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| | | | | | | | | | Van der Waals heterostructures | | Nobel Prize winner Andre Geim and Irina Grigorieva offer a forward-looking review of the potential of layering two-dimensional materials into novel heterostructures held together by weak van der Waals interactions. Dozens of these crystals are known. Graphene is well studied but others, such as monolayers of hexagonal boron nitride, MoS2, WSe2, graphane, fluorographene, mica and silicene are attracting interest. With many other monolayers yet to be examined the authors anticipate exciting new technological innovations. | | | | | | | | | | | | | | Insights into the phylogeny and coding potential of microbial dark matter | | Currently available genome sequences give a narrow view of the remarkable diversity of microorganisms as the vast majority of them have never been cultivated. Tanja Woyke and colleagues use single-cell genomics to target and sequence more than 200 uncultivated archaeal and bacterial cells from nine diverse environments. Based on the new data the authors propose a number of taxonomic revisions, including a proposal to reorganizing the Archaea into three superphyla. | | | | | | | | | | | | | | Vascularized and functional human liver from an iPSC-derived organ bud transplant | | This proof-of-concept study mimics events in the embryo during the development of an organ bud - in this case a liver bud - using an in vitro system containing human induced pluripotent stem cells on the hepatic lineage together with endothelial and mesenchymal cells. Transplantation of the resulting liver buds led to the generation of vascularized and functional human liver tissue in mice. Organ bud creation and transplantation could be a promising new approach to regenerative treatment of organ failure. | | | | | | | | | | | | | | | Roche's X-tremeGENE Transfection Reagents Efficiently transfect difficult cells, including more than 100 cancer cell lines. Free sample and protocols at www.x-tremegene.roche.com For life science research only. Not for use in diagnostic procedures. | | | | | | | | | | | | | | | | | | In this week's podcast: the superbugs resistant to last-resort antibiotics, how flatworms regrow their heads, and why the oil palm genome could be good news for sustainable crop breeding. | | | | | | | |
| | | | | | | | | | | | | | | | | | | | | | | | | | | Plastic fantastic ▶ | | | | A resurgence in organic technology is set to transform the world of electronic devices, offering a way to give the very fabric of life enhanced functionality. | | | | | | | | | | | | Antibiotic threat ▶ | | | | In the fight to combat antibiotic resistance, researchers should strengthen their advocacy. | | | | | | | | | | | | | | | | | | | | | | | | Seven days: 19–25 July 2013 ▶ | | | | The week in science: Elusive tar drop caught on film, Alan Turing set for UK pardon, and plan for Antarctic reserves fails. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | MRSA: Farming up trouble ▶ | | | | Microbiologists are trying to work out whether use of antibiotics on farms is fuelling the human epidemic of drug-resistant bacteria. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Q&A: Mountain guardian ▶ | | | | Dane Maxwell is the specialist in Hawaiian traditional culture advising the US National Solar Observatory and its partners as they build the world's largest solar observatory atop Haleakala on the island of Maui. He talks about the sacred mountain, known as the house of the Sun, and local responses to the Advanced Technology Solar Telescope (ATST). | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The initiation of mammalian protein synthesis and mRNA scanning mechanism ▶ | | | | Ivan B. Lomakin, Thomas A. Steitz | | | | Three structures of the eukaryotic small ribosomal subunit in complex with initiator tRNA, mRNA and the initiation factors eIF1 and eIF1A have been solved; these structures offer insight into the contributions of the initiation factors, the mechanism by which mRNA is scanned, and the interactions that occur in the ribosome's P site. | | | | | | | | | | | | Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease ▶ | | | | Herve Rhinn, Ryousuke Fujita, Liang Qiang et al. | | | | Whole transcriptome differential gene co-expression correlation analysis of cerebral cortex of APOE ε4 allele carriers and late-onset Alzheimer's disease patients reveals an APOE ε4 carrier transcription network pattern that resembles that of late-onset Alzheimer's disease and also identifies new genes of interest for further study. | | | | | | | | | | | | Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds OPEN ▶ | | | | Rajinder Singh, Meilina Ong-Abdullah, Eng-Ti Leslie Low et al. | | | | The genome sequence of the African oil palm, the main source of oil production, is used to predict at least 34,802 genes, including oil biosynthesis genes; comparison with the draft sequence of the South American oil palm reveals that the two species may have diverged in the New World and that segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. | | | | | | | | | | | | Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga OPEN ▶ | | | | Jean-François Flot, Boris Hespeels, Xiang Li et al. | | | | The genome of the asexual rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on the same chromosome in a palindromic fashion, a structure reminiscent of the primate Y chromosome and of other mitotic lineages such as cancer cells. | | | | | | | | | | | | Epithelial junctions maintain tissue architecture by directing planar spindle orientation ▶ | | | | Yu-ichiro Nakajima, Emily J. Meyer, Amanda Kroesen et al. | | | | The Drosophila tumour suppressors Scribbled and Discs large 1 are found to be essential regulators of planar spindle alignment during epithelial cell division; aberrant effects of spindle alignment are shown to be corrected through apoptosis, and the suppression of this mechanism can result in epithelial dysplasia and tumorigenesis. | | | | | | | | | | | | Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations ▶ | | | | Gregory I. Lang, Daniel P. Rice, Mark J. Hickman et al. | | | | Whole-genome whole-population sequencing is used to examine the dynamics of genome-sequence evolution in Saccharomyces cerevisiae populations for 1,000 generations; this reveals patterns of sequence evolution driven by pervasive genetic hitchhiking and interference, and shows that beneficial mutations that escape drift and increase in frequency typically occur in cohorts. | | | | | | | | | | | | The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK ▶ | | | | Rajinder Singh, Eng-Ti Leslie Low, Leslie Cheng-Li Ooi et al. | | | | Genetic mapping and whole-genome sequencing studies identify the SHELL gene (a homologue of Arabidopsis SEEDSTICK) as responsible for the three different fruit forms in oil palm (Elaeis guineesis); this has important economic implications for modulating SHELL activity to breed desired fruit forms and enhance oil yields. | | | | | | | | | | | | Coordination of heart and lung co-development by a multipotent cardiopulmonary progenitor ▶ | | | | Tien Peng, Ying Tian, Cornelis J. Boogerd et al. | | | | A population of multipotent cardiopulmonary mesoderm progenitors (CPPs) within the posterior pole of the heart expresses Wnt2, Gli1 and Isl1; these CPPs arise from cardiac progenitors before lung development, generate the mesoderm lineages within the cardiac inflow tract and lung, and are regulated by hedgehog expression from the foregut endoderm. | | | | | | | | | | | | The molecular logic for planarian regeneration along the anterior–posterior axis ▶ | | | | Yoshihiko Umesono, Junichi Tasaki, Yui Nishimura et al. | | | | More than a century ago, Thomas Hunt Morgan attempted to explain the extraordinary regenerative ability of planarians such as Dugesia japonica, which can regenerate a complete individual even from a tail fragment, by proposing that two opposing morphogenetic gradients along the anterior–posterior axis are required for regeneration; here ERK and β-catenin signalling are shown to form these gradients. | | | | | | | | | | | | Restoration of anterior regeneration in a planarian with limited regenerative ability ▶ | | | | James M. Sikes, Phillip A. Newmark | | | | Although the capacity for tissue regeneration of planarians is exceptional, planarians with more limited regenerative capacities are known; this study of Procotyla fluviatilis, a planarian with restricted ability to replace missing tissues, shows that Wnt signalling is aberrantly regulated in regeneration-deficient tissues and that downregulation of Wnt signalling in these regions restores regenerative abilities, revealing that manipulating a single signalling pathway can reverse the evolutionary loss of regenerative potential. | | | | | | | | | | | | Reactivating head regrowth in a regeneration-deficient planarian species ▶ | | | | S.-Y. Liu, C. Selck, B. Friedrich et al. | | | | Although the capacity for tissue regeneration of planarians is exceptional, planarians with more limited regenerative capacities are known; here knocking down components of the Wnt signalling pathway rescues head regeneration in the regeneration-impaired planarian Dendrocoelum lacteum, revealing that manipulating a single signalling pathway can reverse the evolutionary loss of regenerative potential. | | | | | | | | | | | | The pluripotent genome in three dimensions is shaped around pluripotency factors ▶ | | | | Elzo de Wit, Britta A. M. Bouwman, Yun Zhu et al. | | | | Using 4C technology, higher-order topological features of the pluripotent genome are identified; in pluripotent stem cells, Nanog clusters specifically with other pluripotency genes and this clustering is centred around Nanog-binding sites, suggesting that Nanog helps to shape the three-dimensional structure of the pluripotent genome and thereby contributes to the robustness of the pluripotent state. | | | | | | | | | | | | Optical control of mammalian endogenous transcription and epigenetic states ▶ | | | | Silvana Konermann, Mark D. Brigham, Alexandro Trevino et al. | | | | Here the customizable TALE DNA-binding domain was integrated with the light-sensitive cryptochrome 2 protein and its interacting partner (CIB1) from Arabidopsis thaliana, thereby creating an optogenetic two-hybrid system called light-inducible transcriptional effectors (LITEs); the LITE system establishes a novel mode of optogenetic control of endogenous cellular processes. | | | | | | | | | | | | | | | | Insights into the phylogeny and coding potential of microbial dark matter OPEN ▶ | | | | Christian Rinke, Patrick Schwientek, Alexander Sczyrba et al. | | | | Uncultivated archaeal and bacterial cells of major uncharted branches of the tree of life are targeted and sequenced using single-cell genomics; this enables resolution of many intra- and inter-phylum-level relationships, uncovers unexpected metabolic features that challenge established boundaries between the three domains of life, and leads to the proposal of two new superphyla. | | | | | | | | | | | | Structure of class B GPCR corticotropin-releasing factor receptor 1 ▶ | | | | Kaspar Hollenstein, James Kean, Andrea Bortolato et al. | | | | Approximately 30% of known drugs target G protein-coupled receptors (GPCRs), but all the published structures of GPCRs to date are from the class A family of GPCRs; here the first X-ray crystal structure of a member of the class B family of GPCRs, the human corticotropin-releasing factor receptor 1, is determined. | | | | | | | | | | | | | | | | High frequency of functional extinctions in ecological networks ▶ | | | | Torbjörn Säterberg, Stefan Sellman, Bo Ebenman | | | | A modelling study of the mechanisms of extinction within ecological networks reveals how even a small reduction in the population size of a species may lead to the loss of its ecological functionality—that is, to its functional extinction—by causing extinction of other organisms in the food web, often only indirectly connected to the focal species, revealing the value of conservation strategies that target a broader ecological network. | | | | | | | | | | | | Great ape genetic diversity and population history OPEN ▶ | | | | Javier Prado-Martinez, Peter H. Sudmant, Jeffrey M. Kidd et al. | | | | High-coverage sequencing of 79 (wild and captive) individuals representing all six non-human great ape species has identified over 88 million single nucleotide polymorphisms providing insight into ape genetic variation and evolutionary history and enabling comparison with human genetic diversity. | | | | | | | | | | | | Attention enhances synaptic efficacy and the signal-to-noise ratio in neural circuits ▶ | | | | Farran Briggs, George R. Mangun, W. Martin Usrey | | | | In monkeys performing a visual spatial attention task, stimulation of neurons in the lateral geniculate nucleus and recording of shock-evoked responses from monosynaptically connected primary-visual-cortex neurons shows that attention enhances neuronal communication by increasing the efficacy of presynaptic input, increasing synchronous responses, and by decreasing redundant signals. | | | | | | | | | | | | Vascularized and functional human liver from an iPSC-derived organ bud transplant ▶ | | | | Takanori Takebe, Keisuke Sekine, Masahiro Enomura et al. | | | | Vascularized, functional human liver is generated from human induced pluripotent stem cells (iPSCs) by transplantation of liver buds created in vitro (iPSC-LBs); hepatic cells self-organized into three-dimensional iPSC-LBs, and human vasculatures in iPSC-LB transplants became functional by connecting to host vessels, stimulating maturation of iPSC-LBs into tissue resembling adult liver and performing liver-specific functions. | | | | | | | | | | | | | | | | | | | | Receptor binding by an H7N9 influenza virus from humans ▶ | | | | Xiaoli Xiong, Stephen R. Martin, Lesley F. Haire et al. | | | | An examination of the receptor-binding properties of the H7N9 virus, which has recently emerged in China, shows that the virus has acquired the ability to bind the human α-2,6-linked sialic acid receptor while retaining binding to the avian α-2,3-linked receptor, and therefore does not have the preference for human versus avian receptors characteristic of pandemic viruses. | | | | | | | | | | | | Biological features of novel avian influenza A (H7N9) virus ▶ | | | | Jianfang Zhou, Dayan Wang, Rongbao Gao et al. | | | | An initial characterization of the receptor-binding properties of the novel avian influenza A (H7N9) shows that the virus has acquired the ability to bind human receptors while retaining the ability to bind avian receptors; the virus infects epithelial cells in the human lower respiratory tract and type II pneumocytes in the alveoli, and hypercytokinaemia was seen in infected patients. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Brief Communications Arising | | | | | | | | | | | | | | | | | | | | | | | | Brief Communications Arising | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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| | | | | | | | | | | | | | | | | | | | | | | | | | The pluripotent genome in three dimensions is shaped around pluripotency factors ▶ | | | | Elzo de Wit, Britta A. M. Bouwman, Yun Zhu, Petra Klous, Erik Splinter et al. | | | | Using 4C technology, higher-order topological features of the pluripotent genome are identified; in pluripotent stem cells, Nanog clusters specifically with other pluripotency genes and this clustering is centred around Nanog-binding sites, suggesting that Nanog helps to shape the three-dimensional structure of the pluripotent genome and thereby contributes to the robustness of the pluripotent state. | | | | | | | | | | | | The initiation of mammalian protein synthesis and mRNA scanning mechanism ▶ | | | | Ivan B. Lomakin & Thomas A. Steitz | | | | Three structures of the eukaryotic small ribosomal subunit in complex with initiator tRNA, mRNA and the initiation factors eIF1 and eIF1A have been solved; these structures offer insight into the contributions of the initiation factors, the mechanism by which mRNA is scanned, and the interactions that occur in the ribosome’s P site. | | | | | | | | | | | | | | | | Structure of class B GPCR corticotropin-releasing factor receptor 1 ▶ | | | | Kaspar Hollenstein, James Kean, Andrea Bortolato, Robert K. Y. Cheng, Andrew S. Doré et al. | | | | Approximately 30% of known drugs target G protein-coupled receptors (GPCRs), but all the published structures of GPCRs to date are from the class A family of GPCRs; here the first X-ray crystal structure of a member of the class B family of GPCRs, the human corticotropin-releasing factor receptor 1, is determined. | | | | | | | | | | | | Structure of the human glucagon class B G-protein-coupled receptor ▶ | | | | Fai Yiu Siu, Min He, Chris de Graaf, Gye Won Han, Dehua Yang et al. | | | | The X-ray crystal structure of the human glucagon receptor, a potential drug target for type 2 diabetes, offers a structural basis for molecular recognition by class B G-protein-coupled receptors. | | | | | | | | | | | | | | | | Receptor binding by an H7N9 influenza virus from humans ▶ | | | | Xiaoli Xiong, Stephen R. Martin, Lesley F. Haire, Stephen A. Wharton, Rodney S. Daniels et al. | | | | An examination of the receptor-binding properties of the H7N9 virus, which has recently emerged in China, shows that the virus has acquired the ability to bind the human α-2,6-linked sialic acid receptor while retaining binding to the avian α-2,3-linked receptor, and therefore does not have the preference for human versus avian receptors characteristic of pandemic viruses. | | | | | | | | | | | | | | | | Van der Waals heterostructures ▶ | | | | A. K. Geim & I. V. Grigorieva | | | | Fabrication techniques developed for graphene research allow the disassembly of many layered crystals (so-called van der Waals materials) into individual atomic planes and their reassembly into designer heterostructures, which reveal new properties and phenomena. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Heavy solitons in a fermionic superfluid ▶ | | | | Tarik Yefsah, Ariel T. Sommer, Mark J. H. Ku et al. | | | | Solitons — solitary waves that maintain their shape as they propagate — in a strongly interacting superfluid of fermionic lithium atoms are found to have an effective mass more than 50 times larger than the theoretically predicted value, a sign of strong quantum fluctuations. | | | | | | | | | | | | | | | | | | | | | | | | Van der Waals heterostructures ▶ | | | | A. K. Geim, I. V. Grigorieva | | | | Fabrication techniques developed for graphene research allow the disassembly of many layered crystals (so-called van der Waals materials) into individual atomic planes and their reassembly into designer heterostructures, which reveal new properties and phenomena. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | No increase in global temperature variability despite changing regional patterns ▶ | | | | Chris Huntingford, Philip D. Jones, Valerie N. Livina et al. | | | | Although fluctuations in annual temperature have shown substantial geographical variation over the past few decades, which may be more difficult for society to adapt to than altered mean conditions, the time-evolving standard deviation of globally averaged temperature anomalies reveals that there has been little change. | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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