Showing papers in "Science in 2014"
TL;DR: Perovskite films received a boost in photovoltaic efficiency through controlled formation of charge-generating films and improved current transfer to the electrodes and low-temperature processing steps allowed the use of materials that draw current out of the perovskites layer more efficiently.
Abstract: Advancing perovskite solar cell technologies toward their theoretical power conversion efficiency (PCE) requires delicate control over the carrier dynamics throughout the entire device. By controlling the formation of the perovskite layer and careful choices of other materials, we suppressed carrier recombination in the absorber, facilitated carrier injection into the carrier transport layers, and maintained good carrier extraction at the electrodes. When measured via reverse bias scan, cell PCE is typically boosted to 16.6% on average, with the highest efficiency of ~19.3% in a planar geometry without antireflective coating. The fabrication of our perovskite solar cells was conducted in air and from solution at low temperatures, which should simplify manufacturing of large-area perovskite devices that are inexpensive and perform at high levels.
5,222 citations
TL;DR: The power of the CRISPR-Cas9 technology to systematically analyze gene functions in mammalian cells, study genomic rearrangements and the progression of cancers or other diseases, and potentially correct genetic mutations responsible for inherited disorders is illustrated.
Abstract: The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.
3,761 citations
TL;DR: Electrochemical measurements can distinguish between different types of energy storage materials and their underlying mechanisms, used to recover power in cars and electric mass transit vehicles that would otherwise lose braking energy as heat.
Abstract: Electrochemical measurements can distinguish between different types of energy storage materials and their underlying mechanisms.
3,494 citations
TL;DR: This work shows that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells, and observes a high level of consistency between independent guide RNAs targeting the same gene and a high rate of hit confirmation.
Abstract: The simplicity of programming the CRISPR (clustered regularly interspaced short palindromic repeats)–associated nuclease Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on a genome-wide scale. We show that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells. First, we used the GeCKO library to identify genes essential for cell viability in cancer and pluripotent stem cells. Next, in a melanoma model, we screened for genes whose loss is involved in resistance to vemurafenib, a therapeutic RAF inhibitor. Our highest-ranking candidates include previously validated genes NF1 and MED12 , as well as novel hits NF2 , CUL3 , TADA2B , and TADA1. We observe a high level of consistency between independent guide RNAs targeting the same gene and a high rate of hit confirmation, demonstrating the promise of genome-scale screening with Cas9.
3,399 citations
TL;DR: The genome sequence of single cells isolated from brain glioblastomas was examined, which revealed shared chromosomal changes but also extensive transcription variation, including genes related to signaling, which represent potential therapeutic targets.
Abstract: Human cancers are complex ecosystems composed of cells with distinct phenotypes, genotypes, and epigenetic states, but current models do not adequately reflect tumor composition in patients. We used single-cell RNA sequencing (RNA-seq) to profile 430 cells from five primary glioblastomas, which we found to be inherently variable in their expression of diverse transcriptional programs related to oncogenic signaling, proliferation, complement/immune response, and hypoxia. We also observed a continuum of stemness-related expression states that enabled us to identify putative regulators of stemness in vivo. Finally, we show that established glioblastoma subtype classifiers are variably expressed across individual cells within a tumor and demonstrate the potential prognostic implications of such intratumoral heterogeneity. Thus, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.
2,655 citations
TL;DR: A method in which the cluster centers are recognized as local density maxima that are far away from any points of higher density, and the algorithm depends only on the relative densities rather than their absolute values.
Abstract: Cluster analysis is aimed at classifying elements into categories on the basis of their similarity. Its applications range from astronomy to bioinformatics, bibliometrics, and pattern recognition. We propose an approach based on the idea that cluster centers are characterized by a higher density than their neighbors and by a relatively large distance from points with higher densities. This idea forms the basis of a clustering procedure in which the number of clusters arises intuitively, outliers are automatically spotted and excluded from the analysis, and clusters are recognized regardless of their shape and of the dimensionality of the space in which they are embedded. We demonstrate the power of the algorithm on several test cases.
2,548 citations
TL;DR: Inspired by the brain’s structure, an efficient, scalable, and flexible non–von Neumann architecture is developed that leverages contemporary silicon technology and is well suited to many applications that use complex neural networks in real time, for example, multiobject detection and classification.
Abstract: Inspired by the brain’s structure, we have developed an efficient, scalable, and flexible non–von Neumann architecture that leverages contemporary silicon technology. To demonstrate, we built a 5.4-billion-transistor chip with 4096 neurosynaptic cores interconnected via an intrachip network that integrates 1 million programmable spiking neurons and 256 million configurable synapses. Chips can be tiled in two dimensions via an interchip communication interface, seamlessly scaling the architecture to a cortexlike sheet of arbitrary size. The architecture is well suited to many applications that use complex neural networks in real time, for example, multiobject detection and classification. With 400-pixel-by-240-pixel video input at 30 frames per second, the chip consumes 63 milliwatts.
2,512 citations
TL;DR: This work examined a five-element high-entropy alloy, CrMnFeCoNi, which forms a single-phase face-centered cubic solid solution, and found it to have exceptional damage tolerance with tensile strengths above 1 GPa and fracture toughness values exceeding 200 MPa·m1/2.
Abstract: High-entropy alloys are equiatomic, multi-element systems that can crystallize as a single phase, despite containing multiple elements with different crystal structures. A rationale for this is that the configurational entropy contribution to the total free energy in alloys with five or more major elements may stabilize the solid-solution state relative to multiphase microstructures. We examined a five-element high-entropy alloy, CrMnFeCoNi, which forms a single-phase face-centered cubic solid solution, and found it to have exceptional damage tolerance with tensile strengths above 1 GPa and fracture toughness values exceeding 200 MPa·m(1/2). Furthermore, its mechanical properties actually improve at cryogenic temperatures; we attribute this to a transition from planar-slip dislocation activity at room temperature to deformation by mechanical nanotwinning with decreasing temperature, which results in continuous steady strain hardening.
2,411 citations
TL;DR: A perovskite solar cell that uses a double layer of mesoporous TiO2 and ZrO2 as a scaffold infiltrated with perovSkite and does not require a hole-conducting layer is fabricated and achieves a certified power conversion efficiency of 12.8%.
Abstract: We fabricated a perovskite solar cell that uses a double layer of mesoporous TiO2 and ZrO2 as a scaffold infiltrated with perovskite and does not require a hole-conducting layer. The perovskite was produced by drop-casting a solution of PbI2, methylammonium (MA) iodide, and 5-ammoniumvaleric acid (5-AVA) iodide through a porous carbon film. The 5-AVA templating created mixed-cation perovskite (5-AVA)x(MA)1- xPbI3 crystals with lower defect concentration and better pore filling as well as more complete contact with the TiO2 scaffold, resulting in a longer exciton lifetime and a higher quantum yield for photoinduced charge separation as compared to MAPbI3. The cell achieved a certified power conversion efficiency of 12.8% and was stable for >1000 hours in ambient air under full sunlight.
2,341 citations
TL;DR: Recent developments in genetic engineering, enhanced extraction methods, and a deeper understanding of the structure of lignin are yielding promising opportunities for efficient conversion of this renewable resource to carbon fibers, polymers, commodity chemicals, and fuels.
Abstract: Background Lignin, nature’s dominant aromatic polymer, is found in most terrestrial plants in the approximate range of 15 to 40% dry weight and provides structural integrity. Traditionally, most large-scale industrial processes that use plant polysaccharides have burned lignin to generate the power needed to productively transform biomass. The advent of biorefineries that convert cellulosic biomass into liquid transportation fuels will generate substantially more lignin than necessary to power the operation, and therefore efforts are underway to transform it to value-added products. Production of biofuels from cellulosic biomass requires separation of large quantities of the aromatic polymer lignin. In planta genetic engineering, enhanced extraction methods, and a deeper understanding of the structure of lignin are yielding promising opportunities for efficient conversion of this renewable resource to carbon fibers, polymers, commodity chemicals, and fuels. [Credit: Oak Ridge National Laboratory, U.S. Department of Energy] Advances Bioengineering to modify lignin structure and/or incorporate atypical components has shown promise toward facilitating recovery and chemical transformation of lignin under biorefinery conditions. The flexibility in lignin monomer composition has proven useful for enhancing extraction efficiency. Both the mining of genetic variants in native populations of bioenergy crops and direct genetic manipulation of biosynthesis pathways have produced lignin feedstocks with unique properties for coproduct development. Advances in analytical chemistry and computational modeling detail the structure of the modified lignin and direct bioengineering strategies for targeted properties. Refinement of biomass pretreatment technologies has further facilitated lignin recovery and enables catalytic modifications for desired chemical and physical properties. Outlook Potential high-value products from isolated lignin include low-cost carbon fiber, engineering plastics and thermoplastic elastomers, polymeric foams and membranes, and a variety of fuels and chemicals all currently sourced from petroleum. These lignin coproducts must be low cost and perform as well as petroleum-derived counterparts. Each product stream has its own distinct challenges. Development of renewable lignin-based polymers requires improved processing technologies coupled to tailored bioenergy crops incorporating lignin with the desired chemical and physical properties. For fuels and chemicals, multiple strategies have emerged for lignin depolymerization and upgrading, including thermochemical treatments and homogeneous and heterogeneous catalysis. The multifunctional nature of lignin has historically yielded multiple product streams, which require extensive separation and purification procedures, but engineering plant feedstocks for greater structural homogeneity and tailored functionality reduces this challenge.
2,324 citations
TL;DR: In this paper, a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library was described.
Abstract: The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines and mice with modified alleles. Here, we describe a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library. sgRNA expression cassettes were stably integrated into the genome, which enabled a complex mutant pool to be tracked by massively parallel sequencing. We used a library containing 73,000 sgRNAs to generate knockout collections and performed screens in two human cell lines. A screen for resistance to the nucleotide analog 6-thioguanine identified all expected members of the DNA mismatch repair pathway, whereas another for the DNA topoisomerase II ( TOP2A ) poison etoposide identified TOP2A , as expected, and also cyclin-dependent kinase 6, CDK6. A negative selection screen for essential genes identified numerous gene sets corresponding to fundamental processes. Last, we show that sgRNA efficiency is associated with specific sequence motifs, enabling the prediction of more effective sgRNAs. Collectively, these results establish Cas9/sgRNA screens as a powerful tool for systematic genetic analysis in mammalian cells.
TL;DR: Defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver of global ecological change.
Abstract: We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically, declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining species show 25% average decline in abundance. Invertebrate patterns are equally dire: 67% of monitored populations show 45% mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown about this “Anthropocene defaunation”; these knowledge gaps hinder our capacity to predict and limit defaunation impacts. Clearly, however, defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver of global ecological change.
TL;DR: It is demonstrated that a nanoporous morphology effectively suppresses bulk carrier recombination without additional doping, manifesting an electron-hole separation yield of 0.90 at 1.23 volts (V) versus the reversible hydrogen electrode (RHE).
Abstract: Bismuth vanadate (BiVO4) has a band structure that is well-suited for potential use as a photoanode in solar water splitting, but it suffers from poor electron-hole separation. Here, we demonstrate that a nanoporous morphology (specific surface area of 31.8 square meters per gram) effectively suppresses bulk carrier recombination without additional doping, manifesting an electron-hole separation yield of 0.90 at 1.23 volts (V) versus the reversible hydrogen electrode (RHE). We enhanced the propensity for surface-reaching holes to instigate water-splitting chemistry by serially applying two different oxygen evolution catalyst (OEC) layers, FeOOH and NiOOH, which reduces interface recombination at the BiVO4/OEC junction while creating a more favorable Helmholtz layer potential drop at the OEC/electrolyte junction. The resulting BiVO4/FeOOH/NiOOH photoanode achieves a photocurrent density of 2.73 milliamps per square centimenter at a potential as low as 0.6 V versus RHE.
TL;DR: The status, threats, and ecological importance of the 31 largest mammalian carnivores globally are reviewed and a Global Large Carnivore Initiative is proposed to coordinate local, national, and international research, conservation, and policy.
Abstract: Large carnivores face serious threats and are experiencing massive declines in their populations and geographic ranges around the world. We highlight how these threats have affected the conservation status and ecological functioning of the 31 largest mammalian carnivores on Earth. Consistent with theory, empirical studies increasingly show that large carnivores have substantial effects on the structure and function of diverse ecosystems. Significant cascading trophic interactions, mediated by their prey or sympatric mesopredators, arise when some of these carnivores are extirpated from or repatriated to ecosystems. Unexpected effects of trophic cascades on various taxa and processes include changes to bird, mammal, invertebrate, and herpetofauna abundance or richness; subsidies to scavengers; altered disease dynamics; carbon sequestration; modified stream morphology; and crop damage. Promoting tolerance and coexistence with large carnivores is a crucial societal challenge that will ultimately determine the fate of Earth's largest carnivores and all that depends upon them, including humans.
TL;DR: A highly active and durable class of electrocatalysts is synthesized by exploiting the structural evolution of platinum-nickel (Pt-Ni) bimetallic nanocrystals by exploitingThe starting material, crystalline PtNi3 polyhedra, transforms in solution by interior erosion into Pt3Ni nanoframes with surfaces that offer three-dimensional molecular accessibility.
Abstract: Control of structure at the atomic level can precisely and effectively tune catalytic properties of materials, enabling enhancement in both activity and durability. We synthesized a highly active and durable class of electrocatalysts by exploiting the structural evolution of platinum-nickel (Pt-Ni) bimetallic nanocrystals. The starting material, crystalline PtNi3 polyhedra, transforms in solution by interior erosion into Pt3Ni nanoframes with surfaces that offer three-dimensional molecular accessibility. The edges of the Pt-rich PtNi3 polyhedra are maintained in the final Pt3Ni nanoframes. Both the interior and exterior catalytic surfaces of this open-framework structure are composed of the nanosegregated Pt-skin structure, which exhibits enhanced oxygen reduction reaction (ORR) activity. The Pt3Ni nanoframe catalysts achieved a factor of 36 enhancement in mass activity and a factor of 22 enhancement in specific activity, respectively, for this reaction (relative to state-of-the-art platinum-carbon catalysts) during prolonged exposure to reaction conditions.
TL;DR: The biodiversity of eukaryote species and their extinction rates, distributions, and protection is reviewed, and what the future rates of species extinction will be, how well protected areas will slow extinction Rates, and how the remaining gaps in knowledge might be filled are reviewed.
Abstract: Background A principal function of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is to “perform regular and timely assessments of knowledge on biodiversity.” In December 2013, its second plenary session approved a program to begin a global assessment in 2015. The Convention on Biological Diversity (CBD) and five other biodiversity-related conventions have adopted IPBES as their science-policy interface, so these assessments will be important in evaluating progress toward the CBD’s Aichi Targets of the Strategic Plan for Biodiversity 2011–2020. As a contribution toward such assessment, we review the biodiversity of eukaryote species and their extinction rates, distributions, and protection. We document what we know, how it likely differs from what we do not, and how these differences affect biodiversity statistics. Interestingly, several targets explicitly mention “known species”—a strong, if implicit, statement of incomplete knowledge. We start by asking how many species are known and how many remain undescribed. We then consider by how much human actions inflate extinction rates. Much depends on where species are, because different biomes contain different numbers of species of different susceptibilities. Biomes also suffer different levels of damage and have unequal levels of protection. How extinction rates will change depends on how and where threats expand and whether greater protection counters them. Different visualizations of species biodiversity. ( A ) The distributions of 9927 bird species. ( B ) The 4964 species with smaller than the median geographical range size. ( C ) The 1308 species assessed as threatened with a high risk of extinction by BirdLife International for the Red List of Threatened Species of the International Union for Conservation of Nature. ( D ) The 1080 threatened species with less than the median range size. (D) provides a strong geographical focus on where local conservation actions can have the greatest global impact. Additional biodiversity maps are available at www.biodiversitymapping.org. Advances Recent studies have clarified where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. These data are increasingly accessible, bringing greater transparency to science and governance. Taxonomic catalogs of plants, terrestrial vertebrates, freshwater fish, and some marine taxa are sufficient to assess their status and the limitations of our knowledge. Most species are undescribed, however. The species we know best have large geographical ranges and are often common within them. Most known species have small ranges, however, and such species are typically newer discoveries. The numbers of known species with very small ranges are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. We expect unknown species to share these characteristics. Current rates of extinction are about 1000 times the background rate of extinction. These are higher than previously estimated and likely still underestimated. Future rates will depend on many factors and are poised to increase. Finally, although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity. Outlook Progress on assessing biodiversity will emerge from continued expansion of the many recently created online databases, combining them with new global data sources on changing land and ocean use and with increasingly crowdsourced data on species’ distributions. Examples of practical conservation that follow from using combined data in Colombia and Brazil can be found at www.savingspecies.org and www.youtube.com/watch?v=R3zjeJW2NVk.
TL;DR: It is shown that a pair of perovskite cells connected in series can power the electrochemical breakdown of water into hydrogen and oxygen efficiently, and the combination of the two yields a water-splitting photocurrent density and a solar-to-hydrogen efficiency of 12.3%.
Abstract: Although sunlight-driven water splitting is a promising route to sustainable hydrogen fuel production, widespread implementation is hampered by the expense of the necessary photovoltaic and photoelectrochemical apparatus. Here, we describe a highly efficient and low-cost water-splitting cell combining a state-of-the-art solution-processed perovskite tandem solar cell and a bifunctional Earth-abundant catalyst. The catalyst electrode, a NiFe layered double hydroxide, exhibits high activity toward both the oxygen and hydrogen evolution reactions in alkaline electrolyte. The combination of the two yields a water-splitting photocurrent density of around 10 milliamperes per square centimeter, corresponding to a solar-to-hydrogen efficiency of 12.3%. Currently, the perovskite instability limits the cell lifetime.
TL;DR: Large errors in flu prediction were largely avoidable, which offers lessons for the use of big data.
Abstract: In February 2013, Google Flu Trends (GFT) made headlines but not for a reason that Google executives or the creators of the flu tracking system would have hoped. Nature reported that GFT was predicting more than double the proportion of doctor visits for influenza-like illness (ILI) than the Centers for Disease Control and Prevention (CDC), which bases its estimates on surveillance reports from laboratories across the United States ( 1 , 2 ). This happened despite the fact that GFT was built to predict CDC reports. Given that GFT is often held up as an exemplary use of big data ( 3 , 4 ), what lessons can we draw from this error?
American Museum of Natural History1, University of Tartu2, University of Colombo3, Royal Netherlands Academy of Arts and Sciences4, University of Florida5, University of Palermo6, Goethe University Frankfurt7, Hobart Corporation8, Nakhon Phanom University9, University of Bamenda10, University of Gothenburg11, Naturalis12, Swedish University of Agricultural Sciences13, Royal Botanic Gardens14, Universiti Malaysia Sabah15, United States Department of Agriculture16, Forest Research Institute Malaysia17, Humboldt State University18, Chinese Academy of Sciences19, Landcare Research20, University of Western Australia21, Estonian University of Life Sciences22, University of Southern Queensland23, Botanic Garden Meise24, Manchester Metropolitan University25, James Cook University26
TL;DR: Diversity of most fungal groups peaked in tropical ecosystems, but ectomycorrhizal fungi and several fungal classes were most diverse in temperate or boreal ecosystems, and manyfungal groups exhibited distinct preferences for specific edaphic conditions (such as pH, calcium, or phosphorus).
Abstract: Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
TL;DR: This work investigates permeation through micrometer-thick laminates prepared by means of vacuum filtration of graphene oxide suspensions, which reveal that the GO membrane can attract a high concentration of small ions into the membrane, which may explain the fast ion transport.
Abstract: Graphene-based materials can have well-defined nanometer pores and can exhibit low frictional water flow inside them, making their properties of interest for filtration and separation. We investigate permeation through micrometer-thick laminates prepared by means of vacuum filtration of graphene oxide suspensions. The laminates are vacuum-tight in the dry state but, if immersed in water, act as molecular sieves, blocking all solutes with hydrated radii larger than 4.5 angstroms. Smaller ions permeate through the membranes at rates thousands of times faster than what is expected for simple diffusion. We believe that this behavior is caused by a network of nanocapillaries that open up in the hydrated state and accept only species that fit in. The anomalously fast permeation is attributed to a capillary-like high pressure acting on ions inside graphene capillaries.
TL;DR: The experimental realization and operation of dielectric gradient metasurface optical elements capable of also achieving high efficiencies in transmission mode in the visible spectrum are described.
Abstract: Gradient metasurfaces are two-dimensional optical elements capable of manipulating light by imparting local, space-variant phase changes on an incident electromagnetic wave. These surfaces have thus far been constructed from nanometallic optical antennas, and high diffraction efficiencies have been limited to operation in reflection mode. We describe the experimental realization and operation of dielectric gradient metasurface optical elements capable of also achieving high efficiencies in transmission mode in the visible spectrum. Ultrathin gratings, lenses, and axicons have been realized by patterning a 100-nanometer-thick Si layer into a dense arrangement of Si nanobeam antennas. The use of semiconductors can broaden the general applicability of gradient metasurfaces, as they offer facile integration with electronics and can be realized by mature semiconductor fabrication technologies.
Commonwealth Scientific and Industrial Research Organisation1, Rutgers University2, Heidelberg Institute for Theoretical Studies3, University of Jena4, University of Bonn5, Naturhistorisches Museum6, University of Vienna7, University of Tsukuba8, Landcare Research9, Johns Hopkins University10, University of Hamburg11, Ehime University12, Florida Museum of Natural History13, Staatliches Museum für Naturkunde Stuttgart14, National Evolutionary Synthesis Center15, Macquarie University16, Australian National University17, American Museum of Natural History18, University of Memphis19, University of Guadalajara20, Bavarian Academy of Sciences and Humanities21, Natural History Museum22, Karlsruhe Institute of Technology23, California Academy of Sciences24, South China Agricultural University25, North Carolina State University26, Hokkaido University27
TL;DR: The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
TL;DR: In this article, 3D Dirac fermions with linear dispersions along all momentum directions were detected in 3D topological Dirac semimetals (TDSs) with angle-resolved photoemission spectroscopy.
Abstract: Three-dimensional (3D) topological Dirac semimetals (TDSs) represent an unusual state of quantum matter that can be viewed as “3D graphene.” In contrast to 2D Dirac fermions in graphene or on the surface of 3D topological insulators, TDSs possess 3D Dirac fermions in the bulk. By investigating the electronic structure of Na 3 Bi with angle-resolved photoemission spectroscopy, we detected 3D Dirac fermions with linear dispersions along all momentum directions. Furthermore, we demonstrated the robustness of 3D Dirac fermions in Na 3 Bi against in situ surface doping. Our results establish Na 3 Bi as a model system for 3D TDSs, which can serve as an ideal platform for the systematic study of quantum phase transitions between rich topological quantum states.
TL;DR: A variety of reaction types have now been shown to be amenable to visible light photocatalysis via photoinduced electron transfer to or from the transition metal chromophore, as well as energy-transfer processes.
Abstract: Background Interest in photochemical synthesis has been motivated in part by the realization that sunlight is effectively an inexhaustible energy source.Chemists have also long recognized distinctive patterns of reactivity that are uniquely accessible via photochemical activation. However, most simple organic molecules absorb only ultraviolet (UV) light and cannot be activated by the visible wavelengths that comprise most of the solar energy that reaches Earth’s surface. Consequently, organic photochemistry has generally required the use of UV light sources. Visible light photocatalysis. ( A ) Transition metal photocatalysts, such as Ru(bpy) 3 2+ , readily absorb visible light to access reactive excited states. ( B ) Photoexcited Ru*(bpy) 3 2+ can act as an electron shuttle, interacting with sacrificial electron donors D (path i) or acceptors A (path ii) to yield either a strongly reducing or oxidizing catalyst toward organic substrates S. Ru*(bpy) 3 2+ can also directly transfer energy to an organic substrate to yield electronically excited species (path iii). bpy, 2,29-bipyridine; MLCT, metal-to-ligand charge transfer. Advances Over the past several years, there has been a resurgence of interest in synthetic photochemistry, based on the recognition that the transition metal chromophores that have been so productively exploited in the design of technologies for solar energy conversion can also convert visible light energy into useful chemical potential for synthetic purposes. Visible light enables productive photoreactions of compounds possessing weak bonds that are sensitive toward UV photodegradation. Furthermore, visible light photoreactions can be conducted by using essentially any source of white light, including sunlight, which obviates the need for specialized UV photoreactors. This feature has expanded the accessibility of photochemical reactions to a broader range of synthetic organic chemists. A variety of reaction types have now been shown to be amenable to visible light photocatalysis via photoinduced electron transfer to or from the transition metal chromophore, as well as energy-transfer processes. The predictable reactivity of the intermediates generated and the tolerance of the reaction conditions to a wide range of functional groups have enabled the application of these reactions to the synthesis of increasingly complex target molecules. Outlook This general strategy for the use of visible light in organic synthesis is already being adopted by a growing community of synthetic chemists. Much of the current research in this emerging area is geared toward the discovery of photochemical solutions for increasingly ambitious synthetic goals. Visible light photocatalysis is also attracting the attention of researchers in chemical biology, materials science, and drug discovery, who recognize that these reactions offer opportunities for innovation in areas beyond traditional organic synthesis. The long-term goals of this emerging area are to continue to improve efficiency and synthetic utility and to realize the long-standing goal of performing chemical synthesis using the sun.
Duke University1, University of Texas at Austin2, Heidelberg Institute for Theoretical Studies3, American Museum of Natural History4, Beijing Genomics Institute5, Xi'an Jiaotong University6, New Mexico State University7, University of Sydney8, University of California9, Uppsala University10, University of Copenhagen11, Okinawa Institute of Science and Technology12, University of Georgia13, Griffith University14, Catalan Institution for Research and Advanced Studies15, Joint Institute for Nuclear Research16, Oak Ridge National Laboratory17, Aarhus University18, Washington University in St. Louis19, University of California, Santa Cruz20, Cardiff University21, Kunming Institute of Zoology22, China Agricultural University23, Louisiana State University24, Tulane University25, Copenhagen Zoo26, Oregon Health & Science University27, Federal University of Pará28, Technical University of Denmark29, Canterbury Museum30, Curtin University31, Novosibirsk State University32, Smithsonian Institution33, National University of Singapore34, National Museum of Natural History35, Nova Southeastern University36, Occidental College37, University of Edinburgh38, Harvard University39, University of California, San Francisco40, University of Florida41, University of Illinois at Urbana–Champaign42
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
TL;DR: These studies illustrated two key events in structural organization during organogenesis: cell sorting out and spatially restricted lineage commitment, which are recapitulated in organoids, which self-assemble to form the cellular organization of the organ itself.
Abstract: Classical experiments performed half a century ago demonstrated the immense self-organizing capacity of vertebrate cells. Even after complete dissociation, cells can reaggregate and reconstruct the original architecture of an organ. More recently, this outstanding feature was used to rebuild organ parts or even complete organs from tissue or embryonic stem cells. Such stem cell-derived three-dimensional cultures are called organoids. Because organoids can be grown from human stem cells and from patient-derived induced pluripotent stem cells, they have the potential to model human development and disease. Furthermore, they have potential for drug testing and even future organ replacement strategies. Here, we summarize this rapidly evolving field and outline the potential of organoid technology for future biomedical research.
University of Évry Val d'Essonne1, Crops Research Institute2, Agriculture and Agri-Food Canada3, J. Craig Venter Institute4, Fujian Agriculture and Forestry University5, Plant Genome Mapping Laboratory6, University of Giessen7, French Alternative Energies and Atomic Energy Commission8, Institut national de la recherche agronomique9, National Research Council10, Australian Centre for Plant Functional Genomics11, University of Cologne12, Purdue University13, University of California, Berkeley14, University of British Columbia15, Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain16, Huazhong Agricultural University17, Hunan Agricultural University18, Chungnam National University19, University of Arizona20, University of York21, University of Missouri22, Southern Cross University23, University of Western Australia24, Centre national de la recherche scientifique25
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
TL;DR: An automated massively parallel single-cell RNA sequencing approach for analyzing in vivo transcriptional states in thousands of single cells is introduced and provides the ability to perform a bottom-up characterization of in vivo cell-type landscapes independent of cell markers or prior knowledge.
Abstract: In multicellular organisms, biological function emerges when heterogeneous cell types form complex organs. Nevertheless, dissection of tissues into mixtures of cellular subpopulations is currently challenging. We introduce an automated massively parallel single-cell RNA sequencing (RNA-seq) approach for analyzing in vivo transcriptional states in thousands of single cells. Combined with unsupervised classification algorithms, this facilitates ab initio cell-type characterization of splenic tissues. Modeling single-cell transcriptional states in dendritic cells and additional hematopoietic cell types uncovers rich cell-type heterogeneity and gene-modules activity in steady state and after pathogen activation. Cellular diversity is thereby approached through inference of variable and dynamic pathway activity rather than a fixed preprogrammed cell-type hierarchy. These data demonstrate single-cell RNA-seq as an effective tool for comprehensive cellular decomposition of complex tissues.
Academy of Sciences of the Czech Republic1, University of Saskatchewan2, Bayer3, Kansas State University4, University of California, Riverside5, Blaise Pascal University6, Kyoto University7, University of Dundee8, Punjab Agricultural University9, Indian Agricultural Research Institute10, University of Delhi11, University of Tsukuba12, Yokohama City University13, National Research Council14, Norwegian University of Life Sciences15, Sainsbury Laboratory16, Leibniz Association17, United States Department of Energy18, James Hutton Institute19, Institut national de la recherche agronomique20, University of Zurich21, Sabancı University22, Murdoch University23
TL;DR: Insight into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Abstract: An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Howard Hughes Medical Institute1, Florida State University2, University of the Sciences3, National Institutes of Health4, University of Minnesota5, University of Cambridge6, University of California, San Francisco7, University of Tennessee8, Max Planck Society9, Johns Hopkins University10, Duke University11
TL;DR: A new microscope using ultrathin light sheets derived from two-dimensional optical lattices is developed, demonstrating the performance advantages of lattice light-sheet microscopy compared with previous techniques and highlighted phenomena that, when seen at increased spatiotemporal detail, may hint at previously unknown biological mechanisms.
Abstract: Although fluorescence microscopy provides a crucial window into the physiology of living specimens, many biological processes are too fragile, are too small, or occur too rapidly to see clearly with existing tools. We crafted ultrathin light sheets from two-dimensional optical lattices that allowed us to image three-dimensional (3D) dynamics for hundreds of volumes, often at subsecond intervals, at the diffraction limit and beyond. We applied this to systems spanning four orders of magnitude in space and time, including the diffusion of single transcription factor molecules in stem cell spheroids, the dynamic instability of mitotic microtubules, the immunological synapse, neutrophil motility in a 3D matrix, and embryogenesis in Caenorhabditis elegans and Drosophila melanogaster. The results provide a visceral reminder of the beauty and the complexity of living systems.