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11.
Genome sequencing in microfabricated high-density picolitre reactors 总被引:21,自引:0,他引:21
Margulies M Egholm M Altman WE Attiya S Bader JS Bemben LA Berka J Braverman MS Chen YJ Chen Z Dewell SB Du L Fierro JM Gomes XV Godwin BC He W Helgesen S Ho CH Ho CH Irzyk GP Jando SC Alenquer ML Jarvie TP Jirage KB Kim JB Knight JR Lanza JR Leamon JH Lefkowitz SM Lei M Li J Lohman KL Lu H Makhijani VB McDade KE McKenna MP Myers EW Nickerson E Nobile JR Plant R Puc BP Ronan MT Roth GT Sarkis GJ Simons JF Simpson JW Srinivasan M Tartaro KR Tomasz A Vogt KA Volkmer GA Wang SH Wang Y Weiner MP 《Nature》2005,437(7057):376-380
The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine. 相似文献
12.
The genome sequence of the rice blast fungus Magnaporthe grisea 总被引:8,自引:0,他引:8
Dean RA Talbot NJ Ebbole DJ Farman ML Mitchell TK Orbach MJ Thon M Kulkarni R Xu JR Pan H Read ND Lee YH Carbone I Brown D Oh YY Donofrio N Jeong JS Soanes DM Djonovic S Kolomiets E Rehmeyer C Li W Harding M Kim S Lebrun MH Bohnert H Coughlan S Butler J Calvo S Ma LJ Nicol R Purcell S Nusbaum C Galagan JE Birren BW 《Nature》2005,434(7036):980-986
Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation. 相似文献
13.
Entanglement is recognized as a key resource for quantum computation and quantum cryptography. For quantum metrology, the use of entangled states has been discussed and demonstrated as a means of improving the signal-to-noise ratio. In addition, entangled states have been used in experiments for efficient quantum state detection and for the measurement of scattering lengths. In quantum information processing, manipulation of individual quantum bits allows for the tailored design of specific states that are insensitive to the detrimental influences of an environment. Such 'decoherence-free subspaces' (ref. 10) protect quantum information and yield significantly enhanced coherence times. Here we use a decoherence-free subspace with specifically designed entangled states to demonstrate precision spectroscopy of a pair of trapped Ca+ ions; we obtain the electric quadrupole moment, which is of use for frequency standard applications. We find that entangled states are not only useful for enhancing the signal-to-noise ratio in frequency measurements--a suitably designed pair of atoms also allows clock measurements in the presence of strong technical noise. Our technique makes explicit use of non-locality as an entanglement property and provides an approach for 'designed' quantum metrology. 相似文献
14.
15.
Tissue-specific and reversible RNA interference in transgenic mice 总被引:11,自引:0,他引:11
Dickins RA McJunkin K Hernando E Premsrirut PK Krizhanovsky V Burgess DJ Kim SY Cordon-Cardo C Zender L Hannon GJ Lowe SW 《Nature genetics》2007,39(7):914-921
Genetically engineered mice provide powerful tools for understanding mammalian gene function. These models traditionally rely on gene overexpression from transgenes or targeted, irreversible gene mutation. By adapting the tetracycline (tet)-responsive system previously used for gene overexpression, we have developed a simple transgenic system to reversibly control endogenous gene expression using RNA interference (RNAi) in mice. Transgenic mice harboring a tet-responsive RNA polymerase II promoter driving a microRNA-based short hairpin RNA targeting the tumor suppressor Trp53 reversibly express short hairpin RNA when crossed with existing mouse strains expressing general or tissue-specific 'tet-on' or 'tet-off' transactivators. Reversible Trp53 knockdown can be achieved in several tissues, and restoring Trp53 expression in lymphomas whose development is promoted by Trp53 knockdown leads to tumor regression. By leaving the target gene unaltered, this approach permits tissue-specific, reversible regulation of endogenous gene expression in vivo, with potential broad application in basic biology and drug target validation. 相似文献
16.
Recombination and linkage disequilibrium in Arabidopsis thaliana 总被引:4,自引:0,他引:4
Kim S Plagnol V Hu TT Toomajian C Clark RM Ossowski S Ecker JR Weigel D Nordborg M 《Nature genetics》2007,39(9):1151-1155
Linkage disequilibrium (LD) is a major aspect of the organization of genetic variation in natural populations. Here we describe the genome-wide pattern of LD in a sample of 19 Arabidopsis thaliana accessions using 341,602 non-singleton SNPs. LD decays within 10 kb on average, considerably faster than previously estimated. Tag SNP selection algorithms and 'hide-the-SNP' simulations suggest that genome-wide association mapping will require only 40%-50% of the observed SNPs, a reduction similar to estimates in a sample of African Americans. An Affymetrix genotyping array containing 250,000 SNPs has been designed based on these results; we demonstrate that it should have more than adequate coverage for genome-wide association mapping. The extent of LD is highly variable, and we find clear evidence of recombination hotspots, which seem to occur preferentially in intergenic regions. LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms. 相似文献
17.
Rakesh K. Sahoo Arya Das Saurabh Singh Damin Lee Saroj K. Singh Rajaram S. Mane Je Moon Yun Kwang Ho Kim 《自然科学进展(英文版)》2019,29(4):410-415
A 3D porous carbon-manganese oxide ([email protected]) nanocomposite is successfully synthesized via a thermal plasma deposition method. The chemical bonds and compositions, phase structures, surface morphologies, etc. of as-obtained [email protected] nanocomposite were characterized by the various equipment, such as X-ray diffractometer, X-ray photoelectron spectroscopy, and electron microscopes. The electrochemical performances of the [email protected] nanocomposite electrode showed a specific capacitance of 780 F g?1 at a current density of 2 A g?1 and a capacitance retention rate of 99% after 5000 charge-discharge cycles at a high current density of 10 A g?1. These excellent capacitive performances may be attributed to the encapsulation of MnO nanoparticles by porous carbon sheets in the [email protected] MnO nanocomposite structure. It is believed that the carbon-encapsulated MnO nanoparticles can be protected from a volume deformation during the charge adsorption/desorption cycle and can be electrically improved by the encapsulated carbon sheets, resulting in better overall capacitive performance. In addition, this study also demonstrates the practical applicability by assembling a supercapacitor using the as-obtained [email protected] nanocomposite to glow a light emitting diode. 相似文献
18.
Jinwon Lim Hyo-Jung Lee Bonglee Kim Jeong-Un Choi Yoeok Shin Eun Jung Sohn Sung-Hoon Kim 《科学通报(英文版)》2014,59(25):3127-3133
Though Hongbaekjeong(HBJ),a hebal mixture of three medicinal plants,has been traditionally used for arthritis and muscular pain,its scientific evidence still remains unclear.Thus,in the present study,analgesic and anti-inflammatory mechanism of HBJ was evaluated in vitro and in vivo.HBJ significantly reduced NO production and prostaglandin E2(PGE2)release and also attenuated the expression of cyclooxygenase 2(COX-2)in lipopolysaccharides(LPS)and interferon(IFN)-c treated RAW 264.7 cells.Furthermore,HBJ abrogated the production of proinflammatory cytokines such as interleukin(IL)1b,IL-6,IL-8 and monocyte chemoattractant protein-1(MCP-1)in LPS and IFN-c treated RAW 264.7 cells.In addition,HBJ significantly decreased the number of writhing syndrome induced by acetic acid,and also increased latency in hot-plate method and tail flick test in mice.Consistently,HBJ significantly reduced the edema volume in the hind paw of the rats with arthritis induced by Freund’s complete adjuvant(FCA)compared to untreated control.Collectively,our findings demonstrate the antiinflammatory and analgesic potential of HBJ via inhibition of proinflammatory cytokines and PGE2 release for treatment of arthritis and muscular pain. 相似文献
19.
Network motif is defined as a frequent and unique subgraph pattern in a network, and the search involves counting all the possible instances or listing all patterns, testing isomorphism known as NP-hard and large amounts of repeated processes for statistical evaluation. Although many efficient algorithms have been introduced, exhaustive search methods are still infeasible and feasible approximation methods are yet implausible.Additionally, the fast and continual growth of biological networks makes the problem more challenging. As a consequence, parallel algorithms have been developed and distributed computing has been tested in the cloud computing environment as well. In this paper, we survey current algorithms for network motif detection and existing software tools. Then, we show that some methods have been utilized for parallel network motif search algorithms with static or dynamic load balancing techniques. With the advent of cloud computing services, network motif search has been implemented with MapReduce in Hadoop Distributed File System(HDFS), and with Storm, but without statistical testing. In this paper, we survey network motif search algorithms in general, including existing parallel methods as well as cloud computing based search, and show the promising potentials for the cloud computing based motif search methods. 相似文献
20.
Hessa T Meindl-Beinker NM Bernsel A Kim H Sato Y Lerch-Bader M Nilsson I White SH von Heijne G 《Nature》2007,450(7172):1026-1030