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This press release is copyright Nature.
VOL.461 NO.7265 DATED 08 OCTOBER 2009
This press release contains:
· Summaries of newsworthy papers:
Cancer: Breast cancer evolution
Opinion: A personalized medicine research agenda
Genetics: Mapping diversity
Opinion: Let's celebrate human genetic diversity
Genetics: Scanning and linking for autism
Physics: Quantum fingerprints of chaos
Genomics: Where is the heritability?
Palaeoclimate: Transition to an icehouse world
Ageing: Protein link to long life
Physics: Photonic crystal guides electromagnetic waves with no losses
And finally… Erupting without warning
· Mention of papers to be published at the same time with the same embargo
· Geographical listing of authors
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[1] Cancer: Breast cancer evolution (pp 809-813)
The genetic evolution of a breast tumour is reported this week in Nature. The findings will help researchers to understand the changes that occur in tumours as disease progresses.
As tumours progress, they acquire new genetic mutations that can enable them to continue to grow and spread. Samuel Aparicio and colleagues used next generation sequencing techniques to chart the genetic mutations that occur in an oestrogen-receptor-alpha-positive breast tumour. This tumour type accounts for 15% of all breast cancers. The sample came from the original patient biopsy at diagnosis and from a secondary tumour from the same patient removed 9 years later, after the tumour had spread.
The team find 32 mutations present in the DNA of the secondary tumour, 19 of which were not present at all in the original tumour sample. Combined analysis of genome and transcriptome data revealed RNA-editing events that occur in the tumour, two of which had not been reported before.
Based on their findings, the authors propose that sequencing primary tumours, before therapy and before they become invasive, should make it easier to find gene candidates for understanding the events that trigger the initial cancer. Looking only at more aggressive tumour samples, where mutations are more numerous, will require many more specimens to make sense of the information.
CONTACT
Samuel Aparicio (BC Cancer Research Centre, Vancouver, Canada)
Tel: +1 604 675 8207; Email: [email protected]
The BC Cancer Foundation is holding a press briefing relating to this paper at the BC Cancer Agency Research Centre, 675 West 10th Avenue, Vancouver, Canada, at 0100 Pacific Standard Time, on Wednesday 7 October.
For more information or to arrange interviews with co-authors from the study, please contact:
Judy Hamill (BC Cancer Foundation, Vancouver, Canada)
Tel: +1 604 707 5934; E-mail: [email protected]
Opinion: A personalized medicine research agenda (pp 724-726)
In this week’s Nature, Pauline Ng, J. Craig Venter, Sarah Murphy and Samuel Levy give nine recommendations to improve direct-to-consumer genetic tests. Prompted by debate on the usefulness of such testing, the team compared results from two companies that offer these tests — 23andMe and Navigenics — on 13 diseases for 5 individuals. “Despite this limited data set we find potential implications for personalized medicine,” they write.
They found the raw DNA data to be accurate, but they spotted inconsistencies between the two companies’ disease-risk predictions. For four diseases, the relative risk predictions completely agreed for all individuals. For seven diseases, only 50% or less of the predictions agreed between the two companies across the individuals.
Among other things, the authors urge companies to report how much of the genetic contribution of a disease can be attributed to the markers used in their test, and how much is still unknown. Companies should also focus on better communicating high-risk predictions, test for as many drug response markers as possible, and agree on the strong-effect disease markers.
Meanwhile, the research community should study markers in all ethnicities and look at how tests affect lifestyle and behaviour. The group also calls for more large, long-term studies to measure the predictive value of known markers, and more sequencing of individual genomes.
CONTACT
The authors are available via:
Heather Kowalski (Kowalski Communications, Washington DC, USA)
Tel: +1 301 943 8879; E-mail: [email protected]
[2] Genetics: Mapping diversity (AOP)
DOI: 10.1038/nature08501
***This paper will be published electronically on Nature's website on 07 October at 1800 London time / 1300 US Eastern time (which is also when the embargo lifts) as part of our AOP (ahead of print) programme. Although we have included it on this release to avoid multiple mailings it will not appear in print on 08 October, but at a later date. ***
What makes people different? A working map of regions of genetic variation across the human genome is reported online this week in Nature.
Everybody gets two copies of their DNA — one from each parent — but some regions can be duplicated or deleted, which gives rise to ‘copy number variation’ within the population. Matthew Hurles, Stephen Scherer and colleagues have made a comprehensive map of CNVs in the human genome from 450 individuals of European, African or East Asian ancestry.
The team identify 30 places in the genome that are candidates for influencing human disease susceptibility, including 3 CNVs that have already been linked with disease in genome-wide association studies. Importantly, the authors conclude that CNVs are unlikely to explain much of the dark matter of the genome — the heritability unexplained by SNPs.
The findings also shed light on how this type of genetic variation is introduced to the genome, providing insights into selective forces that act on CNVs and mechanisms that generate them. In a related News & Views article, John Armour predicts that the study “will become the working first-line resource for reliable data on copy number variation for future studies of human variation, genome evolution and disease genetics.”
CONTACT
Matthew Hurles (Wellcome Trust Sanger Institute, Cambridge, UK)
Tel: +44 1223 495377; Email: [email protected]
Stephen Scherer (The Hospital for Sick Children, Toronto, Canada)
Tel: +1 416 813 7613; E-mail: [email protected]
Opinion: Let's celebrate human genetic diversity (pp 726-728)
Society is ill-prepared for research finding group variation in biologically important traits according to Bruce Lahn and Lanny Ebenstein in Nature this week. Studies of human genetic diversity are increasingly finding evidence of biological variation among groups of people, not just among individuals. Some of these traits are superficial − such as skin colour − or non-controversial - such as lactose intolerance − but to ignore the possibility of group diversity is to do poor science and poor medicine, they claim.
Scientists are naturally wary of making claims that may be interpreted as favouring one population group over another, especially when it comes to important biological traits such as brain biology. Some have even called for a halt to such studies of genetic diversity to prevent any misuse of the information.
In recent decades, 'biological egalitarianism' − the view that human groups have no, or very few, meaningful genetically based biological differences − has emerged as the dominant moral position. The authors argue that this position is dangerous. Instead, they urge the science community to embrace genetic diversity, including at the group level, as one of humanity's chief assets.
CONTACT
Bruce Lahn (University of Chicago and Howard Hughes Medical Institute, Chicago, IL, USA)
Tel: +1 773 834 4393; Email: [email protected]
[3] Genetics: Scanning and linking for autism (pp 802-808)
A double-pronged approach to uncovering genetic variants involved in autism is published in Nature this week. The research describes both genome-wide association — to show common variants — and linkage mapping — to find rarer mutations — in over a thousand families with autism. Mark Daly and colleagues find regions to target for rare variation screening, and the team also discover a single novel association on chromosome 5 in the vicinity of a gene implicated in axonal guidance.
Autism is a highly heritable neurodevelopmental disorder and yet only very few specific susceptibility genes have been identified so far. This genome-wide scan uses half a million genome-wide single nucleotide polymorphisms in a common set of 1,031 multiplex autism families and reveals significant linkage and association to autism. The researchers believe that their work provides new insights into the biology and development of this disorder.
CONTACT
Mark Daly (Massachusetts General Hospital, Boston, MA, USA)
Tel: +1 617 643 3290; Email: [email protected]
[4] Physics: Quantum fingerprints of chaos (pp 768-771; N&V)
Signatures of chaos have been clearly spotted in the dynamics of a quantum system. The findings, reported in this week’s Nature, provide long-sought evidence for a connection between the two very different worlds of quantum mechanics and classical chaos.
Chaotic behaviour pervades the world of our senses. As illustrated most famously by the ‘butterfly effect’ in discussions of weather and climate, the behaviour of a chaotic system is extremely sensitive to its initial state. Ironically, this unpredictable behaviour is possible only in the deterministic world described by classical physics, not in the quantum world, where uncertainty rules. Yet if quantum mechanics is to provide a complete theory of the physical world, there must be quantum behaviours that correspond to chaos in the classical realm.
Poul Jessen and colleagues looked for these behaviours in a quantum system designed to mimic a textbook example of chaos known as the ‘kicked top’. The quantum version of the top is the ‘spin’ of a collection of caesium atoms, with the ‘kick’ applied by external magnetic and optical fields. The atomic spin dynamics were observed to respect the boundaries between stability and chaos that characterize the motion of the classical top. Thus, although classical chaos cannot invade the quantum world, its fingerprints can be clearly seen.
CONTACT
Poul Jessen (University of Arizona, Tucson, AZ, USA)
Tel: +1 520 621-8267; Email: [email protected]
Daniel Steck (University of Oregon, Eugene, OR, USA) N&V author
Tel: +1 541 346 5863; Email: [email protected]
[5] Genomics: Where is the heritability? (pp 747-753)
Despite the identification of hundreds of genetic variants linked to human diseases, most variants explain a small proportion of disease risk. A review article in Nature this week asks what strategies should be explored to illuminate the genetics of complex diseases, and examines potential sources of missing heritability.
Heritability analyses attempt to estimate relative contributions of differences in genetic and non-genetic factors to the total phenotypic variance in a population. Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with complex human diseases and traits, and have provided valuable insights into their genetic architecture.
Teri A Manolio and colleagues, who met in February this year at a special National Human Genome Research Institute (NHGRI) workshop on missing heritability, propose research strategies, including and extending beyond current genome-wide association approaches to identify genetic variance involved in disease risk and prognosis. They argue that “although the value of genetic variants in disease prediction and the steps needed to realise this are widely debated […] the search for missing heritability provides a potentially valuable path towards further discoveries
CONTACT
Teri A Manolio (National Human Genome Research Institute, Bethesda, MD, USA)
Tel: +1 301 402 2915; Email: [email protected]
[6] Palaeoclimate: Transition to an icehouse world (pp 776-779)
During the Late Eocene epoch, the Southern Ocean began a long cooling trend while tropical sea surface temperatures (SSTs) remained stable, according to sediment core data published in Nature. The results suggest that if this cooling was caused by decreases in greenhouse gases, additional processes must have been taking place to keep the tropics relatively warm.
The transition from greenhouse to icehouse world at the end of the Eocene epoch is still poorly understood and there are few temperature records from far southern latitudes, particularly from the Pacific sector of the Antarctic margin.
Peter Bijl and colleagues present a continuous record of SST from the East Tasman Plateau, using an index of carbon together with organic compounds called alkenones as proxies for SST. They show that southwest Pacific SSTs rose to present day tropical values of about 35 degrees Celsius during the Early Eocene epoch (about 53 million years ago), but then gradually fell to about 21 degrees Celsius by the beginning of the Late Eocene (about 36 million years ago). The SST in the tropics stayed relatively constant throughout.
The precise role of decreasing atmospheric greenhouse gases in cooling the poles is unclear, as in theory, this should have cooled tropical regions too. The authors suggest that high-latitude climate feedbacks might have been more instrumental in this Middle Eocene cooling than previously thought.
CONTACT
Peter Bijl (Utrecht University, Netherlands)
Tel: +31 30 253 9318; Email: [email protected]
[7] Ageing: Protein link to long life (793-797)
The mitochondrial protein complex prohibitin promotes longevity in the nematode worm Caenorhabditis elegans by influencing fat metabolism, a Nature paper suggests.
Prohibitin deficiency shortens the lifespan of otherwise wild-type animals, Marta Artal-Sanz and Nektarios Tavernarakis report. But ‘knocking down’ prohibitin levels increases the lifespan of worms under dietary restriction.
The authors propose that prohibitin normally promotes longevity by acting as a brake on the worm’s energy supply — moderating fat use and energy production. But under adverse external conditions, such as limited nutrient availability, energy demands outstrip supply and life lasts longer without such a ‘brake’. It is thought that the protein may have a similar key role in modulating energy metabolism during ageing in mammals.
CONTACT
Nektarios Tavernarakis (Foundation for Research & Technology, Heraklion, Greece)
Tel: +30 2810 391066; Email: [email protected]
[8] Physics: Photonic crystal guides electromagnetic waves with no losses (pp 772-775; N&V)
A new class of photonic crystals allows electromagnetic waves to flow freely in one direction only. This result, reported in this week’s Nature, may lead to the design of novel photonic devices, such as optical waveguides with zero scattering loss.
The reported phenomenon is a photonic equivalent of an electronic phenomenon called the quantum Hall effect, where electrons at the edge of a two-dimensional system in a magnetic field flow unimpeded in one direction only. Zheng Wang and colleagues have designed a special kind of photonic crystal — materials with periodic variations of their refractive index — such that electromagnetic waves flows unidirectionally and without scattering at its edges in a photonic analogue of the quantum Hall effect.
The finding of such photonic edge states may lead to the development of new and efficient photonic devices. It also highlights the universality of the quantum Hall effect, as photons belong to a fundamentally different family of particles, bosons, in contrast to electrons which are fermions.
CONTACT
Zheng Wang (Massachusetts Institute of Technology, Cambridge, MA, USA)
Tel: +1 650 704 2405; Email: [email protected]
Eli Yablonovitch (University of California, Berkeley, CA, USA) N&V author
Tel: +1 510 642 6821; Email: [email protected]
[9] And finally… Erupting without warning (pp 780-783)
Scientists document the rapid rise of magma during the 2008 eruption of Chaitén volcano, Chile, in a paper in Nature this week. An analysis of the ash erupted at Chaitén volcano reveals that certain types of eruption can happen very fast and with little warning.
Normally, when volcanoes enter an eruptive phase, geophysical precursors are observed for a period of time before the eruption itself, allowing scientists to estimate how fast the magma is moving. Many eruptions are preceded by weeks to months of unrest, consistent with long magma ascent times. This pattern was broken in May 2008 when Chaitén volcano entered an eruptive phase with almost no warning. This explosive eruption of rhyolite — a very viscous magma — was the first ever to be scientifically monitored.
Jonathan Castro and Donald Dingwell analysed crystals taken from ash deposits to obtain information about pre-eruptive magma storage and ascent — such as its pressure, temperature and water content. They find that the magma ascended very rapidly, being brought up from five kilometres below the Earth’s surface in about four hours. Very short degassing timescales also promoted explosivity during the eruption.
The authors emphasize the need to monitor rhyolite volcanoes that have shown any activity in the last 10,000 years, particularly in more densely populated regions where it would be essential to avoid a major volcanic disaster.
CONTACT
Jonathan Castro (Institut des Sciences de la Terre, Orléans, France)
Tel: +33 2 38 255 382; Email: [email protected]
Donald Dingwell (University of Munich, Germany)
Tel: +49 89 2180 4250; E-mail: [email protected]
ALSO IN THIS ISSUE…
[10] Nucleation, propagation and cleavage of target RNAs in argonaute silencing complexes (pp 754-761; N&V)
ADVANCE ONLINE PUBLICATION
***This paper will be published electronically on Nature's website on 07 October at 1800 London time / 1300 US Eastern time (which is also when the embargo lifts) as part of our AOP (ahead of print) programme. Although we have included it on this release to avoid multiple mailings it will not appear in print on 08 October, but at a later date. ***
[11] A regulatory circuit for piwi by traffic jam, a large Maf, in Drosophila gonadal somas
DOI: 10.1038/nature08434
GEOGRAPHICAL LISTING OF AUTHORS…
The following list of places refers to the whereabouts of authors on the papers numbered in this release. For example, London: 4 - this means that on paper number four, there will be at least one author affiliated to an institute or company in London. The listing may be for an author's main affiliation, or for a place where they are working temporarily. Please see the PDF of the paper for full details.
AUSTRALIA
Brisbane: 5
CANADA:
Alberta: 3
Nova Scotia: 3
Ontario: 2, 4, 3
Quebec: 3
Toronto: 2, 3
Vancouver: 1
Victoria: 3
FINLAND
Helsinki: 3
Oulu : 3
FRANCE
Creteil : 3
Nantes : 2
Orleans : 9
Paris: 3
Toulouse: 3
GERMANY
Frankfurt: 3
Hamburg: 3
Heidelberg: 3
Munich: 9
GREECE
Athens: 7
ICELAND
Reykjavik: 5
IRELAND
Dublin: 3
IRAN
Tehran: 3
ITALY
Bologna: 3
Stella Maris: 3
JAPAN
Saitama: 11
Tokyo: 11
Tokushima: 11
KUWAIT
Kuwait city: 3
NETHERLANDS
Texel: 6
Utrecht: 6, 3
PAKISTAN
Lahore: 3
PORTUGAL
Coimbra: 3
Lisbon: 3
SAUDI ARABIA
Jeddah: 3
SOUTH AFRICA
Cape Town:
SWEDEN
Goteborg: 3
Uppsala: 2
UNITED KINGDOM
Cambridge: 1, 2, 3
London: 3
Manchester: 3
Newcastle: 3
Oxford: 5, 3
UNITED STATES OF AMERICA
Alabama
Birmingham: 3
Arizona
Tucson: 4
California
Berkeley: 5
Los Angeles: 3
San Francisco: 3
Santa Cruz: 6
Stanford: 5, 3
Connecticut
New Haven: 5, 3, 8
Florida
Miami: 3
Illinois
Chicago: 5, 3
Indiana
Indianapolis: 3
Iowa
Iowa City: 3
Maryland
Baltimore: 5, 3
Bethesda: 5
Massachusetts
Boston: 2, 5, 3
Cambridge: 3, 8
Michigan
Ann Arbor: 5, 3
Missouri
Chesterfield:
St Louis: 5
New Jersey
Princeton: 5
New Mexico
Taos: 3
New York
New York: 5, 3, 10
North Carolina
Chapel Hill: 3
Durham: 5
Raleigh: 5
Ohio
Columbus: 3
Pennsylvania
Philadelphia: 3
Pittsburgh: 3
King of Prussia: 5
Rhode Island
Providence: 3
Tennessee
Memphis: 3
Nashville: 5, 3
Utah
Salt Lake City: 3
Washington
Seattle: 5, 3
PRESS CONTACTS…
For North America and Canada
Neda Afsarmanesh, Nature New York
Tel: +1 212 726 9231; E-mail: [email protected]
For Japan, Korea, China, Singapore and Taiwan
Mika Nakano, Nature Tokyo
Tel: +82 3 3267 8752; E-mail: [email protected]
For the UK/Europe/other countries not listed above
Ruth Francis, Nature London
Tel: +44 20 7843 4562; E-mail [email protected]
Jen Middleton, Nature London
Tel: +44 20 7843 4502; E-mail: [email protected]
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