Nature

Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all disciplines of science, as well as News and Views, reviews, news, features, commentaries, web focuses and more, covering all branches of science and how science impacts upon all aspects of society and life.
  • Reconciliation of the carbon budget in the ocean’s twilight zone
    [Mar 2014]

    Reconciliation of the carbon budget in the ocean’s twilight zone

    Nature 507, 7493 (2014). doi:10.1038/nature13123

    Authors: Sarah L. C. Giering, Richard Sanders, Richard S. Lampitt, Thomas R. Anderson, Christian Tamburini, Mehdi Boutrif, Mikhail V. Zubkov, Chris M. Marsay, Stephanie A. Henson, Kevin Saw, Kathryn Cook & Daniel J. Mayor

    Photosynthesis in the surface ocean produces approximately 100 gigatonnes of organic carbon per year, of which 5 to 15 per cent is exported to the deep ocean. The rate at which the sinking carbon is converted into carbon dioxide by heterotrophic organisms at depth is important in controlling oceanic carbon storage. It remains uncertain, however, to what extent surface ocean carbon supply meets the demand of water-column biota; the discrepancy between known carbon sources and sinks is as much as two orders of magnitude. Here we present field measurements, respiration rate estimates and a steady-state model that allow us to balance carbon sources and sinks to within observational uncertainties at the Porcupine Abyssal Plain site in the eastern North Atlantic Ocean. We find that prokaryotes are responsible for 70 to 92 per cent of the estimated remineralization in the twilight zone (depths of 50 to 1,000 metres) despite the fact that much of the organic carbon is exported in the form of large, fast-sinking particles accessible to larger zooplankton. We suggest that this occurs because zooplankton fragment and ingest half of the fast-sinking particles, of which more than 30 per cent may be released as suspended and slowly sinking matter, stimulating the deep-ocean microbial loop. The synergy between microbes and zooplankton in the twilight zone is important to our understanding of the processes controlling the oceanic carbon sink.

    Categories: Journal Articles
  • Methane fluxes show consistent temperature dependence across microbial to ecosystem scales
    [Mar 2014]

    Methane fluxes show consistent temperature dependence across microbial to ecosystem scales

    Nature 507, 7493 (2014). doi:10.1038/nature13164

    Authors: Gabriel Yvon-Durocher, Andrew P. Allen, David Bastviken, Ralf Conrad, Cristian Gudasz, Annick St-Pierre, Nguyen Thanh-Duc & Paul A. del Giorgio

    Methane (CH4) is an important greenhouse gas because it has 25 times the global warming potential of carbon dioxide (CO2) by mass over a century. Recent calculations suggest that atmospheric CH4 emissions have been responsible for approximately 20% of Earth’s warming since pre-industrial times. Understanding how CH4 emissions from ecosystems will respond to expected increases in global temperature is therefore fundamental to predicting whether the carbon cycle will mitigate or accelerate climate change. Methanogenesis is the terminal step in the remineralization of organic matter and is carried out by strictly anaerobic Archaea. Like most other forms of metabolism, methanogenesis is temperature-dependent. However, it is not yet known how this physiological response combines with other biotic processes (for example, methanotrophy, substrate supply, microbial community composition) and abiotic processes (for example, water-table depth) to determine the temperature dependence of ecosystem-level CH4 emissions. It is also not known whether CH4 emissions at the ecosystem level have a fundamentally different temperature dependence than other key fluxes in the carbon cycle, such as photosynthesis and respiration. Here we use meta-analyses to show that seasonal variations in CH4 emissions from a wide range of ecosystems exhibit an average temperature dependence similar to that of CH4 production derived from pure cultures of methanogens and anaerobic microbial communities. This average temperature dependence (0.96 electron volts (eV)), which corresponds to a 57-fold increase between 0 and 30°C, is considerably higher than previously observed for respiration (approximately 0.65 eV) and photosynthesis (approximately 0.3 eV). As a result, we show that both the emission of CH4 and the ratio of CH4 to CO2 emissions increase markedly with seasonal increases in temperature. Our findings suggest that global warming may have a large impact on the relative contributions of CO2 and CH4 to total greenhouse gas emissions from aquatic ecosystems, terrestrial wetlands and rice paddies.

    Categories: Journal Articles
  • Coherent control of the waveforms of recoilless γ-ray photons
    [Mar 2014]

    Coherent control of the waveforms of recoilless γ-ray photons

    Nature 508, 7494 (2014). doi:10.1038/nature13018

    Authors: Farit Vagizov, Vladimir Antonov, Y. V. Radeonychev, R. N. Shakhmuratov & Olga Kocharovskaya

    The concepts and ideas of coherent, nonlinear and quantum optics have been extended to photon energies in the range of 10–100 kiloelectronvolts, corresponding to soft γ-ray radiation (the term used when the radiation is produced in nuclear transitions) or, equivalently, hard X-ray radiation (the term used when the radiation is produced by electron motion). The recent experimental achievements in this energy range include the demonstration of parametric down-conversion in the Langevin regime, electromagnetically induced transparency in a cavity, the collective Lamb shift, vacuum-assisted generation of atomic coherences and single-photon revival in nuclear absorbing multilayer structures. Also, realization of single-photon coherent storage and stimulated Raman adiabatic passage were recently proposed in this regime. More related work is discussed in a recent review. However, the number of tools for the coherent manipulation of interactions between γ-ray photons and nuclear ensembles remains limited. Here we suggest and implement an efficient method to control the waveforms of γ-ray photons coherently. In particular, we demonstrate the conversion of individual recoilless γ-ray photons into a coherent, ultrashort pulse train and into a double pulse. Our method is based on the resonant interaction of γ-ray photons with an ensemble of nuclei with a resonant transition frequency that is periodically modulated in time. The frequency modulation, which is achieved by a uniform vibration of the resonant absorber, owing to the Doppler effect, renders resonant absorption and dispersion both time dependent, allowing us to shape the waveforms of the incident γ-ray photons. We expect that this technique will lead to advances in the emerging fields of coherent and quantum γ-ray photon optics, providing a basis for the realization of γ-ray-photon/nuclear-ensemble interfaces and quantum interference effects at nuclear γ-ray transitions.

    Categories: Journal Articles
  • Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides
    [Mar 2014]

    Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides

    Nature 508, 7494 (2014). doi:10.1038/nature13110

    Authors: Kıvanç Birsoy, Richard Possemato, Franziska K. Lorbeer, Erol C. Bayraktar, Prathapan Thiru, Burcu Yucel, Tim Wang, Walter W. Chen, Clary B. Clish & David M. Sabatini

    As the concentrations of highly consumed nutrients, particularly glucose, are generally lower in tumours than in normal tissues, cancer cells must adapt their metabolism to the tumour microenvironment. A better understanding of these adaptations might reveal cancer cell liabilities that can be exploited for therapeutic benefit. Here we developed a continuous-flow culture apparatus (Nutrostat) for maintaining proliferating cells in low-nutrient media for long periods of time, and used it to undertake competitive proliferation assays on a pooled collection of barcoded cancer cell lines cultured in low-glucose conditions. Sensitivity to low glucose varies amongst cell lines, and an RNA interference (RNAi) screen pinpointed mitochondrial oxidative phosphorylation (OXPHOS) as the major pathway required for optimal proliferation in low glucose. We found that cell lines most sensitive to low glucose are defective in the OXPHOS upregulation that is normally caused by glucose limitation as a result of either mitochondrial DNA (mtDNA) mutations in complex I genes or impaired glucose utilization. These defects predict sensitivity to biguanides, antidiabetic drugs that inhibit OXPHOS, when cancer cells are grown in low glucose or as tumour xenografts. Notably, the biguanide sensitivity of cancer cells with mtDNA mutations was reversed by ectopic expression of yeast NDI1, a ubiquinone oxidoreductase that allows bypass of complex I function. Thus, we conclude that mtDNA mutations and impaired glucose utilization are potential biomarkers for identifying tumours with increased sensitivity to OXPHOS inhibitors.

    Categories: Journal Articles
  • Low-temperature physics: Chaos in the cold
    [Mar 2014]

    Low-temperature physics: Chaos in the cold

    Nature 507, 7493 (2014). doi:10.1038/nature13211

    Authors: Paul S. Julienne

    A marriage between theory and experiment has shown that ultracold erbium atoms trapped with laser light and subjected to a magnetic field undergo collisions that are characterized by quantum chaos. See Letter p.475

    Categories: Journal Articles
  • Quantum chaos in ultracold collisions of gas-phase erbium atoms
    [Mar 2014]

    Quantum chaos in ultracold collisions of gas-phase erbium atoms

    Nature 507, 7493 (2014). doi:10.1038/nature13137

    Authors: Albert Frisch, Michael Mark, Kiyotaka Aikawa, Francesca Ferlaino, John L. Bohn, Constantinos Makrides, Alexander Petrov & Svetlana Kotochigova

    Atomic and molecular samples reduced to temperatures below one microkelvin, yet still in the gas phase, afford unprecedented energy resolution in probing and manipulating the interactions between their constituent particles. As a result of this resolution, atoms can be made to scatter resonantly on demand, through the precise control of a magnetic field. For simple atoms, such as alkalis, scattering resonances are extremely well characterized. However, ultracold physics is now poised to enter a new regime, where much more complex species can be cooled and studied, including magnetic lanthanide atoms and even molecules. For molecules, it has been speculated that a dense set of resonances in ultracold collision cross-sections will probably exhibit essentially random fluctuations, much as the observed energy spectra of nuclear scattering do. According to the Bohigas–Giannoni–Schmit conjecture, such fluctuations would imply chaotic dynamics of the underlying classical motion driving the collision. This would necessitate new ways of looking at the fundamental interactions in ultracold atomic and molecular systems, as well as perhaps new chaos-driven states of ultracold matter. Here we describe the experimental demonstration that random spectra are indeed found at ultralow temperatures. In the experiment, an ultracold gas of erbium atoms is shown to exhibit many Fano–Feshbach resonances, of the order of three per gauss for bosons. Analysis of their statistics verifies that their distribution of nearest-neighbour spacings is what one would expect from random matrix theory. The density and statistics of these resonances are explained by fully quantum mechanical scattering calculations that locate their origin in the anisotropy of the atoms’ potential energy surface. Our results therefore reveal chaotic behaviour in the native interaction between ultracold atoms.

    Categories: Journal Articles
  • Efficient rotational cooling of Coulomb-crystallized molecular ions by a helium buffer gas
    [Mar 2014]

    Efficient rotational cooling of Coulomb-crystallized molecular ions by a helium buffer gas

    Nature 508, 7494 (2014). doi:10.1038/nature12996

    Authors: A. K. Hansen, O. O. Versolato, Ł. Kłosowski, S. B. Kristensen, A. Gingell, M. Schwarz, A. Windberger, J. Ullrich, J. R. Crespo López-Urrutia & M. Drewsen

    The preparation of cold molecules is of great importance in many contexts, such as fundamental physics investigations, high-resolution spectroscopy of complex molecules, cold chemistry and astrochemistry. One versatile and widely applied method to cool molecules is helium buffer-gas cooling in either a supersonic beam expansion or a cryogenic trap environment. Another more recent method applicable to trapped molecular ions relies on sympathetic translational cooling, through collisional interactions with co-trapped, laser-cooled atomic ions, into spatially ordered structures called Coulomb crystals, combined with laser-controlled internal-state preparation. Here we present experimental results on helium buffer-gas cooling of the rotational degrees of freedom of MgH+ molecular ions, which have been trapped and sympathetically cooled in a cryogenic linear radio-frequency quadrupole trap. With helium collision rates of only about ten per second—that is, four to five orders of magnitude lower than in typical buffer-gas cooling settings—we have cooled a single molecular ion to a rotational temperature of  kelvin, the lowest such temperature so far measured. In addition, by varying the shape of, or the number of atomic and molecular ions in, larger Coulomb crystals, or both, we have tuned the effective rotational temperature from about 7 kelvin to about 60 kelvin by changing the translational micromotion energy of the ions. The extremely low helium collision rate may allow for sympathetic sideband cooling of single molecular ions, and eventually make quantum-logic spectroscopy of buffer-gas-cooled molecular ions feasible. Furthermore, application of the present cooling scheme to complex molecular ions should enable single- or few-state manipulations of individual molecules of biological interest.

    Categories: Journal Articles
  • Mechanism of Tc toxin action revealed in molecular detail
    [Feb 2014]

    Mechanism of Tc toxin action revealed in molecular detail

    Nature 508, 7494 (2014). doi:10.1038/nature13015

    Authors: Dominic Meusch, Christos Gatsogiannis, Rouslan G. Efremov, Alexander E. Lang, Oliver Hofnagel, Ingrid R. Vetter, Klaus Aktories & Stefan Raunser

    Tripartite Tc toxin complexes of bacterial pathogens perforate the host membrane and translocate toxic enzymes into the host cell, including in humans. The underlying mechanism is complex but poorly understood. Here we report the first, to our knowledge, high-resolution structures of a TcA subunit in

    Categories: Journal Articles
  • The hippocampal CA2 region is essential for social memory
    [Feb 2014]

    The hippocampal CA2 region is essential for social memory

    Nature 508, 7494 (2014). doi:10.1038/nature13028

    Authors: Frederick L. Hitti & Steven A. Siegelbaum

    The hippocampus is critical for encoding declarative memory, our repository of knowledge of who, what, where and when. Mnemonic information is processed in the hippocampus through several parallel routes involving distinct subregions. In the classic trisynaptic pathway, information proceeds from entorhinal cortex (EC) to dentate gyrus to CA3 and then to CA1, the main hippocampal output. Genetic lesions of EC (ref. 3) and hippocampal dentate gyrus (ref. 4), CA3 (ref. 5) and CA1 (ref. 6) regions have revealed their distinct functions in learning and memory. In contrast, little is known about the role of CA2, a relatively small area interposed between CA3 and CA1 that forms the nexus of a powerful disynaptic circuit linking EC input with CA1 output. Here we report a novel transgenic mouse line that enabled us to selectively examine the synaptic connections and behavioural role of the CA2 region in adult mice. Genetically targeted inactivation of CA2 pyramidal neurons caused a pronounced loss of social memory—the ability of an animal to remember a conspecific—with no change in sociability or several other hippocampus-dependent behaviours, including spatial and contextual memory. These behavioural and anatomical results thus reveal CA2 as a critical hub of sociocognitive memory processing.

    Categories: Journal Articles
  • Mouse liver repopulation with hepatocytes generated from human fibroblasts
    [Feb 2014]

    Mouse liver repopulation with hepatocytes generated from human fibroblasts

    Nature 508, 7494 (2014). doi:10.1038/nature13020

    Authors: Saiyong Zhu, Milad Rezvani, Jack Harbell, Aras N. Mattis, Alan R. Wolfe, Leslie Z. Benet, Holger Willenbring & Sheng Ding

    Human induced pluripotent stem cells (iPSCs) have the capability of revolutionizing research and therapy of liver diseases by providing a source of hepatocytes for autologous cell therapy and disease modelling. However, despite progress in advancing the differentiation of iPSCs into hepatocytes (iPSC-Heps) in vitro, cells that replicate the ability of human primary adult hepatocytes (aHeps) to proliferate extensively in vivo have not been reported. This deficiency has hampered efforts to recreate human liver diseases in mice, and has cast doubt on the potential of iPSC-Heps for liver cell therapy. The reason is that extensive post-transplant expansion is needed to establish and sustain a therapeutically effective liver cell mass in patients, a lesson learned from clinical trials of aHep transplantation. Here, as a solution to this problem, we report the generation of human fibroblast-derived hepatocytes that can repopulate mouse livers. Unlike current protocols for deriving hepatocytes from human fibroblasts, ours did not generate iPSCs but cut short reprogramming to pluripotency to generate an induced multipotent progenitor cell (iMPC) state from which endoderm progenitor cells and subsequently hepatocytes (iMPC-Heps) could be efficiently differentiated. For this purpose we identified small molecules that aided endoderm and hepatocyte differentiation without compromising proliferation. After transplantation into an immune-deficient mouse model of human liver failure, iMPC-Heps proliferated extensively and acquired levels of hepatocyte function similar to those of aHeps. Unfractionated iMPC-Heps did not form tumours, most probably because they never entered a pluripotent state. Our results establish the feasibility of significant liver repopulation of mice with human hepatocytes generated in vitro, which removes a long-standing roadblock on the path to autologous liver cell therapy.

    Categories: Journal Articles
  • The E3 ligase Cbl-b and TAM receptors regulate cancer metastasis via natural killer cells
    [Feb 2014]

    The E3 ligase Cbl-b and TAM receptors regulate cancer metastasis via natural killer cells

    Nature 507, 7493 (2014). doi:10.1038/nature12998

    Authors: Magdalena Paolino, Axel Choidas, Stephanie Wallner, Blanka Pranjic, Iris Uribesalgo, Stefanie Loeser, Amanda M. Jamieson, Wallace Y. Langdon, Fumiyo Ikeda, Juan Pablo Fededa, Shane J. Cronin, Roberto Nitsch, Carsten Schultz-Fademrecht, Jan Eickhoff, Sascha Menninger, Anke Unger, Robert Torka, Thomas Gruber, Reinhard Hinterleitner, Gottfried Baier, Dominik Wolf, Axel Ullrich, Bert M. Klebl & Josef M. Penninger

    Tumour metastasis is the primary cause of mortality in cancer patients and remains the key challenge for cancer therapy. New therapeutic approaches to block inhibitory pathways of the immune system have renewed hopes for the utility of such therapies. Here we show that genetic deletion of the E3 ubiquitin ligase Cbl-b (casitas B-lineage lymphoma-b) or targeted inactivation of its E3 ligase activity licenses natural killer (NK) cells to spontaneously reject metastatic tumours. The TAM tyrosine kinase receptors Tyro3, Axl and Mer (also known as Mertk) were identified as ubiquitylation substrates for Cbl-b. Treatment of wild-type NK cells with a newly developed small molecule TAM kinase inhibitor conferred therapeutic potential, efficiently enhancing anti-metastatic NK cell activity in vivo. Oral or intraperitoneal administration using this TAM inhibitor markedly reduced murine mammary cancer and melanoma metastases dependent on NK cells. We further report that the anticoagulant warfarin exerts anti-metastatic activity in mice via Cbl-b/TAM receptors in NK cells, providing a molecular explanation for a 50-year-old puzzle in cancer biology. This novel TAM/Cbl-b inhibitory pathway shows that it might be possible to develop a ‘pill’ that awakens the innate immune system to kill cancer metastases.

    Categories: Journal Articles
  • Structure-based programming of lymph-node targeting in molecular vaccines
    [Feb 2014]

    Structure-based programming of lymph-node targeting in molecular vaccines

    Nature 507, 7493 (2014). doi:10.1038/nature12978

    Authors: Haipeng Liu, Kelly D. Moynihan, Yiran Zheng, Gregory L. Szeto, Adrienne V. Li, Bonnie Huang, Debra S. Van Egeren, Clara Park & Darrell J. Irvine

    In cancer patients, visual identification of sentinel lymph nodes (LNs) is achieved by the injection of dyes that bind avidly to endogenous albumin, targeting these compounds to LNs, where they are efficiently filtered by resident phagocytes. Here we translate this ‘albumin hitchhiking’ approach to molecular vaccines, through the synthesis of amphiphiles (amph-vaccines) comprising an antigen or adjuvant cargo linked to a lipophilic albumin-binding tail by a solubility-promoting polar polymer chain. Administration of structurally optimized CpG-DNA/peptide amph-vaccines in mice resulted in marked increases in LN accumulation and decreased systemic dissemination relative to their parent compounds, leading to 30-fold increases in T-cell priming and enhanced anti-tumour efficacy while greatly reducing systemic toxicity. Amph-vaccines provide a simple, broadly applicable strategy to simultaneously increase the potency and safety of subunit vaccines.

    Categories: Journal Articles
  • Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans
    [Feb 2014]

    Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans

    Nature 508, 7494 (2014). doi:10.1038/nature13012

    Authors: En-Zhi Shen, Chun-Qing Song, Yuan Lin, Wen-Hong Zhang, Pei-Fang Su, Wen-Yuan Liu, Pan Zhang, Jiejia Xu, Na Lin, Cheng Zhan, Xianhua Wang, Yu Shyr, Heping Cheng & Meng-Qiu Dong

    It has been theorized for decades that mitochondria act as the biological clock of ageing, but the evidence is incomplete. Here we show a strong coupling between mitochondrial function and ageing by in vivo visualization of the mitochondrial flash (mitoflash), a frequency-coded optical readout reflecting free-radical production and energy metabolism at the single-mitochondrion level. Mitoflash activity in Caenorhabditis elegans pharyngeal muscles peaked on adult day 3 during active reproduction and on day 9 when animals started to die off. A plethora of genetic mutations and environmental factors inversely modified the lifespan and the day-3 mitoflash frequency. Even within an isogenic population, the day-3 mitoflash frequency was negatively correlated with the lifespan of individual animals. Furthermore, enhanced activity of the glyoxylate cycle contributed to the decreased day-3 mitoflash frequency and the longevity of daf-2 mutant animals. These results demonstrate that the day-3 mitoflash frequency is a powerful predictor of C. elegans lifespan across genetic, environmental and stochastic factors. They also support the notion that the rate of ageing, although adjustable in later life, has been set to a considerable degree before reproduction ceases.

    Categories: Journal Articles
  • A primitive placoderm sheds light on the origin of the jawed vertebrate face
    [Feb 2014]

    A primitive placoderm sheds light on the origin of the jawed vertebrate face

    Nature 507, 7493 (2014). doi:10.1038/nature12980

    Authors: Vincent Dupret, Sophie Sanchez, Daniel Goujet, Paul Tafforeau & Per E. Ahlberg

    Extant vertebrates form two clades, the jawless Cyclostomata (lampreys and hagfishes) and the jawed Gnathostomata (all other vertebrates), with contrasting facial architectures. These arise during development from just a few key differences in the growth patterns of the cranial primordia: notably, the nasal sacs and hypophysis originate from a single placode in cyclostomes but from separate placodes in gnathostomes, and infraoptic ectomesenchyme migrates forward either side of the single placode in cyclostomes but between the placodes in gnathostomes. Fossil stem gnathostomes preserve cranial anatomies rich in landmarks that provide proxies for developmental processes and allow the transition from jawless to jawed vertebrates to be broken down into evolutionary steps. Here we use propagation phase contrast synchrotron microtomography to image the cranial anatomy of the primitive placoderm (jawed stem gnathostome) Romundina, and show that it combines jawed vertebrate architecture with cranial and cerebral proportions resembling those of cyclostomes and the galeaspid (jawless stem gnathostome) Shuyu. This combination seems to be primitive for jawed vertebrates, and suggests a decoupling between ectomesenchymal growth trajectory, ectomesenchymal proliferation, and cerebral shape change during the origin of gnathostomes.

    Categories: Journal Articles
  • Geographical limits to species-range shifts are suggested by climate velocity
    [Feb 2014]

    Geographical limits to species-range shifts are suggested by climate velocity

    Nature 507, 7493 (2014). doi:10.1038/nature12976

    Authors: Michael T. Burrows, David S. Schoeman, Anthony J. Richardson, Jorge García Molinos, Ary Hoffmann, Lauren B. Buckley, Pippa J. Moore, Christopher J. Brown, John F. Bruno, Carlos M. Duarte, Benjamin S. Halpern, Ove Hoegh-Guldberg, Carrie V. Kappel, Wolfgang Kiessling, Mary I. O’Connor, John M. Pandolfi, Camille Parmesan, William J. Sydeman, Simon Ferrier, Kristen J. Williams & Elvira S. Poloczanska

    The reorganization of patterns of species diversity driven by anthropogenic climate change, and the consequences for humans, are not yet fully understood or appreciated. Nevertheless, changes in climate conditions are useful for predicting shifts in species distributions at global and local scales. Here we use the velocity of climate change to derive spatial trajectories for climatic niches from 1960 to 2009 (ref. 7) and from 2006 to 2100, and use the properties of these trajectories to infer changes in species distributions. Coastlines act as barriers and locally cooler areas act as attractors for trajectories, creating source and sink areas for local climatic conditions. Climate source areas indicate where locally novel conditions are not connected to areas where similar climates previously occurred, and are thereby inaccessible to climate migrants tracking isotherms: 16% of global surface area for 1960 to 2009, and 34% of ocean for the ‘business as usual’ climate scenario (representative concentration pathway (RCP) 8.5) representing continued use of fossil fuels without mitigation. Climate sink areas are where climate conditions locally disappear, potentially blocking the movement of climate migrants. Sink areas comprise 1.0% of ocean area and 3.6% of land and are prevalent on coasts and high ground. Using this approach to infer shifts in species distributions gives global and regional maps of the expected direction and rate of shifts of climate migrants, and suggests areas of potential loss of species richness.

    Categories: Journal Articles
  • Poly(A)-tail profiling reveals an embryonic switch in translational control
    [Jan 2014]

    Poly(A)-tail profiling reveals an embryonic switch in translational control

    Nature 508, 7494 (2014). doi:10.1038/nature13007

    Authors: Alexander O. Subtelny, Stephen W. Eichhorn, Grace R. Chen, Hazel Sive & David P. Bartel

    Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of

    Categories: Journal Articles
  • Transcription factor achaete-scute homologue 2 initiates follicular T-helper-cell development
    [Jan 2014]

    Transcription factor achaete-scute homologue 2 initiates follicular T-helper-cell development

    Nature 507, 7493 (2014). doi:10.1038/nature12910

    Authors: Xindong Liu, Xin Chen, Bo Zhong, Aibo Wang, Xiaohu Wang, Fuliang Chu, Roza I. Nurieva, Xiaowei Yan, Ping Chen, Laurens G. van der Flier, Hiroko Nakatsukasa, Sattva S. Neelapu, Wanjun Chen, Hans Clevers, Qiang Tian, Hai Qi, Lai Wei & Chen Dong

    In immune responses, activated T cells migrate to B-cell follicles and develop into follicular T-helper (TFH) cells, a recently identified subset of CD4+ T cells specialized in providing help to B lymphocytes in the induction of germinal centres. Although Bcl6 has been shown to be essential in TFH-cell function, it may not regulate the initial migration of T cells or the induction of the TFH program, as exemplified by C-X-C chemokine receptor type 5 (CXCR5) upregulation. Here we show that expression of achaete-scute homologue 2 (Ascl2)—a basic helix–loop–helix (bHLH) transcription factor—is selectively upregulated in TFH cells. Ectopic expression of Ascl2 upregulates CXCR5 but not Bcl6, and downregulates C-C chemokine receptor 7 (CCR7) expression in T cells in vitro, as well as accelerating T-cell migration to the follicles and TFH-cell development in vivo in mice. Genome-wide analysis indicates that Ascl2 directly regulates TFH-related genes whereas it inhibits expression of T-helper cell 1 (TH1) and TH17 signature genes. Acute deletion of Ascl2, as well as blockade of its function with the Id3 protein in CD4+ T cells, results in impaired TFH-cell development and germinal centre response. Conversely, mutation of Id3, known to cause antibody-mediated autoimmunity, greatly enhances TFH-cell generation. Thus, Ascl2 directly initiates TFH-cell development.

    Categories: Journal Articles
  • Power to the people
    [Jan 2014]

    Power to the people

    Nature 505, 7483 (2014). doi:10.1038/505261a

    A planned database collating medical information for England’s population is a laudable exercise, with huge potential for research. But people’s right to opt out has been greatly downplayed.

    Categories: Journal Articles
  • Cool heads needed
    [Jan 2014]

    Cool heads needed

    Nature 505, 7483 (2014). doi:10.1038/505261b

    As cold weather rages, it is easy to forget the difference between weather and climate.

    Categories: Journal Articles
  • V is for vortex
    [Jan 2014]

    V is for vortex

    Nature 505, 7483 (2014). doi:10.1038/505262a

    An endangered species helps scientists to learn why migrating birds fly in a familiar formation.

    Categories: Journal Articles