Hidden layer of genome unveils how plants may adapt to environments throughout the world

Mar. 6, 2013 ? Scientists at the Salk Institute for Biological Studies have identified patterns of epigenomic diversity that not only allow plants to adapt to various environments, but could also benefit crop production and the study of human diseases.

Published March 6 in Nature, the findings show that in addition to genetic diversity found in plants throughout the world, their epigenomic makeup is as varied as the environments in which they are found. Epigenomics is the study of the pattern of chemical markers that serve as a regulatory layer on top of the DNA sequence. Depending on where they grow, the plants' epigenomic differences may allow them to rapidly adapt to their environments.

Epigenomic modifications alter gene expression without changing the letters of the DNA alphabet (A-T-C-G), providing cells with an additional tool to fine-tune how genes control the cellular machinery. These changes occur not only in plants, but in humans as well.

"We looked at plants collected from around the world and found that their epigenomes are surprisingly different," says senior author Joseph R. Ecker, a professor in Salk's Plant Biology Laboratory and holder of the Salk International Council Chair in Genetics. "This additional diversity may create a way for plants to rapidly adapt to diverse environments without any genetic change in their DNA, which takes a very long time."

By understanding epigenomic alterations in plants, scientists may be able to manipulate them for various purposes, including biofuels and creating crops that can withstand stressful events such as drought. That knowledge of epigenomic changes in crop plants could tell producers what to breed for and could have a huge impact on identifying plants that can survive certain conditions and adapt to environmental stressors, says Ecker, who is also a Howard Hughes Medical Institute and Gordon and Betty Moore Foundation Investigator.

Using MethylC-Seq, a method for mapping epigenomic changes developed by Ecker, the researchers analyzed methylation patterns from a population of Arabidopsis thaliana, a modest mustard weed that has become to plant biology what laboratory mice are to animal biology. The plants were from a variety of climates in the Northern Hemisphere, from Europe to Asia and Sweden to the Cape Verde Islands. Ecker's team examined the genomes and methylomes of A. thaliana, the makeup of their entire genetic and epigenomic codes, respectively, which is the first step toward understanding the impact of epigenetic changes on the plants' physical characteristics and ability to adapt to their environment.

"We expected variation in methylation patterns among groups of plants from around the globe," says co-lead author Robert J. Schmitz, a postdoctoral researcher in Ecker's lab. "The amount, however, was far greater than we ever anticipated."

By analyzing these patterns, Ecker's team was able to chart their effects on the activity of genes in the plants' genome. Scientists know that methylation can inactivate genes, but in contrast to DNA mutations, methylation patterns are reversible, giving the plants the ability to temporarily activate genes. The identification of genes that are epigenetically regulated has greatly narrowed the potential candidates important for environmental adaptation.

Methylation silencing also occurs in humans -- and that has implications for treating cancer, a hallmark of which is the silencing of tumor suppressor genes. "If these genes are turned off by the epigenome, they could potentially be turned back on by removing the DNA methylation," says study co-lead author Matthew Schultz, a graduate student in Ecker's lab. Understanding how these methylation variants form in the wild will help toward better engineering of epigenomes.

Ecker's team will next study how methylation variations affect the traits of plants. They will examine stress-induced epigenomic changes and how they might provide clues as to which alterations are most important for the plants.

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The above story is reprinted from materials provided by Salk Institute, via Newswise.

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. Robert J. Schmitz, Matthew D. Schultz, Mark A. Urich, Joseph R. Nery, Mattia Pelizzola, Ondrej Libiger, Andrew Alix, Richard B. McCosh, Huaming Chen, Nicholas J. Schork, Joseph R. Ecker. Patterns of population epigenomic diversity. Nature, 2013; DOI: 10.1038/nature11968

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/top_environment/~3/bkrP6omYjNY/130306134356.htm

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Mourning in NY as baby dies after hit-and-run

This undated photo, provided by the New York City Police Department on Monday March 4, 2013, shows Julio Acevedo, 44, who police are looking for in connection with the death of an expectant couple that was killed in a car accident in Brooklyn early Sunday morning and their premature baby, who was delivered alive but did not survive. Police are searching for the driver of a BMW and a passenger who fled on foot after slamming into the livery cab transporting Nachman Glauber and his pregnant wife Raizy, both 21 years old. (AP Photo/NYPD)

This undated photo, provided by the New York City Police Department on Monday March 4, 2013, shows Julio Acevedo, 44, who police are looking for in connection with the death of an expectant couple that was killed in a car accident in Brooklyn early Sunday morning and their premature baby, who was delivered alive but did not survive. Police are searching for the driver of a BMW and a passenger who fled on foot after slamming into the livery cab transporting Nachman Glauber and his pregnant wife Raizy, both 21 years old. (AP Photo/NYPD)

FILE - In this file photo of March 3, 2013, mourners surround a casket outside the Congregation Yetev Lev D'Satmar synagogue at the funeral for two expectant parents who were killed in a car accident early Sunday, in the Brooklyn borough of New York. The baby of Nachman and Raizy Glauber, a boy, was delivered prematurely cesarean section and survived until the next morning but died around 5:30 a.m. on Monday, March 4, 2013. Police were searching for the driver of a BMW and a passenger who fled on foot after slamming into the livery cab that transporting the 21-year-old couple to a hospital. (AP Photo/John Minchillo, File)

In this March 3, 2013, photo provided by VosIzNeias.com, Orthodox Jewish mourners gather outside the Congregation Yetev Lev D'Satmar synagogue in Brooklyn's Williamsburg neighborhood for the funeral of two expectant parents who were killed in a car accident early Sunday, in New York. The baby of Nachman and Raizy Glauber, a boy, was delivered prematurely by cesarean section and survived until the next morning, but died around 5:30 a.m. on Monday, March 4. Police were searching for the driver of a BMW and a passenger who fled on foot after slamming into the livery cab that was transporting the 21-year-old couple to a hospital. (AP Photo/VosIzNeias.com, Eli Wohl)

NEW YORK (AP) ? A close-knit ultra-Orthodox Jewish community in Brooklyn was plunged into a new round of mourning Monday by the death of a baby who was delivered by cesarean section after his parents were killed in a grisly hit-and-run crash a day earlier.

Police hunted for the suspected driver, identified as Julio Acevedo, saying he was barreling down a residential street in a BMW at 60 mph, or twice the speed limit, early Sunday when he collided with a car hired to take the couple to the hospital.

The death of the newborn on Monday piled tragedy upon tragedy and compounded the community's grief.

The baby was buried near the fresh graves of his parents, Nachman and Raizy Glauber, both 21, according to Isaac Abraham, a spokesman for the Hasidic Jewish community. About a thousand community members turned out for the young couple's funeral a day earlier.

"The mood in the neighborhood is very heavy," said Oscar Sabel, a retired printer who lives near the scene of the accident. "We all hoped the baby would survive."

Brooklyn is home to the largest community of ultra-Orthodox Jews outside Israel, more than 250,000. The couple wed last year in a marriage arranged through a matchmaker and were living in the Williamsburg neighborhood.

They were members of the Satmar Hasidic sect, whose men dress in dark coats and hats, wear long beards like their Eastern European ancestors and have limited dealings with the outside world. Raizy Glauber grew up in a prominent rabbinical family. Her husband was studying at a rabbinical college; his family founded a line of clothing for Orthodox Jews.

Sabel, dressed in the traditional long black coat of the Satmar, said it was a terrible tragedy.

"But it's what God wants," he said. "Maybe the baby's death, and his parents', is not for nothing; God doesn't have to give us answers."

Shortly after midnight Sunday, Raizy Glauber, who was seven months pregnant, wasn't feeling well, so the couple decided to go to the hospital, said Sara Glauber, Nachman Glauber's cousin. They called a livery cab, a hired car that is arranged via telephone, not hailed off the street like a yellow cab.

The livery cab had a stop sign, but it's not clear if the driver stopped. Police said the crash with the BMW reduced the cab to a crumpled heap, and Raizy Glauber was thrown from the wreck. The engine ended up in the back seat, Abraham said.

Police said the driver of the BMW ran away.

The baby weighed only about 4 pounds when he was delivered, neighbors and friends said. He died of extreme prematurity, the city medical examiner's office said.

The driver of the livery cab, Pedro Nunez Delacruz, was knocked unconscious but was not seriously hurt. His vehicle should not have been sent to pick up the passengers because an application to use the Toyota as a livery cab had not yet been approved, the city Taxi and Limousine Commission said.

Acevedo, 44, was arrested last month on a charge of driving while under the influence, and the case is pending. He served about a decade in prison in the 1990s for manslaughter. No one answered the door at Acevedo's last known address, in a public housing complex in Brooklyn. Neighbors said his mother lived in the same building, but she did not answer her door.

"We in the community are demanding that the prosecutor charge the driver of BMW that caused the death of this couple and infant ... with triple homicide," Abraham said in a statement. "This coward left the scene of the accident not even bothering to check on the people of the other car."

How Acevedo came to possess the BMW is also under investigation. The registered owner, Takia Walker, was arrested on insurance fraud charges Sunday in a scam involving the car, police said. She was not involved in the crash. A telephone number registered to Walker rang unanswered.

A person familiar with the investigation said Walker bought the car legally, or allowed her identification to be used in the purchase, then gave the vehicle to a middleman who either lent or rented it out to the driver. The person was not authorized to speak publicly and spoke to The Associated Press on condition of anonymity.

___

Associated Press Writer Jim Fitzgerald in Kiryas Joel, N.Y., contributed to this report.

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/3d281c11a96b4ad082fe88aa0db04305/Article_2013-03-04-Expectant%20Parents%20Killed/id-2a03c87727664917af90ab12c0e14c7b

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House, debris over Fla. sinkhole to be removed

SEFFNER, Fla. (AP) ? The gaping sinkhole that swallowed a man from his Florida home last week could be revealed later Monday when demolition crews knock down the remaining walls and begin clearing away the debris.

Crews on Sunday razed more than half the home, managing to salvage some keepsakes for family members who lived there.

The opening of the sinkhole has been covered by the home, but once emergency officials and engineers can see inside it more clearly, they could begin planning how to deal with it. They also need to decide what will happen to the two homes on either side of the now-demolished house. Experts say the sinkhole has "compromised" those homes, but it's unclear whether steps can be taken to save them.

Jeremy Bush, 35, tried to save his brother, Jeff, when the earth opened up and swallowed him Thursday night.

On Sunday morning, Bush and relatives prayed with a pastor as the home ? where he lived with his girlfriend, Rachel Wicker; their daughter, Hannah, 2; and others ? was demolished and waited for firefighters to salvage anything possible from inside. The home was owned by Leland Wicker, Rachel's grandfather, since the 1970s.

The operator of the heavy equipment worked gingerly, first taking off a front wall. Family belongings were scooped onto the lawn gently in hopes of salvaging parts of the family's 40-year history in the home.

As of Sunday afternoon ? when demolition had stopped for the day and only a few walls remained ? a Bible, family photos, a jewelry box and a pink teddy bear for Hannah were among the items saved. Firefighters also were able to pick out the purse of one of the women in the home.

Cheers went up from family, friends and neighbors each time something valuable was salvaged.

Wanda Carter, the daughter of Leland Wicker, cradled the large family Bible in her arms. She said her mother and father had stored baptism certificates, cards and photos between the pages of that Bible over the years.

"It means that God is still in control, and He knew we needed this for closure," she said, crying.

Carter said she spent from age 11 to 20 in the home, and she had to close her eyes as the home was knocked down.

"Thank you for all of the memories and life it gave us," she said.

The Rev. John Martin Bell of Shoals Baptist Church said he had been with the family all morning. "We just prayed with them," he said. He added that all five who lived in the house ? Bush, Wicker, Hannah and two others ages 50 and 45 ? were in need of support and prayers from the community.

Several generations of family members lived in the home at the time of the ground collapse, including Jeff Bush, the man now presumed dead.

Jeremy Bush tried to save his brother by jumping into the sinking dirt hole. He had to be pulled out of the still-shifting hole by a Hillsborough County Sheriff's deputy, who was visibly shaken when talking about the incident more than a day later.

"I've never seen anything move so fast and do so much destruction," Deputy Douglas Duvall said.

The search for Jeff Bush, 37, was called off Saturday. He was in his bedroom Thursday night in Seffner ? a suburb of 8,000 people 15 miles east of downtown Tampa ? when the ground opened and took him and everything else in his room. Five others in the house at the time escape unharmed as the earth crumbled.

The Hillsborough County Sheriff's Office is conducting the investigation. Detective Larry McKinnon said the sheriff's office and the county medical examiner cannot declare Bush dead if his body is still missing. Under Florida law, Bush's family must petition a court to declare him deceased.

"Based on the circumstances, he's presumed dead; however the official death certificate can only be issued by a judge and the family has to petition the court," McKinnon said.

The area around Seffner is known for sinkholes due to the geography of the terrain, but they are rarely deadly. No one ? from longtime public safety officials to geologists ? could remember an incident where a person was sucked into the earth without warning.

___

Follow Tamara Lush on Twitter at http://twitter.com/tamaralush .

Source: http://news.yahoo.com/house-debris-over-fla-sinkhole-removed-091812243.html

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4 Egyptians killed in Port Said clashes: ministry | Morocco World News

CAIRO, March 4, 2013 (AFP) -

Four people including two policemen were killed in overnight clashes between police and protesters in Egypt?s restive canal city of Port Said, the interior ministry said on Monday.

At least 420 people were also injured in the clashes which began on Sunday after authorities decided to move prisoners awaiting a verdict over alleged involvement in a deadly football riot last year.

The two policemen died from gunshots to the head and neck, an interior ministry official said.

A security official said earlier that protesters threw petrol bombs and stones at the police station in Port Said, where a general strike entered its third week. Police responded with tear gas.

The interior ministry said it decided to move prisoners from Port Said, starting with the 39 remaining defendants over the February 2012 football violence, because it wanted to avoid unrest.

The court verdict, expected next Saturday, is for the 39 defendants in a case which resulted in death sentences in January for 21 other defendants, sparking clashes that killed at least 40 people.

Residents of Port Said and other canal cities have long complained that Cairo marginalises them.

Last year?s football riot which killed 74 people, mostly supporters of a visiting Cairo team, exacerbated Port Said?s isolation, residents of the city say.

Source: http://www.moroccoworldnews.com/2013/03/80947/4-egyptians-killed-in-port-said-clashes-ministry/

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Video: Feiler: Family dinner not as productive as once thought

A Second Take on Meeting the Press: From an up-close look at Rachel Maddow's sneakers to an in-depth look at Jon Krakauer's latest book ? it's all fair game in our "Meet the Press: Take Two" web extra. Log on Sundays to see David Gregory's post-show conversations with leading newsmakers, authors and roundtable guests. Videos are available on-demand by 12 p.m. ET on Sundays.

Source: http://www.nbcnews.com/id/3032608/vp/50974043#50974043

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Girl With Rare Disease Can't Sweat

Sarah Larimore, 7, didn't always like summer.

She suffers from a rare genetic metabolic disorder called cystinosis, which prevents her from sweating. She lives in South Carolina, and can't stay in 80-degree weather for longer than 20 minutes, so during the summer she used to stay cooped up inside, her mother, Katie Larimore, told ABCNews.com.

Last summer her family built a swimming pool in their backyard.

"It was her first real, live outside summer," her mother said. "She just stayed in the water for three months."

Sarah is one of at least 25 million Americans who suffer from rare conditions, according to the National Institutes of Health, which recognizes today as Rare Disease Day. The last day of February has been promoted since 2009 by the National Organization for Rare Disorders (NORD) to increase awareness about the common needs of people with illnesses that not many others have.

People with a rare illness -- defined as affecting fewer than 2,000 people -- share common challenges: They have trouble getting an accurate diagnosis, finding treatment, and convincing insurance companies to pay for care, said Mary Dunkle, NORD spokeswoman.

"Even though each disease is different, the challenges of living with a disease that's rare is pretty consistent," she said.

Of the 6,000 to 7,000 rare diseases recorded in the U.S., treatment options exist for only a few hundred of them, Dunkle said. Treatment is more widely available than it was 30 years ago when NORD was founded, but there's a long way to go, a spokeswoman said.

Federal aid for people with rare illnesses is precarious, and it's often tough to persuade a pharmaceutical company to invest in treatment for a rare disease when there isn't a big payoff, Dunkle said.

Sarah, who loves reading and fashion as well as swimming, shares her diagnosis with about 500 Americans, according to the Cystinosis Research Network. A genetic metabolic disorder, cystinosis causes an amino acid, cystine, to accumulate in every cell of the body, damaging organs and blood cells. An estimated 2,000 people suffer from the illness worldwide.

Her daily regimen is grueling and embarrassing.

Sarah has to take 33 pills daily, a number that will increase to about 80 by the time she's a teenager, her mother said. Cystagon, a medication she takes six times a day, including in the middle of the night, makes her breath stink.

Every hour she has to apply eyedrops to prevent blindness. Seven times a day, she eats through a feeding tube, which causes a bump under her shirt. She has to get a daily injection of growth hormone.

Why she can't sweat is a "one of those mysteries of cystinosis," her mother said. If Sarah stays in the heat too long her cheeks turn red, her body temperature rises and she gets very faint.

Her mother visited Sarah's class to talk about her daughter's fragile condition.

"First-graders can be brutal," Katie Larimore said. But after learning about their classmate's condition, "they started talking about every uncle and cousin they had with an ingrown toenail. They felt empowered and embraced Sarah," she said.

Sarah will need a kidney transplant by the time she's about 15. But she can be considered one of the lucky ones. Children diagnosed years earlier than Sarah died by the time they were 15, he said. Now diagnosis is faster, her parents said.

A company is expected to get FDA approval for a new drug in coming months that could replace Cystagon. It would last for 12 hours instead of six, her parents said.

"Our kid would get to sleep all night. We would get to sleep all night," Katie Larimore said.

Larimore and her husband, Jeff, started noticing problems when Sarah was a baby. She was the youngest of their four children. By the time she was a year old she wasn't growing and needed to drink two gallons of water a day, her mother said.

"Being she was my fourth, I knew something was wrong," Katie Larimore said. "Sarah was very, very tiny at this point because she had stopped growing. I went from doctor to doctor until I found one that believed me."

Sarah's parents say they lucked out. They found a doctor who was treating another child in South Carolina for cystinosis. Soon Sarah was diagnosed. Only two labs in the country can test for the disease, her mother said.

"It was confirmed she had cystinosis and it was going to be a battle," she said. "But we had a name for it we knew what we were battling."

At their first national meeting for parents of children with the condition, eerily, the children of the genetic disorder looked like siblings, Katie Larimore said.

"They all kind of look alike. It's kind of scary," she said. "I thought we were going to pass out."

Last month the Larimores traveled with eight other families with children who have cystinosis to the Capitol to meet with legislative aides of 35 members of Congress. As the March 1 sequester budget cuts loomed, they argued in favor of keeping funding for programs designed to help people with rare illnesses, they said.

Those include the Orphan Drug Act of 1983, which gives pharmaceutical companies tax incentives and other help to research rare illnesses.

A Medicare policy known as TEFRA, or the Tax Equity and Fiscal Responsibility Act, allows middle-class families in 26 states to get federal dollars to help pay for care costs involved helping children with disabilities and serious illnesses. Each month the Larimores spend about $5,000 on medication, doctors' visits and supplies, most of which is currently covered by insurance, they said.

Finally the Larimores asked Congress to not slash funding to the National Institute of Health, which performs research on rare diseases.

"Right now we're coming down to the wire," Katie Larimore said. "As a mom, we'll fight for our kids. There's a lot of us out there who need that kind of help."

Also Read

Source: http://news.yahoo.com/girl-rare-disease-cant-sweat-063623862--abc-news-wellness.html

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Moshi Dulcia

Moshi is more of a design-focused company than one known for its earphones, but since we were sufficiently impressed with the performance of the Moshi Vortex Pro, we decided to give its less-expensive sibling a listen. The good-looking Moshi Dulcia ($64.95 direct) offers a healthy dose of bass response without going over the top, while keeping the focus on high-mid-range clarity. Like its older sibling, it suffers from some very minor?nearly negligible?distortion at top volumes, and some may find it overly bright or sibilant. But, with the included inline remote and microphone for mobile devices, it's a solid deal for the price.

Design
The Dulcia's earpieces are thin, narrow, and lightweight, with the plastic beneath its translucent eartips marked red (right) or white (left). The inline one-button remote control and microphone compartment is situated along the cable leading up to the right earpiece. Overall, its design is simple and refined, with the Moshi logo on each earpiece and the flat, linguini-like black cable the only real flourishes that might grab your attention. The earphones are also available in pink/silver and white/silver color combos.

Included with the Dulcia: a snap-shut, felt-lined carrying case, a shirt clip, and three pairs of eartips?small, medium, and large.

Performance
On deep bass tracks at top volumes, like the Knife's "Silent Shout," the Moshi Dulcia does distort ever so slightly. I almost didn't detect it at first, primarily because it wasn't the sub-bass frequencies?the usual suspects?that were distorting, but the lows and low-mids, instead. Typically, the deep bass kick drum thump on that track is the sound that will distort, and while no distortion occurred until it entered the mix at around 15 seconds, it was the other, less bass-heavy drum hit the track starts out with that began distorting. Evidently, the presence of both drum hits was too much for the earphone's drivers.

Either way, this is hardly a deal-breaker?most tracks won't cause this issue, even at top listening levels, and problematic tracks are unlikely to distort wildly. The Dulcia's $65 price tag buys it a little more leniency in this department, as well.

Despite the minor distortion, the earphones sound pretty solid on tracks with deep bass at more moderate listening levels?the sub-bass drum hits in "Silent Shout" are delivered with power and definition, while the high-mids and highs provide enough clarity to ensure things don't get muddy.

On "Drover," Bill Callahan's voice is delivered with a pleasingly crisp treble edge that helps separate it from the mix. This track can sometimes sound muddy on earphones that boost the bass too much and don't also sculpt the high-mids a bit. On the Dulcia, the low-end is strong without being overwhelming, so the insistent beating of the drums gets your attention, but never overtakes the vocals. Sometimes Callahan's vocals sound a little too boosted in high-mids, and the end result is an overly sibilant sound signature. This varies from mix to mix, but it does mean that the high-mids are significantly tweaked on the Dulcia, as this is rarely an issue with this particular recording.

On classical tracks, like John Adams' "The Chairman Dances," this boost of the high-mids and treble allows the higher register strings and percussion to stand out. The lower register strings don't seem to be nearly as boosted, in comparison, and thus the mix shifts toward the brighter end of the spectrum. Still, the big drum hits at the end of the piece are delivered with a nice resonance?just enough low-end to be noticed without stealing the spotlight.

Obviously, if you're looking for audiophile-level performance, you're going to need to spend a bit more money. In this price range, however, the Dulcia is a solid option that provides rich bass that isn't wildly boosted, though its sculpted highs maybe a turn-off some. The Editors' Choice AKG K 350 is another good choice in this range?both pairs have very minor distortion issues with deep bass at top volumes, but the AKG pair is a bit less sibilant. The $120 Shure SE215 is a step-up in price from both options, but offers better overall audio performance and balance, as well as the added value of a detachable cable. If you're looking to spend even less money, the $50 RHA MA450i delivers an impressive amount of bass for the price, and it doesn't distort, but it's not nearly as balanced as the K 350 or the Dulcia. It's easy to recommend the Moshi Dulcia if you're looking for an inexpensive, but quality, upgrade to their mobile device's earbuds?particularly if you favor high-mid definition with crisp vocals over throbbing bass.

More Headphone Reviews:
??? Moshi Dulcia
??? Polk Audio UltraFocus 6000
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Source: http://feedproxy.google.com/~r/ziffdavis/pcmag/~3/FoLHB2-3C_s/0,2817,2415813,00.asp

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