An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing.

Sequencing technologies have undergone a paradigm shift from bulk to single-cell resolution in response to an evolving understanding of the role of cellular heterogeneity in biological systems. However, single-cell sequencing of large populations has been hampered by limitations in processing genomes for sequencing. In this paper, we describe a method for single-cell genome sequencing (SiC-seq) which uses droplet microfluidics to isolate, amplify, and barcode the genomes of single cells. Cell encapsulation in microgels allows the compartmentalized purification and tagmentation of DNA, while a microfluidic merger efficiently pairs each genome with a unique single-cell oligonucleotide barcode, allowing >50,000 single cells to be sequenced per run. The sequencing data is demultiplexed by barcode, generating groups of reads originating from single cells. As a high-throughput and low-bias method of single-cell sequencing, SiC-seq will enable a broader range of genomic studies targeted at diverse cell populations

Rectangular-Mask Coronagraphs for High-Contrast Imaging

We present yet another new family of masks for high-contrast imaging as required for the to-be-built terrestrial planet finder space telescope. The ``best'' design involves a square entrance pupil having a 4-vane spider, a square image-plane mask containing a plus-sign shaped occulter to block the starlight inside 0.6 lambda/D, and a Lyot-plane mask consisting of a rectangular array of rectangular opennings. Using Fraunhofer analysis, we show that the optical system can image a planet 10^{-10} times as bright as an on-axis star in four rectangular regions given by {(xi,zeta): 1.4 < | xi | < 20, 1.4 < | zeta | < 20}. Since the design involves an image plane mask, pointing error is an issue. We show that the design can tolerate pointing errors of about 0.05 lambda/D. The inclusion of a 4-vane spider in the entrance pupil provides the possibility to build a mirror-only on-axis system thereby greatly reducing the negative effects of polarization. Each of the masks can be realized as two masks consisting of stripes of opaque material with the stripes oriented at right angles to each other. We call these striped masks barcode masks. We show that it is sufficient for the barcode masks by themselves to provide 10^{-5} contrast. This then guarantees that the full system will provide the required 10^{-10} contrast.Comment: 12 pages, 5 figure

Australian Sphingidae – DNA Barcodes Challenge Current Species Boundaries and Distributions

© 2014 Rougerie et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines.

Hundreds of genetically characterized cell lines are available for the discovery of genotype-specific cancer vulnerabilities. However, screening large numbers of compounds against large numbers of cell lines is currently impractical, and such experiments are often difficult to control. Here we report a method called PRISM that allows pooled screening of mixtures of cancer cell lines by labeling each cell line with 24-nucleotide barcodes. PRISM revealed the expected patterns of cell killing seen in conventional (unpooled) assays. In a screen of 102 cell lines across 8,400 compounds, PRISM led to the identification of BRD-7880 as a potent and highly specific inhibitor of aurora kinases B and C. Cell line pools also efficiently formed tumors as xenografts, and PRISM recapitulated the expected pattern of erlotinib sensitivity in vivo

Amplified Dispersive Fourier-Transform Imaging for Ultrafast Displacement Sensing and Barcode Reading

Dispersive Fourier transformation is a powerful technique in which the spectrum of an optical pulse is mapped into a time-domain waveform using chromatic dispersion. It replaces a diffraction grating and detector array with a dispersive fiber and single photodetector. This simplifies the system and, more importantly, enables fast real-time measurements. Here we describe a novel ultrafast barcode reader and displacement sensor that employs internally-amplified dispersive Fourier transformation. This technique amplifies and simultaneously maps the spectrally encoded barcode into a temporal waveform. It achieves a record acquisition speed of 25 MHz -- four orders of magnitude faster than the current state-of-the-art.Comment: Submitted to a journa

Wolbachia and DNA barcoding insects: patterns, potential and problems

Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region

Radon-Gabor Barcodes for Medical Image Retrieval

In recent years, with the explosion of digital images on the Web, content-based retrieval has emerged as a significant research area. Shapes, textures, edges and segments may play a key role in describing the content of an image. Radon and Gabor transforms are both powerful techniques that have been widely studied to extract shape-texture-based information. The combined Radon-Gabor features may be more robust against scale/rotation variations, presence of noise, and illumination changes. The objective of this paper is to harness the potentials of both Gabor and Radon transforms in order to introduce expressive binary features, called barcodes, for image annotation/tagging tasks. We propose two different techniques: Gabor-of-Radon-Image Barcodes (GRIBCs), and Guided-Radon-of-Gabor Barcodes (GRGBCs). For validation, we employ the IRMA x-ray dataset with 193 classes, containing 12,677 training images and 1,733 test images. A total error score as low as 322 and 330 were achieved for GRGBCs and GRIBCs, respectively. This corresponds to $\approx 81\%$ retrieval accuracy for the first hit.Comment: To appear in proceedings of the 23rd International Conference on Pattern Recognition (ICPR 2016), Cancun, Mexico, December 201

Creating New β-Globin-Expressing Lentiviral Vectors by High-Resolution Mapping of Locus Control Region Enhancer Sequences.

Hematopoietic stem cell gene therapy is a promising approach for treating disorders of the hematopoietic system. Identifying combinations of cis-regulatory elements that do not impede packaging or transduction efficiency when included in lentiviral vectors has proven challenging. In this study, we deploy LV-MPRA (lentiviral vector-based, massively parallel reporter assay), an approach that simultaneously analyzes thousands of synthetic DNA fragments in parallel to identify sequence-intrinsic and lineage-specific enhancer function at near-base-pair resolution. We demonstrate the power of LV-MPRA in elucidating the boundaries of previously unknown intrinsic enhancer sequences of the human β-globin locus control region. Our approach facilitated the rapid assembly of novel therapeutic βAS3-globin lentiviral vectors harboring strong lineage-specific recombinant control elements capable of correcting a mouse model of sickle cell disease. LV-MPRA can be used to map any genomic locus for enhancer activity and facilitates the rapid development of therapeutic vectors for treating disorders of the hematopoietic system or other specific tissues and cell types

Securing Interactive Sessions Using Mobile Device through Visual Channel and Visual Inspection

Communication channel established from a display to a device's camera is known as visual channel, and it is helpful in securing key exchange protocol. In this paper, we study how visual channel can be exploited by a network terminal and mobile device to jointly verify information in an interactive session, and how such information can be jointly presented in a user-friendly manner, taking into account that the mobile device can only capture and display a small region, and the user may only want to authenticate selective regions-of-interests. Motivated by applications in Kiosk computing and multi-factor authentication, we consider three security models: (1) the mobile device is trusted, (2) at most one of the terminal or the mobile device is dishonest, and (3) both the terminal and device are dishonest but they do not collude or communicate. We give two protocols and investigate them under the abovementioned models. We point out a form of replay attack that renders some other straightforward implementations cumbersome to use. To enhance user-friendliness, we propose a solution using visual cues embedded into the 2D barcodes and incorporate the framework of "augmented reality" for easy verifications through visual inspection. We give a proof-of-concept implementation to show that our scheme is feasible in practice.Comment: 16 pages, 10 figure