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.DNA sequencing has markedly changed the nature of biomedical research and medicine. Reductions in the cost, complexity and time required to sequence large amounts of DNA, including improvements in the ability to sequence bacterial and eukaryotic genomes, will have significant scientific, economic and cultural impact. Largescale sequencing projects, including whole-genome sequencing, have usually required the cloning of DNA fragments into bacterial vectors, amplification and purification of individual templates, followed by Sanger sequencing 1 using fluorescent chain-terminating nucleotide analogues 2 and either slab gel or capillary electrophoresis. Current estimates put the cost of sequencing a human genome between $10 million and $25 million 3 . Alternative sequencing methods have been described 4-8 ; however, no technology has displaced the use of bacterial vectors and Sanger sequencing as the main generators of sequence information.Here we describe an integrated system whose throughput routinely enables applications requiring millions of bases of sequence information, including whole-genome sequencing. Our focus has been on the co-development of an emulsion-based method 9-11 to isolate and amplify DNA fragments in vitro, and of a fabricated substrate and instrument that performs pyrophosphate-based sequencing (pyrosequencing 5,12 ) in picolitre-sized wells.In a typical run we generate over 25 million bases with a Phred quality score of 20 or better (predicted to have an accuracy of 99% or higher). Although this Phred 20 quality throughput is significantly higher than that of Sanger sequencing by capillary electrophoresis, it is currently at the cost of substantially shorter reads and lower average individual read accuracy. Sanger-based capillary electrophoresis sequencing systems produce up to 700 bases of sequence information from each of 96 DNA templates at an average read accuracy of 99.4% in 1 h, or 67,000 bases per hour, with substantially all of the bases having Phred 20 or better quality 23 . We further characterize the performance ...

Abstract:As alternatives to conventional metals, new plasmonic materials offer many advantages in the rapidly growing fields of plasmonics and metamaterials. These advantages include low intrinsic loss, semiconductor-based design, compatibility with standard nanofabrication processes, tunability, and others. Transparent conducting oxides such as Al:ZnO, Ga:ZnO and indium-tin-oxide (ITO) enable many high-performance metamaterial devices operating in the near-IR. Transition-metal nitrides such as TiN or ZrN can be substitutes for conventional metals in the visible frequencies. In this paper we provide the details of fabrication and characterization of these new materials and discuss their suitability for a number of metamaterial and plasmonic applications.

We report the synthesis of unusually thick poly(2-hydroxyethyl methacrylate) (PHEMA) films on gold surfaces by surface-initiated atom transfer radical polymerization (ATRP). Polymerization from the surface occurs rapidly at room temperature in aqueous media, resulting in the formation of 700 nm thick polymer films in just 12 h. Control experiments using neat monomer and catalyst (no water) yield films with thicknesses of only 6 nm, demonstrating the accelerating effect of water on surfaceinitiated ATRP. Kinetic studies reveal a nearly linear increase in thickness with reaction time, indicating that chain growth from the surface is a controlled process with some "living" character. A second block can be grown from dormant initiators at the end of PHEMA chains, providing further evidence of "living" chain ends. Derivatization of the hydroxyl groups of grafted PHEMA with a variety of molecules allows dense functionalization of these films. Reflectance FTIR spectroscopy shows a virtually quantitative yield in derivatization reactions, and the increase in film thickness after surface derivatization correlates with the molecular mass of the newly formed repeat unit.

Although massively parallel sequencing approaches have been widely used to study genomic variation, simple alignment of short reads to a reference genome cannot be used to investigate the full range of structural variation and phased diploid architecture, which are important for precision medicine. By contrast, the single-molecule real-time (SMRT) sequencing platform produces long reads that can resolve repetitive structures effectively. We integrated this technology with several other sequencing approaches to construct a high-quality

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