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Sun Devils looking for road success
TEMPE, Ariz. (AP)
Arizona State made a statement in its last game, routing a ranked opponent for arguably its biggest win in two seasons under coach Todd Graham.
The next step for the 25th-ranked Sun Devils is to build upon it, not let the momentum fizzle after a week of savoring the victory.
But to keep rolling, Arizona State will have to do something it has struggled with in the past: Winning on the road.
And when it comes to that subject, Graham has heard enough about playing in an unfamiliar environment, in cold weather, having to stay in hotel rooms.
''That's all excuses,'' Graham said Monday during his weekly news conference. ''You don't win on the road because you're not prepared, you're not focused and you don't play well. That's it.''
The Sun Devils have been solid at home under Graham, going 4-2 at Sun Devil Stadium last season and 5-0 this season.
Arizona State had a few bumps on the road last season, losing at Missouri, Oregon State and Southern California while beating Colorado, California and Arizona.
The Sun Devils haven't spent much time away from the desert this season, but have yet to win, losing 42-28 to then-No. 5 Stanford and 37-34 to Notre Dame in a neutral-site game.
Thursday night's game against Washington State kicks off a big stretch for Arizona State (5-2, 3-1 Pac-12).
The Sun Devils' last game was a rout over then-No. 20 Washington, a victory that moved them back into the rankings and in control of the Pac-12 race. After playing in Pullman, Arizona State still has games at Utah and UCLA, games that could go a long way toward helping them reach their main goal of winning the Pac-12 championship.
''If you want to be a champion and that's what we say we want to be, that's what we talk about that we want to win a championship, no excuses,'' Graham said. ''You go, rain, sleet, snow, Alaska, Maine, it doesn't matter - you've got to go win. That's the mindset.''
Cold weather has been one of the perceived problems for Arizona State on the road.
The Sun Devils have to deal with heat early in the season, which ends up being to their advantage, but play most of their games in weather that's often more like spring than fall or winter.
And since Arizona State hasn't had many late-season road wins against teams in the Pacific Northwest in recent years - the last one was over Washington in 2008 - there's an impression that the Sun Devils don't like playing in the cold.
The high in Pullman on Thursday is supposed to be around 50 with temperatures dropping into the 30s overnight - not that Graham wants to hear about it.
''If one of my coaches says something about the weather, I'll tell him to go get a meteorologist's job,'' Graham said. ''It's part of it.''
Graham has done his best to make the Sun Devils feel comfortable on the road, bringing the air fresheners and photos from Sun Devil Stadium to put in the visitor's locker room and taking his players through the stadium the day before so they'll know what it's like.
He did alter his bye-week schedule last week, though.
The Sun Devils played one of the toughest stretches that any team in the country will face this season and have several players banged up after facing big, physical teams like Wisconsin, Stanford, Notre Dame and Washington in a little over a month.
To give his players a chance to recover, Graham allowed them to practice without pads for the entire week.
It was a bit of a gamble, one Graham hopes will not have the opposite effect of what he was going for.
''I've never done what I did this past week, taking the pads off the entire week to try to heal them up,'' Graham said. ''I think it was smart, but are we mentally mature enough to handle that? We'll see.''
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From Wikipedia, the free encyclopedia
Look up cartridge or cartridges in Wiktionary, the free dictionary. |
Cartridge may refer to:
- Broadcast cartridge used in radio stations
- 8-track tape cartridge, a 1960s-1980s music storage format
- Compact Cassette used with sound recording and reproduction and data storage for early microcomputers
- Digital Audio Tape cartridge, a recording and playback medium introduced by Sony in 1987
- Digital Data Storage, a format for storing computer data on Digital Audio Tape cartridges
- Digital Linear Tape, a magnetic tape cartridge data storage technology introduced by Digital Equipment Corporation in 1984
- IBM 3480 Family, a magnetic tape cartridge data storage format developed by IBM
- Linear Tape-Open, a magnetic tape cartridge data storage technology developed as an open standards alternative to proprietary formats
- Magnetic cartridge, a component of a record player
- Quarter-inch cartridge, a magnetic tape data storage format introduced by 3M in 1972
- ROM cartridge, a removable component in an electronic device
- RAM pack, a RAM expansion cartridge
- Data cartridge (tape), magnetic tape in a plastic enclosure for data storage
- Stereo-Pak, a 1950s-1970s music storage format
- Videocassette, used with videocassette recorders (VCR)
- Ink cartridge, an ink component of an inkjet printer
- Toner cartridge, a consumable component of a laser printer
Other uses[edit]
- Cartridge (firearms), a round of ammunition
- Cartridge (surname), a surname in the English language, and is considered to be an English surname
- Keymatic cartridge, used to program washing machines
See also[edit]
This disambiguation page lists articles associated with the title Cartridge. If an internal link led you here, you may wish to change the link to point directly to the intended article. |

subset: commoncrawl


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Source: PA
Strike duo set for cup roles
Birmingham boss Alex McLeish has confirmed that summer signings Nikola Zigic and Matt Derbyshire will be handed their chance to impress in the Carling Cup third-round clash against MK Dons.
Alexander Hleb is likely to be given a run-out to improve his match fitness following his loan move from Barcelona. The former Arsenal player made a promising debut against West Brom at the weekend before fading in the second half.
The likes of Maik Taylor, David Murphy, Keith Fahey, Michel, Jean Beausejour and Enric Valles will also be in contention to start.


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Should I transfer my film to DVD myself or farm it out?
Back in the 1980′s you could transfer your film to DVD and get about the same quality using your camcorder as the camera shop down the street. Today, that isn't the case. Even though many companies are still using the same film to DVD machine they did in the 1980′s, other companies have brought professional equipment from the movie studios to use on 8mm, Super and 16mm film.
Today, there are frame by frame machines (still use a camcorder but uses it as a still picture device which produces better quality film to DVD results). In addition, some companies are using professional film scanners. Like a flat bed scanner, these scanners scan the film instead of using a camcorder. Film scanners produce the best film to DVD transfer.
So, today, even though many film transfer companies still use the same film to DVD equipment from the 1980′s, there are companies that have advanced the art of film to DVD transfers to a new level using film scanners.
This entry was posted on Tuesday, May 12th, 2009 at 1:24 pm and is filed under 8mm film to dvd, Film Transfer. You can follow any comments to this post through the RSS 2.0 feed. You can leave a response, or trackback from your own site.


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Scottish Green Party
The Scottish Green Party was a constituent part of the UK Green Party (as it was then called) until 1990, when the Scottish Green Party became a separate party from the party in England and Wales (Northern Ireland also took this route later). The separation was entirely amicable, as part of the green commitment to decentralisation. The Scottish Green Party is now an independent Green Party, and a fully independent member of the European Federation of Green Parties. The UK Green Party renamed itself the Green Party of England and Wales.The Scottish Green Party benefits from the fact that the Labour Party Government created a Scottish Parliament, which includes an element of proportional representation in addition to the seats elected by first-past-the-post. In the first election to this parliament, in 1999, the Scottish Green Party got one Member of the Scottish Parliament (MSP) elected using the top-up proportional representation. On May 1, 2003 the Scottish Greens added six new MSP's to their previous total.
The Scottish Parliament is elected using the Additional Member System of proportional representation. Soon, local authorities in Scotland are to be elected using the Single Transferable Vote system of proportional representation.


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Lexus Autonomous Car: 2013 CES
Lexus shows off its self-driving concept car at CES.
Smartphones continue to be the next big thing for in-car technology. Read More
Porsche and Aha Internet Radio: 2013 Consumer Electronics Show
Porsche partners with Aha Radio for in-car internet music
Hyundai and Kia Add Google Maps and Search: CES
Hyundai's telematics platform will soon allow users to search locally for places using the web's most popular search provider.


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Appearance / Description of Object(s)It was the same colour of a star. Size of Object(s)It was the size of the letter o that i have just typed. Distance to Object(s) & AltitudeIt's very difficult to gauge it's altitude but it could have been at 60000 to 100000 feet Description of Area / SurroundingsIt was flying over my village which is in County Durham England. I don't know of any military bases in this part of country. I don't know of anything that that would warrant attention. (Though i will check) I wonder if it had been picked up on radar. I will try and find out. Full Description & DetailsIt was at high altitude and could have been mistaken for a star had it not moved in a sort of zig zagging way.
Can sighting be explained as any conventional man-made or natural object?I can assure you that the object was a UFO as nothing from earth could match it's performance. I'm aware of aircraft speeds at 60.000 feet and how slow they appear to move at about 700 MPH. This object was so unique in it's movement and speed. Witness BackgroundFor the next year or two i will be working as an advisor in education. My work is both current and leading. If all else fails Education does'nt. It has a solution to every problem and recognises good politics.. Views on UFOs, before and after sightingI knew nothing about UFO's before these last 4 month's. I am quite well versed in the matter. Whilst we are here on earth there's no reason to suppose there arnt other life forms elsewhere. Canada and Mexico acknowledge alien presence. Their word is good enough for me. Other CommentsIf anyone could be labelled a sceptic it would be me as i pefer proof. I know what i saw.
Reported Sighting?YesReported To:I told a friend and will inform others.Name:Colin HuntYour Location:County Durham EnglandAge:62 |


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Mega Inn
With the guests' convenience in mind, each hotel rooms is well designed and fully equipped with air-con, TV,mineral water . All room attached with private bathroom replete with hairdryer. Free Wifi in hotel.
To suit all guests' utmost convenience, hotel provides luggage storage facilities, airport shuttle services, laundry and dry cleaning services.


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Forensic experts inspect a burnt house where the bodies of four... News PhotoBrittany,Burnt,Examining,Expertise,Family,Finistere,Forensic Science,France,Horizontal,Law,People,RepetitionPhotographer FRED TANNEAUCollection: AFP 2012 AFPForensic experts inspect a burnt house where the bodies of four people apparently belonging to the same family were found on December 6, 2012 in Plouescat, Brittany. AFP PHOTO / FRED TANNEAU (Photo credit should read FRED TANNEAU/AFP/Getty Images)


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Command and Control: Nuclear Weapons, the Damascus Incident and the Illusion of Safety. By Eric Schlosser. Penguin Press; 656 pages; $36. Allen Lane; £25. Buy from Amazon.com, Amazon.co.uk
HOW did the world become so complacent about nuclear weapons? Eric Schlosser, an investigative journalist, suspects that rational minds cannot quite grasp the reality of their destructive power. He recalls growing up in the 1970s, amid talk of a nuclear Armageddon, and coming to view such weapons as a terrible fiction.
He felt differently after witnessing the 1999 launch of a Titan II, the largest intercontinental ballistic missile built by America, at a California air-force base. One moment the silver rocket the size of a ten-storey building stood in its silo, hooked up to hissing, humming support units; the next it was gone, vanishing into the sky. The display profoundly rattled Mr Schlosser, the author of "Fast Food Nation", a bestselling look at the costs of cheap eating. While at the launch he heard of a 1980 accident in which a Titan II exploded in its silo, propelling its nuclear warhead to land (without detonating) in a ditch near Damascus, Arkansas. Thus began a decade-long probe into the systems that govern America's nuclear arsenal of nearly 5,000 weapons.
The resulting book, "Command and Control", aims to drive home the real dangers of nuclear accidents. It is not always an easy read. Mr Schlosser digs up tales from once-secret archives of warheads being dropped, burned and crashed into Arctic ice at 600mph, with near-cataclysmic results. Former nuclear commanders talk of handing over bombs to NATO units which, in retrospect, "you wouldn't trust with a .22 rifle." At the height of the Cuban missile crisis an American pilot nearly triggered dogfights over Siberia after getting lost and straying into Soviet airspace. To counter warhead-theft, engineers offered such solutions as storage "igloos" fitted with nozzles to immobilise intruders with very sticky foam.
Pioneers of atomic research pondered jaw-dropping dilemmas. Scientists designing the bombs that would be dropped on Japan debated whether the intense heat of an atom blast might set the atmosphere on fire, killing every living thing on Earth. One Nobel prize-winning physicist put the odds of the world ending at about one in ten: the chance was duly taken.
The book follows dizzying turns in American nuclear strategy. In 1946, after Hiroshima and Nagasaki, a group of generals, politicians and scientists called for the United Nations to control the armed forces of every country—a plan backed by more than half of Americans. But this pacifism was swiftly replaced by secret plans for "nation-killing" first strikes, and for deterrence measured in "megadeaths", a new term for a million fatalities.
The book intercuts cold-war follies straight from "Dr Strangelove" (pictured) with documentary-style chapters on the 1980 Titan II disaster. There are also long accounts of bureaucratic struggles to improve safety in laboratories and bases. This switchback ride may try readers' patience, but the various threads come together in the book's epilogue. Here Mr Schlosser argues that nuclear arsenals are such complex and catastrophic systems that human beings—no matter how well trained or disciplined—cannot prevent a disaster from occurring, sooner or later. A retired general says that nuclear command and control during the cold war felt like "holding an angry tiger by the tail".
Since nuclear weapons cannot be uninvented, the author cites expert witnesses—military commanders and nuclear scientists among them—who think that the least perilous solution might be a "minimum deterrent" of a few hundred American warheads, with foreign powers told in advance where they would land. The status quo, all agree, is terrifying: an accident waiting to happen.
These claims may seem incredible. It is to Mr Schlosser's credit that his patient accumulation of evidence forces readers to give them serious thought.


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Reviews Summary |
All must hail - BBC / A brilliant swan song - CMJ / Genuinely original - Uncut / Catchy and sublime - Under The Radar / Unquestionably, cLOUDDEAD have arrived - Pitchfork / It's golden - Magnet / Original and eccentric - Alarm / Strident and sophisticated - Grooves / Promising and satisfying – Stylus |
Before hearing cLOUDDEAD, I never would've, in a million years, used terms like "haunting," "psychedelic," "ambient," and "mercurial" to describe a hip-hop album. But when I heard the group's debut full-length, those were the only terms that seemed to fit. But whereas their debut was often as sprawling and unfocused as it was fascinating (mainly because it was a collection of ten-inch singles), Ten is a much more focused and concise, though perhaps slightly less ambitious, recording. Of course, terms like "focused" and "concise" are entirely relative when talking about cLOUDDEAD, thanks in large part to odd nosdam's sonic (de)constructions. odd nosdam pilfers a number of antiquated and offbeat sources, resulting in a number of memorable moments, such as the powerdrill solo and British children's singalong that coexist on "The Teen Keen Skip." Or the "squeaky shoes on creaking floorboards" squelches that serve as the beats for "The Velvet Ant." But there are also subtler, more restrained elements as well, like the drowsily somber atmospherics that drift through "3 Twenty" and "Our Name." Ten manages to balance being wildly unpredictable and perplexing with being accessible and intriguing (the only other hip-hop artist that comes close to this feat is Soul-Junk... maybe). Just don't ask me how they do it. Even after reading the production notes, which are just as fragmentary as any of Doseone and why?'s lyrics, I'm still at a loss to really explain how it works. It just does. - Opus |


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Happy Sunday, folks. Bridget Jones's Diary is one of only three films that I have seen twice at the cinema, and it has a pretty fab soundtrack (once you let Geri Halliwell quietly out the back door). Here's Rosey and 'Love'.
Sunday, 6 January 2013
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33-10690 - 4-way Multi Band Splitter
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33-10650 - SMA Male To F-female Adapt
Adapters used to convert XM or Sirius SMA and SMB connections into an "F" connection to mate with RG-6 cables.
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33-10615 - Rg-6 Extension Cable (100 FT)
This antenna extension cable is designed to work with any satellite radio antenna (purchased separately) to extend the cable length 100' (lengths up to 300' can be achieved by cascading three cable kits).
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Operates up to four satellite radios from a single antenna with this amplified splitter. Includes all adapters and accessories. Uses standard RG-6 cable (not included). Maintains proper RF link budget for the radio. Splitter loss at 2.35GHz has been compensated by...
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Honeybees In The Wild Nearly Gone In North America
...every specific to certain crops. "Plus, if we take native wild bees and culture them, we'regoing to generate new problems there, too. If we bring together10 to 20 times the number of bees that were ever together before,we could expect to have disease outbreaks and other challengesoccur. We can't just whimsi...Cooking And Salad Oils Could Lubricate Cars, Boats, Machines
...n cars, boats and machines. Asadauskas, a native of Lithuania, is an intern at the U.S. Department of Agriculture (USDA) oil chemical research laboratory in Peoria, Ill. Perez, who retired from the U.S. Department of Energy about two years ago, is a volunteer faculty member...Asian Beetle, New In This Country, Threatens Brooklyn's Shade Trees
... it," Hoebeke said. "I knew this wasn't a species native to North America." These beetles might prove to be the ultimate Brooklyn dodgers. Short of cutting down the maple and horsechestnut trees, there is little that can be done to curb the Greenpoint infestation, Hoebeke said, adding that there are no kn...Study Shows Songbirds Switch From Bugs To Berries To Fuel Fall Migration
...,for example--ate berries primarily. The fruits of native shrubs, includingnorthern arrowwood, bayberry and ...nd owners to be good land stewards too."Conserving native habitat in a backyard is simple and inexpensive," he said."Native shrubs, such as bayberry, provide ...Duke Ecologist Says Logging Is Creating 'Mahogany Deserts'
...uth and Central America. Another American species native to a few Caribbean islands (Swietenia mahogani) was logged from the 16th to 18th centuries but now lingers in a few isolatedhabitats, including South Florida's Everglades. Meanwhile, African and Philippine"mahoganies" are foreign imposters, she said....... found, it is likely to have a large impact on the native species of foraminifer. The introduction of exoti...ls, clams, crabs and other invertebrates crowd out native species, and if they have no natural predators, can cause major damage to our harbors and waterways....KU Researcher Eyes The Rain Forest Through The Trees
... lost to deforestation annually - clear-cutting of native forests. That's an area roughly equal to half the ... start a reforestation trend and possibly turn the native plant life into a profitable resource. "In the countries where I have worked, such as Panama, Nicara...No Such Luck: Nitrogen From Air Pollution Unlikely to Moderate Global Warming
...wth and high carbon storage in fields dominated by native "warm-season" prairie grasses, the results were ve...at medium and high rates of nitrogen addition, the native prairie species went extinct, the diversity of vegetation dropped sharply, and the ability of the pr......ther exotic species in the East thatsometimes harm native plants and animals. Other biological research andmonitoring efforts will focus on the effects of air quality on biologicalresources and the effects of pollutants on populations and ecosystems. Themonitoring of migratory birds will be enhanced. The po...Fund Aims To Repay Developing Nations For Valuable Genes
... ofgenetic property rights. In 1995, using plants native to West Africa, Ronald isolated the "Xa21"gene, the first cloned gene known to convey disease-resistance to rice.The University of California proceeded to patent the gene. It is likelythat her discovery and subsequent engineering of disease-resistant...Virus May Be Linked To Obesity -- Early Findings Hint At Relationship
...novirus that infectsbirds and is found only in his native India could induce obesity when itwas injected into chickens. Human adenoviruses form a large family of some 50 viruses.Transmitted through the air, they can cause upper respiratory infections,cold symptoms, gastrointestinal problems and eye...Project Shows Native Bacteria Can Destroy Widespread Pollutant In Groundwater
...erts, Stanford researchers determined that feeding native bacteria with the right mixture of oxygen and tolu... the researchers gathered aquifer sands containing native bacteria and tested them in the laboratory to determine how the bacteria would respond to the oxygen...First Planned Release Of Captive Lemurs In Madagascar Wilds Expected In Fall
... and monitoredrelease" of captive-born lemurs to a native rain forest environmentwhere they will live apart ...lem is critical for lemurs' futures becauseall are native only to Madagascar. The MFG, which is headquartered at the San Francisco Zoo, was formedin 1988 to ...New Evidence For Corn's Ancestry Could Lead To Insect And Drought Resistant Crops
...y.And she said that interested Mangelsdorf because native American potterymakers pressed real ears of corn into the wet clay to form botanically accuratemolds. That meant her pottery studies could give him vital clues about how domesticatedcorn looked many centuries before the Spanish conquest. So her res...Captive Lemurs To Depart For Madagascar Oct. 17 For First Release Into The Wild
... for lemurs' futures because all lemur species are native only to Madagascar. The MFG, headquartered at the San Francisco Zoo, was formed in 1988 to coordinate conservation efforts forMalagasy animals there and abroad. Its activities include training Malagasy students, researchers and technicians. Italso a......inkedwith a tragic motor neuron disease afflicting native people on the island ofGuam, in New Guinea and in part of Japan. "Our team has proposed thatcycasin/MAM may slowly kill neurons by damaging their DNA," says Kisby. "Thecumulative death of neurons may trigger a cascade of events that ultimatelyleads ...Natural Variability Is Key To River Restoration
...a have disappeared and many other organisms in the native community are nearly extinct." However, all the human demands for the Colorado's water probably preclude major changes in river management, Bain said, adding: "Fortunately, Grand Canyon looks fine without water; it's a good thing it's supposed to b...Divorce, Insect Style: Termites Swap Mates
... a log." Her studies of Z. nevadensis , a species native to California woodlands,also show what is on the mind of mate-swapping termites: Females usually choosea male with a bigger head the second time around, while males go for femaleswith bigger bodies and more lipid (fat) storage area. Big-headed males...Scientists Work To Restore Native Fish And Habitat To Great Lakes
...ued fish species like the lake trout. The loss of native species and the invasion of exotic species, such a...ervice are looking at new ways to help restore key native fish including the lake trout, coaster brook trout and lake sturgeon in hopes of establishing more b...NIAID Doctor Successfully Treats Longest Case Of Malaria Infection On Record
...or research purposes. The woman, a native of Greece, came to Dr. Vinetz attention in February 1996 when her daughter, a resident of Baltimore, brought her mother for evaluation to a Johns Hopkins University clinic where Dr. Vinetz works part time. On examination, the ...


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program at Nicklaus Children's Hospital, formerly Miami Children's Hospital, is one of the most experienced such programs for pediatric epilepsy patients in the world. For patients with medically resistant seizures, surgery offers hope for cessation of seizures, or a significant reduction in their severity and frequency. Pediatric brain surgery is an exceptionally delicate discipline that often requires precise brain mapping and a high degree of teamwork among the neurosurgeon, neurologist/epileptologist, EEG technologist and other members of the treatment team. Even this highly sophisticated team cannot eliminate all of the risks of surgery, but can minimize that risk as much as possible.
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Half of 2012 is now history and summer keeps on the move, always pushing toward shorter days and cooler weather. As July weather patterns stabilize a bit and daytime temperatures climb into the 90s, a whole new cast of creatures come to the Walla Walla Valley's stage.
These are warm weather animals that until now have remained tucked away underground, under rocks, under and in logs, in cocoons and in so many different forms you would not believe it. They come from eggs, larvae, nymphs, instars, pupa, worms, maggots, caterpillars, galls, oothecae and combs, to name a few.
These are the insects. These creatures are 100 percent perfect when they emerge. They have no flaws or deformities -- if any are deformed their chance of survival is zero.
Most folks only meet up with "summer bugs" on their windshields, walkways, around outdoor lights at night and maybe landing on them or their food at a picnic. Insects are everywhere and they have adapted to this county through thousands of generations of getting it right.
There are 24,000 species of beetles in North America north of Mexico. Today we will explore the beetles and one in particular: a truly amazing creature called the cadaver or burring beetle in the genus Nicrophorus.
An inch-and-a-quarter long, the black beetle has bright orange designs on its elytra, the hard shell on the back of most beetles that protects the soft abdomen and flight wings. The burring beetle sounds like a bumble bee when in flight. It also "squeaks" by rubbing its abdomen against its elytra.
It generally flies no more than five or six feet above ground, constantly scanning the air for signs of decomposition. It is attracted to dead vertebrates such as mice, birds, frogs, bats and shrews, among others. It lands on the dead animal after detecting it from many hundreds of feet away and crawls down along the soil under the carcass, where it digs in an effort to create a shallow trench as it starts to bury the carcass.
As it does so this insect will remove any feathers or fur on the carcass and then mold the whole dead animal into a rotting ball. It conducts war against any competing flies and their eggs by releasing dozens of mites the beetle hosts. These mites then devour fly eggs laid on the carcass, thus eliminating the potential of maggots that would compete for the rotting tissue.
Adult burring beetles also feed on fly maggots as well as rotting fruit. They lay their eggs beside these rotten balls in the ground and then proceed to hang around to protect their young as they hatch and emerge in larva form.
Watch for these brightly colored beetles near or on dead animals, such as road kills along the edge of roads.
Our second wild thing to take note of this month is a beautiful plant: the wavy leaf thistle, which grows along the Snake River in northern Walla Walla County.
This spectacular native thistle produces a very large pale-lavender flower head amid gray-green leaves. These big flowers are very important to native bees, butterflies, wasps, beetles and flies that depend on them for pollen. Growing to a height of five feet, plant develops 6-10 large flowers. The flowers have an outstanding scent that on a warm day can be smelled from many feet away
Who would have thought that a large plant like this would grow in hot weather out of dry soil? Check them out as you enjoy this great county in your travels.
Life is good.
Mike Denny is president of the Blue Mountain chapter of the National Audubon Society. He can be reached at email@example.com, or by calling 6-8 p.m. weekdays at 529-0080.
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Variations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, such as patterns of DNA methylation, are transferred across generations, and therefore it is uncertain what role epigenetic variation may play in adaptation.
In Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differed substantially from that of a domesticated egg laying breed. Expression as well as methylation differences were largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation. Some of the inherited methylation differences were tissue-specific, and the differential methylation at specific loci were little changed after eight generations of intercrossing between Red Junglefowl and domesticated laying hens. There was an over-representation of differentially expressed and methylated genes in selective sweep regions associated with chicken domestication.
Our results show that epigenetic variation is inherited in chickens, and we suggest that selection of favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation states which are inherited independently of sequence differences, may have been an important aspect of chicken domestication.
Domestication; gene expression; tiling array; behaviour; methylationBackground
Chickens were domesticated from the Red Junglefowl (RJF) about 8000 years ago [1,2], and the changes in morphology, physiology and behaviour as a response to this have been immense. For example, most domesticated chickens grow to at least twice the size of RJF, become sexually mature at a lower age, lay manifold more and larger eggs, show a wide variation in plumage colour and structure, and have a different behaviour in a number of contexts, such as reduced fearfulness [3-6]. In general, domestic animals are assumed to have adapted to a life among humans by evolving higher flexibility in diet, better ability to breed in captivity, less stress susceptibility, and a more socially tolerant disposition [5,6]. It has been suggested that epigenetic mechanisms might be involved in cases like this [7] where wide-encompassing phenotypic changes occur in a short evolutionary time.
However, there is limited knowledge of the extent to which expression and epigenetic profiles are inherited in animals. Reliable inheritance is necessary in order for epigenetic variation to be a major component of any evolutionary process. We have earlier shown that stress-induced modifications in both behaviour and brain gene expression profiles in domestic chickens are to some extent transferred to the offspring [8,9], and other studies have shown similar transgenerational transmission in other species, including humans [10-12]. This indicates that some epigenetic variation may indeed be inherited, but the details and significance of this, as well as its putative evolutionary significance, remain to be elucidated.
One of the possible epigenetic mechanisms, which could be related to variation in gene expression, is methylation of cytosine, preferentially in so called CpG-islands of promoter regions [13,14]. Therefore, we targeted methylation and gene expression simultaneously to investigate whether any of those, or both, would differ between two populations of chickens, recently separated by domestication. We hypothesised that both methylation and gene expression would differ between the populations and show transgenerational stability, opening the possibility for both to be involved in domestication-related phenotypic changes.
By using expression and methylation arrays on hypothalamus samples, we show that profiles of gene expression as well as promoter methylation differ between domesticated White Leghorn layer chickens and their ancestors, the Red Junglefowl. There were also similar differences, although less pronounced, between phenotypically different families within breeds. The differences were largely maintained in the offspring, demonstrating a reliable inheritance of epigenetic states, and for some of the genes the differential methylation was maintained after eight generations of intercross. Our results therefore suggest that selection of favourable epigenetic variants may have been an important aspect of chicken domestication.
Results and discussion
Brain gene expression differences within and between populations
In this experiment, we studied variations in gene expression and methylation in brains of RJF and domesticated White Leghorns (WL), and their offspring. We focussed on thalamus and hypothalamus, brain regions involved in fear and stress responses, both of which have changed significantly during domestication [3,6]. Within each population, we selected parental animals with divergent phenotypes in order to maximise the within population genetic variation. Specifically, we used two pairs of each population, with pairs within population differing in their behaviour in a series of previously validated tests of stress reactions in chickens [6,15]. From these, totally 73 offspring were hatched and reared until three weeks of age, when they were tested in a fear test, similar to that used in the parents.
In both breeds, body weights differed between families in both generations, and behavioural scores, as measured in the fear tests, differed between families in both generations of WL, but not RJF (Additional file 1). Hence, morphological, and to some extent behavioural, phenotypes showed a significant and transgenerationally stable variation in the animals used for the present study. It should be noted that phenotyping was done at different ages in the two generations, which may have been the reason for the lack of transgenerational correlation in fear behaviour in RJF. All eight parents were sacrificed at an age of 373 days, and 48 offspring (12 from each pair) at 21 days, and from each brain, the thalamus-hypothalamus region was removed for extraction of both DNA and mRNA. For the offspring, eight pools of both were prepared, each consisting of six same-sex samples within families. Hence, there were in total eight parental single-animal samples, and eight pools of offspring samples. The mRNA was hybridized to a 38K Affymetrix chicken gene expression microarray, and the DNA was used for subsequent tiling array analysis of methylation. Between populations, there were in total 281 significantly (FDR-corrected P < 0.05) differentially expressed (DE) genes in the parents, and 1674 in the offspring. The lower number of DE genes in the parents could possibly be an effect of the lower power of detection given the smaller biological sample size in this generation. Between families within populations, only a few genes were significantly DE, and also DM was less frequent between families (Additional file 2). This indicates that expression and methylation profiles are relatively stable within breeds, but both may have changed considerably during domestication.
Additional file 1. Phenotypes of parents and offspring. The behavioural scores and weight data for the animals in the experiment.
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Additional file 2. Nrs of differentially expressed and methylated genes. Total numbers of significantly differentially expressed genes or methylated promoters (P < 0.05, FDR-corrected) in the different comparisons.
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Transgenerational stability of gene expression profiles
Out of the significantly DE genes in the parents (comparing populations), 86% percent (n = 242) were also significantly DE in the offspring (Additional file 3), and there was a distinct similarity in the expression differences in both generations (Figure 1a). The overall pattern of fold-change levels between populations (regardless of whether they were significant) was strongly correlated over generations (Figure 2 a), further showing a transgenerational stability in gene expression profiles. Also within populations, the overall pattern of fold-change levels between families was highly correlated across generations (Figure 2 b-c).
Additional file 3. Differentially expressed genes. A full list of all genes found to be differentially expressed, comparing breeds, in both generations, including their chromosomal alignment and accession numbers.
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Figure 1. Gene expression and methylation differences between populations and across generations. a. Heat map, showing the clustering of 242 differentially expressed genes, comparing parental Red Junglefowl (RJF) and White Leghorn (WL) layers, and their offspring. b. Heat map, showing clusters of differentially methylated genes comparing parental RJF and WL, and their offspring. Note that the gene set in b is not the same as in a. c. Average methylation levels (signal intensity from the microarray) for RJF and WL in the 145 promoter regions included in the heatmap in panel b. Circle-diagram displays the percentage of the promoter regions which were hypermethylated (green) and hypomethylated (red) in White Leghorns.
Figure 2. Correlations of differential expression and methylation of genes between generations. a-c, Correlations between generations of differential gene expression, comparing Red Junglefowl and White Leghorn (a); families within Red Junglefowl (b); and families within White Leghorns (c); d-f, Correlation between generations of differential methylation, comparing Red Junglefowl and White Leghorn (d); families within Red Junglefowl (e); and families within White Leghorns (f). The genes included in the analyses were selected based on the fact that they simultaneously occurred in both parents and offspring among top 1000 DE or DM, sorted by fold change.
We further used signalling intensities of individual probesets on each microarray to correlate global expression levels between parents and their own offspring, compared to offspring of other birds, and found a significantly higher correlation within families than between (mean difference in correlation coefficients 0.0017 ± 0.0002 (SEM), t = 8.2, P < 0.001). This was true both for RJF and WL, and further supports that specific brain gene expression profiles are indeed inherited.
Gene methylation: inheritance and differences between populations
For analysis of differential methylation (DM), we selected 3623 genes from the list of genes which had the highest fold changes in DE in both generations, both in the between- and within-population comparison. Note that only 281 of these were significant in parents and 1674 in offspring. For each of these genes, 50-75 bp-probes representing a region spanning from -7.25 kb upstream to +3.25 kb downstream of the transcription start point (hence mostly covering promoter regions and other cis-acting regulatory elements) were placed on a custom made tiling array. Methylated DNA immune precipitation (MeDIP) was used to enrich methylated DNA fragments, and after labelling and hybridisation, the relative levels of methylated to un-methylated DNA was assessed for each probe.
Out of the 3623 selected genes, 239 were significantly DM (FDR-corrected P < 0.05) when comparing RJF and WL parents, and 821 were DM in the corresponding comparison in the offspring. A smaller number were classified as DM when comparing between families within population (Table S2). A heat map of the genes classified as DM in both generations showed a highly consistent pattern across generations (Figure 1b). Furthermore, DM levels were significantly correlated between generations when comparing RJF with WL (Figure 2 d), and also to a lesser degree when comparing WL, but not RJF families (Figure 2 e-f).
Of the 145 genes which were significantly DM in both generations (Additional file 4; Additional file 5), 79% were hypermethylated in WL (Figure 1c). This is a highly significant bias (χ2 = 49.8, P < 0.0001), indicating that this breed has acquired novel methylation patterns during its selection history.
Additional file 4. Expression and methylation. Gene expression differences plotted against promoter methylation differences between WL and RJF offspring.
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Additional file 5. Differentially methylated genes. A full list of all genes, where the promotors were found to be differentially methylated, in both generations.
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We further analysed the relationship between DM and DE on the 3623 selected genes. There was no overall correlation between the level of DM of a gene (% of DM probes) and the degree of DE of the same gene (Additional file 4). Furthermore, there was no overrepresentation of DE genes among the top 100 DM promoters when compared to a random sample of 100 DM genes (χ2 = 2.1, P > 0.05). This is contrary to the common notion that methylation causes down-regulation of gene expression, but similar findings have recently been reported from other species, for example humans [16,17]. The finding is quite surprising, and indicates that the specific sites of methylation may be of major importance for gene regulation. For example, there may be a substantial difference between methylation of transcription factors compared to insulator sequences. Since we only analysed a 10 kb region around the transcription start site of each gene, we can not exclude that DM in other, more distant regulatory regions may be more closely connected to the expression level.
To illustrate examples of the transgenerationally stable methylation patterns observed, we show methylation graphs for four genes (ABHD7, GAB1, KSR1 and PCDHAC1) in Figure 3. In all four, the methylation pattern was reliably inherited, shown by the fact that the DM pattern was highly similar in parents and offspring. ABHD7 showed extensive DM ranging several kb downstream of the transcription start site. In none of the four genes, the significantly DM loci were in CpG-islands, so methylation must have targeted cytosines in other genomic contexts. Extensive methylation of non-CpG regions have recently also been reported for the human methylome [16,17], and it remains unknown which functions these epigenetic variants may serve.
Figure 3. Transgenerational stability of methylation patterns in specific genes. a-h, Differential methylation levels (Log2 fold change) of promoter regions, comparing Red Junglefowl and White Leghorn, are shown with a resolution of 50-75 bp-regions in parents and offspring for each of the genes a, b, ABHD7, c, d, GAB1, e, f, KSR1, and g, h, RAPGEF1. Transcription direction and exons (blue boxes) are shown, and red arrows point at bars or groups of bars where significant levels of differential methylation are found (also indicated by red bars). Locations of CpG-islands are indicated in yellow for each region.
Verification of differential methylation with independent animals, tissues and method
To verify the results of the array-based methylation analysis, we arbitrarily selected four genes, which were DM on the tiling arrays in either parents or offspring, FUCA1, PCDHAC1, TXNDC16, and RUFY3, and replicated the findings for those, using a different technique and a different animal material. Hypothalamus/thalamus regions from eight five-weeks old RJF and eight WL (same strains as earlier, but different parents) were dissected and treated as described above. The DNA was bisulfite-treated, and the degree of methylation was determined in the regions that were significantly DM on the tiling array using methylation sensitive high resolution melting (MS-HRM) analysis.
All four genes were significantly DM in the same direction as found on the tiling array (FUCA1 and PCDHAC1 hypermethylated in WL; RUFY3 and TXNDC16 hypomethylated) (Figure 4a). This suggests that the tiling array produced reliable results and that the observed methylation differences are representative for the population differences at large.
Figure 4. Verification of differential methylation of four arbitrarily chosen genes. a. Methylation differences between Red Junglefowl and White Leghorn in three different tissues, estimated by methylation sensitive high resolution melting (MS-HRM) analysis. The table shows the normalized fluorescent intensities together with the statistical analysis of 6-8 individual samples per population, at a temperature where positive and negative methylation controls showed highest intensity difference (Tmd). The right column shows the number of SNPs present in the PCR-product amplified by the primers for the region analysed. b-d, The average methylation level of the promoter regions of three of the genes, FUCA1 (b), PCDHAC1 (c) and RUFY3 (d), in blood samples from F8-generation intercross birds between Red Junglefowl and White Leghorns. The birds differed as indicated in their genotype on an SNP-marker close to the differentially methylated locus.
In order to check for tissue-specificity of the DM, we also performed HRM on the same four genes, using DNA-pools prepared from cerebellum and blood from the offspring samples included in the tiling arrays. All four genes were significantly DM in cerebellum. In blood, FUCA1 and PCDHAC1 were significant, while RUFY3 showed a tendency for DM (P = 0.08) (Figure 4 a). The fact that TXNDC16 was not DM in blood indicates that this gene shows tissue-specific, heritable methylation.
Genetic stability of methylation differences
There is a risk that the methylation differences detected by the MeDIP technique could be affected by sequence differences in the promoter regions used for the arrays. To exclude this possibility, we used the recently published resequencing data of Red Junglefowl and domestic chickens [18] to check the 145 significantly DM probes in both parents and offspring for possible deletions, insertions and SNP density. Apart from occasional SNPs (Additional file 5), no major sequence differences were detected.
The methylation differences observed may be a result of either inheritance of the epigenetic changes independently of genetic changes, or result from sequence differences which secondarily affect methylation at close or remote loci. This is more difficult to differentiate, since it would require extensive resequencing data of the individuals actually used in the study, combined with, for example, methylation QTL-studies.
To suggestively analyse whether differential methylation of specific loci are caused by sequence differences we decided to study its genetic stability and segregation over several generations. For this purpose, we used a total of 18 birds from the eighth generation of an intercross between RJF and WL. In this population, genetic recombinations in each generation have broken up the linkage between adjacent loci, and we could therefore check for both stability of the methylation sites, and for possible cis- or trans-regulation of these.
From this group of advanced intercross birds, we selected individuals, which were homozygous for either the WL or RJF-allele, or heterozygotes, of an SNP located within 176-1449 kb of the locus showing DM. Using HRM analysis on DNA from blood, extracted from these different genotypes, we again analysed the methylation on FUCA1, PCDHAC1 and RUFY3 in these individuals (Figure 4b). For FUCA1, we found two different non-significant, but distinct, methylation levels, where the birds homozygous for the WL-marker were hypermethylated, and heterozygotes were similar to the ones homozygous for the RJF-marker (P = 0.07). With respect to PCDHAC1, the three genotypes were significantly different (P < 0.001), with heterozygotes having a methylation level falling between the hypermethylated WL homozygotes, and the RJF genotypes. RUFY3 showed a high level of methylation, which was not significantly different between the three genotypes. Hence, two of the three DM loci were stable over the eight generations of intercrossing, and tended to segregate according to genotype at the locus. This is consistent with a cis-regulating mechanism, showing a dominant inheritance of hypomethylation in genotypes with RJF alleles for FUCA1, and an intermediate, codominant inheritance in PCDHAC1. RUFY3 may possibly be under control of trans-acting loci, which have segregated during the intercrossing.
Although these results are not conclusive, they suggest that sequence differences may determine the DM for at least two of the three loci, possibly for all of them. This further suggests that selection during domestication may have targeted genotypes which modify the epigenomes, perhaps affecting phenotypes indirectly.
Genetic pathways
To examine which genetic pathways and functions that may have been affected by DE and DM, we performed a gene ontology (GO) analysis. We analysed the DM and the DE genes in each generation separately, and then selected those GO-terms and KEGG pathways (P < 0.1), which were significantly enriched in both generations (Additional file 6).
Additional file 6. Gene function. Gene ontology and KEGG pathway annotation for the genes which were either differentially expressed or differentially methylated in both generations, comparing between breeds.
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A majority of the enriched GO terms are related to phosphorylation and kinase activity, important aspects of intercellular signalling. Looking specifically at the KEGG pathways enriched among DM and DE genes in offspring only (where the biological sample is considerably larger), the analysis shows that MAPK signalling pathway (which, for example, is associated with stress responses), long-term potentiation (affecting memory consolidation), neurotrophin signalling pathway (involved in neural differentiation) and GnRH signalling pathways (related to reproduction) are enriched. All these are potentially interesting from a domestication perspective, in that they may be related to well documented differences between RJF and WL in stress tolerance, behaviour and reproduction.
Over-representation of epigenetically affected genes in selective sweep regions
We considered that the epigenetic differences between the layer breed and their ancestor could reflect general effects of selection during domestication, as suggested above, perhaps being related to differences in the domestication induced phenotypes, such as growth, feeding behaviour and social tolerance. If so, we would expect the epigenetic differences to be accumulated in genomic regions which have been under selection during domestication. Therefore, we compared our data to one of our earlier, and recently published, datasets on chickens [18]. This dataset consists of an extensive list of selective sweeps related to chicken domestication, based on resequencing of populations of RJF and a number of domesticated breeds. In total, 149 selective sweeps present in all domestic chickens, and 134 present in egg laying breeds only, were used. A sweep was defined as a 40 kb region where the heterozygosity Z-score was below -4.
There were 216 DE genes (DE in both generations) with annotated loci within the 975 Mb of the genome covered by the sweep analysis. Five of them were situated within 50 kb of selective sweeps present in all domestic chickens (non-significant association, based on a permutation test; P > 0.1), and nine in the laying breed sweeps (significantly more than expected by chance; P < 0.05).
We performed the same analysis on 134 DM loci, and found that four were within 50 kb of sweeps in all domestic chickens (non-significant; P > 0.1), and six in laying breed sweeps (P < 0.05). The significant overlapping genes in laying breed sweeps are shown in Additional file 7.
Additional file 7. Selective sweep representation. Genes which were differentially expressed or methylated between breeds in both generations, and significantly overrepresented in selective sweeps associated with domestication.
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It is interesting to note that ABHD7, which was the strongest DM and one of the strongest DE genes in our experiment, is positioned in a laying breed sweep. This gene is named EPHX4 in humans, and is related to detoxification of exogenous chemicals [19]. Based on its position in a selective sweep, and its differential methylation and expression, it would appear that the epigenetic variant of the gene (or the genotype affecting the epigenetic state of it) may have been selected during domestication. KSR1, an important gene in MAPK/Ras dependent signalling [20], as well as ADRA2C, an alpha adrenoreceptor that may be related to egg laying [21] and regulation of the sympathetic stress reaction [22], are also situated in laying breed sweeps.
Although our data do not allow us to conclude on which genes and which sweeps that are associated with specific phenotypes, they suggest that selection of epigenetic variation may have been an important part of chicken domestication.
General discussion
Our findings show that differential methylation and gene expression in hypothalamus/thalamus are abundant in a comparison between domesticated White Leghorn layers and their wild ancestors, the Red Junglefowl. Many of these epigenetic differences are inherited, demonstrating transgenerational stability. It is possible that these differences are a result of selection during domestication, targeting either sequence differences which affect epigenetic states of specific loci, or epigenetic states which are not related to sequence differences.
The causal relationship between methylation and gene regulation is not clear, since differential methylation was associated with both up- and down-regulation of the gene expression, or did not affect it at all. Since similar dissociation between methylation and gene expression has recently been found in the human genome as well [17,23], this indicates that epigenetic regulation is more complex than previously assumed. Whereas it is often believed that methylation of promoter regions is associated with down-regulation of gene expression, our results indicate that gene regulation is more complex than so. For example, chromatin structure may be more important than commonly assumed. Furthermore, we found that CpG-islands are not always methylated, so there may also be evolutionary contraints on methylation sites, hence affecting the rate with which epigenetic adaptations may occur in different parts of the genome. Although speculative, these issues should be considered in future research.
Some of the methylation differences observed appear to be tissue-specific, whereas others affect a wider range of cells. The mechanism whereby differential methylation at a particular locus only in, for example, the brain can be transferred from parents to offspring remains elusive. In Drosophila, similar observations have been made with respect to gene expression, where induced differences specifically in the brain can be transmitted via sperm and cause tissue specific effects in the next generation [24]. Possibly, microRNA regulation may be involved [25], and both sperm and eggs may also transfer specific histone variants [26]. There is also a close link between genetics and epigenetics, in that the epigenetic state of a particular locus is determined by both genetic and epigenetic variations at other loci [23,25].
Stable inheritance of epigenetic variants has been demonstrated in plants [7,13,27,28]. Also in mammals (mainly in rodents and humans), there is increasing evidence that this occurs widely [10,29]. Our results are the first to demonstrate the same in birds, and furthermore show a long-term stability over several generations of specific methylation states.
Although we have only studied one population each of Red Junglefowl and domesticated chickens, the observations in this experiment could indicate that selection of favourable epigenomes, or genotypes favourably affecting the epigenome, may have been an important aspect of chicken domestication. However, further studies are needed, where methylation of specific genes are analysed in a wide range of domesticated populations, analogous to the recent study of sequence variation in the domesticated chicken genome [18].
Both gene expression and promoter methylation profiles in hypothalamus differed between White Leghorn chickens and their wild ancestors, the Red Junglefowl. Family differences within breed as well as breed differences were maintained in the offspring, showing a reliable inheritance of epigenetic states, which may have been an important mechanism involved in the rapid evolutionary changes of chickens during domestication.
Ethics statement
The experiment and all its procedures were approved by the regional Ethical Committee.
Animals and selection
We used two breeds of chicken: a domesticated egg layer White Leghorn (WL) and a wild type Red junglefowl (RJF). The population backgrounds have been described elsewhere [30]. The WL was an outbred mixture of different leghorn breeds, established 1970, and since then kept in a closed population at the university. The RJF stem from an outbred zoo population, kept at the university for 10 years (one generation per year) with a generation size of about 100 individuals. For more details about breeding and housing routines, see [6].
From each breed, two breeding pairs were selected based on divergent performance in four different fear tests conducted between 153-168 days of age. The selection criterion in each test was the frequency of standing/sitting alert, where a longer duration signifies a higher fear level [6]. The tests were: 1) Behaviour in an open field during 10 min (this test was repeated at 286 days for check of consistency); 2) Behavioural response for 5 min after novel object introduction; 3) Behaviour 5 min before and 5 min after exposure to an aerial predator model; 4) Fearful behaviour toward a human. All tests were conducted in the same arena (0.5 × 1.5 m), and details of the test procedures have been described elsewhere [6]. All birds were weighed at 373 days of age.
Eggs were collected for five weeks from each individual female in the breeding pairs and incubated in the same incubator in three consecutive batches. Numbers of eggs in the batches were balanced for family. Each batch consisted of 9-18 birds, and the batches were housed separately in mixed groups under the same conditions as the parents. At day 20 all offspring were tested in a similar open field arena as the parents.
For HRM verification of the breed differences in methylation levels, we bred 8 offspring of each breed (four females and four males), using different animals (but same populations) as those above. These chicks were culled and sampled in the same way as described below.
For studying the long-term stability of methylated loci, we used 18 birds from generation eight of an intercross between RJF and WL. The details of this intercross has been described elsewhere [3]. Briefly, one male RJF and three WL (same populations as those used in other parts of the present experiment) were used to breed 36 F1, and these were intercrossed to produce about 1000 F2. From generation F3 onwards, about 100 birds per generation have been maintained by random mating and pedigree hatching up to generation F8.
RNA and DNA isolation
Parents were culled at day 373 after hatch and their offspring at day 21. A sample of six male and six female offspring (balanced between batches) were chosen from each family. A part of the brain enriched of thalamus/hypothalamus was anatomically dissected and immediately snap frozen in liquid nitrogen, and blood was collected immediately after culling. Samples were homogenized in TRI-reagents (Ambion) using the FastPrep® -24 homogenization system with Lyzing matrix D tubes (MP Biomedicals).
RNA was further extracted with the same method as has been used previously [8,9] following the protocol of the TRI-reagent manufacturer, except for a modification adding 0.25 ml isopropanol and 0.25 ml RNA-precipitation solution (1.2 M NaCl, 0.8 M disodium citrate). After the TRI-based RNA extraction, an RNeasy kit (Qiagen) was used to further purify the samples.
DNA was extracted from the same TRI homogenate as the RNA. Precipitation was done on ice by adding 150 μl of 100% ethanol to 300 μl TRI homogenate followed by gentle vortexing and 5 min 4°C incubation. After centrifugation in 12000× g for 10 min, the supernatant was discarded and the pellet resuspended in the ATL buffer of the DNeasy kit (Qiagen). 4 μl of 10 mg/ml Rnase A was then added, incubated 2 min at room temperature, followed by addition of 20 μl of 10 mg/ml proteinase K (Qiagen) and 3 min incubation at 56°C. DNA was then extracted according to the DNeasy protocol for animal tissue. Quality and quantity of both RNA and DNA was measured on a Bioanalyzer® instrument (Agilent Technologies) and NanoDrop® ND-1000 spectrophotometer (Thermo Scientific).
Both RNA and DNA extractions were treated individually for the parents, but as pools of six same-sex samples in the offspring.
Gene expression microarray
This part of the experiment was performed at Uppsala Array Platform at Uppsala University, Sweden http://www.medsci.uu.se/klinfarm/arrayplatform webcite. A total of 16 GeneChip Chicken Genome Arrays (Affymetrix Inc.) were used to measure the expression of 33457 transcripts. Biotinylated fragmented RNA was prepared for each sample using standard procedures in GeneChip ® 3' IVT Express Kit User's manual (Affymetrix Inc., Rev. 1, 2008). This was followed by array hybridization for 16 h in 45°C under constant rotation. Washing and staining was performed in a Fluidics Station 450 and scanned using the GeneChip Scanner 3000 7 G (Affymetrix Inc.).
Gene expression data analysis
Analysis of the gene expression was performed using the statistical software R http://www.r-project.org webcite with Bioconductor packages http://www.bioconductor.org webcite. Normalization was done with the RMA method [31] and differentially expressed genes were evaluated using fold change in combination with a Bayes moderated t-test [32] adjusted for false discovery rate [33].
Correlation analysis, comparing the fold change of differential expression in parents and offspring, was done using Statistica v 9.1. Cluster analysis and heat maps were performed with the Genesis software v 1.7.5 [34].
DNA-methylation tiling array design
For methylation analysis, we selected the genes which had the highest fold change of expression in both generations of the breed comparison in the microarray data. From each gene, the promoter regions, defined as 7.25 kb upstream and 3.25 kb downstream of the transcription start site (Ensemble genebuild WASHUC2), were used to design a custom 385 K DNA-methylation tiling array (Roche-NimbleGen). In total 3623 promoter regions were tiled to the array, with 50-75 mer probes and 100 bp median spacing, by the Madison design team at Roche-NimbleGen.
Methylated DNA Immunoprecipitation (MeDIP)
Protocols of MeDIP with buffer descriptions and general procedures have been published elsewhere [35,36]. Fragmentation of 6 μg thalamus/hypothalamus DNA was performed using a BRANSON sonifier 250 with a 13 mm disruptor horn (101-147-037) and a 3 mm tapered microtip (101-148-062). Samples were diluted with 450 μl 1 × TE in 1.5 ml tubes and sonicated at 10% amplitude by short 0.5 sec pulses (20 in total) with a rest between pulses of 0.5 sec. Fragment lengths of between 300-1000 bp were verified on a Bioanalyzer (Agilent technologies). After sample denaturation 10 min at 95°C, reference samples of 10 μl was taken from each of the original samples and frozen. The remaining samples underwent methylated DNA immunoprecipitation by first diluting them in 1 × TE to 450 μl, adding 51 μl of 10 × IP buffer and 10 μg of 5-meC antibody (Diagenode). Samples were then incubated in 4°C for 2 h on a rotating platform, whereby 50 μl of clean Dynabeads Protein G (Invitrogen) in 1 × IP buffer was added and followed by an identical 2 h incubation. The beads-antibody-antigen complex was washed 3 times by placing the samples on a DynaMag-spin magnet, discarding the supernatant and adding 1 ml of 1 × IP. Complex digestion was done by adding 250 μl of Proteinase K digestion buffer and 5 μl Proteinase K (20 mg/ml), followed by rotation over night in 50°C. DNA was further purified by phenol/chloroform procedures with glycogen/ethanol -80°C precipitation. The pellet were washed in 100% ethanol and resuspended in 60 μl 1 × TE. All samples, references as well as MeDIP's, were then whole genome amplified using the WGA2 kit (Sigma-aldrich) and purified with QIAquick PCR purification kit (Qiagen).
DNA-methylation tiling array labeling and hybridization
Labeling and hybridization was performed at Roche-NimbleGen service lab at Iceland, Reykjavik, using standard protocols [37]. In short, MeDIP and reference samples were labeled with Cy5 and Cy3 respectively, using the NimbleGen Dual-Color DNA Labeling Kit. The MeDIP-Cy5 and reference-Cy3 samples from each tissue sample were then co-hybridised to the DNA-methylation tiling array using the NimbleGen Hybridization Kit and Hybridization System. After washing with NimbleGen Wash Buffer Kit the slides were scanned by a NimbleGen MS 200 Microarray Scanner.
Tiling array data analysis
Methylation data analysis was performed using Bioconductor in the open source R statistical software environment [38]. To not loose genome wide methylation differences, the RINGO package [39] was used to preprocess the data within arrays by Tukey's biweight normalization and between arrays with A-quantile normalization. Significantly differentially methylated probes (FDR adjusted P-values) were extracted using the limma package [32]). Since promoters sometimes involved more than one significant probe, in all comparisons with the gene expression data and correlations across generations, only the most significant probe of each promoter was considered. All significant probes that were stable across generations were checked for the occurrence of SNPs using a list of SNPs detected in a multibreed resequencing study recently published18.
Methylation sensitive high resolution melting analysis
Verification of differentially methylated genes, and analysis of differential methylation in alternative tissues and in F8-intercross birds, was done by methylation sensitivehigh resolutions melting (MS-HRM) analysis, principally as described by [40]. If not said otherwise, all procedures followed manufactures recommendations. DNA was prepared from brain tissues as above and from blood using the DNeasy Blood and Tissue kit adjusted for nucleated blood (Qiagen).
Positive control samples were synthesized by in vitro methylation, using a nuclease-free water diluted reaction mix of 16.5 μl, including an all bird pool of 1 μg DNA, 2 μl 10× NEBuffer2, 2 μl SAM (640 μM), 1 μl SssI methylase (4 U/μl) (New England BioLabs Inc.). After 2 h of incubation at 37°C, an additional 2.5 μl SAM was added to each sample, followed by another 2 h incubation and then termination by heating at 65°C for 20 min.
Negative control samples were synthesized by whole genome amplification on the same all bird DNA pool (10-20 ng/μl) as for the positive control using the REPLI-g Mini Kit (Qiagen). The whole volume of amplified negative controls were then mixed with 200 μl Buffer AL and 200 μl ethanol (99%) and purified with the DNeasy Blood and Tissue kit (Qiagen). 1 μg DNA from both individual samples and controls were bisulfite treated using the EpiTect Bisulfite Kit (Qiagen).
PCR and High resolution melting was performed on a Rotor-Gene 6000 thermocycler (Corbett Research). 1 μl of the bisulfite treated samples/controls were prepared in a 10 μl PCR mix using EpiTect HRM PCR Kit (Qiagen). A calibration series was also amplified using a mixture of positive and negative controls at 100%, 75%, 50%, 25% and 0% of methylated DNA. PCR was performed in 45 cycles as follows: denaturation 10 s at 95°C, annealing at 30 s 54-55°C (primer dependent) and extension 10 s at 72°C. MS-HRM was run in the interval of 70°C to 90°C, with a 2 s 0.05°C steps, acquiring fluorescence data at the Rotor-Gene HRM channel. Primer sequences and annealing temperatures can be seen in Additional file 8. All MS-HRM reactions were run in triplicates.
Additional file 8. Primer structures. The bisulfate converted primers used in HRM.
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This file can be viewed with: Adobe Acrobat Reader
Annotation and GO analysis
Affy Chicken ID, EntrezGene ID, EnsembleGene ID, WikiGene ID and chromosomal regions were extracted from the Affymetrix annotation file (release 29), and further annotated with Ensemble's BioMart tool [41]. We used DAVID 6.7 http://david.abcc.ncifcrf.gov webcite to extract significantly enriched gene ontology terms and KEGG pathways within our datasets [42,43]. To increase the possible DAVID hits we first extracted the homologous human Ensembl ID of our chicken genes in BioMart [41]. CpG island prediction was performed with EMBOSS CpGPlot [44].
Analysis of sweep overlaps
219 DE genes and 134 DM promoters (significant in both parents and offspring) fell within the 975 Mb that previously has been searched for selective sweeps18. To investigate whether genes or promoters were significantly enriched in sweep regions, 1000 sets of random intervals were generated over the 975 Mb for each analysis, each interval in each set chosen to represent one DE or one DM gene. The number of overlaps between the randomly generated interval and a sweep (within 50 kb of the sweep) was compared to the actual number of real overlaps. A probability of the observed coincidence of less than 5% was taken as a significant association between DM/DE genes and sweeps.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
DN performed the experiments, analysis and lab work, JB and MJ assisted in HRM-analysis, CR performed the sweep analysis, DW performed the F8-breeding and genotyping, LA developed the intercross analysis, and PJ, together with DN, planned and conceptualised the experiment, and wrote the paper. All authors read and approved the final manuscript.
Accession numbers
The microarray data from this study have been deposited at ArrayExpress and can be accessed using the following accession numbers: 1) Parents gene expression [E-MTAB-644]; 2) Offspring gene expression [E-MTAB644]; 3) Parents DNA-methylation [E-MTAB-648]; 4) Offspring DNA-methylation [E-MTAB-649]; 4) Tiling array design [E-MEXP-2041])
The project was supported by grants from The Swedish Research Council (2008-14496-59340-36) and The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (221-2007-838).
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text: Darvant Italy Show all reviews | Esprit du Tigre / Spirit of the Tiger by HeeleyAs soon as i inhaled a vial of Esprit du Tigre i thought: medicinal agarwood and aromatic spices. I don't think oudh is present but undoubtedly the juice is a medicinal and spicy bomb which smells anyway cool and slightly aromatic (because of a starring initial chord of peppermint and camfor) further than tasty of cinnamon and finally virile of vetiver. This is a masculine to me and is an almost sporty or anyway dynamic kind of juice. Going on the development the medicinal effect produced by the link of spices and camfor fades a bit and leaves the stage to a peppery and spicy elegant vetiver. An interesting fragrance but nothing else. 18th April, 2012 (Last Edited: 20th August, 2012) |


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Horn Concerto - Rondo
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Reenactors recreate the Battle of Gettysburg on its 150th Anniversary
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Spectators watch a Civil War wedding where three couples in period... News PhotoAnniversary,Arts Culture and Entertainment,Civil War,Couple - Relationship,Dress,Event,Gettysburg,Historical Reenactment,Horizontal,Human Interest,Lifestyles,Spectator,USA,Watching,Wedding,Wedding VowsPhotographer Christian Science MonitorCollection: Christian Science Monitor 2013 The Christian Science MonitorGETTYSBURG, PA - JULY 5: Spectators watch a Civil War wedding where three couples in period dress renewed their vows, during the Battle of Gettysburg reenactment on the 150th anniversary year of the event, on July 5, 2013 in Gettysburg, Pennsylvania. More than 10,000 reenactors came to the biggest ever reenactment of the event, drawing thousands of spectators. (Photo by Melanie Stetson Freeman/The Christian Science Monitor via Getty Images)


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Oracle FAQ | Your Portal to the Oracle Knowledge Grid |
Home -> Community -> Mailing Lists -> Oracle-L -> RE: [VulnWatch] Patch available for multiple critical flaws in Oracle
Now, Now, They also emerge in early spring to produce a very fine =
Maple Syrup. If for no other reason we need to allow them their way of =
Dick Goulet
Senior Oracle DBA
Oracle Certified 8i DBA
-----Original Message-----
From: Ruth Gramolini [mailto:rgramolini_at_tax.state.vt.us]
Sent: Thursday, September 02, 2004 9:58 AM
To: oracle-l_at_freelists.org
Subject: RE: [VulnWatch] Patch available for multiple critical flaws in
You're just jealous. RBG
-----Original Message-----
From: oracle-l-bounce_at_freelists.org
[mailto:oracle-l-bounce_at_freelists.org]On Behalf Of Mercadante, Thomas F
Sent: Thursday, September 02, 2004 8:05 AM
To: 'oracle-l_at_freelists.org'
Subject: RE: [VulnWatch] Patch available for multiple critical flaws in
Ruth lives in a pagan society in a special part of America called =
They also hug trees, worship gnomes, and dance naked during the summer
The rest of the year, they live under deep deep snow, emerging when the =
is warm again.
-----Original Message-----
From: Carel-Jan Engel [mailto:cjpengel.dbalert_at_xs4all.nl]
Sent: Wednesday, September 01, 2004 3:28 PM
To: oracle-l_at_freelists.org
Cc: Claus Lund
Subject: RE: [VulnWatch] Patch available for multiple critical flaws in
Ruth, what country are you in (or at least NGSSoftware?). Here in Europe =
don't have a 31st of november....). Or do you 'celebrate' the leap year =
November ISO February? ;-)
On Wed, 2004-09-01 at 15:19, Ruth Gramolini wrote:
> NGSSoftware are going to withhold details about these flaws for three
> months. Full details will be published on the 31st of November 2004.
> This three month window will allow Oracle database administrators the
> time needed to test and apply the patch set before the details are
> released to the general public. This reflects NGSSoftware's new
> approach to responsible disclosure.
Best regards,
Carel-Jan Engel
If you think education is expensive, try ignorance. (Derek Bok) =
-- Archives are at http://www.freelists.org/archives/oracle-l/ FAQ is at http://www.freelists.org/help/fom-serve/cache/1.html ----------------------------------------------------------------- --- To unsubscribe - = mailto:oracle-l-request_at_freelists.org&subject=3Dunsubscribe To read recent messages - http://freelists.org/archives/oracle-l/09-2004 --- To unsubscribe - = mailto:oracle-l-request_at_freelists.org&subject=3Dunsubscribe=20 To read recent messages - http://freelists.org/archives/oracle-l/09-2004 --- To unsubscribe - mailto:oracle-l-request_at_freelists.org&subject=unsubscribe To read recent messages - http://freelists.org/archives/oracle-l/09-2004Received on Fri Sep 03 2004 - 07:47:49 CDT