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Wednesday, March 6, 2013

Assembling the transcriptome of a noxious weed: New resources for studying how plants invade

Mar. 5, 2013 ? In order to build and maintain cells, DNA is copied into ribonucleic acid (RNA) molecules, also called transcripts. Transcripts are often like a recipe for making proteins, and a collection of all the transcripts in a cell is called a transcriptome.

Pankaj Jaiswal, Assistant Professor of Botany and Plant Pathology at Oregon State University, Samuel Fox, a Postdoctoral Associate in Jaiswal's laboratory, and colleagues assembled transcriptomes of a noxious weed, Brachypodium sylvaticum, or slender false brome. The transcriptome provides an extensive genetic tool for studying how invasive species, like slender false brome, successfully spread into novel ranges. In addition, the genome is available for a closely related species, Brachypodium distachyon. Together, the transcriptome and genome can be used as a reference for pinpointing differences in slender false brome genes and gene activity that may contribute to its invasive capabilities.

Slender false brome is an invasive grass that is native to Europe, Asia, and North Africa. It was introduced into the United States about 100 years ago and is listed as a noxious weed along the West Coast of the United States. "It is aggressively invasive within its current range -- near monocultures of this grass occupy thousands of hectares of mixed coniferous understory and grassland habitats in Oregon," says Mitch Cruzan, coauthor and Associate Professor of Biology at Portland State University.

Slender false brome is ideal as a model for invasive plant evolution. "False brome is in the process of active range expansion and is wildly successful despite experiencing colder, wet winters and drier summers than plants in the native range," explains Cruzan, "so it is a great system for studying ecological and evolutionary aspects of invasion."

Fox and colleagues have assembled the transcriptomes for two slender false brome populations from its native range (Greece, Spain) and one population from its invasive range (Oregon). Comparing transcriptomes across ranges will reveal new changes in gene expression in the highly successful invasive population. "This system has great potential as a comparative framework for studying adaptation to new environments and invasion," comments Jaiswal.

To allow future studies to identify the functions of slender false brome genes, the authors also compared the false brome transcriptome to those of well-studied agricultural species, including rice and sorghum. If false brome possesses a gene that has already been studied in an agricultural species, it will be easier to identify the gene's supposed function. The teams from Jaiswal's and Cruzan's laboratories are exploring these newly developed genetic resources, which may provide insights into how slender false brome has adapted to Oregon's different environmental conditions.

The authors published their results, including details on data retrieval, in the March issue of Applications in Plant Sciences. Fox and Cruzan note, "The seed and genomic resources are publicly available, so it would be relatively easy for any research group to establish a research program focused on slender false brome."

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The above story is reprinted from materials provided by American Journal of Botany, 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:

Samuel E. Fox , Justin Preece , Jeffrey A. Kimbrel , Gina L. Marchini , Abigail Sage , Ken Youens-Clark , Mitchell B. Cruzan , and Pankaj Jaiswal. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). Applications in Plant Sciences, 2013 DOI: 10.3732/apps.1200011

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/~3/8ywEkoQgpjM/130305174635.htm

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Holder promises more openness on national security

Attorney General Eric Holder testifies on Capitol Hill in Washington, Wednesday, March 6, 2013, before the Senate Judiciary Committee hearing: "Oversight of the U.S. Department of Justice." Holder urged Congress to confront gun violence by requiring universal background checks, imposing tougher penalties on traffickers and banning high-capacity magazines and military-style assault weapons. (AP Photo/Evan Vucci)

Attorney General Eric Holder pauses as he testifies on Capitol Hill in Washington, Wednesday, March 6, 2013, before the Senate Judiciary Committee hearing: "Oversight of the U.S. Department of Justice." Holder urged Congress to confront gun violence by requiring universal background checks, imposing tougher penalties on traffickers and banning high-capacity magazines and military-style assault weapons. (AP Photo/Evan Vucci)

Attorney General Eric Holder arrives on Capitol Hill in Washington, Wednesday, March 6, 2013, to testify before the Senate Judiciary Committee hearing: "Oversight of the U.S. Department of Justice." Holder urged Congress to confront gun violence by requiring universal background checks, imposing tougher penalties on traffickers and banning high-capacity magazines and military-style assault weapons. (AP Photo/Evan Vucci)

WASHINGTON (AP) ? Attorney General Eric Holder promised the Senate Judiciary Committee on Wednesday that the Obama administration will share more information with Congress and the American people about national security policies, particularly the government's use of drone strikes.

Holder's comments came at a hearing where both Democratic and Republican senators said they must have access to Justice Department memoranda that form the legal underpinning for precisely when the administration can use drone strikes to kill a suspected terrorist, even if the person is a U.S. citizen.

Committee chairman Patrick Leahy, D-Vt., said the judiciary panel should have the legal opinions, some of which were provided recently to Sen. Dianne Feinstein, D-Calif., and the Senate Intelligence Committee, which she chairs.

"I heard you and the president has heard you," Holder said. The attorney general said he is confident that if the public had more information there would be greater comfort that the administration is acting in conformity with the law.

Without elaborating, Holder said a number of steps are going to be taken and that he expects "the president will be talking about this."

Fueling the senators' questions was a March 4 letter that Holder wrote to Sen. Rand Paul, R-Ky., who asked whether, in the administration's view, the president has the power to authorize lethal force, such as a drone strike, against a U.S. citizen on U.S. soil.

In his letter, the attorney general said the president could conceivably have no choice but to authorize the military use of such force in circumstances of a catastrophic attack like the ones suffered at Pearl Harbor and on Sept. 11, 2001.

But Holder emphasized that administration has no intention of carrying out drone strikes in the United States. Holder said Rand's hypothetical is unlikely "and one we hope no president will ever have to confront."

On another topic, Holder urged Congress to confront gun violence by requiring universal background checks, imposing tougher penalties on traffickers and banning high-capacity magazines and military-style assault weapons.

Holder said Congress should eliminate what he called misguided restrictions requiring federal agents to allow older weapons to be imported into the United States.

The attorney general also urged senators to confirm a new director for the Bureau of Alcohol, Tobacco, Firearms and Explosives. The agency has been without a Senate-confirmed leader for six years. ATF has been mired in a long-running controversy stemming from a botched gun smuggling investigation in Arizona. ATF agents lost track of about 1,400 of more than 2,000 illicitly acquired weapons in the operation.

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/386c25518f464186bf7a2ac026580ce7/Article_2013-03-06-Holder-Senate/id-9194bfd0793f45b3a069e7ffd79be95e

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Bob Hope's iconic estate listed for $50 million

Erika Riggs , Zillow ? ? ? 5 hrs.

Palm Springs, Calif.
For sale: $50 million

Actor Bob Hope owned a collection of homes in Palm Springs and the L.A. area, and two have hit the market ? both snagging buyers within a month of listing. But the real prize of Hope's homes is the John Lautner-designed property, an architectural treasure that hit the market in late February for $50 million.

Architect John Lautner was well-known for his dramatic designs, and his biggest piece was a custom home for Bob and Dolores Hope. Perched in the private neighborhood of Southridge, the estate dominates a corner lot with sweeping views of the Coachella Valley.

Hope's 23,366-square-foot home was designed in 1973 by Lautner to resemble a volcano. The modernist structure is built of concrete and glass, with an undulating copper roof that rises to an open semi-circle at its center.

The home was used primarily as a second residence for the Hope family and was where they entertained most often, inviting friends such as crooner Tony Bennett and country music singer Glen Campbell to enjoy the views from the house.

Listed by Ann Eysenring of Partners Trust in Beverly Hills along with Patrick Jordan and Stewart Smith of Windermere Real Estate in Palm Springs, the home has six bedrooms and 12 baths. Outdoor spaces include a pool, pond, tennis court and outdoor fireplace.

The Lautner home is just the latest of the Hope estates to be listed; the final property, a custom home in Toluca Lake, Los Angeles used by the Hopes as their primary residence, has yet to be listed.

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Tavis Smiley: My Exclusive Conversation With President Hugo Chavez (VIDEO)

The late Venezuelan president Hugo Chavez was a tyrant to some, but a hero to others, especially the poor.

My first meeting with Chavez occurred in Venezuela where I had the opportunity to sit with him for a conversation in the presidential palace.

My second one-on-one with Chavez took place in 2006, in New York City, just after his most controversial address to the United Nations.

In the clip below, he explains why in that speech he called President George W. Bush "the devil."

You can watch more excerpts from our exclusive conversation during a special re-broadcast airing Monday night, March 11, on PBS. Be sure to check www.pbs.org/tavis for your local TV listings.

Follow Tavis Smiley on Twitter: www.twitter.com/tavissmiley

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Source: http://www.huffingtonpost.com/tavis-smiley/my-exclusive-conversation-chavez_b_2815265.html

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Twitter Is Killing TweetDeck's iPhone App, Android App and Desktop App

Twitter is killing off TweetDeck. TweetDeck just announced that it'll be discontinuing its iPhone app, Android app and versatile Air-based multicolumn desktop app. The apps will be removed from all the app stores and stop working "shortly thereafter". Bye, bye multi-column Twitter! More »

Source: http://feeds.gawker.com/~r/gizmodo/full/~3/kj9ZvP4Bsck/twitter-is-killing-tweetdecks-iphone-app-android-app-and-desktop-app

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How can I Dispute Charged-off Debt With the IRS?

Dear Tax Talk,?

I had a charge-off that was apparently reported to the Internal Revenue Service in 2010. In April 2012 I paid back approximately half of this debt. In July 2012 I was informed that I owed the IRS extra tax for 2010 because of this income. I sent them a copy of the receipt to try and get the amount reduced by half, as half had since been paid; therefore it's not income. They were not impressed and are still after me for the full amount. Will I be able to deduct the paid portion on my 2012 taxes? How can I resolve this tax bill dispute with the IRS??

-Ken

Dear Ken,?

There are various defenses to fight this tax bill battle, but your best bet would be to hire an accountant to represent you so that you prevail in this matter. If I understand you right, you owed someone, let's say, a bank, money that you did not repay in 2010. The bank charged this off as an uncollectible account and issued you a Form 1099. It sounds like you didn't include this debt in your 2010 taxes and the IRS probably sent you a correspondence exam letter, known as a CP2000, asking why you didn't record this as income.

For some unknown reason you paid off half of this debt in 2012 and you believe that you shouldn't have to pay tax in 2010 on this debt. I agree with you, the IRS is not seeing it right. Your defenses would be:

Determine if you were insolvent in 2010 when the debt was forgiven. Usually, lenders only forgive debts when they believe they cannot collect, meaning they think you don't have the assets to pay. If, in fact, your debts exceeded the value of your assets at the time the debt was forgiven, the law allows you to exclude the debt from income.
If you repaid the loan in 2012, presumably the bank was still actively trying to collect from you. If this is the case, then the bank did not discharge the debt in 2010 and should retract the 1099. If the bank doesn't retract the 1099, you may be able to convince the IRS that the 1099 was not issued in the right year as the bank continued collection efforts.
If you can't get anywhere with the correspondence unit, which is likely, do not agree to anything. The correspondence unit will issue what is known as a 30-day letter. This means you have 30 days to appeal the decision. Your appeal goes to the IRS Appeals office, which is a higher level of tax examiner that has more flexibility to apply the law fairly.

Good luck and let me know how things turn out.

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Source: http://feeds.foxbusiness.com/~r/foxbusiness/personal_finance/~3/chAUCr5TJ6A/

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Tuesday, March 5, 2013

No, the iWatch Isn't Definitely Coming This Year

There are headlines this morning, in abundance, that an Apple iWatch will be coming in 2013. They are declarative. They are definitive. They are wrong. The iWatch might be coming this year, or might come in 2015, or it might not come at all. And nothing in this Bloomberg report changes that. More »

Source: http://feeds.gawker.com/~r/gizmodo/full/~3/yGLlQJAknag/no-the-iwatch-isnt-a-lock-for-this-year

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