This press release contains:
• Summaries of newsworthy papers:
Palaeontology: When crocodiles ruled
Biology: Genetic variants linked to blood lipids
Astronomy: Sharper images across a wider field
Genetics: Sea sponge genome sheds light on animal evolution
Biology: New antibiotic caught in action
Earth science: Recycling the Earth’s inner core
Chemistry: Tracking valence electrons in real time
Quantum physics: Light–matter entanglement in the solid state
Materials science: Negative refractive index without loss
And finally… Mining the wisdom of the gamers
• Mention of papers to be published at the same time with the same embargo
• Geographical listing of authors
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[1] Palaeontology: When crocodiles ruled (pp 748-751)
A new species of crocodilian from the Cretaceous Period has been discovered in southwestern Tanzania, with dental features previously thought to exist only in mammals.
Around 144 million to 65 million years ago, the notosuchians or 'southern crocodiles' (distantly related to modern crocodiles and alligators), living in the former Gondwanan landmasses, showed a far more impressive level of ecological and morphological diversity than that shown by today’s crocodiles. For instance, instead of having rows of undifferentiated conical fangs, their teeth were often specialized into biting and crushing types.
In this week’s Nature, Patrick O’Connor and colleagues add to this by describing a new, small-bodied species in which the upper and lower rows of teeth were able to make contact in a way that’s only been seen in mammals. O’Connor and his team infer that notosuchians occupied ecological niches in Gondwana that were filled by mammals in the northern continents.
Author Contact:
Patrick O’Connor (Ohio University, Athens, OH, USA)
Tel: +1 740 593 2110
E-mail: [email protected]
** The National Science Foundation are holding a webcast UNDER
STRICT EMBARGO with lead author Patrick O’Connor on Monday 02 August at 1900 London time / 1400 US Eastern Time. Join the webcast at http://www.science360.gov/live (username webcast, password crocs; both are case sensitive). During the webcast, dial +1 888 831 8968 to ask a question, or e-mail questions to [email protected] at any time. **
[2] & [3] Biology: Genetic variants linked to blood lipids (pp 707-719; N&V)
Ninety-five genetic variants linked to serum lipids are revealed in this
week’s Nature. With serum lipid concentration an important risk factor for coronary artery disease (CAD), it is hoped the research will help generate new therapies for heart disease prevention.
The loci, identified through a genome screen of over 100,000 individuals of European ancestry, include variants linked to cholesterol metabolism and known targets of cholesterol-lowering drugs. And they appear relevant to European and non-European populations, Sekar Kathiresan and colleagues report. The authors also validate three of the novel loci using mouse models.
Some of the lipid-related variants are also associated with increased risk of CAD, and a second study lead by Daniel Rader provides a biological mechanism linking the two phenomena. The team describes how one particular variant influences a specific gene, SORT1, and show how manipulating mouse liver SORT1 levels alters plasma levels of LDL-cholesterol and levels of very-low density lipoprotein particles. Teasing apart the steps in complicated pathways such as this should identify new potential targets for drug development.
Author contact:
Sekar Kathiresan (Massachusetts General Hospital, Boston, MA, USA) – Author paper [2]
Tel: +1 617 643 6120
E-mail: [email protected]
Daniel Rader (University of Pennsylvania, Philadelphia, PA, USA)
– Author paper [3]
Tel: +1 215 573 4176
E-mail: [email protected]
Alan Shuldiner (University of Maryland, Baltimore, MD, USA) N&V author
Tel: +1 410 706 1623
E-mail: [email protected]
[4] Astronomy: Sharper images across a wider field (pp 727-729)
Ground-based astronomy takes a leap forward this week, with the report of observations made with a new system for correcting the optical aberrations caused by low-altitude atmospheric turbulence. As described in this week’s Nature, the improvement in telescope resolution, over a wide area, will allow the study of many important processes, such as star formation in massive young clusters.
For two decades, ground-based astronomers have used ‘adaptive optics’ techniques to remove the detrimental effects of atmospheric turbulence on their images. Conventional adaptive optics systems use a single bright ‘guide star’ as a reference for correction — leading to a degradation in image quality with distance from the guide star. Observations requiring high spatial resolution over a wide area can in principle be made by using multiple guide stars. The simplest version of such a system, called ‘ground-layer adaptive optics’ (GLAO), removes distortions originating in the lowest 500 metres of the atmosphere, where much of the damaging turbulence is concentrated.
Michael Hart and colleagues report observations of two star clusters, made with the recently upgraded GLAO system on the 6.5-metre MMT telescope in Arizona. They obtain improvements in resolution by a factor of 2–3 over a field wide enough to image an entire cluster in a single observation.
Author contact:
Michael Hart (University of Arizona, Tucson, AZ, USA)
Tel: +1 585 613 1882
E-mail: [email protected]
[5] Genetics: Sea sponge genome sheds light on animal evolution (pp 720-726)
The newly sequenced genome of one of the earliest multicellular creatures, the humble sea sponge, hints that our founding animal ancestor was remarkably complex. Comparative analyses of the DNA sequence, presented in this week’s Nature, yield important insights into animal evolution and cancer biology.
Sponges form part of the earliest branching lineage in the animal kingdom, and as such their DNA is instructive with regard to identifying the genetic innovations that enabled transition from single-celled to multicellular life some 600 million years ago. This draft DNA sequence of the Great Barrier Reef demosponge Amphimedon queenslandica is no disappointment, incorporating as it does many genes related to inherently multicellular processes such as cell division, growth and specialization.
Mansi Srivastava and colleagues point out that this complex genetic ‘toolkit’ is remarkably similar to other animal genomes in content, structure and organization. Notably, many of the genes linked with the emergence of animals are also implicated in cancer, which arises from defects in basic processes related to animal multicellularity.
Author contact:
Mansi Srivastava (Whitehead Institute for Biomedical Research, Cambridge, MA, USA)
Tel: +1 510 684 8693
E-mail: [email protected]
[6] Biology: New antibiotic caught in action (AOP)
DOI: 10.1038/nature09197
***This paper will be published electronically on Nature's website on 04 August 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 05 August, but at a later date. ***
A ‘molecular snapshot’ of a potent new antibiotic in action is revealed in this week’s Nature. It is hoped that the crystal structure of the drug bound to its target enzyme will aid the design of new antibiotics that are effective against multiresistant pathogens.
The new antibiotics block the activity of type IIA topoisomerases, enzymes that are crucial to relieve the torsional stress that builds up in DNA during processes such as replication or transcription. Michael Gwynn and colleagues present the molecular structure of one such antibiotic in complex with a bacterial topoisomerase and DNA, providing the first detailed structural picture of how these enzymes cleave DNA.
Many drugs act by interfering with topoisomerases, notably the broad-spectrum fluoroquinolone antibiotics that are increasingly losing effectiveness as resistance spreads in bacteria. The team also determined the structure of the enzyme in complex with a fluoroquinolone, thereby providing insight into how the new antibiotic is active against pathogens that are resistant to
fluoroquinolones. As such it provides a much needed platform for the
structure-based design of urgently needed new antibiotic drugs.
Author contact:
Michael Gwynn (GlaxoSmithKline, Collegeville, PA, USA)
Tel: +1 610 917 7749
E-mail: [email protected]
[7] Earth science: Recycling the Earth’s inner core (pp 744-747; N&V)
Some puzzling observations relating to the structure of the Earth’s core may be explained by a proposal in this week’s Nature. Thierry Alboussière and colleagues suggest that the solid inner core is continually moving eastwards relative to the liquid outer core — melting at its leading surface and crystallizing at the back.
The Earth’s solid inner core grows through time by the progressive
crystallization of the liquid outer core. As iron-rich crystals form, light
elements such as sulphur and oxygen are preferentially retained in the liquid; this lighter residual liquid can then rise through the outer core, driving the convective flow that is thought to generate the Earth’s magnetic field.
Against this background, it has been hard to understand seismological observations that seem to indicate a layer of relatively dense liquid lying at the base of the outer core, as well as an east–west hemispherical asymmetry in the inner core’s properties.
Alboussière and colleagues note that the dense liquid layer can be generated if melting is occurring at the top of the inner core. They present a theoretical model, supported by laboratory experiments, in which melting and crystallization occur simultaneously on the opposite sides of the inner core, as it continually moves towards the melting side — entirely renewing itself every 100 million years or so. If the movement takes place from west to east, it may also account for the observed hemispherical asymetry.
Author contact
Thierry Alboussière (Université Joseph Fourier, Grenoble, France)
Tel: +33 4 72 44 83 98
E-mail: [email protected]
Michael Bergman (Bard College at Simon’s Rock, Great Barrington, MA, USA) N&V author
Tel: +1 413 528 7432
E-mail: [email protected]
[8] Chemistry: Tracking valence electrons in real time (pp 739-742; N&V)
Laser pulses lasting less than 150 attoseconds (one attosecond is 10-18 seconds) have been used to observe, in real time, the motion o electrons in the outermost (‘valence’) shell of ionized krypton atoms. This technical achievement, reported this week in Nature, lays the groundwork for observations in more complex systems, which should allow a detailed examination of the fundamental processes underlying the making and breaking of chemical bonds.
‘Pump–probe’ spectroscopy, in which optical pulses separated in time are used to investigate a chemical reaction, is now a well established technique at timescales of the order of femtoseconds (one femtosecond is 10-15 seconds). This timescale is sufficiently fast to follow changes in molecular structure, but the motion of the valence electrons that ultimately drive chemical reactions occurs on faster, sub-femtosecond timescales.
Ferenc Krausz and colleagues have extended the pump–probe technique to these faster timescales, reporting the successful observation of the sub-femtosecond motion of valence electrons over a multi-femtosecond timespan. The authors use an infrared ‘pump’ pulse to ionize a collection of krypton atoms, which is followed by an extreme-ultraviolet probe pulse, lasting less than 150 attoseconds, to take a snapshot of the resulting electron vacancy, or ‘hole’. By varying the delay between pump and probe, the authors are able to reconstruct the motion of the valence electron wave-packet.
In an accompanying News and Views article, Olga Smirnova delves into the quantum-mechanical underpinnings of the authors’ experiment, and explains how the technique may uncover new mechanisms of chemical reactivity.
Author contact
Ferenc Krausz (Max Planck Institute of Quantum Optics, Garching, Germany)
Tel: +49 89 32905 602
E-mail: [email protected]
Eleftherios Goulielmakis (Max Planck Institute of Quantum Optics, Garching, Germany) – Co-author
Tel: +49 89 32 905 632
E-mail: [email protected]
Olga Smirnova (Max Born Institute, Berlin, Germany) N&V author
Tel: +49 306 392 1356
E-mail: [email protected]
[9] Quantum physics: Light–matter entanglement in the solid state (pp 730-734)
An important step on the road to practical quantum networks is reported this week in Nature, with the demonstration of quantum entanglement between an optical photon and a solid-state ‘quantum bit’.
Long-distance quantum communication and distributed quantum computation will require the implementation of quantum networks, in which nodes that process and store quantum states are connected to one another by entanglement. This connection can be made by optical photons, if quantum states can be transferred reliably from matter to light and back again. This can be done by preparing an entangled state between a photon and a quantum bit — a process that has been demonstrated using trapped ions, atoms and atomic ensembles.
Mikhail Lukin and colleagues now show that a single optical photon can also be entangled with a quantum bit in the solid state — specifically, an electron spin associated with a defect (called a nitrogen-vacancy centre) in diamond. This capability may provide a key building block for the solid-state realization of quantum networks, and paves the way for new studies of fundamental quantum phenomena using solid-state quantum bits.
Author contact:
Mikhail Lukin (Harvard University, Cambridge, MA, USA)
Tel: +1 617 495 2862
E-mail: [email protected]
[10] Materials science: Negative refractive index without loss (pp 735-738)
Asubstantial obstacle to using otherwise promising ‘metamaterials’ has been overcome, with the report in Nature of composite materials with negative refractive index that are not compromised by the absorption of incident light.
Artificially engineered composites, known as metamaterials, exhibit electromagnetic properties that cannot be obtained with natural materials. In particular, nanostructured composites combining metals and dielectric insulators can be made to have a negative refractive index — opening the way to applications such as ‘invisibility cloaks’ and ‘perfect’ lenses. But the performance of such negative-index metamaterials (NIMs) has been severely limited, especially at near-infrared and visible wavelengths, by energy losses due to the strong absorption characteristic of metals.
Vladimir Shalaev and colleagues have found a incorporating a light-amplifying material (or ‘gain medium’) in the design of a NIM structure. Previous discussions of this approach were stymied by the apparent impossibility of obtaining sufficient gain without disturbing the special optical properties of the NIM. But by locating the gain medium at those places in the nanostructure where the local electromagnetic field is strong, the authors are able to create enough gain to compensate for the inherent losses while preserving the negative refractive index.
Author contact:
Vladimir Shalaev (Purdue University, West Lafayette, IN, USA)
Tel: +1 765 494 9855
E-mail: [email protected]
[11] And finally… Mining the wisdom of the gamers (pp 756-760)
Complex scientific problems can be ‘crowd-sourced’ effectively using
interactive, online games, reports a paper in this week’s Nature. The combined efforts of tens of thousands of players of a multiplayer online game yielded a rich, new set of search strategies for the prediction of protein structures.
The three-dimensional structure of a protein is crucial for understanding its biological function, but the computational prediction of a protein's structure is a formidable challenge. Seth Cooper and colleagues have developed a multiplayer online game called ’Foldit’, in which incorrectly folded protein structures are presented as puzzles. The players, many of whom do not have any formal scientific training, manipulate the protein structures to optimize the computed energy.
The researchers used ten puzzles, where the target protein structures were not publicly available, to test the players’ abilities: they found that players outperformed the ‘Rosetta’ structure rediction software on five of the puzzles. Many players worked collaboratively and — unlike computational approaches — they explored not only conformational space but also the space of possible search strategies.
The authors believe that further analysis of the strategies used by the top-ranked Foldit players could lead to improved automated algorithms for protein structure prediction and could facilitate research on related problems, such as protein design, that rely on computational algorithms.
Also in this issue, a News Feature by Eric Hand investigates the growing phenomenon of 'human computing' or 'distributed thinking': recruiting volunteers to solve scientific problems — such as protein folding and image analysis —- at which many human brains can still outperform a computer.
Author contact
Seth Cooper (University of Washington, Seattle, WA, USA)
Tel: +1 206 818 2248
E-mail: [email protected]
ALSO IN THIS ISSUE…
[12] Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells (pp 769-773)
[13] Branched tricarboxylic acid metabolism in Plasmodium falciparum (pp 774-778; N&V)
ADVANCE ONLINE PUBLICATION
***This paper will be published electronically on Nature's website on 04 August 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 05 August, but at a later date. ***
[14] Rb regulates fate choice and lineage commitment in vivo
DOI: 10.1038/nature09264
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: 2, 5
Townsville: 1
AUSTRIA
Innsbruck: 2
BELGIUM
Brussels: 6
CANADA
Edmonton: 5
Hamilton: 2
London: 2
Montreal: 2, 3
Ottawa: 2
DENMARK
Copenhagen: 9
Odense: 2
FINLAND
Espoo: 2
Helsinki: 2
Oulu: 2
Tampere: 2
FRANCE
Grenoble: 7
Lyon: 7
Paris: 5
GERMANY
Garching: 8
Göttingen: 5
Hamburg: 3
Heidelburg: 5, 8
Lübeck: 2
München: 2
Munich: 5
Neuherberg: 2
Regensburg: 2
ICELAND
Kopavogur: 2
Reykjavik: 2
ITALY
Cagliari: 2
Florence: 2
Rome: 2
Udine: 2
KINGDOM OF SAUDI ARABIA
Riyadh: 8
KOREA
Seoul: 2
NETHERLANDS
Amsterdam: 2
Rotterdam: 2
NORTH CAROLINA
Chapel Hill: 2
NORWAY
Bergen: 5
PHILIPPINES
Cebu City: 2
SINGAPORE
Singapore: 2
SOUTH AFRICA
Johannesburg: 1
SPAIN
Barcelona: 2
Granada: 12
SWEDEN
Malmö: 2, 3
Stockholm: 2
Uppsala: 2
SWITZERLAND
Lausanne: 2
Zurich: 5
TANZANIA
Dar es Salaam: 2
UNITED KINGDOM
Bristol: 2
Cambridge: 2, 6
Edinburgh: 2
Glasgow: 2
Harlow: 6
Leicester: 2
London: 2
Oxford: 2
Stevenage: 6
UNITED STATES OF AMERICA
Arizona
Tucson: 4
California
Berkeley: 5, 8
Davis: 5
La Jolla: 5
Livermore: 8
Los Angeles: 2
Oakland: 2, 3
Pasadena: 4
Santa Barbara: 5
Stanford: 2
Thousand Oaks: 2
Walnut Creek: 5
Hawaii
Kamuela: 4
Illinois
Argonne: 8
Chicago: 8
Indiana
West Lafayette: 10
Maine
Lewiston: 9
Maryland
Baltimore: 2, 3, 7
Chevy Chase: 12
Massachusetts
Boston: 2, 3
Cambridge: 2, 3, 5, 9, 13
Framingham: 2
Michigan
Ann Arbor: 2, 12
East Lansing: 1
Minnesota
Minneapolis: 3
Mississippi
Jackson: 2
Missouri
St Louis: 2
New Jersey
Princeton: 13
New York
Farmingdale: 6
New York: 2
Stony Brook: 1
North Carolina
Cary: 6
Chapel Hill: 11
Ohio
Athens: 1
Rootstown: 1
Oregon
Hillsboro: 10
Pennsylvania
Collegeville: 6
King of Prussia: 2
Philadelphia: 2, 3, 10, 13
Pittsburgh: 9, 11
Texas
College Station: 9
Houston: 2, 5
Utah
Cedar City: 1
Washington
Seattle: 2, 3, 11
PRESS CONTACTS…
From North America and Canada
Neda Afsarmanesh, Nature New York
Tel: +1 212 726 9231
E-mail: [email protected]
From Japan, Korea, China, Singapore and Taiwan
Mika Nakano, Nature Tokyo
Tel: +81 3 3267 8751
E-mail: [email protected]
From the UK
Rebecca Walton, Nature, London
Tel: +44 20 7843 4502
E-mail: [email protected]
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