News this Week

Science  04 May 2012:
Vol. 336, Issue 6081, pp. 524
  1. Around the World

    1 - Sado Island, Japan
    Back From the Brink
    2 - Washington, D.C.
    Research Agencies Hear About the Possibility of More
    3 - Abrolhos Shelf, Brazil
    Massive Coral Beds Charted off Brazil
    4 - Oshika Peninsula, Japan
    A New Deep-Sea Drilling Record

    Sado Island, Japan

    Back From the Brink

    Japan went gaga last week when three crested ibis chicks pecked through their shells in a nest on Sado Island and became the first of their species born in the wild in the country in 36 years.

    Scientists were equally thrilled. “We've learned a lot about captive breeding, preparing birds for release, and how to monitor them,” says Satoshi Yamagishi, an ornithologist at Niigata University in Japan who heads a Ministry of the Environment task force on reestablishing the birds in the wild. He expects their experience to benefit breeding-and-release programs for other species.

    CREDIT: MINISTRY OF THE ENVIRONMENT, JAPAN

    Nipponia nippon once flew over much of Japan and northeastern Asia, but overhunting (for their feathers) and habitat loss devastated their numbers. In 1981, the environment ministry captured Japan's last five wild birds for breeding, but the last of those birds died in 2003. Efforts continued with birds donated by China, where a small wild population survives. Since 2008, Japan has released 78 birds; 45 are known to remain in the wild. Before claiming success, “we would like to see a second generation born in the wild and a stable population,” Yamagishi says.

    Washington, D.C.

    Research Agencies Hear About the Possibility of More

    Research increases weren't supposed to be an option for next year because the U.S. government was tightening its belt. But the Obama Administration is facing the un expected—and not entirely unpleasant—job of deciding how to respond to preliminary steps by Congress to give some research programs more money in 2013 than the White House had requested.

    A House of Representatives spending panel last week voted to add $76 million to the president's request for fusion research at the Department of Energy, reversing cuts for domestic programs and coming closer to the promised U.S. contribution to the ITER fusion reactor being built in France. Within NASA, the panel had previously added $150 million to the Administration's request for continued work on a Mars sample return mission, and $115 million for two programs supporting planetary missions.

    While Congress is months away from a final decision on spending for next year, these initial moves raise a new issue for the White House: Is more money for research always a good thing? “Yes, as a general matter, increases [in research budgets] are good,” presidential science adviser John Holdren said after a speech last week at the AAAS annual policy forum. “But, of course, under overall caps, whether particular increases are good depends on what they come out of. That's why we need to study the House proposals before offering an opinion.” http://scim.ag/budget_2013

    Abrolhos Shelf, Brazil

    Massive Coral Beds Charted off Brazil

    CREDIT: © RODRIGO L. DE MOURA

    The Abrolhos Shelf of Brazil boasts the world's largest expanse of rhodoliths, a spherical type of coralline algae, according to a survey published last month in PLoS ONE. The beds cover a total area the size of El Salvador and produce an estimated 25 million metric tons of calcium carbonate a year, but face several threats. The slow-growing rhodoliths are made of magnesium-rich calcite, which is particularly vulnerable to ocean acidification. In addition, river sediments from deforestation may be harming the beds. Southern portions are also dredged as a source of lime for use as an additive to agricultural soils.

    Researchers have known about the rhodolith beds since the 1970s, but they had never been mapped in detail. So marine biologist Rodrigo Moura of Rio de Janeiro Federal University, along with colleagues from Brazil and Conservation International, spent 2 years surveying the beds with remotely operated vehicles, sonar, and SCUBA divers. The tennis ball–size rhodoliths cover 20,902 square kilometers. “It was very surprising to find beds these big,” Moura says, adding that the rhodolith beds need to be protected in part because they may be important migration routes for species that live on coral reefs.

    Oshika Peninsula, Japan

    A New Deep-Sea Drilling Record

    CREDIT: KYODO/LANDOV

    The deep-sea drilling vessel Chikyu, operated by the Japan Agency for Marine-Earth Science and Technology, has set the record for the deepest undersea research borehole, extending to a total depth of 7740 meters below sea level (856 meters of which are below the sea floor) in waters off the coast of Oshika Peninsula, the agency announced 27 April. The previous record was set in 1978, when the U.S. vessel Glomar Challenger drilled to a total of 7049.5 meters below sea level in the Mariana Trench—although only about 15.5 meters of that was below the sea floor.

    Chikyu has been probing into the fault zone around the Japan Trench, where the 11 March 2011 Tohoku earthquake and tsunami were generated.

  2. Random Sample

    Noted

    Alvin Ailey, Duke Ellington, and yes, Dr. Seuss—oh, the places you've gone! The International Astronomical Union (IAU) has approved a proposal by the science team of NASA's MESSENGER mission to assign new names to 23 impact craters on Mercury—including Ailey, Ellington, and Seuss.

    Those will join 53 previously named craters since the MESSENGER spacecraft first flew by Mercury in January 2008—all honoring deceased artists, musicians, and authors.

    Psyched About STEM

    CREDIT: MEGHNA SACHDEV/SCIENCE

    Sumo-wrestling LEGO robots (pictured), jumbo squid dissections, and virtual helicopter rides were just a few of the attractions at the second USA Science & Engineering Festival held in Washington, D.C., last weekend. The festival included more than 3000 exhibits, as well as appearances by science celebrities such as Bill Nye the Science Guy, neuroscientist and TV actor Mayim Bialik (of Blossom and The Big Bang Theory), and the MythBusters team.

    Designed to get kids interested in science, technology, math, and engineering (STEM), the festival's Finale Expo was packed with thousands of young attendees eager to build robots, test out fighter jet simulators, and play 3D videogames. It seems to be working, if the opinion of attendee 8-year-old Jacob Morey is any indication. “I like talking to the experts because I get responses and I can ask questions,” Morey says. “I think science is the greatest invention since the Internet!”

    Part Real, Part Fantasy: Disney's Chimpanzee

    CREDIT: © DISNEY

    The Disney film Chimpanzee tells the story of Oscar, an orphan chimp in Ivory Coast's Taï Forest that was adopted by one of his troop's males. The movie tells a scientifically accurate story—in fact, “the main plot was decided by the chimps,” says primatologist Christophe Boesch of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Boesch and his colleagues described the real-life adoption of another young orphan chimp named Victor by an older male in his troop in a 2010 PLoS ONE paper. (The movie blends Victor's story with Oscar's.)

    However, the story is also fictionalized in that it was pieced together from 3 years' worth of footage filmed not only in Taï but also among chimpanzee troops in Ngogo, Uganda—and, to Boesch's disappointment, the movie might not directly benefit its stars. Disney is donating some proceeds to the Jane Goodall Institute's sanctuary for orphaned chimps in the Republic of Congo. But Boesch says he'd hoped proceeds would also go to the Wild Chimpanzee Foundation, which works to protect the chimpanzees in Taï, and the Ngogo Chimpanzee Project, which supports conservation in Uganda. Both populations are severely threatened, he says. “They need support to have them survive.”

    By the Numbers

    12%—Percentage of clinical drug trials that are pediatric trials, although children bear nearly 60% of the disease burden for high-priority conditions such as malaria and HIV/AIDS, according to a study presented 28 April at the Pediatric Academic Societies' annual meeting in Boston.

    7327—Number of family names among a population of 1.28 billion Chinese recorded in a study appearing in an upcoming issue of the American Journal of Physical Anthropology. By contrast, a study of 18 million people in the United States found nearly 900,000 last names.

    ScienceLive

    Join us Thursday, 10 May, at 3 p.m. EDT for a live chat on how conservatives and liberals view science differently. http://scim.ag/science-live

    Understanding the Lords of Time

    CREDIT: ALEXANDRA FLEISCHMAN FOR PENN MUSEUM

    The putative end of the Maya Long Count calendar on 21 December 2012 has unleashed a cottage industry of doomsaying. Books, articles, TV shows, and movies portray myriad cataclysmic events that the Maya are said to have foreseen. This can be a frustrating exercise for scientists; Maya scholars tend to think the end of the calendar is merely the end of a cycle—hardly the end of the world or of time itself. But Simon Martin, a noted Maya epigrapher and associate curator at the University of Pennsylvania's Museum of Archaeology and Anthropology, sees an upside to the doom and gloom. This, he says, is a “once-in-a-lifetime opportunity, when the world is focused on the ancient Maya,” to inform people about the true role time played in the Maya's lives.

    Martin is the co-curator of Maya 2012: Lords of Time, an exhibit opening 5 May at the museum. Despite the forecasts of doom, experts note there is only one reference to the portentous date in all of the Maya glyphs; that reference was found at Tortuguero, a small site in southern Mexico. And although the 2012 date itself is discernible, the inscription that follows is difficult to decipher because of its poor condition.

    “Even in damaged form, (what comes after the date) doesn't appear to refer to 2012,” said Martin. The syntax and structure of this glyph suggest the damaged script would refer to a much earlier event. There's also a reference to a much later date, 4772 C.E., in an inscription at Palenque, which indicates the Maya thought life would continue beyond 2012.

  3. Newsmakers

    Steven Koonin is preparing for a homecoming of sorts: The Brooklyn-born physicist has been named director of New York University's new Center for Urban Science and Progress (CUSP), which will study how to make cities work better. Koonin, once provost of the California Institute of Technology in Pasadena, stepped down last fall as under secretary for science at the U.S. Department of Energy.

    Koonin

    CREDIT: FNAL.GOV

    Last year, New York City Mayor Michael Bloomberg invited proposals to raise the city's academic applied science and engineering IQ. The winner, and recipient of $100 million in city funding, was a team led by Cornell University and the Technion–Israel Institute of Technology. But Koonin, 60, thinks that CUSP, supported by a consortium of universities and high-tech companies, can also make a big splash.

    Q:How will CUSP differ from other research programs on sustainable cities?

    We have the city and its agencies as a deeply engaged partner. That means working with the people who actually run the subways and write the building codes. We have been promised the data and the opportunity to use the city as a living laboratory.

    Q:What will industry contribute?

    I know academics, and I love the freewheeling, curiosity-driven atmosphere of a university. But CUSP is meant to have an impact. That comes through demonstration projects and deployment, and industry knows how to do that.

    Q:Any downsides to returning to New York?

    I'm long enough out of California that I don't miss the sunshine. No, I can only think of upsides.

    They Said It

    “You have the right to prepare for interesting work and economic independence.”

    —Shorma Bianca Bailey, president of the Howard University Chapter of Engineers Without Borders, at a 24 April White House panel offering advice to young women entering science, technology, engineering, or mathematics fields.

    Epidemiologist Among Medal Of Freedom Winners

    William Foege, a leader of the global campaign that wiped out smallpox, has been named a recipient of the Presidential Medal of Freedom, the nation's highest civilian honor.

    Foege

    CREDIT: PHOTO BY EMORY PHOTO/VIDEO

    Foege, 76, is a physician and epidemiologist who helped spearhead the massive immunization effort that eradicated smallpox in the 1970s. He directed the Centers for Disease Control and Prevention from 1977 to 1983, worked to boost immunization rates in the developing world, and served as executive director of The Carter Center in Atlanta. More recently, as a senior fellow at the Bill & Melinda Gates Foundation, he has helped shape the organization's global health efforts.

    Foege is among 13 people recognized by President Barack Obama for their contributions to the United States or to the world who will receive the medal at the White House later this spring.

  4. Genome Sequencing

    Search for Pore-fection

    1. Elizabeth Pennisi

    At long last, nanopore sequencing seems poised to leave the lab, promising a new and better way to decode DNA.

    Threading the pore.

    With nanopore sequencing, single molecules of DNA will be deciphered as they pass through a tiny channel.

    CREDIT: DR. IAN M. DERRINGTON

    In a packed Florida conference center 3 months ago, Clive Brown introduced an audience of scientists, engineers, and biotech analysts to a device resembling an oversized thumb drive. He promised it would decipher almost a billion DNA bases in 6 hours and sell for $900. As backing for that claim, Brown described how Oxford Nanopore Technologies, where he is chief technology officer, had used a prototype to decode the genome of a virus in a single pass of a complete strand of its DNA. “There was an audible gasp from the audience,” recalls Oxford Nanopore's CEO, Gordon Sanghera.

    If Oxford Nanopore's claims and promises are borne out—and some scientists remain skeptical—the company is set to achieve the first commercialization of a long-awaited and oft-doubted technology called nanopore sequencing. The technology, based on protein pores so tiny that 25,000 of them can fit on the cross section of a human hair, could be the next big thing in genome sequencing and analysis.

    Although they've gotten much cheaper and smaller in recent years, machines that read DNA and RNA still usually cost hundreds of thousands of dollars, take up entire lab benches, and require much upfront and postsequencing processing to generate a genome. Nanopore sequencing could change all that. This new technology “really requires you to think about things in a completely different way,” says Elaine Mardis, co-director of the Washington University Genome Institute in St. Louis.

    As the tweeters and bloggers in Brown's audience went wild, sending missives out onto the Internet, David Deamer, a biophysicist at the University of California, Santa Cruz (UCSC), and Harvard University cell biologist Daniel Branton sat in the front row, beaming. In 1996, 7 years after Deamer initially had the idea, they had publicly proposed that threading DNA through a tiny pore and monitoring changes in the current going through the pore could yield a more direct, faster way to sequence genomes. Yet until the Florida meeting, no one had claimed success in reading DNA as it moved through a pore, leaving many to wonder whether the technology would ever pan out. “Over the years, the number of people who truly believed in nanopore sequencing you could probably count on your two hands,” says Mark Akeson, a molecular biologist at UCSC. “Now both companies and academics are seeing [evidence] that this stuff actually works. This technology is going to really take off.”

    Sequencing gold rush

    Over the 2 decades that nanopore sequencing has lingered backstage, many other advances have greatly reduced the cost and increased the speed of reading the strings of adenines, guanines, thymines, and cytosines that compose strands of DNA. Whereas that first human genome sequence cost an estimated $1 billion to complete, the all-inclusive price at a high-throughput sequencing center today is about $18,000, and a few companies are promising costs approaching $1000 per genome. The pace has also quickened. It took 3 years at the turn of the century to produce a draft of a human genome; the same can now be done in a week. Since the human genome sequence was completed in 2003, researchers have decoded hundreds of genomes of plants, animals, cancer cells, and even ancient humans, proving that sequencing is a valuable tool for biomedicine and all sorts of other disciplines, from ecology to anthropology. Researchers are calling for 10,000 vertebrates to be sequenced, for example, and physicians may soon routinely order up a patient's genome sequence for diagnostic or preventive purposes.

    Nanopore sequencing has not been part of this revolution. Instead, it was an appealing idea for which every aspect needed to be developed. When they first considered the concept, Deamer and Branton didn't have an appropriate pore or a way to control DNA's flow through such a pore, and they didn't know for sure that they could distinguish the different bases on a strand of nucleic acid. Ever so slowly, they and a handful of others have made advances on all those fronts, with several key publications in the past 2 years signaling progress, not just with protein pores but also with solid state ones (see sidebar, p. 536).

    Oxford Nanopore has promised to sell its new protein-pore sequencers by the end of the year, and if those machines pan out, it could set off another genomics revolution, many scientists predict. “Current sequencing has an awful lot of complications that just go away with nanopore sequencing,” says Stuart Lindsay, a physicist at Arizona State University, Tempe.

    Nanopore sequencing should require little upfront preparation beyond isolating an organism's DNA, and even that might be done away with in some applications. In contrast, current approaches require that the DNA be copied many times over and, typically, labeled with a fluorescent tag that can be read by an optical sensor. Such preparation takes time and money and erases any of the chemical modifications that result in the epigenetic control of gene expression—something researchers increasingly want to know about that nanopore devices may be able to read.

    Furthermore, current sequencers work by decoding many short stretches of DNA—typically 200 bases or so—and that information has to be painstakingly pieced together. Nanopore technology can read much longer stretches of DNA: At the February meeting, Brown reported decoding a 48,000-base genome of a bacteriophage, a virus that infects bacteria, by first linking the ends of the two strands of its DNA, then threading the entire genome, first one strand and then the other, through a pore in one pass. “That really stunned the audience,” Deamer says.

    While no scientist outside of Oxford Nanopore has reported seeing the prototype sequencers Brown bragged about in Florida, the company says it will eventually have an 8000-pore version—many pores will be needed to sequence genomes much larger than a phage's DNA. With 20 of these machines, it should be possible to reveal a human genome sequence in 15 minutes. “You don't have to wait 2 weeks to do the assembly; you are watching it on the fly,” Akeson says. “If [nanopore sequencing] works, there's not going to be anybody in genomics who is not using the device in some fashion.”

    That's a big “if,” Mardis notes. “It's such a beautiful possibility, but there are many technical hurdles to getting it to actually produce sequence data.”

    Not just an idea

    Deamer began trying to jump those hurdles almost 25 years ago, long before Oxford Nanopore formed. In 1989, Deamer was working on the origins of life and was struggling to figure out how to get the molecule adenosine triphosphate (ATP) across a lipid membrane to supply energy to enzymes trapped inside his synthetic “cell.” He quickly realized that his theoretical solution—to insert a channel of some sort into the membrane—had other possibilities. If ATP could squeeze through, so might DNA. And as DNA crossed the channel, he reasoned, it would alter the ion flow through the channel. Finally, if the changes in this hypothetical channel's ionic current differed with each of DNA's bases, then that could open up a whole new way of sequencing. At the time, the idea seemed fanciful even to Deamer. For starters, he recalls, “there was no pore available.” Nevertheless, he sketched out his idea in a lab notebook.

    Showstopper.

    If it works, this device could enable DNA sequencing to be done from a laptop.

    CREDIT: NIGEL CHAPMAN PHOTOGRAPHY

    Deamer also shared the scheme with Branton, and they approached Harvard about patenting it. They weren't the only ones thinking along those lines: They discovered that a colleague, geneticist George Church, had independently come up with a similar plan to sequence DNA using a pore from a bacteriophage. The three of them decided to join forces and eventually filed for a patent together. The chief missing ingredient was still a big enough pore. Church moved on to other sequencing projects, but Deamer kept an eye out for a way to make his idea reality.

    Nanopore dreamers.

    After David Deamer (top right) sketched out nanopore sequencing in 1989, he teamed up with Daniel Branton (bottom right).

    CREDIT: DAVID DEAMER (2); PAUL HOROWITZ

    Deamer learned about α-hemolysin, a protein that Staphylococcus aureus uses to bust open red blood cells. John Kasianowicz, a researcher at the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, was testing pores formed by this protein as biosensors for toxic heavy metals in solution. Working with Hagan Bayley, now at the University of Oxford in the United Kingdom, he had embedded an α-hemolysin pore in a membrane and applied a voltage to produce an electrical current of potassium and chloride ions through the pore. Sensitive electronics measured the ion flow. Kasianowicz hoped the heavy metals would bind to the pore and alter the ionic current in distinctive ways.

    “It occurred to me that this pore might in fact be large enough” to allow strands of RNA or DNA to move through, Deamer says. In 1993, he went to NIST with some RNA to test the concept. Because DNA and RNA are negatively charged, they would be pulled through the pore. As Deamer suspected, as the strand of RNA passed the narrow point of the pore, it interfered with the ion flow, changing the current. “We immediately got huge numbers of signals from the recorder,” indicating that the RNA was blocking the pore's ionic current as it threaded its way through, Deamer says.

    In 1996, he, Kasianowicz, and Branton published a paper in the Proceedings of the National Academy of Sciences, in which they reported that they could unravel a coiled nucleic acid so that its bases move through the pore single file. They could tell the length of a strand of DNA going through the pore by the amount of time the ionic current signal was altered. In the article, they suggested that this approach could also be used to sequence DNA. “That was the pioneering paper,” says Henry White, a chemist at the University of Utah in Salt Lake City.

    Even with a potential pore in hand, Deamer and his colleagues realized that DNA's bases were whipping through the channel too fast to be identified. One solution was to harness another protein to latch onto the DNA and control its movement through the pore. Reza Ghadiri of the Scripps Research Institute in San Diego, California, was also interested in nanopore sequencing and had taken the first steps toward controlling DNA movement using a polymerase, an enzyme that copies DNA by ratcheting a DNA strand along base by base, like a sprocket moving the links of a bicycle chain, as it adds the complementary base. Independently, Akeson, working with Deamer, started buying and testing various polymerases from different species and other proteins. The first ones he and his colleagues tested quickly fell off the DNA, only briefly moving the strand through the pore. After many years of trying, in 2010, they discovered that a polymerase from a phage called ϕ29 would move long stretches of DNA, one base at a time, at a reasonable pace through α-hemolysin.

    Yet although the ϕ29 polymerase slowed the DNA down as desired, the stem of the mushroom-shaped pore was so long that more than a dozen bases were passing through at any one time, creating a fuzzy ionic current signal at best. The signals weren't distinctive enough to tell one base from another. They needed a different pore.

    A better pore

    Fortunately, Jens Gundlach, a gravitational physicist at the University of Washington, Seattle, had heard about nanopore sequencing and was intrigued enough to move into biophysics. In 2003, Gundlach started looking into alternatives to α-hemolysin. A literature search yielded no promising candidates, but then he saw in Science a pore in a different bacterium with a potentially better geometry—it was shaped like a funnel—for getting a strong ionic current signal. Called MspA (for Mycobacterium smegmatis porin A), this channel has a single narrow section long enough for just four bases. The natural MspA had limitations, however: The constricted section carries a negative charge, making it hard for the similarly charged DNA to get through.

    Gundlach and his colleagues tweaked MspA's gene, changing the protein so that the constricted part of the pore was neutral, and produced the modified pore by expressing the altered gene in bacteria. They had also added some positive charges at the pore entrance to enhance the inflow of DNA. When DNA was suspended in the modified pore, the signal for each base was almost 10 times stronger than the signal for immobilized bases in α-hemolysin, Gundlach's team reported in 2010. A sequencer using this unnatural MspA in theory “could resolve in much finer detail the DNA strands,” Akeson says.

    Perfecting pores.

    Cross sections of the MspA (left) and α-hemolysin (right) pores show their different geometries.

    CREDIT: IAN M. DERRINGTON

    But each base still zipped by in a microsecond, 1000 times faster than could be read. And the only way Gundlach could slow them down required modifying the DNA itself, an impractical solution. So last year, he and Akeson joined forces. “The ϕ29 polymerase provides a mechanism to move the DNA through the pore at a reasonable speed,” about one base every 30 milliseconds, Gundlach says. With the combination of Gundlach's pore and Akeson's polymerase, nanopore sequencing finally made its public debut, at least in the academic sense. Gundlach and his colleagues reported at the Florida meeting and online 25 March in Nature Biotechnology that they had could distinguish the bases in six DNA strands ranging from 42 to 53 bases long. “This is the first paper where somebody has actually [read] DNA,” says chemist Geoffrey Barrall, president of Electronic BioSciences in San Diego, California, which is also developing nanopore sequencing technology. (Oxford Nanopore has yet to publish a scientific paper on the phage genome sequencing Brown described in Florida.) Gundlach says he has since tested longer stretches of DNA.

    A company is born

    While Deamer and the other U.S. researchers were struggling to make nanopore sequencing a reality, Bayley was modifying the α-hemolysin pore with a different primary goal in mind: sensing devices. He had started looking at α-hemolysin in the 1980s to learn how water-soluble proteins made it through membranes, but he got interested in engineering pore proteins for biotechnology. Bayley envisioned pores that would help kill tumor cells or detect metals, sugars, and other proteins, and he had been modifying this pore for these different applications, making much progress. In 2005, he started a company to commercialize these biosensors.

    About the same time, the push for the $1000 genome (Science, 17 March 2006, p. 1544) had resulted in a new U.S. National Human Genome Research Institute (NHGRI) program for technology development. Bayley decided to apply and see what his modified α-hemolysins could do with respect to sensing DNA. Since he knew that he could make pores that could distinguish mirror versions of the same molecule, he was confident he could distinguish DNA's bases. With Ghadiri, he got an NHGRI grant and eventually published that the pore could tell DNA's building blocks apart when they were in solution. He decided to pursue the idea of feeding individual bases through the pore and started looking into using an enzyme that would break off each base as the DNA entered the pore. In 2008, his company, now renamed Oxford Nanopore Technologies, stepped up its efforts in nanopore sequencing, first pursuing the idea of reading cut-up bases and later following the path others had taken, decoding long, intact DNA strands.

    Oxford Nanopore went after a better pore in earnest, developing a high-throughput approach toward testing and modifying potential protein candidates. The company licensed technology developed and patented by Bayley, Deamer, Branton, Akeson, and others. Because the natural lipid bilayers of the cell membrane originally used to hold the pores are not very stable, the company developed a polymer alternative that could withstand exposure to blood or pollutants. And Oxford Nanopore has its own proprietary motor protein to control the DNA's flow through the pore. The company won't disclose any details yet but says it will have data and machines for academics to evaluate in the coming months.

    One challenge, the company acknowledged in Florida, is getting the error rate down from its current 4%. Academics concur that errors are a problem. As a polymerase ratchets along, it sometimes backtracks so that a base is read twice; other times, the base gets through the pore without being read. One can compensate for these random errors by sequencing each DNA strand multiple times. With the pore setup developed by Akeson and Gundlach, they can read the DNA as it is first pulled down through the pore and then again as it is pulled up and turned into double-stranded DNA by the polymerase. In theory, one could repeat those two steps with the same strand as many times as needed. With its sequenced viral genome, Oxford Nanopore showed it could tackle the problem by connecting the DNA's two complementary strands so that each is sequenced, the second providing an accuracy check on the first.

    Neither approach solves another problem, accurately reading long stretches in which the same base is repeated, a not-infrequent occurrence in genomes. But nanopore proponents point out that this repetitive DNA is difficult for all sequencing techniques.

    How solvable this and other problems are and whether they can be overcome in the coming months is not yet clear. Oxford Nanopore has a good reputation, but some rival sequencing companies and genome experts won't believe the sequencers work as advertised until they can test one. They caution that nanopore technology has been “coming” for so long that it's hard to believe the hurdles are finally overcome. However, “if they could pull it off,” Mardis says, “it would be a complete game changer.” And Deamer and Branton's smiles may get even wider.

  5. Genome Sequencing

    Going Solid-State

    1. Elizabeth Pennisi

    The first nanopore sequencers will depend on protein pores, but many in the field envision replacing these biological channels with solid-state ones.

    The first nanopore sequencers will depend on protein pores, but many in the field envision replacing these biological channels with solid-state ones. They also foresee controlling DNA's movement through a sequencer's channels electrically rather than depending on another protein to ratchet the bases along the pore. Ditching the proteins could pave the way to even cheaper devices that take advantage of semiconductor manufacturing technology to mass-produce and shrink these sequencers.

    Since 2005, Tomoji Kawai, a physical chemist at Osaka University in Japan, and his colleagues have experimented with a pore in a silicon wafer. In Kawai's device, a quantum-dynamics effect known as electron tunneling, in which electrons jump from one place to another through what should be a barrier, has replaced the ionic current of the protein pore nanosequencers (see main text, p. 534) as a means of reading the bases. Two nanoelectrodes flank the pore and are close enough to produce quantum tunneling across the pore. As they pass between the electrodes, DNA's four bases alter the tunneling current in specific ways that are detected by the electrodes.

    Quantum sequencing.

    One way to read DNA in a nanopore would be to monitor changes in the tunneling current.

    CREDIT: MASATERU TANIGUCHI/THE INSTITUTE OF SCIENTIFIC AND INDUSTRIAL RESEARCH, OSAKA UNIVERSITY

    Instead of controlling the movement of the RNA or DNA strands with motor proteins, Kawai uses an electrical field that starts and stops the passage of the negatively charged nucleic acids through the wafer. Thus far, he has used the technology to read up to 20 bases of RNA. Toshiba is looking into using the technology to detect viruses, and Toray Industries Inc. plans to develop a test for an RNA cancer marker.

    Working together, IBM and Roche are also exploring an electronics-based approach. At the core of their nanopore-sequencing technology is a “DNA transistor,” a chip that consists of a stack of alternating metal and insulating layers, with the pore drilled through the layers. Sequential electric fields will pull the DNA through base by base. In 2010, researchers at IBM T. J. Watson Research Center in Yorktown Heights, New York, published a simulation showing the potential of this approach, and they have since been working on making a device. “We are pushing the limits” of chip technology, says Gustavo Stolovitzky of IBM.

    Like Kawai, Stolovitzky and his colleagues aim to detect tunneling differences. But his team decided that simply placing the electrode pair in the pore would work poorly, so they approached Stuart Lindsay, a physicist at Arizona State University, Tempe, who has developed a way to fit each electrode with a small organic molecule that is prone to making hydrogen bonds. These molecules recognize and latch onto each DNA base, briefly holding on to it until a signal is registered. In 2011, Lindsay licensed the technology to Roche.

    Neither IBM nor Roche will say exactly where their collaboration is in the development of this nanopore-sequencing technology. The “main challenges” are engineering, Lindsay says—”These are tiny devices that need to be made precisely.”

    Another potential solid-state pore material is graphene, which consists of a layer of carbon molecules arranged in adjoining hexagons. In theory, a graphene pore could be one atomic layer thick, just deep enough for a single base to pass by at one time, which might make detection more precise. In 2010, Daniel Branton and Jene Golovchenko of Harvard University and colleagues, along with two other independent groups, reported that they could detect DNA moving through graphene pores. They have since been working on building pores more reliably.

    The idea would be to apply semiconductor manufacturing technology to build large arrays of solid-state pores that allow for very fast sequencing. If these can be developed, they “offer the possibility to obtain genome sequences in less time than it takes to unravel a stethoscope” and could be a “compelling” technology for personalized genome sequencing, Hagan Bayley, a pioneer in nanopore sequencing at the University of Oxford in the United Kingdom, wrote in 2010.

  6. American Association of Physical Anthropologists

    For Early Hominins in Africa, Many Ways To Take a Walk

    Several new studies of incredibly rare fossils of feet and partial skeletons reported at the meeting reveal the complexity of early bipedalism.

    If the bureaucrats of Monty Python's Ministry of Silly Walks were to establish a hall of fame, they might consider inducting Australopithecus sediba, who walked with its weight balanced oddly on the inside edge of its soles about 2 million years ago in South Africa. Or they might ponder the contrasting way two types of australopithecines strolled across the same region of Ethiopia's Rift Valley about 3.4 million years ago. While one strode much like humans do today, the other tucked in its opposable big toe and swayed from side to side. “The take-home message here this morning is … there were different ways of being a good biped throughout early human evolution,” paleoanthropologist Jeremy DeSilva of Boston University reported.

    Different steps.

    The Burtele foot from Ethiopia (left) and the Au. sediba foot from South Africa show different ways of walking upright.

    CREDIT: COURTESY OF YOHANNES HAILE-SELASSIE/CLEVELAND MUSEUM OF NATURAL HISTORY; JEREMY DESILVA

    Of course, the walks weren't silly to these early hominins, the group that includes humans and our ancestors but not other apes. At the time, these gaits were adaptive, and so they shed light on how upright walking evolved in different habitats. Several new studies of incredibly rare fossils of feet and partial skeletons reported at the meeting reveal the complexity of early bipedalism. “By seeing subtle differences in different species, we're moving beyond the (simple) debate of whether a hominin had a humanlike bipedalism or not,” says paleoanthropologist Brian Richmond of George Washington University in Washington, D.C.

    Until recently, many thought that upright walking—a defining trait of being a hominin—evolved step by step in one lineage relatively quickly, perhaps just before the emergence of Au. afarensis—the species of the famous fossil Lucy—about 3.6 million years ago. But the discovery of older upright walkers, including the 4.4-million-year-old Ardipithecus ramidus and the 6-million-year-old Orrorin tugenensis, have pushed back the origins of bipedalism to 6 million years ago (Science, 2 October 2009, p. 36).

    This spring, researchers unveiled the more primitive foot of a still-unnamed species of Australopithecus from Burtele, near Hadar, Lucy's home in Ethiopia. That showed that at least two kinds of hominins walked upright in different ways at the same time 4 million to 3 million years ago (see http://scim.ag/EarlyAncestor).

    In a talk, paleoanthropologist Yohannes Haile-Selassie of the Cleveland Museum of Natural History in Ohio showed how the new foot shared features such as an opposable big toe with older Ar. ramidus, which suggests that both hominins still spent considerable time in trees. The foot also shared a key trait (the shape of a toe bone) with Au. africanus, which lived about 2 million years ago in South Africa. Neither of those features is found in Au. afarensis, suggesting that Lucy's species cannot be the direct ancestor of Au. africanus. That means that a second hominin lineage, with a different way of walking, must have led to Au. africanus, Haile-Selassie notes. (Lucy's species is still the leading candidate for ancestor to early Homo.)

    Meanwhile, DeSilva reported at the meeting that his analysis of the feet of two newly discovered partial skeletons of Au. sediba, considered a relative of Au. africanus, shows that this species walked with “excessive” pronation. It landed on its primitive, narrow heel and shifted its weight to the inside of its sole. “The big question now is why did it walk this way?” DeSilva says. All this variation in bipedalism shows that “through much of human evolution, there were several experiments in bipedalism going on,” he adds.

    One long-standing hypothesis holds that bipedalism arose because it's energetically more efficient to walk upright on two legs rather than on four. But paleoanthropologist Herman Pontzer of Hunter College in New York City and David Raichlen of the University of Arizona in Tucson reported in a poster that that idea doesn't hold up. They modeled the energy cost of walking and found that long-legged hominins are energetically efficient because they walk with straight legs, with their knees directly over their lower legs. In contrast, the crouched, bent-knee posture of the earliest hominins, such as Ardipithecus, required more muscle activation and energy. Simply walking on two legs instead of four doesn't save energy, so the earliest hominins must have begun walking upright for other reasons. Taken together, the flurry of new reports suggest to Pontzer that “our models of the origins of bipedalism are overly simple.”

  7. American Association of Physical Anthropologists

    How the Modern Body Shaped Up

    1. Ann Gibbons

    A remarkably comprehensive analysis of more than 2000 European skeletons presented at the meeting reveals how cultural changes have altered our physiques.

    Modern humans have gone through a lot of changes in the past 30,000 years. We switched from hunting and gathering to farming and herding; from life as nomads to settling in urban centers; from eating meat, nuts, and tubers to consuming grains, sugars, and dairy products. Now, a remarkably comprehensive analysis of more than 2000 European skeletons presented at the meeting reveals how these cultural changes have altered our physiques. “When you become a modern human, what happens to your body?” asked paleoanthropologist Christopher Ruff of Johns Hopkins University in Baltimore, Maryland, co-chair of the session on skeletal adaptation in recent Europeans.

    Strong-arm tactics.

    Men had stronger right arms, perhaps from throwing spears and other activities, before the invention of agriculture.

    CREDIT: PETER V. BIANCHI/NATIONAL GEOGRAPHIC COLLECTION

    While other studies have documented a decrease in height after the transition to agriculture, this is the first systematic study of how the skeleton changed from the time modern humans spread through Europe 30,000 years ago until they were circling the globe in jets by the 1960s. In 10 posters, Ruff and his colleagues focused on how each part of the body, from the spine to leg and arm bones, evolved over time through both genetic and cultural change.

    One of the most significant findings is a dramatic drop in strength in leg bones. Leg bending strength, or resistance to fracture, declined by 25% to 33% from 27,000 years ago to 1900 C.E., as shown by the cross-sectional dimensions of the upper and lower leg bones of 1834 men and 786 women, according to a poster by Brigitte Holt of the University of Massachusetts, Amherst, and her colleagues. This is “huge,” Ruff says. “We interpret this to reflect the move from a hunting-gathering lifestyle to a more sedentary agricultural lifestyle across Europe.” Our ancestors needed stronger legs to walk farther, especially if carrying goods.

    Over the same 30,000-year period, upper body strength declined after the introduction of agriculture. In males, it then increased in the Medieval period, possibly due to intensive upper-body labor such as blacksmithing. One trend through time is that the right arm lost much of its asymmetric larger size compared to the left arm, perhaps due to fewer strongly lateralized activities such as spear throwing. Women show particularly symmetrical arms from the beginning of agriculture 7000 years ago to Europe's Bronze Age, 3000 years ago. The researchers suspect that this stems from using both arms to make flour with grinding stones.

    As for overall height, about 30,000 years ago, European men stood 1.72 meters tall, almost as tall as Europeans today. Their height and weight dropped steadily until 4000 years ago, probably because of poorer nutrition and health, particularly with the advent of agriculture 10,000 years ago. With a few exceptions—for example, milk-drinking Scandinavians—Europeans got even shorter during the Medieval period and stayed short until 1900.

    The study has produced “an awesomely comprehensive picture of skeletal adaptation,” says bioarchaeologist Clark Spencer Larsen of Ohio State University in Columbus, who was not part of the team. Jay Stock of the University of Cambridge in the United Kingdom agrees that the study is a “major milestone. … It is a major achievement to quantify human variation through time and space with this resolution.”

  8. American Association of Physical Anthropologists

    Older Dads Have Healthier Kids Than You Think

    1. Ann Gibbons

    New data presented at the meeting suggest that children of older fathers and grandfathers may inherit longer telomeres, structures at the tips of chromosomes that may protect against aging and disease.

    Older fathers often get blamed for passing on genetic mutations to their children, causing some types of autism, schizophrenia, and other disorders. But new data presented at the meeting suggest that children of older fathers and grandfathers may inherit at least one advantage from aging patriarchs: longer telomeres, structures at the tips of chromosomes that may protect against aging and disease. And the effect is amplified over the generations: “We've shown that the paternal grandfather's age is associated with longer telomeres in his grandchildren,” graduate student Dan Eisenberg of Northwestern University in Evanston, Illinois, reported in a talk.

    Grandfather effect.

    Older fathers in the Philippines passed on long telomeres to their sons and grandsons.

    CREDIT: E. A. QUINN

    Telomeres are repetitive sequences of DNA that prevent the ends of chromosomes from unraveling, much like the plastic tips on the ends of shoelaces. As cells divide and replicate, telomeres get shorter and eventually can no longer prevent the fraying of DNA and the decay of aging. Recent studies have found a link between living to 100 and having a hyperactive version of telomerase, an enzyme that keeps telomeres long.

    Telomeres in sperm cells, however, are exceptional: Several studies have shown that they grow longer, not shorter, over the years, probably because telomerase activity is high in testes. As a result, sperm cells from older men have longer telomeres than those of younger men. That would suggest that the older a father is at conception, the longer the telomeres his sons and daughters inherit.

    Working with Northwestern biological anthropologist Christopher Kuzawa and anthropological geneticist Geoff Hayes, Eisenberg examined data from a long-term study of 3327 women who were pregnant in 1983 in the Cebu Longitudinal Health and Nutrition Survey in the Philippines. They had gathered the ages of fathers and in 2005 measured telomere length in the blood of 1845 moms and 1681 children.

    Children of older fathers did indeed have longer telomeres than those of younger dads: For each additional decade of age in fathers at conception, sons and daughters had 4% longer telomeres, a finding that corroborates earlier work. The Northwestern group also found that for every additional decade of age in grand fathers, the grandchildren's telomeres added another 4%. But grand fathers did not pass on their longer telomeres to their daughters' children, only their sons', suggesting that this is a paternal effect.

    The increase in telomere length per year of fathers' age is just about the same amount as telomere length lost per year in normal aging, Eisenberg says. So the longer telomeres in sperm roughly offset normal aging, giving children of older dads an advantage. “It's as if you delay reproduction, you earn this kind of higher fitness for your offspring,” says biological anthropologist Koji Lum of Binghamton University in New York.

    Any benefit in telomere length may still be swamped out by the risk of passing on more mutations, Eisenberg warns: “We don't know yet the net health effect.” So at the moment, he's not advising anyone to delay fatherhood.

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