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BMC Structural Biology - Latest Articles   [more] [xml]
 2014-10-18T00:00:00Z A PDB-wide, evolution-based assessment of protein¿protein interfaces
Background: Thanks to the growth in sequence and structure databases, more than 50 million sequences are now available in UniProt and 100,000 structures in the PDB. Rich information about protein?protein interfaces can be obtained by a comprehensive study of protein contacts in the PDB, their sequence conservation and geometric features. Results: An automated computational pipeline was developed to run our Evolutionary Protein?Protein Interface Classifier (EPPIC) software on the entire PDB and store the results in a relational database, currently containing > 800,000 interfaces. This allows the analysis of interface data on a PDB-wide scale. Two large benchmark datasets of biological interfaces and crystal contacts, each containing about 3000 entries, were automatically generated based on criteria thought to be strong indicators of interface type. The BioMany set of biological interfaces includes NMR dimers solved as crystal structures and interfaces that are preserved across diverse crystal forms, as catalogued by the Protein Common Interface Database (ProtCID) from Xu and Dunbrack. The second dataset, XtalMany, is derived from interfaces that would lead to infinite assemblies and are therefore crystal contacts. BioMany and XtalMany were used to benchmark the EPPIC approach. The performance of EPPIC was also compared to classifications from the Protein Interfaces, Surfaces, and Assemblies (PISA) program on a PDB-wide scale, finding that the two approaches give the same call in about 85% of PDB interfaces. By comparing our safest predictions to the PDB author annotations, we provide a lower-bound estimate of the error rate of biological unit annotations in the PDB. Additionally, we developed a PyMOL plugin for direct download and easy visualization of EPPIC interfaces for any PDB entry. Both the datasets and the PyMOL plugin are available at http://www.eppic-web.org/ewui/\#downloads. Conclusions: Our computational pipeline allows us to analyze protein?protein contacts and their sequence conservation across the entire PDB. Two new benchmark datasets are provided, which are over an order of magnitude larger than existing manually curated ones. These tools enable the comprehensive study of several aspects of protein?protein contacts in the PDB and represent a basis for future, even larger scale studies of protein?protein interactions.


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BMC Bioinformatics - Latest Articles   [more] [xml]
 2014-10-31T00:00:00Z CIG-P: Cicular Interaction Graph for Proteomics
Background: A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins co-purifying with the bait (aka prey proteins). Like any other systems biology approach, AP-MS experiments generate a lot of data and visualization has been challenging, especially when integrating AP-MS experiments with orthogonal datasets. Results: We present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data. Through a Java based GUI, the user inputs experimental and reference data as file in csv format. The resulting circular representation can be manipulated live within the GUI before exporting the diagram as vector graphic in pdf format. The strength of CIG-P is the ability to integrate orthogonal datasets with each other, e.g. affinity purification data of kinase PRPF4B in relation to the functional components of the spliceosome. Further, various AP-MS experiments can be compared to each other. Conclusions: CIG-P aids to present AP-MS data to a wider audience and we envision that the tool finds other applications too, e.g. kinase - substrate relationships as a function of perturbation. CIG-P is available under: http://sourceforge.net/projects/cig-p/


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BMC Genomics - Latest Articles   [more] [xml]
 2014-11-01T00:00:00Z Evaluation of variant identification methods for whole genome sequencing data in dairy cattle
Background: Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less well documented. We explored the consequences of commonly recommended preparatory steps and the effects of single and multi sample variant identification methods using four publicly available software applications (Platypus, HaplotypeCaller, Samtools and UnifiedGenotyper) on whole genome sequence data of 65 key ancestors of Swiss dairy cattle populations. Accuracy of calling next-generation sequence variants was assessed by comparison to the same loci from medium and high-density single nucleotide variant (SNV) arrays. Results: The total number of SNVs identified varied by software and method, with single (multi) sample results ranging from 17.7 to 22.0 (16.9 to 22.0) million variants. Computing time varied considerably between software. Preparatory realignment of insertions and deletions and subsequent base quality score recalibration had only minor effects on the number and quality of SNVs identified by different software, but increased computing time considerably. Average concordance for single (multi) sample results with high-density chip data was 58.3% (87.0%) and average genotype concordance in correctly identified SNVs was 99.2% (99.2%) across software. The average quality of SNVs identified, measured as the ratio of transitions to transversions, was higher using single sample methods than multi sample methods. A consensus approach using results of different software generally provided the highest variant quality in terms of transition / transversion ratio. Conclusions: Our findings serve as a reference for variant identification pipeline development in non-human organisms and help assess the implication of preparatory steps in next-generation sequencing pipelines for organisms with incomplete reference genomes (pipeline code is included). Benchmarking this information should prove particularly useful in processing next-generation sequencing data for use in genome-wide association studies and genomic selection.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-10-09T00:00:00Z Alleviation effect of arbutin on oxidative stress generated through tyrosinase reaction with l-tyrosine and l-DOPA
Background: Hydroxyl radical that has the highest reactivity among reactive oxygen species (ROS) is generated through l-tyrosine-tyrosinase reaction. Thus, the melanogenesis might induce oxidative stress in the skin. Arbutin (p-hydroxyphenyl-β-d-glucopyranoside), a well-known tyrosinase inhibitor has been widely used for the purpose of skin whitening. The aim of the present study was to examine if arbutin could suppress the hydroxyl radical generation via tyrosinase reaction with its substrates, l-tyrosine and l-DOPA. Results: The hydroxyl radical, which was determined by an electron spin resonance-spin trapping technique, was generated by the addition of not only l-tyrosine but l-DOPA to tyrosinase in a concentration dependent manner. Arbutin could inhibit the hydroxyl radical generation in the both reactions. Conclusion: It is presumed that arbutin could alleviate oxidative stress derived from the melanogenic pathway in the skin in addition to its function as a whitening agent in cosmetics.


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Nature   [more] [xml]
 2005-01-19 Einstein is dead
Until its next revolution, much of the glory of physics will be in engineering. It is a shame that the physicists who do so much of it keep so quiet about it.

Einstein is dead

Nature 433, 179 (2005). doi:10.1038/433179a

Until its next revolution, much of the glory of physics will be in engineering. It is a shame that the physicists who do so much of it keep so quiet about it.

 2005-01-19 Tales of the unexpected
Unfettered research sometimes leads to highly serendipitous discoveries.

Tales of the unexpected

Nature 433, 179 (2005). doi:10.1038/433179b

Unfettered research sometimes leads to highly serendipitous discoveries.

 2005-01-19 Titan team claims just deserts as probe hits moon of crème brûlée
European space craft successfully parachutes down to Saturn's moon.

Titan team claims just deserts as probe hits moon of crème brûlée

Nature 433, 181 (2005). doi:10.1038/433181a

Author: Alison Abbott

European space craft successfully parachutes down to Saturn's moon.

 2005-01-19 Georgia court bans biology textbook stickers
“Evolution is a theory, not a fact” stickers banned from school texts.

Georgia court bans biology textbook stickers

Nature 433, 182 (2005). doi:10.1038/433182a

Author: Jessica Ebert

“Evolution is a theory, not a fact” stickers banned from school texts.

 2005-01-19 All parties on edge as NIH delays open-access briefing
Both sides of the open-access debate anxious about potential policy changes.

All parties on edge as NIH delays open-access briefing

Nature 433, 182 (2005). doi:10.1038/433182b

Author: Erika Check

Both sides of the open-access debate anxious about potential policy changes.

 2005-01-19 Indian Ocean fault line poses threat of further earthquakes
Energy from 26 December quake could hasten the next rupture.

Indian Ocean fault line poses threat of further earthquakes

Nature 433, 183 (2005). doi:10.1038/433183a

Author: Emma Marris

Energy from 26 December quake could hasten the next rupture.

 2005-01-19 Pasteur board quits in bid to resolve crisis at troubled institute
Staff of Parisian biomedical research facility resign in mass protest.

Pasteur board quits in bid to resolve crisis at troubled institute

Nature 433, 183 (2005). doi:10.1038/433183b

Author: Declan Butler

Staff of Parisian biomedical research facility resign in mass protest.

 2005-01-19 Science lobby urges UK to divert funds from military fields
Public funding too focused on weapons-based research, says report.

Science lobby urges UK to divert funds from military fields

Nature 433, 184 (2005). doi:10.1038/433184a

Author: Philip Ball

Public funding too focused on weapons-based research, says report.

 2005-01-19 Antinuclear groups push to keep treaty review in the air
Nuclear Non-Proliferation Treaty at critical point, observers say.

Antinuclear groups push to keep treaty review in the air

Nature 433, 184 (2005). doi:10.1038/433184b

Author: Michael Hopkin

Nuclear Non-Proliferation Treaty at critical point, observers say.

 2005-01-19 Brain-scan ethics come under the spotlight
Scientists thrash out policies for dealing with scan results.

Brain-scan ethics come under the spotlight

Nature 433, 185 (2005). doi:10.1038/433185a

Author: Erika Check

Scientists thrash out policies for dealing with scan results.

 2005-01-19 news in brief
Paediatrician launches bid to become Iran's next presidentParisA prominent Iranian scientist is set to stand in the nation's presidential elections in June. Mostafa Moin, who was widely respected as science minister, was chosen in late December as the candidate of the reformist party,

news in brief

Nature 433, 186 (2005). doi:10.1038/433186a

Paediatrician launches bid to become Iran's next presidentParisA prominent Iranian scientist is set to stand in the nation's presidential elections in June. Mostafa Moin, who was widely respected as science minister, was chosen in late December as the candidate of the reformist party,

 2005-01-19 All pain, no gain?
Exercise is good for you, or so we always thought. But, as Alison Abbott learns, your genes don't always cooperate.

All pain, no gain?

Nature 433, 188 (2005). doi:10.1038/433188a

Author: Alison Abbott

Exercise is good for you, or so we always thought. But, as Alison Abbott learns, your genes don't always cooperate.

 2005-01-19 The premier division
Since he took over as Harvard president in 2001, Larry Summers' style and vision have divided the university. As his plans for expansion step up a gear, Summers tells Helen Pearson why it is time for Cambridge to face up to the need for change.

The premier division

Nature 433, 190 (2005). doi:10.1038/433190a

Author: Helen Pearson

Since he took over as Harvard president in 2001, Larry Summers' style and vision have divided the university. As his plans for expansion step up a gear, Summers tells Helen Pearson why it is time for Cambridge to face up to the need for change.

 2005-01-19 Croatian minister rejects ‘meddling’ claim
Mediterranean Institute's link with university is intended to ensure academic freedom.

Croatian minister rejects ‘meddling’ claim

Nature 433, 193 (2005). doi:10.1038/433193a

Author: Dragan Primorac

Mediterranean Institute's link with university is intended to ensure academic freedom.

 2005-01-19 Insect collection ready to spread its wings
SirYour News story “Curators bugged by museum's vision for insect collection” (Nature432, 659; 2004) gave the impression that Darwin Centre II (DCII) will be incompatible with a ‘cyber-infrastructure’ future for taxonomy.Although we are certain that taxonomy and collections-based

Insect collection ready to spread its wings

Nature 433, 193 (2005). doi:10.1038/433193b

Author: Quentin D. Wheeler

SirYour News story “Curators bugged by museum's vision for insect collection” (Nature432, 659; 2004) gave the impression that Darwin Centre II (DCII) will be incompatible with a ‘cyber-infrastructure’ future for taxonomy.Although we are certain that taxonomy and collections-based

 2005-01-19 Alternative views of amphibian toe-clipping
SirIn News and Views (“Ethics and amphibians” Nature431, 403; 2004), Robert M. May discusses a study by M. A. McCarthy and K. M. Parris on the effects of toe-clipping on amphibians. This is a standard technique for uniquely marking animals

Alternative views of amphibian toe-clipping

Nature 433, 193 (2005). doi:10.1038/433193c

Authors: W. Chris Funk, Maureen A. Donnelly & Karen R. Lips

SirIn News and Views (“Ethics and amphibians” Nature431, 403; 2004), Robert M. May discusses a study by M. A. McCarthy and K. M. Parris on the effects of toe-clipping on amphibians. This is a standard technique for uniquely marking animals

 2005-01-19 The Einstein chronicles
Two volumes of correspondence put Einstein's work in a historical context.

The Einstein chronicles

Nature 433, 195 (2005). doi:10.1038/433195a

Author: Gerald Holton

Two volumes of correspondence put Einstein's work in a historical context.

 2005-01-19 Relativity revisited
What, another three books on Einstein? At the last count on http://www.amazon.com there were 498 currently in print, and the proliferation of titles such as The Private Albert Einstein, Einstein in Love and Einstein's Daughter should ensure that no corner of

Relativity revisited

Nature 433, 196 (2005). doi:10.1038/433196a

Author: Werner Israel

What, another three books on Einstein? At the last count on http://www.amazon.com there were 498 currently in print, and the proliferation of titles such as The Private Albert Einstein, Einstein in Love and Einstein's Daughter should ensure that no corner of

 2005-01-19 Science in culture
A disputed portrait of Robert Hooke may in fact show a contemporary.

Science in culture

Nature 433, 197 (2005). doi:10.1038/433197a

Author: Philip Ball

A disputed portrait of Robert Hooke may in fact show a contemporary.

 2005-01-19 A novel view of global warming
Jo Public is smarter than we think. When I reviewed the film The Day After Tomorrow for Nature (429, 347–348), I said that it couldn't really do any harm, and it made geophysics look cool, so we

A novel view of global warming

Nature 433, 198 (2005). doi:10.1038/433198a

Author: Myles Allen

Jo Public is smarter than we think. When I reviewed the film The Day After Tomorrow for Nature (429, 347–348), I said that it couldn't really do any harm, and it made geophysics look cool, so we

 2005-01-19  Schrödinger's mousetrap
Part 1: The trap is primed.

Schrödinger's mousetrap

Nature 433, 200 (2005). doi:10.1038/433200a

Author: Ian Stewart

Part 1: The trap is primed.

 2005-01-19 Endocrinology: Fertility hormone in repose
Egg and sperm development are triggered when follicle-stimulating hormone binds to its receptor. A three-dimensional structural snapshot reveals how the hormone slots into its receptor, and how specificity of binding is ensured.

Endocrinology: Fertility hormone in repose

Nature 433, 203 (2005). doi:10.1038/433203a

Author: James A. Dias

Egg and sperm development are triggered when follicle-stimulating hormone binds to its receptor. A three-dimensional structural snapshot reveals how the hormone slots into its receptor, and how specificity of binding is ensured.

 2005-01-19 Climatology: Will soil amplify climate change?
It had been thought by some that rising atmospheric temperatures would have no effect on the rate at which carbon is released from the soil. A study that revisits the data behind this theory now finds otherwise.

Climatology: Will soil amplify climate change?

Nature 433, 204 (2005). doi:10.1038/433204a

Author: David Powlson

It had been thought by some that rising atmospheric temperatures would have no effect on the rate at which carbon is released from the soil. A study that revisits the data behind this theory now finds otherwise.

 2005-01-19 Evolution: A taste for mimicry
Looking inedible is a great way to deter predators, but the warning signs must be learnt first. It seems that unpalatable species employ some unexpected strategies to make the education a quick one.

Evolution: A taste for mimicry

Nature 433, 205 (2005). doi:10.1038/433205a

Authors: Graeme D. Ruxton & Michael P. Speed

Looking inedible is a great way to deter predators, but the warning signs must be learnt first. It seems that unpalatable species employ some unexpected strategies to make the education a quick one.

 2005-01-19 Astronomy: Weighing the baby
Mass is the fundamental parameter in stellar astrophysics, but measuring mass is difficult, especially for young stars. A study of a youthful neighbour of the Sun provides insight into the accuracy of widely used calibrations.

Astronomy: Weighing the baby

Nature 433, 207 (2005). doi:10.1038/433207a

Author: I. Neill Reid

Mass is the fundamental parameter in stellar astrophysics, but measuring mass is difficult, especially for young stars. A study of a youthful neighbour of the Sun provides insight into the accuracy of widely used calibrations.

 2005-01-19 Signal transduction: A new canon
Muscle development in vertebrates relies on signals transmitted from proteins of the Wnt family. But which molecules form the relay that transfers this signal to the cell nucleus? The answer is unexpected.

Signal transduction: A new canon

Nature 433, 208 (2005). doi:10.1038/433208a

Author: Olivier Pourquié

Muscle development in vertebrates relies on signals transmitted from proteins of the Wnt family. But which molecules form the relay that transfers this signal to the cell nucleus? The answer is unexpected.

 2005-01-19 100 and 50 years ago
100 YEARS AGOIndia. By Colonel Sir Thomas Holdich. With climates varying from the ice-bound deserts of the higher Himalayas and the rain-steeped forests of Tenasserim, to the desolation of Makran... where in one part music is produced by stamping on a piece of

100 and 50 years ago

Nature 433, 209 (2005). doi:10.1038/433209a

100 YEARS AGOIndia. By Colonel Sir Thomas Holdich. With climates varying from the ice-bound deserts of the higher Himalayas and the rain-steeped forests of Tenasserim, to the desolation of Makran... where in one part music is produced by stamping on a piece of

 2005-01-19 research highlights
Self-assembly: Algorithmic crystals made to orderPLoS Biol.2, 2041–2053 (2004)Erwin Schrödinger famously predicted that biological information is encoded in an ‘aperiodic crystal’, which turned out to be DNA. Paul W. K. Rothemund et al. now show that DNA's ‘digital logic’ can

research highlights

Nature 433, 210 (2005). doi:10.1038/433210a

Self-assembly: Algorithmic crystals made to orderPLoS Biol.2, 2041–2053 (2004)Erwin Schrödinger famously predicted that biological information is encoded in an ‘aperiodic crystal’, which turned out to be DNA. Paul W. K. Rothemund et al. now show that DNA's ‘digital logic’ can

 2005-01-19 Animal mimicry: Choosing when to be a cleaner-fish mimic
A dangerous fish can discard a seemingly harmless disguise to suit its circumstances.Mimicry in vertebrates is usually a permanent state — mimics resemble and normally accompany their model throughout the life stages during which they act as mimics. Here we show that the bluestriped fangblenny fish (Plagiotremus rhinorhynchos), which aggressively attacks other coral-reef fish, can turn off the mimetic colours that disguise it as the benign bluestreak cleaner wrasse, Labroides dimidiatus, and assume a radically different appearance. This opportunistic facultative mimicry extends the fangblenny's scope by allowing it to blend into shoals of small reef fish as well as to remain inconspicuous at cleaning stations.

Animal mimicry: Choosing when to be a cleaner-fish mimic

Nature 433, 211 (2005). doi:10.1038/433211a

Authors: Isabelle M. Côté & Karen L. Cheney

A dangerous fish can discard a seemingly harmless disguise to suit its circumstances.Mimicry in vertebrates is usually a permanent state — mimics resemble and normally accompany their model throughout the life stages during which they act as mimics. Here we show that the bluestriped fangblenny fish (Plagiotremus rhinorhynchos), which aggressively attacks other coral-reef fish, can turn off the mimetic colours that disguise it as the benign bluestreak cleaner wrasse, Labroides dimidiatus, and assume a radically different appearance. This opportunistic facultative mimicry extends the fangblenny's scope by allowing it to blend into shoals of small reef fish as well as to remain inconspicuous at cleaning stations.

 2005-01-19 Behavioural ecology: Transient sexual mimicry leads to fertilization
Sexual mimicry among animals is widespread, but does it impart a fertilization advantage in the widely accepted ‘sneak–guard’ model of sperm competition? Here we describe field results in which a dramatic facultative switch in sexual phenotype by sneaker-male cuttlefish leads to immediate fertilization success, even in the presence of the consort male. These results are surprising, given the high rate at which females reject copulation attempts by males, the strong mate-guarding behaviour of consort males, and the high level of sperm competition in this complex mating system.

Behavioural ecology: Transient sexual mimicry leads to fertilization

Nature 433, 212 (2005). doi:10.1038/433212a

Authors: Roger T. Hanlon, Marié-Jose Naud, Paul W. Shaw & Jon N. Havenhand

Sexual mimicry among animals is widespread, but does it impart a fertilization advantage in the widely accepted ‘sneak–guard’ model of sperm competition? Here we describe field results in which a dramatic facultative switch in sexual phenotype by sneaker-male cuttlefish leads to immediate fertilization success, even in the presence of the consort male. These results are surprising, given the high rate at which females reject copulation attempts by males, the strong mate-guarding behaviour of consort males, and the high level of sperm competition in this complex mating system.

 2005-01-19 Evolutionary genomics: Codon bias and selection on single genomes
Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature428, 942–945 (2004); see also communication from Nielsen et al.; Chenet al.; Plotkin et al. replyThe idea that natural selection on genes might be detected using only a single genome has been put forward by Plotkin and colleagues, who present a method that they claim can detect selection without the need for comparative data and which, if correct, would confer greater power of analysis with less information. Here we argue that their method depends on assumptions that confound their conclusions and that, even if these assumptions were valid, the authors' inferences about adaptive natural selection are unjustified.

Evolutionary genomics: Codon bias and selection on single genomes

Nature 433, E5 (2005). doi:10.1038/nature03221

Authors: Matthew W. Hahn, Jason G. Mezey, David J. Begun, John H. Gillespie, Andrew D. Kern, Charles H. Langley & Leonie C. Moyle

Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature428, 942–945 (2004); see also communication from Nielsen et al.; Chenet al.; Plotkin et al. replyThe idea that natural selection on genes might be detected using only a single genome has been put forward by Plotkin and colleagues, who present a method that they claim can detect selection without the need for comparative data and which, if correct, would confer greater power of analysis with less information. Here we argue that their method depends on assumptions that confound their conclusions and that, even if these assumptions were valid, the authors' inferences about adaptive natural selection are unjustified.

 2005-01-19 Evolutionary genomics: Detecting selection needs comparative data
Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature428, 942–945 (2004); see also communication from Hahn et al.; Chen et al.; Plotkin et al. replyPositive selection at the molecular level is usually indicated by an increase in the ratio of non-synonymous to synonymous substitutions (dN/dS) in comparative data. However, Plotkin et al. describe a new method for detecting positive selection based on a single nucleotide sequence. We show here that this method is particularly sensitive to assumptions regarding the underlying mutational processes and does not provide a reliable way to identify positive selection.

Evolutionary genomics: Detecting selection needs comparative data

Nature 433, E6 (2005). doi:10.1038/nature03222

Authors: Rasmus Nielsen & Melissa J. Hubisz

Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature428, 942–945 (2004); see also communication from Hahn et al.; Chen et al.; Plotkin et al. replyPositive selection at the molecular level is usually indicated by an increase in the ratio of non-synonymous to synonymous substitutions (dN/dS) in comparative data. However, Plotkin et al. describe a new method for detecting positive selection based on a single nucleotide sequence. We show here that this method is particularly sensitive to assumptions regarding the underlying mutational processes and does not provide a reliable way to identify positive selection.

 2005-01-19 Evolutionary genomics: Codon volatility does not detect selection
Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature428, 942–945 (2004); see also communication from Hahn et al.; Nielsenet al.; Plotkin et al. replyPlotkin et al. introduce a method to detect selection that is based on an index called codon volatility and that uses only the sequence of a single genome, claiming that this method is applicable to a large range of sequenced organisms. Volatility for a given codon is the ratio of non-synonymous codons to all sense codons accessible by one point mutation. The significance of each gene's volatility is assessed by comparison with a simulated distribution of 106 synonymous versions of each gene, with synonymous codons drawn randomly from average genome frequencies. Here we re-examine their method and data and find that codon volatility does not detect selection, and that, even if it did, the genomes of Mycobacterium tuberculosis and Plasmodium falciparum, as well as those of most sequenced organisms, do not meet the assumptions necessary for application of their method.

Evolutionary genomics: Codon volatility does not detect selection

Nature 433, E6 (2005). doi:10.1038/nature03223

Authors: Ying Chen, J. J. Emerson & Todd M. Martin

Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature428, 942–945 (2004); see also communication from Hahn et al.; Nielsenet al.; Plotkin et al. replyPlotkin et al. introduce a method to detect selection that is based on an index called codon volatility and that uses only the sequence of a single genome, claiming that this method is applicable to a large range of sequenced organisms. Volatility for a given codon is the ratio of non-synonymous codons to all sense codons accessible by one point mutation. The significance of each gene's volatility is assessed by comparison with a simulated distribution of 106 synonymous versions of each gene, with synonymous codons drawn randomly from average genome frequencies. Here we re-examine their method and data and find that codon volatility does not detect selection, and that, even if it did, the genomes of Mycobacterium tuberculosis and Plasmodium falciparum, as well as those of most sequenced organisms, do not meet the assumptions necessary for application of their method.

 2005-01-19 Evolutionary genomics: Codon volatility does not detect selection (reply)
Plotkin et al. reply - The criticisms of our results by Hahnet al., Nielsen and Hubisz, and Chen, Emerson and Martin fall into three categories: the formal justification for our method, the potential for confounding factors, and the interpretation of our empirical results.

Evolutionary genomics: Codon volatility does not detect selection (reply)

Nature 433, E7 (2005). doi:10.1038/nature03224

Authors: J. B. Plotkin, J. Dushoff & H. B. Fraser

Plotkin et al. reply - The criticisms of our results by Hahnet al., Nielsen and Hubisz, and Chen, Emerson and Martin fall into three categories: the formal justification for our method, the potential for confounding factors, and the interpretation of our empirical results.

 2005-01-19 Year of physics a celebration
In 1905, Albert Einstein submitted five papers for publication in Annalen der Physik, covering three topics: the photoelectric effect, brownian motion, and the special theory of relativity. Although diverse in subject matter, these contributions are landmarks in their field — and testament to Einstein's

Year of physics a celebration

Nature 433, 213 (2005). doi:10.1038/433213a

Authors: Alison Wright, Karl Ziemelis, Leslie Sage & Karen Southwell

In 1905, Albert Einstein submitted five papers for publication in Annalen der Physik, covering three topics: the photoelectric effect, brownian motion, and the special theory of relativity. Although diverse in subject matter, these contributions are landmarks in their field — and testament to Einstein's

 2005-01-19 1905 and all that
How Einstein claimed his place in the changing landscape of physics during his annus mirabilis.

1905 and all that

Nature 433, 215 (2005). doi:10.1038/433215a

Author: John Stachel

How Einstein claimed his place in the changing landscape of physics during his annus mirabilis.

 2005-01-19 Einstein as icon
How Einstein became the personification of physics.

Einstein as icon

Nature 433, 218 (2005). doi:10.1038/433218a

Author: John D. Barrow

How Einstein became the personification of physics.

 2005-01-19 Brownian motion
“I did not believe that it was possible to study the Brownian motion with such a precision.” From a letter from Albert Einstein to Jean Perrin (1909).

Brownian motion

Nature 433, 221 (2005). doi:10.1038/433221a

Author: Giorgio Parisi

“I did not believe that it was possible to study the Brownian motion with such a precision.” From a letter from Albert Einstein to Jean Perrin (1909).

 2005-01-19 In and out of equilibrium
Albert Einstein's work on brownian motion showed how thermal equilibrium could be brought about by work exchanged through thermal fluctuations and viscous dissipation. Glasses are out-of-equilibrium systems in which this exchange happens at widely different timescales simultaneously. Theory then suggests the fascinating possibility that such

In and out of equilibrium

Nature 433, 222 (2005). doi:10.1038/nature03278

Author: J. Kurchan

Albert Einstein's work on brownian motion showed how thermal equilibrium could be brought about by work exchanged through thermal fluctuations and viscous dissipation. Glasses are out-of-equilibrium systems in which this exchange happens at widely different timescales simultaneously. Theory then suggests the fascinating possibility that such

 2005-01-19 Quantum criticality
As we mark the centenary of Albert Einstein's seminal contribution to both quantum mechanics and special relativity, we approach another anniversary — that of Einstein's foundation of the quantum theory of solids. But 100 years on, the same experimental measurement that puzzled Einstein and his

Quantum criticality

Nature 433, 226 (2005). doi:10.1038/nature03279

Authors: Piers Coleman & Andrew J. Schofield

As we mark the centenary of Albert Einstein's seminal contribution to both quantum mechanics and special relativity, we approach another anniversary — that of Einstein's foundation of the quantum theory of solids. But 100 years on, the same experimental measurement that puzzled Einstein and his

 2005-01-19 Happy centenary, photon
One hundred years ago Albert Einstein introduced the concept of the photon. Although in the early years after 1905 the evidence for the quantum nature of light was not compelling, modern experiments — especially those using photon pairs — have beautifully confirmed its corpuscular character.

Happy centenary, photon

Nature 433, 230 (2005). doi:10.1038/nature03280

Authors: Anton Zeilinger, Gregor Weihs, Thomas Jennewein & Markus Aspelmeyer

One hundred years ago Albert Einstein introduced the concept of the photon. Although in the early years after 1905 the evidence for the quantum nature of light was not compelling, modern experiments — especially those using photon pairs — have beautifully confirmed its corpuscular character.

 2005-01-19 In search of symmetry lost
Powerful symmetry principles have guided physicists in their quest for nature's fundamental laws. The successful gauge theory of electroweak interactions postulates a more extensive symmetry for its equations than are manifest in the world. The discrepancy is ascribed to a pervasive symmetry-breaking field, which fills

In search of symmetry lost

Nature 433, 239 (2005). doi:10.1038/nature03281

Author: Frank Wilczek

Powerful symmetry principles have guided physicists in their quest for nature's fundamental laws. The successful gauge theory of electroweak interactions postulates a more extensive symmetry for its equations than are manifest in the world. The discrepancy is ascribed to a pervasive symmetry-breaking field, which fills

 2005-01-19 The state of the Universe
The past 20 years have seen dramatic advances in cosmology, mostly driven by observations from new telescopes and detectors. These instruments have allowed astronomers to map out the large-scale structure of the Universe and probe the very early stages of its evolution. We seem to

The state of the Universe

Nature 433, 248 (2005). doi:10.1038/nature03282

Author: Peter Coles

The past 20 years have seen dramatic advances in cosmology, mostly driven by observations from new telescopes and detectors. These instruments have allowed astronomers to map out the large-scale structure of the Universe and probe the very early stages of its evolution. We seem to

 2005-01-19 A theory of everything?
In his later years, Einstein sought a unified theory that would extend general relativity and provide an alternative to quantum theory. There is now talk of a ‘theory of everything’ (although Einstein himself never used the phrase). Fifty years after his death, how close are we to such a theory?

A theory of everything?

Nature 433, 257 (2005). doi:10.1038/433257a

In his later years, Einstein sought a unified theory that would extend general relativity and provide an alternative to quantum theory. There is now talk of a ‘theory of everything’ (although Einstein himself never used the phrase). Fifty years after his death, how close are we to such a theory?

  A theoretical look at the direct detection of giant planets outside the Solar System
Astronomy is at times a science of unexpected discovery. When it is, and if we are lucky, new intellectual territories emerge to challenge our views of the cosmos. The recent indirect detections using high-precision Doppler spectroscopy of more than 100 giant planets orbiting more than

A theoretical look at the direct detection of giant planets outside the Solar System

Nature 433, 261 (2005). doi:10.1038/nature03244

Author: Adam Burrows

Astronomy is at times a science of unexpected discovery. When it is, and if we are lucky, new intellectual territories emerge to challenge our views of the cosmos. The recent indirect detections using high-precision Doppler spectroscopy of more than 100 giant planets orbiting more than

  Structure of human follicle-stimulating hormone in complex with its receptor
Follicle-stimulating hormone (FSH) is central to reproduction in mammals. It acts through a G-protein-coupled receptor on the surface of target cells to stimulate testicular and ovarian functions. We present here the 2.9-Å-resolution structure of a partially deglycosylated complex of human FSH bound to the extracellular

Structure of human follicle-stimulating hormone in complex with its receptor

Nature 433, 269 (2005). doi:10.1038/nature03206

Authors: Qing R. Fan & Wayne A. Hendrickson

Follicle-stimulating hormone (FSH) is central to reproduction in mammals. It acts through a G-protein-coupled receptor on the surface of target cells to stimulate testicular and ovarian functions. We present here the 2.9-Å-resolution structure of a partially deglycosylated complex of human FSH bound to the extracellular

  Role of the proto-oncogene Pokemon in cellular transformation and ARF repression
Aberrant transcriptional repression through chromatin remodelling and histone deacetylation has been postulated to represent a driving force underlying tumorigenesis because histone deacetylase inhibitors have been found to be effective in cancer treatment. However, the molecular mechanisms by which transcriptional derepression would be linked to tumour

Role of the proto-oncogene Pokemon in cellular transformation and ARF repression

Nature 433, 278 (2005). doi:10.1038/nature03203

Authors: Takahiro Maeda, Robin M. Hobbs, Taha Merghoub, Ilhem Guernah, Arthur Zelent, Carlos Cordon-Cardo, Julie Teruya-Feldstein & Pier Paolo Pandolfi

Aberrant transcriptional repression through chromatin remodelling and histone deacetylation has been postulated to represent a driving force underlying tumorigenesis because histone deacetylase inhibitors have been found to be effective in cancer treatment. However, the molecular mechanisms by which transcriptional derepression would be linked to tumour

  A dynamical calibration of the mass–luminosity relation at very low stellar masses and young ages
Mass is the most fundamental parameter of a star, yet it is also one of the most difficult to measure directly. In general, astronomers estimate stellar masses by determining the luminosity and using the ‘mass–luminosity’ relationship, but this relationship has never been accurately calibrated for young, low-mass stars and brown dwarfs. Masses for these low-mass objects are therefore constrained only by theoretical models. A new high-contrast adaptive optics camera enabled the discovery of a young (50 million years) companion only 0.156 arcseconds (2.3 au) from the more luminous (> 120 times brighter) star AB Doradus A. Here we report a dynamical determination of the mass of the newly resolved low-mass companion AB Dor C, whose mass is 0.090 ± 0.005 solar masses. Given its measured 1–2-micrometre luminosity, we have found that the standard mass–luminosity relations overestimate the near-infrared luminosity of such objects by about a factor of ∼2.5 at young ages. The young, cool objects hitherto thought to be substellar in mass are therefore about twice as massive, which means that the frequency of brown dwarfs and planetary mass objects in young stellar clusters has been overestimated.

A dynamical calibration of the mass–luminosity relation at very low stellar masses and young ages

Nature 433, 286 (2005). doi:10.1038/nature03225

Authors: Laird M. Close, Rainer Lenzen, Jose C. Guirado, Eric L. Nielsen, Eric E. Mamajek, Wolfgang Brandner, Markus Hartung, Chris Lidman & Beth Biller

Mass is the most fundamental parameter of a star, yet it is also one of the most difficult to measure directly. In general, astronomers estimate stellar masses by determining the luminosity and using the ‘mass–luminosity’ relationship, but this relationship has never been accurately calibrated for young, low-mass stars and brown dwarfs. Masses for these low-mass objects are therefore constrained only by theoretical models. A new high-contrast adaptive optics camera enabled the discovery of a young (50 million years) companion only 0.156 arcseconds (2.3 au) from the more luminous (> 120 times brighter) star AB Doradus A. Here we report a dynamical determination of the mass of the newly resolved low-mass companion AB Dor C, whose mass is 0.090 ± 0.005 solar masses. Given its measured 1–2-micrometre luminosity, we have found that the standard mass–luminosity relations overestimate the near-infrared luminosity of such objects by about a factor of ∼2.5 at young ages. The young, cool objects hitherto thought to be substellar in mass are therefore about twice as massive, which means that the frequency of brown dwarfs and planetary mass objects in young stellar clusters has been overestimated.

  High-velocity streams of dust originating from Saturn
High-velocity submicrometre-sized dust particles expelled from the jovian system have been identified by dust detectors on board several spacecraft. On the basis of periodicities in the dust impact rate, Jupiter's moon Io was found to be the dominant source of the streams. The grains become positively charged within the plasma environment of Jupiter's magnetosphere, and gain energy from its co-rotational electric field. Outside the magnetosphere, the dynamics of the grains are governed by the interaction with the interplanetary magnetic field that eventually forms the streams. A similar process was suggested for Saturn. Here we report the discovery by the Cassini spacecraft of bursts of high-velocity dust particles (≥ 100 km s-1) within ∼70 million kilometres of Saturn. Most of the particles detected at large distances appear to originate from the outskirts of Saturn's outermost main ring. All bursts of dust impacts detected within 150 Saturn radii are characterized by impact directions markedly different from those measured between the bursts, and they clearly coincide with the spacecraft's traversals through streams of compressed solar wind.

High-velocity streams of dust originating from Saturn

Nature 433, 289 (2005). doi:10.1038/nature03218

Authors: Sascha Kempf, Ralf Srama, Mihaly Horányi, Marcia Burton, Stefan Helfert, Georg Moragas-Klostermeyer, Mou Roy & Eberhard Grün

High-velocity submicrometre-sized dust particles expelled from the jovian system have been identified by dust detectors on board several spacecraft. On the basis of periodicities in the dust impact rate, Jupiter's moon Io was found to be the dominant source of the streams. The grains become positively charged within the plasma environment of Jupiter's magnetosphere, and gain energy from its co-rotational electric field. Outside the magnetosphere, the dynamics of the grains are governed by the interaction with the interplanetary magnetic field that eventually forms the streams. A similar process was suggested for Saturn. Here we report the discovery by the Cassini spacecraft of bursts of high-velocity dust particles (≥ 100 km s-1) within ∼70 million kilometres of Saturn. Most of the particles detected at large distances appear to originate from the outskirts of Saturn's outermost main ring. All bursts of dust impacts detected within 150 Saturn radii are characterized by impact directions markedly different from those measured between the bursts, and they clearly coincide with the spacecraft's traversals through streams of compressed solar wind.

 2005-01-05 An all-silicon Raman laser
The possibility of light generation and/or amplification in silicon has attracted a great deal of attention for silicon-based optoelectronic applications owing to the potential for forming inexpensive, monolithic integrated optical components. Because of its indirect bandgap, bulk silicon shows very inefficient band-to-band radiative electron–hole recombination. Light emission in silicon has thus focused on the use of silicon engineered materials such as nanocrystals, Si/SiO2 superlattices, erbium-doped silicon-rich oxides, surface-textured bulk silicon and Si/SiGe quantum cascade structures. Stimulated Raman scattering (SRS) has recently been demonstrated as a mechanism to generate optical gain in planar silicon waveguide structures. In fact, net optical gain in the range 2–11 dB due to SRS has been reported in centimetre-sized silicon waveguides using pulsed pumping. Recently, a lasing experiment involving silicon as the gain medium by way of SRS was reported, where the ring laser cavity was formed by an 8-m-long optical fibre. Here we report the experimental demonstration of Raman lasing in a compact, all-silicon, waveguide cavity on a single silicon chip. This demonstration represents an important step towards producing practical continuous-wave optical amplifiers and lasers that could be integrated with other optoelectronic components onto CMOS-compatible silicon chips.

An all-silicon Raman laser

Nature 433, 292 (2005). doi:10.1038/nature03273

Authors: Haisheng Rong, Ansheng Liu, Richard Jones, Oded Cohen, Dani Hak, Remus Nicolaescu, Alexander Fang & Mario Paniccia

The possibility of light generation and/or amplification in silicon has attracted a great deal of attention for silicon-based optoelectronic applications owing to the potential for forming inexpensive, monolithic integrated optical components. Because of its indirect bandgap, bulk silicon shows very inefficient band-to-band radiative electron–hole recombination. Light emission in silicon has thus focused on the use of silicon engineered materials such as nanocrystals, Si/SiO2 superlattices, erbium-doped silicon-rich oxides, surface-textured bulk silicon and Si/SiGe quantum cascade structures. Stimulated Raman scattering (SRS) has recently been demonstrated as a mechanism to generate optical gain in planar silicon waveguide structures. In fact, net optical gain in the range 2–11 dB due to SRS has been reported in centimetre-sized silicon waveguides using pulsed pumping. Recently, a lasing experiment involving silicon as the gain medium by way of SRS was reported, where the ring laser cavity was formed by an 8-m-long optical fibre. Here we report the experimental demonstration of Raman lasing in a compact, all-silicon, waveguide cavity on a single silicon chip. This demonstration represents an important step towards producing practical continuous-wave optical amplifiers and lasers that could be integrated with other optoelectronic components onto CMOS-compatible silicon chips.

  Stable sea surface temperatures in the western Pacific warm pool over the past 1.75 million years
About 850,000 years ago, the period of the glacial cycles changed from 41,000 to 100,000 years. This mid-Pleistocene climate transition has been attributed to global cooling, possibly caused by a decrease in atmospheric carbon dioxide concentrations. However, evidence for such cooling is currently restricted to the cool upwelling regions in the eastern equatorial oceans, although the tropical warm pools on the western side of the ocean basins are particularly sensitive to changes in radiative forcing. Here we present high-resolution records of sea surface temperatures spanning the past 1.75 million years, obtained from oxygen isotopes and Mg/Ca ratios in planktonic foraminifera from the western Pacific warm pool. In contrast with the eastern equatorial regions, sea surface temperatures in the western Pacific warm pool are relatively stable throughout the Pleistocene epoch, implying little long-term change in the tropical net radiation budget. Our results challenge the hypothesis of a gradual decrease in atmospheric carbon dioxide concentrations as a dominant trigger of the longer glacial cycles since 850,000 years ago. Instead, we infer that the temperature contrast across the equatorial Pacific Ocean increased, which might have had a significant influence on the mid-Pleistocene climate transition.

Stable sea surface temperatures in the western Pacific warm pool over the past 1.75 million years

Nature 433, 294 (2005). doi:10.1038/nature03189

Authors: Thibault de Garidel-Thoron, Yair Rosenthal, Franck Bassinot & Luc Beaufort

About 850,000 years ago, the period of the glacial cycles changed from 41,000 to 100,000 years. This mid-Pleistocene climate transition has been attributed to global cooling, possibly caused by a decrease in atmospheric carbon dioxide concentrations. However, evidence for such cooling is currently restricted to the cool upwelling regions in the eastern equatorial oceans, although the tropical warm pools on the western side of the ocean basins are particularly sensitive to changes in radiative forcing. Here we present high-resolution records of sea surface temperatures spanning the past 1.75 million years, obtained from oxygen isotopes and Mg/Ca ratios in planktonic foraminifera from the western Pacific warm pool. In contrast with the eastern equatorial regions, sea surface temperatures in the western Pacific warm pool are relatively stable throughout the Pleistocene epoch, implying little long-term change in the tropical net radiation budget. Our results challenge the hypothesis of a gradual decrease in atmospheric carbon dioxide concentrations as a dominant trigger of the longer glacial cycles since 850,000 years ago. Instead, we infer that the temperature contrast across the equatorial Pacific Ocean increased, which might have had a significant influence on the mid-Pleistocene climate transition.

  Long-term sensitivity of soil carbon turnover to warming
The sensitivity of soil carbon to warming is a major uncertainty in projections of carbon dioxide concentration and climate. Experimental studies overwhelmingly indicate increased soil organic carbon (SOC) decomposition at higher temperatures, resulting in increased carbon dioxide emissions from soils. However, recent findings have been cited as evidence against increased soil carbon emissions in a warmer world. In soil warming experiments, the initially increased carbon dioxide efflux returns to pre-warming rates within one to three years, and apparent carbon pool turnover times are insensitive to temperature. It has already been suggested that the apparent lack of temperature dependence could be an artefact due to neglecting the extreme heterogeneity of soil carbon, but no explicit model has yet been presented that can reconcile all the above findings. Here we present a simple three-pool model that partitions SOC into components with different intrinsic turnover rates. Using this model, we show that the results of all the soil-warming experiments are compatible with long-term temperature sensitivity of SOC turnover: they can be explained by rapid depletion of labile SOC combined with the negligible response of non-labile SOC on experimental timescales. Furthermore, we present evidence that non-labile SOC is more sensitive to temperature than labile SOC, implying that the long-term positive feedback of soil decomposition in a warming world may be even stronger than predicted by global models.

Long-term sensitivity of soil carbon turnover to warming

Nature 433, 298 (2005). doi:10.1038/nature03226

Authors: W. Knorr, I. C. Prentice, J. I. House & E. A. Holland

The sensitivity of soil carbon to warming is a major uncertainty in projections of carbon dioxide concentration and climate. Experimental studies overwhelmingly indicate increased soil organic carbon (SOC) decomposition at higher temperatures, resulting in increased carbon dioxide emissions from soils. However, recent findings have been cited as evidence against increased soil carbon emissions in a warmer world. In soil warming experiments, the initially increased carbon dioxide efflux returns to pre-warming rates within one to three years, and apparent carbon pool turnover times are insensitive to temperature. It has already been suggested that the apparent lack of temperature dependence could be an artefact due to neglecting the extreme heterogeneity of soil carbon, but no explicit model has yet been presented that can reconcile all the above findings. Here we present a simple three-pool model that partitions SOC into components with different intrinsic turnover rates. Using this model, we show that the results of all the soil-warming experiments are compatible with long-term temperature sensitivity of SOC turnover: they can be explained by rapid depletion of labile SOC combined with the negligible response of non-labile SOC on experimental timescales. Furthermore, we present evidence that non-labile SOC is more sensitive to temperature than labile SOC, implying that the long-term positive feedback of soil decomposition in a warming world may be even stronger than predicted by global models.

  Early Pliocene hominids from Gona, Ethiopia
Comparative biomolecular studies suggest that the last common ancestor of humans and chimpanzees, our closest living relatives, lived during the Late Miocene–Early Pliocene. Fossil evidence of Late Miocene–Early Pliocene hominid evolution is rare and limited to a few sites in Ethiopia, Kenya and Chad. Here we report new Early Pliocene hominid discoveries and their palaeoenvironmental context from the fossiliferous deposits of As Duma, Gona Western Margin (GWM), Afar, Ethiopia. The hominid dental anatomy (occlusal enamel thickness, absolute and relative size of the first and second lower molar crowns, and premolar crown and radicular anatomy) indicates attribution to Ardipithecus ramidus. The combined radioisotopic and palaeomagnetic data suggest an age of between 4.51 and 4.32 million years for the hominid finds at As Duma. Diverse sources of data (sedimentology, faunal composition, ecomorphological variables and stable carbon isotopic evidence from the palaeosols and fossil tooth enamel) indicate that the Early Pliocene As Duma sediments sample a moderate rainfall woodland and woodland/grassland.

Early Pliocene hominids from Gona, Ethiopia

Nature 433, 301 (2005). doi:10.1038/nature03177

Authors: Sileshi Semaw, Scott W. Simpson, Jay Quade, Paul R. Renne, Robert F. Butler, William C. McIntosh, Naomi Levin, Manuel Dominguez-Rodrigo & Michael J. Rogers

Comparative biomolecular studies suggest that the last common ancestor of humans and chimpanzees, our closest living relatives, lived during the Late Miocene–Early Pliocene. Fossil evidence of Late Miocene–Early Pliocene hominid evolution is rare and limited to a few sites in Ethiopia, Kenya and Chad. Here we report new Early Pliocene hominid discoveries and their palaeoenvironmental context from the fossiliferous deposits of As Duma, Gona Western Margin (GWM), Afar, Ethiopia. The hominid dental anatomy (occlusal enamel thickness, absolute and relative size of the first and second lower molar crowns, and premolar crown and radicular anatomy) indicates attribution to Ardipithecus ramidus. The combined radioisotopic and palaeomagnetic data suggest an age of between 4.51 and 4.32 million years for the hominid finds at As Duma. Diverse sources of data (sedimentology, faunal composition, ecomorphological variables and stable carbon isotopic evidence from the palaeosols and fossil tooth enamel) indicate that the Early Pliocene As Duma sediments sample a moderate rainfall woodland and woodland/grassland.

  Definitive fossil evidence for the extant avian radiation in the Cretaceous
Long-standing controversy surrounds the question of whether living bird lineages emerged after non-avian dinosaur extinction at the Cretaceous/Tertiary (K/T) boundary or whether these lineages coexisted with other dinosaurs and passed through this mass extinction event. Inferences from biogeography and molecular sequence data (but see ref. 10) project major avian lineages deep into the Cretaceous period, implying their ‘mass survival’ at the K/T boundary. By contrast, it has been argued that the fossil record refutes this hypothesis, placing a ‘big bang’ of avian radiation only after the end of the Cretaceous. However, other fossil data—fragmentary bones referred to extant bird lineages—have been considered inconclusive. These data have never been subjected to phylogenetic analysis. Here we identify a rare, partial skeleton from the Maastrichtian of Antarctica as the first Cretaceous fossil definitively placed within the extant bird radiation. Several phylogenetic analyses supported by independent histological data indicate that a new species, Vegavis iaai, is a part of Anseriformes (waterfowl) and is most closely related to Anatidae, which includes true ducks. A minimum of five divergences within Aves before the K/T boundary are inferred from the placement of Vegavis; at least duck, chicken and ratite bird relatives were coextant with non-avian dinosaurs.

Definitive fossil evidence for the extant avian radiation in the Cretaceous

Nature 433, 305 (2005). doi:10.1038/nature03150

Authors: Julia A. Clarke, Claudia P. Tambussi, Jorge I. Noriega, Gregory M. Erickson & Richard A. Ketcham

Long-standing controversy surrounds the question of whether living bird lineages emerged after non-avian dinosaur extinction at the Cretaceous/Tertiary (K/T) boundary or whether these lineages coexisted with other dinosaurs and passed through this mass extinction event. Inferences from biogeography and molecular sequence data (but see ref. 10) project major avian lineages deep into the Cretaceous period, implying their ‘mass survival’ at the K/T boundary. By contrast, it has been argued that the fossil record refutes this hypothesis, placing a ‘big bang’ of avian radiation only after the end of the Cretaceous. However, other fossil data—fragmentary bones referred to extant bird lineages—have been considered inconclusive. These data have never been subjected to phylogenetic analysis. Here we identify a rare, partial skeleton from the Maastrichtian of Antarctica as the first Cretaceous fossil definitively placed within the extant bird radiation. Several phylogenetic analyses supported by independent histological data indicate that a new species, Vegavis iaai, is a part of Anseriformes (waterfowl) and is most closely related to Anatidae, which includes true ducks. A minimum of five divergences within Aves before the K/T boundary are inferred from the placement of Vegavis; at least duck, chicken and ratite bird relatives were coextant with non-avian dinosaurs.

  Field parameterization and experimental test of the neutral theory of biodiversity
Ecologists would like to explain general patterns observed across multi-species communities, such as species–area and abundance–frequency relationships, in terms of the fundamental processes of birth, death and migration underlying the dynamics of all constituent species. The unified neutral theory of biodiversity and related theories based on these fundamental population processes have successfully recreated general species-abundance patterns without accounting for either the variation among species and individuals or resource-releasing processes such as predation and disturbance, long emphasized in ecological theory. If ecological communities can be described adequately without estimating variation in species and their interactions, our understanding of ecological community organization and the predicted consequences of reduced biodiversity and environmental change would shift markedly. Here, I introduce a strong method to test the neutral theory that combines field parameterization of the underlying population dynamics with a field experiment, and apply it to a rocky intertidal community. Although the observed abundance–frequency distribution of the system follows that predicted by the neutral theory, the neutral theory predicts poorly the field experimental results, indicating an essential role for variation in species interactions.

Field parameterization and experimental test of the neutral theory of biodiversity

Nature 433, 309 (2005). doi:10.1038/nature03211

Author: J. Timothy Wootton

Ecologists would like to explain general patterns observed across multi-species communities, such as species–area and abundance–frequency relationships, in terms of the fundamental processes of birth, death and migration underlying the dynamics of all constituent species. The unified neutral theory of biodiversity and related theories based on these fundamental population processes have successfully recreated general species-abundance patterns without accounting for either the variation among species and individuals or resource-releasing processes such as predation and disturbance, long emphasized in ecological theory. If ecological communities can be described adequately without estimating variation in species and their interactions, our understanding of ecological community organization and the predicted consequences of reduced biodiversity and environmental change would shift markedly. Here, I introduce a strong method to test the neutral theory that combines field parameterization of the underlying population dynamics with a field experiment, and apply it to a rocky intertidal community. Although the observed abundance–frequency distribution of the system follows that predicted by the neutral theory, the neutral theory predicts poorly the field experimental results, indicating an essential role for variation in species interactions.

  Evolutionary dynamics on graphs
Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

Evolutionary dynamics on graphs

Nature 433, 312 (2005). doi:10.1038/nature03204

Authors: Erez Lieberman, Christoph Hauert & Martin A. Nowak

Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

 2004-11-28 Protein kinase A signalling via CREB controls myogenesis induced by Wnt proteins
Select members of the Wnt family of secreted glycoproteins have been implicated in inducing the myogenic determinant genes Pax3, MyoD and Myf5 during mammalian embryogenesis, but the mechanism of induction has not been defined. We describe an unexpected role for protein kinase A (PKA) signalling via CREB in this induction. Using a combination of in vitro explant assays, mutant analysis and gene delivery into mouse embryos cultured ex vivo, we demonstrate that adenylyl cyclase signalling via PKA and its target transcription factor CREB are required for Wnt-directed myogenic gene expression. Wnt proteins can also stimulate CREB-mediated transcription, providing evidence for a Wnt signalling pathway involving PKA and CREB. Our findings raise the possibility that PKA/CREB signalling may also contribute to other Wnt-regulated processes in embryonic patterning, stem cell renewal and cancer.

Protein kinase A signalling via CREB controls myogenesis induced by Wnt proteins

Nature 433, 317 (2005). doi:10.1038/nature03126

Authors: Alice E. Chen, David D. Ginty & Chen-Ming Fan

Select members of the Wnt family of secreted glycoproteins have been implicated in inducing the myogenic determinant genes Pax3, MyoD and Myf5 during mammalian embryogenesis, but the mechanism of induction has not been defined. We describe an unexpected role for protein kinase A (PKA) signalling via CREB in this induction. Using a combination of in vitro explant assays, mutant analysis and gene delivery into mouse embryos cultured ex vivo, we demonstrate that adenylyl cyclase signalling via PKA and its target transcription factor CREB are required for Wnt-directed myogenic gene expression. Wnt proteins can also stimulate CREB-mediated transcription, providing evidence for a Wnt signalling pathway involving PKA and CREB. Our findings raise the possibility that PKA/CREB signalling may also contribute to other Wnt-regulated processes in embryonic patterning, stem cell renewal and cancer.

  An autoregulatory circuit for long-range self-organization in Dictyostelium cell populations
Nutrient-deprived Dictyostelium amoebae aggregate to form a multicellular structure by chemotaxis, moving towards propagating waves of cyclic AMP that are relayed from cell to cell. Organizing centres are not formed by founder cells, but are dynamic entities consisting of cores of outwardly rotating spiral waves that self-organize in a homogeneous cell population. Spiral waves are ubiquitously observed in chemical reactions as well as in biological systems. Although feedback control of spiral waves in spatially extended chemical reactions has been demonstrated in recent years, the mechanism by which control is achieved in living systems is unknown. Here we show that mutants of the cyclic AMP/protein kinase A pathway show periodic signalling, but fail to organize coherent long-range wave territories, owing to the appearance of numerous spiral cores. A theoretical model suggests that autoregulation of cell excitability mediated by protein kinase A acts to optimize the number of signalling centres.

An autoregulatory circuit for long-range self-organization in Dictyostelium cell populations

Nature 433, 323 (2005). doi:10.1038/nature03228

Authors: Satoshi Sawai, Peter A. Thomason & Edward C. Cox

Nutrient-deprived Dictyostelium amoebae aggregate to form a multicellular structure by chemotaxis, moving towards propagating waves of cyclic AMP that are relayed from cell to cell. Organizing centres are not formed by founder cells, but are dynamic entities consisting of cores of outwardly rotating spiral waves that self-organize in a homogeneous cell population. Spiral waves are ubiquitously observed in chemical reactions as well as in biological systems. Although feedback control of spiral waves in spatially extended chemical reactions has been demonstrated in recent years, the mechanism by which control is achieved in living systems is unknown. Here we show that mutants of the cyclic AMP/protein kinase A pathway show periodic signalling, but fail to organize coherent long-range wave territories, owing to the appearance of numerous spiral cores. A theoretical model suggests that autoregulation of cell excitability mediated by protein kinase A acts to optimize the number of signalling centres.

  A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts
RNA editing is a process of RNA maturation involved in the insertion, deletion or modification of nucleotides. In organellar transcripts of higher plants, specific cytidine residues are converted into uridine residues. In many cases, editing results in the restoration of conserved amino acid residues, a process that is essential for protein function in plastids. Despite the technical breakthrough in establishing systems in vivo and in vitro for analysing RNA editing, its machinery still remains to be identified in higher plants. Here we introduce a genetic approach and report the discovery of a gene responsible for the specific RNA editing event in the chloroplast.

A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts

Nature 433, 326 (2005). doi:10.1038/nature03229

Authors: Emi Kotera, Masao Tasaka & Toshiharu Shikanai

RNA editing is a process of RNA maturation involved in the insertion, deletion or modification of nucleotides. In organellar transcripts of higher plants, specific cytidine residues are converted into uridine residues. In many cases, editing results in the restoration of conserved amino acid residues, a process that is essential for protein function in plastids. Despite the technical breakthrough in establishing systems in vivo and in vitro for analysing RNA editing, its machinery still remains to be identified in higher plants. Here we introduce a genetic approach and report the discovery of a gene responsible for the specific RNA editing event in the chloroplast.

  Molecular dynamics of cyclically contracting insect flight muscle in vivo
Flight in insects—which constitute the largest group of species in the animal kingdom—is powered by specialized muscles located within the thorax. In most insects each contraction is triggered not by a motor neuron spike but by mechanical stretch imposed by antagonistic muscles. Whereas ‘stretch activation’ and its reciprocal phenomenon ‘shortening deactivation’ are observed to varying extents in all striated muscles, both are particularly prominent in the indirect flight muscles of insects. Here we show changes in thick-filament structure and actin–myosin interactions in living, flying Drosophila with the use of synchrotron small-angle X-ray diffraction. To elicit stable flight behaviour and permit the capture of images at specific phases within the 5-ms wingbeat cycle, we tethered flies within a visual flight simulator. We recorded images of 340 µs duration every 625 µs to create an eight-frame diffraction movie, with each frame reflecting the instantaneous structure of the contractile apparatus. These time-resolved measurements of molecular-level structure provide new insight into the unique ability of insect flight muscle to generate elevated power at high frequency.

Molecular dynamics of cyclically contracting insect flight muscle in vivo

Nature 433, 330 (2005). doi:10.1038/nature03230

Authors: Michael Dickinson, Gerrie Farman, Mark Frye, Tanya Bekyarova, David Gore, David Maughan & Thomas Irving

Flight in insects—which constitute the largest group of species in the animal kingdom—is powered by specialized muscles located within the thorax. In most insects each contraction is triggered not by a motor neuron spike but by mechanical stretch imposed by antagonistic muscles. Whereas ‘stretch activation’ and its reciprocal phenomenon ‘shortening deactivation’ are observed to varying extents in all striated muscles, both are particularly prominent in the indirect flight muscles of insects. Here we show changes in thick-filament structure and actin–myosin interactions in living, flying Drosophila with the use of synchrotron small-angle X-ray diffraction. To elicit stable flight behaviour and permit the capture of images at specific phases within the 5-ms wingbeat cycle, we tethered flies within a visual flight simulator. We recorded images of 340 µs duration every 625 µs to create an eight-frame diffraction movie, with each frame reflecting the instantaneous structure of the contractile apparatus. These time-resolved measurements of molecular-level structure provide new insight into the unique ability of insect flight muscle to generate elevated power at high frequency.

 2005-01-19 Closing the gap
In the life sciences, the problems of graduate training are legion, and well-documented. PhDs take an increasingly long time to complete, graduate programmes often don't account for true interdisciplinary learning, and the gap between basic and applied science remains wide. But some key institutions seem

Closing the gap

Nature 433, 335 (2005). doi:10.1038/nj7023-335a

Author: Paul Smaglik

In the life sciences, the problems of graduate training are legion, and well-documented. PhDs take an increasingly long time to complete, graduate programmes often don't account for true interdisciplinary learning, and the gap between basic and applied science remains wide. But some key institutions seem

 2005-01-19 Save now, don't pay later
Should young scientists be tightening their belts to save for the future? Kendall Powell compounds the interest.

Save now, don't pay later

Nature 433, 336 (2005). doi:10.1038/nj7023-336a

Author: Kendal Powell

Should young scientists be tightening their belts to save for the future? Kendall Powell compounds the interest.

 2005-01-19 Graduate Journal: Time to explore new worlds
As 2005 begins, it is gratifying but also disconcerting to say that this year, I will graduate. I'll complete a PhD in molecular biology at the University of California, Los Angeles. But despite this impending accomplishment, I can honestly say that at 30 years old

Graduate Journal: Time to explore new worlds

Nature 433, 338 (2005). doi:10.1038/nj7023-338a

Author: Jason Underwood

As 2005 begins, it is gratifying but also disconcerting to say that this year, I will graduate. I'll complete a PhD in molecular biology at the University of California, Los Angeles. But despite this impending accomplishment, I can honestly say that at 30 years old

 2005-01-19 Scientists & Societies
International Institute for Applied Systems Analysis, AustriaHardly anyone could believe my summer plans. “You're going to work in an Austrian castle?” a fellow graduate student asked. “Well, it's more like a palace,” I explained, somewhat sheepish about planning to research civil war in such

Scientists & Societies

Nature 433, 338 (2005). doi:10.1038/nj7023-338b

Author: Sarah Elizabeth Staveteig

International Institute for Applied Systems Analysis, AustriaHardly anyone could believe my summer plans. “You're going to work in an Austrian castle?” a fellow graduate student asked. “Well, it's more like a palace,” I explained, somewhat sheepish about planning to research civil war in such

 2005-01-19 Movers
Iain Mattaj, director-general, European Molecular Biology Laboratory, Heidelberg, GermanyFrustrated by the slow progress of his work at the beginning of his postgraduate career, Iain Mattaj once considered joining a friend's retail business. But his desire to understand how the world functions at the molecular

Movers

Nature 433, 338 (2005). doi:10.1038/nj7023-338c

Iain Mattaj, director-general, European Molecular Biology Laboratory, Heidelberg, GermanyFrustrated by the slow progress of his work at the beginning of his postgraduate career, Iain Mattaj once considered joining a friend's retail business. But his desire to understand how the world functions at the molecular



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 2014-10-31 [Editorial] Planet at the crossroads
When we think of nature in 2014, chances are that protected areas come to mind: Amazonian rainforests teeming with wildlife, the sweeping plains of the Serengeti, or an Alpine lake surrounded by glaciers. But the world's protected areas are at a crossroads, and next month, when the International Union for Conservation of Nature (IUCN) convenes its once-in-a-decade World Parks Congress in Sydney, Australia, nations will discuss how to address the challenges in protecting ecosystems across the world for the benefit of humanity. Author: Julia Marton-Lefèvre

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