| | | Volume 507 Number 7491 | | | | nature | | The science that matters. Every week. | | | | | | | | | | |  | | | Learn how to identify and mitigate error in NGS projects. This article discusses the sources of experimental error in NGS and presents a simple analysis for characterizing and abating error. The author, Kimberly Robasky, formerly a student of George Church, is currently a Bioinformatics Director at EA|Quintiles. Read More... | | | | | | | | Jump to the content that matters to you | | | | | | | | | | | | | | | Reflection from the strong gravity regime in a lensed quasar at redshift z=0.658 | | Measurements of the spin of a supermassive black hole more than 6 billion light years away - the most distant black hole for which a spin has been measured - offer new clues as to how these objects grow. The reflection-dominated spectrum of a 'lensed' quasar at z=0.658, together with archival X-ray data, show that it is rotating rapidly and that much of its radiation comes from a compact region close to the black hole. The data suggest that the black hole has grown by coherent accretion rather than in a chaotic manner. | | | | | | | | | | | | | Hydrous mantle transition zone indicated by ringwoodite included within diamond | | It is not clear just how much water there is within the solid Earth, or where it is to be found. Graham Pearson and co-authors present evidence from a diamond inclusion from Juína, Brazil, for the first known terrestrial occurrence of ringwoodite - a high-pressure form of olivine mineral first identified in meteorites and thought to be a major constituent of the Earth's mantle transition zone. The water-rich nature of this inclusion provides direct evidence that, at least locally, the transition zone is hydrous, to about one weight per cent. | | | | | | | | | | | | | Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European | | The emergence of agriculture may have caused many of the changes in human physiology evident in the fossil record. Which changes it is hard to say in the absence of a baseline - a record of human physiology just before the advent of farming. We may now have that in the form of genome of a Mesolithic hunter-gatherer from Spain. The genes of this male, alive around 7,000 years ago, had more in common with ancient genomes from Siberia than with other Europeans, suggesting a wide genetic continuity across Eurasia. He was probably lactose intolerant and digested starchy food less effectively than did Neolithic farmers, supporting the idea that these changes came in with agriculture. And he had the unusual combination of dark skin and blue eyes, suggesting that in the Mesolithic, the transition to a lighter 'modern European' skin tone was incomplete and that eye-colour changes came first. | | | | | | | | | | | | | | | | | | | | | | | | | In this week's podcast: This week, how a thirteenth century cosmologist predicted the Big Bang, the ocean of water hidden deep in the Earth's mantle, and what the wolves of Yellowstone tell us about ecosystems. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Don’t hide the decline ▶ | | | | US scientists should not be placated by the ‘flat budget’ myth. Funds are decreasing, and the situation will get worse. | | | | | | | | | | | | An elegant chaos ▶ | | | | Universal theories are few and far between in ecology, but that is what makes it fascinating. | | | | | | | | | | | | Share alike ▶ | | | | Research communities need to agree on standard etiquette for data-sharing. | | | | | | | | | | | | | | | | | | | | | | | | 7 days: 7–13 March 2014 ▶ | | | | The week in science: Infant HIV cure; Craig Venter launches genomics company; and asteroid caught falling apart. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | History: A medieval multiverse ▶ | | | | Ideas in a thirteenth-century treatise on the nature of matter still resonate today, say Tom C. B. McLeish and colleagues. | | | | | | | | | | | | | | | | | | | | In retrospect: Sylva ▶ | | | | Gabriel Hemery celebrates the 350th anniversary of John Evelyn's treatise on the science and practice of forestry. | | | | | | | | | | | | | | | | | | | | | | | | | |  | | | The New York Stem Cell Foundation is accepting proposals for high-risk, high-reward projects exploring the therapeutic potential of stem cells. The awards provide $1.5M USD over 5 years. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Haematopoietic stem cells require a highly regulated protein synthesis rate ▶ | | | | Robert A. J. Signer, Jeffrey A. Magee, Adrian Salic et al. | | | | Haematopoietic stem cells (HSCs) have a lower rate of protein synthesis in vivo than most other haematopoietic cells, and both increases and decreases in the rate of protein synthesis impair HSC function, demonstrating that HSC maintenance—and hence, cellular homeostasis—requires the rate of protein synthesis to be highly regulated. | | | | | | | | | | | | Coupling of angiogenesis and osteogenesis by a specific vessel subtype in bone ▶ | | | | Anjali P. Kusumbe, Saravana K. Ramasamy, Ralf H. Adams | | | | Bone homeostasis and repair declines with ageing and the mechanisms regulating the relationship between bone growth and blood vessel formation have remained unknown; this mouse study identifies the endothelial cells that promote the formation of new bone, a small microvessel subtype that can be identified by high CD31 and high Emcn expression. | | | | | | | | | | | | Unexpected link between an antibiotic, pannexin channels and apoptosis ▶ | | | | Ivan K. H. Poon, Yu-Hsin Chiu, Allison J. Armstrong et al. | | | | The pannexin 1 channel on the plasma membrane of apoptotic cells mediates the release of find-me molecular signals to attract phagocytic cells for clearance of the apoptotic cells; here the quinolone antibiotic trovafloxacin is identified as a direct inhibitor of pannexin 1, which results in dysregulated fragmentation of apoptotic cells and may partly explain quinolone toxicity. | | | | | | | | | | | | Inhibition of miR-25 improves cardiac contractility in the failing heart ▶ | | | | Christine Wahlquist, Dongtak Jeong, Agustin Rojas-Muñoz et al. | | | | Reduced activity of the calcium-transporting ATPase SERCA2a is a hallmark of heart failure; here, microRNAs that downregulate SERCA2a function are identified, and antagonism of one, miR-25, is shown to halt heart failure in mice. | | | | | | | | | | | | | | | | Structure of a type IV secretion system ▶ | | | | Harry H. Low, Francesca Gubellini, Angel Rivera-Calzada et al. | | | | The three-dimensional structure of the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid. | | | | | | | | | | | | A new fossil species supports an early origin for toothed whale echolocation ▶ | | | | Jonathan H. Geisler, Matthew W. Colbert, James L. Carew | | | | Phylogenetic analysis of a new species of fossil toothed whale, Cotylocara macei, from the Oligocene epoch places it in a basal clade of odontocetes, and its features suggest that rudimentary echolocation evolved in the early Oligocene and was followed by convergent evolution in their skulls. | | | | | | | | | | | | Obesity-associated variants within FTO form long-range functional connections with IRX3 ▶ | | | | Scott Smemo, Juan J. Tena, Kyoung-Han Kim et al. | | | | Obesity-associated noncoding sequences within FTO are functionally connected with IRX3, and long-range enhancers in this region recapitulate aspects of IRX3 expression, suggesting that the obesity-associated interval is part of IRX3 regulation; Irx3-deficient mice have lower body weight and are resistant to diet-induced obesity, suggesting IRX3 as a novel determinant of body mass and composition. | | | | | | | | | | | | Herbivores and nutrients control grassland plant diversity via light limitation ▶ | | | | Elizabeth T. Borer, Eric W. Seabloom, Daniel S. Gruner et al. | | | | Experimental data collected from 40 grasslands on 6 continents show that nutrients and herbivores can serve as counteracting forces to control local plant diversity; nutrient addition reduces local diversity through light limitation, and herbivory rescues diversity at sites where it alleviates light limitation. | | | | | | | | | | | | | | | | | | | | Alveolar progenitor and stem cells in lung development, renewal and cancer ▶ | | | | Tushar J. Desai, Douglas G. Brownfield, Mark A. Krasnow | | | | Lung alveoli are lined by two types of alveolar epithelial cells, squamous alveolar type (AT) 1 cells that mediate gas exchange and cuboidal AT2 cells that secrete surfactant to prevent alveolar collapse during breathing; here alveolar markers, genetic lineage tracing and clonal analysis are used in mice to identify alveolar progenitor and stem cells in vivo, and to map their locations and potential during lung development, maintenance and cancer. | | | | | | | | | | | | C9orf72 nucleotide repeat structures initiate molecular cascades of disease ▶ | | | | Aaron R. Haeusler, Christopher J. Donnelly, Goran Periz et al. | | | | Structurally polymorphic C9orf72 hexanucleotide repeats cause an impairment in transcriptional processivity and lead to accumulation of truncated repeat-containing transcripts that bind to specific ribonucleoproteins, such as nucleolin, in a conformation-dependent manner resulting in nucleolar stress and C9orf72-linked pathology in amyotrophic lateral sclerosis and frontotemporal dementia. | | | | | | | | | | | | Proof of principle for epitope-focused vaccine design ▶ | | | | Bruno E. Correia, John T. Bates, Rebecca J. Loomis et al. | | | | Computational protein design methods are used to generate new candidates for a human respiratory syncytial virus (RSV) vaccine; artificial protein scaffolds that mimic the structure of a RSV epitope are shown to induce RSV-specific neutralizing antibodies in macaques. | | | | | | | | | | | | Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European ▶ | | | | Iñigo Olalde, Morten E. Allentoft, Federico Sánchez-Quinto et al. | | | | A complete pre-agricultural European human genome from a ∼7,000-year-old Mesolithic skeleton suggests the existence of a common genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic, and ancestral alleles in several skin pigmentation genes suggest that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. | | | | | | | | | | | | doublesex is a mimicry supergene ▶ | | | | K. Kunte, W. Zhang, A. Tenger-Trolander et al. | | | | The phenomenon of sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio — now, a single gene, doublesex, is shown to control supergene mimicry, a finding that is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci. | | | | | | | | | | | | Dynamic sensory cues shape song structure in Drosophila ▶ | | | | Philip Coen, Jan Clemens, Andrew J. Weinstein et al. | | | | Drosophila male courtship songs were thought to have a fixed structure with song repetition variations introduced unintentionally because of neural noise; this behavioural assay and computational modelling study instead reveals that males use fast changes in sensory information to actively pattern individual song sequences. | | | | | | | | | | | | An excitatory paraventricular nucleus to AgRP neuron circuit that drives hunger ▶ | | | | Michael J. Krashes, Bhavik P. Shah, Joseph C. Madara et al. | | | | The AgRP-expressing neurons in the arcuate nucleus drive food-seeking behaviours during caloric restriction; a mouse study of monosynaptic retrograde rabies spread and optogenetic circuit mapping reveals that these neurons are activated by input from hypothalamic paraventricular nucleus cells and their activation or inhibition can modulate feeding behaviour. | | | | | | | | | | | | L-Myc expression by dendritic cells is required for optimal T-cell priming ▶ | | | | Wumesh KC, Ansuman T. Satpathy, Aaron S. Rapaport et al. | | | | L-Myc, a paralogue of the proto-oncogene c-Myc, is shown to regulate dendritic cell homeostasis and functionality; unlike c-Myc, L-Myc is not repressed by interferons and its expression allows for optimal dendritic cell proliferation and T-cell priming in the presence of inflammation. | | | | | | | | | | | | | | | | A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium ▶ | | | | Abhinav Sinha, Katie R. Hughes, Katarzyna K. Modrzynska et al. | | | | Malaria parasites must produce gametocytes for transmission to the mosquito vector, although the molecular mechanisms underlying commitment to gametocyte production remain unclear; here this process is found to be controlled by PbAP2-G, a member of the ApiAP2 family of DNA-binding proteins, in the rodent-infecting Plasmodium berghei parasite. | | | | | | | | | | | | DNA-guided DNA interference by a prokaryotic Argonaute ▶ | | | | Daan C. Swarts, Matthijs M. Jore, Edze R. Westra et al. | | | | Here, Argonaute from the prokaryote Thermus thermophilus is shown to use small DNA guides to interfere directly with invading foreign DNA, rather than being involved in RNA-guided RNA interference, as observed in eukaryotes. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |  The Structural Genomics Consortium (SGC), Natureconferences, and the São Paulo Research Foundation are pleased to present: Chemical Probe-based Open Science: Uncovering New Human and Plant Biology April 28-29, 2014 Faculdade de Ciências Médicas, State University of Campinas (UNICAMP), Brazil Click here for more information or to register for this conference today! | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Inhibition of miR-25 improves cardiac contractility in the failing heart ▶ | | | | Christine Wahlquist, Dongtak Jeong, Agustin Rojas-Muñoz et al. | | | | Reduced activity of the calcium-transporting ATPase SERCA2a is a hallmark of heart failure; here, microRNAs that downregulate SERCA2a function are identified, and antagonism of one, miR-25, is shown to halt heart failure in mice. | | | | | | | | | | | | | | | | Obesity-associated variants within FTO form long-range functional connections with IRX3 ▶ | | | | Scott Smemo, Juan J. Tena, Kyoung-Han Kim et al. | | | | Obesity-associated noncoding sequences within FTO are functionally connected with IRX3, and long-range enhancers in this region recapitulate aspects of IRX3 expression, suggesting that the obesity-associated interval is part of IRX3 regulation; Irx3-deficient mice have lower body weight and are resistant to diet-induced obesity, suggesting IRX3 as a novel determinant of body mass and composition. | | | | | | | | | | | | | | | | C9orf72 nucleotide repeat structures initiate molecular cascades of disease ▶ | | | | Aaron R. Haeusler, Christopher J. Donnelly, Goran Periz et al. | | | | Structurally polymorphic C9orf72 hexanucleotide repeats cause an impairment in transcriptional processivity and lead to accumulation of truncated repeat-containing transcripts that bind to specific ribonucleoproteins, such as nucleolin, in a conformation-dependent manner resulting in nucleolar stress and C9orf72-linked pathology in amyotrophic lateral sclerosis and frontotemporal dementia. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Efficient rotational cooling of Coulomb-crystallized molecular ions by a helium buffer gas ▶ | | | | A. K. Hansen, O. O. Versolato, Ł. Kłosowski et al. | | | | In combination with sympathetic cooling of translational degrees of freedom (leading to Coulomb crystallization), cooling of the rotational degrees of freedom of magnesium hydride ions using a helium buffer gas leads to temperatures in a tunable range from 60 kelvin down to about 7 kelvin for a single ion, the lowest such temperature so far recorded. | | | | | | | | | | | | | | | | | | | | | | | | Interrogating selectivity in catalysis using molecular vibrations ▶ | | | | Anat Milo, Elizabeth N. Bess, Matthew S. Sigman | | | | A set of parameters based on the response of a molecule’s properties to infrared vibrations can be used to model and predict selectivity trends for molecular reactions with interlinked steric and electronic effects at positions of interest | | | | | | | | | | | | Conformation-induced remote meta-C–H activation of amines ▶ | | | | Ri-Yuan Tang, Gang Li, Jin-Quan Yu | | | | In anilines and benzylic amines, a recyclable chemical template can direct the olefination and acetoxylation of meta-C–H bonds as far as 11 bonds away from a functional group; in particular, it is able to direct the meta-selective C–H functionalization of bicyclic heterocycles via a highly strained, tricyclic-cyclophane-like palladated intermediate. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Brief Communications Arising | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | FREE POSTER: Dyslipidaemia and its treatment
Disorders of plasma lipid and lipoprotein metabolism can cause atherosclerotic cardiovascular disease. This poster displays the main lipid-metabolism pathways in the body, the points at which monogenetic protein mutations lead to dyslipidaemia, and the mechanisms of action of both established and novel lipid-modifying drugs. This poster was produced with support from: | | | | | | | | | | | | | | | | | | | | | | | | Geoscience: Fracking fundamentals ▶ | | | | Scientists in the United States who are looking to ride the gas-exploration boom can find a variety of options for employment, from chemical research to environmental monitoring. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Skewed rankings ▶ | | | | Female researchers avoid collaborating with lower-ranked female colleagues, finds study. | | | | | | | | | | | | | | | | Costs of childcare ▶ | | | | Breaks due to childcare are associated with lower wages for female physicians, says study. | | | | | | | | | | | | | |  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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