Making the paper: Samar Khatiwala
Nature 462, 250 (2009). doi:10.1038/7271250a
Using maths to map the ocean's carbon sink through time.
Making the paper: Samar Khatiwala
Nature 462, 250 (2009). doi:10.1038/7271250a
Using maths to map the ocean's carbon sink through time.
Nature 462, 250 (2009). doi:10.1038/7271250b
Last authorBiologists have wondered for more than a century why separate sexes exist when many plant and animal species reproduce through self-fertilization (selfing). Two theories had emerged to explain why cross-fertilization, or outcrossing, might be beneficial to species despite the cost of a separate
Nature 462, 250 (2009). doi:10.1038/7271250c
Published research articles are now available to rent, writes Frank Norman on his Nature Network blog, Trading Knowledge (http://go.nature.com/GKNUa8). Norman, head of library services at the Medical Research Council's National Institute for Medical Research in London, reviews a new business model for publishing.
Nature 462, 251 (2009). doi:10.1038/462251a
This third special issue in Nature's year-long celebration of Charles Darwin focuses on the dire challenges to Earth's biodiversity — and finds some reason for hope.
Nature 462, 252 (2009). doi:10.1038/462252a
Information-sharing resources are essential to biologists and deserve international support.
Nature 462, 254 (2009). doi:10.1038/462254a
BMC Biol.7, 74 (2009) 10.1186/1741-7007-7-74Feeding off whale bones at the bottom of the ocean, the Osedax genus of marine worms was first described by scientists in 2004. In these creatures, harems of tiny males are wholly encased in
Nature 462, 254 (2009). doi:10.1038/462254b
Geology37, 1011–1014 (2009) 10.1130/G30259A.1A huge meteorite or comet that smashed into North America 1.85 billion years ago was responsible for the abrupt end of certain iron deposits in the rocks around Lake Superior, say John Slack and
Nature 462, 254 (2009). doi:10.1038/462254c
PLoS Genet.5, e1000719 (2009) 10.1371/journal.pgen.1000719A large-scale survey of gene loss or gain in cervical cancer has flagged more than 50 potential genetic drivers of the disease.Heidi Lyng and her colleagues at the Norwegian Radium Hospital in Oslo screened
Nature 462, 254 (2009). doi:10.1038/462254d
Phys. Rev. Lett.103, 198101 (2009); 10.1103/PhysRevLett.103.198101Phys. Rev. Lett.103, 198102 (2009)10.1103/PhysRevLett.103.198102Researchers have taken the first X-ray diffraction images of intact, hydrated cells.Because of their short wavelengths, X-rays can penetrate deep into specimens
Nature 462, 254 (2009). doi:10.1038/462254e
Nature 462, 254 (2009). doi:10.1038/462254f
PLoS ONE4, e7783 (2009) 10.1371/journal.pone.0007783Two methods for estimating animal metabolic rates have been applied to extinct dinosaurs to show which of the bipedal species may have been warm- or cold-blooded. Herman Pontzer of Washington University in St Louis, Missouri,
Nature 462, 255 (2009). doi:10.1038/462255a
In vivo
Nature 462, 255 (2009). doi:10.1038/462255b
J. Exp. Biol.212, 3892–3900 (2009) 10.1242/jeb.034561The marine sponge Halisarca caerulea takes up about two-thirds of its body weight in dissolved carbon each day by filtering massive amounts of water, but it barely grows in size.To
Nature 462, 255 (2009). doi:10.1038/462255c
Geophys. Res. Lett.36, L21203 doi:10.1029/2009GL040634 (2009)After nearly six months of scraping at the polar regions of Mars, NASA's Phoenix lander in 2008 discovered both ice-cemented soil and slabs of pure ice below the surface. It also found
Nature 462, 255 (2009). doi:10.1038/462255d
Proc. Natl Acad. Sci. USA106, 19150–19155 (2009) 10.1073/pnas.0909293106Patients undergoing irradiation for brain tumours often display signs of cognitive dysfunction, owing in part to the loss of healthy neural stem and precursor cells. To investigate possible treatments, Charles
Nature 462, 255 (2009). doi:10.1038/462255e
Author: Matt Friedman
A palaeontologist ponders how biodiversity is spread across the vertebrate tree of life.Why do some biological groups burst at the seams with many different species, whereas others, despite their deep evolutionary heritage, contain only a handful of members? Many of my old vertebrate-biology textbooks
Nature 462, 276 (2009). doi:10.1038/462276a
Authors: Stuart Pimm, Nigel Roulet & Andrew Weaver
In the run-up to next month's climate-change treaty negotiations in Copenhagen, there is a pressing need to inform policy discussions about the importance of carbon management of northern boreal forests, as well as of tropical forests.Boreal carbon pools account for more of the overall
Nature 462, 276 (2009). doi:10.1038/462276b
Author: David Piehler
Authors of research papers should use and cite online patent databases more frequently, according to a recent Correspondence (
Nature 462, 276 (2009). doi:10.1038/462276c
Author: Yulia Timoshkina
Political agreement on water rights and usage should be at the heart of climate-change conference discussions (see http://www.nature.com/roadtocopenhagen). Policy-makers, whose real agenda may be their standing with their electorates, should recognize that water is an ideal vehicle for reaching a useful aggregate agreement.Water
Nature 462, 276 (2009). doi:10.1038/462276d
Author: Saumitra Mukherjee
Satellite-based estimates of groundwater depletion in northwestern India reported by Matthew Rodell and colleagues (Nature460, 999–1002; 2009) should be backed up with precise ground-based information for the whole of India, taking into account regional variations in rock types,
Nature 462, 277 (2009). doi:10.1038/462277a
Author: Pavan Sukhdev
The value of biodiversity must be accounted for, says Pavan Sukhdev. It is time for governments to invest to secure the flow of nature's 'public goods'.
Nature 462, 278 (2009). doi:10.1038/462278a
Authors: Will R. Turner, Michael Oppenheimer & David S. Wilcove
Natural ecosystems and biodiversity must be made a bulwark against climate change, not a casualty of it, argue Will R. Turner, Michael Oppenheimer and David S. Wilcove.
Nature 462, 280 (2009). doi:10.1038/462280a
Authors: Robert J. Smith, Diogo Veríssimo, Nigel Leader-Williams, Richard M. Cowling & Andrew T. Knight
To save biodiversity, on-the-ground agencies need to set the conservation research agenda, not distant academics and non-governmental organizations, argue Robert J. Smith and colleagues.
Nature 462, 282 (2009). doi:10.1038/462282a
Author: Douglas Erwin
Palaeontologists must model the causes of biodiversity rather than simply cataloguing fossils, says Douglas Erwin, as they curate the only record of ecosystems undamaged by humans.
Nature 462, 284 (2009). doi:10.1038/462284a
Author: Jürgen Buchenau
Latin Americans first saw evolution as a reason to 'whiten' their societies, then as a reason to take pride in their mixed lineage, says Jürgen Buchenau in the last of four pieces on Darwin's global influence.
Nature 462, 286 (2009). doi:10.1038/462286a
Author: Alistair Sponsel
Shared experiences on global voyages linked Darwin and his fellow naturalists, explains Alistair Sponsel.
Nature 462, 287 (2009). doi:10.1038/462287a
Author: Mark Schrope
Begun in 2000, the first global marine census is due to be completed next year. In anticipation of the official release of these results, a beautifully illustrated book highlights the findings to date of this massive project. World Ocean Census also hints at the
Nature 462, 288 (2009). doi:10.1038/462288a
Author: Patrick Goymer
Nicky Clayton, a biologist and psychologist who studies the behaviour of birds, and who is also a salsa and tango dancer, collaborated with Rambert Dance Company to create a work commemorating Charles Darwin. As The Comedy of Change tours the United Kingdom, she explains how communicating via motion is common to both dance and the natural world.
Nature 462, 289 (2009). doi:10.1038/462289a
Author: Fausto Barbagli
Ideas about the mutability of species may have been part of Enlightenment imagery before Lamarck.
Nature 462, 289 (2009). doi:10.1038/462289b
In the Book Review 'Amphibian mystery misread' by Alan Pounds and Karen Masters (Nature462, 38–39; 2009) the sentence “Collins and Crump's selection of published work and quoted opinions downplays such links” should have read “Collins and Crump's assessment
Nature 462, 291 (2009). doi:10.1038/462291a
Authors: Giovanni Amelino-Camelia
Light from a distant γ-ray burst backs up a key prediction of Albert Einstein's theory of relativity — that photon speed is the same regardless of energy. But it might set the stage for evolution of the theory.
Nature 462, 292 (2009). doi:10.1038/462292a
Authors: Steven Hahn
A structure for the enzyme RNA polymerase II in combination with the transcription factor TFIIB changes our view of how the polymerase and its helper proteins initiate transcription.
Nature 462, 294 (2009). doi:10.1038/462294a
Authors: Aneil F. Agrawal
On the face of it, self-fertilization is the efficient way to breed: compared with outcrossing, there's usually much less fuss, for a start. So why isn't reproduction by selfing far more prevalent than it is?
Nature 462, 295 (2009). doi:10.1038/462295b
50 Years agoIt has often been suggested that the dark areas of Mars consist partly of vegetation, particularly in view of the seasonal variation of the intensity of the dark regions. Tests for the high near-infra-red reflectivity characteristic of many plants have all given
Nature 462, 295 (2009). doi:10.1038/462295a
Authors: David Noone
Temperature estimates derived from isotopes in polar ice cores reveal much about Earth's past climate. According to the latest analysis, interglacial periods were rather warmer than previously thought.
Nature 462, 296 (2009). doi:10.1038/462296a
Authors: Dirk Schübeler
Genome-wide maps of methylated cytosine bases at single-base-pair resolution in human cells reveal distinct differences between cell types. These maps provide a starting point to decode the function of this enigmatic mark.
Nature 462, 297 (2009). doi:10.1038/462297a
Author: Andrew Mitchinson
Nature 462, 298 (2009). doi:10.1038/462298a
Authors: Yannis Michalakis & François Renaud
Each week some 20,000 people die from malaria. There will be no magic ways of reducing this dreadful toll, not least because the mosquito vector and the parasite itself have formidable abilities to resist control measures. Angles of attack that rest on evolutionary principles are being explored.
Nature 462, 301 (2009). doi:10.1038/nature08556
Authors: Drake Deming & Sara Seager
Exoplanets are distant worlds that orbit stars other than our Sun. More than 370 such planets are known, and a growing fraction of them are discovered because they transit their star as seen from Earth. The special transit geometry enables us to measure masses and radii for dozens of planets, and we have identified gases in the atmospheres of several giant ones. Within the next decade, we expect to find and study a ‘habitable’ rocky planet transiting a cool red dwarf star close to our Sun. Eventually, we will be able to image the light from an Earth-like world orbiting a nearby solar-type star.
Nature 462, 307 (2009). doi:10.1038/nature08532
Authors: Stephen O’Rahilly
Metabolic diseases represent a growing threat to world-wide public health. In general, these disorders result from the interaction of heritable factors with environmental influences. Here, I will focus on two important metabolic disorders, namely type 2 diabetes and obesity, and explore the extent to which human molecular genetic research has illuminated our understanding of their underlying pathophysiological mechanisms.
Nature 462, 315 (2009). doi:10.1038/nature08514
Authors: Ryan Lister, Mattia Pelizzola, Robert H. Dowen, R. David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R. Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A. Harvey Millar, James A. Thomson, Bing Ren & Joseph R. Ecker
DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts,
Nature 462, 323 (2009). doi:10.1038/nature08548
Authors: Dirk Kostrewa, Mirijam E. Zeller, Karim-Jean Armache, Martin Seizl, Kristin Leike, Michael Thomm & Patrick Cramer
To initiate gene transcription, RNA polymerase II (Pol II) requires the transcription factor IIB (B). Here we present the crystal structure of the complete Pol II–B complex at 4.3 Å resolution, and complementary functional data. The results indicate the mechanism of transcription initiation, including the transition to RNA
Nature 462, 331 (2009). doi:10.1038/nature08574
Authors: A. A. Abdo, M. Ackermann, M. Ajello, K. Asano, W. B. Atwood, M. Axelsson, L. Baldini, J. Ballet, G. Barbiellini, M. G. Baring, D. Bastieri, K. Bechtol, R. Bellazzini, B. Berenji, P. N. Bhat, E. Bissaldi, E. D. Bloom, E. Bonamente, J. Bonnell, A. W. Borgland, A. Bouvier, J. Bregeon, A. Brez, M. S. Briggs, M. Brigida, P. Bruel, J. M. Burgess, T. H. Burnett, G. A. Caliandro, R. A. Cameron, P. A. Caraveo, J. M. Casandjian, C. Cecchi, Ö. Çelik, V. Chaplin, E. Charles, C. C. Cheung, J. Chiang, S. Ciprini, R. Claus, J. Cohen-Tanugi, L. R. Cominsky, V. Connaughton, J. Conrad, S. Cutini, C. D. Dermer, A. de Angelis, F. de Palma, S. W. Digel, B. L. Dingus, E. do Couto e Silva, P. S. Drell, R. Dubois, D. Dumora, C. Farnier, C. Favuzzi, S. J. Fegan, J. Finke, G. Fishman, W. B. Focke, L. Foschini, Y. Fukazawa, S. Funk, P. Fusco, F. Gargano, D. Gasparrini, N. Gehrels, S. Germani, L. Gibby, B. Giebels, N. Giglietto, F. Giordano, T. Glanzman, G. Godfrey, J. Granot, J. Greiner, I. A. Grenier, M.-H. Grondin, J. E. Grove, D. Grupe, L. Guillemot, S. Guiriec, Y. Hanabata, A. K. Harding, M. Hayashida, E. Hays, E. A. Hoversten, R. E. Hughes, G. Jóhannesson, A. S. Johnson, R. P. Johnson, W. N. Johnson, T. Kamae, H. Katagiri, J. Kataoka, N. Kawai, M. Kerr, R. M. Kippen, J. Knödlseder, D. Kocevski, C. Kouveliotou, F. Kuehn, M. Kuss, J. Lande, L. Latronico, M. Lemoine-Goumard, F. Longo, F. Loparco, B. Lott, M. N. Lovellette, P. Lubrano, G. M. Madejski, A. Makeev, M. N. Mazziotta, S. McBreen, J. E. McEnery, S. McGlynn, P. Mészáros, C. Meurer, P. F. Michelson, W. Mitthumsiri, T. Mizuno, A. A. Moiseev, C. Monte, M. E. Monzani, E. Moretti, A. Morselli, I. V. Moskalenko, S. Murgia, T. Nakamori, P. L. Nolan, J. P. Norris, E. Nuss, M. Ohno, T. Ohsugi, N. Omodei, E. Orlando, J. F. Ormes, M. Ozaki, W. S. Paciesas, D. Paneque, J. H. Panetta, D. Parent, V. Pelassa, M. Pepe, M. Pesce-Rollins, V. Petrosian, F. Piron, T. A. Porter, R. Preece, S. Rainò, E. Ramirez-Ruiz, R. Rando, M. Razzano, S. Razzaque, A. Reimer, O. Reimer, T. Reposeur, S. Ritz, L. S. Rochester, A. Y. Rodriguez, M. Roth, F. Ryde, H. F.-W. Sadrozinski, D. Sanchez, A. Sander, P. M. Saz Parkinson, J. D. Scargle, T. L. Schalk, C. Sgrò, E. J. Siskind, D. A. Smith, P. D. Smith, G. Spandre, P. Spinelli, M. Stamatikos, F. W. Stecker, M. S. Strickman, D. J. Suson, H. Tajima, H. Takahashi, T. Takahashi, T. Tanaka, J. B. Thayer, J. G. Thayer, D. J. Thompson, L. Tibaldo, K. Toma, D. F. Torres, G. Tosti, E. Troja, Y. Uchiyama, T. Uehara, T. L. Usher, A. J. van der Horst, V. Vasileiou, N. Vilchez, V. Vitale, A. von Kienlin, A. P. Waite, P. Wang, C. Wilson-Hodge, B. L. Winer, K. S. Wood, X. F. Wu, R. Yamazaki, T. Ylinen & M. Ziegler
A cornerstone of Einstein’s special relativity is Lorentz invariance—the postulate that all observers measure exactly the same speed of light in vacuum, independent of photon-energy. While special relativity assumes that there is no fundamental length-scale associated with such invariance, there is a fundamental scale (the Planck scale, lPlanck ≈ 1.62 × 10-33 cm or EPlanck = MPlanckc2 ≈ 1.22 × 1019 GeV), at which quantum effects are expected to strongly affect the nature of space–time. There is great interest in the (not yet validated) idea that Lorentz invariance might break near the Planck scale. A key test of such violation of Lorentz invariance is a possible variation of photon speed with energy. Even a tiny variation in photon speed, when accumulated over cosmological light-travel times, may be revealed by observing sharp features in γ-ray burst (GRB) light-curves. Here we report the detection of emission up to ∼31 GeV from the distant and short GRB 090510. We find no evidence for the violation of Lorentz invariance, and place a lower limit of 1.2EPlanck on the scale of a linear energy dependence (or an inverse wavelength dependence), subject to reasonable assumptions about the emission (equivalently we have an upper limit of lPlanck/1.2 on the length scale of the effect). Our results disfavour quantum-gravity theories in which the quantum nature of space–time on a very small scale linearly alters the speed of light.
Nature 462, 335 (2009). doi:10.1038/nature08521
Authors: Jianqiao Meng, Guodong Liu, Wentao Zhang, Lin Zhao, Haiyun Liu, Xiaowen Jia, Daixiang Mu, Shanyu Liu, Xiaoli Dong, Jun Zhang, Wei Lu, Guiling Wang, Yong Zhou, Yong Zhu, Xiaoyang Wang, Zuyan Xu, Chuangtian Chen & X. J. Zhou
In the pseudogap state of the high-transition-temperature (high-Tc) copper oxide superconductors, angle-resolved photoemission (ARPES) measurements have seen Fermi arcs—that is, open-ended gapless sections in the large Fermi surface—rather than a closed loop expected of an ordinary metal. This is all the more puzzling because Fermi pockets (small closed Fermi surface features) have been suggested by recent quantum oscillation measurements. The Fermi arcs cannot be understood in terms of existing theories, although there is a solution in the form of conventional Fermi surface pockets associated with competing order, but with a back side that is for detailed reasons invisible to photoemission probes. Here we report ARPES measurements of Bi2Sr2-xLaxCuO6+δ (La-Bi2201) that reveal Fermi pockets. The charge carriers in the pockets are holes, and the pockets show an unusual dependence on doping: they exist in underdoped but not overdoped samples. A surprise is that these Fermi pockets appear to coexist with the Fermi arcs. This coexistence has not been expected theoretically.
Nature 462, 339 (2009). doi:10.1038/nature08569
Authors: Chun Hung Lui, Li Liu, Kin Fai Mak, George W. Flynn & Tony F. Heinz
Graphene, a single atomic layer of carbon connected by sp2 hybridized bonds, has attracted intense scientific interest since its recent discovery. Much of the research on graphene has been directed towards exploration of its novel electronic properties, but the structural aspects of this model two-dimensional system are also of great interest and importance. In particular, microscopic corrugations have been observed on all suspended and supported graphene sheets studied so far. This rippling has been invoked to explain the thermodynamic stability of free-standing graphene sheets. Many distinctive electronic and chemical properties of graphene have been attributed to the presence of ripples, which are also predicted to give rise to new physical phenomena that would be absent in a planar two-dimensional material. Direct experimental study of such novel ripple physics has, however, been hindered by the lack of flat graphene layers. Here we demonstrate the fabrication of graphene monolayers that are flat down to the atomic level. These samples are produced by deposition on the atomically flat terraces of cleaved mica surfaces. The apparent height variation in the graphene layers observed by high-resolution atomic force microscopy (AFM) is less than 25 picometres, indicating the suppression of any existing intrinsic ripples in graphene. The availability of such ultraflat samples will permit rigorous testing of the impact of ripples on various physical and chemical properties of graphene.
Nature 462, 342 (2009). doi:10.1038/nature08564
Authors: L. C. Sime, E. W. Wolff, K. I. C. Oliver & J. C. Tindall
Stable isotope ratios of oxygen and hydrogen in the Antarctic ice core record have revolutionized our understanding of Pleistocene climate variations and have allowed reconstructions of Antarctic temperature over the past 800,000 years (800 kyr; refs 1, 2). The relationship between the D/H ratio of mean annual precipitation and mean annual surface air temperature is said to be uniform ±10% over East Antarctica and constant with time ±20% (refs 3–5). In the absence of strong independent temperature proxy evidence allowing us to calibrate individual ice cores, prior general circulation model (GCM) studies have supported the assumption of constant uniform conversion for climates cooler than that of the present day. Here we analyse the three available 340 kyr East Antarctic ice core records alongside input from GCM modelling. We show that for warmer interglacial periods the relationship between temperature and the isotopic signature varies among ice core sites, and that therefore the conversions must be nonlinear for at least some sites. Model results indicate that the isotopic composition of East Antarctic ice is less sensitive to temperature changes during warmer climates. We conclude that previous temperature estimates from interglacial climates are likely to be too low. The available evidence is consistent with a peak Antarctic interglacial temperature that was at least 6 K higher than that of the present day —approximately double the widely quoted 3 ± 1.5 K (refs 5, 6).
Nature 462, 346 (2009). doi:10.1038/nature08526
Authors: S. Khatiwala, F. Primeau & T. Hall
The release of fossil fuel CO2 to the atmosphere by human activity has been implicated as the predominant cause of recent global climate change. The ocean plays a crucial role in mitigating the effects of this perturbation to the climate system, sequestering 20 to 35 per cent of anthropogenic CO2 emissions. Although much progress has been made in recent years in understanding and quantifying this sink, considerable uncertainties remain as to the distribution of anthropogenic CO2 in the ocean, its rate of uptake over the industrial era, and the relative roles of the ocean and terrestrial biosphere in anthropogenic CO2 sequestration. Here we address these questions by presenting an observationally based reconstruction of the spatially resolved, time-dependent history of anthropogenic carbon in the ocean over the industrial era. Our approach is based on the recognition that the transport of tracers in the ocean can be described by a Green’s function, which we estimate from tracer data using a maximum entropy deconvolution technique. Our results indicate that ocean uptake of anthropogenic CO2 has increased sharply since the 1950s, with a small decline in the rate of increase in the last few decades. We estimate the inventory and uptake rate of anthropogenic CO2 in 2008 at 140 ± 25 Pg C and 2.3 ± 0.6 Pg C yr-1, respectively. We find that the Southern Ocean is the primary conduit by which this CO2 enters the ocean (contributing over 40 per cent of the anthropogenic CO2 inventory in the ocean in 2008). Our results also suggest that the terrestrial biosphere was a source of CO2 until the 1940s, subsequently turning into a sink. Taken over the entire industrial period, and accounting for uncertainties, we estimate that the terrestrial biosphere has been anywhere from neutral to a net source of CO2, contributing up to half as much CO2 as has been taken up by the ocean over the same period.
Nature 462, 350 (2009). doi:10.1038/nature08496
Authors: Levi T. Morran, Michelle D. Parmenter & Patrick C. Phillips
The tendency of organisms to reproduce by cross-fertilization despite numerous disadvantages relative to self-fertilization is one of the oldest puzzles in evolutionary biology. For many species, the primary obstacle to the evolution of outcrossing is the cost of production of males, individuals that do not directly contribute offspring and thus diminish the long-term reproductive output of a lineage. Self-fertilizing (‘selfing’) organisms do not incur the cost of males and therefore should possess at least a twofold numerical advantage over most outcrossing organisms. Two competing explanations for the widespread prevalence of outcrossing in nature despite this inherent disadvantage are the avoidance of inbreeding depression generated by selfing and the ability of outcrossing populations to adapt more rapidly to environmental change. Here we show that outcrossing is favoured in populations of Caenorhabditis elegans subject to experimental evolution both under conditions of increased mutation rate and during adaptation to a novel environment. In general, fitness increased with increasing rates of outcrossing. Thus, each of the standard explanations for the maintenance of outcrossing are correct, and it is likely that outcrossing is the predominant mode of reproduction in most species because it is favoured under ecological conditions that are ubiquitous in natural environments.
Nature 462, 353 (2009). doi:10.1038/nature08573
Authors: Laura Lee Colgin, Tobias Denninger, Marianne Fyhn, Torkel Hafting, Tora Bonnevie, Ole Jensen, May-Britt Moser & Edvard I. Moser
Gamma oscillations are thought to transiently link distributed cell assemblies that are processing related information, a function that is probably important for network processes such as perception, attentional selection and memory. This ‘binding’ mechanism requires that spatially distributed cells fire together with millisecond range precision; however, it is not clear how such coordinated timing is achieved given that the frequency of gamma oscillations varies substantially across space and time, from ∼25 to almost 150 Hz. Here we show that gamma oscillations in the CA1 area of the hippocampus split into distinct fast and slow frequency components that differentially couple CA1 to inputs from the medial entorhinal cortex, an area that provides information about the animal’s current position, and CA3, a hippocampal subfield essential for storage of such information. Fast gamma oscillations in CA1 were synchronized with fast gamma in medial entorhinal cortex, and slow gamma oscillations in CA1 were coherent with slow gamma in CA3. Significant proportions of cells in medial entorhinal cortex and CA3 were phase-locked to fast and slow CA1 gamma waves, respectively. The two types of gamma occurred at different phases of the CA1 theta rhythm and mostly on different theta cycles. These results point to routeing of information as a possible function of gamma frequency variations in the brain and provide a mechanism for temporal segregation of potentially interfering information from different sources.
Nature 462, 358 (2009). doi:10.1038/nature08575
Authors: Rong Lu, Florian Markowetz, Richard D. Unwin, Jeffrey T. Leek, Edoardo M. Airoldi, Ben D. MacArthur, Alexander Lachmann, Roye Rozov, Avi Ma’ayan, Laurie A. Boyer, Olga G. Troyanskaya, Anthony D. Whetton & Ihor R. Lemischka
Molecular regulation of embryonic stem cell (ESC) fate involves a coordinated interaction between epigenetic, transcriptional and translational mechanisms. It is unclear how these different molecular regulatory mechanisms interact to regulate changes in stem cell fate. Here we present a dynamic systems-level study of cell fate change in murine ESCs following a well-defined perturbation. Global changes in histone acetylation, chromatin-bound RNA polymerase II, messenger RNA (mRNA), and nuclear protein levels were measured over 5 days after downregulation of Nanog, a key pluripotency regulator. Our data demonstrate how a single genetic perturbation leads to progressive widespread changes in several molecular regulatory layers, and provide a dynamic view of information flow in the epigenome, transcriptome and proteome. We observe that a large proportion of changes in nuclear protein levels are not accompanied by concordant changes in the expression of corresponding mRNAs, indicating important roles for translational and post-translational regulation of ESC fate. Gene-ontology analysis across different molecular layers indicates that although chromatin reconfiguration is important for altering cell fate, it is preceded by transcription-factor-mediated regulatory events. The temporal order of gene expression alterations shows the order of the regulatory network reconfiguration and offers further insight into the gene regulatory network. Our studies extend the conventional systems biology approach to include many molecular species, regulatory layers and temporal series, and underscore the complexity of the multilayer regulatory mechanisms responsible for changes in protein expression that determine stem cell fate.
Nature 462, 363 (2009). doi:10.1038/nature08559
Authors: Giorgos Gouridis, Spyridoula Karamanou, Ioannis Gelis, Charalampos G. Kalodimos & Anastassios Economou
Extra-cytoplasmic polypeptides are usually synthesized as ‘preproteins’ carrying amino-terminal, cleavable signal peptides and secreted across membranes by translocases. The main bacterial translocase comprises the SecYEG protein-conducting channel and the peripheral ATPase motor SecA. Most proteins destined for the periplasm and beyond are exported post-translationally by SecA. Preprotein targeting to SecA is thought to involve signal peptides and chaperones like SecB. Here we show that signal peptides have a new role beyond targeting: they are essential allosteric activators of the translocase. On docking on their binding groove on SecA, signal peptides act in trans to drive three successive states: first, ‘triggering’ that drives the translocase to a lower activation energy state; second, ‘trapping’ that engages non-native preprotein mature domains docked with high affinity on the secretion apparatus; and third, ‘secretion’ during which trapped mature domains undergo several turnovers of translocation in segments. A significant contribution by mature domains renders signal peptides less critical in bacterial secretory protein targeting than currently assumed. Rather, it is their function as allosteric activators of the translocase that renders signal peptides essential for protein secretion. A role for signal peptides and targeting sequences as allosteric activators may be universal in protein translocases.
Nature 462, 368 (2009). doi:10.1038/nature08560
Authors: Shiou-Ru Tzeng & Charalampos G. Kalodimos
Allosteric regulation is used as a very efficient mechanism to control protein activity in most biological processes, including signal transduction, metabolism, catalysis and gene regulation. Allosteric proteins can exist in several conformational states with distinct binding or enzymatic activity. Effectors are considered to function in a purely structural manner by selectively stabilizing a specific conformational state, thereby regulating protein activity. Here we show that allosteric proteins can be regulated predominantly by changes in their structural dynamics. We have used NMR spectroscopy and isothermal titration calorimetry to characterize cyclic AMP (cAMP) binding to the catabolite activator protein (CAP), a transcriptional activator that has been a prototype for understanding effector-mediated allosteric control of protein activity. cAMP switches CAP from the ‘off’ state (inactive), which binds DNA weakly and non-specifically, to the ‘on’ state (active), which binds DNA strongly and specifically. In contrast, cAMP binding to a single CAP mutant, CAP-S62F, fails to elicit the active conformation; yet, cAMP binding to CAP-S62F strongly activates the protein for DNA binding. NMR and thermodynamic analyses show that despite the fact that CAP-S62F-cAMP2 adopts the inactive conformation, its strong binding to DNA is driven by a large conformational entropy originating in enhanced protein motions induced by DNA binding. The results provide strong evidence that changes in protein motions may activate allosteric proteins that are otherwise structurally inactive.
Nature 462, 380 (2009). doi:10.1038/462380a
Author: Ruy José Válka Alves
On the dubious position of Aelfus in the evolutionary tree of mankind.