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Monday, December 17, 2007

New research shows that despite the vast evolutionary gulf between humans and the three-spined stickleback fish

Ocean sticklebacks are dark colored fish that often migrate into new environments. Multiple stickleback populations have evolved lighter gill and skin colors following colonization of new lakes and streams at the end of the last ice age. Ocean (upper) compared to freshwater creek (lower) sticklebacks, both collected near Vancouver, British Columbia. Scientists have identified a genetic change controlling rapid evolution of skin color in fish, and shown that the same mechanism also contributes to recent evolution of skin color in humans. (Credit: Frank Chan, Craig Miller, and David Kingsley; Stanford University.

Skin Color Evolution In Fish And Humans Determined By Same Genetic Machinery
When humans began to migrate out of Africa about 100,000 years ago, their skin color gradually changed to adapt to their new environments. And when the last Ice Age ended about 10,000 years ago, marine ancestors of ocean-dwelling stickleback fish experienced dramatic changes in skin coloring as they colonized newly formed lakes and streams. New research shows that despite the vast evolutionary gulf between humans and the three-spined stickleback fish, the two species have adopted a common genetic strategy to acquire the skin pigmentation that would help each species thrive in their new environments.
The researchers, led by Howard Hughes Medical Institute investigator David Kingsley, published their findings in the December 14, 2007, issue of the journal Cell. Kingsley and first author Craig Miller are at the Stanford University School of Medicine, and other co-authors are from the University of Porto in Portugal, the University of British Columbia, the University of Chicago, and the Pennsylvania State University Further studies of stickleback, they say, may reveal other malleable pieces of genetic machinery both fish and humans have used for adaptation.

The stickleback has become a premier model organism for studying evolution because of its extraordinary evolutionary history, said Kingsley. "Sticklebacks have undergone one of the most recent and dramatic evolutionary radiations on earth," he said. When the last Ice Age ended, giant glaciers melted and created thousands of lakes and streams in North America, Europe, and Asia. These waters were colonized by the stickleback's marine ancestors, which subsequently adapted to life in freshwater. "This created a multitude of little evolutionary experiments, in which these isolated populations of fish adapted to the new food sources, predators, water color, and water temperature that they found in these new environments," Kingsley explained.

Among those adaptations were new colorations that helped the fish camouflage themselves, distinguish species, and attract mates in their new environments. Until now, however, scientists had not understood what genetic factors drove the changes in skin pigmentation.

Human populations have also undergone pigmentation changes as they have adapted to life in new environments. The ecological reasons for those changes may be quite different from the forces driving the evolution of pigmentation in sticklebacks, said Kingsley. As human populations migrated out of Africa into northern climates, the need for darker pigmentation necessary to protect against the intense tropical sun diminished. With skin that was more transparent to sunlight, humans were better able to produce sufficient vitamin D in their new climate.

To begin to understand the genetic basis of skin pigmentation changes in fish, Kingsley and his colleagues crossed stickleback species that had different pigmentation patterns and used genetic markers and the recently completed sequence map of the fish's genome to search for the mechanism regulating stickleback pigmentation. They searched for chromosome segments in the offspring that were always associated with inheritance of dark or light gills and skin. Through detailed mapping of one such segment, Kingsley and his colleagues found that a gene called Kitlg (short for "Kit ligand") was associated with pigmentation inheritance. Kitlg was an excellent candidate for regulating pigmentation because mutant forms of the corresponding gene in mice produce changes in fur color, said Kingsley.

The Kitlg gene is involved in a variety of biological processes, including germ cell development, pigment cell development, and hematopoiesis. Light-colored fish have regulatory mutations that reduce expression of the Kitlg gene in gills and skin, but that do not reduce the gene's function in other tissues. "By altering expression of this gene in one particular place in the body, the fish can fine tune the level of expression of that factor in some tissues but not others," said Kingsley. "That lets evolution produce a big local effect on a trait like color while preserving the other functions of the gene."

Humans also have a Kitlg gene, and Kingsley and his colleagues wondered if it played a role in regulating the pigmentation of human skin. One clue they had came from previous research by other groups that had revealed that the human Kitlg gene has undergone different changes among different human populations, suggesting that it is evolutionarily significant.

Kingsley and his colleagues tested whether the different human versions of the Kitlg gene are associated with changes in skin color. Humans with two copies of the African form of the Kitlg gene had darker skin color than people with one or two copies of the new Kitlg variant that is common in Europe and Asia.

Knowing that people had also adapted lighter skin when they migrated north, Kingsley wondered whether mutations in the same gene accounted for light pigmentation in people living in northern climes. In the north, where less sunlight reaches the ground, lighter coloring helps people absorb enough sunlight to produce vitamin D.

Kingsley and his colleagues collected DNA from people with a variety of skin colors to look for alterations in the Kit ligand gene. Sure enough, people with lighter skin had an altered form of the gene. He said this gene isn’t alone in controlling a person’s skin color, but it does seem to account for about 20 percent of the differences in pigmentation between people of African and northern European descent.

“It is the same genetic mechanism between organisms that are very different from each other,” Kingsley said. This gene is known to make a protein that plays a role in maintaining the melanocyte skin cells that control pigmentation.

In terms of how evolution progresses, this gene would be a large ladle of dye that helps set the paint color apart from the original. Additional genetic changes account for the exact color of each person’s skin.

"Although multiple chromosomal regions contribute to the complex trait of pigmentation in both fish and humans, we have identified one gene that plays a central role in color changes in both species," said Kingsley.

"Since fish and humans look so different, people are often surprised that common mechanisms may extend across both organisms," he said. "But there are real parallels between the evolutionary history of sticklebacks and humans. Sticklebacks migrated out of the ocean into new environments about ten thousand years ago. And they breed about once every one or two years, giving them five thousand to ten thousand generations to adapt to new environments."

Although modern humans arose in Africa, they are thought to have migrated out of Africa in the last 100,000 years. "Humans breed about once every 20 years, giving them about 5,000 generations or so to emerge from an ancestral environment and colonize and adapt to new environments around the world," Kingsley added. "So despite the difference in total years, the underlying process is actually quite similar. Whether it be fish or humans, there were small migrating populations encountering new environments and evolving significant changes in some traits in a relatively short time. And the genetic mechanisms that can produce these changes may be so constrained that evolution will tend to use the same sorts of genes in different organisms."

Kingsley and his colleagues are now exploring the genetic basis of other evolved traits in the stickleback that could find a parallel in humans. "And given the degree to which evolutionary mechanisms appear to be shared between populations and organisms, we're optimistic about finding the particular genes that underlie other recent adaptations to changing environments in both fish and humans," he said.

The Milky Way Released

Largest Digital Survey Of The Milky Way Released.

A collaboration of over 50 astronomers, The IPHAS consortium, led from the UK, with partners in Europe, USA, Australia, has released today (10th December 2007) the first comprehensive optical digital survey of our own Milky Way. Conducted by looking at light emitted by hydrogen ions, using the Isaac Newton Telescope on La Palma, the survey contains stunning red images of nebulae and stars.

To date, the IPHAS survey includes some 200 million unique objects in the newly released catalogue. This immense resource will foster studies that can be at once both comprehensive and subtle, of the stellar demographics of the Milky Way and of its three-dimensional structure.

Professor Janet Drew of the University of Hertfordshire said "Using the distinctive Hydrogen marker we are able to look at some of the least understood stars in the Galaxy -- those at the early and very late stages of their life cycles. These represent less than one in a thousand stars, so the IPHAS data will greatly improve our picture of stellar evolution."

IPHAS is embracing a recent change in the way astronomers share data. As well as being available through traditional web access it is also being published through a Virtual Observatory interface, where it can automatically be cross-referenced with other relevant data catalogues.

Dr Nic Walton of the University of Cambridge said "Using the standard Virtual Observatory interface is a very effective way of exploiting the IPHAS survey data. This is a substantial and significant survey, which aims to eventually contain 7-800 million objects. Access through the AstroGrid Virtual Observatory opens up a full range of analysis options and should allow astronomers to make greater use of the information. IPHAS is the largest dataset published primarily through Virtual Observatory interfaces to date, and as such heralds the future of survey data mining."

This initial data release is of observations of the Northern Plane of the Milky Way (the star filled section) that cover 1600 sq deg, in two broadband colours, and a narrow band filter sensitive to the emission of Hydrogen in the red part of the spectrum (H-alpha emission). The image resolution is high enough to permit the detection of individual stars exhibiting H-alpha emission, in addition to the diffuse gas that makes up the often-beautiful glowing nebulae that lower spatial resolution surveys have made known to us before.

The IPHAS database is already revealing a wealth of new science. For example, IPHAS team members from the University of Southampton, have led an effort to extract and catalogue the brighter H-alpha emission line stars revealed so far by the survey. This list of nearly 5000 objects is already the longest single list of its kind. The distribution of these special objects, across the northern sky, traces 'hot spots' of recently formed stars in our Galaxy much more convincingly than has been possible hitherto.

The IPHAS survey will eventually be extended to cover the entire galactic plane of our galaxy, with a coverage approaching 4000 square degrees (for comparison, the moon on the sky as seen from Earth covers ~0.1 square degrees).

The data is described in a paper submitted to the Monthly Notices of the Royal Astronomical Society.

MIT will lead a 375-million dollar mission to map the moon's interior and reconstruct its thermal history.

MIT mission to study moon's gravity
The Massachusetts Institute of Technology (MIT) will lead a 375-million dollar mission to map the moon's interior and reconstruct its thermal history.

According to a NASA announcement, the Gravity Recovery And Interior Laboratory (GRAIL) mission will be led by MIT professor Maria Zuber and will be launched in 2011.

The mission will put two separate satellites into orbit around the moon to precisely map variations in the moon's gravitational pull.

These changes will reveal differences in density of the moon's crust and mantle, and can be used to answer fundamental questions about the moon's internal structure and its history of collisions with asteroids.

The detailed information about lunar gravity will also significantly facilitate any future manned or unmanned missions to land on the moon.

Such data will be used to program the descent to the surface to avoid a crash landing and will also help target desirable landing sites.

Moreover, the mission's novel technology could eventually be used to explore other interesting worlds such as Mars.

"After the three-month mission is completed, we will know the lunar gravitational field better than we know Earth's," said Zuber, who is the head of the MIT's Department of Earth, Atmospheric and Planetary Sciences and the E.A. Griswold Professor of Geophysics.

She will be the principal investigator for the GRAIL mission.

Former astronaut Sally Ride, the first U.S. woman in space, will lead the project's educational outreach phase, which will include five live MoonKam cameras on each satellite that will be targeted by young students--especially middle-school girls--in their classrooms to get close-up still and video views of the moon's surface.

So far, even such fundamental questions as whether or not the moon has a separate, differentiated core, as Earth does, are unknown, Zuber says.

In addition to answering that question, the new mission should reveal details about lunar history, including the relative timing and effects of the myriads of huge impacts that created the craters and basins seen on the surface today.

The moon, with its airless, un-eroded surface, serves as a kind of Rosetta Stone for understanding the history of all the solar system's inner planets--Mercury, Venus, Earth and Mars--so the mission should also help to unlock secrets of the evolution of all these planets.

"The moon has the best-preserved record of the solar system's early history," Zuber says, while on other planets much of that record has been lost through erosion and other surface changes.

The technology used in the mission is a direct spin-off from the highly successful Gravity Recovery and Climate Experiment (GRACE) mission, which has been mapping Earth's gravitational field since 2002.

Using that technology made this a "low risk" mission for NASA because the necessary instruments had already been developed and tested.

As with that mission, GRAIL measurements of the gravitational field will come from very precise monitoring of changes in the distance between the two satellites.

The resulting measurements will map the moon's gravitational field up to 1,000 times more accurately than any previous mapping.

NASA selected the MIT-led mission from among two-dozen original proposals.

The GRAIL satellites will be built and operated by Lockheed Martin Space Systems of Denver, Colorado.

NASA's Jet Propulsion Laboratory in Pasadena, California will handle project management and developing the communications and navigation systems.

The mission's science team also includes David E. Smith of NASA Goddard Space Flight Center, who will be the deputy principal investigator, and other researchers from JPL, GSFC, the Carnegie Institution of Washington, the University of Arizona, the University of Paris and the Southwest Research Institute.

new kinds of biological research.( 'fire hose')

MIT has developed a new system for sorting cells that involves special "traps" in a silicone layer bonded to a microscope slide. Cells with specific properties are then levitated out of their traps using the pressure of a beam of targeted light from a low-cost laser. A flowing fluid then sweeps the selected cells off to a separate reservoir.

graduate student Joseph Kovac and Joel Voldman, associate professor of electrical engineering and computer science, have developed an inexpensive and easy method for sorting cells for microscope examination, using microfluidics and a laser beam "firehose."

Laser beam 'fire hose' used to sort cells

Separating particular kinds of cells from a sample could become faster, cheaper and easier thanks to a new system developed by MIT researchers that involves pushing up the cells with a laser beam "fire hose."

The system, which can sort up to 10,000 cells on a conventional glass microscope slide, could enable a variety of biological research projects that might not have been feasible before, its inventors say. It could also find applications in clinical testing and diagnosis, genetic screening and cloning research, all of which require the selection of cells with particular characteristics for further testing.

Joel Voldman, an associate professor in MIT's Department of Electrical Engineering and Computer Science, and Joseph Kovac, a graduate student in the department, developed the new system, which is featured as the cover story in the Dec. 15 issue of the journal Analytical Chemistry.

Present methods allow cells to be sorted based on whether or not they emit fluorescent light when mixed with a marker that responds to a particular protein or other compound. The new system allows more precise sorting, separating out cells based not just on the overall average fluorescent response of the whole cell but on responses that occur in specific parts of the cell, such as the nucleus. The system can also pick up responses that vary in how fast they begin or how long they last.

"We've been interested in looking at things inside the cell that either change over time, or are in specific places," Voldman said. Separating out cells with such characteristics "can't be done with traditional cell sorting."

For example, if cells differ in how quickly they respond to a particular compound used in the fluorescent labeling, the new system would make it possible to "select out the ones that are faster or slower, and see what's different," said Voldman, who also has appointments in MIT's Research Laboratory of Electronics and the Microsystems Technology Laboratories.

"It seems like that should be easy, but it isn't," he said. There are other ways of accomplishing the same kind of cell separation, but they require complex and expensive equipment, or are limited in the number of cells they can process.

The new system uses a simple transparent silicone layer bonded to a conventional glass microscope slide. Fabricated in the layer are a series of tiny cavities, or traps, in which cells settle out after being added to the slide in a solution. Up to 10,000 cells could be sorted on a single slide.

Looking through the microscope, either a technician or a computerized system can check each cell to determine whether it has fluorescence in the right area or at the right time to meet the selection criteria. If so, its position is noted by the computer. At the end of the selection process, all of the cells whose positions were recorded are then levitated out of their traps using the pressure of a beam of targeted light from a low-cost laser. A flowing fluid then sweeps the selected cells off to a separate reservoir.

The laser levitation of the cells acts like "a fire hose pushing up a beach ball," Voldman said. But the laser method is gentle enough that the living cells remain viable after the process is complete, allowing further biological testing.

Voldman and Kovac are continuing to refine the system, working on making it easier to use and on improving its ability to keep samples sterile. Voldman said that unlike expensive separation techniques such as optical tweezers, the new system could cost only a few thousand dollars. As a result, it could be employed in a variety of biological research laboratories or clinical settings, not just in big, centralized testing facilities.

The research was funded by the National Institutes of Health and the Singapore-MIT Alliance; Kovac is supported by an ASEE National Defense Science and Engineering Graduate Fellowship.

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