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| | | Special: 2013 Review of the Year | | | | Shutdowns, lethal viruses, typhoons and meteorites — much of this year's science news seemed to come straight from the set of a Hollywood disaster movie. But there were plenty of feel-good moments, too. Space exploration hit a new high, cash poured in to investigate that most cryptic of human organs, the brain, and huge leaps were made in stem-cell therapies and the treatment of HIV. Here, captured in soundbites, statistics and summaries, is everything you need to know about the science that mattered in 2013. ▼ more | | | | | | | Specials - Outlook: Cancer Immunotherapy | | | | A groundswell of research on the immune system is yielding a deeper understanding of how cancer progresses and offering new ways to stop it. As a result of these efforts, a range of cancer therapies are under development that work by turning our own immune cells against tumours. ▼ more | | | | | | | | | Inconsistency in large pharmacogenomic studies | Two large-scale datasets recently determined the sensitivity of many cancer cell lines to drugs, and integrated the data with genomic features, such as mutations and gene expression profiles. This study compares the two studies and finds that while the gene expression data are largely concordant between them, drug sensitivity measures and subsequently their association with genomic features are discordant. The authors call for standardization of drug response measurements as a step towards personalized cancer medicine. | | | | | | | | | | | | | | | | Rapid local acceleration of relativistic radiation-belt electrons by magnetospheric chorus | The magnetic storm of 9 October 2012 has been analysed in detail using the array of instruments onboard NASA's two Van Allen Probes, launched in 2012 to study Earth's magnetosphere. The nature of the force that accelerates electrons trapped in Earth's radiation belts has been a topic of much debate. Data from Van Allen probe A, together with modelling studies, identify the likely source of accelerating energy as chorus scattering, an effect caused locally by structured wave formations. | | | | | | | | | Attention to eyes is present but in decline in 2–6-month-old infants later diagnosed with autism | Infants who go on to develop autism spectrum disorders (ASDs) may exhibit a decline in eye contact within the first 2 to 6 months of life. This finding emerges from a study of 110 infants, 13 of whom were later diagnosed as having ASD. The results may represent some of the earliest manifestations of autism symptoms, but need to be replicated in a larger independent sample before being considered a potential diagnostic marker. | | | | | | | | | | In this week's bumper Christmas podcast: comedian Andy Zaltzman joins the Nature Podcast team to talk pickles, Neanderthals, and the biggest science stories of 2013. In our latest video feature Carley Rutledge is taking part in a trial for a cancer vaccine. She talks about her experience, while her doctors explain how the personalised vaccine works. | | | | | | |
| | | | | | | | | | | | | 365 days: 2013 in review ▶ | | | From the US shutdown to breakthroughs in stem-cell therapies, the past 12 months have seen fluctuating fortunes for science. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| | | | | | | | | | | | | | | | Stem-cell fiasco must be stopped ▶ | | | In the public interest, the Italian health minister should resolve the ongoing uncertainty over a government trial of a controversial therapy. | | | | | | | | Sink or swim? ▶ | | | A rethink on monitoring land-use change is needed to estimate effects on global warming. | | | | | | | | Futures redux ▶ | | | Can you tell a sci-fi tale in just 200 characters? Then the Nature Futures competition is for you. | | | | | | | | | | | | | | | | | Seven days: 13–19 December 2013 ▶ | | | The week in science: China lands rover on the Moon, Israel joins CERN, and the number of animals used for scientific purposes in the European Union falls. | | | | | | | | | | | | | | | | | Quandary over Soviet croplands ▶ | | | Researchers ponder whether Eastern Europe's large areas of abandoned land should be replanted or left as a carbon sink. | | | | | | | | | | | | | | | | | Chemistry: A festive ferment ▶ | | | Harold McGee surveys a seething array of microbially transformed treats — from beard beer and grasshopper sauce to extreme herring and armpit cheese. | | | | | | | | | | | | | | | | | | | | | | | |
| | | nature.com webcasts Macmillan Science Communication presents a custom webcast: Pioneering advances in the next generation sequencing clinical research workflow. Wednesday December 18th at 8am PST / 11am EST / 4pm GMT / 5pm CET Sponsored by: | | | | | |
| | | | | | | | | | | | | | | | | | | | | | | | | CNVs conferring risk of autism or schizophrenia affect cognition in controls ▶ | | | Hreinn Stefansson, Andreas Meyer-Lindenberg, Stacy Steinberg et al. | | | Rare copy-number variants (CNVs) conferring risk of schizophrenia or autism affect fecundity of carriers in Iceland, and carriers of these CNVs who do not suffer disease or have not been diagnosed with intellectual disability show phenotypes in brain structure and cognitive abilities between those of non-carrier controls and patients with schizophrenia. | | | | | | | | A molecular marker of artemisinin-resistant Plasmodium falciparum malaria ▶ | | | Frédéric Ariey, Benoit Witkowski, Chanaki Amaratunga et al. | | | A molecular marker is required to monitor artemisinin-resistant Plasmodium falciparum parasites in southeast Asia; here mutations in K13-propeller are associated with artemisinin resistance in vitro and in vivo and also cluster in Cambodian provinces where resistance is prevalent. | | | | | | | | The complete genome sequence of a Neanderthal from the Altai Mountains ▶ | | | Kay Prüfer, Fernando Racimo, Nick Patterson et al. | | | A complete genome sequence is presented of a female Neanderthal from Siberia, providing information about interbreeding between close relatives and uncovering gene flow events among Neanderthals, Denisovans and early modern humans, as well as establishing substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans. | | | | | | | | | | | Cytokinin signalling inhibitory fields provide robustness to phyllotaxis ▶ | | | Fabrice Besnard, Yassin Refahi, Valérie Morin et al. | | | The regularly spaced arrangement of plant organs around the stem known as phyllotaxis depends on auxin-based inhibitory fields; this study identifies another hormone-based inhibitory field downstream of auxin which is generated by movement of the cytokinin signalling inhibitor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 and regulates the periodicity of organ production. | | | | | | | | | | | | | | | | | The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) OPEN ▶ | | | Juliane C. Dohm, André E. Minoche, Daniela Holtgräwe et al. | | | A full genome sequence is presented of sugar beet Beta vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions. | | | | | | | | | | | Genome-wide dissection of the quorum sensing signalling pathway in Trypanosoma brucei ▶ | | | Binny M. Mony, Paula MacGregor, Alasdair Ivens et al. | | | Here a genome-wide RNAi library screen is used to identify components of the signalling pathway that allow transformation of Trypanosoma brucei spp., the protozoan parasite responsible for important human and livestock diseases in sub-Saharan Africa, from proliferative slender forms to arrested stumpy forms which are transmitted to the tsetse fly vector. | | | | | | | | RNA viruses can hijack vertebrate microRNAs to suppress innate immunity ▶ | | | Derek W. Trobaugh, Christina L. Gardner, Chengqun Sun et al. | | | Here it is proposed that RNA viruses can adapt to use the antiviral properties of microRNAs to limit viral replication and suppress innate immunity in particular cell types, and this restriction can lead to exacerbation of disease severity. | | | | | | | | C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells ▶ | | | Bruno Di Stefano, Jose Luis Sardina, Chris van Oevelen et al. | | | A pulse of C/EBPα followed by overexpression of the transcription factors Oct4, Sox2, Klf4 and Myc leads to fast and very efficient reprogramming of B cell precursors to induced pluripotent stem cells; C/EBPα facilitates transient chromatin accessibility and accelerates expression of pluripotency genes through a mechanism that involves activation of the Tet2 enzyme. | | | | | | | | Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo ▶ | | | Silvi Rouskin, Meghan Zubradt, Stefan Washietl et al. | | | Understanding how RNA structure influences its function has been hampered by a lack of approaches that can accurately quantify RNA structure in vivo; here, RNA structure is revealed on a global scale and with nucleotide-level resolution, showing that there is less structure within cells than expected from in vitro and in silico analyses. | | | | | | | | | | | Astrocytes mediate synapse elimination through MEGF10 and MERTK pathways ▶ | | | Won-Suk Chung, Laura E. Clarke, Gordon X. Wang et al. | | | This study describes comprehensive synaptic engulfment by astrocytes, mediating synapse elimination in an activity-dependent manner; this elimination process involves the MEGF10 and MERTK phagocytic pathways and persists into adulthood, with mutant mice that lack these pathways in astrocytes exhibiting a failure to refine retinogeniculate connections during development. | | | | | | | | DWARF 53 acts as a repressor of strigolactone signalling in rice ▶ | | | Liang Jiang, Xue Liu, Guosheng Xiong et al. | | | Strigolactones (SLs), key regulators of plant growth, are believed to mediate their responses through a proposed receptor (D14) that interacts with an F-box protein (D3) to form a D14–SCFD3 protein complex; here the perception of SLs by the D14–SCFD3 complex and the control of gene expression are linked by the finding that DWARF 53, a repressor protein of SL signalling, interacts with the D14–SCFD3 complex and is ubiquitinated and degraded in a SL-dependent manner. | | | | | | | | D14–SCFD3-dependent degradation of D53 regulates strigolactone signalling ▶ | | | Feng Zhou, Qibing Lin, Lihong Zhu et al. | | | Strigolactones (SLs), key regulators of plant growth, are believed to mediate their responses through a proposed receptor (D14) that interacts with an F-box protein (D3) to form a D14–SCFD3 protein complex; here the perception of SLs by the D14–SCFD3 complex and the control of gene expression are linked by the finding that DWARF 53, a repressor protein of SL function, interacts with the D14–SCFD3 complex and is ubiquitinated and degraded in a SL-dependent manner. | | | | | | | | Attention to eyes is present but in decline in 2–6-month-old infants later diagnosed with autism ▶ | | | Warren Jones, Ami Klin | | | A prospective longitudinal study identifies the earliest known indicator of social disability in human infancy: decline in attention to others' eyes in infants who are later diagnosed with autism; the decline is evident already within the first 2 to 6 months of life, which reveals the early unfolding of the disorder but also offers a promising opportunity for the future of early intervention. | | | | | | | | Dysfunctional nitric oxide signalling increases risk of myocardial infarction ▶ | | | Jeanette Erdmann, Klaus Stark, Ulrike B. Esslinger et al. | | | Two private, heterozygous mutations in two functionally related genes, GUCY1A3 and CCT7, are identified in an extended family with myocardial infarction; these genes encode proteins that work together to inhibit platelet activation after nitric oxide stimulation, suggesting a link between impaired nitric oxide signalling and myocardial infarction risk. | | | | | | | | | | | | | | | | | Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation ▶ | | | Nicholas Arpaia, Clarissa Campbell, Xiying Fan et al. | | | In mice, provision of butyrate—a short-chain fatty acid produced by commensal microorganisms during starch fermentation—facilitates extrathymic generation and differentiation of Foxp3+ regulatory T cells, demonstrating that metabolic by-products are sensed by cells of the immune system and affect the balance between pro- and anti-inflammatory cells. | | | | | | | | | | | Role of Tet1 in erasure of genomic imprinting ▶ | | | Shinpei Yamaguchi, Li Shen, Yuting Liu et al. | | | This study establishes an important role for the enzyme Tet1 in erasing genomic imprinting in vivo — mice with a knockout of paternal Tet1 give rise to progeny with imprinting defects and associated growth and development defects, which leads to early embryonic lethality; furthermore, analysis of the DNA methylation dynamics in reprogramming primordial germ cells (PGCs) suggests that Tet1 is required at a late stage of the reprogramming process, in the second wave of DNA demethylation in PGCs. | | | | | | | | High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation ▶ | | | Matthew D. Simon, Stefan F. Pinter, Rui Fang et al. | | | During mammalian X-chromosome inactivation, the Xist long noncoding RNA coats the future inactive X chromosome and recruits polycomb repressive complex 2 to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear; here high-resolution maps of Xist binding sites across the X chromosome are generated and show that Xist does not spread across the inactive X chromosome uniformly but in two steps, initially targeting gene-rich islands before later spreading to intervening gene-poor domains. | | | | | | | | Inconsistency in large pharmacogenomic studies ▶ | | | Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai Juul Birkbak et al. | | | This Analysis compares two large-scale pharmacogenomic data sets that catalogued the sensitivity of a large number of cancer cell lines to approved and potential drugs, and finds that whereas the gene expression data are largely concordant between the two studies, the reported drug sensitivity measures and subsequently their association with genomic features are highly discordant. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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| | | | | | | | | | | | | | | | Asymmetric synthesis from terminal alkenes by cascades of diboration and cross-coupling ▶ | | | Scott N. Mlynarski, Christopher H. Schuster, James P. Morken | | | A single-flask, catalytic enantioselective conversion of terminal alkenes into a number of chiral products is described: this tandem diboration/cross-coupling reaction works on a broad range of substrates, requires small amounts of commercially available catalysts, and provides products in high yield and high selectivity. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Dislocations in bilayer graphene ▶ | | | Benjamin Butz, Christian Dolle, Florian Niekiel et al. | | | Basal-plane dislocations, identified as fundamental defects in bilayer graphene by transmission electron microscopy and atomistic simulations, reveal striking size effects, most notably a pronounced buckling of the graphene membrane, which drastically alters the strain state and is of key importance for the material's mechanical and electronic properties. | | | | | | | | Asymmetric synthesis from terminal alkenes by cascades of diboration and cross-coupling ▶ | | | Scott N. Mlynarski, Christopher H. Schuster, James P. Morken | | | A single-flask, catalytic enantioselective conversion of terminal alkenes into a number of chiral products is described: this tandem diboration/cross-coupling reaction works on a broad range of substrates, requires small amounts of commercially available catalysts, and provides products in high yield and high selectivity. | | | | | | | | | | | Rapid local acceleration of relativistic radiation-belt electrons by magnetospheric chorus ▶ | | | R. M. Thorne, W. Li, B. Ni et al. | | | High-resolution measurements of electrons obtained by satellite during the geomagnetic storm of 9 October 2012 together with a data-driven global wave model are analysed to show that scattering by a magnetospheric electromagnetic emission, known as 'chorus', can explain the temporal evolution of the observed increase in relativistic electron flux. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Increasing subtropical North Pacific Ocean nitrogen fixation since the Little Ice Age ▶ | | | Owen A. Sherwood, Thomas P. Guilderson, Fabian C. Batista et al. | | | Despite a reduction in nutrient supply to the North Pacific subtropical gyre, it has undergone a recent increase in nitrogen fixation, and here records of nitrogen isotopes preserved in Hawaiian corals show that this is a trend that could be linked to climate change since the end of the Little Ice Age. | | | | | | | | Amazon River carbon dioxide outgassing fuelled by wetlands ▶ | | | Gwenaël Abril, Jean-Michel Martinez, L. Felipe Artigas et al. | | | Global carbon budgets reveal that inland waters emit substantial amounts of carbon, which is believed to originate from the terrestrial biosphere; however, here the carbon emitted from the Amazon River system is shown to originate from temporary wetlands in the flooded area itself, such as flooded forests. | | | | | | | | | | | Worldwide acceleration of mountain erosion under a cooling climate ▶ | | | Frédéric Herman, Diane Seward, Pierre G. Valla et al. | | | To establish what effect the Late Cenozoic cooling climate shift might have had on global erosion, inverse modelling of thermochronometric ages is used to show that erosion rates are increased by cooling, especially in glaciated mountain ranges. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Calling cells to arms ▶ | | | Increased understanding of immune- and tumour-cell biology has led to an explosion of research into potential ways to harness the immune system to kill cancer. By Emily Elert. | | | | | | | | Bacteriology: A caring culture ▶ | | | William Coley found a way to prompt the immune system to fight cancer over a century ago. After years of neglect, scientists are now seeking to replicate his success. | | | | | | | | Drug development: Releasing the brakes ▶ | | | Tumours can put a brake on the immune system, but new therapies work by removing these brakes. Now, researchers have to figure out how to use them most effectively. | | | | | | | | Q&A: Evidence presenter ▶ | | | Immunologist Karolina Palucka, at Baylor Institute for Immunology Research in Dallas, Texas, helped treat Nobel prizewinner Ralph Steinman's pancreatic cancer with dentritic cells — the cells he co-discovered. Here she explains the use of dentritic cells in cancer immunotherapy. | | | | | | | | Medical imaging: Removing the blindfold ▶ | | | Using a variety of creative imaging techniques, researchers are tracking the dynamic interactions of immune and cancer cells. Their results will guide drug development. | | | | | | | | | | | | | | |
| | | Nature Outlook The Spine
Combating paralysis with drugs, stem cells and robotics Access the Outlook free online for six months. Produced with support from: Mesoblast | | | | | |
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| | | | | | | | | | | | | | | Lack of female leaders ▶ | | | Dearth of high-ranking women in UK academia misrepresents faculty members and students, says report. | | | | | | | | | | | Focus on outcomes ▶ | | | Basic research increasingly targets societal outcomes, finds study. | | | | | | | | | | | Internet freedom ▶ | | | Professors are entitled to speak out and publish on social media, argues report. | | | | | | | | Careers related news & comment | | | | | | | | | | | | | | | |  naturejobs.com Science jobs of the week | | | | | | | | | | | | | | | No matter what your career stage, student, postdoc or senior scientist, you will find articles on naturejobs.com to help guide you in your science career. Keep up-to-date with the latest sector trends, vote in our reader poll and sign-up to receive the monthly Naturejobs newsletter. | | | | | | | • Natureevents Directory featured events | | | | | |  natureevents directory featured events | | | | | | | Natureevents Directory is the premier resource for scientists looking for the latest scientific conferences, courses, meetings and symposia. Featured across Nature Publishing Group journals and centrally at natureevents.com it is an essential reference guide to scientific events worldwide. | | | | | | | | | | | | | | | | | Your email address is in the Nature mailing list. You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact subscriptions@nature.com For other enquiries, please contact feedback@nature.com | Nature Publishing Group | 75 Varick Street, 9th floor | New York | NY 10013-1917 | USA
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