Sunday, 23 June 2013

The genome's 3-D structure shapes how genes are expressed

June 23, 2013 ? Scientists from Australia and the United States bring new insights to our understanding of the three-dimensional structure of the genome, one of the biggest challenges currently facing the fields of genomics and genetics. Their findings are published in Nature Genetics, online today.

Roughly 3 metres of DNA is tightly folded into the nucleus of every cell in our body. This folding allows some genes to be 'expressed', or activated, while excluding others.

Dr Tim Mercer and Professor John Mattick from Sydney's Garvan Institute of Medical Research and Professor John Stamatoyannopoulos from Seattle's University of Washington analysed the genome's 3D structure, at high resolution.

Genes are made up of 'exons' and 'introns' - the former being the sequences that code for protein and are expressed, and the latter being stretches of noncoding DNA in-between. As the genes are copied, or 'transcribed', from DNA into RNA, the intron sequences are cut or 'spliced' out and the remaining exons are strung together to form a sequence that encodes a protein. Depending on which exons are strung together, the same gene can generate different proteins.

Using vast amounts of data from the ENCODE project*, Dr Tim Mercer and colleagues have inferred the folding of the genome, finding that even within a gene, selected exons are easily exposed.

"Imagine a long and immensely convoluted grape vine, its twisted branches presenting some grapes to be plucked easily, while concealing others beyond reach," said Dr Mercer. "At the same time, imagine a lazy fruit picker only picking the grapes within easy reach.

"The same principle applies in the genome. Specific genes and even specific exons, are placed within easy reach by folding."

"Over the last few years, we've been starting to appreciate just how the folding of the genome helps determine how it's expressed and regulated,"

"This study provides the first indication that the three-dimensional structure of the genome can influence the splicing of genes."

"We can infer that the genome is folded in such a way that the promoter region -- the sequence that initiates transcription of a gene -- is located alongside exons, and they are all presented to transcription machinery."

"This supports a new way of looking at things, one that the genome is folded around transcription machinery, rather than the other way around. Those genes that come in contact with the transcription machinery get transcribed, while those parts which loop away are ignored."

Source: http://feeds.sciencedaily.com/~r/sciencedaily/~3/459JXnr-9hM/130623145058.htm

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It's scrap, not trash, and it's also one of America's top exports

International scrap dealers educate our reporter on the language of our leftovers.

By Peter Ford,?Staff Writer / June 19, 2013

One thing you learn quickly if you hang around scrap merchants is not to refer to the materials in which they trade as "trash" or "garbage" or "junk."

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Beijing Bureau Chief

Peter Ford is The Christian Science Monitor?s Beijing Bureau Chief. He covers news and features throughout China and also makes reporting trips to Japan and the Korean peninsula.

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At a recent convention here of the Bureau of International Recycling (essentially the global forum for scrap dealers) I drew some very sharp looks and a reprimand or two before I got the message.

Of course, the traders are right. If scrap was indeed trash it would not be worth anything. And scrap is certainly worth something. In fact, according to a recent Bank of America-Merrill Lynch report, the global waste and recycling business is worth $1 trillion a year. And it could be worth double that by 2020.

"Where there's muck, there's brass," runs an old Yorkshire adage.

People in the know at the conference told me that a lot of the participants were millionaires at least. But they work in the shadows of the world economy, attracting little attention.

Did you know, for example, that trash ? I mean scrap ? was America's top export to China in 2011? (Though maybe not for long, because of new Chinese regulations.)

There is one synonym for "scrap" that its devotees more or less allow ? "waste." But, as I was reminded by Surendra Borad, an Indian businessman whose company, Gemini, handles more scrap plastic than any other firm, "waste is not waste until it is wasted."

Source: http://rss.csmonitor.com/~r/csmonitor/globalnews/~3/KDKM3rHWzRo/It-s-scrap-not-trash-and-it-s-also-one-of-America-s-top-exports

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Planetary Resources Kickstarter Meets Its Initial Goal

Just a few days ago (when it was published on theoatmeal.com) I visited that campaign and it was a few thousands of dolars (around 15k, if I recall correctly). Now, Not more than a week later it reached 1,1 million? The number of people who supported it hasn't grown that much from that time. I don't recall the exact figure, unfortunately. I don't know, it just seems kinda fishy. They started the project may, 29 and they've got a little over 10k. Now, after a few days, they got to 1,1 million? Maybe oatmeal

Source: http://rss.slashdot.org/~r/Slashdot/slashdotScience/~3/0Ke-zrPU3Ss/story01.htm

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Saturday, 22 June 2013

Paula Deen Fired From Food Network Following Lawsuit About Racial Slurs

Source: http://www.thehollywoodgossip.com/2013/06/paula-deen-fired-from-food-network-following-lawsuit-about-racia/

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John Kerry to Doha for Syria Talks (Voice Of America)

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Bits of Arthur C. Clarke and 'Star Trek' celebs will sail into deep space

Sunjammer / Celestis

An artist's conception shows the Sunjammer solar sail deployed in orbit.

By Alan Boyle, Science Editor, NBC News

When the Sunjammer solar sail?is launched for a deep-space test next year, small samples from sci-fi guru Arthur C. Clarke and three pioneers of the "Star Trek" TV series will be going along for the ride. And you can send a message as well.

It's all part of a memorial spaceflight organized by the Houston-based Celestis, which has been putting cremated remains into outer space for 16 years. Hundreds of bits of ash, weighing no more than a few grams each, have been launched on suborbital or orbital flights. The remains of planetary scientist Gene Shoemaker were sent to the moon aboard NASA's Lunar Prospector probe in the late 1990s. Celestis is getting set to send another set of remains on a short trip to space and back on Friday, aboard an UP Aerospace SpaceLoft XL rocket launched from Spaceport America in New Mexico.


The Sunjammer flight, set for liftoff from Cape Canaveral in November 2014, will break new ground: It'll be the first Celestis mission to go into deep space. "We're finally able to initiate the Celestis Voyager service, which we've wanted to do for a long time," Charles Chafer, CEO of Space Services Holdings and co-founder of Celestis, told NBC News.

Among those whose ashes will be included on the flight are "Star Trek" creator Gene Roddenberry and his wife, Majel Barrett Roddenberry, who was an actress on several Trek TV series. Remains from James Doohan, who played the irascible chief engineer Montgomery "Scotty" Scott, will go up as well. (Samples from Gene Roddenberry and Doohan have been included on previous Celestis flights.)

Clarke will be represented by a single strand of hair, part of a lock that the late writer donated back in 1999. Chafer recalled that Clarke said, "I'd give you more, but I don't have anything to spare."

Sunjammer's namesake
In a way, Clarke is the most fitting person to ride on Sunjammer: He's the one who came up with the solar sail's name, for a 1963 short story about a sun-yacht race.

Celestis is a commercial partner in the $27 million Sunjammer project, which is funded by NASA and headed up by L'Garde, a California-based company that specializes in inflatable and deployable structures. The 13,000-square-foot (1,208-square-meter) expandable sail will be folded up inside a spacecraft and then placed aboard a SpaceX Falcon 9 rocket as a secondary payload. Sunjammer will be deployed in orbit along with a bigger satellite, the National Oceanic and Atmospheric Administration's Deep Space Climate Observatory.

A promotional video outlines the Sunjammer solar-sail mission.

After separation from the Falcon 9, the Sunjammer spacecraft will open up its sail and head for a position about 1.8 million miles (3 million kilometers) from Earth, propelled by the force of photons from the sun. The aim of the mission is to test solar-sail propulsion techniques as well as monitor solar weather.

"It's the culmination of generations of hopes that we can harness the sun," Chafer said.

He said Sunjammer would remain in space forever, tracing an orbit around the sun between Earth and Venus. The samples from Clarke, Doohan, the Roddenberrys and dozens of others would stay out there as well, protected inside lipstick-sized metal containers.

'Message in a bottle'
Celestis is selling spots on the memorial spaceflight for prices ranging from $12,500 on up. The company will also let people send digitized messages for inclusion aboard the spacecraft, as part of a service it calls MindFiles. Messages are already pouring in via the SunjammerMission.com website. "Greetings from the early 21st century, from an aerospace worker ... who loves space exploration," one message reads.

"It's kind of like a Facebook post," Chafer explained. "You put photos in, or anything you want, and we'll take that information, burn it onto a disk and send it out to deep space. It's like a message in a bottle, but it could also be like a Library of Alexandria."

And if you want to be like Arthur C. Clarke, you can send a BioFile?? a single strand of hair, and/or digital DNA markers, that will be packaged to endure in outer space. Theoretically, it might be possible for an alien civilization to turn that BioFile into a clone, as Clarke hoped would be the case when he donated his hair. Chafer makes no guarantee, however.

"It's a symbolic action more than anything else," he said, "but it's a way to have a little bit of you go on a space mission, and you don't have to die first."

More about space memorials:


Alan Boyle is NBCNews.com's science editor. Connect with the Cosmic Log community by "liking" the NBC News Science Facebook page, following @b0yle on Twitter and adding the Cosmic Log pageto your Google+ presence. To keep up with NBCNews.com's stories about science and space, sign up for the Tech & Science newsletter, delivered to your email in-box every weekday. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.

Source: http://feeds.nbcnews.com/c/35002/f/653377/s/2d9431f3/l/0Lcosmiclog0Bnbcnews0N0C0Inews0C20A130C0A60C20A0C190A613630Ebits0Eof0Earthur0Ec0Eclarke0Eand0Estar0Etrek0Ecelebs0Ewill0Esail0Einto0Edeep0Espace0Dlite/story01.htm

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Friday, 21 June 2013

Immigration reform: new security plan could sway dozen Republicans

Many Republicans have balked at the immigration reform bill, saying it didn't do enough to improve border security. A new compromise amendment in the Senate addresses those concerns and could pave the way for overwhelming approval next week.

By David Grant,?Staff writer / June 20, 2013

Republican Sens. Bob Corker of Tennessee (l.) and John Hoeven of North Dakota talk to reporters at the U.S. Capitol in Washington on Thursday about their amendment to immigration legislation.

Jonathan Ernst/Reuters

Enlarge

Immigration reform got a substantial boost in the Senate Thursday, as Republican Sens. Bob Corker of Tennessee and John Hoeven of North Dakota helped craft a compromise proposal on border security that could pave the way for an overwhelming approval of the bill when it comes to a final vote next week.

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The amendment, together with a handful of others still under negotiation but whose prospects appear favorable, could push the vote total toward 70 senators. That is something of a magic number for proponents of immigration reform, who think a huge, bipartisan vote in the Senate could compel the House to act. Many Republicans in the House have so far shown little enthusiasm for comprehensive immigration reform.?

Yet border security has been among the primary stumbling blocks for Republicans, both in the House and Senate, and Senator Corker is confident that his amendment should allay any concerns.

?If anybody on either side of the aisle had any concerns whatsoever about the border being secure ? certainly securing the border should not be an issue if this amendment passes,? he said Thursday.

The "Gang of Eight" senators that crafted the immigration bill also also hailed the importance of the compromise amendment.?

?If this amendment doesn?t convince people we are securing the border, nothing will,? says Sen. Chuck Schumer (D) of New York, one of the bill?s authors.

The amendment, which will likely come up for a vote early next week, would double the number of border security agents along the US-Mexico divide to 40,000 and require the completion of 700 miles of border fencing, up from 350 in the initial border plan. The measure explicitly spells out the types of technology (including unmanned aerial vehicles and special radar) and infrastructure to be deployed by the Department of Homeland Security (DHS), which will have to provide a border security strategy six months after the bill is enacted.

The Corker-Hoeven compromise addressed concerns on both sides of the aisle.

Republicans pointed out that the DHS has failed to enforce immigration laws in the past. They also were concerned that, under the original bill, DHS was tasked with devising its own border security plan. What if that plan wasn't up to snuff? Republicans said.?

Democrats, on the other hand, feared that an alternative ? putting specific border-security goals in place and then making the pathway to citizenship contingent on their fulfillment ? would allow a future Congress to short-circuit the route to citizenship for the nation?s 11 million undocumented immigrants.

Corker-Hoeven?s answer was to establish five "triggers" that will increase border security significantly, but which can be definitively implemented in a relatively short period. These are:

  • The addition of 20,000 border patrol agents.
  • The construction of 700 miles of fencing.
  • The implementation of more and advanced border-security technology
  • The nationwide implementation of the E-Verify employment verification system.
  • The implementation of electronic scanning systems for foreigners entering and exiting the US at all air and seaports.

Source: http://rss.csmonitor.com/~r/feeds/csm/~3/bJV7EpV_qew/Immigration-reform-new-security-plan-could-sway-dozen-Republicans

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