Showing papers in "Science in 2013"
TL;DR: The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage as discussed by the authors.
Abstract: Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
12,265 citations
TL;DR: Metal-organic frameworks are porous materials that have potential for applications such as gas storage and separation, as well as catalysis, and methods are being developed for making nanocrystals and supercrystals of MOFs for their incorporation into devices.
Abstract: Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.
10,934 citations
TL;DR: In this article, transient absorption and photoluminescence-quenching measurements were performed to determine the electron-hole diffusion lengths, diffusion constants, and lifetimes in mixed halide and triiodide perovskite absorbers.
Abstract: Organic-inorganic perovskites have shown promise as high-performance absorbers in solar cells, first as a coating on a mesoporous metal oxide scaffold and more recently as a solid layer in planar heterojunction architectures. Here, we report transient absorption and photoluminescence-quenching measurements to determine the electron-hole diffusion lengths, diffusion constants, and lifetimes in mixed halide (CH3NH3PbI(3-x)Cl(x)) and triiodide (CH3NH3PbI3) perovskite absorbers. We found that the diffusion lengths are greater than 1 micrometer in the mixed halide perovskite, which is an order of magnitude greater than the absorption depth. In contrast, the triiodide absorber has electron-hole diffusion lengths of ~100 nanometers. These results justify the high efficiency of planar heterojunction perovskite solar cells and identify a critical parameter to optimize for future perovskite absorber development.
8,199 citations
TL;DR: The type II bacterial CRISPR system is engineer to function with custom guide RNA (gRNA) in human cells to establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
Abstract: Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cells. We show that this process relies on CRISPR components; is sequence-specific; and, upon simultaneous introduction of multiple gRNAs, can effect multiplex editing of target loci. We also compute a genome-wide resource of ~190 K unique gRNAs targeting ~40.5% of human exons. Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
8,197 citations
TL;DR: Intensive forestry practiced within subtropical forests resulted in the highest rates of forest change globally, and boreal forest loss due largely to fire and forestry was second to that in the tropics in absolute and proportional terms.
Abstract: Quantification of global forest change has been lacking despite the recognized importance of forest ecosystem services. In this study, Earth observation satellite data were used to map global forest loss (2.3 million square kilometers) and gain (0.8 million square kilometers) from 2000 to 2012 at a spatial resolution of 30 meters. The tropics were the only climate domain to exhibit a trend, with forest loss increasing by 2101 square kilometers per year. Brazil's well-documented reduction in deforestation was offset by increasing forest loss in Indonesia, Malaysia, Paraguay, Bolivia, Zambia, Angola, and elsewhere. Intensive forestry practiced within subtropical forests resulted in the highest rates of forest change globally. Boreal forest loss due largely to fire and forestry was second to that in the tropics in absolute and proportional terms. These results depict a globally consistent and locally relevant record of forest change.
7,890 citations
TL;DR: This work has revealed the genomic landscapes of common forms of human cancer, which consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of "hills" (Genes altered infrequently).
Abstract: Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.
6,441 citations
TL;DR: Two studies show, using a variety of time-resolved absorption and emission spectroscopic techniques, that perovskite materials manifest relatively long diffusion paths for charge carriers energized by light absorption, highlighting effective carrier diffusion as a fruitful parameter for further optimization.
Abstract: Low-temperature solution-processed photovoltaics suffer from low efficiencies because of poor exciton or electron-hole diffusion lengths (typically about 10 nanometers). Recent reports of highly efficient CH3NH3PbI3-based solar cells in a broad range of configurations raise a compelling case for understanding the fundamental photophysical mechanisms in these materials. By applying femtosecond transient optical spectroscopy to bilayers that interface this perovskite with either selective-electron or selective-hole extraction materials, we have uncovered concrete evidence of balanced long-range electron-hole diffusion lengths of at least 100 nanometers in solution-processed CH3NH3PbI3. The high photoconversion efficiencies of these systems stem from the comparable optical absorption length and charge-carrier diffusion lengths, transcending the traditional constraints of solution-processed semiconductors.
5,882 citations
TL;DR: Although not yet providing compelling mechanical strength or electrical or thermal conductivities for many applications, CNT yarns and sheets already have promising performance for applications including supercapacitors, actuators, and lightweight electromagnetic shields.
Abstract: Worldwide commercial interest in carbon nanotubes (CNTs) is reflected in a production capacity that presently exceeds several thousand tons per year. Currently, bulk CNT powders are incorporated in diverse commercial products ranging from rechargeable batteries, automotive parts, and sporting goods to boat hulls and water filters. Advances in CNT synthesis, purification, and chemical modification are enabling integration of CNTs in thin-film electronics and large-area coatings. Although not yet providing compelling mechanical strength or electrical or thermal conductivities for many applications, CNT yarns and sheets already have promising performance for applications including supercapacitors, actuators, and lightweight electromagnetic shields.
4,596 citations
TL;DR: This study determined that short-chain fatty acids, gut microbiota–derived bacterial fermentation products, regulate the size and function of the colonic Treg pool and protect against colitis in a Ffar2-dependent manner in mice, revealing that a class of abundant microbial metabolites underlies adaptive immune microbiota coadaptation and promotes colonic homeostasis and health.
Abstract: Regulatory T cells (T regs ) that express the transcription factor Foxp3 are critical for regulating intestinal inflammation. Candidate microbe approaches have identified bacterial species and strain-specific molecules that can affect intestinal immune responses, including species that modulate T reg responses. Because neither all humans nor mice harbor the same bacterial strains, we posited that more prevalent factors exist that regulate the number and function of colonic T regs . We determined that short-chain fatty acids, gut microbiota–derived bacterial fermentation products, regulate the size and function of the colonic T reg pool and protect against colitis in a Ffar2 -dependent manner in mice. Our study reveals that a class of abundant microbial metabolites underlies adaptive immune microbiota coadaptation and promotes colonic homeostasis and health.
3,733 citations
TL;DR: It is reported that sleep has a critical function in ensuring metabolic homeostasis and convective fluxes of interstitial fluid increased the rate of β-amyloid clearance during sleep, suggesting the restorative function of sleep may be a consequence of the enhanced removal of potentially neurotoxic waste products that accumulate in the awake central nervous system.
Abstract: The conservation of sleep across all animal species suggests that sleep serves a vital function. We here report that sleep has a critical function in ensuring metabolic homeostasis. Using real-time assessments of tetramethylammonium diffusion and two-photon imaging in live mice, we show that natural sleep or anesthesia are associated with a 60% increase in the interstitial space, resulting in a striking increase in convective exchange of cerebrospinal fluid with interstitial fluid. In turn, convective fluxes of interstitial fluid increased the rate of β-amyloid clearance during sleep. Thus, the restorative function of sleep may be a consequence of the enhanced removal of potentially neurotoxic waste products that accumulate in the awake central nervous system.
3,303 citations
Max Planck Society1, McGill University2, University of Toronto3, University of Manchester4, University of Sheffield5, German Aerospace Center6, University of Amsterdam7, ASTRON8, Lebedev Physical Institute9, University of Warwick10, West Virginia University11, University of Virginia12, National Radio Astronomy Observatory13, University of British Columbia14
TL;DR: Pulsar J0348+0432 is only the second neutron star with a precisely determined mass of 2 M☉
Abstract: Many physically motivated extensions to general relativity (GR) predict significant deviations at energies present in massive neutron stars. We report the measurement of a 2.01 \(\pm \) 0.04 solar mass (M\(_\odot \)) pulsar in a 2.46-h orbit around a 0.172 \(\pm \) 0.003 M\(_\odot \) white dwarf. The high pulsar mass and the compact orbit make this system a sensitive laboratory of a previously untested strong-field gravity regime. Thus far, the observed orbital decay agrees with GR, supporting its validity even for the extreme conditions present in the system. The resulting constraints on deviations support the use of GR-based templates for ground-based gravitational wave detection experiments. Additionally, the system strengthens recent constraints on the properties of dense matter and provides novel insight to binary stellar astrophysics and pulsar recycling.
TL;DR: A number of methods have been developed to exfoliate layered materials in order to produce monolayer nanosheets, which are ideal for applications that require surface activity.
Abstract: Background Since at least 400 C.E., when the Mayans first used layered clays to make dyes, people have been harnessing the properties of layered materials. This gradually developed into scientific research, leading to the elucidation of the laminar structure of layered materials, detailed understanding of their properties, and eventually experiments to exfoliate or delaminate them into individual, atomically thin nanosheets. This culminated in the discovery of graphene, resulting in a new explosion of interest in two-dimensional materials. Layered materials consist of two-dimensional platelets weakly stacked to form three-dimensional structures. The archetypal example is graphite, which consists of stacked graphene monolayers. However, there are many others: from MoS 2 and layered clays to more exotic examples such as MoO 3 , GaTe, and Bi 2 Se 3 . These materials display a wide range of electronic, optical, mechanical, and electrochemical properties. Over the past decade, a number of methods have been developed to exfoliate layered materials in order to produce monolayer nanosheets. Such exfoliation creates extremely high-aspect-ratio nanosheets with enormous surface area, which are ideal for applications that require surface activity. More importantly, however, the two-dimensional confinement of electrons upon exfoliation leads to unprecedented optical and electrical properties. Liquid exfoliation of layered crystals allows the production of suspensions of two-dimensional nanosheets, which can be formed into a range of structures. (A) MoS 2 powder. (B) WS 2 dispersed in surfactant solution. (C) An exfoliated MoS 2 nanosheet. (D) A hybrid material consisting of WS 2 nanosheets embedded in a network of carbon nanotubes. Advances An important advance has been the discovery that layered crystals can be exfoliated in liquids. There are a number of methods to do this that involve oxidation, ion intercalation/exchange, or surface passivation by solvents. However, all result in liquid dispersions containing large quantities of nanosheets. This brings considerable advantages: Liquid exfoliation allows the formation of thin films and composites, is potentially scaleable, and may facilitate processing by using standard technologies such as reel-to-reel manufacturing. Although much work has focused on liquid exfoliation of graphene, such processes have also been demonstrated for a host of other materials, including MoS 2 and related structures, layered oxides, and clays. The resultant liquid dispersions have been formed into films, hybrids, and composites for a range of applications. Outlook There is little doubt that the main advances are in the future. Multifunctional composites based on metal and polymer matrices will be developed that will result in enhanced mechanical, electrical, and barrier properties. Applications in energy generation and storage will abound, with layered materials appearing as electrodes or active elements in devices such as displays, solar cells, and batteries. Particularly important will be the use of MoS 2 for water splitting and metal oxides as hydrogen evolution catalysts. In addition, two-dimensional materials will find important roles in printed electronics as dielectrics, optoelectronic devices, and transistors. To achieve this, much needs to be done. Production rates need to be increased dramatically, the degree of exfoliation improved, and methods to control nanosheet properties developed. The range of layered materials that can be exfoliated must be expanded, even as methods for chemical modification must be developed. Success in these areas will lead to a family of materials that will dominate nanomaterials science in the 21st century.
TL;DR: Results indicate that cGAS is a cytosolic DNA sensor that induces interferons by producing the second messenger cGAMP, which belongs to the nucleotidyltransferase family.
Abstract: The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers host immune responses such as the production of type I interferons. Cytosolic DNA induces interferons through the production of cyclic guanosine monophosphate–adenosine monophosphate (cyclic GMP-AMP, or cGAMP), which binds to and activates the adaptor protein STING. Through biochemical fractionation and quantitative mass spectrometry, we identified a cGAMP synthase (cGAS), which belongs to the nucleotidyltransferase family. Overexpression of cGAS activated the transcription factor IRF3 and induced interferon-β in a STING-dependent manner. Knockdown of cGAS inhibited IRF3 activation and interferon-β induction by DNA transfection or DNA virus infection. cGAS bound to DNA in the cytoplasm and catalyzed cGAMP synthesis. These results indicate that cGAS is a cytosolic DNA sensor that induces interferons by producing the second messenger cGAMP.
TL;DR: This study demonstrates the spontaneous intercalation of cations from aqueous salt solutions between two-dimensional (2D) Ti3C2 MXene layers, and provides a basis for exploring a large family of 2D carbides and carbonitrides in electrochemical energy storage applications using single- and multivalent ions.
Abstract: The intercalation of ions into layered compounds has long been exploited in energy storage devices such as batteries and electrochemical capacitors However, few host materials are known for ions much larger than lithium We demonstrate the spontaneous intercalation of cations from aqueous salt solutions between two-dimensional (2D) Ti3C2 MXene layers MXenes combine 2D conductive carbide layers with a hydrophilic, primarily hydroxyl-terminated surface A variety of cations, including Na+, K+, NH4+, Mg2+, and Al3+, can also be intercalated electrochemically, offering capacitance in excess of 300 farads per cubic centimeter (much higher than that of porous carbons) This study provides a basis for exploring a large family of 2D carbides and carbonitrides in electrochemical energy storage applications using single- and multivalent ions
TL;DR: The observation of the quantum anomalous Hall (QAH) effect in thin films of chromium-doped (Bi,Sb)2Te3, a magnetic topological insulator shows a plateau in the Hall resistance as a function of the gating voltage without any applied magnetic fields, signifying the achievement of the QAH state.
Abstract: The quantized version of the anomalous Hall effect has been predicted to occur in magnetic topological insulators, but the experimental realization has been challenging. Here, we report the observation of the quantum anomalous Hall (QAH) effect in thin films of chromium-doped (Bi,Sb)2Te3, a magnetic topological insulator. At zero magnetic field, the gate-tuned anomalous Hall resistance reaches the predicted quantized value of h/e2, accompanied by a considerable drop in the longitudinal resistance. Under a strong magnetic field, the longitudinal resistance vanishes, whereas the Hall resistance remains at the quantized value. The realization of the QAH effect may lead to the development of low-power-consumption electronics.
TL;DR: The results reveal that transmissible and modifiable interactions between diet and microbiota influence host biology and that adiposity is transmissible from human to mouse and that it was associated with changes in serum levels of branched-chain amino acids.
Abstract: How much does the microbiota influence the host's phenotype? Ridaura et al. ([1241214][1] ; see the Perspective by [ Walker and Parkhill ][2]) obtained uncultured fecal microbiota from twin pairs discordant for body mass and transplanted them into adult germ-free mice. It was discovered that adiposity is transmissible from human to mouse and that it was associated with changes in serum levels of branched-chain amino acids. Moreover, obese-phenotype mice were invaded by members of the Bacteroidales from the lean mice, but, happily, the lean animals resisted invasion by the obese microbiota.
[1]: http://www.sciencemag.org/content/341/6150/1241214.full
[2]: /lookup/doi/10.1126/science.1243787
TL;DR: In graphene heterostructures, the edge-contact geometry provides new design possibilities for multilayered structures of complimentary 2D materials, and enables high electronic performance, including low-temperature ballistic transport over distances longer than 15 micrometers, and room-tem temperature mobility comparable to the theoretical phonon-scattering limit.
Abstract: Heterostructures based on layering of two-dimensional (2D) materials such as graphene and hexagonal boron nitride represent a new class of electronic devices. Realizing this potential, however, depends critically on the ability to make high-quality electrical contact. Here, we report a contact geometry in which we metalize only the 1D edge of a 2D graphene layer. In addition to outperforming conventional surface contacts, the edge-contact geometry allows a complete separation of the layer assembly and contact metallization processes. In graphene heterostructures, this enables high electronic performance, including low-temperature ballistic transport over distances longer than 15 micrometers, and room-temperature mobility comparable to the theoretical phonon-scattering limit. The edge-contact geometry provides new design possibilities for multilayered structures of complimentary 2D materials.
TL;DR: Progress in the optics of metasurfaces is reviewed and promising applications for surface-confined planar photonics components are discussed and the studies of new, low-loss, tunable plasmonic materials—such as transparent conducting oxides and intermetallics—that can be used as building blocks for metAsurfaces will complement the exploration of smart designs and advanced switching capabilities.
Abstract: Metamaterials, or engineered materials with rationally designed, subwavelength-scale building blocks, allow us to control the behavior of physical fields in optical, microwave, radio, acoustic, heat transfer, and other applications with flexibility and performance that are unattainable with naturally available materials. In turn, metasurfaces-planar, ultrathin metamaterials-extend these capabilities even further. Optical metasurfaces offer the fascinating possibility of controlling light with surface-confined, flat components. In the planar photonics concept, it is the reduced dimensionality of the optical metasurfaces that enables new physics and, therefore, leads to functionalities and applications that are distinctly different from those achievable with bulk, multilayer metamaterials. Here, we review the progress in developing optical metasurfaces that has occurred over the past few years with an eye toward the promising future directions in the field.
TL;DR: The viability of using the orbital angular momentum (OAM) of light to create orthogonal, spatially distinct streams of data-transmitting channels that are multiplexed in a single fiber is demonstrated and suggest that OAM could provide an additional degree of freedom for data multiplexing in future fiber networks.
Abstract: Internet data traffic capacity is rapidly reaching limits imposed by optical fiber nonlinear effects Having almost exhausted available degrees of freedom to orthogonally multiplex data, the possibility is now being explored of using spatial modes of fibers to enhance data capacity We demonstrate the viability of using the orbital angular momentum (OAM) of light to create orthogonal, spatially distinct streams of data-transmitting channels that are multiplexed in a single fiber Over 11 kilometers of a specially designed optical fiber that minimizes mode coupling, we achieved 400-gigabits-per-second data transmission using four angular momentum modes at a single wavelength, and 16 terabits per second using two OAM modes over 10 wavelengths These demonstrations suggest that OAM could provide an additional degree of freedom for data multiplexing in future fiber networks
TL;DR: Transition metal dichalcogenides sandwiched between two layers of graphene produce an enhanced photoresponse, which allows development of extremely efficient flexible photovoltaic devices with photoresponsivity above 0.1 ampere per watt (corresponding to an external quantum efficiency of above 30%).
Abstract: The isolation of various two-dimensional (2D) materials, and the possibility to combine them in vertical stacks, has created a new paradigm in materials science: heterostructures based on 2D crystals. Such a concept has already proven fruitful for a number of electronic applications in the area of ultrathin and flexible devices. Here, we expand the range of such structures to photoactive ones by using semiconducting transition metal dichalcogenides (TMDCs)/graphene stacks. Van Hove singularities in the electronic density of states of TMDC guarantees enhanced light-matter interactions, leading to enhanced photon absorption and electron-hole creation (which are collected in transparent graphene electrodes). This allows development of extremely efficient flexible photovoltaic devices with photoresponsivity above 0.1 ampere per watt (corresponding to an external quantum efficiency of above 30%).
TL;DR: A role for EMT in the blood-borne dissemination of human breast cancer is supported as both single cells and multicellular clusters, expressing known EMT regulators, including transforming growth factor (TGF)–β pathway components and the FOXC1 transcription factor.
Abstract: Epithelial-mesenchymal transition (EMT) of adherent epithelial cells to a migratory mesenchymal state has been implicated in tumor metastasis in preclinical models. To investigate its role in human cancer, we characterized EMT in circulating tumor cells (CTCs) from breast cancer patients. Rare primary tumor cells simultaneously expressed mesenchymal and epithelial markers, but mesenchymal cells were highly enriched in CTCs. Serial CTC monitoring in 11 patients suggested an association of mesenchymal CTCs with disease progression. In an index patient, reversible shifts between these cell fates accompanied each cycle of response to therapy and disease progression. Mesenchymal CTCs occurred as both single cells and multicellular clusters, expressing known EMT regulators, including transforming growth factor (TGF)–β pathway components and the FOXC1 transcription factor. These data support a role for EMT in the blood-borne dissemination of human breast cancer.
TL;DR: The evidence supports the need for considerable investment in adaptation and mitigation actions toward a “climate-smart food system” that is more resilient to climate change influences on food security.
Abstract: Climate change could potentially interrupt progress toward a world without hunger. A robust and coherent global pattern is discernible of the impacts of climate change on crop productivity that could have consequences for food availability. The stability of whole food systems may be at risk under climate change because of short-term variability in supply. However, the potential impact is less clear at regional scales, but it is likely that climate variability and change will exacerbate food insecurity in areas currently vulnerable to hunger and undernutrition. Likewise, it can be anticipated that food access and utilization will be affected indirectly via collateral effects on household and individual incomes, and food utilization could be impaired by loss of access to drinking water and damage to health. The evidence supports the need for considerable investment in adaptation and mitigation actions toward a “climate-smart food system” that is more resilient to climate change influences on food security.
TL;DR: For the first time, physicists will have to master quantum error correction to design and operate complex active systems that are dissipative in nature, yet remain coherent indefinitely.
Abstract: The performance of superconducting qubits has improved by several orders of magnitude in the past decade. These circuits benefit from the robustness of superconductivity and the Josephson effect, and at present they have not encountered any hard physical limits. However, building an error-corrected information processor with many such qubits will require solving specific architecture problems that constitute a new field of research. For the first time, physicists will have to master quantum error correction to design and operate complex active systems that are dissipative in nature, yet remain coherent indefinitely. We offer a view on some directions for the field and speculate on its future.
National University of Río Negro1, University of Würzburg2, Rutgers University3, National University of Comahue4, Swedish University of Agricultural Sciences5, Commonwealth Scientific and Industrial Research Organisation6, University of California, Berkeley7, Naturalis8, University of Leeds9, University of Calgary10, Hebrew University of Jerusalem11, Lüneburg University12, ETH Zurich13, National University of Tucumán14, Federal University of Ceará15, Federal University of Bahia16, Plant & Food Research17, Michigan State University18, Agriculture and Agri-Food Canada19, The Nature Conservancy20, University of Göttingen21, University of Queensland22, Cornell University23, University of Reading24, Stockholm University25, University of Vermont26, Lund University27, University of Bern28, University of Koblenz and Landau29, Jagiellonian University30, Universidad de las Américas Puebla31, University of California, Davis32
TL;DR: Overall, wild insects pollinated crops more effectively; an increase in wild insect visitation enhanced fruit set by twice as much as an equivalent increase in honey bee visitation.
Abstract: The diversity and abundance of wild insect pollinators have declined in many agricultural landscapes. Whether such declines reduce crop yields, or are mitigated by managed pollinators such as honey bees, is unclear. We found universally positive associations of fruit set with flower visitation by wild insects in 41 crop systems worldwide. In contrast, fruit set increased significantly with flower visitation by honey bees in only 14% of the systems surveyed. Overall, wild insects pollinated crops more effectively; an increase in wild insect visitation enhanced fruit set by twice as much as an equivalent increase in honey bee visitation. Visitation by wild insects and honey bees promoted fruit set independently, so pollination by managed honey bees supplemented, rather than substituted for, pollination by wild insects. Our results suggest that new practices for integrated management of both honey bees and diverse wild insect assemblages will enhance global crop yields.
TL;DR: It is suggested that poverty-related concerns consume mental resources, leaving less for other tasks, because poverty itself reduces cognitive capacity.
Abstract: The poor often behave in less capable ways, which can further perpetuate poverty. We hypothesize that poverty directly impedes cognitive function and present two studies that test this hypothesis. First, we experimentally induced thoughts about finances and found that this reduces cognitive performance among poor but not in well-off participants. Second, we examined the cognitive function of farmers over the planting cycle. We found that the same farmer shows diminished cognitive performance before harvest, when poor, as compared with after harvest, when rich. This cannot be explained by differences in time available, nutrition, or work effort. Nor can it be explained with stress: Although farmers do show more stress before harvest, that does not account for diminished cognitive performance. Instead, it appears that poverty itself reduces cognitive capacity. We suggest that this is because poverty-related concerns consume mental resources, leaving less for other tasks. These data provide a previously unexamined perspective and help explain a spectrum of behaviors among the poor. We discuss some implications for poverty policy.
TL;DR: The current understanding of the causes and mechanics of earthquakes caused by human activity, including injection of wastewater into deep formations and emerging technologies related to oil and gas recovery, is reviewed.
Abstract: Background Human-induced earthquakes have become an important topic of political and scientific discussion, owing to the concern that these events may be responsible for widespread damage and an overall increase in seismicity. It has long been known that impoundment of reservoirs, surface and underground mining, withdrawal of fluids and gas from the subsurface, and injection of fluids into underground formations are capable of inducing earthquakes. In particular, earthquakes caused by injection have become a focal point, as new drilling and well-completion technologies enable the extraction of oil and gas from previously unproductive formations. Earthquakes with magnitude (M) ≥ 3 in the U.S. midcontinent, 1967–2012. After decades of a steady earthquake rate (average of 21 events/year), activity increased starting in 2001 and peaked at 188 earthquakes in 2011. Human-induced earthquakes are suspected to be partially responsible for the increase. Advances Microearthquakes (that is, those with magnitudes below 2) are routinely produced as part of the hydraulic fracturing (or “fracking”) process used to stimulate the production of oil, but the process as currently practiced appears to pose a low risk of inducing destructive earthquakes. More than 100,000 wells have been subjected to fracking in recent years, and the largest induced earthquake was magnitude 3.6, which is too small to pose a serious risk. Yet, wastewater disposal by injection into deep wells poses a higher risk, because this practice can induce larger earthquakes. For example, several of the largest earthquakes in the U.S. midcontinent in 2011 and 2012 may have been triggered by nearby disposal wells. The largest of these was a magnitude 5.6 event in central Oklahoma that destroyed 14 homes and injured two people. The mechanism responsible for inducing these events appears to be the well-understood process of weakening a preexisting fault by elevating the fluid pressure. However, only a small fraction of the more than 30,000 wastewater disposal wells appears to be problematic—typically those that dispose of very large volumes of water and/or communicate pressure perturbations directly into basement faults. Outlook Injection-induced earthquakes, such as those that struck in 2011, clearly contribute to the seismic hazard. Quantifying their contribution presents difficult challenges that will require new research into the physics of induced earthquakes and the potential for inducing large-magnitude events. The petroleum industry needs clear requirements for operation, regulators must have a solid scientific basis for those requirements, and the public needs assurance that the regulations are sufficient and are being followed. The current regulatory frameworks for wastewater disposal wells were designed to protect potable water sources from contamination and do not address seismic safety. One consequence is that both the quantity and timeliness of information on injection volumes and pressures reported to regulatory agencies are far from ideal for managing earthquake risk from injection activities. In addition, seismic monitoring capabilities in many of the areas in which wastewater injection activities have increased are not capable of detecting small earthquake activity that may presage larger seismic events.
TL;DR: Cytosolic DNA induces type I interferons and other cytokines that are important for antimicrobial defense but can also result in autoimmunity, and cGAMP functions as an endogenous second messenger in metazoans and triggers interferon production in response to cytosolicDNA.
Abstract: Cytosolic DNA induces type I interferons and other cytokines that are important for antimicrobial defense but can also result in autoimmunity. This DNA signaling pathway requires the adaptor protein STING and the transcription factor IRF3, but the mechanism of DNA sensing is unclear. We found that mammalian cytosolic extracts synthesized cyclic guanosine monophosphate–adenosine monophosphate (cyclic GMP-AMP, or cGAMP) in vitro from adenosine triphosphate and guanosine triphosphate in the presence of DNA but not RNA. DNA transfection or DNA virus infection of mammalian cells also triggered cGAMP production. cGAMP bound to STING, leading to the activation of IRF3 and induction of interferon-β. Thus, cGAMP functions as an endogenous second messenger in metazoans and triggers interferon production in response to cytosolic DNA.
TL;DR: Low-error sequencing data suggest that initial microbial colonizers of infant guts could persist over the life span of an individual, and members of Bacteroidetes and Actinobacteria are significantly more stable components than the population average.
Abstract: A low-error 16S ribosomal RNA amplicon sequencing method, in combination with whole-genome sequencing of >500 cultured isolates, was used to characterize bacterial strain composition in the fecal microbiota of 37 U.S. adults sampled for up to 5 years. Microbiota stability followed a power-law function, which when extrapolated suggests that most strains in an individual are residents for decades. Shared strains were recovered from family members but not from unrelated individuals. Sampling of individuals who consumed a monotonous liquid diet for up to 32 weeks indicated that changes in strain composition were better predicted by changes in weight than by differences in sampling interval. This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target.
TL;DR: The results extend the knowledge of the unique role of DNA methylation in brain development and function, and offer a new framework for testing the role of the epigenome in healthy function and in pathological disruptions of neural circuits.
Abstract: DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Last, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain and that CG demethylation at these hmC-poised loci depends on Tet2 activity.