Table of contents

indicates content that is available online only



A plan for the ocean p9

Governments have typically regulated their coastal waters as if fishing, shipping and the like were separate entities. A new, integrated approach could change all that — while greatly boosting marine science.


Up in the air p9

Ways to obtain more accurate data can and should be put in place to police greenhouse-gas emissions.


Open to all p10

A new approach to technology assessment would supplement expert opinion with input from society.



Research Highlights

Ecology: Not-so-lonesome lizards p12


Neuroscience: What makes masculinity? p12


Oceanography: Deep-sea biomass boom p12


Atmospheric science: Ozone high and low p12


Microscopy: See through tissue p12


Genomics: Rat sequencing redux p12


Drug development: Virus knockdown p13


Optical devices: Organic light p13


Microbiology: Bacterial break up p13


Cognitive neuroscience: Attention please! p13



Journal Club

Journal club p13

James Noonan




News briefing: 6 May 2010 p14

The week in science


The code within the code p16

Computational biologists grapple with RNA's complexity.

Heidi Ledford


Nurse wants elite UK science focus p16

Incoming head of Royal Society sets out his agenda.

Geoff Brumfiel


Greenhouse-gas numbers up in the air p18

To control emissions, countries must first account accurately for their carbon. That will take considerable effort, reports Jeff Tollefson.

Jeff Tollefson


Green patents corralled p21

Intellectual-property database could ease technology transfer.

Quirin Schiermeier


Greeks hope crisis may spark reform p22

Financial troubles could be the stimulus for a fairer distribution of science research funding.

Alison Abbott


European funding may get simpler p22

Research commissioner promises to cut red tape in framework programmes.

Alison Abbott



News Features

Seismology: The biggest one p24

Fifty years ago this month, a massive earthquake in Chile broke new ground in seismic science. Roff Smith looks back at the largest quake ever recorded.


Neuroscience: Illuminating the brain p26

Systems neuroscientists are pushing aside their electrophysiology rigs to make room for the tools of 'optogenetics'. Lizzie Buchen reports from a field in the process of reinvention.




World view: Brick by brick p29

A small non-profit organization shows how to reduce the vulnerability of poor countries to earthquakes, says Daniel Sarewitz.

Daniel Sarewitz




European money could end delays on essential facilities p31

Massimo Altarelli


Independent research offers freedom and opportunities p31

Bernt Christian Skottun


Earthquake defence and the price of a telescope p31

Leopoldo Infante & Juan Carlos de la Llera


Questionable value of planting thirsty trees in dry regions p31

Shixiong Cao, Guosheng Wang & Li Chen




Financial pain should focus universities p32

The tightening of the US science budgets could improve both teaching and research, argues Diane Auer Jones — by forcing academics and their institutions to play to their strengths.

Diane Auer Jones


Reflections on the ozone hole p34

Jonathan Shanklin, one of the team who discovered the thinning ozone layer over the Antarctic 25 years ago, reflects on lessons learned from a tale of luck, public perception and fast environmental change.

Jonathan Shanklin



Books and Arts

Chemistry's visual origins p36

Vivid imagination was key to unlocking the secrets of molecular structure in the nineteenth century, finds Andrew Robinson.

Andrew Robinson reviews Image and Reality: Kekulé, Kopp, and the Scientific Imagination by Alan J. Rocke


Managing career moves p37

Peter S. Fiske reviews Chasing Stars: The Myth of Talent and the Portability of Performance by Boris Groysberg


Medical treasures on show p37

Marta Paterlini reviews Läke Konst (Art of Medicine)



News and Views

Geophysics: A new turn for Earth's rotation p39

Earth's spin rate varies with time. A six-year periodic signal in the planet's core is partly responsible, and increases the interior magnetic-field strength to much higher levels than previously thought.

Andy Jackson


See also: Editor's summary | Letter by Gillet et al.

Biochemistry: Getting the metal right p40

Controversy has raged over the identity of the metal cofactor of membrane-bound methane monooxygenase, a methane-oxidizing enzyme. A study suggests that the answer is a cluster of two copper ions.

J. Martin Bollinger Jr


See also: Editor's summary | Letter by Balasubramanian et al.

Nonlinear dynamics: Optoelectronic chaos p41

Optoelectronic circuits with delayed feedback provide a convenient bench-top platform to study a wide range of nonlinear dynamic systems, from ultrastable clocks to complex chaotic devices.

Laurent Larger & John M. Dudley


Hepatitis C: An unsuspected drug target p42

Infection with hepatitis C is one of the main causes of liver disease, yet there are no broadly effective treatments. Discovery of a potent inhibitor of this virus shows that researchers must think outside the box.

Catherine L. Murray & Charles M. Rice


See also: Editor's summary | Letter by Gao et al.

50 & 100 years ago p43


Materials science: Muscle mimic p44

An elastic polymer has been made whose molecular structure mimics that of titin, a protein found in muscle. The resulting material is tough, stretchy and dissipates energy — just like muscle itself.

Elliot L. Chaikof


See also: Editor's summary | Letter by Lv et al.

Gene regulation: Breaking the second genetic code p45

Diverse messenger RNAs, and thus proteins, can be generated from a single piece of DNA. A computational approach is helping to uncover complex combinatorial rules by which specific gene instructions are selected.

J. Ramón Tejedor & Juan Valcárcel


See also: Editor's summary | Article by Barash et al.



Addendum p46




Olfactory pattern classification by discrete neuronal network states p47

The brain is apt to sort sensory stimuli into discrete perceptual categories, but the neuronal activity behind this capability has been unclear. Here, the problem has been investigated by presenting zebrafish with different concentrations or types of odours. The results show that the activity of neuronal populations in the olfactory bulb is largely insensitive to changes in odour concentration, but that morphing one odour into another produces abrupt transitions between odour representations.

Jörn Niessing & Rainer W. Friedrich


See also: Editor's summary

Deciphering the splicing code p53

The coding capacity of the genome is greatly expanded by the process of alternative splicing, which enables a single gene to produce more than one distinct protein. Can the expression of these different proteins be predicted from sequence data? Here, modelling based on information theory has been used to develop a 'splicing code', which can predict, with good accuracy, tissue-dependent changes in alternative splicing.

Yoseph Barash, John A. Calarco, Weijun Gao, Qun Pan, Xinchen Wang, Ofer Shai, Benjamin J. Blencowe & Brendan J. Frey


See also: Editor's summary | News and Views by Tejedor & Valcárcel



H2 emission arises outside photodissociation regions in ultraluminous infrared galaxies p60

Ultraluminous infrared galaxies are among the most luminous objects in the local Universe and are thought to be powered by intense star formation. In these objects, the rotational lines of molecular hydrogen (H2) observed at mid-infrared wavelengths are not affected by dust obscuration, but the source of excitation has been unknown. Here it is found that H2 emission originates outside the obscured regions; it is proposed that H2 emission traces shocks in the surrounding material that are excited by interactions with nearby galaxies.

Nadia L. Zakamska


See also: Editor's summary

Phase-preserving amplification near the quantum limit with a Josephson ring modulator p64

Recent progress in solid-state quantum information processing has stimulated the search for amplifiers and frequency converters with quantum-limited performance in the microwave range. Here, a phase-preserving, superconducting parametric amplifier with ultra-low-noise properties has been experimentally realized.

N. Bergeal, F. Schackert, M. Metcalfe, R. Vijay, V. E. Manucharyan, L. Frunzio, D. E. Prober, R. J. Schoelkopf, S. M. Girvin & M. H. Devoret


See also: Editor's summary

Designed biomaterials to mimic the mechanical properties of muscles p69

Here, artificial proteins are described that mimic the molecular architecture of titin — a protein that helps to govern the passive elastic properties of muscle. The new artificial proteins combine structured and unstructured domains, and can be photochemically crosslinked into a solid biomaterial that is resilient at low strains and extensible and tough at high strains. This provides an example of tailoring the macroscopic properties of a material through engineering at the single-molecule level.

Shanshan Lv, Daniel M. Dudek, Yi Cao, M. M. Balamurali, John Gosline & Hongbin Li


See also: Editor's summary | News and Views by Chaikof

Fast torsional waves and strong magnetic field within the Earth’s core p74

The magnetic field inside the Earth's outer core cannot be directly probed. The intensity of the magnetic field at the core–mantle boundary is estimated to be 0.3 mT, and geodynamo models predict a value about ten times larger (3 mT) for the core's interior. Other data, however, indicate an internal field of only around 0.2 mT. This discrepancy has now been resolved: an ensemble inversion of core flow models finds a torsional wave recurring every 6 years, leading to an estimated field strength of around 4 mT inside the core.

Nicolas Gillet, Dominique Jault, Elisabeth Canet & Alexandre Fournier


See also: Editor's summary | News and Views by Jackson

Seismic and aseismic slip on the Central Peru megathrust p78

Slip on a subduction megathrust can occur during an earthquake or aseismically. The size, location and frequency of earthquakes that a megathrust can generate depend on where and when aseismic creep is taking place, and what fraction of the long-term slip it accounts for. Here this issue is addressed by looking at the central Peru megathrust, and specifically at the Pisco earthquake of 2007. The findings show that aseismic creep accounts for 50–70% of the slip budget on the seismogenic portion of the megathrust.

Hugo Perfettini, Jean-Philippe Avouac, Hernando Tavera, Andrew Kositsky, Jean-Mathieu Nocquet, Francis Bondoux, Mohamed Chlieh, Anthony Sladen, Laurence Audin, Daniel L. Farber & Pierre Soler


See also: Editor's summary

Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease p82

Mutations in mitochondrial DNA (mtDNA) are a common cause of human genetic disease. It has been shown in non-human primates that nuclear transfer techniques might be an approach to prevent the transmission of mtDNA mutations. The proof of principle has now been extended to human embryos. Pronuclei were transferred between human zygotes, which developed onwards to the blastocyst stage in vitro. Carry-over of mtDNA from the donor zygotes to the recipients was minimal.

Lyndsey Craven, Helen A. Tuppen, Gareth D. Greggains, Stephen J. Harbottle, Julie L. Murphy, Lynsey M. Cree, Alison P. Murdoch, Patrick F. Chinnery, Robert W. Taylor, Robert N. Lightowlers, Mary Herbert & Douglass M. Turnbull


See also: Editor's summary

Cis-interactions between Notch and Delta generate mutually exclusive signalling states p86

Notch and Delta are transmembrane proteins that allow neighbouring cells to communicate during development. Here, quantitative time-lapse microscopy has been used to show that the response of Notch to Delta on a neighbouring cell is graded, whereas its response to Delta on the same cell is sharp and occurs at a fixed threshold. A mathematical model explores how this new design principle enhances the sharpness of developmental boundaries set by classical lateral inhibition.

David Sprinzak, Amit Lakhanpal, Lauren LeBon, Leah A. Santat, Michelle E. Fontes, Graham A. Anderson, Jordi Garcia-Ojalvo & Michael B. Elowitz


See also: Editor's summary

The molecular basis for water taste in Drosophila p91

Animals must detect water in their environment to stay alive, but the molecular basis for water detection has been unclear. Here the essential mediators of water-sensing and drinking in fruitflies have been identified: an ion channel of the degenerin/epithelial sodium channel family, and the sensory neurons that make it.

Peter Cameron, Makoto Hiroi, John Ngai & Kristin Scott


See also: Editor's summary

Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect p96

Almost 200 million people worldwide are chronically infected with hepatitis C virus. Current treatments are poorly tolerated and not wholly effective, so new drugs are needed. Here, a potent new inhibitor of hepatitis C virus is described. This inhibitor targets the viral protein NS5A, and shows potential as part of a therapeutic regimen based on a combination of viral inhibitors.

Min Gao, Richard E. Nettles, Makonen Belema, Lawrence B. Snyder, Van N. Nguyen, Robert A. Fridell, Michael H. Serrano-Wu, David R. Langley, Jin-Hua Sun, Donald R. O’Boyle II, Julie A. Lemm, Chunfu Wang, Jay O. Knipe, Caly Chien, Richard J. Colonno, Dennis M. Grasela, Nicholas A. Meanwell & Lawrence G. Hamann


See also: Editor's summary | News and Views by Murray & Rice

The scaffold protein Ste5 directly controls a switch-like mating decision in yeast p101

Before mating, a yeast cell must detect a partner cell that is close enough and expresses sufficiently large amounts of a sex pheromone. The mating decision is an all-or-none, switch-like response to pheromone concentration. It is now shown that this decision involves the competition of one kinase and one phosphatase enzyme for multiple phosphorylation sites on a 'scaffold' protein. The results should prompt a re-evaluation of the role of related signalling molecules that have been implicated in cancer.

Mohan K. Malleshaiah, Vahid Shahrezaei, Peter S. Swain & Stephen W. Michnick


See also: Editor's summary

An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation p106

DNA methylation is an important epigenetic mark in many eukaryotes. In Arabidopsis plants, small interfering RNAs bound to the Argonaute 4 (AGO4) protein can direct de novo DNA methylation and consequent gene silencing. Here, a new regulator of RNA-directed DNA methylation has been discovered. This protein, RDM1, is proposed to bind to methylated DNA and to function in the AGO4 effector complex.

Zhihuan Gao, Hai-Liang Liu, Lucia Daxinger, Olga Pontes, Xinjian He, Weiqiang Qian, Huixin Lin, Mingtang Xie, Zdravko J. Lorkovic, Shoudong Zhang, Daisuke Miki, Xiangqiang Zhan, Dominique Pontier, Thierry Lagrange, Hailing Jin, Antonius J. M. Matzke, Marjori Matzke, Craig S. Pikaard & Jian-Kang Zhu


See also: Editor's summary

X-ray crystal structure of the light-independent protochlorophyllide reductase p110

The ability of plants to 'green' in the dark is attributed to the activity of the dark-operative protochlorophyllide oxidoreductase (DPOR). This enzyme catalyses the stereospecific reduction of the C17=C18 double bond of protochlorophyllide to form chlorophyllide a, the direct precursor of chlorophyll a. The X-ray crystal structure of the catalytic component of DPOR has now been solved. A chemical mechanism is proposed by which the reduction of the double bond may occur.

Norifumi Muraki, Jiro Nomata, Kozue Ebata, Tadashi Mizoguchi, Tomoo Shiba, Hitoshi Tamiaki, Genji Kurisu & Yuichi Fujita


See also: Editor's summary

Oxidation of methane by a biological dicopper centre p115

Particulate methane monooxygenase (pMMO) is an integral membrane protein, found in methanotropic bacteria, that can selectively oxidize methane to produce methanol. This metalloenzyme contains three subunits, and the metal composition and exact location of its active site has been the subject of much speculation. Here it is found that the enzyme's activity is dependent on copper, and that the active site is located in the soluble domains of the pmoB subunit.

Ramakrishnan Balasubramanian, Stephen M. Smith, Swati Rawat, Liliya A. Yatsunyk, Timothy L. Stemmler & Amy C. Rosenzweig


See also: Editor's summary | News and Views by Bollinger Jr



Genome sequence of the palaeopolyploid soybean p120

Jeremy Schmutz, Steven B. Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L. Hyten, Qijian Song, Jay J. Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D. May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K. Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T. Nguyen, Rod A. Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C. Shoemaker & Scott A. Jackson




Careers and Recruitment

Kentucky by the numbers p122

With targeted recruiting efforts under way, Kentucky is attempting to build a life-sciences hub.


Careers Q&A

Ben Keeton p122

Ben Keeton, executive director of the Kentucky BioAlliance, discusses the challenges of transforming a state historically dependent on agriculture, mining and manufacturing into a biotech presence.

Paul Smaglik



Side target p123

Augmenting your full-time job with additional work can bring many rewards, says Peter Fiske.

Peter Fiske




KYLE 7 p126

Virtual success.

Giulio Zambon


Extra navigation

  • Japanese table of contents