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A New Way To Compare Genomes
Posted: Friday, February 28, 2003
Source: Lawrence Berkeley National Laboratory
A New Way To Compare Human And Other Primate Genomes
BERKELEY, CA -- Scientists with the U.S. Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, Calif., and the Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a powerful new technique for deciphering biological information encoded in the human genome.
Called "phylogenetic shadowing," this technique enables scientists to make meaningful comparisons between DNA sequences in the human genome and sequences in the genomes of apes, monkeys, and other nonhuman primates. With phylogenetic shadowing, scientists can now study biological traits that are unique to members of the primate family.
"Now that the sequence of the human genome has almost been completed the next challenge will be the development of a vocabulary to read and interpret that sequence," says Edward Rubin, M.D., director of the Joint Genome Institute (JGI) for the U.S. Department of Energy, and Berkeley Lab's Genomics Division, who led the development of the phylogenetic shadowing technique.
"The ability to compare DNA sequences in the human genome to sequences in nonhuman primates will enable us in some ways to better understand ourselves than the study of evolutionarily far-distant relatives such as the mouse or the rat," Rubin adds. "This is important because as valuable as models like the mouse have been, there are many physical and biochemical attributes of humans that only other primates share."
Using phylogenetic shadowing, Rubin and his colleagues were able to identify the DNA sequences that regulate the activation or "expression" of a gene that is an important indicator of the risk for heart disease and is found only in primates. The results of this research are reported in a paper published the February 28 issues of the journal Science. Co-authoring the paper with Rubin were Dario Boffelli, Dmitriy Ovcharenko, Keith Lewis and Ivan Ovcharenko of Berkeley Lab, plus Jon McAuliffe and Lior Pachter, of the University of California at Berkeley.
Why compare genomes?
Comparative genomics, comparing segments of DNA in the human genome to DNA segments in the genomes of other organisms that have been sequenced, such as the mouse, the puffer fish or the sea squirt, has proven to be an effective means of identifying genes, the DNA sequences that code for proteins, and gene regulatory sequences, the DNA sequences which control when a gene is turned on or off.
"The rationale for comparing the genomes of different animals to identify those sequences that are important is based on the understanding that today's different animals arose from common ancestors tens of millions of years ago," Rubin explains. "If segments of the genomes of two different organisms have been conserved (meaning the sequences are the same in both) over the millions of years since those organisms diverged, then the DNA sequences within those segments probably encode important biological functions."
The search for functional DNA sequences that have been conserved between two different organisms across a large distance in evolution is the classical approach to comparative genomics that has been used to interpret the information in the human genome. In order for this technique to work, the conserved functional sequences have to stand out as distinct from the nonfunctional sequences which were not conserved. That degree of distinction requires the passage of time - lots of it - in order for mutations and the lack of selection pressures to cause the nonfunctional sequences in the two genomes to drift apart.
For example, mice and humans last shared a common ancestor about 75 million years ago, plenty of time for the nonfunctional sequences in their respective genomes to go their separate ways. Only about five-percent of the two genomes are conserved and it has been shown that most of the genes and regulatory sequences that have been discovered lie within these conserved DNA segments. On the other hand, humans and nonhuman primates shared common ancestors as recently as 6 to 14 million years ago for apes, 25 million years ago for Old World (African) monkeys, and 40 million years ago for New World (South American) monkeys. This is insufficient time for much genetic divergence to have taken place. Consequently, nonhuman primates have been largely ignored in the effort to interpret the human genome.
"Comparative genomics studies between evolutionarily distant species will readily identify regions of the human genome performing basic biological functions shared with most mammals," says Rubin. "However, it will invariably miss recent changes in DNA sequence that account for primate-specific biological traits."
Rubin has likened comparisons between the human and mouse genomes to comparisons between an automobile and a go-cart: "Only the very basic parts and design features are similar." Whereas, he argues, comparing the human genome to that of a chimp or a baboon, is like comparing a sedan to a station wagon: "Nearly all the parts and design features are almost interchangeable."
The promise of primates
Until now, however, comparing the human genome to that of a chimp or baboon has been a problem since both genomes are so much alike.
As Boffelli, who works with Rubin at both Berkeley Lab and JGI explains, "There is only about a 5-percent difference between the human and the baboon genomes. When you run comparisons between the two, all of the sequences look just about the same. We can't distinguish function from nonfunctional sequences."
Rubin and his colleagues overcame this lack of distinction by comparing segments of the human genome to segments of not one but anywhere from 5 to 15 different genomes of nonhuman primates, including chimpanzees and gorillas, orangutans, baboons, and Old World and New World monkeys. By sequencing specific segments within each of the genomes of the different primates being analyzed, the researchers found enough small differences from genome to genome in the nonhuman primates that could be combined to create a phylogenetic "shadow" which could then be compared to the human genome.
"The additive collective sequence differences or divergence of these nonhuman primates as a group was comparable to that of humans and mice," Rubin says. "This suggests that deep sequence comparisons of numerous primate species should be sufficient to identify significant regions of conservation that encode functional elements shared by all primates including humans."
The phylogenetic shadow that Rubin and his colleagues created was distinct enough for them to see the boundaries between exons (protein-coding DNA sequences) and introns (noncoding DNA sequences) for several genes in addition to discovering the regulatory elements for a gene named "apo(a)" which is associated with low-density lipoproteins (LDLs) in the blood stream of humans. An evolutionary new-comer, apo(a) is found in humans, apes, and Old World monkeys but appears to be lacking in nearly all other mammals. Biomedical researchers want to know the regulatory sequences of apo(a) because high blood levels of apo(a) are an important risk predictor for cardiovascular disease. The desire to study apo(a) is the reason Rubin and his research group began the development of their phylogenetic shadowing technique.
"We could not study apo(a) by comparing human DNA sequences to the sequences of evolutionarily distant species as those species don't have apo(a) so we had to find an alternative method," Rubin says.
Rubin's research group at Berkeley Lab has been at the forefront of using transgenic mice and the mouse genome to decipher the human genome and to identify and study important genetic risk factors in the development of human heart disease. He and his group believe that the ability to do comparative genomic studies with nonhuman primates will prove especially beneficial to human medical research. Their data from this study suggests that sequencing the genomes of as few as four to six primate species in addition to humans may be enough to identify much of the conserved functional DNA sequences in the human genome.
"The argument for sequencing a broad variety of evolutionarily distant species, like the mouse and puffer fish, has been that they would be needed for us to gain a good understanding of the human genome," Rubin says. "These evolutionarily distant creatures have been incredibly useful but maybe now we should be focusing our effort on sequencing the genomes of not one but several different nonhuman primates. Their collective sequences will tell us things about the human genome that we will never to able to learn from our more distant relatives in the animal kingdom."
This research was funded by a grant from the National Heart, Lung, and Blood Institute.
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Posted: Friday, February 28, 2003
Source: Scripps Research Institute
Scripps Scientists Address Mysteries Of Ozone In The Human Body
In what is a first for biology, a team of investigators at The Scripps Research Institute (TSRI) is reporting that the human body makes ozone.
Led by TSRI President Richard Lerner, Ph.D. and Associate Professor in the Department of Chemistry Paul Wentworth, Jr, Ph.D., who made the original discovery, the team has been slowly gathering evidence over the last few years that the human body produces the reactive gas--most famous as the ultraviolet ray-absorbing component of the ozone layer--as part of a mechanism to protect it from bacteria and fungi.
"Ozone was a big surprise," says TSRI Professor Bernard Babior, M.D., Ph.D. "But it seems that biological systems manufacture ozone, and that ozone has an effect on those biological systems."
Now, in an important development in this unfolding story, Babior, Wentworth, and their TSRI colleagues report in an upcoming issue of the journal Proceedings of the National Academy of Sciences that the ozone appears to be produced in a process involving human immune cells known as neutrophils and human immune proteins known as antibodies.
"It is a tremendously efficient chemical and biological process," says Wentworth, who adds that the presence of ozone in the human body may be linked to inflammation, and therefore this work may have tremendous ramifications for treating inflammatory diseases.
The Ozone Hole in Each One of Us
Ozone is a reactive form of oxygen that exists naturally as a trace gas in the atmosphere. It is perhaps best known for its crucial role absorbing ultraviolet radiation in the stratosphere, where it is concentrated in a so-called ozone layer, protecting life on earth from solar radiation. Ozone is also a familiar component of air in industrial and urban settings where the gas is a hazardous component of smog. However, ozone has never before been detected in biology.
Two years ago, Lerner and Wentworth demonstrated that antibodies are able to produce ozone and other chemical oxidants when they are fed a reactive form of oxygen called singlet oxygen. And late last year, Lerner, Wentworth, and Babior demonstrated that the oxidants produced by antibodies can destroy bacteria by poking holes in their cell walls.
This was a completely unexpected development, since for the last 100 years, immunologists believed that antibodies--proteins secreted into the blood by the immune system--acted only to recognize foreign pathogens and attract lethal "effector" immune cells to the site of infection.
Questions, Answers, and More Questions
The question still remained, however, as to how the antibodies were making the ozone. The TSRI team knew that in order to make the ozone and other highly reactive oxidants, the antibodies had to use a starting material known as singlet oxygen, a rare, excited form of oxygen.
Now Babior and Wentworth believe they have found where the singlet oxygen comes from--one of the effector immune cells called neutrophils which are little cellular factories that produce singlet oxygen and other oxidants. During an immune response, the neutrophils engulf and destroy bacteria and fungi by blasting them with these oxidants.
The work of the TSRI scientists suggests that the antibacterial effect of neutrophils is enhanced by antibodies. In addition to killing the bacteria themselves, the neutrophils feed singlet oxygen to the antibodies, which convert it into ozone, adding weapons to the assault.
"This is really something new, and there are a million questions [that follow]," says Babior. "What does the ozone do to the body's proteins and nucleic acids? Can neutrophils make ozone without the antibodies? Is ozone made by other cells? How long does ozone last in the body? And, most importantly, how will these discoveries help to cure disease?"
The research team continues to investigate.
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The article, "Investigating antibody-catalyzed ozone generation by human neutrophils," is authored by Bernard M. Babior, Cindy Takeuchi, Julie Ruedi, Abel Gutierrez, and Paul Wentworth, Jr. The article will be available online this week at: http://www.pnas.org/cgi/doi/10.1073/pnas.0530251100, and it will be published in an upcoming issue of the journal Proceedings of the National Academy of Sciences.
The research was funded by the National Institutes of Health (NIH), through research grants and through a training grant; and by The Skaggs Institute for Chemical Biology.
The original news release can be found here
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Scientists Get First Close Look At Stardust Posted: Friday, February 28, 2003
Source: Washington University In St. Louis
St. Louis, February 26, 2003 -- For the first time, scientists have identified and analyzed single grains of silicate stardust in the laboratory. This breakthrough, to be reported in the Feb. 27 issue of Science Express, provides a new way to study the history of the universe.
"Astronomers have been studying stardust through telescopes for decades," said first author Scott Messenger, Ph.D., senior research scientist in the Laboratory for Space Sciences at Washington University in St. Louis. "And they have derived models of what it must be like, based on wiggles in their spectral recordings. But they never dreamed it would be possible to look this closely at a grain of stardust that has been floating around in the galaxy."
Most stardust is made of tiny silicate grains, much like dust from rocks on earth. Away from city lights, you can see the dust as a dark band across the Milky Way. This dust comes from dying and exploded stars. Scientists think stars form when these dust clouds collapse and that some of this dust became trapped inside asteroids and comets when our own sun formed.
The researchers found the stardust in tiny fragments of asteroids and comets--interplanetary dust particles (IDPs) --collected 20 km above the earth by NASA planes. A typical IDP is a mishmash of more than 100,000 grains gleaned from different parts of space. Until recently, ion probes had to analyze dozens of grains at one time and so were able to deduce only the average properties of a sample.
In 2001, with help from NASA and the National Science Foundation, Washington University bought a newly available and much more sensitive ion probe. Made by Cameca in Paris, the NanoSIMS probe can resolve particles as small as 100 nanometers in diameter. A million such particles side by side would make a centimeter. The grains in IDPs range from 100 to 500 nanometers. "So like the Hubble telescope, the NanoSIMS allows us to see things on a much finer scale than ever before," Messenger said.
Lindsay P. Keller, Ph.D., at NASA's Johnson Space Center in Houston, first examined thin slices of IDPs under the transmission electron microscope. He identified the chemical elements in single grains and determined whether the grains were crystals or coated with organic material.
Using the NanoSIMS probe, the Washington University investigators then measured the relative amounts of two isotopes of oxygen in more than a thousand grains from nine IDPs. The data told them which grains had come from stars. The researchers discovered the first grain of stardust in the first half hour of their first NanoSIMS session. "Finding something that people have been seeking for such a long time was incredibly exciting," Messenger said.
Stardust was surprisingly common in the IDPs. "We found that 1 percent of the mass of these interplanetary dust particles was stardust," Messenger explained. "So stardust is about 50 times as abundant in these particles as in meteorites, which suggests that it comes from far more primitive bodies."
The isotopic measurements identified six stardust grains from outside our solar system. Three appeared to have come from red giants or asymptotic giant branch stars, two late stages in stellar evolution. A fourth was from a star containing little metal. The fifth and sixth possibly came from a metal-rich star or a supernova.
Although this work is just beginning, some novel findings have emerged. For example, one of the grains was crystalline, which contradicts the idea that silicate stardust grains are always amorphous. "A single grain of stardust can bring down a long-established theory," Messenger said.
The researchers will probe the history of stardust with further studies of IDP chemistry and microstructure. "The interstellar medium plays an incredibly important role in star formation, but you can learn only so much by using a telescope," Messenger said. "You can find out so much more by studying actual samples."
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Messenger S, Keller LP, Stadermann FJ, Walker RM, Zinner E. Samples of stars older than the sun: Silicate grains in interplanetary dust. Science Express, Feb. 27, 2003. http://www.sciencemag.org/feature/express/expresstwise.shl
A grant from NASA funded this research. Images of IDPs are available. Further information about stardust can be found at: http://stardust.wustl.edu
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Clovis People Acquitted Of Ancient Killings Posted: Tuesday, February 25, 2003
Source: University Of Washington
Evidence Acquits Clovis People Of Ancient Killings, Archaeologists Say
Archaeologists have uncovered another piece of evidence that seems to exonerate some of the earliest humans in North America of charges of exterminating 35 genera of Pleistocene epoch mammals.
The Clovis people, who roamed large portions of North America 10,800 to 11,500 years ago and left behind highly distinctive and deadly fluted spear points, have been implicated in the exterminations by some scientists.
Now researchers from the University of Washington and Southern Methodist University who examined evidence from all suggested Clovis-age killing sites conclude that there is no proof that people played a significant role in causing the extinction of Pleistocene mammals in the New World. Climate change, not humans, was the culprit.
"Of the 76 localities with asserted associations between people and now-extinct Pleistocene mammals, we found only 14 (12 for mammoth, two for mastodon) with secure evidence linking the two in a way suggestive of predation," write Donald Grayson of the UW and David Meltzer of SMU in the current issue of the Journal of World Prehistory. "This result provides little support for the assertion that big-game hunting was a significant element in Clovis-age subsistence strategies. This is not to say that such hunting never occurred: we have clear evidence that proboscideans (mammoths and mastodons) were taken by Clovis groups. It just did not occur very often."
To locate Clovis-age sites that suggested hunting of now-extinct mammals Grayson and Meltzer used FAUNMAP, an electronic database that documents the distribution of mammals in North America during the last 40,000 years. The search excluded areas above the North American ice sheet and sites that were pre- and post-Clovis because it is the Clovis people who have been targeted by proponents of the so-called "overkill" hypothesis.
This search turned up 75 locations in the United States and one in Canada that Grayson and Meltzer evaluated. Forty-seven of the sites did not exhibit minimally acceptable evidence showing an association between artifacts and extinct mammals. Most of these sites were rejected because they were not sufficiently described or documented.
"In many cases there is no published material, and when something is not published we are not able to weigh evidence of a human connection," said Grayson. "In other cases there was just an anecdotal suggestion of artifacts or remains, or there were very sketchy drawings."
Of the remaining 29 sites only 14 survived closer study. To determine this, the researchers looked for settings in which artifacts and animal remains were so closely associated that there was little doubt that their relationship was not accidental. In addition, Grayson and Meltzer searched published evidence for signs of human hunting and butchering and processing. This included cases where projectile points were found among bones or where there was solid evidence of human-caused bone breakage or cut marks.
Mammoth and mastodon bones were the most commonly found remains at the 14 confirmed predation sites, but horse, camel and bison bones also were identified. However, Grayson said there was no evidence that the two horse bones and one camel bone, all from extinct genera, came from animals that had been hunted by humans. There was quite a bit of evidence of human predation of bison, but this genus did not become extinct.
The survey produced no evidence that humans hunted the 33 other genera of extinct animals, which also include sloths, tapirs, bears and sabertooth cats. In fact, only 15 genera can be shown to have survived beyond 12,000 years ago and into Clovis times, said Grayson.
"There is absolutely no evidence that Clovis people were involved with 33 of the extinct genera. Where's the spear point sticking out of a camel or a ground sloth? If you can kill a mammoth you can kill a lumbering ground sloth. Clovis people absolutely did not chase these now-extinct animals relentlessly across the North American landscape," he said.
"The bottom line is that we need to stop wasting our time looking at people as the cause of these extinctions. We suspect the extinctions were driven by climate change. We need to know what aspects of climate change were involved. We have to tackle this species by species, one at a time, and look at the interaction of each species with the climate and vegetation on the ground."
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New Age For Mungo Man, New Human History Posted: Thursday, February 20, 2003
Source: University Of Melbourne
A University of Melbourne-led study has finally got scientists to agree on the age of Mungo Man, Australia's oldest human remains, and the consensus is he is 22,000 years younger.
A University of Melbourne-led team say Mungo Man's new age is 40,000 years, reigniting the debate for the 'Out of Africa' theory. The research also boosted the age of Mungo Lady, the world's first recorded cremation, by 10,000 years putting her at the same age as Mungo Man. It is the first time scientists have reached a broad agreement on the ages of the Lake Mungo remains.
"The ages paint a new picture of the human and climatic history of Australia," says the discoverer of the Lake Mungo remains, Professor Jim Bowler, a geologist and Professorial Fellow with the University of Melbourne.
The research will be published in the 20 February issue of Nature
In 1999, Australian National University scientists estimated the age of Mungo Man to be 62,000 years. This created a frenzy of excitement and vigorous debate among scientists as this rewrote the history of human occupation in Australia and had profound implications for the origins of modern man.
"Australia's colonisation is one of the keys to our understanding of how Homo sapiens evolved and spread around the world. It is critical we get the story correct," says Bowler.
To solve the long-standing debate, Professor Bowler amassed a multidisciplinary team of experts from the Universities of Melbourne, Adelaide, Wollongong, the Australian National University, CSIRO and the NSW National Parks and Wildlife Service, and used multiple methods and four separate dating laboratories to achieve a final consensus.
"Dr Nigel Spooner (formerly ANU) and Dr Bert Roberts (University of Wollongong), both co-authors on the paper, have advanced current dating techniques and were integral in achieving confidence in the accuracy of our results. They were supported by co-authors Dr Jon Olley (CSIRO) and Professor John Prescott (University of Adelaide)," says Bowler.
"The new age corrects previous estimates and provides a new picture of Homo sapiens adapting to deteriorating climate in Australia," he says.
The data show that maximum human occupation of Lake Mungo occurred between 45,000 and 42,000 years ago, a time when the lake was a lavish water and food supply for humans, animals and plants. This phase of intense occupation occurred at a time of major climatic change that also coincided with the disappearance of Australia's megafauna.
Between 60,000 and 50,000 years ago, the last ice age saw the expansion of freshwater lakes across what are now dry inland plains. By 45,000 years the system was beginning to change. By 40,000 years, at the time of both burials, the onset of drought conditions was associated with the expansion of Australia's desert dunes building to its maximum impact about 20,000 years ago.
"By 20,000 years, the lakes were dry, plants and animals were decimated and sand dunes had spread across the plains," says Bowler.
"The new dates reveal a rich tapestry of archaeological change that is rarely equaled elsewhere in the world and provides an ancient example of humans being forced to adapt to severe drought conditions similar to those that affect much of semi-arid and arid Australia today," he says.
The oldest evidence for human occupation of the Lake Mungo region has been dated from stone tools at about 50,000 years. This is consistent with the oldest artifacts found in Western Australia and Northern Territory.
"Evidence for occupation at 60,000 years or greater remains to be established," says Bowler.
"Lake Mungo confirms that the first Australians had colonised the country by 50,000 years and by 40,000 years had brought with them art and ritual burial," he says.
The Lake Mungo remains are still Australia's oldest human remains. Mungo Man is still the first well-dated evidence found anywhere in the world of such cultural sophistication, in this case, the anointing of the body with ochre before or during burial.
"This research extends far beyond mere academic interest. The Mungo people's story is of major importance to both their present day indigenous descendants and to all non-indigenous Australians," says Bowler.
"Non-indigenous Australians too often have a desperately limited frame of historical reference. The Lake Mungo region provides a record of land and people that we latter day arrivals have failed to incorporate into our own Australian psyche. We have yet to penetrate the depths of time and cultural treasures revealed by those ancestors of indigenous Australians," he says.
"The messages from the ancient Mungo people challenge us to come to terms with the history and dynamics of this strange land, especially with the rights and richness of their descendants.
"Indeed it is those descendants, in the person of the three traditional tribal groups of the Willandra region (the Barkandji, the Mutthi Mutthi and the Nyampaa) who facilitated and cooperated closely with this project. This represents an important new phase in the collaboration between science and traditional owners. Science and the Australian community owe them a special debt of gratitude."
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Dr Wilfred Shawcross (ANU) and Dr Harvey Johnson (NSW National Parks and Wildlife Service) are responsible for the archaeological content of the paper.
The original news release can be found here.
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Undergrads Discover New Class Of Star Posted: Friday, February 14, 2003
Source: University Of Arizona
Undergrads Discover New Class Of Star; "They Pulsate Like Jell-O"
University of Arizona astronomy undergraduates have serendipitously discovered a new class of star that thrills astronomers who specialize in a relatively new field called "astroseismology."
Astronomers worldwide will collaborate in continuous observations of one of these newly found stars for several weeks in May 2003.
"Astronomers are always looking for new and better ways to study stars," said Elizabeth Green, assistant staff astronomer at Steward Observatory, who with her students discovered the new class of stars. They have found sub-dwarf B stars that pulsate like Jello, quivering in space through cycles that typically last an hour.
"We have incredibly sophisticated theoretical models that describe the interior evolution of stars from birth to death. But our observations are usually limited to only what we can see of the outer layers of a star's atmosphere. It is very difficult to check the theoretical calculations with actual evidence of what is happening inside the star," Green said.
Astronomers have begun to study fluctuating light from naturally pulsating stars to understand interior star structure, in much the same way that seismologists use earthquake-generated density waves to study the interior structure of the Earth.
This new community of "astroseismologists" was delighted in 1997 with the discovery that a few sub-dwarf B stars were pulsating in several different modes during short periods, periods of 100 to 200 seconds.
Sub-dwarf B stars are far along in their stellar evolution. These rare, very hot stars burn helium, rather than hydrogen, in their cores. They have somehow lost almost all of their obscuring red giant atmospheres, leaving their tiny helium-burning cores exposed for astronomical study. Pulsating sub-dwarf B stars promised to give astronomers needed new evidence on interior star structure.
But during the past 5 years, astronomers have searched something like 600 such stars and found only 30 "multimode" pulsators. More, the stars are typically faint, and extremely small changes in their brightness during 2-to-4 minute periods make useful observations difficult.
The discovery of this new class of pulsating sub-dwarf B star is exciting because the stars' hour-long periods should make good observations much easier, and because these stars are more common than the short-period pulsators, Green said.
It was one of those discoveries you make but aren't looking for, she added.
When some of Green's undergraduate astronomy students three years ago asked her for hands-on experience in observational astronomy for independent study credit, she trained them to help on her National Science Foundation-funded survey of sub-dwarf B stars in binary systems, a project to better understand how stars evolve.
Students worked in pairs during weekends, changing off working on homework and observing, mostly at the 61-inch Kuiper Telescope on Mount Bigelow, and occasionally at the 90-inch Bok Telescope on Kitt Peak, which by now are two of Steward Observatory's more modestly sized telescopes.
They observed strange, irregular light curves like one that another UA undergraduate working with Green had seen in July 1999.
"The original discovery curve was done by Melissa Giovanni, an undergraduate working for me for the summer. She wanted to do some observing at a real telescope, and we had 5 nights of telescope time at the 90-inch in July," Green said. "But this was during the monsoons. It was raining cats and dogs every afternoon, and cloudy most of the nights. I decided to give up, but Melissa wanted to keep going, hoping the skies might clear. In the last few hours of the last night, she got a light curve that was the funniest looking thing I'd ever seen," Green said.
Green said she knew the irregular light curve wasn't from a star eclipsing another, or reflection effects that she studies in her survey. "I honestly didn't know what it was. I carried this bizarre light curve around to meetings for the next year and half, and showed it to people who asked if it might be simply a result of observing through the Earth's own turbulent atmosphere."
Beginning spring semester 2000, Keith Callerame, Ivo R. Seitenzahl (who have since graduated) Brooke White, Elaina Hyde and other UA undergraduates on Green's survey collected similar light curves on what are now known to be long-period multimode pulsating sub-dwarf B stars. The UA astronomy undergraduates did about two-thirds of the observing work on the project. Astronomers from the University of Montreal and Missouri State University, from Germany, and from the La Palma Observatory in the Canary Islands collaborated with Green and her students in a research paper on the discovery, published Jan. 20 in the Astrophysical Journal Letters.
Green, the UA undergraduates and their colleagues report seven confirmed such stars pulsating in 3 to 5 modes, and possibly in as many as 10 or more modes. And they have by now found 23 such stars in the group of 100 they have examined, including 18 found just last year.
Green and Gilles Fontaine of the University of Montreal are organizing a campaign from March to June 2003 to observe the brightest, coolest and most dramatically pulsating of these newly found stars, PG1627+107.The star is easily visible from both the Northern and Southern Hemispheres.
Astronomers from Germany, South Africa, Australia, South America and Spain will collaborate with Green and her team at Steward Observatory to get around-the-world and around-the-clock coverage of the star for two weeks during the spring campaign.
The original news release can be found here
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Is race only skin-deep? Posted: Sunday, February 9, 2003
Robin McKie and Jo Revill
Sunday February 9, 2003
The Observer
Science can reveal hidden surprises in our family trees that will affect how we think of ourselves
To shine a light across the darkness of centuries, to peer into your own distant heritage, is an extraordinary concept. Yet this is exactly what Len Garrison did last month when a remarkable survey told him something more than the fact that he hailed from Jamaica.
Analysis of his DNA, taken with that of 228 other black men and women living in Britain, revealed a startling secret: Garrison possessed a Y chromosome - the tiny bundle of human genes that confers masculinity - that is of European origin. Somewhere in his distant family history, a white male had 'helped' to conceive one of his ancestors - most probably a white slave-master who sired a child with a black slave.
It is an intriguing discovery, revealed by a revolution in genetics that threatens to transform our understanding of our personal pasts - and uncover all kinds of familial surprises. Certainly, Garrison - a 59-year-old London teacher and historian - was not the only one to be shocked by the survey, which was carried out by Dr Mark Jobling of Leicester University and will be shown on the BBC2 documentary Motherland on Friday. Twenty-six per cent of its black male participants discovered they too possessed a white male predecessor.
Garrison also found out his blood carried traces of genetic material from 15 different tribal groups stretching across Africa, a fact that astounded and delighted him - for he believes studies like these will change the way black British people see themselves.
'What this has begun to unearth is that we have a dual heritage. Afro-Caribbeans in this country have been in a sort of limbo. They have been disowned by Europeans and also by Africans because of their history. This shows they are from the African continent in a very direct way. It also means that people like myself have a right to claim a heritage in this country and that this country has a clear responsibility to Afro-Caribbeans.'
Such revelations are not confined to Afro-Caribbeans, however. Very soon everyone's perspective of their heritage may be altered - from academic surveys of Viking 'genes' among modern Britons to services offered by US companies such as Family Tree DNA and DNA Print Genomics and Oxford Ancestors in the UK.
Take Oxford Ancestors. For a fee, it will tell you, from a scrap of spittle, if you are related to a series of seven notional founding mothers of ancient races: Ursula, from 45,000 years ago, in present-day Greece; Xenia (25,000, the Caucasus); Helena (20,000, the north-east Pyrenean foothills); Tara (17,000, Tuscany); Velda (17,000, the Basque region); Katrine (15,000, northern Italy); and Jasmine (10,000, the Euphrates valley). For their part, Family Tree DNA and DNA Print Genomics will tell you if you are related to Native Americans and other racial groups.
Such studies are carried out in two ways. First, by analysing mitochondrial DNA that is passed, uniquely, through the maternal line. (It is this technique that demonstrated Garrison's shared bloodline with African tribes). Or second, by carrying out studies of the Y chromosome - which is passed on from father to son. This reveals a person's paternal lineage, and explains how Garrison's white 'roots' were uncovered.
In this way, both sides of our family trees would seem to be exposed by science. However, researchers warn that identifying a Y chromosome as being of European origin, or a piece of mitochondrial DNA as being African, by no means provides a definitive picture of someone's ancestry.
'If you look back a generation, you see only two ancestors - our mother and father,' pointed out the historian Lord Renfrew. 'If you look back two generations, you see four ancestors - your grand parents. Three generations reveals eight great-grandparents, and 10 generations exposes more than 1,000 ancestors. Each one of these individuals has contributed to your gene pool, but by studying only the Y chromosome and mitochondrial DNA, you reveal only two lineages: your father's father 10 times removed, and your mother's mother 10 times removed. You miss all the rest.'
In short, the current limitations of modern genetics can give us a skewed picture of our origins. You may see the plantation owner and the exploited slave, but you miss all the others who have gone to make up a person's lineage.
On the other hand, Y chromosome and mitochondrial DNA data can still be very revealing - and not only for people of Afro-Caribbean background. For example, studies of the British Y chromosome by Mark Thomas and colleagues at University College London recently revealed a stark difference between men in England and those in Wales.
The group found that English Y chromosomes are almost identical to those from Friesland, an area of the Netherlands from which the Anglo-Saxons originated 1,500 years ago. Those of the Welsh were markedly different, however - from which Thomas concludes that Anglo-Saxons invaded the area now covered by England, overcoming between 50 and 100 per cent of the indigenous population, but failed to move into Wales.
This interpretation - based on blood taken from living humans - gives solidity to dusty historical analysis. It also contradicts arguments by many postwar historians who have claimed Anglo-Saxon influence on England was limited to political and commercial elites. 'Our work shows the traditional idea of an invasion of Germanic tribes is the more likely one,' says Thomas.
Or take the discovery of the startlingly high incidence of the A blood group among residents around Pembroke, Wales. Scientists believe this has a simple cause. Around 1108 AD, Henry I brought over many craftsmen from Flanders - which has a high incidence of the A blood group - and settled them in Pembroke. 'In short, in the blood of Pembrokeshire people today, the tell-tale signs of their Norman past lingers on,' says the geneticist Sir Walter Bodmer.
And then there is the work of scientists who have discovered the genetic fingerprint of Viking invaders in the blood of Orkney and Shetland islanders and the people of Cumbria. Peering further into the past, geneticist Prof Brian Sykes - founder of Oxford Ancestors - recently discovered the headmaster of a school in Cheddar had the same mitochondrial DNA type as the 9,000-year-old Cheddar Man's skeleton found many decades earlier in the region's caves.
However, it is crucial to note that DNA showed the headmaster was not directly descended from the Cheddar Man. 'It is merely that there is a link through one of Cheddar Man's female ancestors perhaps thousands of years earlier, and far from Cheddar,' says Sykes. Again, we should be careful about simplifying our ancestry.
It is fascinating stuff, though activists warn of dangers. By uncovering these webs of connectivity, we may end up confusing the concept of ethnicity - which defines people through their culture and language - with the idea of racial make-up. 'This has two dangers,' says Dr Helen Wallace, of Genewatch. 'It could exacerbate racism in medicine, perhaps leading to some ethnic groups being considered as genetically unsuitable to take particular medicines, and it could lead to wrongly blaming the incidence of some diseases on genetic differences, rather than factors such as poverty.'
The point is also stressed by Prof Steve Jones, of University College London: 'If genetics shows us one thing, it's that race is a social construct.'
Nevertheless, such surveys can bring joy. Consider Orlene Henry, a 40-year-old London woman who volunteered for the same survey that provided Len Garrison with his genetic 'surprise'. She knew her parents had come from Guyana in South America, but could not find out any more.
However, DNA tests showed that, like Garrison, she shared her genetic make-up with those of the Bubbi tribe, from equatorial Guinea. 'I've always seen myself as a strong, proud black woman, but now I feel even more so, given that I know who my ancestors are,' said Henry, a mature student. 'Why does it matter so much? I can't explain that to you, but I do believe you are more than the product of your environment or your immediate family.'
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Life's Blueprints & Its Energy Source Posted: Tuesday, February 4, 2003
Source: Purdue University
Purdue Researchers Connect Life's Blueprints With Its Energy Source
WEST LAFAYETTE, Ind. - The Purdue University research team that recently created a tiny motor out of synthetic biological molecules has found further evidence that RNA molecules can perform physical work, a discovery that could advance nanotechnology and possibly solve fundamental mysteries about life itself.
Purdue's Peixuan Guo has discovered how viral RNA molecules bind an energy-bearing organic molecule known as ATP. While linking these two substances might seem to create no more than a longer string of letters, the upshot is that now one of life's most mysterious and ancient storehouses of information can be moved by one of its most important fuels. The discovery could shed light on the fundamental role RNA plays in the creation of living things.
"RNA could be even more of a key player than we realize," said Guo, professor of veterinary pathobiology in Purdue's School of Veterinary Medicine. "The fact that it can be made to bind ATP in the phi29 virus could imply that these two molecules were among the first to partner in Earth's dance of life."
On a more practical level, the discovery could have immediate technical applications - such as driving a Lilliputian motor of the sort Guo's team has recently constructed.
"I think RNA can be made to do mechanical work," he said. "ATP binding could power a motor made of six strands of RNA, and we are now exploring the myriad possible applications of such a tiny mechanism."
The research appears in the February Journal of Biological Chemistry.
DNA, RNA and ATP are substances long known to be central to life's processes, but knowledge about their many functions in living things is still emerging. Several years ago, scientists were stunned by the discovery that some forms of RNA - well-known as the "messenger molecule" that carries instructions between DNA strands in a cell's nucleus - could serve as a catalyst for important chemical reactions in the body. The discovery of these RNA catalysts, called ribozymes, convinced many scientists that RNA probably existed on earth before DNA or complex proteins, the two other ingredient molecules necessary to create life.
"There are thousands of kinds of RNA in your body," Guo said. "Most varieties have an unknown function. When ribozymes were discovered, it taught us that RNA was probably responsible for the creation of other complex biological molecules. RNA might be more significant to life on earth than we imagined a few years ago."
Guo's group has discovered another way that RNA might be the keystone for biological processes: they have found that it is able to bind adenosine triphosphate, or ATP, which is the crucial substance used to transfer metabolic energy in living things.
"You couldn't live for one second without ATP," Guo said. "Your muscles, for example, are able to flex because an enzyme called ATPase binds the ATP molecule, breaking one of ATP's chemical bonds and releasing the energy you use when walking or talking."
Guo theorizes that because RNA can also bind ATP, it might be not only life's original seed molecule, but also able to direct the release of the energy needed to create life from that seed.
"We are just beginning to learn about RNA's many functions," he said. "But it is possible that it plays a crucial role in metabolism, too. In that case, RNA would play a more central role in biology than we originally thought. We are seeking fundamental knowledge here."
It is uncertain whether the RNA in living things has ever directed any of ATP's actions, but for the moment, Guo's group has already found a way to make ATP move RNA around. His team has learned to assemble several strands of RNA into a hexagonally-shaped "engine" with a strand of DNA functioning as the axle. When fed a supply of ATP fuel, the RNA strands kick against the axle in succession, much like pistons in a combustion engine. Such minuscule motors could find applications in nanotechnology.
"The world's smallest machines will need equally small motors to propel them," Guo said. "Ours uses organic molecules as fuel, so no special power source would need to be developed."
The motors could also be used not only to spin the DNA strand, but also as potential gene delivery vehicles. Guo's team had already found that the motor could drive its axle into a virus' protein shell, and has recently also learned that the ATP-binding RNA derived from the phi29 virus can deliver a ribozyme that destroys Hepatitis B. A paper detailing this work is forthcoming in the journal Gene Therapy.
"Delivering healthy genes or therapeutic molecules into damaged cells is the goal of gene therapy," Guo said. "With some modifications, we hope our research will enable us to deliver therapeutic molecules to cancerous or other virus-infected cells as well."
Guo's current research is headed in this direction, but he emphasizes that more work also needs to be done on RNA's fundamental capabilities.
"We would like to find other examples of how RNA operates in the body," Guo said. "We know from our research that RNA can be made to perform physical work in a viral system and in the laboratory, so it is possible that it is also involved in the transportation of components within cells."
Such ideas remain speculative for the moment, but Guo said that naturally occurring hexagonal loops of other RNA have been found performing protein transport in drosophila fly embryos.
"The RNA loops in these developing flies are similar to the loops we assembled," he said. "It's a clue that we may be on the right track."
Funding for this research has been provided in part by the National Institutes of Health and the National Science Foundation.
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