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Showing papers in "Nature in 2004"


Journal ArticleDOI
15 Sep 2004-Nature
TL;DR: Evidence is mounting that animal miRNAs are more numerous, and their regulatory impact more pervasive, than was previously suspected.
Abstract: MicroRNAs (miRNAs) are small RNAs that regulate the expression of complementary messenger RNAs. Hundreds of miRNA genes have been found in diverse animals, and many of these are phylogenetically conserved. With miRNA roles identified in developmental timing, cell death, cell proliferation, haematopoiesis and patterning of the nervous system, evidence is mounting that animal miRNAs are more numerous, and their regulatory impact more pervasive, than was previously suspected.

9,986 citations


Journal ArticleDOI
25 Nov 2004-Nature
TL;DR: A novel semiconducting material is proposed—namely, a transparent amorphous oxide semiconductor from the In-Ga-Zn-O system (a-IGZO)—for the active channel in transparent thin-film transistors (TTFTs), which are fabricated on polyethylene terephthalate sheets and exhibit saturation mobilities and device characteristics are stable during repetitive bending of the TTFT sheet.
Abstract: Transparent electronic devices formed on flexible substrates are expected to meet emerging technological demands where silicon-based electronics cannot provide a solution. Examples of active flexible applications include paper displays and wearable computers1. So far, mainly flexible devices based on hydrogenated amorphous silicon (a-Si:H)2,3,4,5 and organic semiconductors2,6,7,8,9,10 have been investigated. However, the performance of these devices has been insufficient for use as transistors in practical computers and current-driven organic light-emitting diode displays. Fabricating high-performance devices is challenging, owing to a trade-off between processing temperature and device performance. Here, we propose to solve this problem by using a novel semiconducting material—namely, a transparent amorphous oxide semiconductor from the In-Ga-Zn-O system (a-IGZO)—for the active channel in transparent thin-film transistors (TTFTs). The a-IGZO is deposited on polyethylene terephthalate at room temperature and exhibits Hall effect mobilities exceeding 10 cm2 V-1 s-1, which is an order of magnitude larger than for hydrogenated amorphous silicon. TTFTs fabricated on polyethylene terephthalate sheets exhibit saturation mobilities of 6–9 cm2 V-1 s-1, and device characteristics are stable during repetitive bending of the TTFT sheet.

7,301 citations


Journal ArticleDOI
18 Nov 2004-Nature
TL;DR: The development of a xenograft assay that identified human brain tumour initiating cells that initiate tumours in vivo gives strong support for the CSC hypothesis as the basis for many solid tumours, and establishes a previously unidentified cellular target for more effective cancer therapies.
Abstract: The cancer stem cell (CSC) hypothesis suggests that neoplastic clones are maintained exclusively by a rare fraction of cells with stem cell properties. Although the existence of CSCs in human leukaemia is established, little evidence exists for CSCs in solid tumours, except for breast cancer. Recently, we prospectively isolated a CD133+ cell subpopulation from human brain tumours that exhibited stem cell properties in vitro. However, the true measures of CSCs are their capacity for self renewal and exact recapitulation of the original tumour. Here we report the development of a xenograft assay that identified human brain tumour initiating cells that initiate tumours in vivo. Only the CD133+ brain tumour fraction contains cells that are capable of tumour initiation in NOD-SCID (non-obese diabetic, severe combined immunodeficient) mouse brains. Injection of as few as 100 CD133+ cells produced a tumour that could be serially transplanted and was a phenocopy of the patient's original tumour, whereas injection of 10(5) CD133- cells engrafted but did not cause a tumour. Thus, the identification of brain tumour initiating cells provides insights into human brain tumour pathogenesis, giving strong support for the CSC hypothesis as the basis for many solid tumours, and establishes a previously unidentified cellular target for more effective cancer therapies.

7,120 citations


Journal ArticleDOI
08 Jan 2004-Nature
TL;DR: Estimates of extinction risks for sample regions that cover some 20% of the Earth's terrestrial surface show the importance of rapid implementation of technologies to decrease greenhouse gas emissions and strategies for carbon sequestration.
Abstract: Climate change over the past approximately 30 years has produced numerous shifts in the distributions and abundances of species and has been implicated in one species-level extinction. Using projections of species' distributions for future climate scenarios, we assess extinction risks for sample regions that cover some 20% of the Earth's terrestrial surface. Exploring three approaches in which the estimated probability of extinction shows a power-law relationship with geographical range size, we predict, on the basis of mid-range climate-warming scenarios for 2050, that 15-37% of species in our sample of regions and taxa will be 'committed to extinction'. When the average of the three methods and two dispersal scenarios is taken, minimal climate-warming scenarios produce lower projections of species committed to extinction ( approximately 18%) than mid-range ( approximately 24%) and maximum-change ( approximately 35%) scenarios. These estimates show the importance of rapid implementation of technologies to decrease greenhouse gas emissions and strategies for carbon sequestration.

7,089 citations


Journal ArticleDOI
22 Apr 2004-Nature
TL;DR: Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.
Abstract: Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.

6,360 citations


Journal ArticleDOI
29 Apr 2004-Nature
TL;DR: The future holds even greater promise for this technology, with an entirely new generation of ultralow-cost, lightweight and even flexible electronic devices in the offing, which will perform functions traditionally accomplished using much more expensive components based on conventional semiconductor materials such as silicon.
Abstract: Organic electronics are beginning to make significant inroads into the commercial world, and if the field continues to progress at its current, rapid pace, electronics based on organic thin-film materials will soon become a mainstay of our technological existence. Already products based on active thin-film organic devices are in the market place, most notably the displays of several mobile electronic appliances. Yet the future holds even greater promise for this technology, with an entirely new generation of ultralow-cost, lightweight and even flexible electronic devices in the offing, which will perform functions traditionally accomplished using much more expensive components based on conventional semiconductor materials such as silicon.

4,967 citations


Journal ArticleDOI
04 Nov 2004-Nature
TL;DR: A lead-free piezoelectric ceramic with an electric-field-induced strain comparable to typical actuator-grade PZT is reported, achieved through the combination of the discovery of a morphotropic phase boundary in an alkaline niobate-based perovskite solid solution, and the development of a processing route leading to highly textured polycrystals.
Abstract: Lead has recently been expelled from many commercial applications and materials (for example, from solder, glass and pottery glaze) owing to concerns regarding its toxicity. Lead zirconium titanate (PZT) ceramics are high-performance piezoelectric materials, which are widely used in sensors, actuators and other electronic devices; they contain more than 60 weight per cent lead. Although there has been a concerted effort to develop lead-free piezoelectric ceramics, no effective alternative to PZT has yet been found. Here we report a lead-free piezoelectric ceramic with an electric-field-induced strain comparable to typical actuator-grade PZT. We achieved this through the combination of the discovery of a morphotropic phase boundary in an alkaline niobate-based perovskite solid solution, and the development of a processing route leading to highly textured polycrystals. The ceramic exhibits a piezoelectric constant d33 (the induced charge per unit force applied in the same direction) of above 300 picocoulombs per newton (pC N(-1)), and texturing the material leads to a peak d33 of 416 pC N(-1). The textured material also exhibits temperature-independent field-induced strain characteristics.

4,689 citations


Journal ArticleDOI
21 Oct 2004-Nature
TL;DR: The current human genome sequence (Build 35) as discussed by the authors contains 2.85 billion nucleotides interrupted by only 341 gaps and is accurate to an error rate of approximately 1 event per 100,000 bases.
Abstract: The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers approximately 99% of the euchromatic genome and is accurate to an error rate of approximately 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.

3,989 citations


Journal ArticleDOI
29 Jan 2004-Nature
TL;DR: A model interface is examined between two insulating perovskite oxides—LaAlO3 and SrTiO3—in which the termination layer at the interface is controlled on an atomic scale, presenting a broad opportunity to tailor low-dimensional charge states by atomically engineered oxide heteroepitaxy.
Abstract: Polarity discontinuities at the interfaces between different crystalline materials (heterointerfaces) can lead to nontrivial local atomic and electronic structure, owing to the presence of dangling bonds and incomplete atomic coordinations. These discontinuities often arise in naturally layered oxide structures, such as the superconducting copper oxides and ferroelectric titanates, as well as in artificial thin film oxide heterostructures such as manganite tunnel junctions. If polarity discontinuities can be atomically controlled, unusual charge states that are inaccessible in bulk materials could be realized. Here we have examined a model interface between two insulating perovskite oxides--LaAlO3 and SrTiO3--in which we control the termination layer at the interface on an atomic scale. In the simple ionic limit, this interface presents an extra half electron or hole per two-dimensional unit cell, depending on the structure of the interface. The hole-doped interface is found to be insulating, whereas the electron-doped interface is conducting, with extremely high carrier mobility exceeding 10,000 cm2 V(-1) s(-1). At low temperature, dramatic magnetoresistance oscillations periodic with the inverse magnetic field are observed, indicating quantum transport. These results present a broad opportunity to tailor low-dimensional charge states by atomically engineered oxide heteroepitaxy.

3,977 citations


Journal ArticleDOI
09 Sep 2004-Nature
TL;DR: It is shown that the strong coupling regime can be attained in a solid-state system, and the concept of circuit quantum electrodynamics opens many new possibilities for studying the strong interaction of light and matter.
Abstract: The interaction of matter and light is one of the fundamental processes occurring in nature, and its most elementary form is realized when a single atom interacts with a single photon. Reaching this regime has been a major focus of research in atomic physics and quantum optics1 for several decades and has generated the field of cavity quantum electrodynamics2,3. Here we perform an experiment in which a superconducting two-level system, playing the role of an artificial atom, is coupled to an on-chip cavity consisting of a superconducting transmission line resonator. We show that the strong coupling regime can be attained in a solid-state system, and we experimentally observe the coherent interaction of a superconducting two-level system with a single microwave photon. The concept of circuit quantum electrodynamics opens many new possibilities for studying the strong interaction of light and matter. This system can also be exploited for quantum information processing and quantum communication and may lead to new approaches for single photon generation and detection.

3,452 citations


Journal ArticleDOI
27 May 2004-Nature
TL;DR: Great potential lies in the development of ‘epigenetic therapies’ — several inhibitors of enzymes controlling epigenetic modifications, specifically DNA methyltransferases and histone deacetylases, have shown promising anti-tumorigenic effects for some malignancies.
Abstract: Epigenetic mechanisms, which involve DNA and histone modifications, result in the heritable silencing of genes without a change in their coding sequence. The study of human disease has focused on genetic mechanisms, but disruption of the balance of epigenetic networks can cause several major pathologies, including cancer, syndromes involving chromosomal instabilities, and mental retardation. The development of new diagnostic tools might reveal other diseases that are caused by epigenetic alterations. Great potential lies in the development of ‘epigenetic therapies’ — several inhibitors of enzymes controlling epigenetic modifications, specifically DNA methyltransferases and histone deacetylases, have shown promising anti-tumorigenic effects for some malignancies.

Journal ArticleDOI
24 Jun 2004-Nature
TL;DR: The ecological roles of critical functional groups (for both corals and reef fishes) that are fundamental to understanding resilience and avoiding phase shifts from coral dominance to less desirable, degraded ecosystems are reviewed.
Abstract: The worldwide decline of coral reefs calls for an urgent reassessment of current management practices. Confronting large-scale crises requires a major scaling-up of management efforts based on an improved understanding of the ecological processes that underlie reef resilience. Managing for improved resilience, incorporating the role of human activity in shaping ecosystems, provides a basis for coping with uncertainty, future changes and ecological surprises. Here we review the ecological roles of critical functional groups (for both corals and reef fishes) that are fundamental to understanding resilience and avoiding phase shifts from coral dominance to less desirable, degraded ecosystems. We identify striking biogeographic differences in the species richness and composition of functional groups, which highlight the vulnerability of Caribbean reef ecosystems. These findings have profound implications for restoration of degraded reefs, management of fisheries, and the focus on marine protected areas and biodiversity hotspots as priorities for conservation.

Journal ArticleDOI
01 Apr 2004-Nature
TL;DR: New challenges and directions in biomaterials research are discussed, including synthetic replacements for biological tissues, designing materials for specific medical applications, and materials for new applications such as diagnostics and array technologies.
Abstract: Biomaterials have played an enormous role in the success of medical devices and drug delivery systems. We discuss here new challenges and directions in biomaterials research. These include synthetic replacements for biological tissues, designing materials for specific medical applications, and materials for new applications such as diagnostics and array technologies.

Journal ArticleDOI
05 Aug 2004-Nature
TL;DR: Rapid progress towards understanding the cellular and molecular alterations that are responsible for the neuron's demise may soon help in developing effective preventative and therapeutic strategies in Alzheimer's disease.
Abstract: Slowly but surely, Alzheimer's disease (AD) patients lose their memory and their cognitive abilities, and even their personalities may change dramatically. These changes are due to the progressive dysfunction and death of nerve cells that are responsible for the storage and processing of information. Although drugs can temporarily improve memory, at present there are no treatments that can stop or reverse the inexorable neurodegenerative process. But rapid progress towards understanding the cellular and molecular alterations that are responsible for the neuron's demise may soon help in developing effective preventative and therapeutic strategies.

Journal ArticleDOI
23 Dec 2004-Nature
TL;DR: The results suggest that the production of amino acids by autophagic degradation of ‘self’ proteins, which allows for the maintenance of energy homeostasis, is important for survival during neonatal starvation.
Abstract: At birth the trans-placental nutrient supply is suddenly interrupted, and neonates face severe starvation until supply can be restored through milk nutrients. Here, we show that neonates adapt to this adverse circumstance by inducing autophagy. Autophagy is the primary means for the degradation of cytoplasmic constituents within lysosomes. The level of autophagy in mice remains low during embryogenesis; however, autophagy is immediately upregulated in various tissues after birth and is maintained at high levels for 3-12 h before returning to basal levels within 1-2 days. Mice deficient for Atg5, which is essential for autophagosome formation, appear almost normal at birth but die within 1 day of delivery. The survival time of starved Atg5-deficient neonates (approximately 12 h) is much shorter than that of wild-type mice (approximately 21 h) but can be prolonged by forced milk feeding. Atg5-deficient neonates exhibit reduced amino acid concentrations in plasma and tissues, and display signs of energy depletion. These results suggest that the production of amino acids by autophagic degradation of 'self' proteins, which allows for the maintenance of energy homeostasis, is important for survival during neonatal starvation.

Journal ArticleDOI
11 Nov 2004-Nature
TL;DR: In vivo knock-down and in vitro reconstitution studies revealed that both components of this smaller complex, termed Microprocessor, are necessary and sufficient in mediating the genesis of miRNAs from the primary miRNA transcript.
Abstract: MicroRNAs (miRNAs) are a growing family of small non-protein-coding regulatory genes that regulate the expression of homologous target-gene transcripts. They have been implicated in the control of cell death and proliferation in flies, haematopoietic lineage differentiation in mammals, neuronal patterning in nematodes and leaf and flower development in plants. miRNAs are processed by the RNA-mediated interference machinery. Drosha is an RNase III enzyme that was recently implicated in miRNA processing. Here we show that human Drosha is a component of two multi-protein complexes. The larger complex contains multiple classes of RNA-associated proteins including RNA helicases, proteins that bind double-stranded RNA, novel heterogeneous nuclear ribonucleoproteins and the Ewing's sarcoma family of proteins. The smaller complex is composed of Drosha and the double-stranded-RNA-binding protein, DGCR8, the product of a gene deleted in DiGeorge syndrome. In vivo knock-down and in vitro reconstitution studies revealed that both components of this smaller complex, termed Microprocessor, are necessary and sufficient in mediating the genesis of miRNAs from the primary miRNA transcript.

Journal ArticleDOI
18 Nov 2004-Nature
TL;DR: All life on earth must cope with constant exposure to DNA-damaging agents such as the Sun's radiation, and how cells respond to DNA damage are critical determinants of whether that individual will develop cancer.
Abstract: All life on earth must cope with constant exposure to DNA-damaging agents such as the Sun's radiation. Highly conserved DNA-repair and cell-cycle checkpoint pathways allow cells to deal with both endogenous and exogenous sources of DNA damage. How much an individual is exposed to these agents and how their cells respond to DNA damage are critical determinants of whether that individual will develop cancer. These cellular responses are also important for determining toxicities and responses to current cancer therapies, most of which target the DNA.

Journal ArticleDOI
09 Sep 2004-Nature
TL;DR: BSCF is presented as a new cathode material for reduced-temperature SOFC operation and demonstrated that BSCF is ideally suited to ‘single-chamber’ fuel-cell operation, where anode and cathode reactions take place within the same physical chamber.
Abstract: Fuel cells directly and efficiently convert chemical energy to electrical energy. Of the various fuel cell types, solid-oxide fuel cells (SOFCs) combine the benefits of environmentally benign power generation with fuel flexibility. However, the necessity for high operating temperatures (800–1,000 °C) has resulted in high costs and materials compatibility challenges. As a consequence, significant effort has been devoted to the development of intermediate-temperature (500–700 °C) SOFCs. A key obstacle to reduced-temperature operation of SOFCs is the poor activity of traditional cathode materials for electrochemical reduction of oxygen in this temperature regime2. Here we present Ba_(0.5_Sr_(0.5)Co_(0.8)Fe_(0.2)O_(3-delta) (BSCF) as a new cathode material for reduced-temperature SOFC operation. BSCF, incorporated into a thin-film doped ceria fuel cell, exhibits high power densities (1,010 mW cm^(-2) and 402 mW cm^(-2) at 600 °C and 500 °C, respectively) when operated with humidified hydrogen as the fuel and air as the cathode gas. We further demonstrate that BSCF is ideally suited to 'single-chamber' fuel-cell operation, where anode and cathode reactions take place within the same physical chamber. The high power output of BSCF cathodes results from the high rate of oxygen diffusion through the material. By enabling operation at reduced temperatures, BSCF cathodes may result in widespread practical implementation of SOFCs.

Journal ArticleDOI
22 Jan 2004-Nature
TL;DR: It is found that an event like that of summer 2003 is statistically extremely unlikely, even when the observed warming is taken into account, and it is proposed that a regime with an increased variability of temperatures (in addition to increases in mean temperature) may be able to account for summer 2003.
Abstract: Instrumental observations1,2 and reconstructions3,4 of global and hemispheric temperature evolution reveal a pronounced warming during the past ∼150 years. One expression of this warming is the observed increase in the occurrence of heatwaves5,6. Conceptually this increase is understood as a shift of the statistical distribution towards warmer temperatures, while changes in the width of the distribution are often considered small7. Here we show that this framework fails to explain the record-breaking central European summer temperatures in 2003, although it is consistent with observations from previous years. We find that an event like that of summer 2003 is statistically extremely unlikely, even when the observed warming is taken into account. We propose that a regime with an increased variability of temperatures (in addition to increases in mean temperature) may be able to account for summer 2003. To test this proposal, we simulate possible future European climate with a regional climate model in a scenario with increased atmospheric greenhouse-gas concentrations, and find that temperature variability increases by up to 100%, with maximum changes in central and eastern Europe.

Journal ArticleDOI
11 Nov 2004-Nature
TL;DR: A role for Pasha is indicated in miRNA maturation and miRNA-mediated gene regulation in mature microRNAs and in the post-transcriptional level.
Abstract: Mature microRNAs (miRNAs) are generated via a two-step processing pathway to yield approximately 22-nucleotide small RNAs that regulate gene expression at the post-transcriptional level. Initial cleavage is catalysed by Drosha, a nuclease of the RNase III family, which acts on primary miRNA transcripts (pri-miRNAs) in the nucleus. Here we show that Drosha exists in a multiprotein complex, the Microprocessor, and begin the process of deconstructing that complex into its constituent components. Along with Drosha, the Microprocessor also contains Pasha (partner of Drosha), a double-stranded RNA binding protein. Suppression of Pasha expression in Drosophila cells or Caenorhabditis elegans interferes with pri-miRNA processing, leading to an accumulation of pri-miRNAs and a reduction in mature miRNAs. Finally, depletion or mutation of pash-1 in C. elegans causes de-repression of a let-7 reporter and the appearance of phenotypic defects overlapping those observed upon examination of worms with lesions in Dicer (dcr-1) or Drosha (drsh-1). Considered together, these results indicate a role for Pasha in miRNA maturation and miRNA-mediated gene regulation.

Journal ArticleDOI
LaDeana W. Hillier1, Webb Miller2, Ewan Birney, Wesley C. Warren1  +171 moreInstitutions (39)
09 Dec 2004-Nature
TL;DR: A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
Abstract: We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Journal ArticleDOI
05 Feb 2004-Nature
TL;DR: The design, synthesis and properties of crystalline Zn4O(1,3,5-benzenetribenzoate)2 are reported, a new metal-organic framework with a surface area estimated at 4,500 m2 g-1 that combines this exceptional level of surface area with an ordered structure that has extra-large pores capable of binding polycyclic organic guest molecules.
Abstract: One of the outstanding challenges in the field of porous materials is the design and synthesis of chemical structures with exceptionally high surface areas Such materials are of critical importance to many applications involving catalysis, separation and gas storage The claim for the highest surface area of a disordered structure is for carbon, at 2,030 m2 g(-1) (ref 2) Until recently, the largest surface area of an ordered structure was that of zeolite Y, recorded at 904 m2 g(-1) (ref 3) But with the introduction of metal-organic framework materials, this has been exceeded, with values up to 3,000 m2 g(-1) (refs 4-7) Despite this, no method of determining the upper limit in surface area for a material has yet been found Here we present a general strategy that has allowed us to realize a structure having by far the highest surface area reported to date We report the design, synthesis and properties of crystalline Zn4O(1,3,5-benzenetribenzoate)2, a new metal-organic framework with a surface area estimated at 4,500 m2 g(-1) This framework, which we name MOF-177, combines this exceptional level of surface area with an ordered structure that has extra-large pores capable of binding polycyclic organic guest molecules--attributes not previously combined in one material

Journal ArticleDOI
09 Sep 2004-Nature
TL;DR: An undisturbed climate record from a North Greenland ice core, which extends back to 123,000 years before the present, within the last interglacial period, shows a slow decline in temperatures that marked the initiation of the last glacial period.
Abstract: High-resolution record of Northern Hemisphere climate extending into the last interglacial period

Journal ArticleDOI
15 Sep 2004-Nature
TL;DR: A key step in known silencing pathways is the processing of dsRNAs into short RNA duplexes of characteristic size and structure, which guide RNA silencing by specific and distinct mechanisms.
Abstract: Double-stranded RNA (dsRNA) is an important regulator of gene expression in many eukaryotes. It triggers different types of gene silencing that are collectively referred to as RNA silencing or RNA interference. A key step in known silencing pathways is the processing of dsRNAs into short RNA duplexes of characteristic size and structure. These short dsRNAs guide RNA silencing by specific and distinct mechanisms. Many components of the RNA silencing machinery still need to be identified and characterized, but a more complete understanding of the process is imminent.

Journal ArticleDOI
27 May 2004-Nature
TL;DR: The results provide a causative link between mtDNA mutations and ageing phenotypes in mammals by creating homozygous knock-in mice that express a proof-reading-deficient version of PolgA, the nucleus-encoded catalytic subunit of mtDNA polymerase.
Abstract: Point mutations and deletions of mitochondrial DNA (mtDNA) accumulate in a variety of tissues during ageing in humans, monkeys and rodents. These mutations are unevenly distributed and can accumulate clonally in certain cells, causing a mosaic pattern of respiratory chain deficiency in tissues such as heart, skeletal muscle and brain. In terms of the ageing process, their possible causative effects have been intensely debated because of their low abundance and purely correlative connection with ageing. We have now addressed this question experimentally by creating homozygous knock-in mice that express a proof-reading-deficient version of PolgA, the nucleus-encoded catalytic subunit of mtDNA polymerase. Here we show that the knock-in mice develop an mtDNA mutator phenotype with a threefold to fivefold increase in the levels of point mutations, as well as increased amounts of deleted mtDNA. This increase in somatic mtDNA mutations is associated with reduced lifespan and premature onset of ageing-related phenotypes such as weight loss, reduced subcutaneous fat, alopecia (hair loss), kyphosis (curvature of the spine), osteoporosis, anaemia, reduced fertility and heart enlargement. Our results thus provide a causative link between mtDNA mutations and ageing phenotypes in mammals.

Journal ArticleDOI
22 Jan 2004-Nature
TL;DR: It is established that S1P1 is essential for lymphocyte recirculation and that it regulates egress from both thymus and peripheral lymphoid organs.
Abstract: Adaptive immunity depends on T-cell exit from the thymus and T and B cells travelling between secondary lymphoid organs to survey for antigens. After activation in lymphoid organs, T cells must again return to circulation to reach sites of infection; however, the mechanisms regulating lymphoid organ exit are unknown. An immunosuppressant drug, FTY720, inhibits lymphocyte emigration from lymphoid organs, and phosphorylated FTY720 binds and activates four of the five known sphingosine-1-phosphate (S1P) receptors1,2,3,4. However, the role of S1P receptors in normal immune cell trafficking is unclear. Here we show that in mice whose haematopoietic cells lack a single S1P receptor (S1P1; also known as Edg1) there are no T cells in the periphery because mature T cells are unable to exit the thymus. Although B cells are present in peripheral lymphoid organs, they are severely deficient in blood and lymph. Adoptive cell transfer experiments establish an intrinsic requirement for S1P1 in T and B cells for lymphoid organ egress. Furthermore, S1P1-dependent chemotactic responsiveness is strongly upregulated in T-cell development before exit from the thymus, whereas S1P1 is downregulated during peripheral lymphocyte activation, and this is associated with retention in lymphoid organs. We find that FTY720 treatment downregulates S1P1, creating a temporary pharmacological S1P1-null state in lymphocytes, providing an explanation for the mechanism of FTY720-induced lymphocyte sequestration. These findings establish that S1P1 is essential for lymphocyte recirculation and that it regulates egress from both thymus and peripheral lymphoid organs.

Journal ArticleDOI
15 Sep 2004-Nature
TL;DR: Diverse biological roles of these pathways have been established, including defence against viruses, regulation of gene expression and the condensation of chromatin into heterochromatin, and the full extent of this functional diversity in genetic and epigenetic mechanisms of genome control is investigated.
Abstract: There are at least three RNA silencing pathways for silencing specific genes in plants. In these pathways, silencing signals can be amplified and transmitted between cells, and may even be self-regulated by feedback mechanisms. Diverse biological roles of these pathways have been established, including defence against viruses, regulation of gene expression and the condensation of chromatin into heterochromatin. We are now in a good position to investigate the full extent of this functional diversity in genetic and epigenetic mechanisms of genome control.

Journal ArticleDOI
11 Nov 2004-Nature
TL;DR: In this article, chemically modified short interfering RNAs (siRNAs) were used to silence an endogenous gene encoding apolipoprotein B (apoB) after intravenous injection in mice.
Abstract: RNA interference (RNAi) holds considerable promise as a therapeutic approach to silence disease-causing genes, particularly those that encode so-called 'non-druggable' targets that are not amenable to conventional therapeutics such as small molecules, proteins, or monoclonal antibodies. The main obstacle to achieving in vivo gene silencing by RNAi technologies is delivery. Here we show that chemically modified short interfering RNAs (siRNAs) can silence an endogenous gene encoding apolipoprotein B (apoB) after intravenous injection in mice. Administration of chemically modified siRNAs resulted in silencing of the apoB messenger RNA in liver and jejunum, decreased plasma levels of apoB protein, and reduced total cholesterol. We also show that these siRNAs can silence human apoB in a transgenic mouse model. In our in vivo study, the mechanism of action for the siRNAs was proven to occur through RNAi-mediated mRNA degradation, and we determined that cleavage of the apoB mRNA occurred specifically at the predicted site. These findings demonstrate the therapeutic potential of siRNAs for the treatment of disease.

Journal ArticleDOI
02 Sep 2004-Nature
TL;DR: An initial map of yeast's transcriptional regulatory code is constructed by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species.
Abstract: DNA-binding transcriptional regulators interpret the genome's regulatory code by binding to specific sequences to induce or repress gene expression. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation, but this information alone does not reveal if or when transcriptional regulators occupy these binding sites. We have constructed an initial map of yeast's transcriptional regulatory code by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. The organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators are discussed. We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators.

Journal ArticleDOI
23 Sep 2004-Nature
TL;DR: It is shown that the inflammatory process triggers hepatocyte NF-κB through upregulation of tumour-necrosis factor-α (TNFα) in adjacent endothelial and inflammatory cells, and is therefore a potential target for cancer prevention in chronic inflammatory diseases.
Abstract: The causes of sporadic human cancer are seldom recognized, but it is estimated that carcinogen exposure and chronic inflammation are two important underlying conditions for tumour development, the latter accounting for approximately 20% of human cancer. Whereas the causal relationship between carcinogen exposure and cancer has been intensely investigated, the molecular and cellular mechanisms linking chronic inflammation to tumorigenesis remain largely unresolved. We proposed that activation of the nuclear factor kappaB (NF-kappaB), a hallmark of inflammatory responses that is frequently detected in tumours, may constitute a missing link between inflammation and cancer. To test this hypothesis, we studied the Mdr2-knockout mouse strain, which spontaneously develops cholestatic hepatitis followed by hepatocellular carcinoma, a prototype of inflammation-associated cancer. We monitored hepatitis and cancer progression in Mdr2-knockout mice, and here we show that the inflammatory process triggers hepatocyte NF-kappaB through upregulation of tumour-necrosis factor-alpha (TNFalpha) in adjacent endothelial and inflammatory cells. Switching off NF-kappaB in mice from birth to seven months of age, using a hepatocyte-specific inducible IkappaB-super-repressor transgene, had no effect on the course of hepatitis, nor did it affect early phases of hepatocyte transformation. By contrast, suppressing NF-kappaB inhibition through anti-TNFalpha treatment or induction of IkappaB-super-repressor in later stages of tumour development resulted in apoptosis of transformed hepatocytes and failure to progress to hepatocellular carcinoma. Our studies thus indicate that NF-kappaB is essential for promoting inflammation-associated cancer, and is therefore a potential target for cancer prevention in chronic inflammatory diseases.