Pig Genome Offers Insights Into the Feistiest of Farm Animals

The pig and its cousin the wild boar have much in common with humans. They are world travelers. They're adaptable, invasive and often damage their own habitat. They are easy to seduce (with food) and susceptible to domestication, but when conditions allow, they revert to a feral lifestyle.
A new genomic analysis reveals some new, unexpected and potentially beneficial similarities between pigs and humans, along with a few distinct differences. The International Swine Genome Sequencing Consortium -- led by researchers at the University of Illinois, Wageningen University in the Netherlands and the University of Edinburgh -- conducted the analysis. Theirs is the most thorough genomic study yet conducted of the domestic pig and its wild boar counterparts.
A report of the study appears as the cover article in the November 15, 2012, issue of the journal Nature.
"It is exciting that the genomic sequence of the domestic pig now is in the public domain and available to enable more powerful approaches to domestic swine and pork improvement," said Ronnie Green, University of Nebraska Vice Chancellor for the Institute of Agriculture and Natural Resources and an early supporter of the pig genome sequencing project at the U.S. Department of Agriculture. "It will also aid efforts to use the pig as a model for biomedical research and the improvement of human health."
"This new analysis helps us understand the genetic mechanisms that enable high-quality pork production, feed efficiency and resistance to disease," said Sonny Ramaswany, the director of the U.S. Department of Agriculture's National Institute of Food and Agriculture. "This knowledge can ultimately help producers breed high-quality swine, lower production costs and improve sustainability."
The researchers compared the genome of a common farm pig, Sus scrofa domesticus, with those of 10 wild boars -- all from different parts of Europe and Asia. They also compared the pig genome with the human, mouse, dog, horse and cow genomes.
The team discovered new details of Sus scrofa evolution after the ancestors of the domestic pig, which most resembled today's wild boars, first emerged in Southeast Asia and gradually migrated across Eurasia.
Comparisons of Asian and European wild boars revealed significant genetic differences, the result of their separating from one another roughly 1 million years ago, said University of Illinois Vice President for Research Lawrence Schook, a principal investigator on the study.
"They have been separated so long that the Asian and European lineages are almost sub-species now," Schook said. The European and Asian wild boars lost a lot of genetic diversity about 20,000 years ago, likely as a result of a global glaciation event.
Comparisons of domestic and wild pigs also "revealed a clear distinction between European and Asian breeds," the researchers wrote. This adds to the evidence that "pigs were independently domesticated in western Eurasia and East Asia."
"We had evidence from previous studies, but those studies focused on the mitochondrial DNA, a small DNA molecule only inherited from the mother," said Wageningen University professor Martien Groenen, also a principal investigator on the study. "With the complete genome sequence of multiple wild boars we now have a much clearer picture about these events."
"This understanding of the genetic origins of modern pigs is important as we breed pigs to meet growing demand more efficiently and to resist old and emerging diseases," said Alan Archibald, a professor at The Roslin Institute at the University of Edinburgh and a principal investigator on the study.
Some gene families are undergoing relatively fast evolution in the domestic pig, with immune genes and (perhaps not surprisingly) olfactory genes quickly expanding. The pig has more unique olfactory genes than humans, mice or dogs, the researchers report.
And while pigs can smell a world of things humans and many other animals can't -- think truffles -- their sense of taste is somewhat impaired.
"Pigs have a high tolerance for eating things that have a lot of salt or that we would find repulsive by taste," Schook said.
Pigs have significantly fewer bitter taste receptor genes than humans, for example, and genes involved in perception of sweet and umami (which humans perceive as meaty) flavors are also different in pigs and humans, the researchers found.
"Understanding the genes that shape the characteristics of pigs can point to how and why they were domesticated by humans," Archibald said. "Perhaps it was their ability to eat stuff that is unpalatable to us humans."
The new analysis also supports the use of the pig in studies of human diseases.
"In total, we found 112 positions where the porcine protein has the same amino acid that is implicated in a disease in humans," the researchers wrote.
By also sequencing the genomes of another 48 pigs, "we identified many more gene variants implicated in human disease, further supporting the pig as a valuable biomedical model," Groenen said.
Some of the protein aberrations pigs share with humans are associated with obesity, diabetes, dyslexia, Parkinson's disease and Alzheimer's disease, the researchers report.
The new analysis also has important implications for agriculture, particularly since the domestic pig still has an ancestor-like wild cousin on the loose, the researchers said. Unlike the domestic cow, whose ancestors, the aurochs, are now extinct, the porcine lineage has a lot of genetic diversity remaining.
"We can easily go find genes that might be still in the wild that we could use for breeding purposes today," said Schook, who is the Gutgsell Professor of Animal Sciences, Bioengineering, Pathobiology, Nutritional Sciences, Pathology and Surgery at Illinois.
"This study demonstrates the benefits of basic genomic research on agricultural animals and their closest living relatives," said U. of I. President Bob Easter, who helped secure funding for the pig genome sequencing effort when he was the dean of the College of Agricultural, Consumer and Environmental Sciences at Illinois. "This work has important implications for agriculture, contributes to our understanding of evolution and will aid in human medicine," said Easter, who also is an emeritus professor of animal sciences and of nutritional sciences.

My Microbes: New Genetic Fingerprint Lives in Your Gut

Our bodies contain far more microbial genes than human genes. And a new study suggests that just as human DNA varies from person to person, so too does the massive collection of microbial DNA in the intestine.
The research is the first to catalog the genetic variation of microbes that live in the gut, where they extract nutrients from food, synthesize vitamins, protect against infections, and produce compounds that naturally reduce inflammation. The widespread genetic diversity uncovered by the scientists can help them understand how our microbial genes work together with our human genes to keep us healthy or, in some cases, to cause disease.
The study, by researchers at Washington University School of Medicine in St. Louis and the European Molecular Biology Laboratory in Heidelberg, Germany, is published online Dec. 5 in Nature.
"Surprisingly, each of us can be identified by the collective DNA of our gut microbes," says corresponding author George Weinstock, PhD, associate director of The Genome Institute at Washington University."That collection is individualized, completely analogous to our human genome. Differences in the way individuals respond to various drugs or the way they use specific nutrients can be traced to the genetic variation in our microbial genes as well as in our human genes."
The researchers analyzed the microbial DNA in 252 stool samples from 207 individuals living in the United States and Europe. All the subjects had participated in one of two recent high-profile initiatives to catalog the diverse species of microbes that live in and on the body. Neither of those studies -- the Human Microbiome Project, funded by the National Institutes of Health, and the Metagenomics of the Human Intestinal Tract (MetaHIT) project, funded by the European Commission -- looked at the genetic variation of the microbial genomes in the body.
For the new study, the researchers zeroed in on 101 species of microbes commonly found in the intestine, identifying more than 10 million single-letter changes in the collective DNA of those microbes. They also found numerous other DNA alterations, including insertions, deletions and structural changes.
In 43 subjects for whom the researchers had two stool samples collected at least a month apart (most were collected six months to a year after the initial sample), the researchers found very little variability in the microbial DNA over time, although the species of microbes in the intestine fluctuated.
"The microbial DNA in the intestine is remarkably stable, like a fingerprint," Weinstock explains. "Even after a year, we could still distinguish individuals by the genetic signature of their microbial DNA."
Babies become colonized with microbes as they pass through the birth canal and into the world. Those microbes come from their mothers and from the environment. Exactly how the microbes shape our lives is not yet known, but in the gut research has suggested that an imbalance of bacteria may contribute to irritable bowel syndrome, Crohn's and even obesity.
With this new catalog, the researchers can begin to understand the selective forces that shape the microbiome -- the collection of microbes and their genes -- in the intestine.
"The DNA of our microbes is a historical record of the microbial evolution in our bodies," says co-author Makendonka Mitreva, PhD, assistant professor of medicine. "Many of these organisms would have colonized us when we were very young and would have grown and evolved with us throughout our lifetimes."
The information gleaned from future studies of the gut microbiome also may help scientists determine how the microbial genes can be manipulated to improve human health and the effectiveness of certain medications, she adds.
http://www.sciencedaily.com/releases/2012/12/121205132159.htm

Sleeping Giants Discovered: Largest Black Holes Ever Measured Found in 'Nearby' Galaxies

Astronomers recently discovered the most massive black holes to date. Found in two separate nearby galaxies roughly 300 million light years away from Earth, each black hole has a mass equivalent to 10 billion suns.
"We knew that really large quasars, which are powered by matter falling into black holes, existed in the early universe," said Chung-Pei Ma, an astrophysicist at the University of California, Berkeley and co-author of an article that will be published in Nature on Dec. 8.
"What we hadn't yet found was where the remnants of those quasars--equally large black holes--were in the current universe," she said. "The boisterous quasars may have passed through a turbulent youth to become the quiescent giant elliptical galaxies we see today, harboring hidden black holes at their centers."
Black holes are made of matter so dense that even light can't escape their intense gravitational fields. Exploding stars--known as supernovae--can create relatively small black holes only a few times more massive than the sun, but researchers think these monster black holes are formed in different ways, such as multiple smaller black holes merging into one, or voracious growth by swallowing vast amounts of stars and gas while galaxies are forming.
The gigantic black holes discovered by Ma and her colleagues are so enormous they are capable of consuming anything within a region five times the size of Earth's solar system.
Researchers think that most, if not all, galaxies have a black hole at the center. The larger the galaxy, the larger the black hole it contains. Researchers suggest these blacks holes consume tremendous quantities of gas and dust from the central regions of the galaxy, at which point they become "dormant." The surviving gas may become stars that orbit peacefully within the galaxy.
Their quiet nature is part of what makes these sleeping giants so difficult to observe. "Since black holes cannot be seen, we have to detect them by carefully observing their immediate surroundings," said Nicholas McConnell, first author of the paper. "These galaxies contained enormous masses within a small central volume--too much mass to come from stars alone." These and other factors led the group to conclude that most of the mass is contained in massive black holes.
With support from the National Science Foundation (NSF), and using telescopes at the NSF-supported International Gemini Observatory, as well as the Keck and McDonald observatories, McConnell and Ma were able to map the velocities of stars orbiting the centers of massive elliptical galaxies--data the research team did not have the technical capability to obtain just a few years ago. The new results may help astronomers determine how black holes and galaxies form and develop together over the history of the universe.
"Galaxies are the places where stars and planetary systems form, and supermassive black holes in the early universe set the stage for their formation," said Tom Statler, program director for NSF's division of Astronomical Sciences.
"Black holes played a big role in making our universe what it is today."
http://www.sciencedaily.com/releases/2011/12/111206115258.htm

Giant Black Hole Could Upset Galaxy Evolution Models

A group of astronomers led by Remco van den Bosch from the Max Planck Institute for Astronomy (MPIA) have discovered a black hole that could shake the foundations of current models of galaxy evolution. At 17 billion times the mass of the Sun, its mass is much greater than current models predict -- in particular since the surrounding galaxy is comparatively small. This could be the most massive black hole found to date.
To the best of our astronomical knowledge, almost every galaxy should contain in its central region what is called a supermassive black hole: a black hole with a mass between that of hundreds of thousands and billions of Suns. The best-studied super-massive black hole sits in the center of our home galaxy, the Milky Way, with a mass of about four million Suns.
For the masses of galaxies and their central black holes, an intriguing trend has emerged: a direct relationship between the mass of a galaxy's black hole and that of the galaxy's stars.
Typically, the black hole mass is a tiny fraction of the galaxy's total mass. But now a search led by Remco van den Bosch (MPIA) has discovered a massive black hole that could upset the accepted relationship between black hole mass and galaxy mass, which plays a key role in all current theories of galaxy evolution. The observations used the Hobby-Eberly Telescope and existing images from the Hubble Space Telescope.
With a mass 17 billion times that of the Sun, the newly discovered black hole in the center of the disk galaxy NGC 1277 might even be the biggest known black hole of all: the mass of the current record holder is estimated to lie between 6 and 37 billion solar masses (McConnell et al. 2011); if the true value lies towards the lower end of that range, NGC 1277 breaks the record. At the least, NGC 1277 harbors the second-biggest known black hole.
The big surprise is that the black hole mass for NGC 1277 amounts to 14% of the total galaxy mass, instead of usual values around 0,1%. This beats the old record by more than a factor 10. Astronomers would have expected a black hole of this size inside blob-like ("elliptical") galaxies ten times larger. Instead, this black hole sits inside a fairly small disk galaxy.
Is this surprisingly massive black hole a freak accident? Preliminary analysis of additional data suggests otherwise -- so far, the search has uncovered five additional galaxies that are comparatively small, yet, going by first estimates, seemed to harbor unusually large black holes too. More definite conclusions have to await detailed images of these galaxies.
If the additional candidates are confirmed, and there are indeed more black holes like this, astronomers will need to rethink fundamentally their models of galaxy evolution. In particular, they will need to look at the early universe: The galaxy hosting the new black hole appears to have formed more than 8 billion years ago, and does not appear to have changed much since then. Whatever created this giant black hole must have happened a long time ago.
http://www.sciencedaily.com/releases/2012/11/121128132116.htm

Searching for the Best Black Hole Recipe

In this holiday season of home cooking and carefully-honed recipes, some astronomers are asking: what is the best mix of ingredients for stars to make the largest number of plump black holes?
They are tackling this problem by studying the number of black holes in galaxies with different compositions. One of these galaxies, the ring galaxy NGC 922, is seen in this composite image containing X-rays from NASA's Chandra X-ray Observatory (red) and optical data from the Hubble Space Telescope (appearing as pink, yellow and blue).
NGC 922 was formed by the collision between two galaxies -- one seen in this image and another located outside the field of view. This collision triggered the formation of new stars in the shape of a ring. Some of these were massive stars that evolved and collapsed to form black holes.
Most of the bright X-ray sources in Chandra's image of NGC 922 are black holes pulling material in from the winds of massive companion stars. Seven of these are what astronomers classify as "ultraluminous X-ray sources" (ULXs). These are thought to contain stellar-mass black holes that are at least ten times more massive than the sun, which places them in the upper range for this class of black hole. They are a different class from the supermassive black holes found at the centers of galaxies, which are millions to billions of times the mass of the sun.

Theoretical work suggests that the most massive stellar-mass black holes should form in environments containing a relatively small fraction of elements heavier than hydrogen and helium, called "metals" by astronomers. In massive stars, the processes that drive matter away from the stars in stellar winds work less efficiently if the fraction of metals is smaller. Thus, stars with fewer of these metals among their ingredients should lose less of their mass through winds as they evolve. A consequence of this reduced mass loss is that a larger proportion of massive stars will collapse to form black holes when their nuclear fuel is exhausted. This theory appeared to be supported by the detection of a large number (12) of ULXs in the Cartwheel galaxy, where stars typically contain only about 30% of the metals found in the sun.
To test this theory, scientists studied NGC 922, which contains about the same fraction of metals as the sun, meaning that this galaxy is about three times richer in metals than the Cartwheel galaxy. Perhaps surprisingly, the number of ULXs found in NGC 922 is comparable to the number seen in the Cartwheel galaxy. Rather, the ULX tally appears to depend only on the rate at which stars are forming in the two galaxies, not on the fraction of metals they contain.
One explanation for these results is that the theory predicting the most massive stellar-mass black holes should form in metal poor conditions is incorrect. Another explanation is that the metal fraction in the Cartwheel galaxy is not low enough to have a clear effect on the production of unusually massive stellar-mass black holes, and therefore will not cause an enhancement in the number of ULXs. Recent models incorporating the evolution of stars suggest that a clear enhancement in the number of ULXs might only be seen when the metal fraction falls below about 15%. Astronomers are investigating this possibility by observing galaxies with extremely low metal fractions using Chandra. The number of ULXs is being compared with the number found in galaxies with higher metal content. The results of this work will be published in a future paper.
A paper describing the results for NGC 922 was published in the March 10, 2012 issue of the Astrophysical Journal. The authors were Andrea Prestwich and Jose Luis Galache of the Harvard-Smithsonian Center for Astrophysics (CfA) in Cambridge, MA; Tim Linden from University of Santa Cruz in Santa Cruz, CA; Vicky Kalogera from Northwestern University in Evanston, IL; Andreas Zezas from CfA and University of Crete in Crete, Greece; Tim Roberts from University of Durham in Durham, UK; Roy Kilgard from Wesleyan University in Middletown, CT; Anna Wolter and Ginevra Trinchieri from INAF in Milano, Italy.
NASA's Marshall Space Flight Center in Huntsville, Ala., manages the Chandra program for NASA's Science Mission Directorate in Washington. The Smithsonian Astrophysical Observatory controls Chandra's science and flight operations from Cambridge, Mass.
http://www.sciencedaily.com/releases/2012/12/121206121736.htm

Compact Blue Dwarf Can’t Hide from Hubble

The NASA/ESA Hubble Space Telescope has captured a new view of the dwarf galaxy UGC 5497, which looks a bit like salt sprinkled on black velvet in the image.
The object is a compact blue dwarf galaxy that is infused with newly formed clusters of stars. The bright, blue stars that arise in these clusters help to give the galaxy an overall bluish appearance that lasts for several million years until these fast-burning stars explode as supernovae.
UGC 5497 is considered part of the M 81 group of galaxies, which is located about 12 million light-years away in the constellation Ursa Major (The Great Bear). UGC 5497 turned up in a ground-based telescope survey back in 2008 looking for new dwarf galaxy candidates associated with Messier 81.
According to the leading cosmological theory of galaxy formation, called Lambda Cold Dark Matter, there should be far more satellite dwarf galaxies associated with big galaxies like the Milky Way and Messier 81 than are currently known. Finding previously overlooked objects such as this one has helped cut into the expected tally -- but only by a small amount.
Astrophysicists therefore remain puzzled over the so-called "missing satellite" problem.
The field of view in this image, which is a combination of visible and infrared exposures from Hubble's Advanced Camera for Surveys, is approximately 3.4 by 3.4 arcminutes.
http://www.sciencedaily.com/releases/2012/06/120619105101.htm

Little Telescope Spies Gigantic Galaxy Clusters

Our solar system, with its colorful collection of planets, asteroids and comets, is a fleck in the grander cosmos. Hundreds of billions of solar systems are thought to reside in our Milky Way galaxy, which is itself just a drop in a sea of galaxies.
The rarest and largest of galaxy groupings, called galaxy clusters, can be the hardest to find. That's where NASA's Wide-field Infrared Survey Explorer (WISE) can help. The mission's all-sky infrared maps have revealed one distant galaxy cluster and are expected to uncover thousands more.
These massive structures are collections of up to thousands of galaxies bound together by gravity. They were born out of seeds of matter formed in the very early universe, and grew rapidly by a process called inflation.
"One of the key questions in cosmology is how did the first bumps and wiggles in the distribution of matter in our universe rapidly evolve into the massive structures of galaxies we see today," said Anthony Gonzalez of University of Florida, Gainesville, who led the research program. The results are published in the Astrophysical Journal.
"By uncovering the most massive of galaxy clusters billions of light-years away with WISE, we can test theories of the universe's early inflation period."
WISE completed its all-sky survey in 2011, after surveying the entire sky twice at infrared wavelengths. The 16-inch (40-centimeter) telescope ran out of its coolant as expected in 2010, but went on to complete the second sky scan using two of its four infrared channels, which still functioned without coolant. At that time, the goal of the mission extension was to hunt for more near-Earth asteroids via a project called NEOWISE.
NASA has since funded the WISE team to combine all that data, allowing astronomers to study everything from nearby stars to distant galaxies. These next-generation all-sky images, part of a new project called "AllWISE," will be significantly more sensitive than those previously released, and will be publicly available in late 2013.
Gonzalez and his team plan to use the enhanced WISE data to hunt for more massive galaxy clusters. The first one they spotted, MOO J2342.0+1301, is located more than 7 billion light-years away, or halfway back to the time of the Big Bang. It is hundreds of times more massive than our Milky Way.
By scanning the whole sky with the improved AllWISE data, the team will sleuth out the true monsters of the bunch, clusters as big as thousands of times the mass of the Milky Way, assembled even earlier in the history of the universe.
Galaxy clusters from the first half of the universe are hard to find because they are so far away and because not very many had time to assemble by then. What's more, they are especially hard to see using visible-light telescopes: light that left these faraway structures in visible wavelengths has been stretched into longer, infrared wavelengths due to the expansion of space. WISE can hunt some of these rare colossal structures down because it scanned the whole sky in infrared light.
"I had pretty much written off using WISE to find distant galaxy clusters because we had to reduce the telescope diameter to only 16 inches [40 centimeters] to stay within our cost guidelines, so I am thrilled that we can find them after all," said Peter Eisenhardt, the WISE project scientist at NASA's Jet Propulsion Laboratory, Pasadena, Calif. and an author of the new paper. "The longer exposures from AllWISE open the door wide to see the most massive structures forming in the distant universe."
Other projects planned for the enhanced WISE data include the search for nearby, hidden cool stars, including those with masses as low as planets. If a large planet or tiny star does exist close to our solar system, an object some call "Tyche," then WISE's infrared data may reveal it.
Other authors of the new study are: Daniel Gettings and Conor Mancone of the University of Florida; Adam Stanford of Lawrence Livermore National Laboratory, Livermore, Calif., and University of California, Davis; Mark Brodwin of University of Missouri, Kansas City; Daniel Stern of JPL; Gregory Zeimann of University of California, Davis; Frank Masci of the Infrared Processing and Analysis Center at the California Institute of Technology, Pasadena; Casey Papovich of Texas A&M University, College Station; Ichi Tanaka of the National Astronomical Observatory of Japan; and Edward (Ned) Wright of UCLA.
JPL manages, and operated, WISE for NASA's Science Mission Directorate. Edward Wright is the principal investigator and is at UCLA. The mission was selected competitively under NASA's Explorers Program managed by the agency's Goddard Space Flight Center in Greenbelt, Md. The science instrument was built by the Space Dynamics Laboratory in Logan, Utah. The spacecraft was built by Ball Aerospace & Technologies Corp. in Boulder, Colo. Science operations and data processing take place at the Infrared Processing and Analysis Center at the California Institute of Technology in Pasadena. Caltech manages JPL for NASA. More information is online at http://www.nasa.gov/wise , http://wise.astro.ucla.edu and http://www.jpl.nasa.gov/wise .
http://www.sciencedaily.com/releases/2012/12/121206160001.htm