16,105 research outputs found

    Chromosomal bar codes produced by multicolor fluorescence in situ hybridization with multiple YAC clones and whole chromosome painting probes

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    Colored chromosome staining patterns, termed chromosomal ‘bar codes’ (CBCs), were obtained on human chromosomes by fluorescence in situ hybridization (FISH) with pools of Alu-PCR products from YAC dones containing human DNA inserts ranging from 100 kbp to 1 Mbp. In contrast to conventional G- or R-bands, the chromosomal position, extent, Individual color and relative signal intensity of each ‘bar’ could be modified depending on probe selection and labeling procedures. Alu-PCR amplification products were generated from 31 YAC clones which mapped to 37 different chromosome bands. For multiple color FISH, Alu-PCR amplification products from various clones were either biotinylated or labeled with digoxigenin. Probes from up to twenty YAC clones were used simultaneously to produce CBCs on selected human chromosomes. Evaluation using a cooled CCD camera and digital image analysis confirmed the high reproducibility of the bars from one metaphase spread to another. Combinatorial FISH with mixtures of whole chromosome paint probes was applied to paint seven chromosomes simultaneously in different colors along with a set of YAC clones which map to these chromosomes. We discuss the potential to construct analytical chromosomal bar codes adapted to particular needs of cytogenetic investigations and automated image analysis

    Development and evaluation of a Hadamard transform imaging spectrometer and a Hadamard transform thermal imager

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    A spectrometric imager and a thermal imager, which achieve multiplexing by the use of binary optical encoding masks, were developed. The masks are based on orthogonal, pseudorandom digital codes derived from Hadamard matrices. Spatial and/or spectral data is obtained in the form of a Hadamard transform of the spatial and/or spectral scene; computer algorithms are then used to decode the data and reconstruct images of the original scene. The hardware, algorithms and processing/display facility are described. A number of spatial and spatial/spectral images are presented. The achievement of a signal-to-noise improvement due to the signal multiplexing was also demonstrated. An analysis of the results indicates both the situations for which the multiplex advantage may be gained, and the limitations of the technique. A number of potential applications of the spectrometric imager are discussed

    A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

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    Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells

    Analysis and preliminary design of optical sensors for propulsion control

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    A fiber-optic sensor concept screening study was performed. Twenty sensor subsystems were identified and evaluated. Two concepts selected for further study were the Fabry-Perot fiber-optic temperature sensor and the pulse-width-modulated phosphorescent temperature sensor. Various designs suitable for a Fabry-Perot temperature sensor to be used as a remote fiber-optic transducer were investigated. As a result, a particular design was selected and constructed. Tests on this device show that spectral peaks are produced from visible white light, and the change in wavelength of the spectral peaks produced by a change in temperature is consistent with theory and is 36 nm/C for the first order peak. A literature search to determine a suitable phosphor for implementing the pulse-width-modulated fiber optic temperature sensor was conducted. This search indicated that such a device could be made to function for temperatures up to approximately 200 C. Materials like ZnCdS and ZnSe activated with copper will be particularly applicable to temperature sensing in the cryogenic to room temperature region. While this sensing concept is probably not applicable to jet engines, the simplicity and potential reliability make the concept highly desirable for other applications

    Fourier Magnetic Imaging with Nanoscale Resolution and Compressed Sensing Speed-up using Electronic Spins in Diamond

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    Optically-detected magnetic resonance using Nitrogen Vacancy (NV) color centres in diamond is a leading modality for nanoscale magnetic field imaging, as it provides single electron spin sensitivity, three-dimensional resolution better than 1 nm, and applicability to a wide range of physical and biological samples under ambient conditions. To date, however, NV-diamond magnetic imaging has been performed using real space techniques, which are either limited by optical diffraction to 250 nm resolution or require slow, point-by-point scanning for nanoscale resolution, e.g., using an atomic force microscope, magnetic tip, or super-resolution optical imaging. Here we introduce an alternative technique of Fourier magnetic imaging using NV-diamond. In analogy with conventional magnetic resonance imaging (MRI), we employ pulsed magnetic field gradients to phase-encode spatial information on NV electronic spins in wavenumber or k-space followed by a fast Fourier transform to yield real-space images with nanoscale resolution, wide field-of-view (FOV), and compressed sensing speed-up.Comment: 31 pages, 10 figure

    Prototype Packages for Managing and Animating Longitudinal Network Data: dynamicnetwork and rSoNIA

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    Work with longitudinal network survey data and the dynamic network outputs of the statnet ERGMs has demonstrated the need for consistent frameworks and data structures for expressing, storing, and manipulating information about networks that change in time. Motivated by our requirements for exchanging data among researchers and various analysis and visualization processes, we have created an R package dynamicnetwork that builds upon previous work in the network, statnet and sna packages and provides a limited functional implementation. This paper discusses design issues and considerations, describes classes and forms of dynamic data, and works through several examples to demonstrate the utility of the package. The functionality of the rSoNIA package that uses dynamicnetwork to exchange data with the Social Network Image Animator (SoNIA) software to create animated movies of changing networks from within R is also demonstrated.

    Investigation of marmoset hybrids (Cebuella pygmaea x Callithrix jacchus) and related Callitrichinae (Platyrrhini) by cross-species chromosome painting and comparative genomic hybridization

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    We report on the cytogenetics of twin offspring from an interspecies cross in marmosets (Callitrichinae, Platyrrhini), resulting from a pairing between a female Common marmoset (Callithrix jacchus, 2n = 46) and a male Pygmy marmoset (Cebuella pygmaea, 2n = 44). We analyzed their karyotypes by multi-directional chromosome painting employing human, Saguinus oedipus and Lagothrix lagothricha chromosome-specific probes. Both hybrid individuals had a karyotype with a diploid chromosome number of 2n = 45. As a complementary tool, interspecies comparative genomic hybridization (iCGH) was performed in order to screen for genomic imbalances between the hybrids and their parental species, and between Callithrix argentata and S. oedipus, respectively. Copyright (C) 2005 S. Karger AG, Basel
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