Making the paper: Richard Mathies
Nature 462, 135 (2009). doi:10.1038/7270135a
Tracking the structural evolution of chemical reactions.
Making the paper: Richard Mathies
Nature 462, 135 (2009). doi:10.1038/7270135a
Tracking the structural evolution of chemical reactions.
Nature 462, 135 (2009). doi:10.1038/7270135b
Last authorThe genetic changes underlying the evolution of language in humans remain mysterious. FOXP2 is the only gene to be linked so far to inherited speech and language dysfunction — prompting researchers to probe its evolutionary significance. On page 213, Daniel Geschwind
Nature 462, 135 (2009). doi:10.1038/7270135c
In an exclusive interview on The Great Beyond, Nature reporter Geoff Brumfiel explores Romanian hopes to launch a balloon to the Moon. Bogdan Sburlea, project manager of the non-profit Aeronautics and Cosmonautics Romanian Association (ARCA), talks about plans to test-launch 'Helen', ARCA's proof-of-concept rocket
Nature 462, 137 (2009). doi:10.1038/462137a
The ad-hoc proliferation of high-security biological labs must be controlled, and should be tied in more closely to broader research and public-health goals.
Nature 462, 137 (2009). doi:10.1038/462137b
Spain should not use the recession as an excuse to stall plans to boost its scientific enterprise.
Nature 462, 138 (2009). doi:10.1038/462138a
The recently launched World Health Summit offers a rare chance for dialogue.
Nature 462, 140 (2009). doi:10.1038/462140a
Nature 462, 140 (2009). doi:10.1038/462140b
Nature 462, 140 (2009). doi:10.1038/462140c
Cell Metab.10, 379–391 (2009) 10.1016/j.cmet.2009.10.003Nematode worms fed on a diet spiked with glucose die about 20% earlier than those consuming just the bacterium Escherichia coli.Cynthia Kenyon and her colleagues at the University of California, San
Nature 462, 140 (2009). doi:10.1038/462140d
Nature 462, 140 (2009). doi:10.1038/462140e
Nature 462, 140 (2009). doi:10.1038/462140f
Nature 462, 141 (2009). doi:10.1038/462141a
Nature 462, 141 (2009). doi:10.1038/462141b
Atmos. Chem. Phys.9, 7737–7751 (2009)Earth's natural sunscreen — the stratospheric ozone layer — has thinned during the past few decades because of the rise in atmospheric pollutants such as chlorofluorocarbons. This has allowed more ultraviolet (UV) radiation to reach many parts of
Nature 462, 141 (2009). doi:10.1038/462141c
Nature 462, 141 (2009). doi:10.1038/462141d
Nature 462, 141 (2009). doi:10.1038/462141e
Author: Robert Blelloch
A computational biologist looks at how mRNA length changes during development.I am always amazed by how we start as a fertilized egg and develop into a complex, multicellular organism. This feat occurs despite the fact that the DNA in every cell — even the
Nature 462, 158 (2009). doi:10.1038/462158a
Author: Jay Davis
SirYour Editorial on resistance to non-proliferation of nuclear weapons is, in my view, a good example of selective presentation of data (
Nature 462, 158 (2009). doi:10.1038/462158b
Author: Gerald E. Marsh
SirYou are correct to state that the Reliable Replacement Warhead (RRW) programme would do nothing to improve the reliability of the US nuclear arsenal (
Nature 462, 158 (2009). doi:10.1038/462158c
Author: Mike Hulme
SirSanjay Khanna's survey of climate-campaign activities (Nature461, 1058–1059; 2009) implies that the arts and advertising ought to be helping to bring into being a “worldwide consensus for action”. But the point is not to engineer a global
Nature 462, 158 (2009). doi:10.1038/462158d
Author: Roger A. Pielke
SirIn their Opinion articles, Rajendra Pachauri (
Nature 462, 159 (2009). doi:10.1038/462159a
Author: Iain Scott
SirAs a scientist working in a foreign laboratory, I can understand Colin Stoneking's frustration at the UK visa system for students (
Nature 462, 159 (2009). doi:10.1038/462159b
Authors: Dabo Guan & David M. Reiner
SirAs the climate-change conference in Copenhagen approaches, attention is focused on the dialogue between developed and developing countries (see http://www.nature.com/roadtocopenhagen). But the impact of the growing links between developing countries should not be overlooked.China is investing heavily in African countries, focusing mainly
Nature 462, 159 (2009). doi:10.1038/462159c
Author: Michael J. Castellano
SirThere is an upside to the potential future phosphorus shortage highlighted in your News Feature 'The disappearing nutrient' (Nature461, 716–718; 2009). Long before a global phosphorus crisis occurs, declining supplies may present a windfall for water quality and sustainable agriculture.
Nature 462, 160 (2009). doi:10.1038/462160a
Author: Indira V. Samarasekera
To reconcile solution-driven research and blue-skies thinking, academic institutions urgently need innovative collaborations and new funding models, says Indira V. Samarasekera.
Nature 462, 162 (2009). doi:10.1038/462162a
Author: James Pusey
In China, under the threat of Western imperialism, interpretations of Darwin's ideas paved the way for Marx, Lenin and Mao, argues James Pusey in the third in our series on reactions to evolutionary theory.
Nature 462, 164 (2009). doi:10.1038/462164a
Author: William J. Nuttall
Two books reveal the spirit of adventure behind the history of nuclear technology, finds William J. Nuttall.
Nature 462, 165 (2009). doi:10.1038/462165a
Author: John Gilbey
Information technology has clearly had an impact on our daily lives. It has also altered the global economy. But how can you measure the worth of a web search or an electronic file format? In this slender volume, Erik Brynjolfsson and Adam Saunders examine the
Nature 462, 165 (2009). doi:10.1038/462165b
Author: Asha Gopinathan
As an executive coach who works with companies to recruit, retain and develop their female talent, Suzanne Doyle-Morris has long had an interest in issues concerning women in male-dominated professions, including academia and science. In her book, she offers advice to anyone who wishes to
Nature 462, 166 (2009). doi:10.1038/462166a
Author: Daniel Cressey
Having moved from engineering to art, Jean-Pierre Hébert applies mathematical rules to generate artworks that explore themes of chaos and determinism. As resident artist at the Kavli Institute for Theoretical Physics, and with an exhibition on in Los Angeles, Hébert explains his interest in algorithms.
Nature 462, 167 (2009). doi:10.1038/462167a
Authors: Andrew L. Hopkins
Computational methods that reliably predict the biological activities of compounds have long been sought. The validation of one such method suggests that in silico predictions for drug discovery have come of age.
Nature 462, 168 (2009). doi:10.1038/462168a
Authors: Marc Pinsonneault
Stars that host planets experience more mixing of their internal elements than do stars that lack such companions. This correlation may serve as a useful diagnostic in the search for planets around stars other than the Sun.
Nature 462, 169 (2009). doi:10.1038/462169a
Authors: Martin H. Dominguez & Pasko Rakic
The FOXP2 gene is implicated in the development of human speech and language. A comparison of the human and chimpanzee FOXP2 proteins highlights the differences in function in the two species.
Nature 462, 170 (2009). doi:10.1038/462170a
Authors: Alberto F. Morpurgo
Graphene continues to surprise physicists with its remarkable electronic properties. Experiments now show that electrons in the material can team up to behave as if they are only fragments of themselves.
Nature 462, 171 (2009). doi:10.1038/462171a
Authors: Paramjit S. Arora & Aseem Z. Ansari
A tenet of drug discovery states that molecules greater than a certain size don't enter cells. But not only do certain synthetic peptides refute this idea, they also inhibit 'undruggable' biological targets.
Nature 462, 175 (2009). doi:10.1038/nature08506
Authors: Michael J. Keiser, Vincent Setola, John J. Irwin, Christian Laggner, Atheir I. Abbas, Sandra J. Hufeisen, Niels H. Jensen, Michael B. Kuijer, Roberto C. Matos, Thuy B. Tran, Ryan Whaley, Richard A. Glennon, Jérôme Hert, Kelan L. H. Thomas, Douglas D. Edwards, Brian K. Shoichet & Bryan L. Roth
Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. Because many drug–target combinations exist, it would be useful to explore possible interactions computationally. Here we compared 3,665 US Food and Drug Administration (FDA)-approved and
Nature 462, 182 (2009). doi:10.1038/nature08543
Authors: Raymond E. Moellering, Melanie Cornejo, Tina N. Davis, Cristina Del Bianco, Jon C. Aster, Stephen C. Blacklow, Andrew L. Kung, D. Gary Gilliland, Gregory L. Verdine & James E. Bradner
Direct inhibition of transcription factor complexes remains a central challenge in the discipline of ligand discovery. In general, these proteins lack surface involutions suitable for high-affinity binding by small molecules. Here we report the design of synthetic, cell-permeable, stabilized α-helical peptides that target a critical
Nature 462, 189 (2009). doi:10.1038/nature08483
Authors: Garik Israelian, Elisa Delgado Mena, Nuno C. Santos, Sergio G. Sousa, Michel Mayor, Stephane Udry, Carolina Domínguez Cerdeña, Rafael Rebolo & Sofia Randich
The surface abundance of lithium on the Sun is 140 times less than the protosolar value, yet the temperature at the base of the surface convective zone is not hot enough to burn—and hence deplete—Li (refs 2, 3). A large range of Li abundances is observed in solar-type stars of the same age, mass and metallicity as the Sun, but such a range is theoretically difficult to understand. An earlier suggestion that Li is more depleted in stars with planets was weakened by the lack of a proper comparison sample of stars without detected planets. Here we report Li abundances for an unbiased sample of solar-analogue stars with and without detected planets. We find that the planet-bearing stars have less than one per cent of the primordial Li abundance, while about 50 per cent of the solar analogues without detected planets have on average ten times more Li. The presence of planets may increase the amount of mixing and deepen the convective zone to such an extent that the Li can be burned.
Nature 462, 192 (2009). doi:10.1038/nature08522
Authors: Xu Du, Ivan Skachko, Fabian Duerr, Adina Luican & Eva Y. Andrei
In graphene, which is an atomic layer of crystalline carbon, two of the distinguishing properties of the material are the charge carriers’ two-dimensional and relativistic character. The first experimental evidence of the two-dimensional nature of graphene came from the observation of a sequence of plateaus in measurements of its transport properties in the presence of an applied magnetic field. These are signatures of the so-called integer quantum Hall effect. However, as a consequence of the relativistic character of the charge carriers, the integer quantum Hall effect observed in graphene is qualitatively different from its semiconductor analogue. As a third distinguishing feature of graphene, it has been conjectured that interactions and correlations should be important in this material, but surprisingly, evidence of collective behaviour in graphene is lacking. In particular, the quintessential collective quantum behaviour in two dimensions, the fractional quantum Hall effect (FQHE), has so far resisted observation in graphene despite intense efforts and theoretical predictions of its existence. Here we report the observation of the FQHE in graphene. Our observations are made possible by using suspended graphene devices probed by two-terminal charge transport measurements. This allows us to isolate the sample from substrate-induced perturbations that usually obscure the effects of interactions in this system and to avoid effects of finite geometry. At low carrier density, we find a field-induced transition to an insulator that competes with the FQHE, allowing its observation only in the highest quality samples. We believe that these results will open the door to the physics of FQHE and other collective behaviour in graphene.
Nature 462, 196 (2009). doi:10.1038/nature08582
Authors: Kirill I. Bolotin, Fereshte Ghahari, Michael D. Shulman, Horst L. Stormer & Philip Kim
When electrons are confined in two dimensions and subject to strong magnetic fields, the Coulomb interactions between them can become very strong, leading to the formation of correlated states of matter, such as the fractional quantum Hall liquid. In this strong quantum regime, electrons and magnetic flux quanta bind to form complex composite quasiparticles with fractional electronic charge; these are manifest in transport measurements of the Hall conductivity as rational fractions of the elementary conductance quantum. The experimental discovery of an anomalous integer quantum Hall effect in graphene has enabled the study of a correlated two-dimensional electronic system, in which the interacting electrons behave like massless chiral fermions. However, owing to the prevailing disorder, graphene has so far exhibited only weak signatures of correlated electron phenomena, despite intense experimental and theoretical efforts. Here we report the observation of the fractional quantum Hall effect in ultraclean, suspended graphene. In addition, we show that at low carrier density graphene becomes an insulator with a magnetic-field-tunable energy gap. These newly discovered quantum states offer the opportunity to study correlated Dirac fermions in graphene in the presence of large magnetic fields.
Nature 462, 200 (2009). doi:10.1038/nature08527
Authors: Chong Fang, Renee R. Frontiera, Rosalie Tran & Richard A. Mathies
Tracing the transient atomic motions that lie at the heart of chemical reactions requires high-resolution multidimensional structural information on the timescale of molecular vibrations, which commonly range from 10 fs to 1 ps. For simple chemical systems, it has been possible to map out in considerable detail the reactive potential-energy surfaces describing atomic motions and resultant reaction dynamics, but such studies remain challenging for complex chemical and biological transformations. A case in point is the green fluorescent protein (GFP) from the jellyfish Aequorea victoria, which is a widely used gene expression marker owing to its efficient bioluminescence. This feature is known to arise from excited-state proton transfer (ESPT), yet the atomistic details of the process are still not fully understood. Here we show that femtosecond stimulated Raman spectroscopy provides sufficiently detailed and time-resolved vibrational spectra of the electronically excited chromophore of GFP to reveal skeletal motions involved in the proton transfer that produces the fluorescent form of the protein. In particular, we observe that the frequencies and intensities of two marker bands, the C–O and C = N stretching modes at opposite ends of the conjugated chromophore, oscillate out of phase with a period of 280 fs; we attribute these oscillations to impulsively excited low-frequency phenoxyl-ring motions, which optimize the geometry of the chromophore for ESPT. Our findings illustrate that femtosecond simulated Raman spectroscopy is a powerful approach to revealing the real-time nuclear dynamics that make up a multidimensional polyatomic reaction coordinate.
Nature 462, 205 (2009). doi:10.1038/nature08518
Authors: M. T. Hren, M. M. Tice & C. P. Chamberlain
Stable oxygen isotope ratios (δ18O) of Precambrian cherts have been used to establish much of our understanding of the early climate history of Earth and suggest that ocean temperatures during the Archaean era (∼3.5 billion years ago) were between 55 °C and 85 °C (ref. 2). But, because of uncertainty in the δ18O of the primitive ocean, there is considerable debate regarding this conclusion. Examination of modern and ancient cherts indicates that another approach, using a combined analysis of δ18O and hydrogen isotopes (δD) rather than δ18O alone, can provide a firmer constraint on formational temperatures without independent knowledge of the isotopic composition of ambient waters. Here we show that δ18O and δD sampled from 3.42-billion-year-old Buck Reef Chert rocks in South Africa are consistent with formation from waters at varied low temperatures. The most 18O-enriched Buck Reef Chert rocks record the lowest diagenetic temperatures and were formed in equilibrium with waters below ∼40 °C. Geochemical and sedimentary evidence suggests that the Buck Reef Chert was formed in shallow to deep marine conditions, so our results indicate that the Palaeoarchaean ocean was isotopically depleted relative to the modern ocean and far cooler (≤40 °C) than previously thought.
Nature 462, 209 (2009). doi:10.1038/nature08517
Authors: James A. D. Connolly, Max W. Schmidt, Giulio Solferino & Nikolai Bagdassarov
Magmatic production on Earth is dominated by asthenospheric melts of basaltic composition that have mostly erupted at mid-ocean ridges. The timescale for segregation and transport of these melts, which are ultimately responsible for formation of the Earth’s crust, is critically dependent on the permeability of the partly molten asthenospheric mantle, yet this permeability is known mainly from semi-empirical and analogue models. Here we use a high-pressure, high-temperature centrifuge, at accelerations of 400g–700g, to measure the rate of basalt melt flow in olivine aggregates with porosities of 5–12 per cent. The resulting permeabilities are consistent with a microscopic model in which melt is completely connected, and are one to two orders of magnitude larger than predicted by current parameterizations. Extrapolation of the measurements to conditions characteristic of asthenosphere below mid-ocean ridges yields proportionally higher transport speeds. Application of these results in a model of porous-media channelling instabilities yields melt transport times of ∼1–2.5 kyr across the entire asthenosphere, which is sufficient to preserve the observed 230Th excess of mid-ocean-ridge basalts and the mantle signatures of even shorter-lived isotopes such as 226Ra (refs 5,11–14).
Nature 462, 213 (2009). doi:10.1038/nature08549
Authors: Genevieve Konopka, Jamee M. Bomar, Kellen Winden, Giovanni Coppola, Zophonias O. Jonsson, Fuying Gao, Sophia Peng, Todd M. Preuss, James A. Wohlschlegel & Daniel H. Geschwind
The signalling pathways controlling both the evolution and development of language in the human brain remain unknown. So far, the transcription factor FOXP2 (forkhead box P2) is the only gene implicated in Mendelian forms of human speech and language dysfunction. It has been proposed that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this two-amino-acid change occurred around the time of language emergence in humans. However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested. Here we demonstrate that these two human-specific amino acids alter FOXP2 function by conferring differential transcriptional regulation in vitro. We extend these observations in vivo to human and chimpanzee brain, and use network analysis to identify novel relationships among the differentially expressed genes. These data provide experimental support for the functional relevance of changes in FOXP2 that occur on the human lineage, highlighting specific pathways with direct consequences for human brain development and disease in the central nervous system (CNS). Because FOXP2 has an important role in speech and language in humans, the identified targets may have a critical function in the development and evolution of language circuitry in humans.
Nature 462, 218 (2009). doi:10.1038/nature08485
Authors: Yoko Yazaki-Sugiyama, Siu Kang, Hideyuki Câteau, Tomoki Fukai & Takao K. Hensch
Experience-dependent plasticity in the brain requires balanced excitation–inhibition. How individual circuit elements contribute to plasticity outcome in complex neocortical networks remains unknown. Here we report an intracellular analysis of ocular dominance plasticity—the loss of acuity and cortical responsiveness for an eye deprived of vision in early life. Unlike the typical progressive loss of pyramidal-cell bias, direct recording from fast-spiking cells in vivo reveals a counterintuitive initial shift towards the occluded eye followed by a late preference for the open eye, consistent with a spike-timing-dependent plasticity rule for these inhibitory neurons. Intracellular pharmacology confirms a dynamic switch of GABA (γ-aminobutyric acid) impact to pyramidal cells following deprivation in juvenile mice only. Together these results suggest that the bidirectional recruitment of an initially binocular GABA circuit may contribute to experience-dependent plasticity in the developing visual cortex.
Nature 462, 222 (2009). doi:10.1038/nature08562
Authors: Kehkooi Kee, Vanessa T. Angeles, Martha Flores, Ha Nam Nguyen & Renee A. Reijo Pera
The leading cause of infertility in men and women is quantitative and qualitative defects in human germ-cell (oocyte and sperm) development. Yet, it has not been possible to examine the unique developmental genetics of human germ-cell formation and differentiation owing to inaccessibility of germ cells during fetal development. Although several studies have shown that germ cells can be differentiated from mouse and human embryonic stem cells, human germ cells differentiated in these studies generally did not develop beyond the earliest stages. Here we used a germ-cell reporter to quantify and isolate primordial germ cells derived from both male and female human embryonic stem cells. By silencing and overexpressing genes that encode germ-cell-specific cytoplasmic RNA-binding proteins (not transcription factors), we modulated human germ-cell formation and developmental progression. We observed that human DAZL (deleted in azoospermia-like) functions in primordial germ-cell formation, whereas closely related genes DAZ and BOULE (also called BOLL) promote later stages of meiosis and development of haploid gametes. These results are significant to the generation of gametes for future basic science and potential clinical applications.
Nature 462, 226 (2009). doi:10.1038/nature08529
Authors: Koji Hase, Kazuya Kawano, Tomonori Nochi, Gemilson Soares Pontes, Shinji Fukuda, Masashi Ebisawa, Kazunori Kadokura, Toru Tobe, Yumiko Fujimura, Sayaka Kawano, Atsuko Yabashi, Satoshi Waguri, Gaku Nakato, Shunsuke Kimura, Takaya Murakami, Mitsutoshi Iimura, Kimiyo Hamura, Shin-Ichi Fukuoka, Anson W. Lowe, Kikuji Itoh, Hiroshi Kiyono & Hiroshi Ohno
The mucosal immune system forms the largest part of the entire immune system, containing about three-quarters of all lymphocytes and producing grams of secretory IgA daily to protect the mucosal surface from pathogens. To evoke the mucosal immune response, antigens on the mucosal surface must be transported across the epithelial barrier into organized lymphoid structures such as Peyer’s patches. This function, called antigen transcytosis, is mediated by specialized epithelial M cells. The molecular mechanisms promoting this antigen uptake, however, are largely unknown. Here we report that glycoprotein 2 (GP2), specifically expressed on the apical plasma membrane of M cells among enterocytes, serves as a transcytotic receptor for mucosal antigens. Recombinant GP2 protein selectively bound a subset of commensal and pathogenic enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium (S. Typhimurium), by recognizing FimH, a component of type I pili on the bacterial outer membrane. Consistently, these bacteria were colocalized with endogenous GP2 on the apical plasma membrane as well as in cytoplasmic vesicles in M cells. Moreover, deficiency of bacterial FimH or host GP2 led to defects in transcytosis of type-I-piliated bacteria through M cells, resulting in an attenuation of antigen-specific immune responses in Peyer’s patches. GP2 is therefore a previously unrecognized transcytotic receptor on M cells for type-I-piliated bacteria and is a prerequisite for the mucosal immune response to these bacteria. Given that M cells are considered a promising target for oral vaccination against various infectious diseases, the GP2-dependent transcytotic pathway could provide a new target for the development of M-cell-targeted mucosal vaccines.
Nature 462, 231 (2009). doi:10.1038/nature08550
Authors: Marie-Emilie Terret, Rebecca Sherwood, Sadia Rahman, Jun Qin & Prasad V. Jallepalli
Cohesin not only links sister chromatids but also inhibits the transcriptional machinery’s interaction with and movement along chromatin. In contrast, replication forks must traverse such cohesin-associated obstructions to duplicate the entire genome in S phase. How this occurs is unknown. Through single-molecule analysis, we demonstrate that the replication factor C (RFC)–CTF18 clamp loader (RFCCTF18) controls the velocity, spacing and restart activity of replication forks in human cells and is required for robust acetylation of cohesin’s SMC3 subunit and sister chromatid cohesion. Unexpectedly, we discovered that cohesin acetylation itself is a central determinant of fork processivity, as slow-moving replication forks were found in cells lacking the Eco1-related acetyltransferases ESCO1 or ESCO2 (refs 8–10) (including those derived from Roberts’ syndrome patients, in whom ESCO2 is biallelically mutated) and in cells expressing a form of SMC3 that cannot be acetylated. This defect was a consequence of cohesin’s hyperstable interaction with two regulatory cofactors, WAPL and PDS5A (refs 12, 13); removal of either cofactor allowed forks to progress rapidly without ESCO1, ESCO2, or RFCCTF18. Our results show a novel mechanism for clamp-loader-dependent fork progression, mediated by the post-translational modification and structural remodelling of the cohesin ring. Loss of this regulatory mechanism leads to the spontaneous accrual of DNA damage and may contribute to the abnormalities of the Roberts’ syndrome cohesinopathy.
Nature 462, 242 (2009). doi:10.1038/462242a
Author: Martin Hayes
To any impressionable young school leavers who are considering joining the space corps.