scispace - formally typeset
Search or ask a question

Showing papers in "Science in 2008"


Journal ArticleDOI
Changgu Lee1, Xiaoding Wei1, Jeffrey W. Kysar1, James Hone1, James Hone2 
18 Jul 2008-Science
TL;DR: Graphene is established as the strongest material ever measured, and atomically perfect nanoscale materials can be mechanically tested to deformations well beyond the linear regime.
Abstract: We measured the elastic properties and intrinsic breaking strength of free-standing monolayer graphene membranes by nanoindentation in an atomic force microscope. The force-displacement behavior is interpreted within a framework of nonlinear elastic stress-strain response, and yields second- and third-order elastic stiffnesses of 340 newtons per meter (N m(-1)) and -690 Nm(-1), respectively. The breaking strength is 42 N m(-1) and represents the intrinsic strength of a defect-free sheet. These quantities correspond to a Young's modulus of E = 1.0 terapascals, third-order elastic stiffness of D = -2.0 terapascals, and intrinsic strength of sigma(int) = 130 gigapascals for bulk graphite. These experiments establish graphene as the strongest material ever measured, and show that atomically perfect nanoscale materials can be mechanically tested to deformations well beyond the linear regime.

18,008 citations


Journal ArticleDOI
06 Jun 2008-Science
TL;DR: It is shown that the opacity of suspended graphene is defined solely by the fine structure constant, a = e2/hc � 1/137 (where c is the speed of light), the parameter that describes coupling between light and relativistic electrons and that is traditionally associated with quantum electrodynamics rather than materials science.
Abstract: There are few phenomena in condensed matter physics that are defined only by the fundamental constants and do not depend on material parameters. Examples are the resistivity quantum, h/e2 (h is Planck's constant and e the electron charge), that appears in a variety of transport experiments and the magnetic flux quantum, h/e, playing an important role in the physics of superconductivity. By and large, sophisticated facilities and special measurement conditions are required to observe any of these phenomena. We show that the opacity of suspended graphene is defined solely by the fine structure constant, a = e2/hc feminine 1/137 (where c is the speed of light), the parameter that describes coupling between light and relativistic electrons and that is traditionally associated with quantum electrodynamics rather than materials science. Despite being only one atom thick, graphene is found to absorb a significant (pa = 2.3%) fraction of incident white light, a consequence of graphene's unique electronic structure.

7,952 citations


Journal ArticleDOI
15 Feb 2008-Science
TL;DR: This article developed an ecosystem-specific, multiscale spatial model to synthesize 17 global data sets of anthropogenic drivers of ecological change for 20 marine ecosystems and found that no area is unaffected by human influence and that a large fraction (41%) is strongly affected by multiple drivers.
Abstract: The management and conservation of the world's oceans require synthesis of spatial data on the distribution and intensity of human activities and the overlap of their impacts on marine ecosystems. We developed an ecosystem-specific, multiscale spatial model to synthesize 17 global data sets of anthropogenic drivers of ecological change for 20 marine ecosystems. Our analysis indicates that no area is unaffected by human influence and that a large fraction (41%) is strongly affected by multiple drivers. However, large areas of relatively little human impact remain, particularly near the poles. The analytical process and resulting maps provide flexible tools for regional and global efforts to allocate conservation resources; to implement ecosystem-based management; and to inform marine spatial planning, education, and basic research.

5,365 citations


Journal ArticleDOI
26 Sep 2008-Science
TL;DR: Recurrent mutations in the active site of isocitrate dehydrogenase 1 (IDH1) occurred in a large fraction of young patients and in most patients with secondary GBMs and were associated with an increase in overall survival.
Abstract: Glioblastoma multiforme (GBM) is the most common and lethal type of brain cancer. To identify the genetic alterations in GBMs, we sequenced 20,661 protein coding genes, determined the presence of amplifications and deletions using high-density oligonucleotide arrays, and performed gene expression analyses using next-generation sequencing technologies in 22 human tumor samples. This comprehensive analysis led to the discovery of a variety of genes that were not known to be altered in GBMs. Most notably, we found recurrent mutations in the active site of isocitrate dehydrogenase 1 (IDH1) in 12% of GBM patients. Mutations in IDH1 occurred in a large fraction of young patients and in most patients with secondary GBMs and were associated with an increase in overall survival. These studies demonstrate the value of unbiased genomic analyses in the characterization of human brain cancer and identify a potentially useful genetic alteration for the classification and targeted therapy of GBMs.

5,250 citations


Journal ArticleDOI
16 May 2008-Science
TL;DR: Optimizing the need for a key human resource while minimizing its negative consequences requires an integrated interdisciplinary approach and the development of strategies to decrease nitrogen-containing waste.
Abstract: Humans continue to transform the global nitrogen cycle at a record pace, reflecting an increased combustion of fossil fuels, growing demand for nitrogen in agriculture and industry, and pervasive inefficiencies in its use. Much anthropogenic nitrogen is lost to air, water, and land to cause a cascade of environmental and human health problems. Simultaneously, food production in some parts of the world is nitrogen-deficient, highlighting inequities in the distribution of nitrogen-containing fertilizers. Optimizing the need for a key human resource while minimizing its negative consequences requires an integrated interdisciplinary approach and the development of strategies to decrease nitrogen-containing waste.

5,249 citations


Journal ArticleDOI
08 Feb 2008-Science
TL;DR: Urban ecology integrates natural and social sciences to study these radically altered local environments and their regional and global effects of an increasingly urbanized world.
Abstract: Urban areas are hot spots that drive environmental change at multiple scales. Material demands of production and human consumption alter land use and cover, biodiversity, and hydrosystems locally to regionally, and urban waste discharge affects local to global biogeochemical cycles and climate. For urbanites, however, global environmental changes are swamped by dramatic changes in the local environment. Urban ecology integrates natural and social sciences to study these radically altered local environments and their regional and global effects. Cities themselves present both the problems and solutions to sustainability challenges of an increasingly urbanized world.

5,096 citations


Journal ArticleDOI
12 Sep 2008-Science
TL;DR: Thermoelectric materials are solid-state energy converters whose combination of thermal, electrical, and semiconductor properties allows them to be used to convert waste heat into electricity or electrical power directly into cooling and heating.
Abstract: Thermoelectric materials are solid-state energy converters whose combination of thermal, electrical, and semiconducting properties allows them to be used to convert waste heat into electricity or electrical power directly into cooling and heating. These materials can be competitive with fluid-based systems, such as two-phase air-conditioning compressors or heat pumps, or used in smaller-scale applications such as in automobile seats, night-vision systems, and electrical-enclosure cooling. More widespread use of thermoelectrics requires not only improving the intrinsic energy-conversion efficiency of the materials but also implementing recent advancements in system architecture. These principles are illustrated with several proven and potential applications of thermoelectrics.

4,700 citations


Journal ArticleDOI
29 Feb 2008-Science
TL;DR: This article found that corn-based ethanol, instead of producing a 20% savings, nearly doubled greenhouse emissions over 30 years and increased greenhouse gases for 167 years, by using a worldwide agricultural model to estimate emissions from land-use change.
Abstract: Most prior studies have found that substituting biofuels for gasoline will reduce greenhouse gases because biofuels sequester carbon through the growth of the feedstock. These analyses have failed to count the carbon emissions that occur as farmers worldwide respond to higher prices and convert forest and grassland to new cropland to replace the grain (or cropland) diverted to biofuels. By using a worldwide agricultural model to estimate emissions from land-use change, we found that corn-based ethanol, instead of producing a 20% savings, nearly doubles greenhouse emissions over 30 years and increases greenhouse gases for 167 years. Biofuels from switchgrass, if grown on U.S. corn lands, increase emissions by 50%. This result raises concerns about large biofuel mandates and highlights the value of using waste products.

4,696 citations


Journal ArticleDOI
02 May 2008-Science
TL;DR: Electrical transport measurements, coupled with microstructure studies and modeling, show that the ZT improvement is the result of low thermal conductivity caused by the increased phonon scattering by grain boundaries and defects, which makes these materials useful for cooling and power generation.
Abstract: The dimensionless thermoelectric figure of merit (ZT) in bismuth antimony telluride (BiSbTe) bulk alloys has remained around 1 for more than 50 years. We show that a peak ZT of 1.4 at 100°C can be achieved in a p-type nanocrystalline BiSbTe bulk alloy. These nanocrystalline bulk materials were made by hot pressing nanopowders that were ball-milled from crystalline ingots under inert conditions. Electrical transport measurements, coupled with microstructure studies and modeling, show that the ZT improvement is the result of low thermal conductivity caused by the increased phonon scattering by grain boundaries and defects. More importantly, ZT is about 1.2 at room temperature and 0.8 at 250°C, which makes these materials useful for cooling and power generation. Cooling devices that use these materials have produced high-temperature differences of 86°, 106°, and 119°C with hot-side temperatures set at 50°, 100°, and 150°C, respectively. This discovery sets the stage for use of a new nanocomposite approach in developing high-performance low-cost bulk thermoelectric materials.

4,695 citations


Journal ArticleDOI
15 Aug 2008-Science
TL;DR: Dead zones in the coastal oceans have spread exponentially since the 1960s and have serious consequences for ecosystem functioning, exacerbated by the increase in primary production and consequent worldwide coastal eutrophication fueled by riverine runoff of fertilizers and the burning of fossil fuels.
Abstract: Dead zones in the coastal oceans have spread exponentially since the 1960s and have serious consequences for ecosystem functioning. The formation of dead zones has been exacerbated by the increase in primary production and consequent worldwide coastal eutrophication fueled by riverine runoff of fertilizers and the burning of fossil fuels. Enhanced primary production results in an accumulation of particulate organic matter, which encourages microbial activity and the consumption of dissolved oxygen in bottom waters. Dead zones have now been reported from more than 400 systems, affecting a total area of more than 245,000 square kilometers, and are probably a key stressor on marine ecosystems.

4,667 citations


Journal ArticleDOI
Xiaolin Li1, Xinran Wang1, Li Zhang1, Sangwon Lee1, Hongjie Dai1 
29 Feb 2008-Science
TL;DR: A chemical route to produce graphene nanoribbons with width below 10 nanometers was developed, as well as single ribbons with varying widths along their lengths or containing lattice-defined graphene junctions for potential molecular electronics.
Abstract: We developed a chemical route to produce graphene nanoribbons (GNR) with width below 10 nanometers, as well as single ribbons with varying widths along their lengths or containing lattice-defined graphene junctions for potential molecular electronics. The GNRs were solution-phase-derived, stably suspended in solvents with noncovalent polymer functionalization, and exhibited ultrasmooth edges with possibly well-defined zigzag or armchair-edge structures. Electrical transport experiments showed that, unlike single-walled carbon nanotubes, all of the sub-10-nanometer GNRs produced were semiconductors and afforded graphene field effect transistors with on-off ratios of about 10(7) at room temperature.

Journal ArticleDOI
13 Jun 2008-Science
TL;DR: Interdisciplinary science that integrates knowledge of the many interacting climate services of forests with the impacts of global change is necessary to identify and understand as yet unexplored feedbacks in the Earth system and the potential of forests to mitigate climate change.
Abstract: The world's forests influence climate through physical, chemical, and biological processes that affect planetary energetics, the hydrologic cycle, and atmospheric composition. These complex and nonlinear forest-atmosphere interactions can dampen or amplify anthropogenic climate change. Tropical, temperate, and boreal reforestation and afforestation attenuate global warming through carbon sequestration. Biogeophysical feedbacks can enhance or diminish this negative climate forcing. Tropical forests mitigate warming through evaporative cooling, but the low albedo of boreal forests is a positive climate forcing. The evaporative effect of temperate forests is unclear. The net climate forcing from these and other processes is not known. Forests are under tremendous pressure from global change. Interdisciplinary science that integrates knowledge of the many interacting climate services of forests with the impacts of global change is necessary to identify and understand as yet unexplored feedbacks in the Earth system and the potential of forests to mitigate climate change.

Journal ArticleDOI
01 Aug 2008-Science
TL;DR: Electrochemical capacitors enable rapid storage and efficient delivery of electrical energy in heavy-duty applications and are being enabled by electrochemical capacitor technology.
Abstract: Rapid storage and efficient delivery of electrical energy in heavy-duty applications are being enabled by electrochemical capacitors.

Journal ArticleDOI
11 Apr 2008-Science
TL;DR: The racetrack memory described in this review comprises an array of magnetic nanowires arranged horizontally or vertically on a silicon chip and is an example of the move toward innately three-dimensional microelectronic devices.
Abstract: Recent developments in the controlled movement of domain walls in magnetic nanowires by short pulses of spin-polarized current give promise of a nonvolatile memory device with the high performance and reliability of conventional solid-state memory but at the low cost of conventional magnetic disk drive storage. The racetrack memory described in this review comprises an array of magnetic nanowires arranged horizontally or vertically on a silicon chip. Individual spintronic reading and writing nanodevices are used to modify or read a train of ∼10 to 100 domain walls, which store a series of data bits in each nanowire. This racetrack memory is an example of the move toward innately three-dimensional microelectronic devices.

Journal ArticleDOI
29 Feb 2008-Science
TL;DR: Converting rainforests, peatlands, savannas, or grasslands to produce food crop–based biofuels in Brazil, Southeast Asia, and the United States creates a “biofuel carbon debt” by releasing 17 to 420 times more CO2 than the annual greenhouse gas reductions that these biofuel reductions would provide by displacing fossil fuels.
Abstract: Increasing energy use, climate change, and carbon dioxide (CO2) emissions from fossil fuels make switching to lowcarbon fuels a high priority. Biofuels are a potential lowcarbon energy source, but whether biofuels offer carbon savings depends on how they are produced. Converting rainforests, peatlands, savannas, or grasslands to produce food-based biofuels in Brazil, Southeast Asia, and the United States creates a ‘biofuel carbon debt’ by releasing 17 to 420 times more CO2 than the annual greenhouse gas (GHG) reductions these biofuels provide by displacing fossil fuels. In contrast, biofuels made from waste biomass or from biomass grown on abandoned agricultural lands planted with perennials incur little or no carbon debt and offer immediate and sustained GHG advantages. Demand for alternatives to petroleum is increasing the production of biofuels from food crops such as corn, sugarcane, soybeans and palms. As a result, land in

Journal ArticleDOI
26 Sep 2008-Science
TL;DR: It is found that pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations, which defined a core set of 12 cellular signaling pathways and processes that were each genetically altered in 67 to 100% of the tumors.
Abstract: There are currently few therapeutic options for patients with pancreatic cancer, and new insights into the pathogenesis of this lethal disease are urgently needed. Toward this end, we performed a comprehensive genetic analysis of 24 pancreatic cancers. We first determined the sequences of 23,219 transcripts, representing 20,661 protein-coding genes, in these samples. Then, we searched for homozygous deletions and amplifications in the tumor DNA by using microarrays containing probes for approximately 10(6) single-nucleotide polymorphisms. We found that pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations. These alterations defined a core set of 12 cellular signaling pathways and processes that were each genetically altered in 67 to 100% of the tumors. Analysis of these tumors' transcriptomes with next-generation sequencing-by-synthesis technologies provided independent evidence for the importance of these pathways and processes. Our data indicate that genetically altered core pathways and regulatory processes only become evident once the coding regions of the genome are analyzed in depth. Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis.

Journal ArticleDOI
22 Aug 2008-Science
TL;DR: A catalyst that forms upon the oxidative polarization of an inert indium tin oxide electrode in phosphate-buffered water containing cobalt (II) ions is reported that not only forms in situ from earth-abundant materials but also operates in neutral water under ambient conditions.
Abstract: The utilization of solar energy on a large scale requires its storage. In natural photosynthesis, energy from sunlight is used to rearrange the bonds of water to oxygen and hydrogen equivalents. The realization of artificial systems that perform "water splitting" requires catalysts that produce oxygen from water without the need for excessive driving potentials. Here we report such a catalyst that forms upon the oxidative polarization of an inert indium tin oxide electrode in phosphate-buffered water containing cobalt (II) ions. A variety of analytical techniques indicates the presence of phosphate in an approximate 1:2 ratio with cobalt in this material. The pH dependence of the catalytic activity also implicates the hydrogen phosphate ion as the proton acceptor in the oxygen-producing reaction. This catalyst not only forms in situ from earth-abundant materials but also operates in neutral water under ambient conditions.

Journal ArticleDOI
01 Feb 2008-Science
TL;DR: Climate change undermines a basic assumption that historically has facilitated management of water supplies, demands, and risks and threatens to derail efforts to conserve and manage water resources.
Abstract: Climate change undermines a basic assumption that historically has facilitated management of water supplies, demands, and risks.

Journal ArticleDOI
25 Jul 2008-Science
TL;DR: A successful implementation through the use of the thallium impurity levels in lead telluride (PbTe) is reported, which results in a doubling of zT in p-type PbTe to above 1.5 at 773 kelvin.
Abstract: The efficiency of thermoelectric energy converters is limited by the material thermoelectric figure of merit (zT). The recent advances in zT based on nanostructures limiting the phonon heat conduction is nearing a fundamental limit: The thermal conductivity cannot be reduced below the amorphous limit. We explored enhancing the Seebeck coefficient through a distortion of the electronic density of states and report a successful implementation through the use of the thallium impurity levels in lead telluride (PbTe). Such band structure engineering results in a doubling of zT in p-type PbTe to above 1.5 at 773 kelvin. Use of this new physical principle in conjunction with nanostructuring to lower the thermal conductivity could further enhance zT and enable more widespread use of thermoelectric systems.

Journal ArticleDOI
15 Feb 2008-Science
TL;DR: Members of a selection of zeolitic imidazolate frameworks have high thermal stability and chemical stability in refluxing organic and aqueous media, and they exhibit unusual selectivity for CO2 capture from CO2/CO mixtures and extraordinary capacity for storing CO2.
Abstract: A high-throughput protocol was developed for the synthesis of zeolitic imidazolate frameworks (ZIFs). Twenty-five different ZIF crystals were synthesized from only 9600 microreactions of either zinc(II)/cobalt(II) and imidazolate/imidazolate-type linkers. All of the ZIF structures have tetrahedral frameworks: 10 of which have two different links (heterolinks), 16 of which are previously unobserved compositions and structures, and 5 of which have topologies as yet unobserved in zeolites. Members of a selection of these ZIFs (termed ZIF-68, ZIF-69, and ZIF-70) have high thermal stability (up to 390°C) and chemical stability in refluxing organic and aqueous media. Their frameworks have high porosity (with surface areas up to 1970 square meters per gram), and they exhibit unusual selectivity for CO 2 capture from CO 2 /CO mixtures and extraordinary capacity for storing CO 2 : 1 liter of ZIF-69 can hold ∼83 liters of CO 2 at 273 kelvin under ambient pressure.

Journal ArticleDOI
20 Jun 2008-Science
TL;DR: It is indicated that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
Abstract: Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.

Journal ArticleDOI
01 Feb 2008-Science
TL;DR: Results indicate South Asia and Southern Africa as two regions that, without sufficient adaptation measures, will likely suffer negative impacts on several crops that are important to large food-insecure human populations.
Abstract: Investments aimed at improving agricultural adaptation to climate change inevitably favor some crops and regions over others. An analysis of climate risks for crops in 12 food-insecure regions was conducted to identify adaptation priorities, based on statistical crop models and climate projections for 2030 from 20 general circulation models. Results indicate South Asia and Southern Africa as two regions that, without sufficient adaptation measures, will likely suffer negative impacts on several crops that are important to large food-insecure human populations. We also find that uncertainties vary widely by crop, and therefore priorities will depend on the risk attitudes of investment institutions.

Journal ArticleDOI
29 Feb 2008-Science
TL;DR: It is found that cargo is segregated into distinct subdomains on the endosomal membrane and that the transfer of exosome-associated domains into the lumen of theendosome did not depend on the function of the ESCRT (endosomal sorting complex required for transport) machinery, but required the sphingolipid ceramide.
Abstract: Intraluminal vesicles of multivesicular endosomes are either sorted for cargo degradation into lysosomes or secreted as exosomes into the extracellular milieu. The mechanisms underlying the sorting of membrane into the different populations of intraluminal vesicles are unknown. Here, we find that cargo is segregated into distinct subdomains on the endosomal membrane and that the transfer of exosome-associated domains into the lumen of the endosome did not depend on the function of the ESCRT (endosomal sorting complex required for transport) machinery, but required the sphingolipid ceramide. Purified exosomes were enriched in ceramide, and the release of exosomes was reduced after the inhibition of neutral sphingomyelinases. These results establish a pathway in intraendosomal membrane transport and exosome formation.

PatentDOI
08 Oct 2008-Science
TL;DR: Based on analysis of exons representing 20,857 transcripts from 18,191 genes, the authors concluded that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene "mountains" and a much larger number of gene "hills" that are mutated at low frequency.
Abstract: Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalogue the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene “mountains” and a much larger number of gene “hills” that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.

Journal ArticleDOI
22 Feb 2008-Science
TL;DR: In six of eight MCV-positive MCCs, viral DNA was integrated within the tumor genome in a clonal pattern, suggesting that MCV infection and integration preceded clonal expansion of the tumor cells, and MCV may be a contributing factor in the pathogenesis of MCC.
Abstract: Merkel cell carcinoma (MCC) is a rare but aggressive human skin cancer that typically affects elderly and immunosuppressed individuals, a feature suggestive of an infectious origin. We studied MCC samples by digital transcriptome subtraction and detected a fusion transcript between a previously undescribed virus T antigen and a human receptor tyrosine phosphatase. Further investigation led to identification and sequence analysis of the 5387-base-pair genome of a previously unknown polyomavirus that we call Merkel cell polyomavirus (MCV or MCPyV). MCV sequences were detected in 8 of 10 (80%) MCC tumors but only 5 of 59 (8%) control tissues from various body sites and 4 of 25 (16%) control skin tissues. In six of eight MCV-positive MCCs, viral DNA was integrated within the tumor genome in a clonal pattern, suggesting that MCV infection and integration preceded clonal expansion of the tumor cells. Thus, MCV may be a contributing factor in the pathogenesis of MCC.

Journal ArticleDOI
10 Oct 2008-Science
TL;DR: It is shown that a specific deficiency of cytotoxic T lymphocyte antigen 4 (CTLA-4) in Tregs results in spontaneous development of systemic lymphoproliferation, fatal T cell–mediated autoimmune disease, and hyperproduction of immunoglobulin E in mice.
Abstract: Naturally occurring Foxp3+CD4+ regulatory T cells (Tregs) are essential for maintaining immunological self-tolerance and immune homeostasis. Here, we show that a specific deficiency of cytotoxic T lymphocyte antigen 4 (CTLA-4) in Tregs results in spontaneous development of systemic lymphoproliferation, fatal T cell-mediated autoimmune disease, and hyperproduction of immunoglobulin E in mice, and it also produces potent tumor immunity. Treg-specific CTLA-4 deficiency impairs in vivo and in vitro suppressive function of Tregs-in particular, Treg-mediated down-regulation of CD80 and CD86 expression on dendritic cells. Thus, natural Tregs may critically require CTLA-4 to suppress immune responses by affecting the potency of antigen-presenting cells to activate other T cells.

Journal ArticleDOI
08 Feb 2008-Science
TL;DR: 3D stochastic optical reconstruction microscopy (STORM) is demonstrated by using optical astigmatism to determine both axial and lateral positions of individual fluorophores with nanometer accuracy, allowing the 3D morphology of nanoscopic cellular structures to be resolved.
Abstract: Recent advances in far-field fluorescence microscopy have led to substantial improvements in image resolution, achieving a near-molecular resolution of 20 to 30 nanometers in the two lateral dimensions. Three-dimensional (3D) nanoscale-resolution imaging, however, remains a challenge. We demonstrated 3D stochastic optical reconstruction microscopy (STORM) by using optical astigmatism to determine both axial and lateral positions of individual fluorophores with nanometer accuracy. Iterative, stochastic activation of photoswitchable probes enables high-precision 3D localization of each probe, and thus the construction of a 3D image, without scanning the sample. Using this approach, we achieved an image resolution of 20 to 30 nanometers in the lateral dimensions and 50 to 60 nanometers in the axial dimension. This development allowed us to resolve the 3D morphology of nanoscopic cellular structures.

Journal ArticleDOI
06 Jun 2008-Science
TL;DR: A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.
Abstract: The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.

Journal ArticleDOI
13 Jun 2008-Science
TL;DR: It is found that the Rag proteins—a family of four related small guanosine triphosphatases (GTPases)—interact with mTORC1 in an amino acid–sensitive manner and are necessary for the activation of the m TORC1 pathway by amino acids.
Abstract: The multiprotein mTORC1 protein kinase complex is the central component of a pathway that promotes growth in response to insulin, energy levels, and amino acids and is deregulated in common cancers. We find that the Rag proteins--a family of four related small guanosine triphosphatases (GTPases)--interact with mTORC1 in an amino acid-sensitive manner and are necessary for the activation of the mTORC1 pathway by amino acids. A Rag mutant that is constitutively bound to guanosine triphosphate interacted strongly with mTORC1, and its expression within cells made the mTORC1 pathway resistant to amino acid deprivation. Conversely, expression of a guanosine diphosphate-bound Rag mutant prevented stimulation of mTORC1 by amino acids. The Rag proteins do not directly stimulate the kinase activity of mTORC1, but, like amino acids, promote the intracellular localization of mTOR to a compartment that also contains its activator Rheb.

Journal ArticleDOI
21 Mar 2008-Science
TL;DR: The evidence suggests a pathophysiological link between TDP-43 and ALS, and neighboring mutations in a highly conserved region of TARDBP in sporadic and familial ALS cases.
Abstract: Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disorder characterized pathologically by ubiquitinated TAR DNA binding protein (TDP-43) inclusions. The function of TDP-43 in the nervous system is uncertain, and a mechanistic role in neurodegeneration remains speculative. We identified neighboring mutations in a highly conserved region of TARDBP in sporadic and familial ALS cases. TARDBPM337V segregated with disease within one kindred and a genome-wide scan confirmed that linkage was restricted to chromosome 1p36, which contains the TARDBP locus. Mutant forms of TDP-43 fragmented in vitro more readily than wild type and, in vivo, caused neural apoptosis and developmental delay in the chick embryo. Our evidence suggests a pathophysiological link between TDP-43 and ALS.