1,700 research outputs found
Ultracompact quantum splitter of degenerate photon pairs
Integrated sources of indistinguishable photons have attracted a lot of
attention because of their applications in quantum communication and optical
quantum computing. Here, we demonstrate an ultra-compact quantum splitter for
degenerate single photons based on a monolithic chip incorporating Sagnac loop
and a micro-ring resonator with a footprint of 0.011 mm2, generating and
deterministically splitting indistinguishable photon pairs using time-reversed
Hong-Ou-Mandel interference. The ring resonator provides enhanced photon
generation rate, and the Sagnac loop ensures the photons travel through equal
path lengths and interfere with the correct phase to enable the reversed HOM
effect to take place. In the experiment, we observed a HOM dip visibility of
94.5 +- 3.3 %, indicating the photons generated by the degenerate single photon
source are in a suitable state for further integration with other components
for quantum applications, such as controlled-NOT gates
Rapid Assembly of Multiple-Exon cDNA Directly from Genomic DNA
Backgrouud. Polymerase chain reaction (PCR) is extensively applied in gene cloning. But due to the existence of introns, low copy number of particular genes and high complexity of the eukaryotic genome, it is usually impossible to amplify and clone a gene as a full-length sequence directly from the genome by ordinary PCR based techniques. Cloning of cDNA instead of genomic DNA involves multiple steps: harvest of tissues that express the gene of interest, RNA isolation, cDNA synthesis (reverse transcription), and PCR amplification. To simplify the cloning procedures and avoid the problems caused by ubiquitously distributed durable RNases, we have developed a novel strategy allowing the cloning of any cDNA or open reading frame (ORF) with wild type sequence in any spliced form from a single genomic DNA preparation. Methodology. Our Genomic DNA Splicing technique contains the following steps: first, all exons of the gene are amplified from a genomic DNA preparation, using software-optimized, highly efficient primers residing in flanking introns. Next, the tissue-specific exon sequences are assembled into one full-length sequence by overlapping PCR with deliberately designed primers located at the splicing sites. Finally, software-optimized outmost primers are exploited for efficient amplification of the assembled full-length products. Conclusions. The Genomic DNA Splicing protocol avoids RNA preparation and reverse transcription steps, and the entire assembly process can be finished within hours, Since genamic DNA is more stable than RNA, it may be a more practical cloning strategy for many genes, especially the ones that are very large and difficult to generate a full length cDNA using oligo-dT primed reverse transcription. With this technique, we successfully doned the full-length wild type coding sequence of human polymeric immunoglobulin receptor, which is 2295 bp in length and composed of 10 exons. © 2007 An et al.published_or_final_versio
Tunable entangled photon states from a nonlinear directional coupler
Integrated optical platforms enable the realization of complex quantum photonic circuits for a variety of applications including quantum simulations, computations, and communications. The development of on-chip integrated photon sources, providing photon quantum states with on-demand tunability, is currently an important
research area. A flexible approach for on-chip generation of entangled photons is based on spontaneous nonlinear
frequency conversion, with possibilities to integrate several photon-pair sources [1] and realize subsequent post
processing using thermo-optically or electro-optically controlled interference [2, 3]. However, deterministic postprocessing can only provide a limited set of output states, whereas quantum gates with probabilistic operation are
needed to generate arbitrary two-photon states [4]
Discrete Particle Swarm Optimization for the minimum labelling Steiner tree problem
Particle Swarm Optimization is an evolutionary method inspired by the
social behaviour of individuals inside swarms in nature. Solutions of the problem are
modelled as members of the swarm which fly in the solution space. The evolution is
obtained from the continuous movement of the particles that constitute the swarm
submitted to the effect of the inertia and the attraction of the members who lead the
swarm. This work focuses on a recent Discrete Particle Swarm Optimization for combinatorial optimization, called Jumping Particle Swarm Optimization. Its effectiveness is
illustrated on the minimum labelling Steiner tree problem: given an undirected labelled
connected graph, the aim is to find a spanning tree covering a given subset of nodes,
whose edges have the smallest number of distinct labels
A Simple and Accurate Two-Step Long DNA Sequences Synthesis Strategy to Improve Heterologous Gene Expression in Pichia
In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE) was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200–500 bp fragments with 20–25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp) and Aspergillus niger phytase gene phyA (1404 bp). Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application
Twinning superlattices in indium phosphide nanowires
Here, we show that we control the crystal structure of indium phosphide (InP)
nanowires by impurity dopants. We have found that zinc decreases the activation
barrier for 2D nucleation growth of zinc-blende InP and therefore promotes the
InP nanowires to crystallise in the zinc blende, instead of the commonly found
wurtzite crystal structure. More importantly, we demonstrate that we can, by
controlling the crystal structure, induce twinning superlattices with
long-range order in InP nanowires. We can tune the spacing of the superlattices
by the wire diameter and the zinc concentration and present a model based on
the cross-sectional shape of the zinc-blende InP nanowires to quantitatively
explain the formation of the periodic twinning.Comment: 18 pages, 4 figure
Interaction Between Convection and Pulsation
This article reviews our current understanding of modelling convection
dynamics in stars. Several semi-analytical time-dependent convection models
have been proposed for pulsating one-dimensional stellar structures with
different formulations for how the convective turbulent velocity field couples
with the global stellar oscillations. In this review we put emphasis on two,
widely used, time-dependent convection formulations for estimating pulsation
properties in one-dimensional stellar models. Applications to pulsating stars
are presented with results for oscillation properties, such as the effects of
convection dynamics on the oscillation frequencies, or the stability of
pulsation modes, in classical pulsators and in stars supporting solar-type
oscillations.Comment: Invited review article for Living Reviews in Solar Physics. 88 pages,
14 figure
Efficient assembly of very short oligonucleotides using T4 DNA Ligase
<p>Abstract</p> <p>Background</p> <p>In principle, a pre-constructed library of all possible short oligonucleotides could be used to construct many distinct gene sequences. In order to assess the feasibility of such an approach, we characterized T4 DNA Ligase activity on short oligonucleotide substrates and defined conditions suitable for assembly of a plurality of oligonucleotides.</p> <p>Findings</p> <p>Ligation by T4 DNA Ligase was found to be dependent on the formation of a double stranded DNA duplex of at least five base pairs surrounding the site of ligation. However, ligations could be performed effectively with overhangs smaller than five base pairs and oligonucleotides as small as octamers, in the presence of a second, complementary oligonucleotide. We demonstrate the feasibility of simultaneous oligonucleotide phosphorylation and ligation and, as a proof of principle for DNA synthesis through the assembly of short oligonucleotides, we performed a hierarchical ligation procedure whereby octamers were combined to construct a target 128-bp segment of the beta-actin gene.</p> <p>Conclusions</p> <p>Oligonucleotides as short as 8 nucleotides can be efficiently assembled using T4 DNA Ligase. Thus, the construction of synthetic genes, without the need for custom oligonucleotide synthesis, appears feasible.</p
WiseEye: next generation expandable and programmable camera trap platform for wildlife research
Funding: The work was supported by the RCUK Digital Economy programme to the dot.rural Digital Economy Hub; award reference: EP/G066051/1. The work of S. Newey and RJI was part funded by the Scottish Government's Rural and Environment Science and Analytical Services (RESAS). Details published as an Open Source Toolkit, PLOS Journals at: http://dx.doi.org/10.1371/journal.pone.0169758Peer reviewedPublisher PD
Processing DNA molecules as text
Polymerase Chain Reaction (PCR) is the DNA-equivalent of Gutenberg’s movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting, both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Biology labs engage daily in DNA processing—the creation of variations and combinations of existing DNA—using a plethora of manual labor-intensive methods such as site-directed mutagenesis, error-prone PCR, assembly PCR, overlap extension PCR, cleavage and ligation, homologous recombination, and others. So far no universal method for DNA processing has been proposed and, consequently, no engineering discipline that could eliminate this manual labor has emerged. Here we present a novel operation on DNA molecules, called Y, which joins two DNA fragments into one, and show that it provides a foundation for DNA processing as it can implement all basic text processing operations on DNA molecules including insert, delete, replace, cut and paste and copy and paste. In addition, complicated DNA processing tasks such as the creation of libraries of DNA variants, chimeras and extensions can be accomplished with DNA processing plans consisting of multiple Y operations, which can be executed automatically under computer control. The resulting DNA processing system, which incorporates our earlier work on recursive DNA composition and error correction, is the first demonstration of a unified approach to DNA synthesis, editing, and library construction
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