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Sample records for 2d barcode detection

  1. Integrating Mobile Multimedia into Textbooks: 2D Barcodes

    ERIC Educational Resources Information Center

    Uluyol, Celebi; Agca, R. Kagan

    2012-01-01

    The major goal of this study was to empirically compare text-plus-mobile phone learning using an integrated 2D barcode tag in a printed text with three other conditions described in multimedia learning theory. The method examined in the study involved modifications of the instructional material such that: a 2D barcode was used near the text, the…

  2. Field depth extension of 2D barcode scanner based on wavefront coding and projection algorithm

    NASA Astrophysics Data System (ADS)

    Zhao, Tingyu; Ye, Zi; Zhang, Wenzi; Huang, Weiwei; Yu, Feihong

    2008-03-01

    Wavefront coding (WFC) used in 2D barcode scanners can extend the depth of field into a great extent with simpler structure compared to the autofocus microscope system. With a cubic phase mask (CPM) employed in the STOP, blurred images will be obtained in charge coupled device (CCD), which can be restored by digital filters. Direct methods are used widely in real-time restoration with good computational efficiency but with details smoothed. Here, the results of direct method are firstly filtered by hard-threshold function. The positions of the steps can be detected by simple differential operators. With the positions corrected by projection algorithm, the exact barcode information is restored. A wavefront coding system with 7mm effective focal length and 6 F-number is designed as an example. Although with the different magnification, images of different object distances can be restored by one point spread function (PSF) with 200mm object distance. A QR code (Quickly Response Code) of 31mm X 27mm is used as a target object. The simulation results showed that the sharp imaging objective distance is from 80mm to 355mm. The 2D barcode scanner with wavefront coding extends field depth with simple structure, low cost and large manufacture tolerance. This combination of the direct filter and projection algorithm proposed here could get the exact 2D barcode information with good computational efficiency.

  3. PiCode: A New Picture-Embedding 2D Barcode.

    PubMed

    Chen, Changsheng; Huang, Wenjian; Zhou, Baojian; Liu, Chenchen; Mow, Wai Ho

    2016-08-01

    Nowadays, 2D barcodes have been widely used as an interface to connect potential customers and advertisement contents. However, the appearance of a conventional 2D barcode pattern is often too obtrusive for integrating into an aesthetically designed advertisement. Besides, no human readable information is provided before the barcode is successfully decoded. This paper proposes a new picture-embedding 2D barcode, called PiCode, which mitigates these two limitations by equipping a scannable 2D barcode with a picturesque appearance. PiCode is designed with careful considerations on both the perceptual quality of the embedded image and the decoding robustness of the encoded message. Comparisons with the existing beautified 2D barcodes show that PiCode achieves one of the best perceptual qualities for the embedded image, and maintains a better tradeoff between image quality and decoding robustness in various application conditions. PiCode has been implemented in the MATLAB on a PC and some key building blocks have also been ported to Android and iOS platforms. Its practicality for real-world applications has been successfully demonstrated.

  4. Developing Mobile BIM/2D Barcode-Based Automated Facility Management System

    PubMed Central

    Chen, Yen-Pei

    2014-01-01

    Facility management (FM) has become an important topic in research on the operation and maintenance phase. Managing the work of FM effectively is extremely difficult owing to the variety of environments. One of the difficulties is the performance of two-dimensional (2D) graphics when depicting facilities. Building information modeling (BIM) uses precise geometry and relevant data to support the facilities depicted in three-dimensional (3D) object-oriented computer-aided design (CAD). This paper proposes a new and practical methodology with application to FM that uses an integrated 2D barcode and the BIM approach. Using 2D barcode and BIM technologies, this study proposes a mobile automated BIM-based facility management (BIMFM) system for FM staff in the operation and maintenance phase. The mobile automated BIMFM system is then applied in a selected case study of a commercial building project in Taiwan to verify the proposed methodology and demonstrate its effectiveness in FM practice. The combined results demonstrate that a BIMFM-like system can be an effective mobile automated FM tool. The advantage of the mobile automated BIMFM system lies not only in improving FM work efficiency for the FM staff but also in facilitating FM updates and transfers in the BIM environment. PMID:25250373

  5. Developing mobile BIM/2D barcode-based automated facility management system.

    PubMed

    Lin, Yu-Cheng; Su, Yu-Chih; Chen, Yen-Pei

    2014-01-01

    Facility management (FM) has become an important topic in research on the operation and maintenance phase. Managing the work of FM effectively is extremely difficult owing to the variety of environments. One of the difficulties is the performance of two-dimensional (2D) graphics when depicting facilities. Building information modeling (BIM) uses precise geometry and relevant data to support the facilities depicted in three-dimensional (3D) object-oriented computer-aided design (CAD). This paper proposes a new and practical methodology with application to FM that uses an integrated 2D barcode and the BIM approach. Using 2D barcode and BIM technologies, this study proposes a mobile automated BIM-based facility management (BIMFM) system for FM staff in the operation and maintenance phase. The mobile automated BIMFM system is then applied in a selected case study of a commercial building project in Taiwan to verify the proposed methodology and demonstrate its effectiveness in FM practice. The combined results demonstrate that a BIMFM-like system can be an effective mobile automated FM tool. The advantage of the mobile automated BIMFM system lies not only in improving FM work efficiency for the FM staff but also in facilitating FM updates and transfers in the BIM environment.

  6. Magnetic barcoded hydrogel microparticles for multiplexed detection.

    PubMed

    Bong, Ki Wan; Chapin, Stephen C; Doyle, Patrick S

    2010-06-01

    Magnetic polymer particles have been used in a wide variety of applications ranging from targeting and separation to diagnostics and imaging. Current synthesis methods have limited these particles to spherical or deformations of spherical morphologies. In this paper, we report the use of stop flow lithography to produce magnetic hydrogel microparticles with a graphical code region, a probe region, and a magnetic tail region. These anisotropic multifunctional magnetic polymer particles are an enhanced version of previously synthesized "barcoded" particles (Science, 2007, 315, 1393-1396) developed for the sensitive and rapid multiplexed sensing of nucleic acids. The newly added magnetic region has acquired dipole moments in the presence of weak homogeneous magnetic fields, allowing the particles to align along the applied field direction. The novel magnetic properties have led to practical applications in the efficient orientation and separation of the barcoded microparticles during biological assays without disrupting detection capabilities.

  7. The optical system design and application of micro 2D barcode

    NASA Astrophysics Data System (ADS)

    Zhu, Yi-jia; Li, Liang-liang; Qian, Cheng; Liang, Zhong-cheng

    2010-11-01

    We show an optical system of micro visual tag which is based on the principle of microscope and the property of QR Code. Unlike current optical tag, such as barcodes, must be read within a short rang and occupy valuable physical space on products, the new tags can be shrunk to several millimeters and captured from a distance of over 0.5 meters. We design the transmitter according to the parameters of camera lens. We also take the detection range and apertures into account, meanwhile conduct simulations and experiments. The result shows that: the tag can be captured from a long distance, and the amplified image is able to accurately be decoded.

  8. Hybrid hydrogel photonic barcodes for multiplex detection of tumor markers.

    PubMed

    Xu, Yueshuang; Zhang, Xiaoping; Luan, Chengxin; Wang, Huan; Chen, Baoan; Zhao, Yuanjin

    2017-01-15

    Barcodes-based suspension array have for demonstrated values in multiplex assay of tumor markers. Photonic barcodes which are encoded by their characteristic reflection peaks are the important supports for suspension array due to their stable code, low fluorescent background and high surface-volume ratio. Attempts to develop this technology tend to improve the function of the photonic barcodes. Here, we present a new type of hybrid hydrogel photonic barcodes for efficient multiplex assays. This photonic barcodes are hybrid inverse opal hydrogel composed of poly(ethylene glycol) diacrylate (PEG-DA) and agarose. The polymerized PEG-DA hydrogel could guarantee the stabilities of the inverse opal structure and its resultant code, while the agarose could offer active chemical groups for the probe immobilization and homogeneous water surrounding for the bioassay. In addition, the interconnected pores inverse opal structure could provide channels for biomolecules diffusing and reaction into the voids of barcodes. These features imparted the hybrid hydrogel photonic barcodes with limits of detection (LOD) of 0.78ng/mL for carcinoembryonic antigen (CEA) and 0.21ng/mL for α-fetoprotein (AFP), respectively. It was also demonstrated that the proposed barcodes showed acceptable accuracy and detection reproducibility, and the results were in acceptable agreement with those from common clinic method for the detections of practical clinical samples. Thus, our technique provides a new platform for simultaneous multiplex immunoassay.

  9. Noninvasive deep Raman detection with 2D correlation analysis

    NASA Astrophysics Data System (ADS)

    Kim, Hyung Min; Park, Hyo Sun; Cho, Youngho; Jin, Seung Min; Lee, Kang Taek; Jung, Young Mee; Suh, Yung Doug

    2014-07-01

    The detection of poisonous chemicals enclosed in daily necessaries is prerequisite essential for homeland security with the increasing threat of terrorism. For the detection of toxic chemicals, we combined a sensitive deep Raman spectroscopic method with 2D correlation analysis. We obtained the Raman spectra from concealed chemicals employing spatially offset Raman spectroscopy in which incident line-shaped light experiences multiple scatterings before being delivered to inner component and yielding deep Raman signal. Furthermore, we restored the pure Raman spectrum of each component using 2D correlation spectroscopic analysis with chemical inspection. Using this method, we could elucidate subsurface component under thick powder and packed contents in a bottle.

  10. 2D signature for detection and identification of drugs

    NASA Astrophysics Data System (ADS)

    Trofimov, Vyacheslav A.; Varentsova, Svetlana A.; Shen, Jingling; Zhang, Cunlin; Zhou, Qingli; Shi, Yulei

    2011-06-01

    The method of spectral dynamics analysis (SDA-method) is used for obtaining the2D THz signature of drugs. This signature is used for the detection and identification of drugs with similar Fourier spectra by transmitted THz signal. We discuss the efficiency of SDA method for the identification problem of pure methamphetamine (MA), methylenedioxyamphetamine (MDA), 3, 4-methylenedioxymethamphetamine (MDMA) and Ketamine.

  11. Genetic barcodes

    DOEpatents

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  12. 3D surface configuration modulates 2D symmetry detection.

    PubMed

    Chen, Chien-Chung; Sio, Lok-Teng

    2015-02-01

    We investigated whether three-dimensional (3D) information in a scene can affect symmetry detection. The stimuli were random dot patterns with 15% dot density. We measured the coherence threshold, or the proportion of dots that were the mirror reflection of the other dots in the other half of the image about a central vertical axis, at 75% accuracy with a 2AFC paradigm under various 3D configurations produced by the disparity between the left and right eye images. The results showed that symmetry detection was difficult when the corresponding dots across the symmetry axis were on different frontoparallel or inclined planes. However, this effect was not due to a difference in distance, as the observers could detect symmetry on a slanted surface, where the depth of the two sides of the symmetric axis was different. The threshold was reduced for a hinge configuration where the join of two slanted surfaces coincided with the axis of symmetry. Our result suggests that the detection of two-dimensional (2D) symmetry patterns is subject to the 3D configuration of the scene; and that coplanarity across the symmetry axis and consistency between the 2D pattern and 3D structure are important factors for symmetry detection.

  13. Multiplexed Detection of Cytokines Based on Dual Bar-Code Strategy and Single-Molecule Counting.

    PubMed

    Li, Wei; Jiang, Wei; Dai, Shuang; Wang, Lei

    2016-02-02

    Cytokines play important roles in the immune system and have been regarded as biomarkers. While single cytokine is not specific and accurate enough to meet the strict diagnosis in practice, in this work, we constructed a multiplexed detection method for cytokines based on dual bar-code strategy and single-molecule counting. Taking interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) as model analytes, first, the magnetic nanobead was functionalized with the second antibody and primary bar-code strands, forming a magnetic nanoprobe. Then, through the specific reaction of the second antibody and the antigen that fixed by the primary antibody, sandwich-type immunocomplex was formed on the substrate. Next, the primary bar-code strands as amplification units triggered multibranched hybridization chain reaction (mHCR), producing nicked double-stranded polymers with multiple branched arms, which were served as secondary bar-code strands. Finally, the secondary bar-code strands hybridized with the multimolecule labeled fluorescence probes, generating enhanced fluorescence signals. The numbers of fluorescence dots were counted one by one for quantification with epi-fluorescence microscope. By integrating the primary and secondary bar-code-based amplification strategy and the multimolecule labeled fluorescence probes, this method displayed an excellent sensitivity with the detection limits were both 5 fM. Unlike the typical bar-code assay that the bar-code strands should be released and identified on a microarray, this method is more direct. Moreover, because of the selective immune reaction and the dual bar-code mechanism, the resulting method could detect the two targets simultaneously. Multiple analysis in human serum was also performed, suggesting that our strategy was reliable and had a great potential application in early clinical diagnosis.

  14. Symmetry detection of auxetic behaviour in 2D frameworks

    NASA Astrophysics Data System (ADS)

    Mitschke, H.; Schröder-Turk, G. E.; Mecke, K.; Fowler, P. W.; Guest, S. D.

    2013-06-01

    A symmetry-extended Maxwell treatment of the net mobility of periodic bar-and-joint frameworks is used to derive a sufficient condition for auxetic behaviour of a 2D material. The type of auxetic behaviour that can be detected by symmetry has Poisson's ratio -1, with equal expansion/contraction in all directions, and is here termed equiauxetic. A framework may have a symmetry-detectable equiauxetic mechanism if it belongs to a plane group that includes rotational axes of order n = 6, 4, or 3. If the reducible representation for the net mobility contains mechanisms that preserve full rotational symmetry (A modes), these are equiauxetic. In addition, for n = 6, mechanisms that halve rotational symmetry (B modes) are also equiauxetic.

  15. A large 2D PSD for thermal neutron detection

    SciTech Connect

    Knott, R.B.; Watt, G.; Boldeman, J.W.; Smith, G.C.

    1996-12-31

    A 2D PSD based on a MWPC has been constructed for a small angle neutron scattering instrument. The active area of the detector was 640 x 640 mm{sup 2}. To meet the specifications for neutron detection efficiency and spatial resolution, and to minimize parallax, the gas mixture was 190 kPa {sup 3}He plus 100 kPa CF{sub 4} and the active volume had a thickness of 30 mm. The design maximum neutron count-rate of the detector was 10{sup 5} events per second. The (calculated) neutron detection efficiency was 60% for 2{angstrom} neutrons and the (measured) neutron energy resolution on the anode grid was typically 20% (fwhm). The location of a neutron detection event within the active area was determined using the wire-by-wire method: the spatial resolution (5 x 5 mm{sup 2}) was thereby defined by the wire geometry. A 16 channel charge-sensitive preamplifier/amplifier/comparator module has been developed with a channel sensitivity of 0.1 V/fC, noise linewidth of 0.4 fC (fwhm) and channel-to-channel cross-talk of less than 5%. The Proportional Counter Operating System (PCOS III) (LeCroy Corp USA) was used for event encoding. The ECL signals produced by the 16 channel modules were latched in PCOS III by a trigger pulse from the anode and the fast encoders produce a position and width for each event. The information was transferred to a UNIX workstation for accumulation and online display.

  16. A large 2D PSD for thermal neutron detection

    NASA Astrophysics Data System (ADS)

    Knott, R. B.; Smith, G. C.; Watt, G.; Boldeman, J. W.

    1997-02-01

    A 2D PSD based on a MWPC has been constructed for a small angle neutron scattering instrument. The active area of the detector was 640 × 640 mm 2. To meet the specifications for neutron detection efficiency and spatial resolution, and to minimise parallax, the gas mixture was 190 kPa 3He plus 100 kPa CF 4, and the active volume had a thickness of 30 mm. The design maximum neutron count rate of the detector was 10 5 events per secod. The (calculated) neutron detection efficiency was 60% for 2 Å neutrons and the (measured) neutron energy resolution on the anode grid was typically 20% (fwhm). The location of a neutron detection event within the active area was determined using the wire-by-wire method: the spatial resolution (5 × 5 mm 2) was thereby defined by the wire geometry. A 16-channel charge-sensitive preamplifier/amplifier/comparator module has been developed with a channel sensitivity of 0.1 V/fC, noise line width of 0.4 fC (fwhm) and channel-to-channel cross-talk of less than 5%. The Proportional Counter Operating System (PCOS III) (LeCroy Corp, USA) was used for event encoding. The ECL signals produced by the 16 channel modules were latched in PCOS III by a trigger pulse from the anode and the fast encoders produce a position and width for each event. The information was transferred to a UNIX workstation for accumulation and online display.

  17. A practicable detection system for genetically modified rice by SERS-barcoded nanosensors.

    PubMed

    Chen, Kun; Han, Heyou; Luo, Zhihui; Wang, Yanjun; Wang, Xiuping

    2012-04-15

    Since the global cultivation of genetically modified crops constantly expands, it remains a high demand to establish different ways to sort food and feed that consist or contain genetically modified organisms. Surface-enhanced Raman scattering (SERS) spectroscopy is a flexible tool for biological analysis due to its excellent properties for detecting wide varieties of target biomolecules including nucleic acids. In the present study, a SERS-barcoded nanosensor was developed to detect Bacillus thuringiensis (Bt) gene-transformed rice expressing insecticidal proteins. The barcoded sensor was designed by encapsulation of gold nanoparticles with silica and conjugation of oligonucleotide strands for targeting DNA strands. The transition between the cry1A(b) and cry1A(c) fusion gene sequence was used to construct a specific SERS-based detection method with a detection limit of 0.1 pg/mL. In order to build the determination models to screen transgene, a series mixture of Bt rice and normal rice were prepared for SERS assay, and the limit of detection was 0.1% (w/w) transgenic Bt rice relative to normal rice. The sensitivity and accuracy of the SERS-based assay was comparable with real-time PCR. The SERS-barcoded analytical method would provide precise detection of transgenic rice varieties but also informative supplement to avoid false positive outcomes.

  18. The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data

    PubMed Central

    2014-01-01

    Background Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade. Results The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation’ barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity. Conclusions The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is

  19. Barcode DNA length polymorphisms vs fatty acid profiling for adulteration detection in olive oil.

    PubMed

    Uncu, Ali Tevfik; Uncu, Ayse Ozgur; Frary, Anne; Doganlar, Sami

    2017-04-15

    The aim of this study was to compare the performance of a DNA-barcode assay with fatty acid profile analysis to authenticate the botanical origin of olive oil. To achieve this aim, we performed a PCR-capillary electrophoresis (PCR-CE) approach on olive oil: seed oil blends using the plastid trnL (UAA) intron barcode. In parallel to genomic analysis, we subjected the samples to gas chromatography analysis of fatty acid composition. While the PCR-CE assay proved equally efficient as gas chromatography analysis in detecting adulteration with soybean, palm, rapeseed, sunflower, sesame, cottonseed and peanut oils, it was superior to the widely utilized analytical chemistry approach in revealing the adulterant species and detecting small quantities of corn and safflower oils in olive oil. Moreover, the DNA-based test correctly identified all tested olive oil: hazelnut oil blends whereas it was not feasible to detect hazelnut oil adulteration through fatty acid profile analysis. Thus, the present research has shown the feasibility of a PCR-CE barcode assay to detect adulteration in olive oil.

  20. Automatic Constraint Detection for 2D Layout Regularization.

    PubMed

    Jiang, Haiyong; Nan, Liangliang; Yan, Dong-Ming; Dong, Weiming; Zhang, Xiaopeng; Wonka, Peter

    2016-08-01

    In this paper, we address the problem of constraint detection for layout regularization. The layout we consider is a set of two-dimensional elements where each element is represented by its bounding box. Layout regularization is important in digitizing plans or images, such as floor plans and facade images, and in the improvement of user-created contents, such as architectural drawings and slide layouts. To regularize a layout, we aim to improve the input by detecting and subsequently enforcing alignment, size, and distance constraints between layout elements. Similar to previous work, we formulate layout regularization as a quadratic programming problem. In addition, we propose a novel optimization algorithm that automatically detects constraints. We evaluate the proposed framework using a variety of input layouts from different applications. Our results demonstrate that our method has superior performance to the state of the art.

  1. A novel hybrid motion detection algorithm based on 2D histogram

    NASA Astrophysics Data System (ADS)

    Su, Xiaomeng; Wang, Haiying

    2015-03-01

    This article proposes a novel hybrid motion detection algorithm based on 2-D (2-Dimensional) spatio-temporal states histogram. The new algorithm combines the idea of image change detection based on 2-D histogram and spatio-temporal entropy image segmentation. It quantifies the continuity of pixel state in time and space domain which are called TDF (Time Domain Filter) and SDF (Space Domain Filter) respectively. After this, put both channels of output data from TDF and SDF into a 2-D histogram. In the 2-D histogram, a curve division method helps to separate the foreground state points and the background ones more accurately. Innovatively, the new algorithm converts the video sequence to its histogram sequence, and transforms the difference of pixel's value in the video sequence into the difference of pixel's position in the 2-D histogram. Experimental results on different types of scenes added Gaussian noise shows that the proposed technique has strong ability of detecting moving objects.

  2. Automatic barcode recognition method based on adaptive edge detection and a mapping model

    NASA Astrophysics Data System (ADS)

    Yang, Hua; Chen, Lianzheng; Chen, Yifan; Lee, Yong; Yin, Zhouping

    2016-09-01

    An adaptive edge detection and mapping (AEDM) algorithm to address the challenging one-dimensional barcode recognition task with the existence of both image degradation and barcode shape deformation is presented. AEDM is an edge detection-based method that has three consecutive phases. The first phase extracts the scan lines from a cropped image. The second phase involves detecting the edge points in a scan line. The edge positions are assumed to be the intersecting points between a scan line and a corresponding well-designed reference line. The third phase involves adjusting the preliminary edge positions to more reasonable positions by employing prior information of the coding rules. Thus, a universal edge mapping model is established to obtain the coding positions of each edge in this phase, followed by a decoding procedure. The Levenberg-Marquardt method is utilized to solve this nonlinear model. The computational complexity and convergence analysis of AEDM are also provided. Several experiments were implemented to evaluate the performance of AEDM algorithm. The results indicate that the efficient AEDM algorithm outperforms state-of-the-art methods and adequately addresses multiple issues, such as out-of-focus blur, nonlinear distortion, noise, nonlinear optical illumination, and situations that involve the combinations of these issues.

  3. Interferometric Motion Detection in Atomic Layer 2D Nanostructures: Visualizing Signal Transduction Efficiency and Optimization Pathways

    PubMed Central

    Wang, Zenghui; Feng, Philip X.-L.

    2016-01-01

    Atomic layer crystals are emerging building blocks for enabling new two-dimensional (2D) nanomechanical systems, whose motions can be coupled to other attractive physical properties in such 2D systems. Optical interferometry has been very effective in reading out the infinitesimal motions of these 2D structures and spatially resolving different modes. To quantitatively understand the detection efficiency and its dependence on the device parameters and interferometric conditions, here we present a systematic study of the intrinsic motion responsivity in 2D nanomechanical systems using a Fresnel-law-based model. We find that in monolayer to 14-layer structures, MoS2 offers the highest responsivity among graphene, h-BN, and MoS2 devices and for the three commonly used visible laser wavelengths (633, 532, and 405 nm). We also find that the vacuum gap resulting from the widely used 300 nm-oxide substrate in making 2D devices, fortunately, leads to close-to-optimal responsivity for a wide range of 2D flakes. Our results elucidate and graphically visualize the dependence of motion transduction responsivity upon 2D material type and number of layers, vacuum gap, oxide thickness, and detecting wavelength, thus providing design guidelines for constructing 2D nanomechanical systems with optimal optical motion readout. PMID:27464908

  4. Interferometric Motion Detection in Atomic Layer 2D Nanostructures: Visualizing Signal Transduction Efficiency and Optimization Pathways

    NASA Astrophysics Data System (ADS)

    Wang, Zenghui; Feng, Philip X.-L.

    2016-07-01

    Atomic layer crystals are emerging building blocks for enabling new two-dimensional (2D) nanomechanical systems, whose motions can be coupled to other attractive physical properties in such 2D systems. Optical interferometry has been very effective in reading out the infinitesimal motions of these 2D structures and spatially resolving different modes. To quantitatively understand the detection efficiency and its dependence on the device parameters and interferometric conditions, here we present a systematic study of the intrinsic motion responsivity in 2D nanomechanical systems using a Fresnel-law-based model. We find that in monolayer to 14-layer structures, MoS2 offers the highest responsivity among graphene, h-BN, and MoS2 devices and for the three commonly used visible laser wavelengths (633, 532, and 405 nm). We also find that the vacuum gap resulting from the widely used 300 nm-oxide substrate in making 2D devices, fortunately, leads to close-to-optimal responsivity for a wide range of 2D flakes. Our results elucidate and graphically visualize the dependence of motion transduction responsivity upon 2D material type and number of layers, vacuum gap, oxide thickness, and detecting wavelength, thus providing design guidelines for constructing 2D nanomechanical systems with optimal optical motion readout.

  5. Interferometric Motion Detection in Atomic Layer 2D Nanostructures: Visualizing Signal Transduction Efficiency and Optimization Pathways.

    PubMed

    Wang, Zenghui; Feng, Philip X-L

    2016-07-28

    Atomic layer crystals are emerging building blocks for enabling new two-dimensional (2D) nanomechanical systems, whose motions can be coupled to other attractive physical properties in such 2D systems. Optical interferometry has been very effective in reading out the infinitesimal motions of these 2D structures and spatially resolving different modes. To quantitatively understand the detection efficiency and its dependence on the device parameters and interferometric conditions, here we present a systematic study of the intrinsic motion responsivity in 2D nanomechanical systems using a Fresnel-law-based model. We find that in monolayer to 14-layer structures, MoS2 offers the highest responsivity among graphene, h-BN, and MoS2 devices and for the three commonly used visible laser wavelengths (633, 532, and 405 nm). We also find that the vacuum gap resulting from the widely used 300 nm-oxide substrate in making 2D devices, fortunately, leads to close-to-optimal responsivity for a wide range of 2D flakes. Our results elucidate and graphically visualize the dependence of motion transduction responsivity upon 2D material type and number of layers, vacuum gap, oxide thickness, and detecting wavelength, thus providing design guidelines for constructing 2D nanomechanical systems with optimal optical motion readout.

  6. Presynaptic GluN2D receptors detect glutamate spillover and regulate cerebellar GABA release

    PubMed Central

    Dubois, Christophe J.; Lachamp, Philippe M.; Sun, Lu; Mishina, Masayoshi

    2015-01-01

    Glutamate directly activates N-methyl-d-aspartate (NMDA) receptors on presynaptic inhibitory interneurons and enhances GABA release, altering the excitatory-inhibitory balance within a neuronal circuit. However, which class of NMDA receptors is involved in the detection of glutamate spillover is not known. GluN2D subunit-containing NMDA receptors are ideal candidates as they exhibit a high affinity for glutamate. We now show that cerebellar stellate cells express both GluN2B and GluN2D NMDA receptor subunits. Genetic deletion of GluN2D subunits prevented a physiologically relevant, stimulation-induced, lasting increase in GABA release from stellate cells [long-term potentiation of inhibitory transmission (I-LTP)]. NMDA receptors are tetramers composed of two GluN1 subunits associated to either two identical subunits (di-heteromeric receptors) or to two different subunits (tri-heteromeric receptors). To determine whether tri-heteromeric GluN2B/2D NMDA receptors mediate I-LTP, we tested the prediction that deletion of GluN2D converts tri-heteromeric GluN2B/2D to di-heteromeric GluN2B NMDA receptors. We find that prolonged stimulation rescued I-LTP in GluN2D knockout mice, and this was abolished by GluN2B receptor blockers that failed to prevent I-LTP in wild-type mice. Therefore, NMDA receptors that contain both GluN2D and GluN2B mediate the induction of I-LTP. Because these receptors are not present in the soma and dendrites, presynaptic tri-heteromeric GluN2B/2D NMDA receptors in inhibitory interneurons are likely to mediate the cross talk between excitatory and inhibitory transmission. PMID:26510761

  7. Encapsulated Solid-Liquid Phase Change Nanoparticles as Thermal Barcodes for Highly Sensitive Detections of Multiple Lung Cancer Biomarkers

    DTIC Science & Technology

    2012-10-01

    nanoparticles as thermal barcodes for highly sensitive detections of multiple lung cancer biomarkers PRINCIPAL INVESTIGATOR: Ming Su...nanoparticles to detect multiple cancer biomarkers for enhanced cancer detection at early stage. With the support from DOD-LCRP, we have proved the new signal...been used to obtain an NSF-CAREER project in 2011, as well as two grants to NIH and National Institute of Justice in 2012. 15. SUBJECT TERMS Cancer

  8. 2D View Aggregation for Lymph Node Detection Using a Shallow Hierarchy of Linear Classifiers

    PubMed Central

    Seff, Ari; Lu, Le; Cherry, Kevin M.; Roth, Holger; Liu, Jiamin; Wang, Shijun; Hoffman, Joanne; Turkbey, Evrim B.; Summers, Ronald M.

    2015-01-01

    Enlarged lymph nodes (LNs) can provide important information for cancer diagnosis, staging, and measuring treatment reactions, making automated detection a highly sought goal. In this paper, we propose a new algorithm representation of decomposing the LN detection problem into a set of 2D object detection subtasks on sampled CT slices, largely alleviating the curse of dimensionality issue. Our 2D detection can be effectively formulated as linear classification on a single image feature type of Histogram of Oriented Gradients (HOG), covering a moderate field-of-view of 45 by 45 voxels. We exploit both simple pooling and sparse linear fusion schemes to aggregate these 2D detection scores for the final 3D LN detection. In this manner, detection is more tractable and does not need to perform perfectly at instance level (as weak hypotheses) since our aggregation process will robustly harness collective information for LN detection. Two datasets (90 patients with 389 mediastinal LNs and 86 patients with 595 abdominal LNs) are used for validation. Cross-validation demonstrates 78.0% sensitivity at 6 false positives/volume (FP/vol.) (86.1% at 10 FP/vol.) and 73.1% sensitivity at 6 FP/vol. (87.2% at 10 FP/vol.), for the mediastinal and abdominal datasets respectively. Our results compare favorably to previous state-of-the-art methods. PMID:25333161

  9. 2D view aggregation for lymph node detection using a shallow hierarchy of linear classifiers.

    PubMed

    Seff, Ari; Lu, Le; Cherry, Kevin M; Roth, Holger R; Liu, Jiamin; Wang, Shijun; Hoffman, Joanne; Turkbey, Evrim B; Summers, Ronald M

    2014-01-01

    Enlarged lymph nodes (LNs) can provide important information for cancer diagnosis, staging, and measuring treatment reactions, making automated detection a highly sought goal. In this paper, we propose a new algorithm representation of decomposing the LN detection problem into a set of 2D object detection subtasks on sampled CT slices, largely alleviating the curse of dimensionality issue. Our 2D detection can be effectively formulated as linear classification on a single image feature type of Histogram of Oriented Gradients (HOG), covering a moderate field-of-view of 45 by 45 voxels. We exploit both max-pooling and sparse linear fusion schemes to aggregate these 2D detection scores for the final 3D LN detection. In this manner, detection is more tractable and does not need to perform perfectly at instance level (as weak hypotheses) since our aggregation process will robustly harness collective information for LN detection. Two datasets (90 patients with 389 mediastinal LNs and 86 patients with 595 abdominal LNs) are used for validation. Cross-validation demonstrates 78.0% sensitivity at 6 false positives/volume (FP/vol.) (86.1% at 10 FP/vol.) and 73.1% sensitivity at 6 FP/vol. (87.2% at 10 FP/vol.), for the mediastinal and abdominal datasets respectively. Our results compare favorably to previous state-of-the-art methods.

  10. A nanoparticle-based bio-barcode assay for ultrasensitive detection of ricin toxin.

    PubMed

    Yin, Hui-qiong; Jia, Min-xian; Yang, Shu; Wang, Sheng-qi; Zhang, Jin-gang

    2012-01-01

    The ultrasensitive bio-barcode amplification assay (BCA) technique was developed for the specific detection of the A chain of ricin toxin. The target antigen A chain was first captured by gold nanoparticles (GNPs) coated with polyclonal antibodies. Magnetic microparticles (MMPs) coated with A chain monoclonal antibody were then added to form a sandwich immuno-complex. After the immuno-complex was formed, signal DNA annealed to DNA strands covalently bound to the GNPs were released by heating and characterized by PCR and real-time fluorescence PCR. A detection limit of 1fg/ml was measured for A chain, six orders of magnitude more sensitive than that of conventional antigen-capture ELISA. The coefficient of variation (CV) of intra-assay and inter-assay ranged from 3.39% to 6.84%. The BCA can detect the A chain in milk and water mimic samples. In the following work it is demonstrated that this assay is a highly sensitive method for the detection of ricin proteins that could be adapted to measure other proteins.

  11. Acute myocarditis with normal wall motion detected with 2D speckle tracking echocardiography

    PubMed Central

    Niel, Johannes; Aichinger, Josef; Ebner, Christian

    2016-01-01

    Summary We present the case of a 26-year-old male with acute tonsillitis who was referred for coronary angiography because of chest pain, elevated cardiac biomarkers, and biphasic T waves. The patient had no cardiovascular risk factors. Echocardiography showed no wall motion abnormalities and no pericardial effusion. 2D speckle tracking revealed distinct decreased regional peak longitudinal systolic strain in the lateral and posterior walls. Ischemic disease was extremely unlikely in view of his young age, negative family history regarding coronary artery disease, and lack of regional wall motion abnormalities on the conventional 2D echocardiogram. Coronary angiography was deferred as myocarditis was suspected. To confirm the diagnosis, cardiac magnetic resonance tomography (MRT) was performed, showing subepicardial delayed hyperenhancement in the lateral and posterior walls correlating closely with the strain pattern obtained by 2D speckle tracking echocardiography. With a working diagnosis of acute myocarditis associated with acute tonsillitis, we prescribed antibiotics and nonsteroidal anti-inflammatory drugs. The patient’s clinical signs resolved along with normalization of serum creatine kinase (CK) levels, and the patient was discharged on the third day after admission. Learning points Acute myocarditis can mimic acute coronary syndromes.Conventional 2D echocardiography lacks specific features for detection of subtle regional wall motion abnormalities.2D speckle tracking expands the scope of echocardiography in identifying myocardial dysfunction derived from edema in acute myocarditis. PMID:27249814

  12. Interactive Boundary Detection for Automatic Definition of 2D Opacity Transfer Function

    NASA Astrophysics Data System (ADS)

    Rauberger, Martin; Overhoff, Heinrich Martin

    In computer assisted diagnostics nowadays, high-value 3-D visualization intake a supporting role to the traditional 2-D slice wise visualization. 3-D visualization may create intuitive visual appearances of the spatial relations of anatomical structures, based upon transfer functions mapping data values to visual parameters, e.g. color or opacity. Manual definition of these transfer functions however requires expert knowledge and can be tedious. In this paper an approach to automatizing 2-D opacity transfer function definition is presented. Upon few parameters characterizing the image volume and an user-depicted area of interest, the procedure detects organ surfaces automatically, upon which transfer functions may automatically be defined. Parameter setting still requires experience about the imaging properties of modalities, and improper setting can cause falsely detected organ surfaces. Procedure tests with CT and MRI image volumes show, that real time structure detection is even possible for noisy image volumes.

  13. DETECTION OF N{sub 2}D{sup +} IN A PROTOPLANETARY DISK

    SciTech Connect

    Huang, Jane; Öberg, Karin I.

    2015-08-20

    Observations of deuterium fractionation in the solar system, and in interstellar and circumstellar material, are commonly used to constrain the formation environment of volatiles. Toward protoplanetary disks, this approach has been limited by the small number of detected deuterated molecules, i.e., DCO{sup +} and DCN. Based on ALMA Cycle 2 observations toward the disk around the T Tauri star AS 209, we report the first detection of N{sub 2}D{sup +} (J = 3–2) in a protoplanetary disk. These data are used together with previous Submillimeter Array observations of N{sub 2}H{sup +} (J = 3–2) to estimate a disk-averaged D/H ratio of 0.3–0.5, an order of magnitude higher than disk-averaged ratios previously derived for DCN/HCN and DCO{sup +}/HCO{sup +} around other young stars. The high fractionation in N{sub 2}H{sup +} is consistent with model predictions. The presence of abundant N{sub 2}D{sup +} toward AS 209 also suggests that N{sub 2}D{sup +} and the N{sub 2}D{sup +}/N{sub 2}H{sup +} ratio can be developed into effective probes of deuterium chemistry, kinematics, and ionization processes outside the CO snow line of disks.

  14. Detection of IMRT delivery errors using a quantitative 2D dosimetric verification system

    SciTech Connect

    Childress, Nathan L.; Bloch, Charles; White, R. Allen; Salehpour, Mohammad; Rosen, Isaac I.

    2005-01-01

    We investigated the feasibility of detecting intensity modulated radiotherapy delivery errors automatically using a scalar evaluation of two-dimensional (2D) transverse dose measurement of the complete treatment delivery. Techniques using the gamma index and the normalized agreement test (NAT) index were used to parametrize the agreement between measured and computed dose distributions to seven different scalar metrics. Simulated verifications with delivery errors calculated using a commercially available treatment planning system for 9 prostate and 7 paranasal sinus cases were compared to 433 clinical verifications. The NAT index with 5% and 3 mm criteria that included cold areas outside the planning target volume detected the largest percent of delivery errors. Assuming a false positive rate of 5%, it was able to detect 88% of beam energy changes, 94% of a different patient's plan being delivered, 25% of plans with one beam's collimator rotated by 90 deg., 81% of rotating one beam's gantry angle by 10 deg., and 100% of omitting the delivery of one beam. However, no instances of changing one beam's monitor unit setting by 10% or shifting the isocenter by 5 mm were detected. Although the phantom shift could not be detected by the small change it made in the dose distribution, our autopositioning algorithm clearly identified the spatial anomaly. Using tighter 3%/2 mm criteria or combining dose and distance disagreements in an either/or fashion resulted in poorer delivery error detection. The mean value of the 2D gamma index distribution was less sensitive to delivery errors than the other scalar metrics studied. Although we found that scalar metrics do not have sufficient delivery error detection rates to be used as the sole clinical analysis technique, manually examining 2D dose comparison images would result in a near 100% detection rate while performing an ion chamber measurement alone would only detect 54% of these errors.

  15. Tetrodotoxin detection and species identification of pufferfish in retail roasted fish fillet by DNA barcoding in China.

    PubMed

    Li, Nan; Shen, Qing; Wang, Jiahui; Han, Chunhui; Ji, Rong; Li, Fengqin; Jiang, Tao

    2015-01-01

    This study identifies the pufferfish species and detects tetrodotoxin (TTX) in roasted fish fillet samples collected in Beijing, Qingdao and Xiamen, China. The cytochrome c oxidase I (COI) gene was used as the target gene for identification of the pufferfish species in the samples. Enzyme-linked immunosorbent assay (ELISA) screened the TTX levels in samples that had been detected as containing pufferfish by DNA barcode. A total of 125 samples were identified by DNA barcodes; 32 (26%) samples contained pufferfish composition and, among them, 26 (81%) were the highly toxic species Lagocephalus lunaris. All 32 samples containing the pufferfish composition were positive for TTX with levels ranging from 100 to 63,800 ng g(-1). Most of the 32 samples contained the highly toxic L. lunaris. Based on the results, we suggest that the monitoring of roasted fish fillet should be strengthened and the processing procedures should be standardised to minimise TTX poisoning caused by pufferfish.

  16. Detection of Leptomeningeal Metastasis by Contrast-Enhanced 3D T1-SPACE: Comparison with 2D FLAIR and Contrast-Enhanced 2D T1-Weighted Images

    PubMed Central

    Gil, Bomi; Hwang, Eo-Jin; Lee, Song; Jang, Jinhee; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Bum-soo

    2016-01-01

    Introduction To compare the diagnostic accuracy of contrast-enhanced 3D(dimensional) T1-weighted sampling perfection with application-optimized contrasts by using different flip angle evolutions (T1-SPACE), 2D fluid attenuated inversion recovery (FLAIR) images and 2D contrast-enhanced T1-weighted image in detection of leptomeningeal metastasis except for invasive procedures such as a CSF tapping. Materials and Methods Three groups of patients were included retrospectively for 9 months (from 2013-04-01 to 2013-12-31). Group 1 patients with positive malignant cells in CSF cytology (n = 22); group 2, stroke patients with steno-occlusion in ICA or MCA (n = 16); and group 3, patients with negative results on MRI, whose symptom were dizziness or headache (n = 25). A total of 63 sets of MR images are separately collected and randomly arranged: (1) CE 3D T1-SPACE; (2) 2D FLAIR; and (3) CE T1-GRE using a 3-Tesla MR system. A faculty neuroradiologist with 8-year-experience and another 2nd grade trainee in radiology reviewed each MR image- blinded by the results of CSF cytology and coded their observations as positives or negatives of leptomeningeal metastasis. The CSF cytology result was considered as a gold standard. Sensitivity and specificity of each MR images were calculated. Diagnostic accuracy was compared using a McNemar’s test. A Cohen's kappa analysis was performed to assess inter-observer agreements. Results Diagnostic accuracy was not different between 3D T1-SPACE and CSF cytology by both raters. However, the accuracy test of 2D FLAIR and 2D contrast-enhanced T1-weighted GRE was inconsistent by the two raters. The Kappa statistic results were 0.657 (3D T1-SPACE), 0.420 (2D FLAIR), and 0.160 (2D contrast-enhanced T1-weighted GRE). The 3D T1-SPACE images showed the highest inter-observer agreements between the raters. Conclusions Compared to 2D FLAIR and 2D contrast-enhanced T1-weighted GRE, contrast-enhanced 3D T1 SPACE showed a better detection rate of

  17. Fluorescence bio-barcode DNA assay based on gold and magnetic nanoparticles for detection of Exotoxin A gene sequence.

    PubMed

    Amini, Bahram; Kamali, Mehdi; Salouti, Mojtaba; Yaghmaei, Parichehreh

    2017-06-15

    Bio-barcode DNA based on gold nanoparticle (bDNA-GNPs) as a new generation of biosensor based detection tools, holds promise for biological science studies. They are of enormous importance in the emergence of rapid and sensitive procedures for detecting toxins of microorganisms. Exotoxin A (ETA) is the most toxic virulence factor of Pseudomonas aeruginosa. ETA has ADP-ribosylation activity and decisively affects the protein synthesis of the host cells. In the present study, we developed a fluorescence bio-barcode technology to trace P. aeruginosa ETA. The GNPs were coated with the first target-specific DNA probe 1 (1pDNA) and bio-barcode DNA, which acted as a signal reporter. The magnetic nanoparticles (MNPs) were coated with the second target-specific DNA probe 2 (2pDNA) that was able to recognize the other end of the target DNA. After binding the nanoparticles with the target DNA, the following sandwich structure was formed: MNP 2pDNA/tDNA/1pDNA-GNP-bDNA. After isolating the sandwiches by a magnetic field, the DNAs of the probes which have been hybridized to their complementary DNA, GNPs and MNPs, via the hydrogen, electrostatic and covalently bonds, were released from the sandwiches after dissolving in dithiothreitol solution (DTT 0.8M). This bio-barcode DNA with known DNA sequence was then detected by fluorescence spectrophotometry. The findings showed that the new method has the advantages of fast, high sensitivity (the detection limit was 1.2ng/ml), good selectivity, and wide linear range of 5-200ng/ml. The regression analysis also showed that there was a good linear relationship (∆F=0.57 [target DNA]+21.31, R(2)=0.9984) between the fluorescent intensity and the target DNA concentration in the samples.

  18. 2D-ELDOR detection of magnetization transfer of nitroxides in disordered solid polymers

    NASA Astrophysics Data System (ADS)

    Maresch, G. G.; Weber, M.; Dubinskii, A. A.; Spiess, H. W.

    1992-05-01

    Two-dimensional electron—electron double resonance (2D-ELDOR) experiments on nitroxide spin labels in solid liquid-crystalline side-group polymers have been performed employing narrow-band microwave excitation pulses followed by a rapid magnetic field step during a mixing time and detection at the new selected point of the EPR spectrum. Information about magnetization transfer throughout the full EPR spectrum is obtained by sweeping both pumping and detecting fields. In the two-dimensional representation of experimental ELDOR data, the different processes causing magnetization transfer through the EPR spectrum, i.e. electron spin diffusion, nuclear relaxation, and slow rotational motions lead to different patterns and can be distinguished by recording 2D-ELDOR spectra as a function of temperature. In the specific system studied, the 2D-ELDOR spectra show the dominance of magnetization transfer between states with close molecular orientations but different nitrogen nuclear spin projections caused by flips of nuclear spins. The results are discussed in terms of dynamic processes in glasses.

  19. Limitations and challenges of genetic barcode quantification

    PubMed Central

    Thielecke, Lars; Aranyossy, Tim; Dahl, Andreas; Tiwari, Rajiv; Roeder, Ingo; Geiger, Hartmut; Fehse, Boris; Glauche, Ingmar; Cornils, Kerstin

    2017-01-01

    Genetic barcodes are increasingly used to track individual cells and to quantitatively assess their clonal contributions over time. Although barcode quantification relies entirely on counting sequencing reads, detailed studies about the method’s accuracy are still limited. We report on a systematic investigation of the relation between barcode abundance and resulting read counts after amplification and sequencing using cell-mixtures that contain barcodes with known frequencies (“miniBulks”). We evaluated the influence of protocol modifications to identify potential sources of error and elucidate possible limitations of the quantification approach. Based on these findings we designed an advanced barcode construct (BC32) to improved barcode calling and quantification, and to ensure a sensitive detection of even highly diluted barcodes. Our results emphasize the importance of using curated barcode libraries to obtain interpretable quantitative data and underline the need for rigorous analyses of any utilized barcode library in terms of reliability and reproducibility. PMID:28256524

  20. Detection and assessment of damage in 2D structures using measured modal response

    NASA Astrophysics Data System (ADS)

    Banan, Mohammad Reza; Mehdi-pour, Yousef

    2007-10-01

    Motivated by one of the concepts in the field of health monitoring for structural systems, a damage detection procedure is developed. In order to perform the system health monitoring, structural health along with sensor and actuator malfunction must be continuously checked. As a step toward developing a system health-monitoring scheme, this paper investigated structural damage detection, using a constrained eigenstructure assignment. The proposed damage detection method is constructed based on a concept of control theory and subspace rotation for two-dimensional (2D)-structural systems. To demonstrate the capabilities of the developed damage detection algorithm, the behavior of a simulated degraded braced-frame structure is studied. Using Monte Carlo simulation, the performance of the approach is evaluated. It shows that the proposed algorithm is potentially promising for application to real cases.

  1. Low-frequency phased-array 2D fluorescence localization in breast cancer detection

    NASA Astrophysics Data System (ADS)

    Liu, Qian; Chen, Yu; Chance, Britton; Luo, Qingming

    2003-12-01

    A method for rapid, non-invasive 2D fluorescence localization of breast cancer using low frequency phased array near-infrared technique is presented in this article. In our study, we have developed a dual-channel fluorescence detection system to locate breast cancer. This system consists two pair of in-phase and out-of-phase light emitting diodes (LEDs) as the light sources and Photomultiplier Tube (PMT) as the detector. Two null planes generated by cancellation of diffusion photon density waves (DPDW) will indicate the 2D position of breast cancer with exogenous contrast agents. The fluorescent contrast agent used in this study is Indocyanine Green (ICG) and the minimum amount of ICG detected by our system is 0.5 μM. With the 2 cm separation of sources and detector, the maximum depth our system can detect is 10 mm. The whole system is in compact size and portable. Phantom experiments show that the system can provide real time detection and localization of small hidden absorbing-fluorescent objects inside the highly scattering medium with high accuracy of +/-3 mm. The potential application is that it is low-cost and can be used for breast cancer localization as operation aid and self-examination.

  2. Holographic method for site-resolved detection of a 2D array of ultracold atoms

    NASA Astrophysics Data System (ADS)

    Hoffmann, Daniel Kai; Deissler, Benjamin; Limmer, Wolfgang; Hecker Denschlag, Johannes

    2016-08-01

    We propose a novel approach to site-resolved detection of a 2D gas of ultracold atoms in an optical lattice. A near-resonant laser beam is coherently scattered by the atomic array, and after passing a lens its interference pattern is holographically recorded by superimposing it with a reference laser beam on a CCD chip. Fourier transformation of the recorded intensity pattern reconstructs the atomic distribution in the lattice with single-site resolution. The holographic detection method requires only about two hundred scattered photons per atom in order to achieve a high reconstruction fidelity of 99.9 %. Therefore, additional cooling during detection might not be necessary even for light atomic elements such as lithium. Furthermore, first investigations suggest that small aberrations of the lens can be post-corrected in imaging processing.

  3. Directional statistics for realistic weakly interacting massive particle direct detection experiments. II. 2D readout

    NASA Astrophysics Data System (ADS)

    Morgan, Ben; Green, Anne M.

    2005-12-01

    The direction dependence of the WIMP direct detection rate provides a powerful tool for distinguishing a WIMP signal from possible backgrounds. We study the number of events required to discriminate a WIMP signal from an isotropic background for a detector with 2-d readout using nonparametric circular statistics. We also examine the number of events needed to (i) detect a deviation from rotational symmetry, due to flattening of the Milky Way halo and (ii) detect a deviation in the mean direction due to a tidal stream. If the senses of the recoils are measured then of order 20--70 events (depending on the plane of the 2-d readout and the detector location) will be sufficient to reject isotropy of the raw recoil angles at 90% confidence. If the senses can not be measured these number increase by roughly 2 orders of magnitude (compared with an increase of 1 order of magnitude for the case of full 3-d readout). The distributions of the reduced angles, with the (time-dependent) direction of solar motion subtracted, are far more anisotropic, however, and if the isotropy tests are applied to these angles then the numbers of events required are similar to the case of 3-d readout. A deviation from rotational symmetry will only be detectable if the Milky Way halo is significantly flattened. The deviation in the mean direction due to a tidal stream is potentially detectable, however, depending on the density and direction of the stream. The meridian plane (which contains the Earth’s spin axis) is, for all detector locations, the optimum readout plane for rejecting isotropy. However readout in this plane can not be used for detecting flattening of the Milky Way halo or a stream with direction perpendicular to the galactic plane. In these cases the optimum readout plane depends on the detector location.

  4. Barcoded microchips for biomolecular assays.

    PubMed

    Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu

    2015-01-20

    Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

  5. Comparison of 2D and 3D Displays and Sensor Fusion for Threat Detection, Surveillance, and Telepresence

    DTIC Science & Technology

    2003-05-19

    Comparison of 2D and 3D displays and sensor fusion for threat detection, surveillance, and telepresence T. Meitzler, Ph. D.a, D. Bednarz, Ph.D.a, K...camouflaged threats are compared on a two dimensional (2D) display and a three dimensional ( 3D ) display. A 3D display is compared alongside a 2D...technologies that take advantage of 3D and sensor fusion will be discussed. 1. INTRODUCTION Computer driven interactive 3D imaging has made

  6. Evaluation of the channelized Hotelling observer for signal detection in 2D tomographic imaging

    NASA Astrophysics Data System (ADS)

    LaRoque, Samuel J.; Sidky, Emil Y.; Edwards, Darrin C.; Pan, Xiaochuan

    2007-03-01

    Signal detection by the channelized Hotelling (ch-Hotelling) observer is studied for tomographic application by employing a small, tractable 2D model of a computed tomography (CT) system. The primary goal of this manuscript is to develop a practical method for evaluating the ch-Hotelling observer that can generalize to larger 3D cone-beam CT systems. The use of the ch-Hotelling observer for evaluating tomographic image reconstruction algorithms is also demonstrated. For a realistic model for CT, the ch-Hotelling observer can be a good approximation to the ideal observer. The ch-Hotelling observer is applied to both the projection data and the reconstructed images. The difference in signal-to-noise ratio for signal detection in both of these domains provides a metric for evaluating the image reconstruction algorithm.

  7. Tamper-indicating barcode and method

    DOEpatents

    Cummings, Eric B.; Even, Jr., William R.; Simmons, Blake A.; Dentinger, Paul Michael

    2005-03-22

    A novel tamper-indicating barcode methodology is disclosed that allows for detection of alteration to the barcode. The tamper-indicating methodology makes use of a tamper-indicating means that may be comprised of a particulate indicator, an optical indicator, a deformable substrate, and/or may be an integrated aspect of the barcode itself. This tamper-indicating information provides greater security for the contents of containers sealed with the tamper-indicating barcodes.

  8. A multiplex nanoparticle-based bio-barcoded DNA sensor for the simultaneous detection of multiple pathogens.

    PubMed

    Zhang, Deng; Huarng, Michael C; Alocilja, Evangelyn C

    2010-12-15

    A highly amplified, nanoparticle-based, bio-barcoded electrochemical biosensor for the simultaneous multiple detection of the protective antigen A (pagA) gene (accession number, M22589) of Bacillus anthracis and the insertion element (Iel) gene (accession number, Z83734) of Salmonella enteritidis is reported in this paper. The biosensor system is mainly composed of three nanoparticles: gold nanoparticles (AuNPs), magnetic nanoparticles (MNPs), and nanoparticle tracers (NTs, such as PbS and CdS). The AuNPs are coated with the first target-specific DNA probe (1pDNA), which can recognize one end of the target DNA sequence (tDNA), and many NT-terminated bio-barcode ssDNA (bDNA-NT), which act as signal reporter and amplifier. The MNPs are coated with the second target-specific DNA probe (2pDNA) that can recognize the other end of the target gene. After binding the nanoparticles with the target DNA, the following sandwich structure is formed: MNP-2pDNA/tDNA/1pDNA-AuNP-bDNA-NTs. A magnetic field is applied to separate the sandwich structure from the unreacted materials. Because the AuNPs have a large number of nanoparticle tracers per DNA probe binding event, there is substantial amplification. After the nanoparticle tracer is dissolved in 1M nitric acid, the NT(2+) ions are detected by square wave anodic stripping voltammetry (SWASV) on screen-printed carbon electrode (SPCE) chips. The results show that the detection limit of this multiplex bio-barcoded DNA sensor are 0.5 ng/mL of the insertion element (Iel) gene of S. enteritidis using CdS, and 50 pg/mL of the pagA gene of B. anthracis using PbS NTs. The nanoparticle-based bio-barcoded DNA sensor has potential application in rapid detection of multiple pathogenic agents in the same sample.

  9. A New Method for Detecting Goaf Area of Coal Mine :2D Microtremor Profiling Technique

    NASA Astrophysics Data System (ADS)

    Xu, P.; Ling, S.; Guo, H.; Shi, W.; Li, S.; Tian, B.

    2012-12-01

    A goaf area is referred to as a cavity where coal has been removed or mined out. These cavities will change the original geostress equilibrium of stratigraphic system and cause local geostress focusing or concentration. Consequently, the surrounding rock of a goaf may be deformed, fractured, displaced and caved resulting from the combined effect of gravity and geostress. In the cases of little or no effective mining control, widespread cracks, fractures and even subsidence of the rock mass above the goaf will not only lead to groundwater depletion, farmland destruction and deterioration of ecological environment, but also present a serious threat to the mining safety, engineering construction, and even people's lives and property. So, it is important to locate the boundary of the goaf and to evaluate its stability in order to provide the basis for comprehensive control in the latter period of mining. This article attempts to explore a new geophysical method - 2D microtremor profiling technique for goaf detection and mapping. 2D microtremor profiling technique is based on the microtremor array theory (Aki, 1957; Ling, 1994; Okada, 2003) utilizing spatial autocorrelation analysis to obtain Rayleigh-wave dispersion curves for apparent S-wave velocity (Vx) calculation (Ling & Miwa, 2006;Xu et al.,2012). A laterally continuous S-wave velocity section can then be obtained through data interpolation. The final result will be used for interpreting lateral changes in lithology and geological structures. Let's take a case study in Henan Province of China as an example. The coal seams in the survey area were about 150 ~ 250m deep. A triple-circular array was adopted for acquiring microtremor data, with the observation radius in 20, 40 and 80m, respectively, and a sampling the interval of 50m. We observed the following characteristics of the goaf area from the microtremor Vx section: (1) obvious low pseudo velocity anomaly corresponding to limestone layer below the goaf; (2

  10. DNA barcoding detects contamination and substitution in North American herbal products

    PubMed Central

    2013-01-01

    Background Herbal products available to consumers in the marketplace may be contaminated or substituted with alternative plant species and fillers that are not listed on the labels. According to the World Health Organization, the adulteration of herbal products is a threat to consumer safety. Our research aimed to investigate herbal product integrity and authenticity with the goal of protecting consumers from health risks associated with product substitution and contamination. Methods We used DNA barcoding to conduct a blind test of the authenticity for (i) 44 herbal products representing 12 companies and 30 different species of herbs, and (ii) 50 leaf samples collected from 42 herbal species. Our laboratory also assembled the first standard reference material (SRM) herbal barcode library from 100 herbal species of known provenance that were used to identify the unknown herbal products and leaf samples. Results We recovered DNA barcodes from most herbal products (91%) and all leaf samples (100%), with 95% species resolution using a tiered approach (rbcL + ITS2). Most (59%) of the products tested contained DNA barcodes from plant species not listed on the labels. Although we were able to authenticate almost half (48%) of the products, one-third of these also contained contaminants and or fillers not listed on the label. Product substitution occurred in 30/44 of the products tested and only 2/12 companies had products without any substitution, contamination or fillers. Some of the contaminants we found pose serious health risks to consumers. Conclusions Most of the herbal products tested were of poor quality, including considerable product substitution, contamination and use of fillers. These activities dilute the effectiveness of otherwise useful remedies, lowering the perceived value of all related products because of a lack of consumer confidence in them. We suggest that the herbal industry should embrace DNA barcoding for authenticating herbal products through

  11. Detection of an endogenous urinary biomarker associated with CYP2D6 activity using global metabolomics

    PubMed Central

    Tay-Sontheimer, Jessica; Shireman, Laura M; Beyer, Richard P; Senn, Taurence; Witten, Daniela; Pearce, Robin E; Gaedigk, Andrea; Fomban, Cletus L Gana; Lutz, Justin D; Isoherranen, Nina; Thummel, Kenneth E; Fiehn, Oliver; Leeder, J Steven; Lin, Yvonne S

    2015-01-01

    Aim We sought to discover endogenous urinary biomarkers of human CYP2D6 activity. Patients & methods Healthy pediatric subjects (n = 189) were phenotyped using dextromethorphan and randomized for candidate biomarker selection and validation. Global urinary metabolomics was performed using liquid chromatography quadrupole time-of-flight mass spectrometry. Candidate biomarkers were tested in adults receiving fluoxetine, a CYP2D6 inhibitor. Results A biomarker, M1 (m/z 444.3102) was correlated with CYP2D6 activity in both the pediatric training and validation sets. Poor metabolizers had undetectable levels of M1, whereas it was present in subjects with other phenotypes. In adult subjects, a 9.56-fold decrease in M1 abundance was observed during CYP2D6 inhibition. Conclusion Identification and validation of M1 may provide a noninvasive means of CYP2D6 phenotyping. PMID:25521354

  12. DNA Barcoding of Marine Metazoa

    NASA Astrophysics Data System (ADS)

    Bucklin, Ann; Steinke, Dirk; Blanco-Bercial, Leocadio

    2011-01-01

    More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may outpace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a ˜648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.

  13. Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding.

    PubMed

    Asis, Angelli Marie Jacynth M; Lacsamana, Joanne Krisha M; Santos, Mudjekeewis D

    2016-01-01

    Illegal trade has greatly affected marine fish stocks, decreasing fish populations worldwide. Despite having a number of aquatic species being regulated, illegal trade still persists through the transport of dried or processed products and juvenile species trafficking. In this regard, accurate species identification of illegally traded marine fish stocks by DNA barcoding is deemed to be a more efficient method in regulating and monitoring trade than by morphological means which is very difficult due to the absence of key morphological characters in juveniles and processed products. Here, live juvenile eels (elvers) and dried products of sharks and rays confiscated for illegal trade were identified. Twenty out of 23 (87%) randomly selected "elvers" were identified as Anguilla bicolor pacifica and 3 (13%) samples as Anguilla marmorata. On the other hand, 4 out of 11 (36%) of the randomly selected dried samples of sharks and rays were Manta birostris. The rest of the samples were identified as Alopias pelagicus, Taeniura meyeni, Carcharhinus falciformis, Himantura fai and Mobula japonica. These results confirm that wild juvenile eels and species of manta rays are still being caught in the country regardless of its protected status under Philippine and international laws. It is evident that the illegal trade of protected aquatic species is happening in the guise of dried or processed products thus the need to put emphasis on strengthening conservation measures. This study aims to underscore the importance of accurate species identification in such cases of illegal trade and the effectivity of DNA barcoding as a tool to do this.

  14. iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast

    PubMed Central

    Jaffe, Mia; Sherlock, Gavin; Levy, Sasha F.

    2016-01-01

    Systematic screens for genetic interactions are a cornerstone of both network and systems biology. However, most screens have been limited to characterizing interaction networks in a single environment. Moving beyond this static view of the cell requires a major technological advance to increase the throughput and ease of replication in these assays. Here, we introduce iSeq—a platform to build large double barcode libraries and rapidly assay genetic interactions across environments. We use iSeq in yeast to measure fitness in three conditions of nearly 400 clonal strains, representing 45 possible single or double gene deletions, including multiple replicate strains per genotype. We show that iSeq fitness and interaction scores are highly reproducible for the same clonal strain across replicate cultures. However, consistent with previous work, we find that replicates with the same putative genotype have highly variable genetic interaction scores. By whole-genome sequencing 102 of our strains, we find that segregating variation and de novo mutations, including aneuploidy, occur frequently during strain construction, and can have large effects on genetic interaction scores. Additionally, we uncover several new environment-dependent genetic interactions, suggesting that barcode-based genetic interaction assays have the potential to significantly expand our knowledge of genetic interaction networks. PMID:27821633

  15. Integrating early detection with DNA barcoding: species identification of a non-native monitor lizard (Squamata: Varanidae) carcass in Mississippi, U.S.A.

    USGS Publications Warehouse

    Reed, Robert N.; Hopken, Matthew W.; Steen, David A.; Falk, Bryan G.; Piaggio, Antoinette J.

    2016-01-01

    Early detection of invasive species is critical to increasing the probability of successful management. At the primary stage of an invasion, invasive species are easier to control as the population is likely represented by just a few individuals. Detection of these first few individuals can be challenging, particularly if they are cryptic or otherwise characterized by low detectability. The engagement of members of the public may be critical to early detection as there are far more citizen s on the landscape than trained biologists. However, it can be difficult to assess the credibility of public reporting, especially when a diagnostic digital image or a physical specimen in good condition are lacking. DNA barcoding can be used for verification when morphological identification of a specimen is not possible or uncertain (i.e., degraded or partial specimen). DNA barcoding relies on obtaining a DNA sequence from a relatively small fragment of mitochondrial DNA and comparing it to a database of sequences containing a variety of expertly identified species. He rein we report the successful identification of a degraded specimen of a non-native, potentially invasive reptile species (Varanus niloticus) via DNA barcoding, after discovery and reporting by a member of the public.

  16. Highly sensitive detection of human IgG using a novel bio-barcode assay combined with DNA chip technology

    NASA Astrophysics Data System (ADS)

    Liu, Zhenbao; Zhou, Bo; Wang, Haiqing; Lu, Feng; Liu, Tianjun; Song, Cunxian; Leng, Xigang

    2013-09-01

    A simple and ultrasensitive detection of human IgG based on signal amplification using a novel bio-barcode assay and DNA chip technology was developed. The sensing platform was a sandwich system made up of antibody-modified magnetic microparticles (Ab-MMPs)/human IgG/Cy3-labeled single-stranded DNA and antibody-modified gold nanoparticles (Cy3-ssDNA-Ab-AuNPs). The MMPs (2.5 μm in diameter) modified with mouse anti-human IgG monoclonal-antibodies could capture human IgG and further be separated and enriched via a magnetic field. The AuNPs (13 nm in diameter) conjugated with goat anti-human IgG polyclonal-antibodies and Cy3-ssDNA could further combine with the human IgG/Ab-MMP complex. The Cy3-ssDNA on AuNPs was then released by TCEP to hybridize with the DNA chip, thus generating a detectable signal by the fluorescence intensity of Cy3. In order to improve detection sensitivity, a three-level cascaded signal amplification was developed: (1) The MMP enrichment as the first-level; (2) Large quantities of Cy3-ssDNA on AuNPs as the second-level; (3) The Cy3-ssDNA conjugate with DNA chip as the third-level. The highly sensitive technique showed an increased response of the fluorescence intensity to the increased concentration of human IgG through a detection range from 1 pg mL-1 to 10 ng mL-1. This sensing technique could not only improve the detection sensitivity for the low concentration of human IgG but also present a robust and efficient signal amplification model. The detection method has good stability, specificity, and reproducibility and could be applied in the detection of human IgG in the real samples.

  17. Toward a two-dimensional barcode with visual information using perceptual shaping watermarking in mobile applications

    NASA Astrophysics Data System (ADS)

    Liu, Jen-Chang; Shieh, Hsiang-An

    2011-01-01

    Traditional two-dimensional (2-D) barcodes, such as the QR code and PDF417, do not carry visual information. This work proposes a visually meaningful 2-D barcode (or 2-D image code) that carries not only hidden information, but also visual information. Watermarking is employed to hide information in a meaningful cover image to produce the 2-D image code. The 2-D image code can be printed or displayed and then captured using a camera-equipped mobile device. The hidden information is extracted for innovative applications. To resist distortions in the print-and-photo process, a perceptual shaping algorithm, based on Watson's DCT-based perceptual model, is proposed for use in the data hiding procedure. The detection performance that can be achieved using two classes of position-detection patterns is evaluated, and the best pattern is then used as a part of the 2-D image code. A web service is provided for generating the 2-D image codes and a Java-based decoder is developed for mobile phones. The results of practical experiments reveal the applicability, robustness, and high capacity of the proposed 2-D image code.

  18. Enhanced detection limit by dark mode perturbation in 2D photonic crystal slab refractive index sensors.

    PubMed

    Nicolaou, Costa; Lau, Wah Tung; Gad, Raanan; Akhavan, Hooman; Schilling, Ryan; Levi, Ofer

    2013-12-16

    We demonstrate for the first time a 300nm thick, 300μm × 300μm 2D dielectric photonic crystal slab membrane with a quality factor of 10,600 by coupling light to slightly perturbed dark modes through alternating nano-hole sizes. The newly created fundamental guided resonances greatly reduce nano-fabrication accuracy requirements. Moreover, we created a new layer architecture resulting in electric field enhancement at the interface between the slab and sensing regions, and spectral sensitivity of >800 nm/RIU, that is, >0.8 of the single-mode theoretical upper limit of spectral sensitivity.

  19. Detection of CYP2D6 polymorphism using Luminex xTAG technology in autism spectrum disorder: CYP2D6 activity score and its association with risperidone levels.

    PubMed

    Vanwong, Natchaya; Ngamsamut, Nattawat; Hongkaew, Yaowaluck; Nuntamool, Nopphadol; Puangpetch, Apichaya; Chamnanphon, Montri; Sinrachatanant, Ananya; Limsila, Penkhae; Sukasem, Chonlaphat

    2016-04-01

    CYP2D6 is involved in the biotransformation of a large number of drugs, including risperidone. This study was designed to detect CYP2D6 polymorphisms with a Luminex assay, including assessment the relationship of CYP2D6 polymorphisms and risperidone plasma concentration in autism spectrum disorder children (ASD) treated with risperidone. All 84 ASD patients included in this study had been receiving risperidone at least for 1 month. The CYP2D6 genotypes were determined by Luminex assay. Plasma concentrations of risperidone and 9-hydroxyrisperidone were measured using LC/MS/MS. Among the 84 patients, there were 46 (55.42%) classified as EM, 33 (39.76%) as IM, and 4(4.82%) as UM. The plasma concentration of risperidone and risperidone/9-hydroxyrisperidone ratio in the patients were significant differences among the CYP2D6 predicted phenotype group (P = 0.001 and P < 0.0001 respectively). Moreover, the plasma concentration of risperidone and risperidone/9-hydroxyrisperidone ratio in the patients with CYP2D6 activity score 0.5 were significantly higher than those with the CYP2D6 activity score 2.0 (P = 0.004 and P = 0.002 respectively). These findings suggested that the determination of the accurate CYP2D6 genotype-predicted phenotype is essential in the clinical setting and individualization of drug therapy. The use of the Luminex assay for detection of CYP2D6 polymorphisms could help us more accurately identify an individual's CYP2D6 phenotype.

  20. Phase-Resolved Heterodyne-Detected Transient Grating Enhances the Capabilities of 2D IR Echo Spectroscopy.

    PubMed

    Jin, Geun Young; Kim, Yung Sam

    2017-02-09

    2D IR echo spectroscopy, with high sensitivity and femtosecond time resolution, enables us to understand structure and ultrafast dynamics of molecular systems. Application of this experimental technique on weakly absorbing samples, however, had been limited by the precise and unambiguous phase determination of the echo signals. In this study, we propose a new experimental scheme that significantly increases the phase stability of the involved IR pulses. We have demonstrated that the incorporation of phase-resolved heterodyne-detected transient grating (PR-HDTG) spectroscopy greatly enhances the capabilities of 2D IR spectroscopy. The new experimental scheme has been used to obtain 2D IR spectra on weakly absorbing azide ions (N3(-)) in H2O (absorbance ∼0.025), free of phase ambiguity even at large waiting times. We report the estimated spectral diffusion time scale (1.056 ps) of azide ions in aqueous solution from the 2D IR spectra and the vibrational lifetime (750 ± 3 fs) and the reorientation time (1108 ± 24 fs) from the PR-HDTG spectra.

  1. An aptamer-based bio-barcode assay with isothermal recombinase polymerase amplification for cytochrome-c detection and anti-cancer drug screening.

    PubMed

    Loo, Jacky F C; Lau, P M; Ho, H P; Kong, S K

    2013-10-15

    Based on a recently reported ultra-sensitive bio-barcode (BBC) assay, we have developed an aptamer-based bio-barcode (ABC) alternative to detect a cell death marker cytochrome-c (Cyto-c) and its subsequent application to screen anti-cancer drugs. Aptamer is a short single-stranded DNA selected from a synthetic DNA library by virtue of its high binding affinity and specificity to its target based on its unique 3D structure from the nucleotide sequence after folding. In the BBC assay, an antigen (Ag) in analytes is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Abs). Gold nanoparticles (NPs) with another recognition Ab against the same target and hundreds of identical DNA molecules of known sequence are subsequently added to allow the formation of sandwich structures ([MMP-Ab1]-Ag-[Ab2-NP-DNA]). After isolating the sandwiches by a magnetic field, the DNAs hybridized to their complementary DNAs covalently bound on the NPs are released from the sandwiches after heating. Acting as an Ag identification tag, these bio-barcode DNAs with known DNA sequence are then amplified by polymerase chain reaction (PCR) and detected by fluorescence. In our ABC assay, we employed a Cyto-c-specific aptamer to substitute both the recognition Ab and barcode DNAs on the NPs in the BBC assay; and a novel isothermal recombinase polymerase amplification for the time-consuming PCR. The detection limit of our ABC assay for the Cyto-c was found to be 10 ng/mL and this new assay can be completed within 3h. Several potential anti-cancer drugs have been tested in vitro for their efficacy to kill liver cancer with or without multi-drug resistance.

  2. Random forest learning of ultrasonic statistical physics and object spaces for lesion detection in 2D sonomammography

    NASA Astrophysics Data System (ADS)

    Sheet, Debdoot; Karamalis, Athanasios; Kraft, Silvan; Noël, Peter B.; Vag, Tibor; Sadhu, Anup; Katouzian, Amin; Navab, Nassir; Chatterjee, Jyotirmoy; Ray, Ajoy K.

    2013-03-01

    Breast cancer is the most common form of cancer in women. Early diagnosis can significantly improve lifeexpectancy and allow different treatment options. Clinicians favor 2D ultrasonography for breast tissue abnormality screening due to high sensitivity and specificity compared to competing technologies. However, inter- and intra-observer variability in visual assessment and reporting of lesions often handicaps its performance. Existing Computer Assisted Diagnosis (CAD) systems though being able to detect solid lesions are often restricted in performance. These restrictions are inability to (1) detect lesion of multiple sizes and shapes, and (2) differentiate between hypo-echoic lesions from their posterior acoustic shadowing. In this work we present a completely automatic system for detection and segmentation of breast lesions in 2D ultrasound images. We employ random forests for learning of tissue specific primal to discriminate breast lesions from surrounding normal tissues. This enables it to detect lesions of multiple shapes and sizes, as well as discriminate between hypo-echoic lesion from associated posterior acoustic shadowing. The primal comprises of (i) multiscale estimated ultrasonic statistical physics and (ii) scale-space characteristics. The random forest learns lesion vs. background primal from a database of 2D ultrasound images with labeled lesions. For segmentation, the posterior probabilities of lesion pixels estimated by the learnt random forest are hard thresholded to provide a random walks segmentation stage with starting seeds. Our method achieves detection with 99.19% accuracy and segmentation with mean contour-to-contour error < 3 pixels on a set of 40 images with 49 lesions.

  3. A Pedestrian Detection Scheme Using a Coherent Phase Difference Method Based on 2D Range-Doppler FMCW Radar.

    PubMed

    Hyun, Eugin; Jin, Young-Seok; Lee, Jong-Hun

    2016-01-20

    For an automotive pedestrian detection radar system, fast-ramp based 2D range-Doppler Frequency Modulated Continuous Wave (FMCW) radar is effective for distinguishing between moving targets and unwanted clutter. However, when a weak moving target such as a pedestrian exists together with strong clutter, the pedestrian may be masked by the side-lobe of the clutter even though they are notably separated in the Doppler dimension. To prevent this problem, one popular solution is the use of a windowing scheme with a weighting function. However, this method leads to a spread spectrum, so the pedestrian with weak signal power and slow Doppler may also be masked by the main-lobe of clutter. With a fast-ramp based FMCW radar, if the target is moving, the complex spectrum of the range- Fast Fourier Transform (FFT) is changed with a constant phase difference over ramps. In contrast, the clutter exhibits constant phase irrespective of the ramps. Based on this fact, in this paper we propose a pedestrian detection for highly cluttered environments using a coherent phase difference method. By detecting the coherent phase difference from the complex spectrum of the range-FFT, we first extract the range profile of the moving pedestrians. Then, through the Doppler FFT, we obtain the 2D range-Doppler map for only the pedestrian. To test the proposed detection scheme, we have developed a real-time data logging system with a 24 GHz FMCW transceiver. In laboratory tests, we verified that the signal processing results from the proposed method were much better than those expected from the conventional 2D FFT-based detection method.

  4. A Pedestrian Detection Scheme Using a Coherent Phase Difference Method Based on 2D Range-Doppler FMCW Radar

    PubMed Central

    Hyun, Eugin; Jin, Young-Seok; Lee, Jong-Hun

    2016-01-01

    For an automotive pedestrian detection radar system, fast-ramp based 2D range-Doppler Frequency Modulated Continuous Wave (FMCW) radar is effective for distinguishing between moving targets and unwanted clutter. However, when a weak moving target such as a pedestrian exists together with strong clutter, the pedestrian may be masked by the side-lobe of the clutter even though they are notably separated in the Doppler dimension. To prevent this problem, one popular solution is the use of a windowing scheme with a weighting function. However, this method leads to a spread spectrum, so the pedestrian with weak signal power and slow Doppler may also be masked by the main-lobe of clutter. With a fast-ramp based FMCW radar, if the target is moving, the complex spectrum of the range- Fast Fourier Transform (FFT) is changed with a constant phase difference over ramps. In contrast, the clutter exhibits constant phase irrespective of the ramps. Based on this fact, in this paper we propose a pedestrian detection for highly cluttered environments using a coherent phase difference method. By detecting the coherent phase difference from the complex spectrum of the range-FFT, we first extract the range profile of the moving pedestrians. Then, through the Doppler FFT, we obtain the 2D range-Doppler map for only the pedestrian. To test the proposed detection scheme, we have developed a real-time data logging system with a 24 GHz FMCW transceiver. In laboratory tests, we verified that the signal processing results from the proposed method were much better than those expected from the conventional 2D FFT-based detection method. PMID:26805835

  5. Multichannel response analysis on 2D projection views for detection of clustered microcalcifications in digital breast tomosynthesis

    SciTech Connect

    Wei, Jun Chan, Heang-Ping; Hadjiiski, Lubomir M.; Helvie, Mark A.; Lu, Yao; Zhou, Chuan; Samala, Ravi

    2014-04-15

    Purpose: To investigate the feasibility of a new two-dimensional (2D) multichannel response (MCR) analysis approach for the detection of clustered microcalcifications (MCs) in digital breast tomosynthesis (DBT). Methods: With IRB approval and informed consent, a data set of two-view DBTs from 42 breasts containing biopsy-proven MC clusters was collected in this study. The authors developed a 2D approach for MC detection using projection view (PV) images rather than the reconstructed three-dimensional (3D) DBT volume. Signal-to-noise ratio (SNR) enhancement processing was first applied to each PV to enhance the potential MCs. The locations of MC candidates were then identified with iterative thresholding. The individual MCs were decomposed with Hermite–Gaussian (HG) and Laguerre–Gaussian (LG) basis functions and the channelized Hotelling model was trained to produce the MCRs for each MC on the 2D images. The MCRs from the PVs were fused in 3D by a coincidence counting method that backprojects the MC candidates on the PVs and traces the coincidence of their ray paths in 3D. The 3D MCR was used to differentiate the true MCs from false positives (FPs). Finally a dynamic clustering method was used to identify the potential MC clusters in the DBT volume based on the fact that true MCs of clinical significance appear in clusters. Using two-fold cross validation, the performance of the 3D MCR for classification of true and false MCs was estimated by the area under the receiver operating characteristic (ROC) curve and the overall performance of the MCR approach for detection of clustered MCs was assessed by free response receiver operating characteristic (FROC) analysis. Results: When the HG basis function was used for MCR analysis, the detection of MC cluster achieved case-based test sensitivities of 80% and 90% at the average FP rates of 0.65 and 1.55 FPs per DBT volume, respectively. With LG basis function, the average FP rates were 0.62 and 1.57 per DBT volume at

  6. Highly specific SNP detection using 2D graphene electronics and DNA strand displacement.

    PubMed

    Hwang, Michael T; Landon, Preston B; Lee, Joon; Choi, Duyoung; Mo, Alexander H; Glinsky, Gennadi; Lal, Ratnesh

    2016-06-28

    Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.

  7. Highly specific SNP detection using 2D graphene electronics and DNA strand displacement

    PubMed Central

    Hwang, Michael T.; Landon, Preston B.; Lee, Joon; Choi, Duyoung; Mo, Alexander H.; Glinsky, Gennadi; Lal, Ratnesh

    2016-01-01

    Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine. PMID:27298347

  8. A fast moving object detection method based on 2D laser scanner and infrared camera

    NASA Astrophysics Data System (ADS)

    Zeng, Lina; Ding, Meng; Zhang, Tianci; Sun, Zejun

    2015-10-01

    Moving object detection is a major research direction of video surveillance systems. This paper proposes a novel approach for moving object detection by fusing information from the laser scanner and infrared camera. First, in accordance with the feature of laser scanner data, we apply robust principal component analysis (RPCA) to studying moving object detection. Then the depth and angle information of moving objects is mapped to the infrared image pixels so as to obtain the regions of interest (ROI). Finally, moving objects can be recognized by making investigation of the ROI. Experimental results show that this method has good real-time performance and accuracy.

  9. Image Outlier Detection and Feature Extraction via L1-Norm-Based 2D Probabilistic PCA.

    PubMed

    Ju, Fujiao; Sun, Yanfeng; Gao, Junbin; Hu, Yongli; Yin, Baocai

    2015-12-01

    This paper introduces an L1-norm-based probabilistic principal component analysis model on 2D data (L1-2DPPCA) based on the assumption of the Laplacian noise model. The Laplacian or L1 density function can be expressed as a superposition of an infinite number of Gaussian distributions. Under this expression, a Bayesian inference can be established based on the variational expectation maximization approach. All the key parameters in the probabilistic model can be learned by the proposed variational algorithm. It has experimentally been demonstrated that the newly introduced hidden variables in the superposition can serve as an effective indicator for data outliers. Experiments on some publicly available databases show that the performance of L1-2DPPCA has largely been improved after identifying and removing sample outliers, resulting in more accurate image reconstruction than the existing PCA-based methods. The performance of feature extraction of the proposed method generally outperforms other existing algorithms in terms of reconstruction errors and classification accuracy.

  10. A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium.

    PubMed

    Chen, W; Seifert, K A; Lévesque, C A

    2009-05-01

    We developed a COX1 barcode oligonucleotide array based on 358 sequences, including 58 known and two new species of Penicillium subgenus Penicillium, and 12 allied species. The array was robotically spotted at near microarray density on membranes. Species and clade-specific oligonucleotides were selected using the computer programs SigOli and Array Designer. Robotic spotting allowed 768 spots with duplicate sets of perfect match and the corresponding mismatch and positive control oligonucleotides, to be printed on 2 × 6 cm(2) nylon membranes. The array was validated with hybridizations between the array and digoxigenin (DIG)-labelled COX1 polymerase chain reaction amplicons from 70 pure DNA samples, and directly from environmental samples (cheese and plants) without culturing. DNA hybridization conditions were optimized, but undesired cross-reactions were detected frequently, reflecting the relatively high sequence similarity of the COX1 gene among Penicillium species. Approximately 60% of the perfect match oligonucleotides were rejected because of low specificity and 76 delivered useful group-specific or species-specific reactions and could be used for detecting certain species of Penicillium in environmental samples. In practice, the presence of weak signals on arrays exposed to amplicons from environmental samples, which could have represented weak detections or weak cross reactions, made interpretation difficult for over half of the oligonucleotides. DNA regions with very few single nucleotide polymorphisms or lacking insertions/deletions among closely related species are not ideal for oligonucleotide-based diagnostics, and supplementing the COX1-based array with oligonucleotides derived from additional genes would result in a more robust hierarchical identification system.

  11. Emission-Line Galaxies from the PEARS Hubble Ultra Deep Field: A 2-D Detection Method and First Results

    NASA Technical Reports Server (NTRS)

    Gardner, J. P.; Straughn, Amber N.; Meurer, Gerhardt R.; Pirzkal, Norbert; Cohen, Seth H.; Malhotra, Sangeeta; Rhoads, james; Windhorst, Rogier A.; Gardner, Jonathan P.; Hathi, Nimish P.; Xu, Chun; Gronwall, Caryl; Koekemoer, Anton M.; Walsh, Jeremy; diSeregoAlighieri, Sperello

    2007-01-01

    The Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) grism PEARS (Probing Evolution And Reionization Spectroscopically) survey provides a large dataset of low-resolution spectra from thousands of galaxies in the GOODS North and South fields. One important subset of objects in these data are emission-line galaxies (ELGs), and we have investigated several different methods aimed at systematically selecting these galaxies. Here we present a new methodology and results of a search for these ELGs in the PEARS observations of the Hubble Ultra Deep Field (HUDF) using a 2D detection method that utilizes the observation that many emission lines originate from clumpy knots within galaxies. This 2D line-finding method proves to be useful in detecting emission lines from compact knots within galaxies that might not otherwise be detected using more traditional 1D line-finding techniques. We find in total 96 emission lines in the HUDF, originating from 81 distinct "knots" within 63 individual galaxies. We find in general that [0 1111 emitters are the most common, comprising 44% of the sample, and on average have high equivalent widths (70% of [0 1111 emitters having rest-frame EW> 100A). There are 12 galaxies with multiple emitting knots; several show evidence of variations in H-alpha flux in the knots, suggesting that the differing star formation properties across a single galaxy can in general be probed at redshifts approximately greater than 0.2 - 0.4. The most prevalent morphologies are large face-on spirals and clumpy interacting systems, many being unique detections owing to the 2D method described here, thus highlighting the strength of this technique.

  12. Ex vivo evaluation of new 2D and 3D dental radiographic technology for detecting caries

    PubMed Central

    Tyndall, Donald; Mol, André; Everett, Eric T; Bangdiwala, Ananta

    2016-01-01

    Objectives: Proximal dental caries remains a prevalent disease with only modest detection rates by current diagnostic systems. Many new systems are available without controlled validation of diagnostic efficacy. The objective of this study was to evaluate the diagnostic efficacy of three potentially promising new imaging systems. Methods: This study evaluated the caries detection efficacy of Schick 33 (Sirona Dental, Salzburg, Austria) intraoral digital detector images employing an advanced sharpening filter, Planmeca ProMax® (Planmeca Inc., Helsinki, Finland) extraoral “panoramic bitewing” images and Sirona Orthophos XG3D (Sirona Dental) CBCT images with advanced artefact reduction. Conventional photostimulable phosphor images served as the control modality. An ex vivo study design using extracted human teeth, ten expert observers and micro-CT ground truth was employed. Results: Receiver operating characteristic analysis indicated similar diagnostic efficacy of all systems (ANOVA p > 0.05). The sensitivity of the Schick 33 images (0.48) was significantly lower than the other modalities (0.53–0.62). The specificity of the Planmeca images (0.86) was significantly lower than Schick 33 (0.96) and XG3D (0.97). The XG3D showed significantly better cavitation detection sensitivity (0.62) than the other modalities (0.48–0.57). Conclusions: The Schick 33 images demonstrated reduced caries sensitivity, whereas the Planmeca panoramic bitewing images demonstrated reduced specificity. XG3D with artefact reduction demonstrated elevated sensitivity and specificity for caries detection, improved depth accuracy and substantially improved cavitation detection. Care must be taken to recognize potential false-positive caries lesions with Planmeca panoramic bitewing images. Use of CBCT for caries detection must be carefully balanced with the presence of metal artefacts, time commitment, financial cost and radiation dose. PMID:26670605

  13. Detection of metallic and plastic landmines using the GPR and 2-D resistivity techniques

    NASA Astrophysics Data System (ADS)

    Metwaly, M.

    2007-12-01

    Low and non-metallic landmines are one of the most difficult subsurface targets to be detected using several geophysical techniques. Ground penetrating radar (GPR) performance at different field sites shows great success in detecting metallic landmines. However significant limitations are taking place in the case of low and non-metallic landmines. Electrical resistivity imaging (ERI) technique is tested to be an alternative or confirmation technique for detecting the metallic and non-metallic landmines in suspicious cleared areas. The electrical resistivity responses using forward modeling for metallic and non-metallic landmines buried in dry and wet environments utilizing the common electrode configurations have been achieved. Roughly all the utilized electrode arrays can establish the buried metallic and plastic mines correctly in dry and wet soil. The accuracy differs from one array to the other based on the relative resistivity contrast to the host soil and the subsurface distribution of current and potential lines as well as the amplitude of the noises in the data. The ERI technique proved to be fast and effective tool for detecting the non-metallic mines especially in the conductive environment whereas the performances of the other metal detector (MD) and GPR techniques show great limitation.

  14. Location detection and tracking of moving targets by a 2D IR-UWB radar system.

    PubMed

    Nguyen, Van-Han; Pyun, Jae-Young

    2015-03-19

    In indoor environments, the Global Positioning System (GPS) and long-range tracking radar systems are not optimal, because of signal propagation limitations in the indoor environment. In recent years, the use of ultra-wide band (UWB) technology has become a possible solution for object detection, localization and tracking in indoor environments, because of its high range resolution, compact size and low cost. This paper presents improved target detection and tracking techniques for moving objects with impulse-radio UWB (IR-UWB) radar in a short-range indoor area. This is achieved through signal-processing steps, such as clutter reduction, target detection, target localization and tracking. In this paper, we introduce a new combination consisting of our proposed signal-processing procedures. In the clutter-reduction step, a filtering method that uses a Kalman filter (KF) is proposed. Then, in the target detection step, a modification of the conventional CLEAN algorithm which is used to estimate the impulse response from observation region is applied for the advanced elimination of false alarms. Then, the output is fed into the target localization and tracking step, in which the target location and trajectory are determined and tracked by using unscented KF in two-dimensional coordinates. In each step, the proposed methods are compared to conventional methods to demonstrate the differences in performance. The experiments are carried out using actual IR-UWB radar under different scenarios. The results verify that the proposed methods can improve the probability and efficiency of target detection and tracking.

  15. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding.

    PubMed

    Jørgensen, Tina; Kjaer, Kurt H; Haile, James; Rasmussen, Morten; Boessenkool, Sanne; Andersen, Kenneth; Coissac, Eric; Taberlet, Pierre; Brochmann, Christian; Orlando, Ludovic; Gilbert, M Thomas P; Willerslev, Eske

    2012-04-01

    Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in 'oceans' of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km(2) of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes probably being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.

  16. Feasibility and Limitations of Vaccine Two-Dimensional Barcoding Using Mobile Devices

    PubMed Central

    Bell, Cameron; Guerinet, Julien

    2016-01-01

    Background Two-dimensional (2D) barcoding has the potential to enhance documentation of vaccine encounters at the point of care. However, this is currently limited to environments equipped with dedicated barcode scanners and compatible record systems. Mobile devices may present a cost-effective alternative to leverage 2D vaccine vial barcodes and improve vaccine product-specific information residing in digital health records. Objective Mobile devices have the potential to capture product-specific information from 2D vaccine vial barcodes. We sought to examine the feasibility, performance, and potential limitations of scanning 2D barcodes on vaccine vials using 4 different mobile phones. Methods A unique barcode scanning app was developed for Android and iOS operating systems. The impact of 4 variables on the scan success rate, data accuracy, and time to scan were examined: barcode size, curvature, fading, and ambient lighting conditions. Two experimenters performed 4 trials 10 times each, amounting to a total of 2160 barcode scan attempts. Results Of the 1832 successful scans performed in this evaluation, zero produced incorrect data. Five-millimeter barcodes were the slowest to scan, although only by 0.5 seconds on average. Barcodes with up to 50% fading had a 100% success rate, but success rate deteriorated beyond 60% fading. Curved barcodes took longer to scan compared with flat, but success rate deterioration was only observed at a vial diameter of 10 mm. Light conditions did not affect success rate or scan time between 500 lux and 20 lux. Conditions below 20 lux impeded the device’s ability to scan successfully. Variability in scan time was observed across devices in all trials performed. Conclusions 2D vaccine barcoding is possible using mobile devices and is successful under the majority of conditions examined. Manufacturers utilizing 2D barcodes should take into consideration the impact of factors that limit scan success rates. Future studies should

  17. Applying a 2D based CAD scheme for detecting micro-calcification clusters using digital breast tomosynthesis images: an assessment

    NASA Astrophysics Data System (ADS)

    Park, Sang Cheol; Zheng, Bin; Wang, Xiao-Hui; Gur, David

    2008-03-01

    Digital breast tomosynthesis (DBT) has emerged as a promising imaging modality for screening mammography. However, visually detecting micro-calcification clusters depicted on DBT images is a difficult task. Computer-aided detection (CAD) schemes for detecting micro-calcification clusters depicted on mammograms can achieve high performance and the use of CAD results can assist radiologists in detecting subtle micro-calcification clusters. In this study, we compared the performance of an available 2D based CAD scheme with one that includes a new grouping and scoring method when applied to both projection and reconstructed DBT images. We selected a dataset involving 96 DBT examinations acquired on 45 women. Each DBT image set included 11 low dose projection images and a varying number of reconstructed image slices ranging from 18 to 87. In this dataset 20 true-positive micro-calcification clusters were visually detected on the projection images and 40 were visually detected on the reconstructed images, respectively. We first applied the CAD scheme that was previously developed in our laboratory to the DBT dataset. We then tested a new grouping method that defines an independent cluster by grouping the same cluster detected on different projection or reconstructed images. We then compared four scoring methods to assess the CAD performance. The maximum sensitivity level observed for the different grouping and scoring methods were 70% and 88% for the projection and reconstructed images with a maximum false-positive rate of 4.0 and 15.9 per examination, respectively. This preliminary study demonstrates that (1) among the maximum, the minimum or the average CAD generated scores, using the maximum score of the grouped cluster regions achieved the highest performance level, (2) the histogram based scoring method is reasonably effective in reducing false-positive detections on the projection images but the overall CAD sensitivity is lower due to lower signal-to-noise ratio

  18. Tool breakage detection from 2D workpiece profile using vision method

    NASA Astrophysics Data System (ADS)

    Lee, W. K.; Ratnam, M. M.; Ahmad, Z. A.

    2016-02-01

    In-process tool breakage monitoring can significantly save cost and prevent damages to machine tool. In this paper, a machine vision approach was employed to detect the tool fracture in commercial aluminium oxide ceramic cutting tool during turning of AISI 52100 hardened steel. The contour of the workpiece profile was captured with the aid of backlighting during turning using a high-resolution DSLR camera with a shutter speed of 1/4000 s. The surface profile of the workpiece was extracted to sub-pixel accuracy using the invariant moment method. The effect of fracture in ceramic cutting tools on the surface profile signature of the machined workpiece using autocorrelation was studied. Fracture in the aluminum oxide ceramic tool was found to cause the peaks of autocorrelation function of the workpiece profile to decrease rapidly as the lag distance increased. The envelope of the peaks of the autocorrelation function was observed to deviate significantly from one another at different workpiece angles when the tool has fractured due to the continuous fracture of ceramic cutting insert during machining.

  19. Antibody-free detection of infectious bacteria using quantum dots-based barcode assay.

    PubMed

    Cihalova, Kristyna; Hegerova, Dagmar; Jimenez, Ana Maria; Milosavljevic, Vedran; Kudr, Jiri; Skalickova, Sylvie; Hynek, David; Kopel, Pavel; Vaculovicova, Marketa; Adam, Vojtech

    2017-02-05

    Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae are the most representative bacteria causing infectious diseases. Due to the increased application of antibiotics, the bacterial resistance is growing causing severe complications. Therefore, a sensitive determination of these pathogens is crucial for effective treatment. The aim of this study was to design an effective method for multiplex detection of Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae taking advantage from properties of magnetic particles as well as fluorescent nanoparticles (quantum dots). The method was able to detect as low concentrations of bacteria as 10(2) CFU/mL using the bacteria-specific genes (fnbA, mecA and wcaG).

  20. Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging

    NASA Astrophysics Data System (ADS)

    Afik, Eldad

    2015-09-01

    Three-dimensional particle tracking is an essential tool in studying dynamics under the microscope, namely, fluid dynamics in microfluidic devices, bacteria taxis, cellular trafficking. The 3d position can be determined using 2d imaging alone by measuring the diffraction rings generated by an out-of-focus fluorescent particle, imaged on a single camera. Here I present a ring detection algorithm exhibiting a high detection rate, which is robust to the challenges arising from ring occlusion, inclusions and overlaps, and allows resolving particles even when near to each other. It is capable of real time analysis thanks to its high performance and low memory footprint. The proposed algorithm, an offspring of the circle Hough transform, addresses the need to efficiently trace the trajectories of many particles concurrently, when their number in not necessarily fixed, by solving a classification problem, and overcomes the challenges of finding local maxima in the complex parameter space which results from ring clusters and noise. Several algorithmic concepts introduced here can be advantageous in other cases, particularly when dealing with noisy and sparse data. The implementation is based on open-source and cross-platform software packages only, making it easy to distribute and modify. It is implemented in a microfluidic experiment allowing real-time multi-particle tracking at 70 Hz, achieving a detection rate which exceeds 94% and only 1% false-detection.

  1. Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging

    PubMed Central

    Afik, Eldad

    2015-01-01

    Three-dimensional particle tracking is an essential tool in studying dynamics under the microscope, namely, fluid dynamics in microfluidic devices, bacteria taxis, cellular trafficking. The 3d position can be determined using 2d imaging alone by measuring the diffraction rings generated by an out-of-focus fluorescent particle, imaged on a single camera. Here I present a ring detection algorithm exhibiting a high detection rate, which is robust to the challenges arising from ring occlusion, inclusions and overlaps, and allows resolving particles even when near to each other. It is capable of real time analysis thanks to its high performance and low memory footprint. The proposed algorithm, an offspring of the circle Hough transform, addresses the need to efficiently trace the trajectories of many particles concurrently, when their number in not necessarily fixed, by solving a classification problem, and overcomes the challenges of finding local maxima in the complex parameter space which results from ring clusters and noise. Several algorithmic concepts introduced here can be advantageous in other cases, particularly when dealing with noisy and sparse data. The implementation is based on open-source and cross-platform software packages only, making it easy to distribute and modify. It is implemented in a microfluidic experiment allowing real-time multi-particle tracking at 70 Hz, achieving a detection rate which exceeds 94% and only 1% false-detection. PMID:26329642

  2. Simultaneous detection of single nucleotide polymorphisms and copy number variations in the CYP2D6 gene by multiplex polymerase chain reaction combined with capillary electrophoresis.

    PubMed

    Liao, Hsiao-Wei; Tsai, I-Lin; Chen, Guan-Yuan; Kuo, Chun-Ting; Wei, Ming-Feng; Hwang, Tzung-Jeng; Chen, Wei J; Shen, Li-Jiuan; Kuo, Ching-Hua

    2013-02-06

    CYP2D6 (cytochrome P450 2D6) is one of the most important enzymes involved in drug metabolism, and CYP2D6 gene variants may cause toxic effects of therapeutic drugs or treatment failure. In this research, a rapid and simple method for genotyping the most common mutant alleles in the Asian population (CYP2D6*1/*1, CYP2D6*1/*10, CYP2D6*10/*10, CYP2D6*1/*5, CYP2D6*5/*10, and CYP2D6*5/*5) was developed by allele-specific polymerase chain reaction (AS-PCR) combined with capillary electrophoresis (CE). We designed a second mismatch nucleotide next to the single nucleotide polymorphism (SNP) site in allele-specific primers to increase the difference in PCR amplification. Besides, we established simulation equations to predict the CYP2D6 genotypes by analyzing the DNA patterns in the CE chromatograms. The multiplex PCR combined with CE method was applied to test 50 patients, and all of the test results were compared with the DNA sequencing method, long-PCR method and real-time PCR method. The correlation of the analytical results between the proposed method and other methods were higher than 90%, and the proposed method is superior to other methods for being able to simultaneous detection of SNPs and copy number variations (CNV). Furthermore, we compared the plasma concentration of aripiprazole (a CYP2D6 substrate) and its major metabolites with the genotype of 25 patients. The results demonstrate the proposed genotyping method is effective for estimating the activity of the CYP2D6 enzyme and shows potential for application in personalized medicine. Similar approach can be applied to simultaneous detection of SNPs and CNVs of other genes.

  3. A rapidly modulated multifocal detection scheme for parallel acquisition of Raman spectra from a 2-D focal array.

    PubMed

    Kong, Lingbo; Chan, James

    2014-07-01

    We report the development of a rapidly modulated multifocal detection scheme that enables full Raman spectra (~500-2000 cm(-1)) from a 2-D focal array to be acquired simultaneously. A spatial light modulator splits a laser beam to generate an m × n multifocal array. Raman signals generated within each focus are projected simultaneously into a spectrometer and imaged onto a TE-cooled CCD camera. A shuttering system using different masks is constructed to collect the superimposed Raman spectra of different multifocal patterns. The individual Raman spectrum from each focus is then retrieved from the superimposed spectra with no crosstalk using a postacquisition data processing algorithm. This system is expected to significantly improve the speed of current Raman-based instruments such as laser tweezers Raman spectroscopy and hyperspectral Raman imaging.

  4. Color two-dimensional barcode patterns for extra encrypting sinusoidal-function scrambled data

    NASA Astrophysics Data System (ADS)

    Yeh, Sheng Lih; Lin, Kuang Tsan; Lin, Shyh-Tsong

    2016-06-01

    Conventional two-dimensional (2-D) barcode patterns are printed with black and white squares to encode texts. A few papers have proposed special 2-D barcode patterns with extra encrypted data, but the security of extra encrypted data is not emphasized usually. Therefore, this paper proposes color 2-D barcode patterns composed of black, blue, white, and yellow subsquares to extra encrypt binary data with higher security. Because blue looks like black and yellow looks like white, a color 2-D barcode pattern performs like a conventional 2-D barcode pattern. On the other hand, black, blue, white, and yellow subsquares are used to denote binary data. The security of extra encrypted data depends on an image scrambling algorithm by using the sinusoidal function, and the image scrambling algorithm can make a scrambled image have a high image scrambling degree percentage even after image scrambling is operated only one time.

  5. The effect of system geometry and dose on the threshold detectable calcification diameter in 2D-mammography and digital breast tomosynthesis

    NASA Astrophysics Data System (ADS)

    Hadjipanteli, Andria; Elangovan, Premkumar; Mackenzie, Alistair; Looney, Padraig T.; Wells, Kevin; Dance, David R.; Young, Kenneth C.

    2017-02-01

    Digital breast tomosynthesis (DBT) is under consideration to replace or to be used in combination with 2D-mammography in breast screening. The aim of this study was the comparison of the detection of microcalcification clusters by human observers in simulated breast images using 2D-mammography, narrow angle (15°/15 projections) and wide angle (50°/25 projections) DBT. The effects of the cluster height in the breast and the dose to the breast on calcification detection were also tested. Simulated images of 6 cm thick compressed breasts were produced with and without microcalcification clusters inserted, using a set of image modelling tools for 2D-mammography and DBT. Image processing and reconstruction were performed using commercial software. A series of 4-alternative forced choice (4AFC) experiments was conducted for signal detection with the microcalcification clusters as targets. Threshold detectable calcification diameter was found for each imaging modality with standard dose: 2D-mammography: 2D-mammography (165  ±  9 µm), narrow angle DBT (211  ±  11 µm) and wide angle DBT (257  ±  14 µm). Statistically significant differences were found when using different doses, but different geometries had a greater effect. No differences were found between the threshold detectable calcification diameters at different heights in the breast. Calcification clusters may have a lower detectability using DBT than 2D imaging.

  6. DNA barcoding for detecting market substitution in salted cod fillets and battered cod chunks.

    PubMed

    Di Pinto, Angela; Di Pinto, Pietro; Terio, Valentina; Bozzo, Giancarlo; Bonerba, Elisabetta; Ceci, Edmondo; Tantillo, Giuseppina

    2013-12-01

    The Italian Ministry of Agricultural, Food and Forestry Policies (MiPAAF) Decree dated 31 January 2008, which reports the Italian name for fish species of commercial interest, establishes that baccalà can be obtained exclusively from G. macrocephalus (Pacific cod) and G. morhua (Atlantic cod). This paper describes the COI-based DNA identification system to verify the substitution or misbranding of gadoid fish species and, consequently, its concordance with the labels on salted cod fillets shown as baccalà and on battered cod chunks labelled as bocconcini di baccalà. The analysis of interpretable sequences revealed that 55/65 dried salted cod fillet samples were detected as belonging to the family Gadidae, while 10/65 samples appeared to belong to the Lotidae family, while among battered cod chunks labelled as bocconcini di baccalà, the post-sequencing data analysis shows that the labels were completely wrong, with 28/40 samples from Pollachius virens and 12/40 samples from Brosme brosme. The substitution rate for products labelled on the market as baccalà in this study raises significant issues relating to food safety and consumer protection.

  7. Computer-aided detection of masses in digital tomosynthesis mammography: combination of 3D and 2D detection information

    NASA Astrophysics Data System (ADS)

    Chan, Heang-Ping; Wei, Jun; Zhang, Yiheng; Moore, Richard H.; Kopans, Daniel B.; Hadjiiski, Lubomir; Sahiner, Berkman; Roubidoux, Marilyn A.; Helvie, Mark A.

    2007-03-01

    We are developing a computer-aided detection (CAD) system for masses on digital breast tomosynthesis mammograms (DBTs). The CAD system includes two parallel processes. In the first process, mass detection and feature analysis are performed in the reconstructed 3D DBT volume. A mass likelihood score is estimated for each mass candidate using a linear discriminant (LDA) classifier. In the second process, mass detection and feature analysis are applied to the individual projection view (PV) images. A mass likelihood score is estimated for each mass candidate using another LDA classifier. The mass likelihood images derived from the PVs are back-projected to the breast volume to estimate the 3D spatial distribution of the mass likelihood scores. The mass likelihood scores estimated by the two processes at the corresponding 3D location are then merged and evaluated using FROC analysis. In this preliminary study, a data set of 52 DBT cases acquired with a GE prototype system at the Massachusetts General Hospital was used. The LDA classifiers with stepwise feature selection were designed with leave-one-case-out resampling. In an FROC analysis, the CAD system for detection in the DBT volume alone achieved test sensitivities of 80% and 90% at an average FP rate of 1.6 and 3.0 per breast, respectively. In comparison, the average FP rates of the combined system were 1.2 and 2.3 per breast, respectively, at the same sensitivities. The combined system is a promising approach to improving mass detection on DBTs.

  8. Barcode V1.0

    SciTech Connect

    2003-03-03

    This software produces barcode images for printing and reads barcodes from digital images according to the mathematical and algorithmic description from a Sandia patent application titled "A Self-Registering Sread-Spectrum Barcode". A novel spread spectrum barcode methodology is disclosed that allows a barcode to be read in its entirety even when a significant fraction or majority of the barcode is obscured. The barcode methodology makes use of registration or clocking information that is distributed along with the encoded user data across the barcode image. This registration information allows for the barcode image to be corrected for imaging distortion such as zoom, rotation, tilt, curvature and perspective.

  9. Luminance level of a monitor: influence on detectability and detection rate of breast cancer in 2D mammography

    NASA Astrophysics Data System (ADS)

    Bemelmans, Frédéric; Rashidnasab, Alaleh; Chesterman, Frédérique; Kimpe, Tom; Bosmans, Hilde

    2016-03-01

    Purpose: To evaluate lesion detectability and reading time as a function of luminance level of the monitor. Material and Methods: 3D mass models and microcalcification clusters were simulated into ROIs of for processing mammograms. Randomly selected ROIs were subdivided in three groups according to their background glandularity: high (>30%), medium (15-30%) and low (<15%). 6 non-spiculated masses (9 - 11mm), 6 spiculated masses (5 - 7mm) and 6 microcalcification clusters (2 - 4mm) were scaled in 3D to create a range of sizes. The linear attenuation coefficient (AC) of the masses was adjusted from 100% glandular tissue to 90%, 80%, 70%, to create different contrasts. Six physicists read the full database on Barco's Coronis Uniti monitor for four different luminance levels (300, 800, 1000 and 1200 Cd/m2), using a 4-AFC tool. Percentage correct (PC) and time were computed for all different conditions. A paired t-test was performed to evaluate the effect of luminance on PC and time. A multi-factorial analysis was performed using MANOVA.. Results: Paired t-test indicated a statistically significant difference for the average time per session between 300 and 1200; 800 and 1200; 1000 and 1200 Cd/m2, for all participants combined. There was no effect on PC. MANOVA denoted significantly lower reading times for high glandularity images at 1200 Cd/m2. Both types of masses were significantly faster detected at 1200 Cd/m2, for the contrast study. In the size study, microcalcification clusters and spiculated masses had a significantly higher detection rate at 1200 Cd/m2. Conclusion: These results demonstrate a significant decrease in reading time, while detectability remained constant.

  10. Automated clean-up, separation and detection of polycyclic aromatic hydrocarbons in particulate matter extracts from urban dust and diesel standard reference materials using a 2D-LC/2D-GC system.

    PubMed

    Ahmed, Trifa M; Lim, Hwanmi; Bergvall, Christoffer; Westerholm, Roger

    2013-10-01

    A multidimensional, on-line coupled liquid chromatographic/gas chromatographic system was developed for the quantification of polycyclic aromatic hydrocarbons (PAHs). A two-dimensional liquid chromatographic system (2D-liquid chromatography (LC)), with three columns having different selectivities, was connected on-line to a two-dimensional gas chromatographic system (2D-gas chromatography (GC)). Samples were cleaned up by combining normal elution and column back-flush of the LC columns to selectively remove matrix constituents and isolate well-defined, PAH enriched fractions. Using this system, the sequential removal of polar, mono/diaromatic, olefinic and alkane compounds from crude extracts was achieved. The LC/GC coupling was performed using a fused silica transfer line into a programmable temperature vaporizer (PTV) GC injector. Using the PTV in the solvent vent mode, excess solvent was removed and the enriched PAH sample extract was injected into the GC. The 2D-GC setup consisted of two capillary columns with different stationary phase selectivities. Heart-cutting of selected PAH compounds in the first GC column (first dimension) and transfer of these to the second GC column (second dimension) increased the baseline resolutions of closely eluting PAHs. The on-line system was validated using the standard reference materials SRM 1649a (urban dust) and SRM 1975 (diesel particulate extract). The PAH concentrations measured were comparable to the certified values and the fully automated LC/GC system performed the clean-up, separation and detection of PAHs in 16 extracts in less than 24 h. The multidimensional, on-line 2D-LC/2D-GC system eliminated manual handling of the sample extracts and minimised the risk of sample loss and contamination, while increasing accuracy and precision.

  11. Very Fast Algorithms and Detection Performance of Multi-Channel and 2-D Parametric Adaptive Matched Filters for Airborne Radar

    DTIC Science & Technology

    2007-06-05

    tive to the AMF, [1] and [5] discovered that multi-channel and two-dimensional parametric estimation approaches could (1) reduce the computational...dimensional (2-D) parametric estimation using the 2-D least-squares-based lattice algorithm [4]. The specifics of the inverse are found in the next...non- parametric estimation techniques • Least square error (LSE) vs mean square error (MSE) • Primarily multi-channel (M-C) structures; also try 2-D

  12. Detection of toxin proteins from Bacillus thuringiensis strain 4.0718 by strategy of 2D-LC-MS/MS.

    PubMed

    Yang, Qi; Tang, Sijia; Rang, Jie; Zuo, Mingxing; Ding, Xuezhi; Sun, Yunjun; Feng, Pinghui; Xia, Liqiu

    2015-04-01

    Bacillus thuringiensis is a kind of insecticidal microorganism which can produce a variety of toxin proteins, it is particularly important to find an effective strategy to identify novel toxin proteins rapidly and comprehensively with the discovery of the wild-type strains. Multi-dimensional high-performance liquid chromatography combined with mass spectrometry has become one of the main methods to detect and identify toxin proteins and proteome of B. thuringiensis. In this study, protein samples from B. thuringiensis strain 4.0718 were analyzed on the basis of two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS), and tryptic peptides of whole cell from the late sporulation phase were eluted at different concentration gradients of ammonium chloride and followed by secondary mass spectrum identification. 831 and 894 proteins were identified from two biological replicates, respectively, while 1,770 and 1,859 peptides were detected correspondingly. Among the identified proteins and peptides, 606 proteins and 1,259 peptides were detected in both replicates, which mean that 1,119 proteins and 2,370 peptides were unique to the proteome of this strain. A total of 15 toxins have been identified successfully, and seven of them were firstly discovered in B. thuringiensis strain 4.0718 that were Crystal protein (A1E259), pesticidal protein (U5KS09), Cry2Af1 (A4GVF0), Cry2Ad (Q9RM89), Cry1 (K4HMB5), Cry1Bc (Q45774), and Cry1Ga (Q45746). The proteomic strategy employed in the present study has provided quick and exhaustive identification of toxins produced by B. thuringiensis.

  13. Αutomated 2D shoreline detection from coastal video imagery: an example from the island of Crete

    NASA Astrophysics Data System (ADS)

    Velegrakis, A. F.; Trygonis, V.; Vousdoukas, M. I.; Ghionis, G.; Chatzipavlis, A.; Andreadis, O.; Psarros, F.; Hasiotis, Th.

    2015-06-01

    Beaches are both sensitive and critical coastal system components as they: (i) are vulnerable to coastal erosion (due to e.g. wave regime changes and the short- and long-term sea level rise) and (ii) form valuable ecosystems and economic resources. In order to identify/understand the current and future beach morphodynamics, effective monitoring of the beach spatial characteristics (e.g. the shoreline position) at adequate spatio-temporal resolutions is required. In this contribution we present the results of a new, fully-automated detection method of the (2-D) shoreline positions using high resolution video imaging from a Greek island beach (Ammoudara, Crete). A fully-automated feature detection method was developed/used to monitor the shoreline position in geo-rectified coastal imagery obtained through a video system set to collect 10 min videos every daylight hour with a sampling rate of 5 Hz, from which snapshot, time-averaged (TIMEX) and variance images (SIGMA) were generated. The developed coastal feature detector is based on a very fast algorithm using a localised kernel that progressively grows along the SIGMA or TIMEX digital image, following the maximum backscatter intensity along the feature of interest; the detector results were found to compare very well with those obtained from a semi-automated `manual' shoreline detection procedure. The automated procedure was tested on video imagery obtained from the eastern part of Ammoudara beach in two 5-day periods, a low wave energy period (6-10 April 2014) and a high wave energy period (1 -5 November 2014). The results showed that, during the high wave energy event, there have been much higher levels of shoreline variance which, however, appeared to be similarly unevenly distributed along the shoreline as that related to the low wave energy event, Shoreline variance `hot spots' were found to be related to the presence/architecture of an offshore submerged shallow beachrock reef, found at a distance of 50-80 m

  14. A novel sandwich-type electrochemical immunosensor for PSA detection based on PtCu bimetallic hybrid (2D/2D) rGO/g-C3N4.

    PubMed

    Feng, Jinhui; Li, Yueyun; Li, Mingdang; Li, Faying; Han, Jian; Dong, Yunhui; Chen, Zhiwei; Wang, Ping; Liu, Hui; Wei, Qin

    2017-05-15

    In this work, a sensitive sandwich-type electrochemical immunosensor was designed for the quantitative detection of prostate-specific antigen (PSA) by amperometric i-t. The Au loaded on thionine functionalized graphene oxide (Au@Th/GO) was used as a platform to immobilize primary antibodies (Ab1) and accelerate the electron transfer on the electrode interface. PtCu bimetallic hybrid were loaded on 2D/2D reduced graphene oxide/graphitic carbon nitride (PtCu@rGO/g-C3N4) with large surface area and biocompatibility, which were employed as labels for combining secondary antibodies (Ab2) and amplifying signals to improve the sensitivity of the designed immunosensor which attributes to its good activity for the reduction of hydrogen peroxide (H2O2). Under optimal conditions, the designed immunosensor exhibited a linear concentration range from 50fg/mL to 40ng/mL, with a low detection limit of 16.6fg/mL (S/N=3) for PSA. Additionally, the designed immunosensor showed acceptable selectivity, reproducibility and stability. The satisfactory results in analyze human serum samples indicated potential application promising in clinical monitoring of tumor markers.

  15. Comprehensive DNA barcoding of the herpetofauna of Germany.

    PubMed

    Hawlitschek, O; Morinière, J; Dunz, A; Franzen, M; Rödder, D; Glaw, F; Haszprunar, G

    2016-01-01

    We present the first comprehensive DNA barcoding study of German reptiles and amphibians representing likewise the first on the European herpetofauna. A total of 248 barcodes for all native species and subspecies in the country and a few additional taxa were obtained in the framework of the projects 'Barcoding Fauna Bavarica' (BFB) and 'German Barcode of Life' (GBOL). In contrast to many invertebrate groups, the success rate of the identification of mitochondrial lineages representing species via DNA barcode was almost 100% because no cases of Barcode Index Number (BIN) sharing were detected within German native reptiles and amphibians. However, as expected, a reliable identification of the hybridogenetic species complex in the frog genus Pelophylax was not possible. Deep conspecific lineages resulting in the identification of more than one BIN were found in Lissotriton vulgaris, Natrix natrix and the hybridogenetic Pelophylax complex. A high variety of lineages with different BINs was also found in the barcodes of wall lizards (Podarcis muralis), confirming the existence of many introduced lineages and the frequent occurrence of multiple introductions. Besides the reliable species identification of all life stages and even of tissue remains, our study highlights other potential applications of DNA barcoding concerning German amphibians and reptiles, such as the detection of allochthonous lineages, monitoring of gene flow and also noninvasive sampling via environmental DNA. DNA barcoding based on COI has now proven to be a reliable and efficient tool for studying most amphibians and reptiles as it is already for many other organism groups in zoology.

  16. Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining1

    PubMed Central

    Behbehani, Gregory K.; Thom, Colin; Zunder, Eli R.; Finck, Rachel; Gaudilliere, Brice; Fragiadakis, Gabriela K.; Fantl, Wendy J.; Nolan, Garry P.

    2015-01-01

    Fluorescent cellular barcoding and mass-tag cellular barcoding are cytometric methods that enable high sample throughput, minimize inter-sample variation, and reduce reagent consumption. Previously employed barcoding protocols require that barcoding be performed after surface marker staining, complicating combining the technique with measurement of alcohol-sensitive surface epitopes. This report describes a method of barcoding fixed cells after a transient partial permeabilization with 0.02% saponin that results in efficient and consistent barcode staining with fluorescent or mass-tagged reagents while preserving surface marker staining. This approach simplifies barcoding protocols and allows direct comparison of surface marker staining of multiple samples without concern for variations in the antibody cocktail volume, antigen-antibody ratio, or machine sensitivity. Using this protocol, cellular barcoding can be used to reliably detect subtle differences in surface marker expression. PMID:25274027

  17. 2D heterodyne-detected sum frequency generation study on the ultrafast vibrational dynamics of H{sub 2}O and HOD water at charged interfaces

    SciTech Connect

    Inoue, Ken-ichi; Singh, Prashant C.; Nihonyanagi, Satoshi; Tahara, Tahei; Yamaguchi, Shoichi

    2015-06-07

    Two-dimensional heterodyne-detected vibrational sum-frequency generation (2D HD-VSFG) spectroscopy is applied to study the ultrafast vibrational dynamics of water at positively charged aqueous interfaces, and 2D HD-VSFG spectra of cetyltrimethylammonium bromide (CTAB)/water interfaces in the whole hydrogen-bonded OH stretch region (3000 cm{sup −1} ≤ ω{sub pump} ≤ 3600 cm{sup −1}) are measured. 2D HD-VSFG spectrum of the CTAB/isotopically diluted water (HOD-D{sub 2}O) interface exhibits a diagonally elongated bleaching lobe immediately after excitation, which becomes round with a time constant of ∼0.3 ps due to spectral diffusion. In contrast, 2D HD-VSFG spectrum of the CTAB/H{sub 2}O interface at 0.0 ps clearly shows two diagonal peaks and their cross peaks in the bleaching region, corresponding to the double peaks observed at 3230 cm{sup −1} and 3420 cm{sup −1} in the steady-state HD-VSFG spectrum. Horizontal slices of the 2D spectrum show that the relative intensity of the two peaks of the bleaching at the CTAB/H{sub 2}O interface gradually change with the change of the pump frequency. We simulate the pump-frequency dependence of the bleaching feature using a model that takes account of the Fermi resonance and inhomogeneity of the OH stretch vibration, and the simulated spectra reproduce the essential features of the 2D HD-VSFG spectra of the CTAB/H{sub 2}O interface. The present study demonstrates that heterodyne detection of the time-resolved VSFG is critically important for studying the ultrafast dynamics of water interfaces and for unveiling the underlying mechanism.

  18. Novel silicon compatible p-WS2 2D/3D heterojunction devices exhibiting broadband photoresponse and superior detectivity

    NASA Astrophysics Data System (ADS)

    Chowdhury, Rup K.; Maiti, Rishi; Ghorai, Arup; Midya, Anupam; Ray, Samit K.

    2016-07-01

    We report for the first time, the fabrication of novel two-dimensional (2D) p-WS2/n-Si vertical heterostructures with superior junction and photoresponse characteristics. Few layer WS2 has been synthesized by a lithium-ion intercalation technique in hexane and coated on Si substrates for realization of CMOS compatible devices. Atomic force microscopy and Raman spectroscopy have been used to confirm the 2D nature of WS2 layers. Sharp band-edge absorption and emission peaks have indicated the formation of mono-to-few-layers thick direct band gap WS2 films. The electrical and optical responses of the heterostructures have exhibited superior properties revealing the formation of an abrupt heterojunction. The fabricated photodetector device depicts a peak responsivity of 1.11 A W-1 at -2 V with a broadband spectral response of 400-1100 nm and a moderate photo-to-dark current ratio of ~103. The optical switching characteristics have been studied as a function of applied bias and illuminated power density. A comparative study of the reported results on 2D transition metal chalcogenides indicates the superior characteristics of WS2/n-Si heterostructures for future photonic devices.

  19. Authentication of Chinese crude drug gecko by DNA barcoding.

    PubMed

    Gu, Hai-Feng; Xia, Yun; Penga, Rui; Mo, Bang-Hui; Li, Li; Zenga, Xiao-Mao

    2011-01-01

    Gekko gecko, an animal used as a valued traditional Chinese medicine, has been widely used for over 2000 years. Due to localized habitat destruction, the amount of G. gecko has dramatically decreased in recent years. As a result, more and more adulterants have been detected in the traditional medicine, which has resulted in a chaotic market. Therefore, a correct identification method is badly needed. In this study, we employed a new molecular method of DNA barcoding for discriminating gecko from its adulterants. Fifty-seven specimens of gecko and its adulterants were collected as test samples. The full-barcode and mini-barcode sequences of these specimens were separately amplified and sequenced separately. Together with other published barcode sequences, we detected that the intra-specific sequence diversity was far lower than the inter-specific diversity in G. gecko and its adulterants (3% compared with 35% in full-length barcode; 4% compared with 33.5% in mini-barcode). These results showed that both the full-length and mini-barcodes were effective for identifying gecko, which suggested that the DNA barcode could be an effective and powerful tool for identifying the Chinese crude drug gecko.

  20. Label-free optical detection of C-reactive protein by nanoimprint lithography-based 2D-photonic crystal film.

    PubMed

    Endo, Tatsuro; Kajita, Hiroshi; Kawaguchi, Yukio; Kosaka, Terumasa; Himi, Toshiyuki

    2016-06-01

    The development of high-sensitive, and cost-effective novel biosensors have been strongly desired for future medical diagnostics. To develop novel biosensor, the authors focused on the specific optical characteristics of photonic crystal. In this study, a label-free optical biosensor, polymer-based two-dimensional photonic crystal (2D-PhC) film fabricated using nanoimprint lithography (NIL), was developed for detection of C-reactive protein (CRP) in human serum. The nano-hole array constructed NIL-based 2D-PhC (hole diameter: 230 nm, distance: 230, depth: 200 nm) was fabricated on a cyclo-olefin polymer (COP) film (100 µm) using thermal NIL and required surface modifications to reduce nonspecific adsorption of target proteins. Antigen-antibody reactions on the NIL-based 2D-PhC caused changes to the surrounding refractive index, which was monitored as reflection spectrum changes in the visible region. By using surface modified 2D-PhC, the calculated detection limit for CRP was 12.24 pg/mL at an extremely short reaction time (5 min) without the need for additional labeling procedures and secondary antibody. Furthermore, using the dual-functional random copolymer, CRP could be detected in a pooled blood serum diluted 100× with dramatic reduction of nonspecific adsorption. From these results, the NIL-based 2D-PhC film has great potential for development of an on-site, high-sensitivity, cost-effective, label-free biosensor for medical diagnostics applications.

  1. Does a global DNA barcoding gap exist in Annelida?

    PubMed

    Kvist, Sebastian

    2016-05-01

    Accurate identification of unknown specimens by means of DNA barcoding is contingent on the presence of a DNA barcoding gap, among other factors, as its absence may result in dubious specimen identifications - false negatives or positives. Whereas the utility of DNA barcoding would be greatly reduced in the absence of a distinct and sufficiently sized barcoding gap, the limits of intraspecific and interspecific distances are seldom thoroughly inspected across comprehensive sampling. The present study aims to illuminate this aspect of barcoding in a comprehensive manner for the animal phylum Annelida. All cytochrome c oxidase subunit I sequences (cox1 gene; the chosen region for zoological DNA barcoding) present in GenBank for Annelida, as well as for "Polychaeta", "Oligochaeta", and Hirudinea separately, were downloaded and curated for length, coverage and potential contaminations. The final datasets consisted of 9782 (Annelida), 5545 ("Polychaeta"), 3639 ("Oligochaeta"), and 598 (Hirudinea) cox1 sequences and these were either (i) used as is in an automated global barcoding gap detection analysis or (ii) further analyzed for genetic distances, separated into bins containing intraspecific and interspecific comparisons and plotted in a graph to visualize any potential global barcoding gap. Over 70 million pairwise genetic comparisons were made and results suggest that although there is a tendency towards separation, no distinct or sufficiently sized global barcoding gap exists in either of the datasets rendering future barcoding efforts at risk of erroneous specimen identifications (but local barcoding gaps may still exist allowing for the identification of specimens at lower taxonomic ranks). This seems to be especially true for earthworm taxa, which account for fully 35% of the total number of interspecific comparisons that show 0% divergence.

  2. Atomic-Scale Variations of the Mechanical Response of 2D Materials Detected by Noncontact Atomic Force Microscopy.

    PubMed

    de la Torre, B; Ellner, M; Pou, P; Nicoara, N; Pérez, Rubén; Gómez-Rodríguez, J M

    2016-06-17

    We show that noncontact atomic force microscopy (AFM) is sensitive to the local stiffness in the atomic-scale limit on weakly coupled 2D materials, as graphene on metals. Our large amplitude AFM topography and dissipation images under ultrahigh vacuum and low temperature resolve the atomic and moiré patterns in graphene on Pt(111), despite its extremely low geometric corrugation. The imaging mechanisms are identified with a multiscale model based on density-functional theory calculations, where the energy cost of global and local deformations of graphene competes with short-range chemical and long-range van der Waals interactions. Atomic contrast is related with short-range tip-sample interactions, while the dissipation can be understood in terms of global deformations in the weakly coupled graphene layer. Remarkably, the observed moiré modulation is linked with the subtle variations of the local interplanar graphene-substrate interaction, opening a new route to explore the local mechanical properties of 2D materials at the atomic scale.

  3. Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding.

    PubMed

    Zou, Shanmei; Li, Qi

    2016-06-01

    With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.

  4. Feasibility of vibro-acoustography with a quasi-2D ultrasound array transducer for detection and localizing of permanent prostate brachytherapy seeds: A pilot ex vivo study

    SciTech Connect

    Mehrmohammadi, Mohammad; Kinnick, Randall R.; Fatemi, Mostafa; Alizad, Azra; Davis, Brian J.

    2014-09-15

    Purpose: Effective permanent prostate brachytherapy (PPB) requires precise placement of radioactive seeds in and around the prostate. The impetus for this research is to examine a new ultrasound-based imaging modality, vibro-acoustography (VA), which may serve to provide a high rate of PPB seed detection while also effecting enhanced prostate imaging. The authors investigate the ability of VA, implemented on a clinical ultrasound (US) scanner and equipped with a quasi-2D (Q2D) array US transducer, to detect and localize PPB seeds in excised prostate specimens. Methods: Nonradioactive brachytherapy seeds were implanted into four excised cadaver prostates. A clinical US scanner equipped with a Q2D array US transducer was customized to acquire both US and C-scan VA images at various depths. The VA images were then used to detect and localize the implanted seeds in prostate tissue. To validate the VA results, computed tomography (CT) images of the same tissue samples were obtained to serve as the reference by which to evaluate the performance of VA in PPB seed detection. Results: The results indicate that VA is capable of accurately identifying the presence and distribution of PPB seeds with a high imaging contrast. Moreover, a large ratio of the PPB seeds implanted into prostate tissue samples could be detected through acquired VA images. Using CT-based seed identification as the standard, VA was capable of detecting 74%–92% of the implanted seeds. Additionally, the angular independency of VA in detecting PPB seeds was demonstrated through a well-controlled phantom experiment. Conclusions: Q2DVA detected a substantial portion of the seeds by using a 2D array US transducer in excised prostate tissue specimens. While VA has inherent advantages associated with conventional US imaging, it has the additional advantage of permitting detection of PPB seeds independent of their orientation. These results suggest the potential of VA as a method for PPB imaging that

  5. Automatic organ localizations on 3D CT images by using majority-voting of multiple 2D detections based on local binary patterns and Haar-like features

    NASA Astrophysics Data System (ADS)

    Zhou, Xiangrong; Yamaguchi, Shoutarou; Zhou, Xinxin; Chen, Huayue; Hara, Takeshi; Yokoyama, Ryujiro; Kanematsu, Masayuki; Fujita, Hiroshi

    2013-02-01

    This paper describes an approach to accomplish the fast and automatic localization of the different inner organ regions on 3D CT scans. The proposed approach combines object detections and the majority voting technique to achieve the robust and quick organ localization. The basic idea of proposed method is to detect a number of 2D partial appearances of a 3D target region on CT images from multiple body directions, on multiple image scales, by using multiple feature spaces, and vote all the 2D detecting results back to the 3D image space to statistically decide one 3D bounding rectangle of the target organ. Ensemble learning was used to train the multiple 2D detectors based on template matching on local binary patterns and Haar-like feature spaces. A collaborative voting was used to decide the corner coordinates of the 3D bounding rectangle of the target organ region based on the coordinate histograms from detection results in three body directions. Since the architecture of the proposed method (multiple independent detections connected to a majority voting) naturally fits the parallel computing paradigm and multi-core CPU hardware, the proposed algorithm was easy to achieve a high computational efficiently for the organ localizations on a whole body CT scan by using general-purpose computers. We applied this approach to localization of 12 kinds of major organ regions independently on 1,300 torso CT scans. In our experiments, we randomly selected 300 CT scans (with human indicated organ and tissue locations) for training, and then, applied the proposed approach with the training results to localize each of the target regions on the other 1,000 CT scans for the performance testing. The experimental results showed the possibility of the proposed approach to automatically locate different kinds of organs on the whole body CT scans.

  6. [Detection of hybrid DQ molecules by the use of T cell clone and 2D-gel analyses].

    PubMed

    Hawkin, S

    1986-11-01

    The HLA-D region incorporates three subregions, DR, DQ and DP, encoding for three sets of Ia molecules. Whereas DR antigens consist of a constant alpha chain and an extremely polymorphic beta chain, both of alpha and beta chain of DQ antigens show moderate polymorphism. This indicated us the existence of hybrid HLA-DQ molecules in HLA-D heterozygous cells, resulting from the association of an alpha chain and a beta chain encoded by genes located on the two separate haplotypes. In this report, hybrid DQ antigens were demonstrated by using cytotoxic T cell-clone. A cytotoxic T cell clone, which was generated by mixed lymphocyte reaction against a lymphoblastoid B cell line, EBV-Fuk (HLA-DR1/4, DQw1/Wa), recognized only heterogenous lymphoblastoid B cell lines (HLA-DR1/4, DQw1/Wa). Cytotoxic T cell clone, however, didn't react with B cell lines which are homozygous for HLA-DR1, DQw1 or DR4/DQWa. This suggests the T cell clone recognized the hybrid DQ molecules expressed only on heterozygous cell lines. Further confirmation was obtained by inhibition test using monoclonal antibody and biochemically by 2-D gel analyses. Biological significance of hybrid DQ antigens were discussed.

  7. Implementing a Serials Barcoding Project.

    ERIC Educational Resources Information Center

    Lennertz, Lora L.; Conway, Cheryl L.

    1997-01-01

    Discusses the process of planning and implementing a barcode project for library serials based on experiences at the University of Arkansas Fayetteville library. Topics include dumb versus smart barcodes, cataloging, classification, application rate of barcode labels, and library staff participation. (Author/LRW)

  8. Graphene Paper Decorated with a 2D Array of Dendritic Platinum Nanoparticles for Ultrasensitive Electrochemical Detection of Dopamine Secreted by Live Cells

    PubMed Central

    Zan, Xiaoli; Wang, Chenxu

    2016-01-01

    Abstract To circumvent the bottlenecks of non‐flexibility, low sensitivity, and narrow workable detection range of conventional biosensors for biological molecule detection (e.g., dopamine (DA) secreted by living cells), a new hybrid flexible electrochemical biosensor has been created by decorating closely packed dendritic Pt nanoparticles (NPs) on freestanding graphene paper. This innovative structural integration of ultrathin graphene paper and uniform 2D arrays of dendritic NPs by tailored wet chemical synthesis has been achieved by a modular strategy through a facile and delicately controlled oil–water interfacial assembly method, whereby the uniform distribution of catalytic dendritic NPs on the graphene paper is maximized. In this way, the performance is improved by several orders of magnitude. The developed hybrid electrode shows a high sensitivity of 2 μA cm−2 μm −1, up to about 33 times higher than those of conventional sensors, a low detection limit of 5 nm, and a wide linear range of 87 nm to 100 μm. These combined features enable the ultrasensitive detection of DA released from pheochromocytoma (PC 12) cells. The unique features of this flexible sensor can be attributed to the well‐tailored uniform 2D array of dendritic Pt NPs and the modular electrode assembly at the oil–water interface. Its excellent performance holds much promise for the future development of optimized flexible electrochemical sensors for a diverse range of electroactive molecules to better serve society. PMID:26918612

  9. Imprinted gold 2D nanoarray for highly sensitive and convenient PSA detection via plasmon excited quantum dots.

    PubMed

    Song, Hong Yan; Wong, Ten It; Sadovoy, Anton; Wu, Lin; Bai, Ping; Deng, Jie; Guo, Shifeng; Wang, Yi; Knoll, Wolfgang; Zhou, Xiaodong

    2015-01-07

    We designed and fabricated two new nanostructured biosensing chips, with which the sensitive detection of prostate specific antigen (PSA) as low as 100 pg ml(-1) can be achieved, by measuring the plasmon enhanced fluorescence through a conventional dark field microscope. The gold nanostructure arrays, one with gold nanopillars of 140 nm, the other with gold nanoholes of 140 nm, were fabricated via nanoimprinting onto glass substrate, as localized surface plasmon resonance (LSPR) generators to enhance the fluorescent emission of fluorophore, e.g. quantum dot (QD). A sandwich bioassay of capture anti-PSA antibody (cAb)/PSA/detection anti-PSA (dAb) labeled by QD-655 was established on the nanostructures, and the perfect LSPR excitation distance (10-15 nm) between the nanostructure and QD-655 was simulated and controlled by a cleft cAb fragment and streptavidin modified QD. QD was chosen in this study due to its photo stability, broad Stokes shift, and long lifetime. As far as we know, this is the first time that QD is applied for PSA detection on the uniform nanostructured sensing chips based on the LSPR enhanced fluorescence. Due to the miniaturized nanoarray sensing chip (1.8 mm × 1.8 mm), the convenience and specificity for the detection of PSA via the sandwich assay, and the high optical detection sensitivity, the platform has great potential for the development of a portable point-of-care (POC) system for outpatient diagnosis and treatment monitoring.

  10. Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles.

    PubMed

    Hawlitschek, Oliver; Nagy, Zoltán T; Berger, Johannes; Glaw, Frank

    2013-01-01

    In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.

  11. An electrochemical sensor for detection of neurotransmitter-acetylcholine using metal nanoparticles, 2D material and conducting polymer modified electrode.

    PubMed

    Chauhan, Nidhi; Chawla, Sheetal; Pundir, C S; Jain, Utkarsh

    2017-03-15

    An essential biological sensor for acetylcholine (ACh) detection is constructed by immobilizing enzymes, acetylcholinesterase (AChE) and choline oxidase (ChO), on the surface of iron oxide nanoparticles (Fe2O3NPs), poly(3,4-ethylenedioxythiophene) (PEDOT)-reduced graphene oxide (rGO) nanocomposite modified fluorine doped tin oxide (FTO). The qualitative and quantitative measurements of nanocomposites properties were accomplished by scanning electron microscope (SEM), electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). This prepared biological sensor delineated a wide linear range of 4.0nM to 800μM with a response time less than 4s and detection limit (based on S/N ratio) of 4.0nM. The sensor showed perfect sensitivity, excessive selectivity and stability for longer period of time during storage. Besides its very high-sensitivity, the biosensor has displayed a low detection limit which is reported for the first time in comparison to previously reported ACh sensors. By fabricating Fe2O3NPs/rGO/PEDOT modified FTO electrode for determining ACh level in serum samples, the applicability of biosensor has increased immensely as the detection of the level neurotransmitter is first priority for patients suffering from memory loss or Alzheimer's disease (AD).

  12. Effect of image processing version on detection of non-calcification cancers in 2D digital mammography imaging

    NASA Astrophysics Data System (ADS)

    Warren, L. M.; Cooke, J.; Given-Wilson, R. M.; Wallis, M. G.; Halling-Brown, M.; Mackenzie, A.; Chakraborty, D. P.; Bosmans, H.; Dance, D. R.; Young, K. C.

    2013-03-01

    Image processing (IP) is the last step in the digital mammography imaging chain before interpretation by a radiologist. Each manufacturer has their own IP algorithm(s) and the appearance of an image after IP can vary greatly depending upon the algorithm and version used. It is unclear whether these differences can affect cancer detection. This work investigates the effect of IP on the detection of non-calcification cancers by expert observers. Digital mammography images for 190 patients were collected from two screening sites using Hologic amorphous selenium detectors. Eighty of these cases contained non-calcification cancers. The images were processed using three versions of IP from Hologic - default (full enhancement), low contrast (intermediate enhancement) and pseudo screen-film (no enhancement). Seven experienced observers inspected the images and marked the location of regions suspected to be non-calcification cancers assigning a score for likelihood of malignancy. This data was analysed using JAFROC analysis. The observers also scored the clinical interpretation of the entire case using the BSBR classification scale. This was analysed using ROC analysis. The breast density in the region surrounding each cancer and the number of times each cancer was detected were calculated. IP did not have a significant effect on the radiologists' judgment of the likelihood of malignancy of individual lesions or their clinical interpretation of the entire case. No correlation was found between number of times each cancer was detected and the density of breast tissue surrounding that cancer.

  13. Barcode uses and abuses

    SciTech Connect

    KEENEN,MARTHA JANE; NUSBAUM,ANNA W.

    2000-05-18

    Barcodes are something that everybody sees every day; so common as to be taken for granted and normally unnoticed. Readable, no one reads them. They are used to allow machines to identify a wide variety of non-electronic, real life objects. Barcode is one of the earliest types of what is now called ``Automatic Identification and Data Capture'' (AIDC), meaning ``data was transmitted into whatever system by something other than typing or hand-writing.'' There are 18 technologies, broken down into six categories--biometrics, electromagnetic, magnetic, optical, Smart Cards, Touch--included in the AIDC concept. Many are used jointly with or as adjuncts to a basic barcode system of some type. All are based on assignment of a unique identifier to the object, usually a number. The uniqueness presumption makes barcode systems very applicable and appropriate to the nuclear information management venue as they inherently comply with the Nuclear Quality Assurance (NQA-1) requirements. Barcode systems belong to the optical category of AIDC. It is very old in usage as these technologies go, having first been patented in 1949. It astonished me, in researching this paper, to find that there are over 250 types of barcode (symbologies), each with its own specialized attributes, though only a few dozen are in active use. The initial uses were in the early 1950s and diversity of use is ever increasing as people find new ways to make this versatile old technology work. To what else could it be applied, in the future? This paper attempts to answer this.

  14. Polarization shaping in the mid-IR and polarization-based balanced heterodyne detection with application to 2D IR spectroscopy.

    PubMed

    Middleton, Chris T; Strasfeld, David B; Zanni, Martin T

    2009-08-17

    We demonstrate amplitude, phase and polarization shaping of femtosecond mid-IR pulses using a germanium acousto-optical modulator by independently shaping the frequency-dependent amplitudes and phases of two orthogonally polarized pulses which are then collinearly overlapped using a wire-grid polarizer. We use a feedback loop to set and stabilize the relative phase of the orthogonal pulses. We have also used a wire-grid polarizer to implement polarization-based balanced heterodyne detection for improved signal-to-noise of 2D IR spectra collected in a pump-probe geometry. Applications include coherent control of molecular vibrations and improvements in multidimensional IR spectroscopy.

  15. Digital breast tomosynthesis: application of 2D digital mammography CAD to detection of microcalcification clusters on planar projection image

    NASA Astrophysics Data System (ADS)

    Samala, Ravi K.; Chan, Heang-Ping; Lu, Yao; Hadjiiski, Lubomir; Wei, Jun; Helvie, Mark

    2015-03-01

    Computer-aided detection (CAD) has the potential to aid radiologists in detection of microcalcification clusters (MCs). CAD for digital breast tomosynthesis (DBT) can be developed by using the reconstructed volume, the projection views or other derivatives as input. We have developed a novel method of generating a single planar projection (PPJ) image from a regularized DBT volume to emphasize the high contrast objects such as microcalcifications while removing the anatomical background and noise. In this work, we adapted a CAD system developed for digital mammography (CADDM) to the PPJ image and compared its performance with our CAD system developed for DBT volumes (CADDBT) in the same set of cases. For microcalcification detection in the PPJ image using the CADDM system, the background removal preprocessing step designed for DM was not needed. The other methods and processing steps in the CADDM system were kept without modification while the parameters were optimized with a training set. The linear discriminant analysis classifier using cluster based features was retrained to generate a discriminant score to be used as decision variable. For view-based FROC analysis, at 80% sensitivity, an FP rate of 1.95/volume and 1.54/image were achieved, respectively, for CADDBT and CADDM in an independent test set. At a threshold of 1.2 FPs per image or per DBT volume, the nonparametric analysis of the area under the FROC curve shows that the optimized CADDM for PPJ is significantly better than CADDBT. However, the performance of CADDM drops at higher sensitivity or FP rate, resulting in similar overall performance between the two CAD systems. The higher sensitivity of the CADDM in the low FP rate region and vice versa for the CADDBT indicate that a joint CAD system combining detection in the DBT volume and the PPJ image has the potential to increase the sensitivity and reduce the FP rate.

  16. Preliminary clinical results: an analyzing tool for 2D optical imaging in detection of active inflammation in rheumatoid arthritis

    NASA Astrophysics Data System (ADS)

    Adi Aizudin Bin Radin Nasirudin, Radin; Meier, Reinhard; Ahari, Carmen; Sievert, Matti; Fiebich, Martin; Rummeny, Ernst J.; No"l, Peter B.

    2011-03-01

    Optical imaging (OI) is a relatively new method in detecting active inflammation of hand joints of patients suffering from rheumatoid arthritis (RA). With the high number of people affected by this disease especially in western countries, the availability of OI as an early diagnostic imaging method is clinically highly relevant. In this paper, we present a newly in-house developed OI analyzing tool and a clinical evaluation study. Our analyzing tool extends the capability of existing OI tools. We include many features in the tool, such as region-based image analysis, hyper perfusion curve analysis, and multi-modality image fusion to aid clinicians in localizing and determining the intensity of inflammation in joints. Additionally, image data management options, such as the full integration of PACS/RIS, are included. In our clinical study we demonstrate how OI facilitates the detection of active inflammation in rheumatoid arthritis. The preliminary clinical results indicate a sensitivity of 43.5%, a specificity of 80.3%, an accuracy of 65.7%, a positive predictive value of 76.6%, and a negative predictive value of 64.9% in relation to clinical results from MRI. The accuracy of inflammation detection serves as evidence to the potential of OI as a useful imaging modality for early detection of active inflammation in patients with rheumatoid arthritis. With our in-house developed tool we extend the usefulness of OI imaging in the clinical arena. Overall, we show that OI is a fast, inexpensive, non-invasive and nonionizing yet highly sensitive and accurate imaging modality.-

  17. Photoelectrochemical Immunosensor for Detection of Carcinoembryonic Antigen Based on 2D TiO2 Nanosheets and Carboxylated Graphitic Carbon Nitride

    PubMed Central

    Wang, Huan; Wang, Yaoguang; Zhang, Yong; Wang, Qi; Ren, Xiang; Wu, Dan; Wei, Qin

    2016-01-01

    Carcinoembryonic antigen (CEA) was used as the model, an ultrasensitive label-free photoelectrochemical immunosensor was developed using 2D TiO2 nanosheets and carboxylated graphitic carbon nitride (g-C3N4) as photoactive materials and ascorbic acid as an efficient electron donor. 2D TiO2 nanosheets was sythsized by surfactant self-assembly method and proved to have higher photoelectrochemical signals than TiO2 nanoparticles. Firstly, carboxylated g-C3N4 could be attached to 2D TiO2 nanosheets through the bond formed between carboxyl group of carboxylated g-C3N4 and TiO2. And the photocurrent of g-C3N4/TiO2 drastically enhances compared to carboxylated g-C3N4 and TiO2. Then, antibody of CEA was bonded to TiO2 through the dentate bond formed between carboxyl group of anti-CEA and TiO2, leading to the decrease of the photocurrents. As proven by PEC experiments and electrochemical impedance spectroscopy (EIS) analysis, the fabrication process of the immunosensor is successful. Under the optimal conditions, the intensity decreased linearly with CEA concentration in the range of 0.01~10 ng/mL. The detection limit is 2.1 pg/mL. The work provides an effective method for the detection of tumor markers and can be extended for the application in food safety and environmental monitoring analysis. PMID:27263659

  18. Application of 2-D geoelectrical resistivity tomography for mountain permafrost detection in sporadic permafrost environments: Experiences from Eastern Austria

    NASA Astrophysics Data System (ADS)

    Kellerer-Pirklbauer, Andreas

    2015-04-01

    Mountain permafrost covers some 2000 km² of the Austrian Alps which is less than 2.5% of the national territory. Delineating the altitudinal lower limit of permafrost in the mountains of Austria is difficult due the complex topography, the rather sparseness of field verification data and the lack of long-term permafrost monitoring data. Such monitoring data should cover different slope aspects, different elevations, different substrates and different mountain regions of Austria. In this study it was attempted to delineate the lower limit of permafrost at two study sites in the Tauern Range, Austria, applying two-dimensional geoelectrical resistivity tomography (ERT). In addition, multi-annual ground temperature data collected by miniature temperature datalogger (MDT) were used to validate the results. At the study site Hochreichart (maximum elevation 2416 m asl), located in the Seckauer Tauern Range, 14 ERT profiles (lengths 48-196 m; electrode spacing 2, 2.5 or 4 m) were measured at elevations between 1805 and 2416 m asl. Measurements were carried out at two cirques (Reichart, Schöneben) and at the summit plateau of Hochreichart. Results at this site indicate that permafrost lenses are detectable at elevations down to c.1900 m asl at radiation-sheltered sites. Furthermore, at the summit plateau permafrost only occurs as rather small lenses. The ERT-based permafrost pattern is generally confirmed by the MTD data with negative mean annual ground temperature values at only a few monitoring sites. However, the possibility of air-filled cavities causing higher resistive zones faking permafrost existence cannot be excluded because coarse-grained sediments (i.e. relict rock glaciers and autochthonous block fields) are widespread at this study site. At the second study site Kögele Cirque (maximum elevation 3030 m asl) located in the Schober Mountains 12 ERT profiles (lengths 48 m; electrode spacing 2 m) were measured at elevations between 2631 and 2740 m asl. Spatially

  19. An estimation method for echo signal energy of pipe inner surface longitudinal crack detection by 2-D energy coefficients integration

    SciTech Connect

    Zhou, Shiyuan Sun, Haoyu Xu, Chunguang Cao, Xiandong Cui, Liming Xiao, Dingguo

    2015-03-31

    The echo signal energy is directly affected by the incident sound beam eccentricity or angle for thick-walled pipes inner longitudinal cracks detection. A method for analyzing the relationship between echo signal energy between the values of incident eccentricity is brought forward, which can be used to estimate echo signal energy when testing inside wall longitudinal crack of pipe, using mode-transformed compression wave adaptation of shear wave with water-immersion method, by making a two-dimension integration of “energy coefficient” in both circumferential and axial directions. The calculation model is founded for cylinder sound beam case, in which the refraction and reflection energy coefficients of different rays in the whole sound beam are considered different. The echo signal energy is calculated for a particular cylinder sound beam testing different pipes: a beam with a diameter of 0.5 inch (12.7mm) testing a φ279.4mm pipe and a φ79.4mm one. As a comparison, both the results of two-dimension integration and one-dimension (circumferential direction) integration are listed, and only the former agrees well with experimental results. The estimation method proves to be valid and shows that the usual method of simplifying the sound beam as a single ray for estimating echo signal energy and choosing optimal incident eccentricity is not so appropriate.

  20. DNA Barcoding Identifies Argentine Fishes from Marine and Brackish Waters

    PubMed Central

    Mabragaña, Ezequiel; Díaz de Astarloa, Juan Martín; Hanner, Robert; Zhang, Junbin; González Castro, Mariano

    2011-01-01

    Background DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. Methodology/Principal Findings Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species), and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org). Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125) examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. Conclusions/Significance This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha taxonomy, barcodes provide

  1. Quantitative phenotyping via deep barcode sequencing.

    PubMed

    Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

    2009-10-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

  2. eDNA Barcoding: Using Next-Generation Sequencing of Environmental DNA for Detection and Identification of Cetacean Species

    DTIC Science & Technology

    2015-09-30

    Environmental DNA for Detection and Identification of Cetacean Species Scott Baker Oregon State University Hatfield Marine Science Center Newport...identification of cetaceans using environmental (e) DNA collected from seawater. Referred to here as ‘(e) DNA barcoding’, this new methodology can be used...the first year, we have conducted a series of (e) DNA sampling experiments in the vicinity of killer whales Orcinus orca near San Juan Island in Puget

  3. Highly Selective and Repeatable Surface-Enhanced Resonance Raman Scattering Detection for Epinephrine in Serum Based on Interface Self-Assembled 2D Nanoparticles Arrays.

    PubMed

    Zhou, Binbin; Li, Xiaoyun; Tang, Xianghu; Li, Pan; Yang, Liangbao; Liu, Jinhuai

    2017-03-01

    Target analyte detection in complex systems with high selectivity and repeatability is crucial to analytical technology and science. Here we present a two-dimensional (2D) surface-enhanced resonance Raman scattering (SERRS) platform, which takes advantages of the high selectivity of the SERRS sensor as well as the sensitivity and reproducibility of the interfacial SERS platform, for detecting trace epinephrine (EP) in the serum. To realize sensitive and selective detection of EP in a complex system, Au NPs are modified with α,β-nitriloacetic acid and Fe(NO3)3 to form the Au NP-(Fe-NTA) sensor, and as a consequence, EP can be rapidly captured by the sensor on the surface of Au NPs and then delivered at the cyclohexane/water interface. More importantly, we synthesized the extremely stable Au NPs (PVP-stabilized Au NPs), where the presence of PVP prevents aggregation of Au NPs during the self-assembly process and then makes a more uniform distribution of Au NPs with analytes at the cyclohexane/water interface, approximately 2 nm interparticle distance between the Au NPs, which has been proved by synchrotron radiation grazing incidence small-angle X-ray scattering (SR-GISAXS) experiments. The self-assembly method not only effectively avoids the aggregation of Au NPs and decreases the influence of the background signal but also can capture and enrich EP molecules in the cyclohexane/water interface, realizing the sensitive and selective detection of EP in complex serum sample. This strategy overcomes the difficulty of bringing nanostructures together to form efficient interparticle distance with simple fabrication and maximum uniformity and also provides a powerful nanosensor for tracing amounts of analyte molecules in a complex system with the advantages of capturing and enriching of target molecules in the liquid/liquid interface during the self-assembly process. Our SERRS platform opens vast possibilities for repeatability, sensitivity, and selectivity detection of

  4. Rapidly evolving homing CRISPR barcodes.

    PubMed

    Kalhor, Reza; Mali, Prashant; Church, George M

    2017-02-01

    We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing. This integrated approach will have wide-ranging applications, such as in deep lineage tracing, cellular barcoding, molecular recording, dissecting cancer biology, and connectome mapping.

  5. Design of mini-barcode for catfishes for assessment of archival biodiversity.

    PubMed

    Bhattacharjee, Maloyjo J; Ghosh, Sankar K

    2014-05-01

    Recovery of DNA barcode sequences is often challenging from the archived specimens. However, short fragments of DNA may be recovered, which would significantly improve many unresolved taxonomic conflicts. Here, we designed a mini-barcode for catfishes comprising several species and many cryptic taxa. We analysed a data set of 3048 publicly available COI barcode sequences representing 547 worldwide catfish species and performed 152 628 interspecies comparisons. A significantly more positively correlated interspecies distance was detected with transversion (0.78, P < 0.001) than with transition (0.70, P < 0.001). This suggested that transversions were better diagnostics for species identification. In the aligned data set, two transversion-rich fragments (53 bp and 119 bp) were identified. Transition/transversion bias value was 1.04 in 53-bp fragment, 1.23 in 119-bp fragment and 1.50 in full-length barcode. The interspecies distance with full-length barcode was 0.212 ± 0.037, while that with 53-bp and 119-bp fragments was 0.325 ± 0.039 and 0.218 ± 0.045, respectively. Survey of 53-bp fragment showed a possibility of only 1144 barcodes, while that of 119-bp fragment showed >4 million barcodes. Thus, the 119-bp fragment is a viable mini-barcode for catfishes comprising >3000 extant species. Experiment with 82 archived catfishes showed successful recovery of this mini-barcode using the designed primer. The mini-barcode sequences showed species-specific similarity in the range of 98-100% with the global database. Therefore, survey of a transversion-rich fragment within the full-length barcode would be an ideal approach of mini-barcode design for biodiversity assessment.

  6. Identification of Amazonian Trees with DNA Barcodes

    PubMed Central

    Gonzalez, Mailyn Adriana; Baraloto, Christopher; Engel, Julien; Mori, Scott A.; Pétronelli, Pascal; Riéra, Bernard; Roger, Aurélien; Thébaud, Christophe; Chave, Jérôme

    2009-01-01

    Background Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests. Methodology/Principal Findings Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon. Conclusion/Significance We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs. PMID:19834612

  7. DNA barcode goes two-dimensions: DNA QR code web server.

    PubMed

    Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

    2012-01-01

    The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

  8. Metal imaging in non-denaturating 2D electrophoresis gels by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) for the detection of metalloproteins.

    PubMed

    Becker, J Susanne; Lobinski, Ryszard; Becker, J Sabine

    2009-01-01

    Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was developed as a powerful analytical technique for metal imaging of 2D gels for the detection of metalloproteins in rat kidney after electrophoretic separation. Protein complexes, extracted with water, were separated in their native state in the first and second dimension by blue native gel electrophoresis (BN-PAGE). Essential and toxic metals, such as zinc, copper, iron, manganese and lead, were monitored by LA-ICP-MS after gel ablation by a focused laser beam in a way that the total surface of a selected fragment of the gel was totally ablated. The metal distribution of this part of the gel was then constructed by plotting the metal (isotope) signal intensity as a function of the x,y (isoelectric point, molecular mass) coordinates of the gel. The proteins at locations rich in metals were cut out, digested with trypsin and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS).

  9. A Novel Assessment of Various Bio-Imaging Methods for Lung Tumor Detection and Treatment by using 4-D and 2-D CT Images

    PubMed Central

    Judice A., Antony; Geetha, Dr. K. Parimala

    2013-01-01

    Lung Cancer is known as one of the most difficult cancer to cure, and the number of deaths that it causes generally increasing. A detection of the Lung Cancer in its early stage can be helpful for Medical treatment to limit the danger, but it is a challenging problem due to Cancer cell structure. Interpretation of Medical image is often difficult and time consuming, even for the experienced Physicians. The aid of image analysis Based on machine learning can make this process easier. This paper describes fully Automatic Decision Support system for Lung Cancer diagnostic from CT Lung images. Most traditional medical diagnosis systems are founded on huge quantity of training data and takes long processing time. However, on the occasion that very little volume of data is available, the traditional diagnosis systems derive defects such as larger error, Time complexity. Focused on the solution to this problem, a Medical Diagnosis System based on Hidden Markov Model (HMM) is presented. In this paper we describe a pre-processing stage involving some Noise removal techniques help to solve this problem, we preprocess an images (by Mean Error Square Filtering and Histogram analysis)obtained after scanning the Lung CT images. Secondly separate the lung areas from an image by a segmentation process (by Thresholding and region growing techniques). Finally we developed HMM for the classification of Cancer Nodule. Results are checked for 2D and 4D CT images. This automation process reduces the time complexity and increases the diagnosis confidence. PMID:23847454

  10. Development of an iterative reconstruction method to overcome 2D detector low resolution limitations in MLC leaf position error detection for 3D dose verification in IMRT.

    PubMed

    Visser, R; Godart, J; Wauben, D J L; Langendijk, J A; Van't Veld, A A; Korevaar, E W

    2016-05-21

    The objective of this study was to introduce a new iterative method to reconstruct multi leaf collimator (MLC) positions based on low resolution ionization detector array measurements and to evaluate its error detection performance. The iterative reconstruction method consists of a fluence model, a detector model and an optimizer. Expected detector response was calculated using a radiotherapy treatment plan in combination with the fluence model and detector model. MLC leaf positions were reconstructed by minimizing differences between expected and measured detector response. The iterative reconstruction method was evaluated for an Elekta SLi with 10.0 mm MLC leafs in combination with the COMPASS system and the MatriXX Evolution (IBA Dosimetry) detector with a spacing of 7.62 mm. The detector was positioned in such a way that each leaf pair of the MLC was aligned with one row of ionization chambers. Known leaf displacements were introduced in various field geometries ranging from  -10.0 mm to 10.0 mm. Error detection performance was tested for MLC leaf position dependency relative to the detector position, gantry angle dependency, monitor unit dependency, and for ten clinical intensity modulated radiotherapy (IMRT) treatment beams. For one clinical head and neck IMRT treatment beam, influence of the iterative reconstruction method on existing 3D dose reconstruction artifacts was evaluated. The described iterative reconstruction method was capable of individual MLC leaf position reconstruction with millimeter accuracy, independent of the relative detector position within the range of clinically applied MU's for IMRT. Dose reconstruction artifacts in a clinical IMRT treatment beam were considerably reduced as compared to the current dose verification procedure. The iterative reconstruction method allows high accuracy 3D dose verification by including actual MLC leaf positions reconstructed from low resolution 2D measurements.

  11. Development of an iterative reconstruction method to overcome 2D detector low resolution limitations in MLC leaf position error detection for 3D dose verification in IMRT

    NASA Astrophysics Data System (ADS)

    Visser, R.; Godart, J.; Wauben, D. J. L.; Langendijk, J. A.; van't Veld, A. A.; Korevaar, E. W.

    2016-05-01

    The objective of this study was to introduce a new iterative method to reconstruct multi leaf collimator (MLC) positions based on low resolution ionization detector array measurements and to evaluate its error detection performance. The iterative reconstruction method consists of a fluence model, a detector model and an optimizer. Expected detector response was calculated using a radiotherapy treatment plan in combination with the fluence model and detector model. MLC leaf positions were reconstructed by minimizing differences between expected and measured detector response. The iterative reconstruction method was evaluated for an Elekta SLi with 10.0 mm MLC leafs in combination with the COMPASS system and the MatriXX Evolution (IBA Dosimetry) detector with a spacing of 7.62 mm. The detector was positioned in such a way that each leaf pair of the MLC was aligned with one row of ionization chambers. Known leaf displacements were introduced in various field geometries ranging from  -10.0 mm to 10.0 mm. Error detection performance was tested for MLC leaf position dependency relative to the detector position, gantry angle dependency, monitor unit dependency, and for ten clinical intensity modulated radiotherapy (IMRT) treatment beams. For one clinical head and neck IMRT treatment beam, influence of the iterative reconstruction method on existing 3D dose reconstruction artifacts was evaluated. The described iterative reconstruction method was capable of individual MLC leaf position reconstruction with millimeter accuracy, independent of the relative detector position within the range of clinically applied MU’s for IMRT. Dose reconstruction artifacts in a clinical IMRT treatment beam were considerably reduced as compared to the current dose verification procedure. The iterative reconstruction method allows high accuracy 3D dose verification by including actual MLC leaf positions reconstructed from low resolution 2D measurements.

  12. Performance of a Micro-Strip Gas Chamber for event wise, high rate thermal neutron detection with accurate 2D position determination

    NASA Astrophysics Data System (ADS)

    Mindur, B.; Alimov, S.; Fiutowski, T.; Schulz, C.; Wilpert, T.

    2014-12-01

    A two-dimensional (2D) position sensitive detector for neutron scattering applications based on low-pressure gas amplification and micro-strip technology was built and tested with an innovative readout electronics and data acquisition system. This detector contains a thin solid neutron converter and was developed for time- and thus wavelength-resolved neutron detection in single-event counting mode, which improves the image contrast in comparison with integrating detectors. The prototype detector of a Micro-Strip Gas Chamber (MSGC) was built with a solid natGd/CsI thermal neutron converter for spatial resolutions of about 100 μm and counting rates up to 107 neutrons/s. For attaining very high spatial resolutions and counting rates via micro-strip readout with centre-of-gravity evaluation of the signal amplitude distributions, a fast, channel-wise, self-triggering ASIC was developed. The front-end chips (MSGCROCs), which are very first signal processing components, are read out into powerful ADC-FPGA boards for on-line data processing and thereafter via Gigabit Ethernet link into the data receiving PC. The workstation PC is controlled by a modular, high performance dedicated software suite. Such a fast and accurate system is crucial for efficient radiography/tomography, diffraction or imaging applications based on high flux thermal neutron beam. In this paper a brief description of the detector concept with its operation principles, readout electronics requirements and design together with the signals processing stages performed in hardware and software are presented. In more detail the neutron test beam conditions and measurement results are reported. The focus of this paper is on the system integration, two dimensional spatial resolution, the time resolution of the readout system and the imaging capabilities of the overall setup. The detection efficiency of the detector prototype is estimated as well.

  13. Automation and validation of micronucleus detection in the 3D EpiDerm™ human reconstructed skin assay and correlation with 2D dose responses

    PubMed Central

    Chapman, K. E.; Thomas, A. D.; Jenkins, G. J. S.

    2014-01-01

    Recent restrictions on the testing of cosmetic ingredients in animals have resulted in the need to test the genotoxic potential of chemicals exclusively in vitro prior to licensing. However, as current in vitro tests produce some misleading positive results, sole reliance on such tests could prevent some chemicals with safe or beneficial exposure levels from being marketed. The 3D human reconstructed skin micronucleus (RSMN) assay is a promising new in vitro approach designed to assess genotoxicity of dermally applied compounds. The assay utilises a highly differentiated in vitro model of the human epidermis. For the first time, we have applied automated micronucleus detection to this assay using MetaSystems Metafer Slide Scanning Platform (Metafer), demonstrating concordance with manual scoring. The RSMN assay’s fixation protocol was found to be compatible with the Metafer, providing a considerably shorter alternative to the recommended Metafer protocol. Lowest observed genotoxic effect levels (LOGELs) were observed for mitomycin-C at 4.8 µg/ml and methyl methanesulfonate (MMS) at 1750 µg/ml when applied topically to the skin surface. In-medium dosing with MMS produced a LOGEL of 20 µg/ml, which was very similar to the topical LOGEL when considering the total mass of MMS added. Comparisons between 3D medium and 2D LOGELs resulted in a 7-fold difference in total mass of MMS applied to each system, suggesting a protective function of the 3D microarchitecture. Interestingly, hydrogen peroxide (H2O2), a positive clastogen in 2D systems, tested negative in this assay. A non-genotoxic carcinogen, methyl carbamate, produced negative results, as expected. We also demonstrated expression of the DNA repair protein N-methylpurine-DNA glycosylase in EpiDerm™. Our preliminary validation here demonstrates that the RSMN assay may be a valuable follow-up to the current in vitro test battery, and together with its automation, could contribute to minimising unnecessary in

  14. Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms.

    PubMed

    Saunders, Gary W; McDevit, Daniel C

    2012-01-01

    This chapter outlines the current practices used in our laboratory for routine DNA barcode analyses of the three major marine macroalgal groups, viz., brown (Phaeophyceae), red (Rhodophyta), and green (Chlorophyta) algae, as well as for the microscopic diatoms (Bacillariophyta). We start with an outline of current streamlined field protocols, which facilitate the collection of substantial (hundreds to thousands) specimens during short (days to weeks) field excursions. We present the current high-throughput DNA extraction protocols, which can, nonetheless, be easily modified for manual molecular laboratory use. We are advocating a two-marker approach for the DNA barcoding of protists with each major lineage having a designated primary and secondary barcode marker of which one is always the LSU D2/D3 (divergent domains D2/D3 of the nuclear ribosomal large subunit DNA). We provide a listing of the primers that we currently use in our laboratory for amplification of DNA barcode markers from the groups that we study: LSU D2/D3, which we advocate as a eukaryote-wide barcode marker to facilitate broad ecological and environmental surveys (secondary barcode marker in this capacity); COI-5P (the standard DNA barcode region of the mitochondrial cytochrome c oxidase 1 gene) as the primary barcode marker for brown and red algae; rbcL-3P (the 3' region of the plastid large subunit of ribulose-l-5-bisphosphate carboxylase/oxygenase) as the primary barcode marker for diatoms; and tufA (plastid elongation factor Tu gene) as the primary barcode marker for chlorophytan green algae. We outline our polymerase chain reaction and DNA sequencing methodologies, which have been streamlined for efficiency and to reduce unnecessary cleaning steps. The combined information should provide a helpful guide to those seeking to complete barcode research on these and related "protistan" groups (the term protist is not used in a phylogenetic context; it is simply a catch-all term for the bulk of

  15. Wolbachia and DNA barcoding insects: patterns, potential, and problems.

    PubMed

    Smith, M Alex; Bertrand, Claudia; Crosby, Kate; Eveleigh, Eldon S; Fernandez-Triana, Jose; Fisher, Brian L; Gibbs, Jason; Hajibabaei, Mehrdad; Hallwachs, Winnie; Hind, Katharine; Hrcek, Jan; Huang, Da-Wei; Janda, Milan; Janzen, Daniel H; Li, Yanwei; Miller, Scott E; Packer, Laurence; Quicke, Donald; Ratnasingham, Sujeevan; Rodriguez, Josephine; Rougerie, Rodolphe; Shaw, Mark R; Sheffield, Cory; Stahlhut, Julie K; Steinke, Dirk; Whitfield, James; Wood, Monty; Zhou, Xin

    2012-01-01

    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--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.

  16. Photocleavable DNA Barcoding Antibodies for Multiplexed Protein Analysis in Single Cells.

    PubMed

    Ullal, Adeeti V; Weissleder, Ralph

    2015-01-01

    We describe a DNA-barcoded antibody sensing technique for single cell protein analysis in which the barcodes are photocleaved and digitally detected without amplification steps (Ullal et al., Sci Transl Med 6:219, 2014). After photocleaving the unique ~70 mer DNA barcodes we use a fluorescent hybridization technology for detection, similar to what is commonly done for nucleic acid readouts. This protocol offers a simple method for multiplexed protein detection using 100+ antibodies and can be performed on clinical samples as well as single cells.

  17. DNA barcoding of European Herbertus (Marchantiopsida, Herbertaceae) and the discovery and description of a new species.

    PubMed

    Bell, David; Long, David G; Forrest, Alan D; Hollingsworth, Michelle L; Blom, Hans H; Hollingsworth, Peter M

    2012-01-01

    DNA barcoding of a group of European liverwort species from the genus Herbertus was undertaken using three plastid (matK, rbcL and trnH-psbA) and one nuclear (ITS) marker. The DNA barcode data were effective in discriminating among the sampled species of Herbertus and contributed towards the detection of a previously overlooked European Herbertus species, described here as H. norenus sp. nov. This species shows clear-cut differences in DNA sequence for multiple barcode regions and is also morphologically distinct. The DNA barcode data were also useful in clarifying taxonomic relationships of the European species with some species from Asia and North America. In terms of the discriminatory power of the different barcode markers, ITS was the most informative region, followed closely by matK. All species were distinguishable by ITS alone, rbcL + matK and various other multimarker combinations.

  18. Diagnostic performance of 3D TSE MRI versus 2D TSE MRI of the knee at 1.5 T, with prompt arthroscopic correlation, in the detection of meniscal and cruciate ligament tears*

    PubMed Central

    Chagas-Neto, Francisco Abaeté; Nogueira-Barbosa, Marcello Henrique; Lorenzato, Mário Müller; Salim, Rodrigo; Kfuri-Junior, Maurício; Crema, Michel Daoud

    2016-01-01

    Objective To compare the diagnostic performance of the three-dimensional turbo spin-echo (3D TSE) magnetic resonance imaging (MRI) technique with the performance of the standard two-dimensional turbo spin-echo (2D TSE) protocol at 1.5 T, in the detection of meniscal and ligament tears. Materials and Methods Thirty-eight patients were imaged twice, first with a standard multiplanar 2D TSE MR technique, and then with a 3D TSE technique, both in the same 1.5 T MRI scanner. The patients underwent knee arthroscopy within the first three days after the MRI. Using arthroscopy as the reference standard, we determined the diagnostic performance and agreement. Results For detecting anterior cruciate ligament tears, the 3D TSE and routine 2D TSE techniques showed similar values for sensitivity (93% and 93%, respectively) and specificity (80% and 85%, respectively). For detecting medial meniscal tears, the two techniques also had similar sensitivity (85% and 83%, respectively) and specificity (68% and 71%, respectively). In addition, for detecting lateral meniscal tears, the two techniques had similar sensitivity (58% and 54%, respectively) and specificity (82% and 92%, respectively). There was a substantial to almost perfect intraobserver and interobserver agreement when comparing the readings for both techniques. Conclusion The 3D TSE technique has a diagnostic performance similar to that of the routine 2D TSE protocol for detecting meniscal and anterior cruciate ligament tears at 1.5 T, with the advantage of faster acquisition. PMID:27141127

  19. A comparative analysis of DNA barcode microarray feature size

    PubMed Central

    Ammar, Ron; Smith, Andrew M; Heisler, Lawrence E; Giaever, Guri; Nislow, Corey

    2009-01-01

    Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO) collection used for screens of pooled yeast (Saccharomyces cerevisiae) deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density. PMID:19825181

  20. Identifying Canadian Freshwater Fishes through DNA Barcodes

    PubMed Central

    Hubert, Nicolas; Hanner, Robert; Holm, Erling; Mandrak, Nicholas E.; Taylor, Eric; Burridge, Mary; Watkinson, Douglas; Dumont, Pierre; Curry, Allen; Bentzen, Paul; Zhang, Junbin; April, Julien; Bernatchez, Louis

    2008-01-01

    Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. Methodology/Principal Findings We bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. Conclusions/Significance The present study evidenced that freshwater fish species can be

  1. Digital barcodes of suspension array using laser induced breakdown spectroscopy

    PubMed Central

    He, Qinghua; Liu, Yixi; He, Yonghong; Zhu, Liang; Zhang, Yilong; Shen, Zhiyuan

    2016-01-01

    We show a coding method of suspension array based on the laser induced breakdown spectroscopy (LIBS), which promotes the barcodes from analog to digital. As the foundation of digital optical barcodes, nanocrystals encoded microspheres are prepared with self-assembly encapsulation method. We confirm that digital multiplexing of LIBS-based coding method becomes feasible since the microsphere can be coded with direct read-out data of wavelengths, and the method can avoid fluorescence signal crosstalk between barcodes and analyte tags, which lead to overall advantages in accuracy and stability to current fluorescent multicolor coding method. This demonstration increases the capability of multiplexed detection and accurate filtrating, expanding more extensive applications of suspension array in life science. PMID:27808270

  2. Staring 2-D hadamard transform spectral imager

    DOEpatents

    Gentry, Stephen M.; Wehlburg, Christine M.; Wehlburg, Joseph C.; Smith, Mark W.; Smith, Jody L.

    2006-02-07

    A staring imaging system inputs a 2D spatial image containing multi-frequency spectral information. This image is encoded in one dimension of the image with a cyclic Hadamarid S-matrix. The resulting image is detecting with a spatial 2D detector; and a computer applies a Hadamard transform to recover the encoded image.

  3. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

    Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.

  4. 77 FR 12764 - POSTNET Barcode Discontinuation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-02

    ... between the barcode and top line or bottom line of the address block must not exceed 0.625 (\\5/8\\) inch... Intelligent Mail barcode and the top and bottom window edges must be at least 0.028 inch. These clearances... the top and bottom edges of the address label must be at least 0.028 inch. * * * * * 5.7 Barcode...

  5. A Ranking System for Reference Libraries of DNA Barcodes: Application to Marine Fish Species from Portugal

    PubMed Central

    Costa, Filipe O.; Landi, Monica; Martins, Rogelia; Costa, Maria H.; Costa, Maria E.; Carneiro, Miguel; Alves, Maria J.; Steinke, Dirk; Carvalho, Gary R.

    2012-01-01

    Background The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal. Methodology/Principal Findings Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A–E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E). Conclusion/Significance We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the

  6. Counting animal species with DNA barcodes: Canadian insects

    PubMed Central

    Ratnasingham, Sujeevan; Zakharov, Evgeny V.; Telfer, Angela C.; Levesque-Beaudin, Valerie; Milton, Megan A.; Pedersen, Stephanie; Jannetta, Paul; deWaard, Jeremy R.

    2016-01-01

    Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy. This article is part of the

  7. 2D semiconductor optoelectronics

    NASA Astrophysics Data System (ADS)

    Novoselov, Kostya

    The advent of graphene and related 2D materials has recently led to a new technology: heterostructures based on these atomically thin crystals. The paradigm proved itself extremely versatile and led to rapid demonstration of tunnelling diodes with negative differential resistance, tunnelling transistors, photovoltaic devices, etc. By taking the complexity and functionality of such van der Waals heterostructures to the next level we introduce quantum wells engineered with one atomic plane precision. Light emission from such quantum wells, quantum dots and polaritonic effects will be discussed.

  8. Prospective cost-benefit analysis of a two-dimensional barcode for vaccine production, clinical documentation, and public health reporting and tracking.

    PubMed

    O'Connor, Alan C; Kennedy, Erin D; Loomis, Ross J; Haque, Saira N; Layton, Christine M; Williams, Warren W; Amoozegar, Jacqueline B; Braun, Fern M; Honeycutt, Amanda A; Weinbaum, Cindy

    2013-06-28

    In the United States recording accurate vaccine lot numbers in immunization records is required by the National Childhood Vaccine Injury Act and is necessary for public health surveillance and implementation of vaccine product recalls. However, this information is often missing or inaccurate in records. The Food and Drug Administration (FDA) requires a linear barcode of the National Drug Code (NDC) on vaccine product labels as a medication verification measure, but lot number and expiration date must still be recorded by hand. Beginning in 2011, FDA permitted manufacturers to replace linear barcodes with two-dimensional (2D) barcodes on unit-of-use product labels. A 2D barcode can contain the NDC, expiration date, and lot number in a symbol small enough to fit on a unit-of-use label. All three data elements could be scanned into a patient record. To assess 2D barcodes' potential impacts, a mixed-methods approach of time-motion data analysis, interview and survey data collection, and cost-benefit analysis was employed. Analysis of a time-motion study conducted at 33 practices suggests scanning 2D-barcoded vaccines could reduce immunization documentation time by 36-39 s per dose. Data from an internet survey of primary care providers and local health officials indicate that 60% of pediatric practices, 54% of family medicine practices, and 39% of health departments would use the 2D barcode, with more indicating they would do so if they used electronic health records. Inclusive of manufacturer and immunization provider costs and benefits, we forecast lower-bound net benefits to be $310-334 million between 2011 and 2023 with a benefit-to-cost ratio of 3.1:1-3.2:1. Although we were unable to monetize benefits for expected improved immunization coverage, surveillance, or reduced medication errors, based on our findings, we expect that using 2D barcodes will lower vaccine documentation costs, facilitate data capture, and enhance immunization data quality.

  9. Determination of vitamins D2, D3, K1 and K3 and some hydroxy metabolites of vitamin D3 in plasma using a continuous clean-up-preconcentration procedure coupled on-line with liquid chromatography-UV detection.

    PubMed

    Ortiz Boyer, F; Fernández Romero, J M; Luque de Castro, M D; Quesada, J M

    1999-03-01

    A semi-automatic procedure for the continuous clean-up and concentration of several fat-soluble vitamins prior to their separation by HPLC and UV detection is reported. The procedure is based on the use of a minicolumn packed with aminopropylsilica as sorbent located prior to the chromatographic detection system. The overall process was developed and applied to the main liposoluble vitamins (A, D2, D3, E, K1, K3) and several hydroxy metabolites of vitamin D3 [25-(OH)-D3,24,25-(OH)2-D3 and 1,25-(OH)2-D3]. All the analytes were monitored at a compromise wavelength of 270 nm. Calibration graphs were constructed between 0.01 and 100 ng ml-1 for vitamin D2 and D3 and their hydroxy metabolites, between 0.1 and 100 ng ml-1 for vitamin A, K1 and K3 and between 1 and 100 ng ml-1 for vitamin E, with excellent regression coefficients (> or = 0.9901) in all cases. The precision was established at two concentration levels with acceptable RSDs in all instances (between 3.6 and 8.7%). The method was appropriate for the determination of vitamin D2, D3, K1 and K3 and the 24,25-dihydroxy and 25-hydroxy metabolites of vitamin D3 in human plasma. The method was applied to plasma samples spiked with the target analytes and the recoveries ranged between 78 and 109%.

  10. Barcoding a Small Academic Library: Avoiding the Pitfalls.

    ERIC Educational Resources Information Center

    Linsley, Laurie S.; Jones, Leona

    1994-01-01

    Relates the Seminole Community College (Florida) library's experience barcoding a collection of materials and provides practical suggestions on how to implement barcoding in other libraries. Highlights include a barcode plan (smart barcodes and dumb barcodes), worker guidelines, problems encountered, and costs. An annotated bibliography and seven…

  11. Heterogeneity and Disorder in Ti{1-x}Fe{y}O{2-d) Nanocrystal Rutile-based Flower Like Aggregates: Detection of Anatase

    SciTech Connect

    Bozin, E.S.; Kremenovic, A.; Antic, B.; Blanusa, J.; Comor, M.; Columban, P.; Mazerolles, L.

    2011-03-24

    Here we report results of systematic investigation of heterogeneity and disorder in Ti{sub 1-x}Fe{sub y}O{sub 2-d} nanorod rutile-based flowerlike aggregates. It was found that Ti{sub 1-x}Fe{sub y}O{sub 2-d} aggregates are composed of two crystalline phases: rutile as a dominant and anatase as a minor phase. Flowerlike aggregates were found to grow from an isometric core ca. 5-10 nm in diameter that was built from anatase and rutile nanorods ca. 5 x 100 nm that were grown on the anatase surface having base plane (001) intergrowth with an anatase plane. The direction of rutile nanorods growth, i.e., direction of the nanorod elongation, was [001]. Highly nonisometric rutile crystals produce anisotropic X-ray powder diffraction line broadening and doubling of vibrational bands in Raman spectra. Both these techniques confirmed nonisometric character of rutile crystals and gave a quantitative measure of crystal shape anisotropy in excellent agreement with high-resolution transmission electron microscopy measurements. In addition, from the atomic pair distribution function and Raman spectral analyses the level of vacancy concentration was determined in rutile and anatase phases of investigated samples.

  12. Denture barcoding in forensic dentistry: A future option.

    PubMed

    Basavanna, Jayaprakash Mugur; Jain, Abhishek; Misra, Sumit Kumar

    2016-01-01

    Neurodegenerative disorders are commonly seen in elderly individuals. Parkinson's disease (PD) is the most common example with memory loss, lack of logic, reasoning and analytical thinking. In this case report simple method of 2D Bar code technique of denture marking has been explained which will not only useful in patients with memory loss but it is very helpful in identifying the individuals in case of natural calamities like floods, earthquake, tornedo, state of unconsciousness and accidents. Such patients can be traced easily by denture barcoding. This technique is a major breakthrough in the field of forensic dentistry.

  13. Denture barcoding in forensic dentistry: A future option

    PubMed Central

    Basavanna, Jayaprakash Mugur; Jain, Abhishek; Misra, Sumit Kumar

    2016-01-01

    Neurodegenerative disorders are commonly seen in elderly individuals. Parkinson's disease (PD) is the most common example with memory loss, lack of logic, reasoning and analytical thinking. In this case report simple method of 2D Bar code technique of denture marking has been explained which will not only useful in patients with memory loss but it is very helpful in identifying the individuals in case of natural calamities like floods, earthquake, tornedo, state of unconsciousness and accidents. Such patients can be traced easily by denture barcoding. This technique is a major breakthrough in the field of forensic dentistry. PMID:27051224

  14. Clinical Validation of Quantum Dot Barcode Diagnostic Technology.

    PubMed

    Kim, Jisung; Biondi, Mia J; Feld, Jordan J; Chan, Warren C W

    2016-04-26

    There has been a major focus on the clinical translation of emerging technologies for diagnosing patients with infectious diseases, cancer, heart disease, and diabetes. However, most developments still remain at the academic stage where researchers use spiked target molecules to demonstrate the utility of a technology and assess the analytical performance. This approach does not account for the biological complexities and variabilities of human patient samples. As a technology matures and potentially becomes clinically viable, one important intermediate step in the translation process is to conduct a full clinical validation of the technology using a large number of patient samples. Here, we present a full detailed clinical validation of Quantum Dot (QD) barcode technology for diagnosing patients infected with Hepatitis B Virus (HBV). We further demonstrate that the detection of multiple regions of the viral genome using multiplexed QD barcodes improved clinical sensitivity from 54.9-66.7% to 80.4-90.5%, and describe how to use QD barcodes for optimal clinical diagnosis of patients. The use of QDs in biology and medicine was first introduced in 1998 but has not reached clinical care. This study describes our long-term systematic development strategy to advance QD technology to a clinically feasible product for diagnosing patients. Our "blueprint" for translating the QD barcode research concept could be adapted for other nanotechnologies, to efficiently advance diagnostic techniques discovered in the academic laboratory to patient care.

  15. A Retrospective Approach to Testing the DNA Barcoding Method

    PubMed Central

    Chapple, David G.; Ritchie, Peter A.

    2013-01-01

    A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters), and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%), and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%). But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%). For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity. PMID:24244283

  16. Multiplex single-molecule interaction profiling of DNA barcoded proteins

    PubMed Central

    Gu, Liangcai; Li, Chao; Aach, John; Hill, David E.; Vidal, Marc; Church, George M.

    2014-01-01

    In contrast with advances in massively parallel DNA sequencing1, high-throughput protein analyses2-4 are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule (SM) protein detection achieved using optical methods5 is limited by the number of spectrally nonoverlapping chromophores. Here, we introduce a single molecular interaction-sequencing (SMI-Seq) technology for parallel protein interaction profiling leveraging SM advantages. DNA barcodes are attached to proteins collectively via ribosome display6 or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide (PAA) thin film to construct a random SM array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies)7 and analyzed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimeter. Furthermore, protein interactions can be measured based on the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor (GPCR) and antibody binding profiling, were demonstrated. SMI-Seq enables “library vs. library” screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity. PMID:25252978

  17. Volumetry and biomechanical parameters detected by 3D and 2D ultrasound in patients with and without an abdominal aortic aneurysm.

    PubMed

    Batagini, Nayara Cioffi; Ventura, Carlos Augusto Pinto; Raghavan, Madhavan L; Chammas, Maria Cristina; Tachibana, Adriano; da Silva, Erasmo Simão

    2016-06-01

    The objective was to demonstrate the ability of ultrasound (US) with 3D properties to evaluate volumetry and biomechanical parameters of the aorta in patients with and without abdominal aortic aneurysm (AAA). Thirty-one patients with normal aortas (group 1), 46 patients with AAA measuring 3.0-5.5 cm (group 2) and 31 patients with AAA ⩾ 5.5 cm (group 3) underwent a 2D/3D-US examination of the infra-renal aorta, and the images were post-processed prior to being analyzed. In the maximum diameter, the global circumferential strain and the global maximum rotation assessed by 2D speckle-tracking algorithms were compared among the three groups. The volumetry data obtained using 3D-US from 40 AAA patients were compared with the volumetry data obtained by a contemporary computed tomography (CT) scan. The median global circumferential strain was 2.0% (interquartile range (IR): 1.0-3.0), 1.0% (IR: 1.0-2.0) and 1.0% (IR: 1.0-1.75) in groups 1, 2 and 3, respectively (p < 0.001). The median global maximum rotation decreased progressively from group 1 to group 3 (1.38º (IR: 0.77-2.13), 0.80º (IR: 0.57-1.0) and 0.50º (IR: 0.31-0.75), p < 0.001). AAA volume estimations by 3D-US correlated well with CT (R(2) = 0.76). In conclusion, US with 3D properties is non-invasive and has the potential to evaluate volumetry and biomechanical characteristics of AAA.

  18. Automating quantum dot barcode assays using microfluidics and magnetism for the development of a point-of-care device.

    PubMed

    Gao, Yali; Lam, Albert W Y; Chan, Warren C W

    2013-04-24

    The impact of detecting multiple infectious diseases simultaneously at point-of-care with good sensitivity, specificity, and reproducibility would be enormous for containing the spread of diseases in both resource-limited and rich countries. Many barcoding technologies have been introduced for addressing this need as barcodes can be applied to detecting thousands of genetic and protein biomarkers simultaneously. However, the assay process is not automated and is tedious and requires skilled technicians. Barcoding technology is currently limited to use in resource-rich settings. Here we used magnetism and microfluidics technology to automate the multiple steps in a quantum dot barcode assay. The quantum dot-barcoded microbeads are sequentially (a) introduced into the chip, (b) magnetically moved to a stream containing target molecules, (c) moved back to the original stream containing secondary probes, (d) washed, and (e) finally aligned for detection. The assay requires 20 min, has a limit of detection of 1.2 nM, and can detect genetic targets for HIV, hepatitis B, and syphilis. This study provides a simple strategy to automate the entire barcode assay process and moves barcoding technologies one step closer to point-of-care applications.

  19. Self-registering spread-spectrum barcode method

    DOEpatents

    Cummings, Eric B.; Even Jr., William R.

    2004-11-09

    A novel spread spectrum barcode methodology is disclosed that allows a barcode to be read in its entirety even when a significant fraction or majority of the barcode is obscured. The barcode methodology makes use of registration or clocking information that is distributed along with the encoded user data across the barcode image. This registration information allows for the barcode image to be corrected for imaging distortion such as zoom, rotation, tilt, curvature, and perspective.

  20. DNA barcoding of Dutch birds

    PubMed Central

    Aliabadian, Mansour; Beentjes, Kevin K.; Roselaar, C.S. (Kees); van Brandwijk, Hans; Nijman, Vincent; Vonk, Ronald

    2013-01-01

    Abstract The mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification of animal species, and has been applied in a number of studies on birds. We here sequenced the COI gene for 387 individuals of 147 species of birds from the Netherlands, with 83 species being represented by > 2 sequences. The Netherlands occupies a small geographic area and 95% of all samples were collected within a 50 km radius from one another. The intraspecific divergences averaged 0.29% among this assemblage, but most values were lower; the interspecific divergences averaged 9.54%. In all, 95% of species were represented by a unique barcode, with 6 species of gulls and skua (Larus and Stercorarius) having at least one shared barcode. This is best explained by these species representing recent radiations with ongoing hybridization. In contrast, one species, the Lesser Whitethroat Sylvia curruca showed deep divergences, averaging 5.76% and up to 8.68% between individuals. These possibly represent two distinct taxa, S. curruca and S. blythi, both clearly separated in a haplotype network analysis. Our study adds to a growing body of DNA barcodes that have become available for birds, and shows that a DNA barcoding approach enables to identify known Dutch bird species with a very high resolution. In addition some species were flagged up for further detailed taxonomic investigation, illustrating that even in ornithologically well-known areas such as the Netherlands, more is to be learned about the birds that are present. PMID:24453549

  1. Detection of Anisotropic Hyperfine Components of Chemically Prepared Carotenoid Radical Cations:1D and 2D ESEEM and Pulsed ENDOR Study

    SciTech Connect

    Konovalova, Tatyana A.; Dikanov, Sergei A.; Bowman, Michael K.; Kispert, Lowell D.

    2001-09-06

    Canthaxanthin and 8'-apo-B-caroten-8'-al radical cations chemically prepared on activated silica-alumina and in CH2CI2 solution containing A1C13 were studied by pulsed EPR and ENDOR spectroscopies. Both the 1D three-pulse ESEEM and the 2D HYSCORE spectra of the carotenoid-A1C13 mixtures exhibited the 27 A1 nuclei peak at 3.75 MHz. This indicates electron-transfer interactions between carotenoids and A1III ions resulting in the formation and stabilization of carotenoid radical cations. Davies ENDOR measurements of the canthaxanthin radical cation on silica-alumina determined the hyperfine couplings of B protons belonging to three different methyl groups with ahI=2.6 MHz, aH2=8.6MHz, and ah3 ca. 13 MHz. The principal components of the proton hyperfine tensors were obtained from HYSCORE spectra in A1C13 solutions and on the solid support. Identification of the protons was made on the basis of isotropic hyperfine couplings determined by RHF-INDO/SP molecular orbital calculations. In frozen A1C13 solution, the C(7, 7')Ha and C(14, 14')-Ha a protons were observed for Canthaxanthin and the C(8 or 14')-Ha, C(15')-Ha were observed for 8'-apo-B-caroten-8'-al. On the silica-alumina support, the C(10, 10')-Ha, C(11, 11')-Ha, and C(15,15')-Ha a protons were measured for Canthaxanthin and the C(12)-Ha and C(15')-Ha were measured for 8' apo-B-caroten-8'-al. Some protons with large isotropic couplings (>10 MHz) determined from HYSCORE analysis could be assigned to B protons, but the principal components of their hyperfine tensors are much more anisotropic than those reported previously for B protons. We suggest that cis/trans isomerization of carotenoids on silica-alumina results in stabilization of di-cis isomers with large isotropic couplings for some a protons which are comparable to those of B protons.

  2. Ten years of barcoding at the African Centre for DNA barcoding.

    PubMed

    Bezeng, Simeon Bezeng; Davies, T Jonathan; Daru, Barnabas H; Kabongo, Ronny Mukala; Maurin, Olivier; Yessoufou, Kowiyou; van der Bank, Herman; Van der Bank, Michelle

    2017-03-24

    The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that the two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants. To date, numerous studies continue to test the discriminatory power of these markers across various plant lineages. Over the past decade, we at the African Centre for DNA Barcoding, have used these core DNA barcodes to generate a barcode library for southern Africa. To date, the ACDB has contributed more than 21 000 plant barcodes and over 3 000 CO1 barcodes for animals to the Barcode of Life Database (BOLD). Building upon this effort, we at the ACDB have addressed questions related to community assembly, biogeography, phylogenetic diversification, and invasion biology. Collectively, our work demonstrates the diverse applications of DNA barcoding in ecology, systematics, evolutionary biology, and conservation.

  3. DNA Barcoding the Geometrid Fauna of Bavaria (Lepidoptera): Successes, Surprises, and Questions

    PubMed Central

    Hausmann, Axel; Haszprunar, Gerhard; Hebert, Paul D. N.

    2011-01-01

    Background The State of Bavaria is involved in a research program that will lead to the construction of a DNA barcode library for all animal species within its territorial boundaries. The present study provides a comprehensive DNA barcode library for the Geometridae, one of the most diverse of insect families. Methodology/Principal Findings This study reports DNA barcodes for 400 Bavarian geometrid species, 98 per cent of the known fauna, and approximately one per cent of all Bavarian animal species. Although 98.5% of these species possess diagnostic barcode sequences in Bavaria, records from neighbouring countries suggest that species-level resolution may be compromised in up to 3.5% of cases. All taxa which apparently share barcodes are discussed in detail. One case of modest divergence (1.4%) revealed a species overlooked by the current taxonomic system: Eupithecia goossensiata Mabille, 1869 stat.n. is raised from synonymy with Eupithecia absinthiata (Clerck, 1759) to species rank. Deep intraspecific sequence divergences (>2%) were detected in 20 traditionally recognized species. Conclusions/Significance The study emphasizes the effectiveness of DNA barcoding as a tool for monitoring biodiversity. Open access is provided to a data set that includes records for 1,395 geometrid specimens (331 species) from Bavaria, with 69 additional species from neighbouring regions. Taxa with deep intraspecific sequence divergences are undergoing more detailed analysis to ascertain if they represent cases of cryptic diversity. PMID:21423340

  4. Fluorescent genetic barcoding in mammalian cells for enhanced multiplexing capabilities in flow cytometry.

    PubMed

    Smurthwaite, Cameron A; Hilton, Brett J; O'Hanlon, Ryan; Stolp, Zachary D; Hancock, Bryan M; Abbadessa, Darin; Stotland, Aleksandr; Sklar, Larry A; Wolkowicz, Roland

    2014-01-01

    The discovery of the green fluorescent protein from Aequorea victoria has revolutionized the field of cell and molecular biology. Since its discovery a growing panel of fluorescent proteins, fluorophores and fluorescent-coupled staining methodologies, have expanded the analytical capabilities of flow cytometry. Here, we exploit the power of genetic engineering to barcode individual cells with genes encoding fluorescent proteins. For genetic engineering, we utilize retroviral technology, which allows for the expression of ectopic genetic information in a stable manner in mammalian cells. We have genetically barcoded both adherent and nonadherent cells with different fluorescent proteins. Multiplexing power was increased by combining both the number of distinct fluorescent proteins, and the fluorescence intensity in each channel. Moreover, retroviral expression has proven to be stable for at least a 6-month period, which is critical for applications such as biological screens. We have shown the applicability of fluorescent barcoded multiplexing to cell-based assays that rely themselves on genetic barcoding, or on classical staining protocols. Fluorescent genetic barcoding gives the cell an inherited characteristic that distinguishes it from its counterpart. Once cell lines are developed, no further manipulation or staining is required, decreasing time, nonspecific background associated with staining protocols, and cost. The increasing number of discovered and/or engineered fluorescent proteins with unique absorbance/emission spectra, combined with the growing number of detection devices and lasers, increases multiplexing versatility, making fluorescent genetic barcoding a powerful tool for flow cytometry-based analysis.

  5. Insights into the Oxidation Mechanism of sp(2)-sp(3) Hybrid Carbon Materials: Preparation of a Water-Soluble 2D Porous Conductive Network and Detectable Molecule Separation.

    PubMed

    Yang, Siwei; Yang, Yucheng; He, Peng; Wang, Gang; Ding, Guqiao; Xie, Xiaoming

    2017-01-31

    A thorough investigation of the oxidation mechanism of sp(2)-sp(3) hybrid carbon materials is helpful for the morphological trimming of graphene. Here, porous graphene (PGN) was obtained via a free radical oxidation process. We further demonstrated the difference between traditional and free radical oxidation processes in sp(2)-sp(3) hybrid carbon materials. The sp(3) part of graphene oxide was oxidized first, and well-crystallized sp(2) domains were reserved, which is different from the oxidation mechanism in a traditional approach. The obtained PGN shows excellent performance in the design of PGN-based detectable molecule separation or other biomedical applications.

  6. Qualitative and quantitative analysis of the unsaponifiable fraction of vegetable oils by using comprehensive 2D GC with dual MS/FID detection.

    PubMed

    Tranchida, Peter Q; Salivo, Simona; Franchina, Flavio A; Bonaccorsi, Ivana; Dugo, Paola; Mondello, Luigi

    2013-05-01

    The present investigation is focused on the development of a comprehensive two-dimensional GC (GC × GC) method, with dual MS/FID detection, for the qualitative and quantitative analysis of the entire unsaponifiable fraction of vegetable oils. The unsaponifiable fraction forms a minor, highly specific part of a vegetable oil, and can be used as an indicator of genuineness. The column set used consisted of a low-polarity first dimension, and a medium-polarity secondary one, both characterized by a high thermal stability. The use of dual detection enabled the attainment of both mass spectral information and relative % FID data. The complexity of the fingerprint, generated by the unsaponifiable fraction, fully justified the employment of the two-dimensional GC technology. Furthermore, two other GC × GC benefits contributed greatly to the attainment of promising results, namely sensitivity enhancement and the formation of group-type patterns. The method herein proposed could potentially open a new opportunity for the more in-depth knowledge of the unsaponifiable fraction of vegetable oils.

  7. E-2D Advanced Hawkeye Aircraft (E-2D AHE)

    DTIC Science & Technology

    2015-12-01

    Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-364 E-2D Advanced Hawkeye Aircraft (E-2D AHE) As of FY 2017 President’s Budget Defense...Office Estimate RDT&E - Research, Development, Test, and Evaluation SAR - Selected Acquisition Report SCP - Service Cost Position TBD - To Be Determined

  8. 76 FR 34871 - Mobile Barcode Promotion

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-15

    ... 111 Mobile Barcode Promotion AGENCY: Postal Service TM . ACTION: Final rule. SUMMARY: The Postal... ) 709.4 to add a temporary promotion for First-Class Mail cards, letters and flats, and Standard Mail... barcode promotion, and the new mailing standards to implement the promotion. To be eligible,...

  9. DNA Barcoding Investigations Bring Biology to Life

    ERIC Educational Resources Information Center

    Musante, Susan

    2010-01-01

    This article describes how DNA barcoding investigations bring biology to life. Biologists recognize the power of DNA barcoding not just to teach biology through connections to the real world but also to immerse students in the exciting process of science. As an investigator in the Program for the Human Environment at Rockefeller University in New…

  10. Long-range barcode labeling-sequencing

    SciTech Connect

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  11. Pilot Study on the Detection of Simulated Lesions Using a 2D and 3D Digital Full-Field Mammography System with a Newly Developed High Resolution Detector Based on Two Shifts of a-Se.

    PubMed

    Schulz-Wendtland, R; Bani, M; Lux, M P; Schwab, S; Loehberg, C R; Jud, S M; Rauh, C; Bayer, C M; Beckmann, M W; Uder, M; Fasching, P A; Adamietz, B; Meier-Meitinger, M

    2012-05-01

    Purpose: Experimental study of a new system for digital 2D and 3D full-field mammography (FFDM) using a high resolution detector based on two shifts of a-Se. Material and Methods: Images were acquired using the new FFDM system Amulet® (FujiFilm, Tokio, Japan), an a-Se detector (receptor 24 × 30 cm(2), pixel size 50 µm, memory depth 12 bit, spatial resolution 10 lp/mm, DQE > 0.50). Integrated in the detector is a new method for data transfer, based on optical switch technology. The object of investigation was the Wisconsin Mammographic Random Phantom, Model 152A (Radiation Measurement Inc., Middleton, WI, USA) and the same parameters and exposure data (Tungsten, 100 mAs, 30 kV) were consistently used. We acquired 3 different pairs of images in the c-c and ml planes (2D) and in the c-c and c-c planes with an angle of 4 degrees (3D). Five radiologists experienced in mammography (experience ranging from 3 months to more than 5 years) analyzed the images (monitoring) which had been randomly encoded (random generator) with regard to the recognition of details such as specks of aluminum oxide (200-740 µm), nylon fibers (0.4-1.6 mm) and round lesions/masses (diameters 5-14 mm), using special linear glasses for 3D visualization, and compared the results. Results: A total of 225 correct positive decisions could be detected: we found 222 (98.7 %) correct positive results for 2D and 3D visualization in each case. Conclusion: The results of this phantom study showed the same detection rates for both 2D and 3D imaging using full field digital mammography. Our results must be confirmed in further clinical trials.

  12. Label Free Cell-Tracking and Division Detection Based on 2D Time-Lapse Images For Lineage Analysis of Early Embryo Development

    PubMed Central

    Cicconet, Marcelo; Gutwein, Michelle; Gunsalus, Kristin C; Geiger, Davi

    2014-01-01

    In this paper we report a database and a series of techniques related to the problem of tracking cells, and detecting their divisions, in time-lapse movies of mammalian embryos. Our contributions are: (1) a method for counting embryos in a well, and cropping each individual embryo across frames, to create individual movies for cell tracking; (2) a semi-automated method for cell tracking that works up to the 8-cell stage, along with a software implementation available to the public (this software was used to build the reported database); (3) an algorithm for automatic tracking up to the 4-cell stage, based on histograms of mirror symmetry coefficients captured using wavelets; (4) a cell-tracking database containing 100 annotated examples of mammalian embryos up to the 8-cell stage; (5) statistical analysis of various timing distributions obtained from those examples. PMID:24873887

  13. DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples.

    PubMed

    Loh, W K W; Bond, P; Ashton, K J; Roberts, D T; Tibbetts, I R

    2014-08-01

    The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0.52 ± 0.10 and 23.8 ± 2.20% respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples.

  14. Species Identification of Marine Fishes in China with DNA Barcoding

    PubMed Central

    Zhang, Junbin

    2011-01-01

    DNA barcoding is a molecular method that uses a short standardized DNA sequence as a species identification tool. In this study, the standard 652 base-pair region of the mitochondrial cytochrome oxidase subunit I gene (COI) was sequenced in marine fish specimens captured in China. The average genetic distance was 50-fold higher between species than within species, as Kimura two parameter (K2P) genetic distances averaged 15.742% among congeners and only 0.319% for intraspecific individuals. There are no overlaps of pairwise genetic variations between conspecific and interspecific comparisons apart from the genera Pampus in which the introgressive hybridization was detected. High efficiency of species identification was demonstrated in the present study by DNA barcoding. Due to the incidence of cryptic species, an assumed threshold is suggested to expedite discovering of new species and biodiversity, especially involving biotas of few studies. PMID:21687792

  15. Droplet barcoding for massively parallel single-molecule deep sequencing

    PubMed Central

    Lan, Freeman; Haliburton, John R.; Yuan, Aaron; Abate, Adam R.

    2016-01-01

    The ability to accurately sequence long DNA molecules is important across biology, but existing sequencers are limited in read length and accuracy. Here, we demonstrate a method to leverage short-read sequencing to obtain long and accurate reads. Using droplet microfluidics, we isolate, amplify, fragment and barcode single DNA molecules in aqueous picolitre droplets, allowing the full-length molecules to be sequenced with multi-fold coverage using short-read sequencing. We show that this approach can provide accurate sequences of up to 10 kb, allowing us to identify rare mutations below the detection limit of conventional sequencing and directly link them into haplotypes. This barcoding methodology can be a powerful tool in sequencing heterogeneous populations such as viruses. PMID:27353563

  16. Isoflavone determination in spontaneous legumes identified by DNA barcodes.

    PubMed

    Cunha, Sara C; Faria, Miguel A; Sousa, Tiago; Nunes, Eugénia

    2012-10-15

    Isoflavones have been associated with several health protective effects. In this work spontaneous legume plants were screened as putative sources of dietary isoflavones. A molecular identification of the collected species was performed throughout DNA barcoding using ITS, rbcL, rpoC1 and matK sequences. The use of a multi-locus barcoding system complemented with basic morphological information allowed the unequivocal identification at the species level of 90% of the samples. The determination of isoflavone content was performed by high-performance liquid chromatography with diode-array detection. Total average contents in the studied species were significantly different, Ononis natrix and Cytisus scoparius possessing the highest total isoflavones content (396 and 273 mg kg(-1), respectively) and Lotus creticus, the lowest (20 mg kg(-1)). The correlation of total isoflavone content with the phylogeny of this set of plants as determined by the rpoC1 sequences was evaluated for the first time.

  17. DNA barcoding methods for land plants.

    PubMed

    Fazekas, Aron J; Kuzmina, Maria L; Newmaster, Steven G; Hollingsworth, Peter M

    2012-01-01

    DNA barcoding in the land plants presents a number of challenges compared to DNA barcoding in many animal clades. The CO1 animal DNA barcode is not effective for plants. Plant species hybridize frequently, and there are many cases of recent speciation via mechanisms, such as polyploidy and breeding system transitions. Additionally, there are many life-history trait combinations, which combine to reduce the likelihood of a small number of markers effectively tracking plant species boundaries. Recent results, however, from the two chosen core plant DNA barcode regions rbcL and matK plus two supplementary regions trnH-psbA and internal transcribed spacer (ITS) (or ITS2) have demonstrated reasonable levels of species discrimination in both floristic and taxonomically focused studies. We describe sampling techniques, extraction protocols, and PCR methods for each of these two core and two supplementary plant DNA barcode regions, with extensive notes supporting their implementation for both low- and high-throughput facilities.

  18. ABGD, Automatic Barcode Gap Discovery for primary species delimitation.

    PubMed

    Puillandre, N; Lambert, A; Brouillet, S; Achaz, G

    2012-04-01

    Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

  19. Forensic identification of CITES protected slimming cactus (Hoodia) using DNA barcoding.

    PubMed

    Gathier, Gerard; van der Niet, Timotheus; Peelen, Tamara; van Vugt, Rogier R; Eurlings, Marcel C M; Gravendeel, Barbara

    2013-11-01

    Slimming cactus (Hoodia), found only in southwestern Africa, is a well-known herbal product for losing weight. Consequently, Hoodia extracts are sought-after worldwide despite a CITES Appendix II status. The failure to eradicate illegal trade is due to problems with detecting and identifying Hoodia using morphological and chemical characters. Our aim was to evaluate the potential of molecular identification of Hoodia based on DNA barcoding. Screening of nrITS1 and psbA-trnH DNA sequences from 26 accessions of Ceropegieae resulted in successful identification, while conventional chemical profiling using DLI-MS led to inaccurate detection and identification of Hoodia. The presence of Hoodia in herbal products was also successfully established using DNA sequences. A validation procedure of our DNA barcoding protocol demonstrated its robustness to changes in PCR conditions. We conclude that DNA barcoding is an effective tool for Hoodia detection and identification which can contribute to preventing illegal trade.

  20. Species identification through DNA "barcodes".

    PubMed

    Ferri, Gianmarco; Alù, Milena; Corradini, Beatrice; Licata, Manuela; Beduschi, Giovanni

    2009-06-01

    Conventional methods for forensic species identification are mainly based on immunological procedures, which have limited applications for old and degraded specimens. The mitochondrial cytochrome b gene sequence has emerged in forensics among molecular methods. Recent investigations in the taxonomic field have suggested that a DNA-based identification system may aid the resolution of animal diversity and classification using sequence analysis and phylogenetic links. Selected gene sequences can be viewed as a genetic "barcode," which is enclosed in every cell, and barcoding is a standardized approach for characterizing species using short DNA sequences as a diagnostic biomarker for organisms. The aim of this study was to evaluate the potential of barcode mitochondrial genes, such as the cytochrome c oxidase sub 1 (COI) and the 16S rRNA gene, as a forensic tool. We developed a new approach for species testing and identification with a singleplex PCR amplification that will be useful not only in criminal casework but also in biosecurity, food authentication, investigation against poaching or illegal trade of endangered species, and wildlife enforcement. Seven fragments ranging from 157 to 541 bp (base pairs) in humans were selected from COI and 16S rRNA genes by different redesigned sets of primers suitable for forensic purposes. The specificity of each primer pair was evaluated with a single PCR reaction on different substrates, and the diversity values were calculated by statistical tests to select a set of markers that could be useful in different caseworks. A case example of forensic species identification is also presented.

  1. Integrated quantum dot barcode smartphone optical device for wireless multiplexed diagnosis of infected patients.

    PubMed

    Ming, Kevin; Kim, Jisung; Biondi, Mia J; Syed, Abdullah; Chen, Kun; Lam, Albert; Ostrowski, Mario; Rebbapragada, Anu; Feld, Jordan J; Chan, Warren C W

    2015-03-24

    Inorganic nanoparticles are ideal precursors for engineering barcodes for rapidly detecting diseases. Despite advances in the chemical design of these barcodes, they have not advanced to clinical use because they lack sensitivity and are not cost-effective due to requirement of a large read-out system. Here we combined recent advances in quantum dot barcode technology with smartphones and isothermal amplification to engineer a simple and low-cost chip-based wireless multiplex diagnostic device. We characterized the analytical performance of this device and demonstrated that the device is capable of detecting down to 1000 viral genetic copies per milliliter, and this enabled the diagnosis of patients infected with HIV or hepatitis B. More importantly, the barcoding enabled us to detect multiple infectious pathogens simultaneously, in a single test, in less than 1 h. This multiplexing capability of the device enables the diagnosis of infections that are difficult to differentiate clinically due to common symptoms such as a fever or rash. The integration of quantum dot barcoding technology with a smartphone reader provides a capacity for global surveillance of infectious diseases and the potential to accelerate knowledge exchange transfer of emerging or exigent disease threats with healthcare and military organizations in real time.

  2. Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections

    PubMed Central

    Baniecki, Mary Lynn; Faust, Aubrey L.; Schaffner, Stephen F.; Park, Daniel J.; Galinsky, Kevin; Daniels, Rachel F.; Hamilton, Elizabeth; Ferreira, Marcelo U.; Karunaweera, Nadira D.; Serre, David; Zimmerman, Peter A.; Sá, Juliana M.; Wellems, Thomas E.; Musset, Lise; Legrand, Eric; Melnikov, Alexandre; Neafsey, Daniel E.; Volkman, Sarah K.; Wirth, Dyann F.; Sabeti, Pardis C.

    2015-01-01

    Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections. PMID:25781890

  3. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology

    PubMed Central

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct “beyond graphene” domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  4. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology.

    PubMed

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-02-06

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct "beyond graphene" domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials.

  5. An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding.

    PubMed

    De Ley, Paul; De Ley, Irma Tandingan; Morris, Krystalynne; Abebe, Eyualem; Mundo-Ocampo, Manuel; Yoder, Melissa; Heras, Joseph; Waumann, Dora; Rocha-Olivares, Axayácatl; Jay Burr, A H; Baldwin, James G; Thomas, W Kelley

    2005-10-29

    Molecular surveys of meiofaunal diversity face some interesting methodological challenges when it comes to interstitial nematodes from soils and sediments. Morphology-based surveys are greatly limited in processing speed, while barcoding approaches for nematodes are hampered by difficulties of matching sequence data with traditional taxonomy. Intermediate technology is needed to bridge the gap between both approaches. An example of such technology is video capture and editing microscopy, which consists of the recording of taxonomically informative multifocal series of microscopy images as digital video clips. The integration of multifocal imaging with sequence analysis of the D2D3 region of large subunit (LSU) rDNA is illustrated here in the context of a combined morphological and barcode sequencing survey of marine nematodes from Baja California and California. The resulting video clips and sequence data are made available online in the database NemATOL (http://nematol.unh.edu/). Analyses of 37 barcoded nematodes suggest that these represent at least 32 species, none of which matches available D2D3 sequences in public databases. The recorded multifocal vouchers allowed us to identify most specimens to genus, and will be used to match specimens with subsequent species identifications and descriptions of preserved specimens. Like molecular barcodes, multifocal voucher archives are part of a wider effort at structuring and changing the process of biodiversity discovery. We argue that data-rich surveys and phylogenetic tools for analysis of barcode sequences are an essential component of the exploration of phyla with a high fraction of undiscovered species. Our methods are also directly applicable to other meiofauna such as for example gastrotrichs and tardigrades.

  6. Learning to classify species with barcodes

    PubMed Central

    Bertolazzi, Paola; Felici, Giovanni; Weitschek, Emanuel

    2009-01-01

    Background According to many field experts, specimens classification based on morphological keys needs to be supported with automated techniques based on the analysis of DNA fragments. The most successful results in this area are those obtained from a particular fragment of mitochondrial DNA, the gene cytochrome c oxidase I (COI) (the "barcode"). Since 2004 the Consortium for the Barcode of Life (CBOL) promotes the collection of barcode specimens and the development of methods to analyze the barcode for several tasks, among which the identification of rules to correctly classify an individual into its species by reading its barcode. Results We adopt a Logic Mining method based on two optimization models and present the results obtained on two datasets where a number of COI fragments are used to describe the individuals that belong to different species. The method proposed exhibits high correct recognition rates on a training-testing split of the available data using a small proportion of the information available (e.g., correct recognition approx. 97% when only 20 sites of the 648 available are used). The method is able to provide compact formulas on the values (A, C, G, T) at the selected sites that synthesize the characteristic of each species, a relevant information for taxonomists. Conclusion We have presented a Logic Mining technique designed to analyze barcode data and to provide detailed output of interest to the taxonomists and the barcode community represented in the CBOL Consortium. The method has proven to be effective, efficient and precise. PMID:19900303

  7. DNA Barcoding and Pharmacovigilance of Herbal Medicines.

    PubMed

    de Boer, Hugo J; Ichim, Mihael C; Newmaster, Steven G

    2015-07-01

    Pharmacovigilance of herbal medicines relies on the product label information regarding the ingredients and the adherence to good manufacturing practices along the commercialisation chain. Several studies have shown that substitution of plant species occurs in herbal medicines, and this in turn poses a challenge to herbal pharmacovigilance as adverse reactions might be due to adulterated or added ingredients. Authentication of constituents in herbal medicines using analytical chemistry methods can help detect contaminants and toxins, but are often limited or incapable of detecting the source of the contamination. Recent developments in molecular plant identification using DNA sequence data enable accurate identification of plant species from herbal medicines using defined DNA markers. Identification of multiple constituent species from compound herbal medicines using amplicon metabarcoding enables verification of labelled ingredients and detection of substituted, adulterated and added species. DNA barcoding is proving to be a powerful method to assess species composition in herbal medicines and has the potential to be used as a standard method in herbal pharmacovigilance research of adverse reactions to specific products.

  8. Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring

    PubMed Central

    Vivien, Régis; Wyler, Sofia; Lafont, Michel; Pawlowski, Jan

    2015-01-01

    Aquatic oligochaetes are well recognized bioindicators of quality of sediments and water in watercourses and lakes. However, the difficult taxonomic determination based on morphological features compromises their more common use in eco-diagnostic analyses. To overcome this limitation, we investigated molecular barcodes as identification tool for broad range of taxa of aquatic oligochaetes. We report 185 COI and 52 ITS2 rDNA sequences for specimens collected in Switzerland and belonging to the families Naididae, Lumbriculidae, Enchytraeidae and Lumbricidae. Phylogenetic analyses allowed distinguishing 41 lineages separated by more than 10 % divergence in COI sequences. The lineage distinction was confirmed by Automatic Barcode Gap Discovery (ABGD) method and by ITS2 data. Our results showed that morphological identification underestimates the oligochaete diversity. Only 26 of the lineages could be assigned to morphospecies, of which seven were sequenced for the first time. Several cryptic species were detected within common morphospecies. Many juvenile specimens that could not be assigned morphologically have found their home after genetic analysis. Our study showed that COI barcodes performed very well as species identifiers in aquatic oligochaetes. Their easy amplification and good taxonomic resolution might help promoting aquatic oligochaetes as bioindicators for next generation environmental DNA biomonitoring of aquatic ecosystems. PMID:25856230

  9. Identifying the ichthyoplankton of a coral reef using DNA barcodes.

    PubMed

    Hubert, Nicolas; Espiau, Benoit; Meyer, Christopher; Planes, Serge

    2015-01-01

    Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.

  10. Genetic Barcodes for Improved Environmental Tracking of an Anthrax Simulant

    PubMed Central

    Buckley, Patricia; Rivers, Bryan; Katoski, Sarah; Kim, Michael H.; Kragl, F. Joseph; Broomall, Stacey; Krepps, Michael; Skowronski, Evan W.; Rosenzweig, C. Nicole; Paikoff, Sari; Emanuel, Peter

    2012-01-01

    The development of realistic risk models that predict the dissemination, dispersion and persistence of potential biothreat agents have utilized nonpathogenic surrogate organisms such as Bacillus atrophaeus subsp. globigii or commercial products such as Bacillus thuringiensis subsp. kurstaki. Comparison of results from outdoor tests under different conditions requires the use of genetically identical strains; however, the requirement for isogenic strains limits the ability to compare other desirable properties, such as the behavior in the environment of the same strain prepared using different methods. Finally, current methods do not allow long-term studies of persistence or reaerosolization in test sites where simulants are heavily used or in areas where B. thuringiensis subsp. kurstaki is applied as a biopesticide. To create a set of genetically heterogeneous yet phenotypically indistinguishable strains so that variables intrinsic to simulations (e.g., sample preparation) can be varied and the strains can be tested under otherwise identical conditions, we have developed a strategy of introducing small genetic signatures (“barcodes”) into neutral regions of the genome. The barcodes are stable over 300 generations and do not impact in vitro growth or sporulation. Each barcode contains common and specific tags that allow differentiation of marked strains from wild-type strains and from each other. Each tag is paired with specific real-time PCR assays that facilitate discrimination of barcoded strains from wild-type strains and from each other. These uniquely barcoded strains will be valuable tools for research into the environmental fate of released organisms by providing specific artificial detection signatures. PMID:23001658

  11. DNA barcoding amphibians and reptiles.

    PubMed

    Vences, Miguel; Nagy, Zoltán T; Sonet, Gontran; Verheyen, Erik

    2012-01-01

    Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.

  12. DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market

    PubMed Central

    Lee, Shiou Yih; Ng, Wei Lun; Mahat, Mohd Noor; Nazre, Mohd; Mohamed, Rozi

    2016-01-01

    The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication. PMID:27128309

  13. DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market.

    PubMed

    Lee, Shiou Yih; Ng, Wei Lun; Mahat, Mohd Noor; Nazre, Mohd; Mohamed, Rozi

    2016-01-01

    The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.

  14. Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes.

    PubMed

    Geiger, M F; Herder, F; Monaghan, M T; Almada, V; Barbieri, R; Bariche, M; Berrebi, P; Bohlen, J; Casal-Lopez, M; Delmastro, G B; Denys, G P J; Dettai, A; Doadrio, I; Kalogianni, E; Kärst, H; Kottelat, M; Kovačić, M; Laporte, M; Lorenzoni, M; Marčić, Z; Özuluğ, M; Perdices, A; Perea, S; Persat, H; Porcelotti, S; Puzzi, C; Robalo, J; Šanda, R; Schneider, M; Šlechtová, V; Stoumboudi, M; Walter, S; Freyhof, J

    2014-11-01

    Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean BH (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the general mixed Yule-coalescent (GMYC) model-based approach (83% of all species recovered as GMYC entity). Overall, genetic morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared with analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated Evolutionarily Distinct and Globally Endangered scores in order to identify candidate species for conservation priority and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.

  15. A Competitive Bio-Barcode Amplification Immunoassay for Small Molecules Based on Nanoparticles

    PubMed Central

    Du, Pengfei; Jin, Maojun; Chen, Ge; Zhang, Chan; Jiang, Zejun; Zhang, Yanxin; Zou, Pan; She, Yongxin; Jin, Fen; Shao, Hua; Wang, Shanshan; Zheng, Lufei; Wang, Jing

    2016-01-01

    A novel detection method of small molecules, competitive bio-barcode amplification immunoassay, was developed and described in this report. Through the gold nanoparticles (AuNPs) probe and magnetic nanoparticles (MNPs) probe we prepared, only one monoclonal antibody can be used to detect small molecules. The competitive bio-barcode amplification immunoassay overcomes the obstacle that the bio-barcode assay cannot be used in small molecular detection, as two antibodies are unable to combine to one small molecule due to its small molecular structure. The small molecular compounds, triazophos, were selected as targets for the competitive bio-barcode amplification immunoassay. The linear range of detection was from 0.04 ng mL−1 to 10 ng mL−1, and the limit of detection (LOD) was 0.02 ng mL−1, which was 10–20 folds lower than ELISA (Enzyme Linked Immunosorbent Assay). A practical application of the proposed immunoassay was evaluated by detecting triazophos in real samples. The recovery rate ranged from 72.5% to 110.5%, and the RSD was less than 20%. These results were validated by GC-MS, which indicated that this convenient and sensitive method has great potential for small molecular in real samples. PMID:27924952

  16. DNA barcoding in Mexico: an introduction.

    PubMed

    Elías-Gutiérrez, M; León-Regagnon, V

    2013-11-01

    DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire sets of specimens. This tendency resulted in the creation of a national network named Mexican Barcode of Life (MEXBOL) which main goals are to train students, and to promote the interaction and collective work among researchers interested in this topic. As a result, the number of records in the Barcode of Life Database (BOLD) for some groups, such as the Mammalia, Actinopterygii, Polychaeta, Branchiopoda, Ostracoda, Maxillopoda, Nematoda, Pinophyta, Ascomycota and Basidiomycota place Mexico among the top ten countries in the generation of these data. This special number presents only few of the many interesting findings in this region of the world, after the use of this technique and its integration with other methodologies.

  17. Intracellular polysilicon barcodes for cell tracking.

    PubMed

    Fernandez-Rosas, Elisabet; Gómez, Rodrigo; Ibañez, Elena; Barrios, Leonardo; Duch, Marta; Esteve, Jaume; Nogués, Carme; Plaza, José Antonio

    2009-11-01

    During the past decade, diverse types of barcode have been designed in order to track living cells in vivo or in vitro, but none of them offer the possibility to follow an individual cell up to ten or more days. Using silicon microtechnologies a barcode sufficiently small to be introduced into a cell, yet visible and readily identifiable under an optical microscope, is designed. Cultured human macrophages are able to engulf the barcodes due to their phagocytic ability and their viability is not affected. The utility of the barcodes for cell tracking is demonstrated by following individual cells for up to ten days in culture and recording their locomotion. Interestingly, silicon microtechnology allows the mass production of reproducible codes at low cost with small features (bits) in the micrometer range that are additionally biocompatible.

  18. Optoelectronics with 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Mueller, Thomas

    2015-03-01

    Two-dimensional (2D) atomic crystals, such as graphene and layered transition-metal dichalcogenides, are currently receiving a lot of attention for applications in electronics and optoelectronics. In this talk, I will review our research activities on electrically driven light emission, photovoltaic energy conversion and photodetection in 2D semiconductors. In particular, WSe2 monolayer p-n junctions formed by electrostatic doping using a pair of split gate electrodes, type-II heterojunctions based on MoS2/WSe2 and MoS2/phosphorene van der Waals stacks, 2D multi-junction solar cells, and 3D/2D semiconductor interfaces will be presented. Upon optical illumination, conversion of light into electrical energy occurs in these devices. If an electrical current is driven, efficient electroluminescence is obtained. I will present measurements of the electrical characteristics, the optical properties, and the gate voltage dependence of the device response. In the second part of my talk, I will discuss photoconductivity studies of MoS2 field-effect transistors. We identify photovoltaic and photoconductive effects, which both show strong photoconductive gain. A model will be presented that reproduces our experimental findings, such as the dependence on optical power and gate voltage. We envision that the efficient photon conversion and light emission, combined with the advantages of 2D semiconductors, such as flexibility, high mechanical stability and low costs of production, could lead to new optoelectronic technologies.

  19. Barcode extension for analysis and reconstruction of structures.

    PubMed

    Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

    2017-03-13

    Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

  20. Barcode extension for analysis and reconstruction of structures

    NASA Astrophysics Data System (ADS)

    Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L.; Gootenberg, Jonathan S.; Yin, Peng

    2017-03-01

    Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

  1. Bio-barcode gel assay for microRNA

    NASA Astrophysics Data System (ADS)

    Lee, Hyojin; Park, Jeong-Eun; Nam, Jwa-Min

    2014-02-01

    MicroRNA has been identified as a potential biomarker because expression level of microRNA is correlated with various cancers. Its detection at low concentrations would be highly beneficial for cancer diagnosis. Here, we develop a new type of a DNA-modified gold nanoparticle-based bio-barcode assay that uses a conventional gel electrophoresis platform and potassium cyanide chemistry and show this assay can detect microRNA at aM levels without enzymatic amplification. It is also shown that single-base-mismatched microRNA can be differentiated from perfectly matched microRNA and the multiplexed detection of various combinations of microRNA sequences is possible with this approach. Finally, differently expressed microRNA levels are selectively detected from cancer cells using the bio-barcode gel assay, and the results are compared with conventional polymerase chain reaction-based results. The method and results shown herein pave the way for practical use of a conventional gel electrophoresis for detecting biomolecules of interest even at aM level without polymerase chain reaction amplification.

  2. Recommendations for Using Barcode in Hospital Process

    PubMed Central

    Hachesu, Peyman Rezaei; Zyaei, Leila; Hassankhani, Hadi

    2016-01-01

    Background: Lack of attention to the proper barcode using leads to lack of use or misuse in the hospitals. The present research aimed to investigate the requirements and barrier for using barcode technology and presenting suggestions to use it. Methods: The research is observational-descriptive. The data was collected using the designed checklist which its validity was assessed. This check list consists of two parts: “Requirements” and “barrier” of using the barcodes. Research community included 10 teaching hospitals and a class of 65 participants included people in the hospitals. The collected data was analyzed using descriptive statistics. Results: Required changes of workflow processes in the hospital and compliance them with the hospital policy are such requirements that had been infringed in the 90 % of hospitals. Prioritization of some hospital processes for barcoding, system integration with Hospital Information system (HIS), training of staff and budgeting are requirements for the successful implementation which had been infringed in the 80% of hospitals. Dissatisfaction with the quality of barcode labels and lacks of adequate scanners both whit the rate of 100 %, and the lack of understanding of the necessary requirements for implementation of barcodes as 80% were the most important barrier. Conclusion: Integrate bar code system with clinical workflow should be considered. Lack of knowledge and understanding toward the infrastructure, inadequate staff training and technologic problems are considered as the greatest barriers. PMID:27482137

  3. DNA Barcoding through Quaternary LDPC Codes

    PubMed Central

    Tapia, Elizabeth; Spetale, Flavio; Krsticevic, Flavia; Angelone, Laura; Bulacio, Pilar

    2015-01-01

    For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10−2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10−9 at the expense of a rate of read losses just in the order of 10−6. PMID:26492348

  4. DNA Barcodes for Nearctic Auchenorrhyncha (Insecta: Hemiptera)

    PubMed Central

    Foottit, Robert G.; Maw, Eric; Hebert, P. D. N.

    2014-01-01

    Background Many studies have shown the suitability of sequence variation in the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene as a DNA barcode for the identification of species in a wide range of animal groups. We examined 471 species in 147 genera of Hemiptera: Auchenorrhyncha drawn from specimens in the Canadian National Collection of Insects to assess the effectiveness of DNA barcoding in this group. Methodology/Principal Findings Analysis of the COI gene revealed less than 2% intra-specific divergence in 93% of the taxa examined, while minimum interspecific distances exceeded 2% in 70% of congeneric species pairs. Although most species are characterized by a distinct sequence cluster, sequences for members of many groups of closely related species either shared sequences or showed close similarity, with 25% of species separated from their nearest neighbor by less than 1%. Conclusions/Significance This study, although preliminary, provides DNA barcodes for about 8% of the species of this hemipteran suborder found in North America north of Mexico. Barcodes can enable the identification of many species of Auchenorrhyncha, but members of some species groups cannot be discriminated. Future use of DNA barcodes in regulatory, pest management, and environmental applications will be possible as the barcode library for Auchenorrhyncha expands to include more species and broader geographic coverage. PMID:25004106

  5. DNA Barcoding through Quaternary LDPC Codes.

    PubMed

    Tapia, Elizabeth; Spetale, Flavio; Krsticevic, Flavia; Angelone, Laura; Bulacio, Pilar

    2015-01-01

    For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2) per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9) at the expense of a rate of read losses just in the order of 10(-6).

  6. Scanning-time evaluation of Digimarc Barcode

    NASA Astrophysics Data System (ADS)

    Gerlach, Rebecca; Pinard, Dan; Weaver, Matt; Alattar, Adnan

    2015-03-01

    This paper presents a speed comparison between the use of Digimarc® Barcodes and the Universal Product Code (UPC) for customer checkout at point of sale (POS). The recently introduced Digimarc Barcode promises to increase the speed of scanning packaged goods at POS. When this increase is exploited by workforce optimization systems, the retail industry could potentially save billions of dollars. The Digimarc Barcode is based on Digimarc's watermarking technology, and it is imperceptible, very robust, and does not require any special ink, material, or printing processes. Using an image-based scanner, a checker can quickly scan consumer packaged goods (CPG) embedded with the Digimarc Barcode without the need to reorient the packages with respect to the scanner. Faster scanning of packages saves money and enhances customer satisfaction. It reduces the length of the queues at checkout, reduces the cost of cashier labor, and makes self-checkout more convenient. This paper quantifies the increase in POS scanning rates resulting from the use of the Digimarc Barcode versus the traditional UPC. It explains the testing methodology, describes the experimental setup, and analyzes the obtained results. It concludes that the Digimarc Barcode increases number of items per minute (IPM) scanned at least 50% over traditional UPC.

  7. DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera

    PubMed Central

    Bello, Abubakar; Daru, Barnabas H.; Stirton, Charles H.; Chimphango, Samson B. M.; van der Bank, Michelle; Maurin, Olivier; Muasya, A. Muthama

    2015-01-01

    Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK + rbcLa) data set as a better barcode than single regions. We found a high score (100 %) of correct identification of individuals to their respective genera but a very low score (<50 %) in identifying them to species. We found a considerable match (54 %) between genetic species and morphologically delimited species. We also found that different lineages showed a weak but significant phylogenetic conservatism in their response to fire as reseeders or resprouters, with more clustering of resprouters than would be expected by chance. These novel microevolutionary patterns might be acting continuously over time to produce multi-scale regularities of biodiversity. This study provides the first insight into the DNA barcoding campaign of land plants in species identification and detection of the phylogenetic signal in recently diverged lineages of the CFR. PMID:26507570

  8. Integrative taxonomy at work: DNA barcoding of taeniids harboured by wild and domestic cats.

    PubMed

    Galimberti, A; Romano, D F; Genchi, M; Paoloni, D; Vercillo, F; Bizzarri, L; Sassera, D; Bandi, C; Genchi, C; Ragni, B; Casiraghi, M

    2012-05-01

    In modern taxonomy, DNA barcoding is particularly useful where biometric parameters are difficult to determine or useless owing to the poor quality of samples. These situations are frequent in parasitology. Here, we present an integrated study, based on both DNA barcoding and morphological analysis, on cestodes belonging to the genus Taenia, for which biodiversity is still largely underestimated. In particular, we characterized cestodes from Italian wildcats (Felis silvestris silvestris), free-ranging domestic cats (Felis silvestris catus) and hybrids populations. Adult taeniids were collected by post-mortem examinations of the hosts and morphologically identified as Taenia taeniaeformis. We produced cox1 barcode sequences for all the analysed specimens, and we compared them with reference sequences of individuals belonging to the genus Taenia retrieved from GenBank. In order to evaluate the performance of a DNA barcoding approach to discriminate these parasites, the strength of correlation between species identification based on classical morphology and the molecular divergence of cox1 sequences was measured. Our study provides clear evidence that DNA barcoding is highly efficient to reveal the presence of cryptic lineages within already-described taeniid species. Indeed, we detected three well-defined molecular lineages within the whole panel of specimens morphologically identified as T. taeniaeformis. Two of these molecular groups were already identified by other authors and should be ranked at species level. The third molecular group encompasses only samples collected in Italy during this study, and it represents a third candidate species, still morphologically undescribed.

  9. Role of DNA barcoding in marine biodiversity assessment and conservation: An update

    PubMed Central

    Trivedi, Subrata; Aloufi, Abdulhadi A.; Ansari, Abid A.; Ghosh, Sankar K.

    2015-01-01

    More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation. PMID:26980996

  10. DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes

    PubMed Central

    Iftikhar, Romana; Ashfaq, Muhammad; Rasool, Akhtar; Hebert, Paul D. N.

    2016-01-01

    Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5ʹ (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips. PMID:26741134

  11. DNA barcoding Australia's fish species

    PubMed Central

    Ward, Robert D; Zemlak, Tyler S; Innes, Bronwyn H; Last, Peter R; Hebert, Paul D.N

    2005-01-01

    Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus—were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species. PMID:16214743

  12. The basics of 2D DIGE.

    PubMed

    Beckett, Phil

    2012-01-01

    The technique of two-dimensional (2D) gel electrophoresis is a powerful tool for separating complex mixtures of proteins, but since its inception in the mid 1970s, it acquired the stigma of being a very difficult application to master and was generally used to its best effect by experts. The introduction of commercially available immobilized pH gradients in the early 1990s provided enhanced reproducibility and easier protocols, leading to a pronounced increase in popularity of the technique. However gel-to-gel variation was still difficult to control without the use of technical replicates. In the mid 1990s (at the same time as the birth of "proteomics"), the concept of multiplexing fluorescently labeled proteins for 2D gel separation was realized by Jon Minden's group and has led to the ability to design experiments to virtually eliminate gel-to-gel variation, resulting in biological replicates being used for statistical analysis with the ability to detect very small changes in relative protein abundance. This technology is referred to as 2D difference gel electrophoresis (2D DIGE).

  13. Determination of phosphine and other fumigants in air samples by thermal desorption and 2D heart-cutting gas chromatography with synchronous SIM/Scan mass spectrometry and flame photometric detection.

    PubMed

    Fahrenholtz, Svea; Hühnerfuss, Heinrich; Baur, Xaver; Budnik, Lygia Therese

    2010-12-24

    Fumigants and volatile industrial chemicals are particularly hazardous to health when a freight container is fumigated or the contaminated material is introduced into its enclosed environment. Phosphine is now increasingly used as a fumigant, after bromomethane--the former fumigant of choice--has been banned by the Montreal Protocol. We have enhanced our previously established thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) method by integrating a second gas chromatographic dimension and a flame photometric detector to allow the simultaneous detection of phosphine and volatile organic compounds (VOCs), providing a novel application. A thermal desorption system is coupled to a two dimensional gas chromatograph using both mass spectrometric and flame photometric detection (TD-2D-GC-MS/FPD). Additionally, the collection of mass spectrometric SIM and Scan data has been synchronised, so only a single analysis is now sufficient for qualitative scanning of the whole sample and for sensitive quantification. Though detection limits for the herewith described method are slightly higher than in the previous method, they are in the low μL m(-3) range, which is not only below the respective occupational exposure and intervention limits but also allows the detection of residual contamination after ventilation. The method was developed for the separation and identification of 44 volatile substances. For 12 of these compounds (bromomethane, iodomethane, dichloromethane, 1,2-dichlorethane, benzene, tetrachloromethane, 1,2-dichloropropane, toluene, trichloronitromethane, ethyl benzene, phosphine, carbon disulfide) the method was validated as we chose the target compounds due to their relevance in freight container handling.

  14. Barcoding the food chain: from Sanger to high-throughput sequencing.

    PubMed

    Littlefair, Joanne E; Clare, Elizabeth L

    2016-11-01

    Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace "environmental DNA", and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.

  15. Self-healing encapsulation strategy for preparing highly stable, functionalized quantum-dot barcodes.

    PubMed

    Song, Tao; Liu, Junqing; Li, Wenbin; Li, Yunhong; Yang, Qiuhua; Gong, Xiaoqun; Xuan, Lixue; Chang, Jin

    2014-02-26

    Quantum dot (QD) barcodes are becoming an urgent requirement for researchers and clinicians to obtain high-density information in multiplexed suspension (bead-based) assay. However, how to improve the stability of quantum dot barcodes is a longstanding issue. Here, we present a new self-healing encapsulation strategy to generate functionalized uniform quantum dots barcodes with high physical and chemical stability. This efficient and facile strategy could make porous polymer microspheres self-heal to encapsulate QDs via the thermal motion and interaction of the molecular chains. Consequently, the new strategy solved especially the QDs leakage problem and improved the chemical stability under different pH physiological conditions as well as the longtime storage stability. In the meantime, the encoding capacity and the spatial distribution uniformity of quantum dots could be also improved. Furthermore, immunofluorescence assays for alpha fetoprotein (AFP) detections indicated that carboxyl groups on the surface of QD-encoded microspheres could facilitate efficient attachment of biomacromolecules.

  16. DNA Barcoding and Molecular Phylogeny of Drosophila lini and Its Sibling Species.

    PubMed

    Li, Yi-Feng; Wen, Shuo-Yang; Kawai, Kuniko; Gao, Jian-Jun; Hu, Yao-Guang; Segawa, Ryoko; Toda, Masanori J

    2012-01-01

    Drosophila lini and its two sibling species, D. ohnishii and D. ogumai, are hardly distinguishable from one another in morphology. These species are more or less reproductively isolated. The mitochondrial ND2 and COI-COII and the nuclear ITS1-ITS2 regions were sequenced to seek for the possibility of DNA barcoding and to reconstruct the phylogeny of them. The character-based approach for DNA barcoding detected some diagnostic nucleotides only for monophyletic D. ogumai, but no informative sites for the other two very closely species, D. lini and D. ohnishii, of which strains intermingled in the molecular phylogenetic trees. Thus, this study provides another case of limited applicability of DNA barcoding in species delineation, as in other cases of related Drosophila species. The molecular phylogenetic tree inferred from the concatenated sequences strongly supported the monophyly of the cluster of the three species, that is, the lini clade. We propose some hypotheses of evolutionary events in this clade.

  17. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  18. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  19. Quality Traceability System of Traditional Chinese Medicine Based on Two Dimensional Barcode Using Mobile Intelligent Technology

    PubMed Central

    Cai, Yong; Li, Xiwen; Wang, Runmiao; Yang, Qing; Li, Peng; Hu, Hao

    2016-01-01

    Currently, the chemical fingerprint comparison and analysis is mainly based on professional equipment and software, it’s expensive and inconvenient. This study aims to integrate QR (Quick Response) code with quality data and mobile intelligent technology to develop a convenient query terminal for tracing quality in the whole industrial chain of TCM (traditional Chinese medicine). Three herbal medicines were randomly selected and their chemical two-dimensional barcode (2D) barcodes fingerprints were constructed. Smartphone application (APP) based on Android system was developed to read initial data of 2D chemical barcodes, and compared multiple fingerprints from different batches of same species or different species. It was demonstrated that there were no significant differences between original and scanned TCM chemical fingerprints. Meanwhile, different TCM chemical fingerprint QR codes could be rendered in the same coordinate and showed the differences very intuitively. To be able to distinguish the variations of chemical fingerprint more directly, linear interpolation angle cosine similarity algorithm (LIACSA) was proposed to get similarity ratio. This study showed that QR codes can be used as an effective information carrier to transfer quality data. Smartphone application can rapidly read quality information in QR codes and convert data into TCM chemical fingerprints. PMID:27780256

  20. Quality Traceability System of Traditional Chinese Medicine Based on Two Dimensional Barcode Using Mobile Intelligent Technology.

    PubMed

    Cai, Yong; Li, Xiwen; Wang, Runmiao; Yang, Qing; Li, Peng; Hu, Hao

    2016-01-01

    Currently, the chemical fingerprint comparison and analysis is mainly based on professional equipment and software, it's expensive and inconvenient. This study aims to integrate QR (Quick Response) code with quality data and mobile intelligent technology to develop a convenient query terminal for tracing quality in the whole industrial chain of TCM (traditional Chinese medicine). Three herbal medicines were randomly selected and their chemical two-dimensional barcode (2D) barcodes fingerprints were constructed. Smartphone application (APP) based on Android system was developed to read initial data of 2D chemical barcodes, and compared multiple fingerprints from different batches of same species or different species. It was demonstrated that there were no significant differences between original and scanned TCM chemical fingerprints. Meanwhile, different TCM chemical fingerprint QR codes could be rendered in the same coordinate and showed the differences very intuitively. To be able to distinguish the variations of chemical fingerprint more directly, linear interpolation angle cosine similarity algorithm (LIACSA) was proposed to get similarity ratio. This study showed that QR codes can be used as an effective information carrier to transfer quality data. Smartphone application can rapidly read quality information in QR codes and convert data into TCM chemical fingerprints.

  1. Highly crystalline 2D superconductors

    NASA Astrophysics Data System (ADS)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-12-01

    Recent advances in materials fabrication have enabled the manufacturing of ordered 2D electron systems, such as heterogeneous interfaces, atomic layers grown by molecular beam epitaxy, exfoliated thin flakes and field-effect devices. These 2D electron systems are highly crystalline, and some of them, despite their single-layer thickness, exhibit a sheet resistance more than an order of magnitude lower than that of conventional amorphous or granular thin films. In this Review, we explore recent developments in the field of highly crystalline 2D superconductors and highlight the unprecedented physical properties of these systems. In particular, we explore the quantum metallic state (or possible metallic ground state), the quantum Griffiths phase observed in out-of-plane magnetic fields and the superconducting state maintained in anomalously large in-plane magnetic fields. These phenomena are examined in the context of weakened disorder and/or broken spatial inversion symmetry. We conclude with a discussion of how these unconventional properties make highly crystalline 2D systems promising platforms for the exploration of new quantum physics and high-temperature superconductors.

  2. Extensions of 2D gravity

    SciTech Connect

    Sevrin, A.

    1993-06-01

    After reviewing some aspects of gravity in two dimensions, I show that non-trivial embeddings of sl(2) in a semi-simple (super) Lie algebra give rise to a very large class of extensions of 2D gravity. The induced action is constructed as a gauged WZW model and an exact expression for the effective action is given.

  3. Fluorine detected 2D NMR experiments for the practical determination of size and sign of homonuclear F-F and heteronuclear C-F multiple bond J-coupling constants in multiple fluorinated compounds.

    PubMed

    Aspers, Ruud L E G; Ampt, Kirsten A M; Dvortsak, Peter; Jaeger, Martin; Wijmenga, Sybren S

    2013-06-01

    The use of fluorine in molecules obtained from chemical synthesis has become increasingly important within the pharmaceutical and agricultural industry. NMR characterization of these compounds is of great value with respect to their structure elucidation, their screening in metabolomics investigations and binding studies. The favorable NMR properties of the fluorine nucleus make NMR with fluorine detection of great value in this respect. A suite of NMR 2D F-F- and F-C-correlation experiments with fluorine detection was applied to the assignment of resonances, (n)J(CF)- and (n)J(FF)-couplings as well as the determination of their size and sign. The utilization of this experiment suite was exemplarily demonstrated for a highly fluorinated vinyl alkyl ether. Especially F-C HSQC and J-scaled F-C HMBC experiments allowed determining the size of the J-couplings of this compound. The relative sign of its homo- and heteronuclear couplings was achieved by different combinations of 2D NMR experiments, including non-selective and F2-selective F-C XLOC, F2-selective F-C HMQC, and F-F COSY. The F2-one/two-site selective F-C XLOC versions were found highly useful, as they led to simplifications of the common E.COSY patterns and resulted in a higher confidence level of the assignment by using selective excitation. The combination of F2-one/two-site selective F-C XLOC experiments with a F2-one-site selective F-C HMQC experiment provided the signs of all (n)J(CF)- and (n)J(FF)-couplings in the vinyl moiety of the test compound. Other combinations of experiments were found useful as well for special purposes when focusing for example on homonuclear couplings a combination of F-F COSY-10 with a F2-one-site selective F-C HMQC could be used. The E.COSY patterns in the spectra demonstrated were analyzed by use of the spin-selective displacement vectors, and in case of the XLOC also by use of the DQ- and ZQ-displacement vectors. The variety of experiments presented shall contribute to

  4. Generating barcoded libraries for multiplex high-throughput sequencing.

    PubMed

    Knapp, Michael; Stiller, Mathias; Meyer, Matthias

    2012-01-01

    Molecular barcoding is an essential tool to use the high throughput of next generation sequencing platforms optimally in studies involving more than one sample. Various barcoding strategies allow for the incorporation of short recognition sequences (barcodes) into sequencing libraries, either by ligation or polymerase chain reaction (PCR). Here, we present two approaches optimized for generating barcoded sequencing libraries from low copy number extracts and amplification products typical of ancient DNA studies.

  5. QR Codes in the Library: "It's Not Your Mother's Barcode!"

    ERIC Educational Resources Information Center

    Dobbs, Cheri

    2011-01-01

    Barcode scanning has become more than just fun. Now libraries and businesses are leveraging barcode technology as an innovative tool to market their products and ideas. Developed and popularized in Japan, these Quick Response (QR) or two-dimensional barcodes allow marketers to provide interactive content in an otherwise static environment. In this…

  6. VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

    PubMed

    Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

    2014-07-01

    Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

  7. Establishing a community-wide DNA barcode library as a new tool for arctic research.

    PubMed

    Wirta, H; Várkonyi, G; Rasmussen, C; Kaartinen, R; Schmidt, N M; Hebert, P D N; Barták, M; Blagoev, G; Disney, H; Ertl, S; Gjelstrup, P; Gwiazdowicz, D J; Huldén, L; Ilmonen, J; Jakovlev, J; Jaschhof, M; Kahanpää, J; Kankaanpää, T; Krogh, P H; Labbee, R; Lettner, C; Michelsen, V; Nielsen, S A; Nielsen, T R; Paasivirta, L; Pedersen, S; Pohjoismäki, J; Salmela, J; Vilkamaa, P; Väre, H; von Tschirnhaus, M; Roslin, T

    2016-05-01

    DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.

  8. DNA barcoding of recently diverged species: relative performance of matching methods.

    PubMed

    van Velzen, Robin; Weitschek, Emanuel; Felici, Giovanni; Bakker, Freek T

    2012-01-01

    Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.

  9. Biological identifications through DNA barcodes.

    PubMed Central

    Hebert, Paul D N; Cywinska, Alina; Ball, Shelley L; deWaard, Jeremy R

    2003-01-01

    Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution. PMID:12614582

  10. 2D vs. 3D mammography observer study

    NASA Astrophysics Data System (ADS)

    Fernandez, James Reza F.; Hovanessian-Larsen, Linda; Liu, Brent

    2011-03-01

    Breast cancer is the most common type of non-skin cancer in women. 2D mammography is a screening tool to aid in the early detection of breast cancer, but has diagnostic limitations of overlapping tissues, especially in dense breasts. 3D mammography has the potential to improve detection outcomes by increasing specificity, and a new 3D screening tool with a 3D display for mammography aims to improve performance and efficiency as compared to 2D mammography. An observer study using a mammography phantom was performed to compare traditional 2D mammography with this ne 3D mammography technique. In comparing 3D and 2D mammography there was no difference in calcification detection, and mass detection was better in 2D as compared to 3D. There was a significant decrease in reading time for masses, calcifications, and normals in 3D compared to 2D, however, as well as more favorable confidence levels in reading normal cases. Given the limitations of the mammography phantom used, however, a clearer picture in comparing 3D and 2D mammography may be better acquired with the incorporation of human studies in the future.

  11. DNA barcodes for ecology, evolution, and conservation.

    PubMed

    Kress, W John; García-Robledo, Carlos; Uriarte, Maria; Erickson, David L

    2015-01-01

    The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed.

  12. Dual resolution two-dimensional color barcode

    NASA Astrophysics Data System (ADS)

    Fan, Zhigang; Zhao, Yonghui; Wang, Shenge; Ding, Hengzhou

    2013-03-01

    In this paper, a QR code is presented with a dual resolution structure. It contains a high resolution layer that is coded in luminance and is in consistency with the conventional QR code, and a low resolution layer providing additional error checking information, that is coded in chrominance and is robust to blurring. The proposed QR code is compatible to its underlying conventional black and white barcode as it can be read by their decoders. Its advantage is additional reliability when a color decoder is used. In particular, it enhances the decoding accuracy for devices such as mobile devices for barcodes printed in small sizes.

  13. Direct Reading of Bona Fide Barcode Assays for Diagnostics with Smartphone Apps

    PubMed Central

    Wong, Jessica X. H.; Li, Xiaochun; Liu, Frank S. F.; Yu, Hua-Zhong

    2015-01-01

    The desire to develop new point-of-care (POC) diagnostic tools has led to the adaptation of smartphones to tackle limitations in state-of-the-art instrumentation and centralized laboratory facilities. Today’s smartphones possess the computer-like ability to image and process data using mobile apps; barcode scanners are one such type of apps. We demonstrate herein that a diagnostic assay can be performed by patterning immunoassay strips in a bona fide barcode format such that after target binding and signal enhancement, the linear barcode can be read directly with a standard smartphone app. Quantitative analysis can then be performed based on the grayscale intensities with a customized mobile app. This novel diagnostic concept has been validated for a real-world application, i.e., the detection of human chorionic gonadotropin, a pregnancy hormone. With the possibility of multiplex detection, the barcode assay protocol promises to boost POC diagnosis research by the direct adaptation of mobile devices and apps. PMID:26122608

  14. Direct Reading of Bona Fide Barcode Assays for Diagnostics with Smartphone Apps

    NASA Astrophysics Data System (ADS)

    Wong, Jessica X. H.; Li, Xiaochun; Liu, Frank S. F.; Yu, Hua-Zhong

    2015-06-01

    The desire to develop new point-of-care (POC) diagnostic tools has led to the adaptation of smartphones to tackle limitations in state-of-the-art instrumentation and centralized laboratory facilities. Today’s smartphones possess the computer-like ability to image and process data using mobile apps; barcode scanners are one such type of apps. We demonstrate herein that a diagnostic assay can be performed by patterning immunoassay strips in a bona fide barcode format such that after target binding and signal enhancement, the linear barcode can be read directly with a standard smartphone app. Quantitative analysis can then be performed based on the grayscale intensities with a customized mobile app. This novel diagnostic concept has been validated for a real-world application, i.e., the detection of human chorionic gonadotropin, a pregnancy hormone. With the possibility of multiplex detection, the barcode assay protocol promises to boost POC diagnosis research by the direct adaptation of mobile devices and apps.

  15. Constructing DNA Barcode Sets based on Particle Swarm Optimization.

    PubMed

    Waang, Bin; Zheng, Xuedong; Zhou, Shihua; Zhou, Changjun; Wei, Xiaopeng; Zhang, Qiang; Wei, Ziqi

    2017-03-07

    Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.

  16. Assessment of snake DNA barcodes based on mitochondrial COI and Cytb genes revealed multiple putative cryptic species in Thailand.

    PubMed

    Laopichienpong, Nararat; Muangmai, Narongrit; Supikamolseni, Arrjaree; Twilprawat, Panupon; Chanhome, Lawan; Suntrarachun, Sunutcha; Peyachoknagul, Surin; Srikulnath, Kornsorn

    2016-12-15

    DNA barcodes of mitochondrial cytochrome c oxidase I (COI), cytochrome b (Cytb) genes, and their combined data sets were constructed from 35 snake species in Thailand. No barcoding gap was detected in either of the two genes from the observed intra- and interspecific sequence divergences. Intra- and interspecific sequence divergences of the COI gene differed 14 times, with barcode cut-off scores ranging over 2%-4% for threshold values differentiated among most of the different species; the Cytb gene differed 6 times with cut-off scores ranging over 2%-6%. Thirty-five specific nucleotide mutations were also found at interspecific level in the COI gene, identifying 18 snake species, but no specific nucleotide mutation was observed for Cytb in any single species. This suggests that COI barcoding was a better marker than Cytb. Phylogenetic clustering analysis indicated that most species were represented by monophyletic clusters, suggesting that these snake species could be clearly differentiated using COI barcodes. However, the two-marker combination of both COI and Cytb was more effective, differentiating snake species by over 2%-4%, and reducing species numbers in the overlap value between intra- and interspecific divergences. Three species delimitation algorithms (general mixed Yule-coalescent, automatic barcoding gap detection, and statistical parsimony network analysis) were extensively applied to a wide range of snakes based on both barcodes. This revealed cryptic diversity for eleven snake species in Thailand. In addition, eleven accessions from the database previously grouped under the same species were represented at different species level, suggesting either high genetic diversity, or the misidentification of these sequences in the database as a consequence of cryptic species.

  17. Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north-eastern part of the Congo basin.

    PubMed

    Decru, Eva; Moelants, Tuur; De Gelas, Koen; Vreven, Emmanuel; Verheyen, Erik; Snoeks, Jos

    2016-01-01

    This study evaluates the utility of DNA barcoding to traditional morphology-based species identifications for the fish fauna of the north-eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio 'nearest-neighbour distance/maximum intraspecific divergence' was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.

  18. DNA BARCODING: CO1 DNA barcoding amphibians: take the chance, meet the challenge.

    PubMed

    Smith, M Alex; Poyarkov, Nikolai A; Hebert, Paul D N

    2008-03-01

    Although a mitochondrial DNA barcode has been shown to be of great utility for species identification and discovery in an increasing number of diverse taxa, caution has been urged with its application to one of the most taxonomically diverse vertebrate groups - the amphibians. Here, we test three of the perceived shortcomings of a CO1 DNA barcode's utility with a group of Holarctic amphibians: primer fit, sequence variability and overlapping intra- and interspecific variability. We found that although the CO1 DNA barcode priming regions were variable, we were able to reliably amplify a CO1 fragment from degenerate primers and primers with G-C residues at the 3' end. Any overlap between intra- and interspecific variation in our taxonomic sampling was due to introgressive hybridization (Bufo/Anaxyrus), complex genetics (Ambystoma) or incomplete taxonomy (Triturus). Rates of hybridization and species discovery are not expected to be greater for amphibians than for other vertebrate groups, and thus problems with the utility of using a single mitochondrial gene for species identification will not be specific to amphibians. Therefore, we conclude that there is greater potential for a CO1 barcode's use with amphibians than has been reported to date. A large-scale effort to barcode the amphibians of the world, using the same primary barcode region of CO1, will yield important findings for science and conservation.

  19. Regulation of ligands for the NKG2D activating receptor

    PubMed Central

    Raulet, David H.; Gasser, Stephan; Gowen, Benjamin G.; Deng, Weiwen; Jung, Heiyoun

    2014-01-01

    NKG2D is an activating receptor expressed by all NK cells and subsets of T cells. It serves as a major recognition receptor for detection and elimination of transformed and infected cells and participates in the genesis of several inflammatory diseases. The ligands for NKG2D are self-proteins that are induced by pathways that are active in certain pathophysiological states. NKG2D ligands are regulated transcriptionally, at the level of mRNA and protein stability, and by cleavage from the cell surface. In some cases, ligand induction can be attributed to pathways that are activated specifically in cancer cells or infected cells. We review the numerous pathways that have been implicated in the regulation of NKG2D ligands, discuss the pathologic states in which those pathways are likely to act, and attempt to synthesize the findings into general schemes of NKG2D ligand regulation in NK cell responses to cancer and infection. PMID:23298206

  20. 2D quasiperiodic plasmonic crystals

    PubMed Central

    Bauer, Christina; Kobiela, Georg; Giessen, Harald

    2012-01-01

    Nanophotonic structures with irregular symmetry, such as quasiperiodic plasmonic crystals, have gained an increasing amount of attention, in particular as potential candidates to enhance the absorption of solar cells in an angular insensitive fashion. To examine the photonic bandstructure of such systems that determines their optical properties, it is necessary to measure and model normal and oblique light interaction with plasmonic crystals. We determine the different propagation vectors and consider the interaction of all possible waveguide modes and particle plasmons in a 2D metallic photonic quasicrystal, in conjunction with the dispersion relations of a slab waveguide. Using a Fano model, we calculate the optical properties for normal and inclined light incidence. Comparing measurements of a quasiperiodic lattice to the modelled spectra for angle of incidence variation in both azimuthal and polar direction of the sample gives excellent agreement and confirms the predictive power of our model. PMID:23209871

  1. Valleytronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Schaibley, John R.; Yu, Hongyi; Clark, Genevieve; Rivera, Pasqual; Ross, Jason S.; Seyler, Kyle L.; Yao, Wang; Xu, Xiaodong

    2016-11-01

    Semiconductor technology is currently based on the manipulation of electronic charge; however, electrons have additional degrees of freedom, such as spin and valley, that can be used to encode and process information. Over the past several decades, there has been significant progress in manipulating electron spin for semiconductor spintronic devices, motivated by potential spin-based information processing and storage applications. However, experimental progress towards manipulating the valley degree of freedom for potential valleytronic devices has been limited until very recently. We review the latest advances in valleytronics, which have largely been enabled by the isolation of 2D materials (such as graphene and semiconducting transition metal dichalcogenides) that host an easily accessible electronic valley degree of freedom, allowing for dynamic control.

  2. Unparticle example in 2D.

    PubMed

    Georgi, Howard; Kats, Yevgeny

    2008-09-26

    We discuss what can be learned about unparticle physics by studying simple quantum field theories in one space and one time dimension. We argue that the exactly soluble 2D theory of a massless fermion coupled to a massive vector boson, the Sommerfield model, is an interesting analog of a Banks-Zaks model, approaching a free theory at high energies and a scale-invariant theory with nontrivial anomalous dimensions at low energies. We construct a toy standard model coupling to the fermions in the Sommerfield model and study how the transition from unparticle behavior at low energies to free particle behavior at high energies manifests itself in interactions with the toy standard model particles.

  3. 77 FR 33314 - POSTNET Barcode Discontinuation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-06

    ... Periodicals automation letters and flats) that were inadvertently omitted in the original final rule, but does... and allow only Intelligent Mail barcodes (IMbs) for automation price eligibility purposes, including... January 28, 2013, the use of the IMb will be required for all automation letters, including Business...

  4. 77 FR 26185 - POSTNET Barcode Discontinuation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-03

    ... Mailpiece * * * * * 3.0 Placement and Content of Mail Markings * * * * * 3.5 Exceptions to Markings Exceptions are as follows: a. Automation letters. Automation letters do not require an ``AUTO'' marking if... obscure the address, barcode, postage, and any marking or endorsement applied to the piece when it...

  5. DNA Barcoding in Fragaria L. (Strawberry) Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA barcoding for species identification using a short DNA sequence has been successful in animals due to rapid mutation rates of the mitochondrial genome where the animal DNA barocode, cytochrome c oxidase 1 gene is located. The chloroplast PsbA-trnH spacer and the nuclear ribosomal internal transc...

  6. Universal COI primers for DNA barcoding amphibians.

    PubMed

    Che, Jing; Chen, Hong-Man; Yang, Jun-Xiao; Jin, Jie-Qiong; Jiang, Ke; Yuan, Zhi-Yong; Murphy, Robert W; Zhang, Ya-Ping

    2012-03-01

    DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.

  7. Quantum coherence selective 2D Raman–2D electronic spectroscopy

    PubMed Central

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-01-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational–vibrational, electronic–vibrational and electronic–electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment–protein complexes. PMID:28281541

  8. Quantum coherence selective 2D Raman-2D electronic spectroscopy

    NASA Astrophysics Data System (ADS)

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-03-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  9. Quantum coherence selective 2D Raman-2D electronic spectroscopy.

    PubMed

    Spencer, Austin P; Hutson, William O; Harel, Elad

    2017-03-10

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  10. Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes.

    PubMed

    Oliveira, L M; Knebelsberger, T; Landi, M; Soares, P; Raupach, M J; Costa, F O

    2016-12-01

    A large-scale comprehensive reference library of DNA barcodes for European marine fishes was assembled, allowing the evaluation of taxonomic uncertainties and species genetic diversity that were otherwise hidden in geographically restricted studies. A total of 4118 DNA barcodes were assigned to 358 species generating 366 Barcode Index Numbers (BIN). Initial examination revealed as much as 141 BIN discordances (more than one species in each BIN). After implementing an auditing and five-grade (A-E) annotation protocol, the number of discordant species BINs was reduced to 44 (13% grade E), while concordant species BINs amounted to 271 (78% grades A and B) and 14 other had insufficient data (grade D). Fifteen species displayed comparatively high intraspecific divergences ranging from 2·6 to 18·5% (grade C), which is biologically paramount information to be considered in fish species monitoring and stock assessment. On balance, this compilation contributed to the detection of 59 European fish species probably in need of taxonomic clarification or re-evaluation. The generalized implementation of an auditing and annotation protocol for reference libraries of DNA barcodes is recommended.

  11. Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology.

    PubMed

    Cao, Xiaowei; Liu, Jie; Chen, Jian; Zheng, Guo; Kuntner, Matjaž; Agnarsson, Ingi

    2016-12-19

    The taxonomic impediment is characterized by dwindling classical taxonomic expertise, and slow pace of revisionary work, thus more rapid taxonomic assessments are needed. Here we pair rapid DNA barcoding methods with swift assessment of morphology in an effort to gauge diversity, establish species limits, and rapidly disseminate taxonomic information prior to completion of formal taxonomic revisions. We focus on a poorly studied, but diverse spider genus, Pseudopoda, from East Asia. We augmented the standard barcoding locus (COI) with nuclear DNA sequence data (ITS2) and analyzed congruence among datasets and species delimitation methods for a total of 572 individuals representing 23 described species and many potentially new species. Our results suggest that a combination of CO1 + ITS2 fragments identify and diagnose species better than the mitochondrial barcodes alone, and that certain tree based methods yield considerably higher diversity estimates than the distance-based approaches and morphology. Combined, through an extensive field survey, we detect a twofold increase in species diversity in the surveyed area, at 42-45, with most species representing short range endemics. Our study demonstrates the power of biodiversity assessments and swift dissemination of taxonomic data through rapid inventory, and through a combination of morphological and multi-locus DNA barcoding diagnoses of diverse arthropod lineages.

  12. Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology

    PubMed Central

    Cao, Xiaowei; Liu, Jie; Chen, Jian; Zheng, Guo; Kuntner, Matjaž; Agnarsson, Ingi

    2016-01-01

    The taxonomic impediment is characterized by dwindling classical taxonomic expertise, and slow pace of revisionary work, thus more rapid taxonomic assessments are needed. Here we pair rapid DNA barcoding methods with swift assessment of morphology in an effort to gauge diversity, establish species limits, and rapidly disseminate taxonomic information prior to completion of formal taxonomic revisions. We focus on a poorly studied, but diverse spider genus, Pseudopoda, from East Asia. We augmented the standard barcoding locus (COI) with nuclear DNA sequence data (ITS2) and analyzed congruence among datasets and species delimitation methods for a total of 572 individuals representing 23 described species and many potentially new species. Our results suggest that a combination of CO1 + ITS2 fragments identify and diagnose species better than the mitochondrial barcodes alone, and that certain tree based methods yield considerably higher diversity estimates than the distance-based approaches and morphology. Combined, through an extensive field survey, we detect a twofold increase in species diversity in the surveyed area, at 42–45, with most species representing short range endemics. Our study demonstrates the power of biodiversity assessments and swift dissemination of taxonomic data through rapid inventory, and through a combination of morphological and multi-locus DNA barcoding diagnoses of diverse arthropod lineages. PMID:27991489

  13. Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

    PubMed

    Gu, Liangcai; Li, Chao; Aach, John; Hill, David E; Vidal, Marc; Church, George M

    2014-11-27

    In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.

  14. The campaign to DNA barcode all fishes, FISH-BOL.

    PubMed

    Ward, R D; Hanner, R; Hebert, P D N

    2009-02-01

    FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.

  15. DNA barcoding of Orchidaceae in Korea.

    PubMed

    Kim, Hye Min; Oh, Sang-Hun; Bhandari, Gauri Shankar; Kim, Chan-Soo; Park, Chong-Wook

    2014-05-01

    Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK-psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF-atpH IGS (0.0648), trnH-psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH-psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.

  16. DNA Barcoding Bromeliaceae: Achievements and Pitfalls

    PubMed Central

    Franco, Luciana Ozório; Cardoso, Mônica Aires; Cardoso, Sérgio Ricardo Sodré; Hemerly, Adriana Silva; Ferreira, Paulo Cavalcanti Gomes

    2012-01-01

    Background DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost. Methodology/Principal Findings It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH–psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling. Conclusions/Significance Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these

  17. Aspergillus and Penicillium identification using DNA sequences: barcode or MLST?

    PubMed

    Peterson, Stephen W

    2012-07-01

    Current methods in DNA technology can detect single nucleotide polymorphisms with measurable accuracy using several different approaches appropriate for different uses. If there are even single nucleotide differences that are invariant markers of the species, we can accomplish identification through rapid DNA-based tests. The question of whether we can reliably detect and identify species of Aspergillus and Penicillium turns mainly upon the completeness of our alpha taxonomy, our species concepts, and how well the available DNA data coincide with the taxonomic diversity in the family Trichocomaceae. No single gene is yet known that is invariant within species and variable between species as would be optimal for the barcode approach. Data are published that would make an MLST approach to isolate identification possible in the most well-studied clades of Aspergillus and Penicillium.

  18. Double resonance rotational spectroscopy of CH2D+

    NASA Astrophysics Data System (ADS)

    Töpfer, Matthias; Jusko, Pavol; Schlemmer, Stephan; Asvany, Oskar

    2016-09-01

    Context. Deuterated forms of CH are thought to be responsible for deuterium enrichment in lukewarm astronomical environments. There is no unambiguous detection of CH2D+ in space to date. Aims: Four submillimetre rotational lines of CH2D+ are documented in the literature. Our aim is to present a complete dataset of highly resolved rotational lines, including millimetre (mm) lines needed for a potential detection. Methods: We used a low-temperature ion trap and applied a novel IR-mm-wave double resonance method to measure the rotational lines of CH2D+. Results: We measured 21 low-lying (J ≤ 4) rotational transitions of CH2D+ between 23 GHz and 1.1 THz with accuracies close to 2 ppb.

  19. Barcoding, types and the Hirudo files: using information content to critically evaluate the identity of DNA barcodes.

    PubMed

    Kvist, Sebastian; Oceguera-Figueroa, Alejandro; Siddall, Mark E; Erséus, Christer

    2010-12-01

    Species identifications based on DNA barcoding rely on the correct identity of previously barcoded specimens, but little attention has been given to whether deposited barcodes include correspondence to the species' name-bearing type. The information content associated with COX1 sequences in the two most commonly used repositories of barcodes, GenBank and the Barcode of Life Data System (BOLD), is often insufficient for subsequent evaluation of the robustness of the identification procedure. We argue that DNA barcoding and taxonomy alike will benefit from more information content in the annotations of barcoded specimens as this will allow for validation and re-evaluation of the initial specimen identification. The aim should be to closely connect specimens from which reference barcodes are generated with the holotype through straight-forward taxonomy, and geographical and genetic correlations. Annotated information should also include voucher specimens and collector/identifier information. We examine two case studies based on empirical data, in which barcoding and taxonomy benefit from increased information content. On the basis of data from the first case study, we designate a barcoded neotype of the European medicinal leech, Hirudo medicinalis, on morphological and geographical grounds.

  20. NKG2D receptor and its ligands in host defense

    PubMed Central

    Lanier, Lewis L.

    2015-01-01

    NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8+ T cells, and subsets of CD4+ T cells, iNKT cells, and γδ T cells. In humans NKG2D transmits signals by its association with the DAP10 adapter subunit and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least 8 genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and post-translation. In general healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyper-proliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves a mechanism for the immune system to detect and eliminate cells that have undergone “stress”. Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases. PMID:26041808

  1. NKG2D Receptor and Its Ligands in Host Defense.

    PubMed

    Lanier, Lewis L

    2015-06-01

    NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8(+) T cells, and subsets of CD4(+) T cells, invariant NKT cells (iNKT), and γδ T cells. In humans, NKG2D transmits signals by its association with the DAP10 adapter subunit, and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least eight genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and posttranslation. In general, healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyperproliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves as a mechanism for the immune system to detect and eliminate cells that have undergone "stress." Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system, and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases.

  2. Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau

    PubMed Central

    Jin, Qian; Han, Huilin; Hu, XiMin; Li, XinHai; Zhu, ChaoDong; Ho, Simon Y. W.; Ward, Robert D.; Zhang, Ai-bing

    2013-01-01

    With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of , which is about four times larger than the mean intraspecific distance (). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau. PMID:23741330

  3. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago

    PubMed Central

    Simó-Riudalbas, Marc; Sindaco, Roberto; Santos, Xavier; Fasola, Mauro; Llorente, Gustavo; Razzetti, Edoardo; Carranza, Salvador

    2016-01-01

    Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra’s most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8–54.4%. This has implications in the species’ ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework. PMID:26930572

  4. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago.

    PubMed

    Vasconcelos, Raquel; Montero-Mendieta, Santiago; Simó-Riudalbas, Marc; Sindaco, Roberto; Santos, Xavier; Fasola, Mauro; Llorente, Gustavo; Razzetti, Edoardo; Carranza, Salvador

    2016-01-01

    Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.

  5. Character-based DNA barcoding: a superior tool for species classification.

    PubMed

    Bergmann, Tjard; Hadrys, Heike; Breves, Gerhard; Schierwater, Bernd

    2009-01-01

    In zoonosis research only correct assigned host-agent-vector associations can lead to success. If most biological species on Earth, from agent to host and from procaryotes to vertebrates, are still undetected, the development of a reliable and universal diversity detection tool becomes a conditio sine qua non. In this context, in breathtaking speed, modern molecular-genetic techniques have become acknowledged tools for the classification of life forms at all taxonomic levels. While previous DNA-barcoding techniques were criticised for several reasons (Moritz and Cicero, 2004; Rubinoff et al., 2006a, b; Rubinoff, 2006; Rubinoff and Haines, 2006) a new approach, the so called CAOS-barcoding (Character Attribute Organisation System), avoids most of the weak points. Traditional DNA-barcoding approaches are based on distances, i. e. they use genetic distances and tree construction algorithms for the classification of species or lineages. The definition of limit values is enforced and prohibits a discrete or clear assignment. In comparison, the new character-based barcoding (CAOS-barcoding; DeSalle et al., 2005; DeSalle, 2006; Rach et al., 2008) works with discrete single characters and character combinations which permits a clear, unambiguous classification. In Hannover (Germany) we are optimising this system and developing a semiautomatic high-throughput procedure for hosts, agents and vectors being studied within the Zoonosis Centre of the "Stiftung Tierärztliche Hochschule Hannover". Our primary research is concentrated on insects, the most successful and species-rich animal group on Earth (every fourth animal is a bug). One subgroup, the winged insects (Pterygota), represents the outstanding majority of all zoonosis relevant animal vectors.

  6. A DNA mini-barcode for land plants.

    PubMed

    Little, Damon P

    2014-05-01

    Small portions of the barcode region - mini-barcodes - may be used in place of full-length barcodes to overcome DNA degradation for samples with poor DNA preservation. 591,491,286 rbcL mini-barcode primer combinations were electronically evaluated for PCR universality, and two novel highly universal sets of priming sites were identified. Novel and published rbcL mini-barcode primers were evaluated for PCR amplification [determined with a validated electronic simulation (n = 2765) and empirically (n = 188)], Sanger sequence quality [determined empirically (n = 188)], and taxonomic discrimination [determined empirically (n = 30,472)]. PCR amplification for all mini-barcodes, as estimated by validated electronic simulation, was successful for 90.2-99.8% of species. Overall Sanger sequence quality for mini-barcodes was very low - the best mini-barcode tested produced sequences of adequate quality (B20 ≥ 0.5) for 74.5% of samples. The majority of mini-barcodes provide correct identifications of families in excess of 70.1% of the time. Discriminatory power noticeably decreased at lower taxonomic levels. At the species level, the discriminatory power of the best mini-barcode was less than 38.2%. For samples believed to contain DNA from only one species, an investigator should attempt to sequence, in decreasing order of utility and probability of success, mini-barcodes F (rbcL1/rbcLB), D (F52/R193) and K (F517/R604). For samples believed to contain DNA from more than one species, an investigator should amplify and sequence mini-barcode D (F52/R193).

  7. A DNA Barcode Library for Korean Chironomidae (Insecta: Diptera) and Indexes for Defining Barcode Gap

    PubMed Central

    Kim, Sungmin; Song, Kyo-Hong; Ree, Han-Il; Kim, Won

    2012-01-01

    Non-biting midges (Diptera: Chironomidae) are a diverse population that commonly causes respiratory allergies in humans. Chironomid larvae can be used to indicate freshwater pollution, but accurate identification on the basis of morphological characteristics is difficult. In this study, we constructed a mitochondrial cytochrome c oxidase subunit I (COI)-based DNA barcode library for Korean chironomids. This library consists of 211 specimens from 49 species, including adults and unidentified larvae. The interspecies and intraspecies COI sequence variations were analyzed. Sophisticated indexes were developed in order to properly evaluate indistinct barcode gaps that are created by insufficient sampling on both the interspecies and intraspecies levels and by variable mutation rates across taxa. In a variety of insect datasets, these indexes were useful for re-evaluating large barcode datasets and for defining COI barcode gaps. The COI-based DNA barcode library will provide a rapid and reliable tool for the molecular identification of Korean chironomid species. Furthermore, this reverse-taxonomic approach will be improved by the continuous addition of other speceis’ sequences to the library. PMID:22138764

  8. Microfluidic generation of multifunctional quantum dot barcode particles.

    PubMed

    Zhao, Yuanjin; Shum, Ho Cheung; Chen, Haosheng; Adams, Laura L A; Gu, Zhongze; Weitz, David A

    2011-06-15

    We develop a new strategy to prepare quantum dot (QD) barcode particles by polymerizing double-emulsion droplets prepared in capillary microfluidic devices. The resultant barcode particles are composed of stable QD-tagged core particles surrounded by hydrogel shells. These particles exhibit uniform spectral characteristics and excellent coding capability, as confirmed by photoluminescence analyses. By using double-emulsion droplets with two inner droplets of distinct phases as templates, we have also fabricated anisotropic magnetic barcode particles with two separate cores or with a Janus core. These particles enable optical encoding and magnetic separation, thus making them excellent functional barcode particles in biomedical applications.

  9. DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach.

    PubMed

    Radulovici, Adriana E; Sainte-Marie, Bernard; Dufresne, France

    2009-05-01

    Marine crustaceans are known as a group with a high level of morphological and ecological diversity but are difficult to identify by traditional approaches and usually require the help of highly trained taxonomists. A faster identification method, DNA barcoding, was found to be an effective tool for species identification in many metazoan groups including some crustaceans. Here we expand the DNA barcode database with a case study involving 80 malacostracan species from the Estuary and Gulf of St Lawrence. DNA sequences for 460 specimens grouped into clusters corresponding to known morphological species in 95% of cases. Genetic distances between species were on average 25 times higher than within species. Intraspecific divergence was high (3.78-13.6%) in specimens belonging to four morphological species, suggesting the occurrence of cryptic species. Moreover, we detected the presence of an invasive amphipod species in the St Lawrence Estuary. This study reconfirms the usefulness of DNA barcoding for the identification of marine crustaceans.

  10. Theranostic barcoded nanoparticles for personalized cancer medicine

    PubMed Central

    Yaari, Zvi; da Silva, Dana; Zinger, Assaf; Goldman, Evgeniya; Kajal, Ashima; Tshuva, Rafi; Barak, Efrat; Dahan, Nitsan; Hershkovitz, Dov; Goldfeder, Mor; Roitman, Janna Shainsky; Schroeder, Avi

    2016-01-01

    Personalized medicine promises to revolutionize cancer therapy by matching the most effective treatment to the individual patient. Using a nanoparticle-based system, we predict the therapeutic potency of anticancer medicines in a personalized manner. We carry out the diagnostic stage through a multidrug screen performed inside the tumour, extracting drug activity information with single cell sensitivity. By using 100 nm liposomes, loaded with various cancer drugs and corresponding synthetic DNA barcodes, we find a correlation between the cell viability and the drug it was exposed to, according to the matching barcodes. Based on this screen, we devise a treatment protocol for mice bearing triple-negative breast-cancer tumours, and its results confirm the diagnostic prediction. We show that the use of nanotechnology in cancer care is effective for generating personalized treatment protocols. PMID:27830705

  11. Laboratory information management systems for DNA barcoding.

    PubMed

    Parker, Meaghan; Stones-Havas, Steven; Starger, Craig; Meyer, Christopher

    2012-01-01

    In the field of molecular biology, laboratory information management systems (LIMSs) have been created to track workflows through a process pipeline. For the purposes of DNA barcoding, this workflow involves tracking tissues through extraction, PCR, cycle sequencing, and consensus assembly. Importantly, a LIMS that serves the DNA barcoding community must link required elements for public submissions (e.g., primers, trace files) that are generated in the molecular lab with specimen metadata. Here, we demonstrate an example workflow of a specimen's entry into the LIMS database to the publishing of the specimen's genetic data to a public database using Geneious bioinformatics software. Throughout the process, the connections between steps in the workflow are maintained to facilitate post-processing annotation, structured reporting, and fully transparent edits to reduce subjectivity and increase repeatability.

  12. Bar-code automated waste tracking system

    SciTech Connect

    Hull, T.E.

    1994-10-01

    The Bar-Code Automated Waste Tracking System was designed to be a site-Specific program with a general purpose application for transportability to other facilities. The system is user-friendly, totally automated, and incorporates the use of a drive-up window that is close to the areas dealing in container preparation, delivery, pickup, and disposal. The system features ``stop-and-go`` operation rather than a long, tedious, error-prone manual entry. The system is designed for automation but allows operators to concentrate on proper handling of waste while maintaining manual entry of data as a backup. A large wall plaque filled with bar-code labels is used to input specific details about any movement of waste.

  13. DNA barcoding of endangered Indian Paphiopedilum species.

    PubMed

    Parveen, Iffat; Singh, Hemant K; Raghuvanshi, Saurabh; Pradhan, Udai C; Babbar, Shashi B

    2012-01-01

    The indiscriminate collections of Paphiopedilum species from the wild for their exotic ornamental flowers have rendered these plants endangered. Although the trade of these endangered species from the wild is strictly forbidden, it continues unabated in one or other forms that elude the current identification methods. DNA barcoding that offers identification of a species even if only a small fragment of the organism at any stage of development is available could be of great utility in scrutinizing the illegal trade of both endangered plant and animal species. Therefore, this study was undertaken to develop DNA barcodes of Indian species of Paphiopedilum along with their three natural hybrids using loci from both the chloroplast and nuclear genomes. The five loci tested for their potential as effective barcodes were RNA polymerase-β subunit (rpoB), RNA polymerase-β' subunit (rpoC1), Rubisco large subunit (rbcL) and maturase K (matK) from the chloroplast genome and nuclear ribosomal internal transcribed spacer (nrITS) from the nuclear genome. The intra- and inter-specific divergence values and species discrimination rates were calculated by Kimura 2 parameter (K2P) method using mega 4.0. The matK with 0.9% average inter-specific divergence value yielded 100% species resolution, thus could distinguish all the eight species of Paphiopedilum unequivocally. The species identification capability of these sequences was further confirmed as each of the matK sequences was found to be unique for the species when a blast analysis of these sequences was carried out on NCBI. nrITS, although had 4.4% average inter-specific divergence value, afforded only 50% species resolution. DNA barcodes of the three hybrids also reflected their parentage.

  14. 2D Hexagonal Boron Nitride (2D-hBN) Explored for the Electrochemical Sensing of Dopamine.

    PubMed

    Khan, Aamar F; Brownson, Dale A C; Randviir, Edward P; Smith, Graham C; Banks, Craig E

    2016-10-04

    Crystalline 2D hexagonal boron nitride (2D-hBN) nanosheets are explored as a potential electrocatalyst toward the electroanalytical sensing of dopamine (DA). The 2D-hBN nanosheets are electrically wired via a drop-casting modification process onto a range of commercially available carbon supporting electrodes, including glassy carbon (GC), boron-doped diamond (BDD), and screen-printed graphitic electrodes (SPEs). 2D-hBN has not previously been explored toward the electrochemical detection/electrochemical sensing of DA. We critically evaluate the potential electrocatalytic performance of 2D-hBN modified electrodes, the effect of supporting carbon electrode platforms, and the effect of "mass coverage" (which is commonly neglected in the 2D material literature) toward the detection of DA. The response of 2D-hBN modified electrodes is found to be largely dependent upon the interaction between 2D-hBN and the underlying supporting electrode material. For example, in the case of SPEs, modification with 2D-hBN (324 ng) improves the electrochemical response, decreasing the electrochemical oxidation potential of DA by ∼90 mV compared to an unmodified SPE. Conversely, modification of a GC electrode with 2D-hBN (324 ng) resulted in an increased oxidation potential of DA by ∼80 mV when compared to the unmodified electrode. We explore the underlying mechanisms of the aforementioned examples and infer that electrode surface interactions and roughness factors are critical considerations. 2D-hBN is utilized toward the sensing of DA in the presence of the common interferents ascorbic acid (AA) and uric acid (UA). 2D-hBN is found to be an effective electrocatalyst in the simultaneous detection of DA and UA at both pH 5.0 and 7.4. The peak separations/resolution between DA and UA increases by ∼70 and 50 mV (at pH 5.0 and 7.4, respectively, when utilizing 108 ng of 2D-hBN) compared to unmodified SPEs, with a particularly favorable response evident in pH 5.0, giving rise to a

  15. NKG2D ligands as therapeutic targets

    PubMed Central

    Spear, Paul; Wu, Ming-Ru; Sentman, Marie-Louise; Sentman, Charles L.

    2013-01-01

    The Natural Killer Group 2D (NKG2D) receptor plays an important role in protecting the host from infections and cancer. By recognizing ligands induced on infected or tumor cells, NKG2D modulates lymphocyte activation and promotes immunity to eliminate ligand-expressing cells. Because these ligands are not widely expressed on healthy adult tissue, NKG2D ligands may present a useful target for immunotherapeutic approaches in cancer. Novel therapies targeting NKG2D ligands for the treatment of cancer have shown preclinical success and are poised to enter into clinical trials. In this review, the NKG2D receptor and its ligands are discussed in the context of cancer, infection, and autoimmunity. In addition, therapies targeting NKG2D ligands in cancer are also reviewed. PMID:23833565

  16. Advancing taxonomy and bioinventories with DNA barcodes

    PubMed Central

    2016-01-01

    We use three examples—field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae—to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the ‘taxonomic impediment’, especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481791

  17. Advancing taxonomy and bioinventories with DNA barcodes.

    PubMed

    Miller, Scott E; Hausmann, Axel; Hallwachs, Winnie; Janzen, Daniel H

    2016-09-05

    We use three examples-field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae-to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the 'taxonomic impediment', especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication.This article is part of the themed issue 'From DNA barcodes to biomes'.

  18. Bayesian Cosmic Web Reconstruction: BARCODE for Clusters

    NASA Astrophysics Data System (ADS)

    Bos, E. G. Patrick; van de Weygaert, Rien; Kitaura, Francisco; Cautun, Marius

    2016-10-01

    We describe the Bayesian \\barcode\\ formalism that has been designed towards the reconstruction of the Cosmic Web in a given volume on the basis of the sampled galaxy cluster distribution. Based on the realization that the massive compact clusters are responsible for the major share of the large scale tidal force field shaping the anisotropic and in particular filamentary features in the Cosmic Web. Given the nonlinearity of the constraints imposed by the cluster configurations, we resort to a state-of-the-art constrained reconstruction technique to find a proper statistically sampled realization of the original initial density and velocity field in the same cosmic region. Ultimately, the subsequent gravitational evolution of these initial conditions towards the implied Cosmic Web configuration can be followed on the basis of a proper analytical model or an N-body computer simulation. The BARCODE formalism includes an implicit treatment for redshift space distortions. This enables a direct reconstruction on the basis of observational data, without the need for a correction of redshift space artifacts. In this contribution we provide a general overview of the the Cosmic Web connection with clusters and a description of the Bayesian BARCODE formalism. We conclude with a presentation of its successful workings with respect to test runs based on a simulated large scale matter distribution, in physical space as well as in redshift space.

  19. Highlighting Astyanax Species Diversity through DNA Barcoding

    PubMed Central

    Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

    2016-01-01

    DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

  20. Role of cytochrome P450 2D6 genetic polymorphism in carvedilol hydroxylation in vitro

    PubMed Central

    Wang, Zhe; Wang, Li; Xu, Ren-ai; Zhan, Yun-yun; Huang, Cheng-ke; Dai, Da-peng; Cai, Jian-ping; Hu, Guo-xin

    2016-01-01

    Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic enzyme that catalyzes the metabolism of a great number of therapeutic drugs. Up to now, >100 allelic variants of CYP2D6 have been reported. Recently, we identified 22 novel variants in the Chinese population in these variants. The purpose of this study was to examine the enzymatic activity of the variants toward the CYP2D6 substrate carvedilol in vitro. The CYP2D6 proteins, including CYP2D6.1 (wild type), CYP2D6.2, CYP2D6.10, and 22 other novel CYP2D6 variants, were expressed from insect microsomes and incubated with carvedilol ranging from 1.0 μM to 50 μM at 37°C for 30 minutes. After termination, the carvedilol metabolites were extracted and detected using ultra-performance liquid chromatography tandem mass-spectrometry. Among the 24 CYP2D6 variants, CYP2D6.92 and CYP2D6.96 were catalytically inactive and the remaining 22 variants exhibited significantly decreased intrinsic clearance values (ranging from ~25% to 95%) compared with CYP2D6.1. The present data in vitro suggest that the newly found variants significantly reduced catalytic activities compared with CYP2D6.1. Given that CYP2D6 protein activities could affect carvedilol plasma levels, these findings are greatly relevant to personalized medicine. PMID:27354764

  1. Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum).

    PubMed

    Guo, Yan-Yan; Huang, Lai-Qiang; Liu, Zhong-Jian; Wang, Xiao-Quan

    2016-01-01

    Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.

  2. Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum)

    PubMed Central

    Guo, Yan-Yan; Huang, Lai-Qiang; Liu, Zhong-Jian; Wang, Xiao-Quan

    2016-01-01

    Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation. PMID:26752741

  3. The agreement between 3D, standard 2D and triplane 2D speckle tracking: effects of image quality and 3D volume rate.

    PubMed

    Trache, Tudor; Stöbe, Stephan; Tarr, Adrienn; Pfeiffer, Dietrich; Hagendorff, Andreas

    2014-12-01

    Comparison of 3D and 2D speckle tracking performed on standard 2D and triplane 2D datasets of normal and pathological left ventricular (LV) wall-motion patterns with a focus on the effect that 3D volume rate (3DVR), image quality and tracking artifacts have on the agreement between 2D and 3D speckle tracking. 37 patients with normal LV function and 18 patients with ischaemic wall-motion abnormalities underwent 2D and 3D echocardiography, followed by offline speckle tracking measurements. The values of 3D global, regional and segmental strain were compared with the standard 2D and triplane 2D strain values. Correlation analysis with the LV ejection fraction (LVEF) was also performed. The 3D and 2D global strain values correlated good in both normally and abnormally contracting hearts, though systematic differences between the two methods were observed. Of the 3D strain parameters, the area strain showed the best correlation with the LVEF. The numerical agreement of 3D and 2D analyses varied significantly with the volume rate and image quality of the 3D datasets. The highest correlation between 2D and 3D peak systolic strain values was found between 3D area and standard 2D longitudinal strain. Regional wall-motion abnormalities were similarly detected by 2D and 3D speckle tracking. 2DST of triplane datasets showed similar results to those of conventional 2D datasets. 2D and 3D speckle tracking similarly detect normal and pathological wall-motion patterns. Limited image quality has a significant impact on the agreement between 3D and 2D numerical strain values.

  4. 75 FR 56922 - Implementation of the Intelligent Mail Package Barcode

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-17

    ... 111 Implementation of the Intelligent Mail Package Barcode AGENCY: Postal Service TM . ACTION: Advance... Mailing Standards of the United States Postal Service, Domestic Mail Manual (DMM ) for the optional use of Intelligent Mail package barcodes (IMpb), no later than January of 2011; and expects to require the...

  5. Multilocus inference of species trees and DNA barcoding

    PubMed Central

    2016-01-01

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481787

  6. Dissecting host-associated communities with DNA barcodes

    PubMed Central

    Pierce, Naomi E.

    2016-01-01

    DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes. Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481780

  7. DNA Barcoding of Catfish: Species Authentication and Phylogenetic Assessment

    PubMed Central

    Wong, Li Lian; Peatman, Eric; Lu, Jianguo; Kucuktas, Huseyin; He, Shunping; Zhou, Chuanjiang; Na-nakorn, Uthairat; Liu, Zhanjiang

    2011-01-01

    As the global market for fisheries and aquaculture products expands, mislabeling of these products has become a growing concern in the food safety arena. Molecular species identification techniques hold the potential for rapid, accurate assessment of proper labeling. Here we developed and evaluated DNA barcodes for use in differentiating United States domestic and imported catfish species. First, we sequenced 651 base-pair barcodes from the cytochrome oxidase I (COI) gene from individuals of 9 species (and an Ictalurid hybrid) of domestic and imported catfish in accordance with standard DNA barcoding protocols. These included domestic Ictalurid catfish, and representative imported species from the families of Clariidae and Pangasiidae. Alignment of individual sequences from within a given species revealed highly consistent barcodes (98% similarity on average). These alignments allowed the development and analyses of consensus barcode sequences for each species and comparison with limited sequences in public databases (GenBank and Barcode of Life Data Systems). Validation tests carried out in blinded studies and with commercially purchased catfish samples (both frozen and fresh) revealed the reliability of DNA barcoding for differentiating between these catfish species. The developed protocols and consensus barcodes are valuable resources as increasing market and governmental scrutiny is placed on catfish and other fisheries and aquaculture products labeling in the United States. PMID:21423623

  8. DNA Barcoding of Metazoan Zooplankton Copepods from South Korea

    PubMed Central

    Ryu, Shi Hyun; Kim, Sang Ki; Lee, Jin Hee; Lim, Young Jin; Lee, Jimin; Jun, Jumin; Kwak, Myounghai; Lee, Young-Sup; Hwang, Jae-Sam; Venmathi Maran, Balu Alagar; Chang, Cheon Young; Kim, Il-Hoi; Hwang, Ui Wook

    2016-01-01

    Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis–Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae–Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica–Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica–Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula. PMID:27383475

  9. Quantitative 2D liquid-state NMR.

    PubMed

    Giraudeau, Patrick

    2014-06-01

    Two-dimensional (2D) liquid-state NMR has a very high potential to simultaneously determine the absolute concentration of small molecules in complex mixtures, thanks to its capacity to separate overlapping resonances. However, it suffers from two main drawbacks that probably explain its relatively late development. First, the 2D NMR signal is strongly molecule-dependent and site-dependent; second, the long duration of 2D NMR experiments prevents its general use for high-throughput quantitative applications and affects its quantitative performance. Fortunately, the last 10 years has witnessed an increasing number of contributions where quantitative approaches based on 2D NMR were developed and applied to solve real analytical issues. This review aims at presenting these recent efforts to reach a high trueness and precision in quantitative measurements by 2D NMR. After highlighting the interest of 2D NMR for quantitative analysis, the different strategies to determine the absolute concentrations from 2D NMR spectra are described and illustrated by recent applications. The last part of the manuscript concerns the recent development of fast quantitative 2D NMR approaches, aiming at reducing the experiment duration while preserving - or even increasing - the analytical performance. We hope that this comprehensive review will help readers to apprehend the current landscape of quantitative 2D NMR, as well as the perspectives that may arise from it.

  10. Identification of Indian crocodile species through DNA barcodes.

    PubMed

    Meganathan, P R; Dubey, Bhawna; Jogayya, Kothakota Naga; Haque, Ikramul

    2013-07-01

    The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species.

  11. Commercial Teas Highlight Plant DNA Barcode Identification Successes and Obstacles

    PubMed Central

    Stoeckle, Mark Y.; Gamble, Catherine C.; Kirpekar, Rohan; Young, Grace; Ahmed, Selena; Little, Damon P.

    2011-01-01

    Appearance does not easily identify the dried plant fragments used to prepare teas to species. Here we test recovery of standard DNA barcodes for land plants from a large array of commercial tea products and analyze their performance in identifying tea constituents using existing databases. Most (90%) of 146 tea products yielded rbcL or matK barcodes using a standard protocol. Matching DNA identifications to listed ingredients was limited by incomplete databases for the two markers, shared or nearly identical barcodes among some species, and lack of standard common names for plant species. About 1/3 of herbal teas generated DNA identifications not found on labels. Broad scale adoption of plant DNA barcoding may require algorithms that place search results in context of standard plant names and character-based keys for distinguishing closely-related species. Demonstrating the importance of accessible plant barcoding, our findings indicate unlisted ingredients are common in herbal teas. PMID:22355561

  12. The multiple applications of DNA barcodes in avian evolutionary studies.

    PubMed

    Barreira, Ana S; Lijtmaer, Darío A; Tubaro, Pablo L

    2016-11-01

    DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer evolutionary questions. We review studies that have used DNA barcodes to investigate evolutionary processes in birds using diverse approaches. We also review studies that have investigated species in depth where taxonomy and DNA barcodes present inconsistencies. Species that showed low genetic interspecific divergence and lack of reciprocal monophyly either are the result of recent radiation and (or) hybridize, while species with large genetic splits in their COI sequences were determined to be more than one independent evolutionary unit. In addition, we review studies that employed large DNA barcode datasets to study the molecular evolution of mitochondrial genes and the biogeography of islands, continents, and even at a multi-continental scale. These studies showed that DNA barcodes offer high-quality data well beyond their main purpose of serving as a molecular tool for species identification.

  13. Commercial teas highlight plant DNA barcode identification successes and obstacles.

    PubMed

    Stoeckle, Mark Y; Gamble, Catherine C; Kirpekar, Rohan; Young, Grace; Ahmed, Selena; Little, Damon P

    2011-01-01

    Appearance does not easily identify the dried plant fragments used to prepare teas to species. Here we test recovery of standard DNA barcodes for land plants from a large array of commercial tea products and analyze their performance in identifying tea constituents using existing databases. Most (90%) of 146 tea products yielded rbcL or matK barcodes using a standard protocol. Matching DNA identifications to listed ingredients was limited by incomplete databases for the two markers, shared or nearly identical barcodes among some species, and lack of standard common names for plant species. About 1/3 of herbal teas generated DNA identifications not found on labels. Broad scale adoption of plant DNA barcoding may require algorithms that place search results in context of standard plant names and character-based keys for distinguishing closely-related species. Demonstrating the importance of accessible plant barcoding, our findings indicate unlisted ingredients are common in herbal teas.

  14. An In silico approach for the evaluation of DNA barcodes

    PubMed Central

    2010-01-01

    Background DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR Results Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples. Conclusions In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims. PMID:20637073

  15. Enhanced spin-dependent parity-nonconservation effect in the 7 s 1/2 2S →6 d 5/2 2D transition in Fr: A possibility for unambiguous detection of the nuclear anapole moment

    NASA Astrophysics Data System (ADS)

    Sahoo, B. K.; Aoki, T.; Das, B. P.; Sakemi, Y.

    2016-03-01

    Employing the relativistic coupled-cluster method, comparative studies of the parity nonconserving electric dipole amplitudes for the 7 s 1/2 2S →6 d 5/2 2D transitions in 210Fr and 211Fr isotopes have been carried out. It is found that these transition amplitudes, sensitive only to the nuclear spin-dependent effects, are enhanced substantially owing to the very large contributions from the electron core-polarization effects in Fr. This translates to a relatively large and, in principle, measurable induced light shift, which would be a signature of nuclear spin-dependent parity nonconservation that is dominated by the nuclear anapole moment in a heavy atom like Fr. A plausible scheme to measure this quantity using the Cyclotron and Radioisotope Center (CYRIC) facility at Tohoku University has been outlined.

  16. DNA barcoding of bark and ambrosia beetles reveals excessive NUMTs and consistent east-west divergence across Palearctic forests.

    PubMed

    Jordal, Bjarte H; Kambestad, Marius

    2014-01-01

    A comprehensive DNA barcoding library is very useful for rapid identification and detection of invasive pest species. We tested the performance of species identification in the economically most damaging group of wood-boring insects - the bark and ambrosia beetles - with particular focus on broad geographical sampling across the boreal Palearctic forests. Neighbour-joining and Bayesian analyses of cytochrome oxidase I (COI) sequences from 151 species in 40 genera revealed high congruence between morphology-based identification and sequence clusters. Inconsistencies with morphological identifications included the discovery of a likely cryptic Nearctic species of Dryocoetes autographus, the possible hybrid origin of shared mitochondrial haplotypes in Pityophthorus micrographus and P. pityographus, and a possible paraphyletic Xyleborinus saxeseni. The first record of Orthotomicus suturalis in North America was confirmed by DNA barcoding. The mitochondrial data also revealed consistent divergence across the Palearctic or Holarctic, confirmed in part by data from the large ribosomal subunit (28S). Some populations had considerable variation in the mitochondrial barcoding marker, but were invariant in the nuclear ribosomal marker. These findings must be viewed in light of the high number of nuclear insertions of mitochondrial DNA (NUMTs) detected in eight bark beetle species, suggesting the possible presence of additional cryptic NUMTs. The occurrence of paralogous COI copies, hybridization or cryptic speciation demands a stronger focus on data quality assessment in the construction of DNA barcoding databases.

  17. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  18. Competing coexisting phases in 2D water

    NASA Astrophysics Data System (ADS)

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-05-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules.

  19. Competing coexisting phases in 2D water

    PubMed Central

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  20. Advances of Community-Level Plant DNA Barcoding in China.

    PubMed

    Pei, Nancai; Chen, Bufeng; Kress, W J

    2017-01-01

    DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation. Lastly, we raised five possible directions; specifically, proposing a "purpose-driven barcode" fit for multi-level applications, developing new integrative sequencing strategies, pushing DNA barcoding beyond terrestrial ecosystem, constructing national-level DNA barcode sequence libraries for special plant groups, and establishing intelligent identification systems or online server platforms. These efforts will be potentially valuable to explore large-scale biodiversity patterns, the origin and evolution of life, and will also facilitate preservation and utilization of biodiversity resources.

  1. Rapid-scan coherent 2D fluorescence spectroscopy.

    PubMed

    Draeger, Simon; Roeding, Sebastian; Brixner, Tobias

    2017-02-20

    We developed pulse-shaper-assisted coherent two-dimensional (2D) electronic spectroscopy in liquids using fluorescence detection. A customized pulse shaper facilitates shot-to-shot modulation at 1 kHz and is employed for rapid scanning over all time delays. A full 2D spectrum with 15 × 15 pixels is obtained in approximately 6 s of measurement time (plus further averaging if needed). Coherent information is extracted from the incoherent fluorescence signal via 27-step phase cycling. We exemplify the technique on cresyl violet in ethanol and recover literature-known oscillations as a function of population time. Signal-to-noise behavior is analyzed as a function of the amount of averaging. Rapid scanning provides a 2D spectrum with a root-mean-square error of < 0.05 after 1 min of measurement time.

  2. Use of DNA barcoding to distinguish the malaria vector Anopheles neivai in Colombia.

    PubMed

    López-Rubio, Andrés; Suaza-Vasco, Juan; Marcet, Paula L; Ruíz-Molina, Natalia; Cáceres, Lorenzo; Porter, Charles; Uribe, Sandra

    2016-10-17

    A reference 535 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI), acquired from specimens of An. neivai Howard, Dyar & Knab, 1913 from its type locality in Panama, was used as a tool for distinguishing this species from others in the subgenus Kerteszia. Comparisons with corresponding regions of COI between An. neivai and other species in the subgenus (An. bellator Dyar & Knab 1906, An. homunculus Komp 1937, An cruzii Dyar & Knab, 1908 and An. laneanus Corrêa & Cerqueira, 1944) produced K2P genetic distances of 8.3-12.6%, values well above those associated with intraspecific variation. In contrast, genetic distances among 55 specimens from five municipalities in the Colombian Pacific coastal state of Chocó were all within the range of 0-2.5%, with an optimized barcode threshold of 1.3%, the limit for unambiguous differentiation of An. neivai. Among specimens from the Chocó region, 18 haplotypes were detected, two of which were widely distributed over the municipalities sampled. The barcode sequence permits discrimination of An. neivai from sympatric species and indicates genetic variability within the species; aspects key to malaria surveillance and control as well as defining geographic distribution and dispersion patterns.

  3. Use of DNA barcoding to distinguish the malaria vector Anopheles neivai in Colombia

    PubMed Central

    LÓPEZ-RUBIO, ANDRÉS; SUAZA-VASCO, JUAN; MARCET, PAULA L; RUÍZ-MOLINA, NATALIA; CÁCERES, LORENZO; PORTER, CHARLES; URIBE, SANDRA

    2016-01-01

    A reference 535 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI), acquired from specimens of An. neivai Howard, Dyar & Knab, 1913 from its type locality in Panama, was used as a tool for distinguishing this species from others in the subgenus Kerteszia. Comparisons with corresponding regions of COI between An. neivai and other species in the subgenus (An. bellator Dyar & Knab 1906, An. homunculus Komp 1937, An cruzii Dyar & Knab, 1908 and An. laneanus Corrêa & Cerqueira, 1944) produced K2P genetic distances of 8.3–12.6%, values well above those associated with intraspecific variation. In contrast, genetic distances among 55 specimens from five municipalities in the Colombian Pacific coastal state of Chocó were all within the range of 0–2.5%, with an optimized barcode threshold of 1.3%, the limit for unambiguous differentiation of An. neivai. Among specimens from the Chocó region, 18 haplotypes were detected, two of which were widely distributed over the municipalities sampled. The barcode sequence permits discrimination of An. neivai from sympatric species and indicates genetic variability within the species; aspects key to malaria surveillance and control as well as defining geographic distribution and dispersion patterns. PMID:27811749

  4. Using DNA barcoding to link cystacanths and adults of the acanthocephalan Polymorphus brevis in central Mexico.

    PubMed

    Alcántar-Escalera, F J; García-Varela, M; Vázquez-Domínguez, E; Pérez-Ponce de León, G

    2013-11-01

    In parasitic organisms, particularly helminths, the usage of the mitochondrial cytochrome c oxidase subunit I gene as the standard DNA barcoding region for species identification and discovery has been very limited. Here, we present an integrated study, based on both DNA barcoding and morphological analyses, for acanthocephalans belonging to the genus Polymorphus, whose larvae (cystacanths) are commonly found in the mesentery of freshwater fishes, while adults are found in the intestine of fish-eating birds. The alpha taxonomy of parasitic helminths is based on adult morphological traits, and because of that larval forms cannot be identified to species level based on morphology alone. DNA barcoding offers an alternative tool for linking larval stages of parasitic organisms to known adults. We sequenced cystacanths collected from freshwater fishes in localities across central Mexico and adults obtained from fish-eating birds, to determine whether they were conspecific. To corroborate the molecular results, we conducted a morphometric analysis with 'Proboscis profiler', which is a software tool developed to detect heterogeneity in morphologically similar acanthocephalans based on the multivariate statistical analysis of proboscis hook dimensions. Both sources of information indicate that cystacanths infecting freshwater fishes in central Mexico belong to a single species, Polymorphus brevis.

  5. Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case.

    PubMed

    Seifert, Keith A; Samson, Robert A; Dewaard, Jeremy R; Houbraken, Jos; Lévesque, C André; Moncalvo, Jean-Marc; Louis-Seize, Gerry; Hebert, Paul D N

    2007-03-06

    DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or beta-tubulin sequences (BenA). CO1 divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.

  6. Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments

    PubMed Central

    Stern, Rowena F.; Horak, Ales; Andrew, Rose L.; Coffroth, Mary-Alice; Andersen, Robert A.; Küpper, Frithjof C.; Jameson, Ian; Hoppenrath, Mona; Véron, Benoît; Kasai, Fumai; Brand, Jerry; James, Erick R.; Keeling, Patrick J.

    2010-01-01

    Background Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known “species”, as a reference to measure the natural diversity in three marine environments. Methodology/Principal Findings In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. Conclusions/Significance COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of

  7. DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China.

    PubMed

    Li, Jing; Zheng, Xin; Cai, Yansen; Zhang, Xiuyue; Yang, Min; Yue, Bisong; Li, Jing

    2015-01-01

    Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.

  8. 2D DIGE saturation labeling for minute sample amounts.

    PubMed

    Arnold, Georg J; Fröhlich, Thomas

    2012-01-01

    The 2D DIGE technique, based on fluorophores covalently linked to amino acid side chain residues and the concept of an internal standard, has significantly improved reproducibility, sensitivity, and the dynamic range of protein quantification. In saturation DIGE, sulfhydryl groups of cysteines are labeled with cyanine dyes to completion, providing a so far unraveled sensitivity for protein detection and quantification in 2D gel-based proteomic experiments. Only a few micrograms of protein per 2D gel facilitate the analysis of about 2,000 analytes from complex mammalian cell or tissue samples. As a consequence, 2D saturation DIGE is the method of choice when only minute sample amounts are available for quantitative proteome analysis at the level of proteins rather than peptides. Since very low amounts of samples have to be handled in a reproducible manner, saturation DIGE-based proteomic experiments are technically demanding. Moreover, successful saturation DIGE approaches require a strict adherence to adequate reaction conditions at each step. This chapter is dedicated to colleagues already experienced in 2D PAGE protein separation and intends to support the establishment of this ultrasensitive technique in proteomic workgroups. We provide basic guidelines for the experimental design and discuss crucial aspects concerning labeling chemistry, sample preparation, and pitfalls caused by labeling artifacts. A detailed step-by-step protocol comprises all aspects from initial sample preparation to image analysis and statistical evaluation. Furthermore, we describe the generation of preparative saturation DIGE gels necessary for mass spectrometry-based spot identification.

  9. Exploring Canadian Echinoderm Diversity through DNA Barcodes

    PubMed Central

    2016-01-01

    DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs. PMID:27870868

  10. Covert thermal barcodes based on phase change nanoparticles

    PubMed Central

    Duong, Binh; Liu, Helin; Ma, Liyuan; Su, Ming

    2014-01-01

    An unmet need is to develop covert barcodes that can be used to track-trace objects, and authenticate documents. This paper describes a new nanoparticle-based covert barcode system, in which a selected panel of solid-to-liquid phase change nanoparticles with discrete and sharp melting peaks is added in a variety of objects such as explosive derivative, drug, polymer, and ink. This method has high labeling capacity owing to the small sizes of nanoparticles, sharp melting peaks, and large scan range of thermal analysis. The thermal barcode can enhance forensic investigation by its technical readiness, structural covertness, and robustness. PMID:24901064

  11. Testing DNA Barcode Performance in 1000 Species of European Lepidoptera: Large Geographic Distances Have Small Genetic Impacts

    PubMed Central

    Huemer, Peter; Mutanen, Marko; Sefc, Kristina M.; Hebert, Paul D. N.

    2014-01-01

    This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections. PMID:25541991

  12. Dietary Niche Partitioning of Euphaea formosa and Matrona cyanoptera (Odonata: Zygoptera) on the Basis of DNA Barcoding of Larval Feces

    PubMed Central

    Cheng, Yun-Chieh; Lin, Chung-Ping

    2016-01-01

    Odonate larvae are commonly considered opportunistic general predators in freshwater ecosystems. However, the dietary breadth of most odonate larvae in forest streams is still poorly documented. We characterized the prey species and estimated the level of dietary niche overlap of two damselflies, Euphaea formosa Hagen 1869 and Matrona cyanoptera Hämäläinen and Yeh, 2000 in a forest stream of central Taiwan on the basis of DNA barcoding of larval feces. A collection of 23 successfully identified cytochrome c oxidase 1 (CO1) barcoding sequences suggested that the mayflies (Ephemeroptera), caddisflies (Trichoptera), and midges (Diptera) comprise the majority (43%, 6/14) of prey species consumed by E. formosa larvae, whereas the identified prey for M. cyanoptera were mainly zooplankton (56%, 5/9). Statistical analysis of dietary overlap indicated that these two species occupy different dietary niches (Pianka’s index = 0.219). DNA barcoding analysis of damselfly larval feces was effective in detecting less sclerotized prey such as vertebrates (fish and frog) and small zooplankton. However, a moderately successful rate (<70%) of PCR amplification by universal CO1 primers and a low percentage (<60%) of identifiable sequences in public databases indicate the limitations of naive DNA barcoding in fecal analysis. PMID:27432350

  13. Dietary Niche Partitioning of Euphaea formosa and Matrona cyanoptera (Odonata: Zygoptera) on the Basis of DNA Barcoding of Larval Feces.

    PubMed

    Cheng, Yun-Chieh; Lin, Chung-Ping

    2016-01-01

    Odonate larvae are commonly considered opportunistic general predators in freshwater ecosystems. However, the dietary breadth of most odonate larvae in forest streams is still poorly documented. We characterized the prey species and estimated the level of dietary niche overlap of two damselflies, Euphaea formosa Hagen 1869 and Matrona cyanoptera Hämäläinen and Yeh, 2000 in a forest stream of central Taiwan on the basis of DNA barcoding of larval feces. A collection of 23 successfully identified cytochrome c oxidase 1 (CO1) barcoding sequences suggested that the mayflies (Ephemeroptera), caddisflies (Trichoptera), and midges (Diptera) comprise the majority (43%, 6/14) of prey species consumed by E. formosa larvae, whereas the identified prey for M. cyanoptera were mainly zooplankton (56%, 5/9). Statistical analysis of dietary overlap indicated that these two species occupy different dietary niches (Pianka's index = 0.219). DNA barcoding analysis of damselfly larval feces was effective in detecting less sclerotized prey such as vertebrates (fish and frog) and small zooplankton. However, a moderately successful rate (<70%) of PCR amplification by universal CO1 primers and a low percentage (<60%) of identifiable sequences in public databases indicate the limitations of naive DNA barcoding in fecal analysis.

  14. Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.

    PubMed

    Huemer, Peter; Mutanen, Marko; Sefc, Kristina M; Hebert, Paul D N

    2014-01-01

    This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

  15. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  16. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  17. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

    DYNA2D is an explicit Lagrangian finite element code used to model dynamic events where stress wave interactions influence the overall response of the system. DYNA2D is often used to model penetration problems involving ductile-to-ductile impacts; however, with the advent of the use of ceramics in the armor-anti-armor community and the need to model damage to laser optics components, good brittle damage models are now needed in DYNA2D. This report will detail the implementation of four brittle damage models in DYNA2D, three scalar damage models and one tensor damage model. These new brittle damage models are then used to predict experimental results from three distinctly different glass damage problems.

  18. 2D/3D switchable displays

    NASA Astrophysics Data System (ADS)

    Dekker, T.; de Zwart, S. T.; Willemsen, O. H.; Hiddink, M. G. H.; IJzerman, W. L.

    2006-02-01

    A prerequisite for a wide market acceptance of 3D displays is the ability to switch between 3D and full resolution 2D. In this paper we present a robust and cost effective concept for an auto-stereoscopic switchable 2D/3D display. The display is based on an LCD panel, equipped with switchable LC-filled lenticular lenses. We will discuss 3D image quality, with the focus on display uniformity. We show that slanting the lenticulars in combination with a good lens design can minimize non-uniformities in our 20" 2D/3D monitors. Furthermore, we introduce fractional viewing systems as a very robust concept to further improve uniformity in the case slanting the lenticulars and optimizing the lens design are not sufficient. We will discuss measurements and numerical simulations of the key optical characteristics of this display. Finally, we discuss 2D image quality, the switching characteristics and the residual lens effect.

  19. 2-d Finite Element Code Postprocessor

    SciTech Connect

    Sanford, L. A.; Hallquist, J. O.

    1996-07-15

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forces along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  20. Optoelectronics of supported and suspended 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Bolotin, Kirill

    2014-03-01

    Two-dimensional semiconductors, materials such monolayer molybdenum disulfide (MoS2) are characterized by strong spin-orbit and electron-electron interactions. However, both electronic and optoelectronic properties of these materials are dominated by disorder-related scattering. In this talk, we investigate approaches to reduce scattering and explore physical phenomena arising in intrinsic 2D semiconductors. First, we discuss fabrication of pristine suspended monolayer MoS2 and use photocurrent spectroscopy measurements to study excitons in this material. We observe band-edge and van Hove singularity excitons and estimate their binding energies. Furthermore, we study dissociation of these excitons and uncover the mechanism of their contribution to photoresponse of MoS2. Second, we study strain-induced modification of bandstructures of 2D semiconductors. With increasing strain, we find large and controllable band gap reduction of both single- and bi-layer MoS2. We also detect experimental signatures consistent with strain-induced transition from direct to indirect band gap in monolayer MoS2. Finally, we fabricate heterostructures of dissimilar 2D semiconductors and study their photoresponse. For closely spaced 2D semiconductors we detect charge transfer, while for separation larger than 10nm we observe Forster-like energy transfer between excitations in different layers.

  1. Development of a MEMS 2D separations device

    NASA Astrophysics Data System (ADS)

    Bloschock, Kristen P.; Flyer, Jonathan N.; Schneider, Thomas W.; Hussam, Abul; Van Keuren, Edward R.

    2004-12-01

    A polymer based biochip for rapid 2D separations of peptides, proteins, and other biomedically relevant molecules was designed and fabricated. Like traditional 2D polyacrylamide gel electrophoresis (2D-PAGE) methods, the device will allow molecules to separate based on isoelectric point (pI) and molecular weight (MW). Our design, however, integrates both an initial capillary isoelectric focusing (cIEF) step followed by capillary electrophoresis (CE) in multiple parallel channels, all on a single microfluidic chip. Not only is the "lab-on-a-chip" design easier to use and less expensive, but the miniaturization of the device produces very rapid separations. Compared to traditional 2D-PAGE, which can take hours to complete, we estimate separation times on the order of seconds. Fluorescence detection will be used in the preliminary stages of testing, but the device also is equipped with integrated electrodes in the electrophoresis channels to perform multiplexed electrochemical detection for quantitative analysis. We will present preliminary results of the chip development and testing.

  2. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

    Chemistry plays an ever-increasing role in the production, functionalization, processing and applications of graphene and other 2D materials. This special issue highlights a selection of enlightening chemical approaches to 2D materials, which nicely reflect the breadth of the field and convey the excitement of the individuals involved in it, who are trying to translate graphene and related materials from the laboratory into a real, high-impact technology.

  3. Use of admixture and association for detection of quantitative trait loci in the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples (T2D-GENES) study

    PubMed Central

    2014-01-01

    Admixture mapping and association testing have been successfully applied to the detection of genes for complex diseases. Methods have also been developed to combine these approaches. As an initial step to determine the feasibility of combining admixture and association mapping in the context of whole genome sequencing, we have applied several methods to data from the Genetic Analysis Workshop 18. Here, we describe the steps necessary to carry out such a study from selection of reference populations and preprocessing of data through to the testing itself. We detected one significant result with a Bonferroni corrected p-value of 0.032 at single nucleotide polymorphism rs12639065. Computing local ancestry for Hispanic populations was challenging because there are relatively few methods by which to handle 3-way admixture, and publicly available Native American reference panels are scarce. However, combining admixture and association is a promising approach for detection of quantitative trait loci because it might be able to elevate the power of detection by combining 2 different sources of genetic signal. PMID:25519335

  4. Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia.

    PubMed

    Salvi, Daniele; Mariottini, Paolo

    2012-11-01

    In this study, we analyzed the nuclear ITS2 rRNA primary sequence and secondary structure in Veneridae and comparatively with 20 Bivalvia taxa to test the phylogenetic resolution of this marker and its suitability for molecular diagnosis at different taxonomic levels. Maximum likelihood and Bayesian trees based on primary sequences were congruent with (profile-) neighbor-joining trees based on a combined model of sequence-structure evolution. ITS2 showed higher resolution below the subfamily level, providing a phylogenetic signal comparable to (mitochondrial/nuclear) gene fragments 2-5 times longer. Structural elements of the ITS2 folding, such as specific mismatch pairing and compensatory base changes, provided further support for the monophyly of some groups and for their phylogenetic relationships. Veneridae ITS2 folding is structured in six domains (DI-VI) and shows five striking sequence-structure features. Two of them, the Basal and Apical STEMs, are common to Bivalvia, while the presence of both the Branched STEM and the Y/R stretches occurs in five superfamilies of the two Heterodonta orders Myoida and Veneroida, thus questioning their reciprocal monophyly. Our results validated the ITS2 as a suitable marker for venerids phylogenetics and taxonomy, and underlined the significance of including secondary structure information for both applications at several systematic levels within bivalves.

  5. DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines.

    PubMed

    Casas, Princess Angelie S; Sing, Kong-Wah; Lee, Ping-Shin; Nuñeza, Olga M; Villanueva, Reagan Joseph T; Wilson, John-James

    2017-02-03

    Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.

  6. Engineering multifunctional magnetic-quantum dot barcodes by flow focusing.

    PubMed

    Giri, Supratim; Li, Dawei; Chan, Warren C W

    2011-04-14

    A simple one-step flow focusing method was used to embed both magnetic nanoparticles and quantum dots in microbeads in controlled ratios to generate a large library of molecular barcodes for biological applications.

  7. DNA barcode authentication of saw palmetto herbal dietary supplements.

    PubMed

    Little, Damon P; Jeanson, Marc L

    2013-12-17

    Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini-barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74-1.00); sensitivity = 1.00 (95% confidence interval = 0.66-1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini-barcodes were used to estimate the frequency of mislabeled saw palmetto herbal dietary supplements on the market in the United States of America. Of the 37 supplements examined, amplifiable DNA could be extracted from 34 (92%). Mini-barcode analysis of these supplements demonstrated that 29 (85%) contain saw palmetto and that 2 (6%) supplements contain related species that cannot be legally sold as herbal dietary supplements in the United States of America. The identity of 3 (9%) supplements could not be conclusively determined.

  8. DNA Barcodes for the Northern European Tachinid Flies (Diptera: Tachinidae)

    PubMed Central

    Kahanpää, Jere; Mutanen, Marko

    2016-01-01

    This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera. PMID:27814365

  9. Testing evolutionary hypotheses for DNA barcoding failure in willows.

    PubMed

    Twyford, Alex D

    2014-10-01

    The goal of DNA barcoding is to enable the rapid identification of taxa from short diagnostic DNA sequence profiles. But how feasible is this objective when many evolutionary processes, such as hybridization and selective sweeps, cause alleles to be shared among related taxa? In this issue of Molecular Ecology, Percy et al. (2014) test the full suite of seven candidate plant barcoding loci in a broad geographic sample of willow species. They show exceptional plastid haplotype sharing between species across continents, with most taxa not possessing a unique barcode sequence. Using population genetic and molecular dating analyses, they implicate hybridization and selective sweeps, but not incomplete lineage sorting, as the historical processes causing widespread haplotype sharing among willow taxa. This study represents an exceptional case of how poorly barcoding can perform, and highlights methodological issues using universal organellar regions for species identification.

  10. Does DNA barcoding improve performance of traditional stream bioassessment metrics?

    EPA Science Inventory

    Benthic macroinvertebrate community composition is used to assess wetland and stream condition and to help differentiate the effects of stressors among sites. Deoxyribonucleic acid (DNA) barcoding has been promoted as a way to increase taxonomic resolution and, thereby, to increa...

  11. DNA barcoding Satyrine butterflies (Lepidoptera: Nymphalidae) in China.

    PubMed

    Yang, Mingsheng; Zhai, Qing; Yang, Zhaofu; Zhang, Yalin

    2016-07-01

    We investigated the effectiveness of the standard 648 bp mitochondrial COI barcode region in discriminating among Satyrine species from China. A total of 214 COI sequences were obtained from 90 species, including 34 species that have never been barcoded. Analyses of genetic divergence show that the mean interspecific genetic divergence is about 16-fold higher than within species, and little overlap occurs between them. Neighbour-joining (NJ) analyses showed that 48 of the 50 species with two or more individuals, including two cases with deep intraspecific divergence (>3%), are monophyletic. Furthermore, when our sequences are combined with the conspecific sequences sampled from distantly geographic regions, the "barcoding gap" still exists, and all related species are recovered to be monophyletic in NJ analysis. Our study demonstrates that COI barcoding is effective in discriminating among the satyrine species of China, and provides a reference library for their future molecular identification.

  12. Marmoset cytochrome P450 2D8 in livers and small intestines metabolizes typical human P450 2D6 substrates, metoprolol, bufuralol and dextromethorphan.

    PubMed

    Uehara, Shotaro; Uno, Yasuhiro; Hagihira, Yuya; Murayama, Norie; Shimizu, Makiko; Inoue, Takashi; Sasaki, Erika; Yamazaki, Hiroshi

    2015-01-01

    1. Although the New World non-human primate, the common marmoset (Callithrix jacchus), is a potentially useful animal model, comprehensive understanding of drug metabolizing enzymes is insufficient. 2. A cDNA encoding a novel cytochrome P450 (P450) 2D8 was identified in marmosets. The amino acid sequence deduced from P450 2D8 cDNA showed a high sequence identity (83-86%) with other primate P450 2Ds. Phylogenetic analysis showed that marmoset P450 2D8 was closely clustered with human P450 2D6, unlike P450 2Ds of miniature pig, dog, rabbit, guinea pig, mouse or rat. 3. Marmoset P450 2D8 mRNA was predominantly expressed in the liver and small intestine among the tissues types analyzed, whereas marmoset P450 2D6 mRNA was expressed predominantly in the liver where P450 2D protein was detected by immunoblotting. 4. By metabolic assays using marmoset P450 2D8 protein heterologously expressed in Escherichia coli, although P450 2D8 exhibits lower catalytic efficiency compared to marmoset and human P450 2D6 enzymes, P450 2D8 mediated O-demethylations of metoprolol and dextromethorphan and bufuralol 1'-hydroxylation. 5. These results suggest that marmoset P450 2D8 (also expressed in the extrahepatic tissues) has potential roles in drug metabolism in a similar manner to those of human and marmoset P450 2D6.

  13. Supervised DNA Barcodes species classification: analysis, comparisons and results

    PubMed Central

    2014-01-01

    Background Specific fragments, coming from short portions of DNA (e.g., mitochondrial, nuclear, and plastid sequences), have been defined as DNA Barcode and can be used as markers for organisms of the main life kingdoms. Species classification with DNA Barcode sequences has been proven effective on different organisms. Indeed, specific gene regions have been identified as Barcode: COI in animals, rbcL and matK in plants, and ITS in fungi. The classification problem assigns an unknown specimen to a known species by analyzing its Barcode. This task has to be supported with reliable methods and algorithms. Methods In this work the efficacy of supervised machine learning methods to classify species with DNA Barcode sequences is shown. The Weka software suite, which includes a collection of supervised classification methods, is adopted to address the task of DNA Barcode analysis. Classifier families are tested on synthetic and empirical datasets belonging to the animal, fungus, and plant kingdoms. In particular, the function-based method Support Vector Machines (SVM), the rule-based RIPPER, the decision tree C4.5, and the Naïve Bayes method are considered. Additionally, the classification results are compared with respect to ad-hoc and well-established DNA Barcode classification methods. Results A software that converts the DNA Barcode FASTA sequences to the Weka format is released, to adapt different input formats and to allow the execution of the classification procedure. The analysis of results on synthetic and real datasets shows that SVM and Naïve Bayes outperform on average the other considered classifiers, although they do not provide a human interpretable classification model. Rule-based methods have slightly inferior classification performances, but deliver the species specific positions and nucleotide assignments. On synthetic data the supervised machine learning methods obtain superior classification performances with respect to the traditional DNA Barcode

  14. Improved COI barcoding primers for Southeast Asian perching birds (Aves: Passeriformes).

    PubMed

    Lohman, David J; Prawiradilaga, Dewi M; Meier, Rudolf

    2009-01-01

    The All Birds Barcoding Initiative aims to assemble a DNA barcode database for all bird species, but the 648-bp 'barcoding' region of cytochrome c oxidase subunit I (COI) can be difficult to amplify in Southeast Asian perching birds (Aves: Passeriformes). Using COI sequences from complete mitochondrial genomes, we designed a primer pair that more reliably amplifies and sequences the COI barcoding region of Southeast Asian passerine birds. The 655-bp region amplified with these primers overlaps the COI region amplified with other barcoding primer pairs, enabling direct comparison of sequences with previously published DNA barcodes.

  15. DNA barcoding the native flowering plants and conifers of Wales.

    PubMed

    de Vere, Natasha; Rich, Tim C G; Ford, Col R; Trinder, Sarah A; Long, Charlotte; Moore, Chris W; Satterthwaite, Danielle; Davies, Helena; Allainguillaume, Joel; Ronca, Sandra; Tatarinova, Tatiana; Garbett, Hannah; Walker, Kevin; Wilkinson, Mike J

    2012-01-01

    We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.

  16. Graded core/shell semiconductor nanorods and nanorod barcodes

    DOEpatents

    Alivisatos, A. Paul; Scher, Erik C.; Manna, Liberato

    2010-12-14

    Graded core/shell semiconductor nanorods and shaped nanorods are disclosed comprising Group II-VI, Group III-V and Group IV semiconductors and methods of making the same. Also disclosed are nanorod barcodes using core/shell nanorods where the core is a semiconductor or metal material, and with or without a shell. Methods of labeling analytes using the nanorod barcodes are also disclosed.

  17. Graded core/shell semiconductor nanorods and nanorod barcodes

    SciTech Connect

    Alivisatos, A. Paul; Scher, Erik C.; Manna, Liberato

    2013-03-26

    Graded core/shell semiconductor nanorods and shapped nanorods are disclosed comprising Group II-VI, Group III-V and Group IV semiconductors and methods of making the same. Also disclosed are nanorod barcodes using core/shell nanorods where the core is a semiconductor or metal material, and with or without a shell. Methods of labeling analytes using the nanorod barcodes are also disclosed.

  18. DNA Barcoding the Native Flowering Plants and Conifers of Wales

    PubMed Central

    de Vere, Natasha; Rich, Tim C. G.; Ford, Col R.; Trinder, Sarah A.; Long, Charlotte; Moore, Chris W.; Satterthwaite, Danielle; Davies, Helena; Allainguillaume, Joel; Ronca, Sandra; Tatarinova, Tatiana; Garbett, Hannah; Walker, Kevin; Wilkinson, Mike J.

    2012-01-01

    We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification. PMID:22701588

  19. Reading 1D Barcodes with Mobile Phones Using Deformable Templates.

    PubMed

    Gallo, Orazio; Manduchi, Roberto

    2011-09-01

    Camera cellphones have become ubiquitous, thus opening a plethora of opportunities for mobile vision applications. For instance, they can enable users to access reviews or price comparisons for a product from a picture of its barcode while still in the store. Barcode reading needs to be robust to challenging conditions such as blur, noise, low resolution, or low-quality camera lenses, all of which are extremely common. Surprisingly, even state-of-the-art barcode reading algorithms fail when some of these factors come into play. One reason resides in the early commitment strategy that virtually all existing algorithms adopt: The image is first binarized and then only the binary data are processed. We propose a new approach to barcode decoding that bypasses binarization. Our technique relies on deformable templates and exploits all of the gray-level information of each pixel. Due to our parameterization of these templates, we can efficiently perform maximum likelihood estimation independently on each digit and enforce spatial coherence in a subsequent step. We show by way of experiments on challenging UPC-A barcode images from five different databases that our approach outperforms competing algorithms. Implemented on a Nokia N95 phone, our algorithm can localize and decode a barcode on a VGA image (640 × 480, JPEG compressed) in an average time of 400-500 ms.

  20. Advances of Community-Level Plant DNA Barcoding in China

    PubMed Central

    Pei, Nancai; Chen, Bufeng; Kress, W. J.

    2017-01-01

    DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation. Lastly, we raised five possible directions; specifically, proposing a “purpose-driven barcode” fit for multi-level applications, developing new integrative sequencing strategies, pushing DNA barcoding beyond terrestrial ecosystem, constructing national-level DNA barcode sequence libraries for special plant groups, and establishing intelligent identification systems or online server platforms. These efforts will be potentially valuable to explore large-scale biodiversity patterns, the origin and evolution of life, and will also facilitate preservation and utilization of biodiversity resources. PMID:28270824

  1. Nematode molecular diagnostics: from bands to barcodes.

    PubMed

    Powers, Tom

    2004-01-01

    Nematodes are considered among the most difficult animals to identify. DNA-based diagnostic methods have already gained acceptance in applications ranging from quarantine determinations to assessments of biodiversity. Researchers are currently in an information-gathering mode, with intensive efforts applied to accumulating nucleotide sequence of 18S and 28S ribosomal genes, internally transcribed spacer regions, and mitochondrial genes. Important linkages with collateral data such as digitized images, video clips and specimen voucher web pages are being established on GenBank and NemATOL, the nematode-specific Tree of Life database. The growing DNA taxonomy of nematodes has lead to their use in testing specific short sequences of DNA as a "barcode" for the identification of all nematode species.

  2. Identifying Fishes through DNA Barcodes and Microarrays

    PubMed Central

    Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N.; Weber, Hannes; Blohm, Dietmar

    2010-01-01

    Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products. PMID

  3. Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

    PubMed

    Serrao, Natasha R; Steinke, Dirk; Hanner, Robert H

    2014-01-01

    Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis.

  4. Calibrating Snakehead Diversity with DNA Barcodes: Expanding Taxonomic Coverage to Enable Identification of Potential and Established Invasive Species

    PubMed Central

    Serrao, Natasha R.; Steinke, Dirk; Hanner, Robert H.

    2014-01-01

    Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis. PMID

  5. Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix

    PubMed Central

    Morinière, Jérôme; Cancian de Araujo, Bruno; Hausmann, Axel; Balke, Michael; Hendrich, Lars; Doczkal, Dieter; Arvidsson, Samuel; Haszprunar, Gerhard

    2016-01-01

    The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5’ fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage ≥10; CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples; whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming presorting process will yield approximately 30% more high score BINs compared to the non-sorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline. PMID:27191722

  6. Orthotropic Piezoelectricity in 2D Nanocellulose

    NASA Astrophysics Data System (ADS)

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-10-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V‑1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

  7. Orthotropic Piezoelectricity in 2D Nanocellulose

    PubMed Central

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-01-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V−1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies. PMID:27708364

  8. Orthotropic Piezoelectricity in 2D Nanocellulose.

    PubMed

    García, Y; Ruiz-Blanco, Yasser B; Marrero-Ponce, Yovani; Sotomayor-Torres, C M

    2016-10-06

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V(-1), ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

  9. 2D microwave imaging reflectometer electronics

    SciTech Connect

    Spear, A. G.; Domier, C. W. Hu, X.; Muscatello, C. M.; Ren, X.; Luhmann, N. C.; Tobias, B. J.

    2014-11-15

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  10. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

    Transition metal dichalcogenides (TMDs) have generated significant interest for numerous applications including sensors, flexible electronics, heterostructures and optoelectronics due to their interesting, thickness-dependent properties. Despite recent progress, the synthesis of high-quality and highly uniform TMDs on a large scale is still a challenge. In this talk, synthesis routes for WSe2 and MoS2 that achieve monolayer thickness uniformity across large area substrates with electrical properties equivalent to geological crystals will be described. Controlled doping of 2D semiconductors is also critically required. However, methods established for conventional semiconductors, such as ion implantation, are not easily applicable to 2D materials because of their atomically thin structure. Redox-active molecular dopants will be demonstrated which provide large changes in carrier density and workfunction through the choice of dopant, treatment time, and the solution concentration. Finally, several applications of these large-area, uniform 2D materials will be described including heterostructures, biosensors and strain sensors.

  11. 2D microwave imaging reflectometer electronics.

    PubMed

    Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  12. Assessing 2D electrophoretic mobility spectroscopy (2D MOSY) for analytical applications.

    PubMed

    Fang, Yuan; Yushmanov, Pavel V; Furó, István

    2016-12-08

    Electrophoretic displacement of charged entity phase modulates the spectrum acquired in electrophoretic NMR experiments, and this modulation can be presented via 2D FT as 2D mobility spectroscopy (MOSY) spectra. We compare in various mixed solutions the chemical selectivity provided by 2D MOSY spectra with that provided by 2D diffusion-ordered spectroscopy (DOSY) spectra and demonstrate, under the conditions explored, a superior performance of the former method. 2D MOSY compares also favourably with closely related LC-NMR methods. The shape of 2D MOSY spectra in complex mixtures is strongly modulated by the pH of the sample, a feature that has potential for areas such as in drug discovery and metabolomics. Copyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd. StartCopTextCopyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.

  13. 2D Distributed Sensing Via TDR

    DTIC Science & Technology

    2007-11-02

    plate VEGF CompositeSensor Experimental Setup Air 279 mm 61 78 VARTM profile: slope RTM profile: rectangle 22 1 Jul 2003© 2003 University of Delaware...2003 University of Delaware All rights reserved Vision: Non-contact 2D sensing ü VARTM setup constructed within TL can be sensed by its EM field: 2D...300.0 mm/ns. 1 2 1 Jul 2003© 2003 University of Delaware All rights reserved Model Validation “ RTM Flow” TDR Response to 139 mm VEGC

  14. Inkjet printing of 2D layered materials.

    PubMed

    Li, Jiantong; Lemme, Max C; Östling, Mikael

    2014-11-10

    Inkjet printing of 2D layered materials, such as graphene and MoS2, has attracted great interests for emerging electronics. However, incompatible rheology, low concentration, severe aggregation and toxicity of solvents constitute critical challenges which hamper the manufacturing efficiency and product quality. Here, we introduce a simple and general technology concept (distillation-assisted solvent exchange) to efficiently overcome these challenges. By implementing the concept, we have demonstrated excellent jetting performance, ideal printing patterns and a variety of promising applications for inkjet printing of 2D layered materials.

  15. Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding.

    PubMed

    Little, Damon P

    2014-09-01

    Ginkgo biloba L. (known as ginkgo or maidenhair tree) is a phylogenetically isolated, charismatic, gymnosperm tree. Herbal dietary supplements, prepared from G. biloba leaves, are consumed to boost cognitive capacity via improved blood perfusion and mitochondrial function. A novel DNA mini-barcode assay was designed and validated for the authentication of G. biloba in herbal dietary supplements (n = 22; sensitivity = 1.00, 95% CI = 0.59-1.00; specificity = 1.00, 95% CI = 0.64-1.00). This assay was further used to estimate the frequency of mislabeled ginkgo herbal dietary supplements on the market in the United States of America: DNA amenable to PCR could not be extracted from three (7.5%) of the 40 supplements sampled, 31 of 37 (83.8%) assayable supplements contained identifiable G. biloba DNA, and six supplements (16.2%) contained fillers without any detectable G. biloba DNA. It is hoped that this assay will be used by supplement manufacturers to ensure that their supplements contain G. biloba.

  16. An embedded barcode for "connected" malaria rapid diagnostic tests.

    PubMed

    Scherr, Thomas F; Gupta, Sparsh; Wright, David W; Haselton, Frederick R

    2017-03-29

    Many countries are shifting their efforts from malaria control to disease elimination. New technologies will be necessary to meet the more stringent demands of elimination campaigns, including improved quality control of malaria diagnostic tests, as well as an improved means for communicating test results among field healthcare workers, test manufacturers, and national ministries of health. In this report, we describe and evaluate an embedded barcode within standard rapid diagnostic tests as one potential solution. This information-augmented diagnostic test operates on the familiar principles of traditional lateral flow assays and simply replaces the control line with a control grid patterned in the shape of a QR (quick response) code. After the test is processed, the QR code appears on both positive or negative tests. In this report we demonstrate how this multipurpose code can be used not only to fulfill the control line role of test validation, but also to embed test manufacturing details, serve as a trigger for image capture, enable registration for image analysis, and correct for lighting effects. An accompanying mobile phone application automatically captures an image of the test when the QR code is recognized, decodes the QR code, performs image processing to determine the concentration of the malarial biomarker histidine-rich protein 2 at the test line, and transmits the test results and QR code payload to a secure web portal. This approach blends automated, sub-nanomolar biomarker detection, with near real-time reporting to provide quality assurance data that will help to achieve malaria elimination.

  17. Ultrathin 2D Metal-Organic Framework Nanosheets.

    PubMed

    Zhao, Meiting; Wang, Yixian; Ma, Qinglang; Huang, Ying; Zhang, Xiao; Ping, Jianfeng; Zhang, Zhicheng; Lu, Qipeng; Yu, Yifu; Xu, Huan; Zhao, Yanli; Zhang, Hua

    2015-12-02

    A facile surfactant-assisted bottom-up synthetic method to prepare a series of freestanding ultrathin 2D M-TCPP (M = Zn, Cu, Cd or Co, TCPP = tetrakis(4-carboxyphenyl)porphyrin) nanosheets with a thickness of sub-10 nm is developed. As a proof-of-concept application, some of them are successfully used as new platforms for DNA detection. The Cu-TCPP nanosheet-based sensor shows excellent fluorescent sensing performance and is used for the simultaneous detection of multiple DNA targets.

  18. DNA barcoding in the media: does coverage of cool science reflect its social context?

    PubMed

    Geary, Janis; Camicioli, Emma; Bubela, Tania

    2016-09-01

    Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.

  19. DNA barcoding of the vegetable leafminer Liriomyza sativae Blanchard (Diptera: Agromyzidae) in Bangladesh

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA barcoding revealed the presence of the polyphagous leafminer pest Liriomyza sativae Blanchard in Bangladesh. DNA barcode sequences for mitochondrial COI were generated for Agromyzidae larvae, pupae and adults collected from field populations across Bangladesh. BLAST sequence similarity searches ...

  20. Parallel Stitching of 2D Materials.

    PubMed

    Ling, Xi; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; Hsu, Allen L; Bie, Yaqing; Lee, Yi-Hsien; Zhu, Yimei; Wu, Lijun; Li, Ju; Jarillo-Herrero, Pablo; Dresselhaus, Mildred; Palacios, Tomás; Kong, Jing

    2016-03-23

    Diverse parallel stitched 2D heterostructures, including metal-semiconductor, semiconductor-semiconductor, and insulator-semiconductor, are synthesized directly through selective "sowing" of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. The methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  1. Parallel stitching of 2D materials

    DOE PAGES

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; ...

    2016-01-27

    Diverse parallel stitched 2D heterostructures, including metal–semiconductor, semiconductor–semiconductor, and insulator–semiconductor, are synthesized directly through selective “sowing” of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. Lastly, the methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  2. International Barcode of Life: Evolution of a global research community.

    PubMed

    Adamowicz, Sarah J

    2015-05-01

    The 6th International Barcode of Life Conference (Guelph, Canada, 18-21 August 2015), themed Barcodes to Biomes, showcases the latest developments in DNA barcoding research and its diverse applications. The meeting also provides a venue for a global research community to share ideas and to initiate collaborations. All plenary and contributed abstracts are being published as an open-access special issue of Genome. Here, I use a comparison with the 3rd Conference (Mexico City, 2009) to highlight 10 recent and emerging trends that are apparent among the contributed abstracts. One of the outstanding trends is the rising proportion of abstracts that focus upon multiple socio-economically important applications of DNA barcoding, including studies of agricultural pests, quarantine and invasive species, wildlife forensics, disease vectors, biomonitoring of ecosystem health, and marketplace surveys evaluating the authenticity of seafood products and medicinal plants. Other key movements include the use of barcoding and metabarcoding approaches for dietary analyses-and for studies of food webs spanning three or more trophic levels-as well as the spread of next-generation sequencing methods in multiple contexts. In combination with the rising taxonomic and geographic scope of many barcoding iniatives, these developments suggest that several important questions in biology are becoming tractable. "What is this specimen on an agricultural shipment?", "Who eats whom in this whole food web?", and even "How many species are there?" are questions that may be answered in time periods ranging from a few years to one or a few decades. The next phases of DNA barcoding may expand yet further into prediction of community shifts with climate change and improved management of biological resources.

  3. 2D/3D Image Registration using Regression Learning

    PubMed Central

    Chou, Chen-Rui; Frederick, Brandon; Mageras, Gig; Chang, Sha; Pizer, Stephen

    2013-01-01

    In computer vision and image analysis, image registration between 2D projections and a 3D image that achieves high accuracy and near real-time computation is challenging. In this paper, we propose a novel method that can rapidly detect an object’s 3D rigid motion or deformation from a 2D projection image or a small set thereof. The method is called CLARET (Correction via Limited-Angle Residues in External Beam Therapy) and consists of two stages: registration preceded by shape space and regression learning. In the registration stage, linear operators are used to iteratively estimate the motion/deformation parameters based on the current intensity residue between the target projec-tion(s) and the digitally reconstructed radiograph(s) (DRRs) of the estimated 3D image. The method determines the linear operators via a two-step learning process. First, it builds a low-order parametric model of the image region’s motion/deformation shape space from its prior 3D images. Second, using learning-time samples produced from the 3D images, it formulates the relationships between the model parameters and the co-varying 2D projection intensity residues by multi-scale linear regressions. The calculated multi-scale regression matrices yield the coarse-to-fine linear operators used in estimating the model parameters from the 2D projection intensity residues in the registration. The method’s application to Image-guided Radiation Therapy (IGRT) requires only a few seconds and yields good results in localizing a tumor under rigid motion in the head and neck and under respiratory deformation in the lung, using one treatment-time imaging 2D projection or a small set thereof. PMID:24058278

  4. Identification of Scleractinian Coral Recruits Using Fluorescent Censusing and DNA Barcoding Techniques

    PubMed Central

    Hsu, Chia-Min; de Palmas, Stéphane; Kuo, Chao-Yang; Denis, Vianney; Chen, Chaolun Allen

    2014-01-01

    The identification of coral recruits has been problematic due to a lack of definitive morphological characters being available for higher taxonomic resolution. In this study, we tested whether fluorescent detection of coral recruits used in combinations of different DNA-barcoding markers (cytochrome oxidase I gene [COI], open reading frame [ORF], and nuclear Pax-C intron [PaxC]) could be useful for increasing the resolution of coral spat identification in ecological studies. One hundred and fifty settlement plates were emplaced at nine sites on the fringing reefs of Kenting National Park in southern Taiwan between April 2011 and September 2012. A total of 248 living coral spats and juveniles (with basal areas ranging from 0.21 to 134.57 mm2) were detected on the plates with the aid of fluorescent light and collected for molecular analyses. Using the COI DNA barcoding technique, 90.3% (224/248) of coral spats were successfully identified into six genera, including Acropora, Isopora, Montipora, Pocillopora, Porites, and Pavona. PaxC further separated I. cuneata and I. palifera of Isopora from Acropora, and ORF successfully identified the species of Pocillopora (except P. meandrina and P. eydouxi). Moreover, other cnidarian species such as actinarians, zoanthids, and Millepora species were visually found using fluorescence and identified by COI DNA barcoding. This combination of existing approaches greatly improved the taxonomic resolution of early coral life stages, which to date has been mainly limited to the family level based on skeletal identification. Overall, this study suggests important improvements for the identification of coral recruits in ecological studies. PMID:25211345

  5. Barcodes in a Medical Office Computer System: Experience with Eight Million Data Entry Operations

    PubMed Central

    Willard, Oliver T.

    1985-01-01

    A medical office management software package has been developed which utilizes barcodes to enhance data entry. The system has been in use in our practice since 1982. Currently, there are over twenty-five installations of this system with a combined experience of some eight million data entry operations using barcodes. The barcode system design and our experience with it is described.

  6. 76 FR 59504 - Intelligent Mail Package Barcode (IMpb) Implementation for Commercial Parcels

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-27

    ... unique tracking barcodes or IMpb. Mailers requiring an exception may direct their request to vice... Intelligent Mail unique tracking barcode on all commercial parcels, except Standard Mail parcels, claiming presort or destination entry pricing; to encourage use of IMpb unique tracking barcodes by providing...

  7. Managing Archival Collections in an Automated Environment: The Joys of Barcoding

    ERIC Educational Resources Information Center

    Hamburger, Susan; Charles, Jane Veronica

    2006-01-01

    In a desire for automated collection control, archival repositories are adopting barcoding from their library and records center colleagues. This article discusses the planning, design, and implementation phases of barcoding. The authors focus on reasons for barcoding, security benefits, in-room circulation tracking, potential for gathering…

  8. 2D resistivity method in delineating subsurface problems in urban area

    NASA Astrophysics Data System (ADS)

    Nordiana, M. M.; Saad, Rosli; Teh Saufia, A. H. A.; Azwin, I. N.; Ali, Nisa'; Hidayah, Noer El

    2013-05-01

    2D resistivity is carried out to detect spread saturated zone and subsurface problems cause by the presence of underground river, which resulted from selected urban area at Selangor, Malaysia. Six 2D resistivity survey lines with minimum 5 m electrode spacing were executed using Pole-dipole array. Borehole was carried out at multiple locations in the study area. Subsequently, the borehole was used to verify the 2D resistivity results. Interpretation of 2D resistivity data showed a low resistivity value (< 40 ohm-m), which appears to be a zone that is fully saturated with sandy silt and this could be an influence factor the increasing water level because sandy silt is highly permeable in nature. The borehole, support the results of 2D resistivity method relating a saturated zone in the survey area. There is a good correlation between the 2D resistivity investigations and the results of borehole records.

  9. Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS).

    PubMed

    Widom, Julia R; Johnson, Neil P; von Hippel, Peter H; Marcus, Andrew H

    2013-02-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analog of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS) - a fluorescence-detected variation of 2D electronic spectroscopy - to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point-dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R12 = 3.5 Å ± 0.5 Å, twist angle θ12 = 5° ± 5°), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV-2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein-nucleic acid complexes.

  10. DNA barcoding of tropical black flies (Diptera: Simuliidae) of Thailand.

    PubMed

    Pramual, Pairot; Adler, Peter H

    2014-03-01

    The ecological and medical importance of black flies drives the need for rapid and reliable identification of these minute, structurally uniform insects. We assessed the efficiency of DNA barcoding for species identification of tropical black flies. A total of 351 cytochrome c oxidase subunit 1 sequences were obtained from 41 species in six subgenera of the genus Simulium in Thailand. Despite high intraspecific genetic divergence (mean = 2.00%, maximum = 9.27%), DNA barcodes provided 96% correct identification. Barcodes also differentiated cytoforms of selected species complexes, albeit with varying levels of success. Perfect differentiation was achieved for two cytoforms of Simulium feuerborni, and 91% correct identification was obtained for the Simulium angulistylum complex. Low success (33%), however, was obtained for the Simulium siamense complex. The differential efficiency of DNA barcodes to discriminate cytoforms was attributed to different levels of genetic structure and demographic histories of the taxa. DNA barcode trees were largely congruent with phylogenies based on previous molecular, chromosomal and morphological analyses, but revealed inconsistencies that will require further evaluation.

  11. Evaluating the diversity of Neotropical anurans using DNA barcodes

    PubMed Central

    Estupiñán, Ruth A.; Ferrari, Stephen F.; Gonçalves, Evonnildo C.; Barbosa, Maria Silvanira R.; Vallinoto, Marcelo; Schneider, Maria Paula C.

    2016-01-01

    Abstract This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4–19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11–39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study. PMID:28138277

  12. Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms

    PubMed Central

    Shukla, Virendra; Tuli, Rakesh

    2010-01-01

    Background DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species. Methodology and Principal Findings A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR. Conclusions/Significance Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies. PMID:20808837

  13. Automation and workflow considerations for embedding Digimarc Barcodes at scale

    NASA Astrophysics Data System (ADS)

    Rodriguez, Tony; Haaga, Don; Calhoon, Sean

    2015-03-01

    The Digimarc® Barcode is a digital watermark applied to packages and variable data labels that carries GS1 standard GTIN-14 data traditionally carried by a 1-D barcode. The Digimarc Barcode can be read with smartphones and imaging-based barcode readers commonly used in grocery and retail environments. Using smartphones, consumers can engage with products and retailers can materially increase the speed of check-out, increasing store margins and providing a better experience for shoppers. Internal testing has shown an average of 53% increase in scanning throughput, enabling 100's of millions of dollars in cost savings [1] for retailers when deployed at scale. To get to scale, the process of embedding a digital watermark must be automated and integrated within existing workflows. Creating the tools and processes to do so represents a new challenge for the watermarking community. This paper presents a description and an analysis of the workflow implemented by Digimarc to deploy the Digimarc Barcode at scale. An overview of the tools created and lessons learned during the introduction of technology to the market are provided.

  14. DNA barcodes for 1/1000 of the animal kingdom.

    PubMed

    Hebert, Paul D N; Dewaard, Jeremy R; Landry, Jean-François

    2010-06-23

    This study reports DNA barcodes for more than 1300 Lepidoptera species from the eastern half of North America, establishing that 99.3 per cent of these species possess diagnostic barcode sequences. Intraspecific divergences averaged just 0.43 per cent among this assemblage, but most values were lower. The mean was elevated by deep barcode divergences (greater than 2%) in 5.1 per cent of the species, often involving the sympatric occurrence of two barcode clusters. A few of these cases have been analysed in detail, revealing species overlooked by the current taxonomic system. This study also provided a large-scale test of the extent of regional divergence in barcode sequences, indicating that geographical differentiation in the Lepidoptera of eastern North America is small, even when comparisons involve populations as much as 2800 km apart. The present results affirm that a highly effective system for the identification of Lepidoptera in this region can be built with few records per species because of the limited intra-specific variation. As most terrestrial and marine taxa are likely to possess a similar pattern of population structure, an effective DNA-based identification system can be developed with modest effort.

  15. Efficiency of ITS sequences for DNA barcoding in Passiflora (Passifloraceae).

    PubMed

    Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

    2015-04-01

    DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using "best match" and "best close match" methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

  16. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)

    PubMed Central

    Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

    2015-01-01

    DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species. PMID:25837628

  17. Compatible embedding for 2D shape animation.

    PubMed

    Baxter, William V; Barla, Pascal; Anjyo, Ken-Ichi

    2009-01-01

    We present new algorithms for the compatible embedding of 2D shapes. Such embeddings offer a convenient way to interpolate shapes having complex, detailed features. Compared to existing techniques, our approach requires less user input, and is faster, more robust, and simpler to implement, making it ideal for interactive use in practical applications. Our new approach consists of three parts. First, our boundary matching algorithm locates salient features using the perceptually motivated principles of scale-space and uses these as automatic correspondences to guide an elastic curve matching algorithm. Second, we simplify boundaries while maintaining their parametric correspondence and the embedding of the original shapes. Finally, we extend the mapping to shapes' interiors via a new compatible triangulation algorithm. The combination of our algorithms allows us to demonstrate 2D shape interpolation with instant feedback. The proposed algorithms exhibit a combination of simplicity, speed, and accuracy that has not been achieved in previous work.

  18. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

    Sahoo, Nanda Gopal; Esteves, Richard J.; Punetha, Vinay Deep; Pestov, Dmitry; Arachchige, Indika U.; McLeskey, James T.

    2016-07-01

    We report on the fabrication and characterization of a Schottky diode made using 2D germanane (hydrogenated germanene). When compared to germanium, the 2D structure has higher electron mobility, an optimal band-gap, and exceptional stability making germanane an outstanding candidate for a variety of opto-electronic devices. One-atom-thick sheets of hydrogenated puckered germanium atoms have been synthesized from a CaGe2 framework via intercalation and characterized by XRD, Raman, and FTIR techniques. The material was then used to fabricate Schottky diodes by suspending the germanane in benzonitrile and drop-casting it onto interdigitated metal electrodes. The devices demonstrate significant rectifying behavior and the outstanding potential of this material.

  19. Extrinsic Cation Selectivity of 2D Membranes

    PubMed Central

    2017-01-01

    From a systematic study of the concentration driven diffusion of positive and negative ions across porous 2D membranes of graphene and hexagonal boron nitride (h-BN), we prove their cation selectivity. Using the current–voltage characteristics of graphene and h-BN monolayers separating reservoirs of different salt concentrations, we calculate the reversal potential as a measure of selectivity. We tune the Debye screening length by exchanging the salt concentrations and demonstrate that negative surface charge gives rise to cation selectivity. Surprisingly, h-BN and graphene membranes show similar characteristics, strongly suggesting a common origin of selectivity in aqueous solvents. For the first time, we demonstrate that the cation flux can be increased by using ozone to create additional pores in graphene while maintaining excellent selectivity. We discuss opportunities to exploit our scalable method to use 2D membranes for applications including osmotic power conversion. PMID:28157333

  20. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surface contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.

  1. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Lin, Jerry

    1996-08-07

    DYNA2D* is a vectorized, explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. DYNA2D* contains 13 material models and 9 equations of state (EOS) to cover a wide range of material behavior. The material models implemented in all machine versions are: elastic, orthotropic elastic, kinematic/isotropic elastic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, rubber, high explosive burn, isotropic elastic-plastic, temperature-dependent elastic-plastic. The isotropic and temperature-dependent elastic-plastic models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state including linear polynomial, JWL high explosive, Sack Tuesday high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, and tabulated.

  2. Quasiparticle interference in unconventional 2D systems

    NASA Astrophysics Data System (ADS)

    Chen, Lan; Cheng, Peng; Wu, Kehui

    2017-03-01

    At present, research of 2D systems mainly focuses on two kinds of materials: graphene-like materials and transition-metal dichalcogenides (TMDs). Both of them host unconventional 2D electronic properties: pseudospin and the associated chirality of electrons in graphene-like materials, and spin-valley-coupled electronic structures in the TMDs. These exotic electronic properties have attracted tremendous interest for possible applications in nanodevices in the future. Investigation on the quasiparticle interference (QPI) in 2D systems is an effective way to uncover these properties. In this review, we will begin with a brief introduction to 2D systems, including their atomic structures and electronic bands. Then, we will discuss the formation of Friedel oscillation due to QPI in constant energy contours of electron bands, and show the basic concept of Fourier-transform scanning tunneling microscopy/spectroscopy (FT-STM/STS), which can resolve Friedel oscillation patterns in real space and consequently obtain the QPI patterns in reciprocal space. In the next two parts, we will summarize some pivotal results in the investigation of QPI in graphene and silicene, in which systems the low-energy quasiparticles are described by the massless Dirac equation. The FT-STM experiments show there are two different interference channels (intervalley and intravalley scattering) and backscattering suppression, which associate with the Dirac cones and the chirality of quasiparticles. The monolayer and bilayer graphene on different substrates (SiC and metal surfaces), and the monolayer and multilayer silicene on a Ag(1 1 1) surface will be addressed. The fifth part will introduce the FT-STM research on QPI in TMDs (monolayer and bilayer of WSe2), which allow us to infer the spin texture of both conduction and valence bands, and present spin-valley coupling by tracking allowed and forbidden scattering channels.

  3. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Vračko, Marjan; Zupan, Jure; Novič, Marjana

    2003-05-01

    We present a novel 2-D graphical representation for DNA sequences which has an important advantage over the existing graphical representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the 'worm' curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.

  4. 2D Metals by Repeated Size Reduction.

    PubMed

    Liu, Hanwen; Tang, Hao; Fang, Minghao; Si, Wenjie; Zhang, Qinghua; Huang, Zhaohui; Gu, Lin; Pan, Wei; Yao, Jie; Nan, Cewen; Wu, Hui

    2016-10-01

    A general and convenient strategy for manufacturing freestanding metal nanolayers is developed on large scale. By the simple process of repeatedly folding and calendering stacked metal sheets followed by chemical etching, free-standing 2D metal (e.g., Ag, Au, Fe, Cu, and Ni) nanosheets are obtained with thicknesses as small as 1 nm and with sizes of the order of several micrometers.

  5. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

    Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

  6. DNA barcode sequencing from old type specimens as a tool in taxonomy: a case study in the diverse genus Eois (Lepidoptera: Geometridae).

    PubMed

    Strutzenberger, Patrick; Brehm, Gunnar; Fiedler, Konrad

    2012-01-01

    In this study we report on the sequencing of the COI barcode region from 96 historical specimens (92 type specimens +4 non-types) of Eois. Eois is a diverse clade of tropical geometrid moths and is the target of a number of ongoing studies on life-histories, phylogeny, co-evolution with host plants or parasitoids, and diversity patterns across temporal and spatial dimensions. The unequivocal application of valid names is crucial for all aspects of biodiversity research as well as monitoring and conservation efforts. The availability of barcodes from historical type specimens has the potential to facilitate the much-needed acceleration of species description. We performed non-destructive DNA extraction on the abdomens of Eois specimens between 79 and 157 years of age. We used six primer combinations (recovering between 109 and 130 bp each) to target the full-length barcode sequence of each specimen. We were able to obtain sequences for 91 of 96 specimens (success rate 94.8%). Sequence length ranged from 121 bp to full barcode sequences (658 bp), the average sequence length was ~500 bp. We detected a moderately strong and statistically significant negative correlation between specimen age and total sequence length, which is in agreement with expectations. The abdomen proved to be an exceedingly valuable source of DNA in old specimens of Lepidoptera. Barcode sequences obtained in this study are currently being used in an effort towards a step-wise taxonomic revision of Eois. We encourage that DNA barcodes obtained from types specimens should be included in all species descriptions and revisions whenever feasible.

  7. DNA Barcode Sequencing from Old Type Specimens as a Tool in Taxonomy: A Case Study in the Diverse Genus Eois (Lepidoptera: Geometridae)

    PubMed Central

    Strutzenberger, Patrick; Brehm, Gunnar; Fiedler, Konrad

    2012-01-01

    In this study we report on the sequencing of the COI barcode region from 96 historical specimens (92 type specimens +4 non-types) of Eois. Eois is a diverse clade of tropical geometrid moths and is the target of a number of ongoing studies on life-histories, phylogeny, co-evolution with host plants or parasitoids, and diversity patterns across temporal and spatial dimensions. The unequivocal application of valid names is crucial for all aspects of biodiversity research as well as monitoring and conservation efforts. The availability of barcodes from historical type specimens has the potential to facilitate the much-needed acceleration of species description. We performed non-destructive DNA extraction on the abdomens of Eois specimens between 79 and 157 years of age. We used six primer combinations (recovering between 109 and 130 bp each) to target the full-length barcode sequence of each specimen. We were able to obtain sequences for 91 of 96 specimens (success rate 94.8%). Sequence length ranged from 121 bp to full barcode sequences (658 bp), the average sequence length was ∼500 bp. We detected a moderately strong and statistically significant negative correlation between specimen age and total sequence length, which is in agreement with expectations. The abdomen proved to be an exceedingly valuable source of DNA in old specimens of Lepidoptera. Barcode sequences obtained in this study are currently being used in an effort towards a step-wise taxonomic revision of Eois. We encourage that DNA barcodes obtained from types specimens should be included in all species descriptions and revisions whenever feasible. PMID:23185414

  8. Building-Up of a DNA Barcode Library for True Bugs (Insecta: Hemiptera: Heteroptera) of Germany Reveals Taxonomic Uncertainties and Surprises

    PubMed Central

    Raupach, Michael J.; Hendrich, Lars; Küchler, Stefan M.; Deister, Fabian; Morinière, Jérome; Gossner, Martin M.

    2014-01-01

    During the last few years, DNA barcoding has become an efficient method for the identification of species. In the case of insects, most published DNA barcoding studies focus on species of the Ephemeroptera, Trichoptera, Hymenoptera and especially Lepidoptera. In this study we test the efficiency of DNA barcoding for true bugs (Hemiptera: Heteroptera), an ecological and economical highly important as well as morphologically diverse insect taxon. As part of our study we analyzed DNA barcodes for 1742 specimens of 457 species, comprising 39 families of the Heteroptera. We found low nucleotide distances with a minimum pairwise K2P distance <2.2% within 21 species pairs (39 species). For ten of these species pairs (18 species), minimum pairwise distances were zero. In contrast to this, deep intraspecific sequence divergences with maximum pairwise distances >2.2% were detected for 16 traditionally recognized and valid species. With a successful identification rate of 91.5% (418 species) our study emphasizes the use of DNA barcodes for the identification of true bugs and represents an important step in building-up a comprehensive barcode library for true bugs in Germany and Central Europe as well. Our study also highlights the urgent necessity of taxonomic revisions for various taxa of the Heteroptera, with a special focus on various species of the Miridae. In this context we found evidence for on-going hybridization events within various taxonomically challenging genera (e.g. Nabis Latreille, 1802 (Nabidae), Lygus Hahn, 1833 (Miridae), Phytocoris Fallén, 1814 (Miridae)) as well as the putative existence of cryptic species (e.g. Aneurus avenius (Duffour, 1833) (Aradidae) or Orius niger (Wolff, 1811) (Anthocoridae)). PMID:25203616

  9. Building-up of a DNA barcode library for true bugs (insecta: hemiptera: heteroptera) of Germany reveals taxonomic uncertainties and surprises.

    PubMed

    Raupach, Michael J; Hendrich, Lars; Küchler, Stefan M; Deister, Fabian; Morinière, Jérome; Gossner, Martin M

    2014-01-01

    During the last few years, DNA barcoding has become an efficient method for the identification of species. In the case of insects, most published DNA barcoding studies focus on species of the Ephemeroptera, Trichoptera, Hymenoptera and especially Lepidoptera. In this study we test the efficiency of DNA barcoding for true bugs (Hemiptera: Heteroptera), an ecological and economical highly important as well as morphologically diverse insect taxon. As part of our study we analyzed DNA barcodes for 1742 specimens of 457 species, comprising 39 families of the Heteroptera. We found low nucleotide distances with a minimum pairwise K2P distance <2.2% within 21 species pairs (39 species). For ten of these species pairs (18 species), minimum pairwise distances were zero. In contrast to this, deep intraspecific sequence divergences with maximum pairwise distances >2.2% were detected for 16 traditionally recognized and valid species. With a successful identification rate of 91.5% (418 species) our study emphasizes the use of DNA barcodes for the identification of true bugs and represents an important step in building-up a comprehensive barcode library for true bugs in Germany and Central Europe as well. Our study also highlights the urgent necessity of taxonomic revisions for various taxa of the Heteroptera, with a special focus on various species of the Miridae. In this context we found evidence for on-going hybridization events within various taxonomically challenging genera (e.g. Nabis Latreille, 1802 (Nabidae), Lygus Hahn, 1833 (Miridae), Phytocoris Fallén, 1814 (Miridae)) as well as the putative existence of cryptic species (e.g. Aneurus avenius (Duffour, 1833) (Aradidae) or Orius niger (Wolff, 1811) (Anthocoridae)).

  10. Engineering light outcoupling in 2D materials.

    PubMed

    Lien, Der-Hsien; Kang, Jeong Seuk; Amani, Matin; Chen, Kevin; Tosun, Mahmut; Wang, Hsin-Ping; Roy, Tania; Eggleston, Michael S; Wu, Ming C; Dubey, Madan; Lee, Si-Chen; He, Jr-Hau; Javey, Ali

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells.

  11. Irreversibility-inversions in 2D turbulence

    NASA Astrophysics Data System (ADS)

    Bragg, Andrew; de Lillo, Filippo; Boffetta, Guido

    2016-11-01

    We consider a recent theoretical prediction that for inertial particles in 2D turbulence, the nature of the irreversibility of their pair dispersion inverts when the particle inertia exceeds a certain value. In particular, when the particle Stokes number, St , is below a certain value, the forward-in-time (FIT) dispersion should be faster than the backward-in-time (BIT) dispersion, but for St above this value, this should invert so that BIT becomes faster than FIT dispersion. This non-trivial behavior arises because of the competition between two physically distinct irreversibility mechanisms that operate in different regimes of St . In 3D turbulence, both mechanisms act to produce faster BIT than FIT dispersion, but in 2D, the two mechanisms have opposite effects because of the inverse energy cascade in the turbulent velocity field. We supplement the qualitative argument given by Bragg et al. by deriving quantitative predictions of this effect in the short-time dispersion limit. These predictions are then confirmed by results of inertial particle dispersion in a direct numerical simulation of 2D turbulence.

  12. DNA Barcoding Identifies Illegal Parrot Trade.

    PubMed

    Gonçalves, Priscila F M; Oliveira-Marques, Adriana R; Matsumoto, Tania E; Miyaki, Cristina Y

    2015-01-01

    Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool.

  13. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

    2D superconductivity is attracting a renewed interest due to the discoveries of new highly crystalline 2D superconductors in the past decade. Superconductivity at the oxide interfaces triggered by LaAlO3/SrTiO3 has become one of the promising routes for creation of new 2D superconductors. Also, the MBE grown metallic monolayers including FeSe are also offering a new platform of 2D superconductors. In the last two years, there appear a variety of monolayer/bilayer superconductors fabricated by CVD or mechanical exfoliation. Among these, electric field induced superconductivity by electric double layer transistor (EDLT) is a unique platform of 2D superconductivity, because of its ability of high density charge accumulation, and also because of the versatility in terms of materials, stemming from oxides to organics and layered chalcogenides. In this presentation, the following issues of electric filed induced superconductivity will be addressed; (1) Tunable carrier density, (2) Weak pinning, (3) Absence of inversion symmetry. (1) Since the sheet carrier density is quasi-continuously tunable from 0 to the order of 1014 cm-2, one is able to establish an electronic phase diagram of superconductivity, which will be compared with that of bulk superconductors. (2) The thickness of superconductivity can be estimated as 2 - 10 nm, dependent on materials, and is much smaller than the in-plane coherence length. Such a thin but low resistance at normal state results in extremely weak pinning beyond the dirty Boson model in the amorphous metallic films. (3) Due to the electric filed, the inversion symmetry is inherently broken in EDLT. This feature appears in the enhancement of Pauli limit of the upper critical field for the in-plane magnetic fields. In transition metal dichalcogenide with a substantial spin-orbit interactions, we were able to confirm the stabilization of Cooper pair due to its spin-valley locking. This work has been supported by Grant-in-Aid for Specially

  14. DNA Barcoding the Heliothinae (Lepidoptera: Noctuidae) of Australia and Utility of DNA Barcodes for Pest Identification in Helicoverpa and Relatives

    PubMed Central

    Gopurenko, David

    2016-01-01

    Helicoverpa and Heliothis species include some of the world’s most significant crop pests, causing billions of dollars of losses globally. As such, a number are regulated quarantine species. For quarantine agencies, the most crucial issue is distinguishing native species from exotics, yet even this task is often not feasible because of poorly known local faunas and the difficulties of identifying closely related species, especially the immature stages. DNA barcoding is a scalable molecular diagnostic method that could provide the solution to this problem, however there has been no large-scale test of the efficacy of DNA barcodes for identifying the Heliothinae of any region of the world to date. This study fills that gap by DNA barcoding the entire heliothine moth fauna of Australia, bar one rare species, and comparing results with existing public domain resources. We find that DNA barcodes provide robust discrimination of all of the major pest species sampled, but poor discrimination of Australian Heliocheilus species, and we discuss ways to improve the use of DNA barcodes for identification of pests. PMID:27509042

  15. DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae)

    PubMed Central

    Zhu, Xi-Chao; Chen, Jing; Chen, Rui; Jiang, Li-Yun; Qiao, Ge-Xia

    2017-01-01

    Abstract Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process). The genetic interspecific divergence was clearly larger than the intraspecific divergence for four molecular markers. COI and COII genes were found to be more suitable for Chaitophorinae DNA barcoding. For species delimitation, at least one distance-based method combined with one tree-based method would be preferable. Based on the data for Chaitophorus saliniger and Laingia psammae, DNA barcoding may also reveal geographical variation. PMID:28331401

  16. Pollen DNA barcoding: current applications and future prospects.

    PubMed

    Bell, Karen L; de Vere, Natasha; Keller, Alexander; Richardson, Rodney T; Gous, Annemarie; Burgess, Kevin S; Brosi, Berry J

    2016-09-01

    Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.

  17. A laboratory information management system for DNA barcoding workflows.

    PubMed

    Vu, Thuy Duong; Eberhardt, Ursula; Szöke, Szániszló; Groenewald, Marizeth; Robert, Vincent

    2012-07-01

    This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.

  18. DNA barcoding of fungi causing infections in humans and animals.

    PubMed

    Irinyi, Laszlo; Lackner, Michaela; de Hoog, G Sybren; Meyer, Wieland

    2016-02-01

    Correct species identification is becoming increasingly important in clinical diagnostics. Till now, many mycological laboratories rely on conventional phenotypic identification. But this is slow and strongly operator-dependent. Therefore, to improve the quality of pathogen identification, rapid, reliable, and objective identification methods are essential. One of the most encouraging approaches is molecular barcoding using the internal transcribed spacer (ITS) of the rDNA, which is rapid, easily achievable, accurate, and applicable directly from clinical specimens. It relies on the comparison of a single ITS sequence with a curated reference database. The International Society for Human and Animal Mycology (ISHAM) working group for DNA barcoding has recently established such a database, focusing on the majority of human and animal pathogenic fungi (ISHAM-ITS, freely accessible at http://www.isham.org/ or directly from http://its.mycologylab.org). For some fungi the use of secondary barcodes may be necessary.

  19. Detecting Dangerous Substances from Their 2D Spectra

    DTIC Science & Technology

    2011-04-01

    their 16S ribosomal DNA sequences. For example, we can distinguish between B . cereus and B . thuringien- sis, which are genetically similar to within...ABSTRACT Same as Report (SAR) 18. NUMBER OF PAGES 4 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b . ABSTRACT unclassified c. THIS PAGE

  20. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity.

    PubMed

    Leray, Matthieu; Knowlton, Nancy

    2015-02-17

    Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼ 15.64 m(2) and volume of ∼ 0.09 m(3), 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼ 2 m were significantly more similar than samples separated by ∼ 100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence-absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring.

  1. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

    PubMed Central

    Leray, Matthieu; Knowlton, Nancy

    2015-01-01

    Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼15.64 m2 and volume of ∼0.09 m3, 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼2 m were significantly more similar than samples separated by ∼100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence–absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring. PMID:25646458

  2. FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

    PubMed Central

    Dodt, Matthias; Roehr, Johannes T.; Ahmed, Rina; Dieterich, Christoph

    2012-01-01

    Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to the sequencing platform and library construction method (e.g., adapter sequences); (b) have been introduced by experimental design (e.g., sample barcodes); or (c) constitute some biological signal (e.g., splice leader sequences in nematodes). Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/. PMID:24832523

  3. Beyond genome sequencing: lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer.

    PubMed

    Blundell, Jamie R; Levy, Sasha F

    2014-12-01

    Evolving cellular communities, such as the gut microbiome, pathogenic infections, and cancer, consist of large populations of ~10(7)-10(14) cells. Because of their large population sizes, adaptation within these populations can be driven by many beneficial mutations that never rise above extremely low frequencies. Genome sequencing methods such as clonal, single cell, or whole population sequencing are poorly suited to detect these rare beneficial lineages, and, more generally, to characterize which mutations are most important to the population dynamics. Here, we introduce an alternative approach: high-resolution lineage tracking with DNA barcodes. In contrast to whole genome sequencing, lineage tracking can detect a beneficial mutation at an extremely low frequency within the population, and estimate its time of occurrence and fitness effect. Many lineage trajectories can be observed in parallel, allowing one to observe the population dynamics in exquisite detail. We describe some of the technical and analytical challenges to lineage tracking with DNA barcodes and discuss its applications to studies of evolution, infectious disease and cancer.

  4. Broadband THz Spectroscopy of 2D Nanoscale Materials

    NASA Astrophysics Data System (ADS)

    Chen, Lu; Tripathi, Shivendra; Huang, Mengchen; Hsu, Jen-Feng; D'Urso, Brian; Lee, Hyungwoo; Eom, Chang-Beom; Irvin, Patrick; Levy, Jeremy

    Two-dimensional (2D) materials such as graphene and transition-metal dichalcogenides (TMDC) have attracted intense research interest in the past decade. Their unique electronic and optical properties offer the promise of novel optoelectronic applications in the terahertz regime. Recently, generation and detection of broadband terahertz (10 THz bandwidth) emission from 10-nm-scale LaAlO3/SrTiO3 nanostructures created by conductive atomic force microscope (c-AFM) lithography has been demonstrated . This unprecedented control of THz emission at 10 nm length scales creates a pathway toward hybrid THz functionality in 2D-material/LaAlO3/SrTiO3 heterostructures. Here we report initial efforts in THz spectroscopy of 2D nanoscale materials with resolution comparable to the dimensions of the nanowire (10 nm). Systems under investigation include graphene, single-layer molybdenum disulfide (MoS2), and tungsten diselenide (WSe2) nanoflakes. 1. Y. Ma, et al., Nano Lett. 13, 2884 (2013). We gratefully acknowledge financial support from the following agencies and grants: AFOSR (FA9550-12-1-0268 (JL, PRI), FA9550-12-1-0342 (CBE)), ONR (N00014-13-1-0806 (JL, CBE), N00014-15-1-2847 (JL)), NSF DMR-1124131 (JL, CBE) and DMR-1234096 (CBE).

  5. The changing epitome of species identification - DNA barcoding.

    PubMed

    Ajmal Ali, M; Gyulai, Gábor; Hidvégi, Norbert; Kerti, Balázs; Al Hemaid, Fahad M A; Pandey, Arun K; Lee, Joongku

    2014-07-01

    The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.

  6. DNA barcoding of commercially important catfishes in the Philippines.

    PubMed

    Quilang, Jonas P; Yu, Shiny Cathlynne S

    2015-06-01

    Many species of catfish are important resources for human consumption, for sport fishing and for use in aquarium industry. In the Philippines, some species are cultivated and some are caught in the wild for food and a few introduced species have become invasive. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was done on commercially and economically important Philippine catfishes. A total of 75 specimens belonging to 11 species and 5 families were DNA barcoded. The genetic distances were computed and Neighbor-Joining (NJ) trees were constructed based on the Kimura 2-Parameter (K2P) method. The average K2P distances within species, genus, family and order were 0.2, 8.2, 12.7 and 21.9%, respectively. COI sequences clustered according to their species designation for 7 of the 11 catfishes. DNA barcoding was not able to discriminate between Arius dispar and A. manillensis and between Pterygoplichthys disjunctivus and P. pardalis. The morphological characters that are used to distinguish between these species do not complement molecular identification through DNA barcoding. DNA barcoding also showed that Clarias batrachus from the Philippines is different from the species found in India and Thailand, which supports earlier suggestions based on morphology that those found in India should be designated as C. magur and those in mainland Southeast Asia as C. aff. batrachus "Indochina". This study has shown that DNA barcoding can be used for species delineation and for tagging some species for further taxonomic investigation, which has implications on proper management and conservation strategies.

  7. Selective and universal primers for trematode barcoding in freshwater snails.

    PubMed

    Routtu, J; Grunberg, D; Izhar, R; Dagan, Y; Guttel, Y; Ucko, M; Ben-Ami, F

    2014-07-01

    Trematodes are significant pathogens of high medical, veterinary, and environmental importance. They are hard to isolate from their intermediate hosts, and their early life stages are difficult to identify morphologically. Therefore, primers were developed for trematodes to create a species barcoding system and allow selective PCR amplification in mixed samples. The specific oligonucleotide primer was universal for trematodes that infected several freshwater snail species in Israel. The diagnostic tool is based on the 18S rDNA gene. In contrast to morphological identification, trematode barcoding is rapid as it is based on a sequence of only 800 bp, and it classifies species accurately due to high polymorphism between conserved areas.

  8. Denture bar-coding: An innovative technique in forensic dentistry.

    PubMed

    Dineshshankar, Janardhanam; Venkateshwaran, Rajendran; Vidhya, J; Anuradha, R; Mary, Gold Pealin; Pradeep, R; Senthileagappan, A R

    2015-08-01

    Denture markers play an important role in forensic odontology and also in identifying a person. A number of methods are there for identifying dentures from a less expensive technique to a more expensive technique. Out of different denture markers, the bar-coding system is a way of collecting data from the mobile. Even a huge amount of data can be stored in that. It can be easily incorporated during acrylization of the denture and thus could be helpful in identification. This article reviews the strengths of bar-coding and how easily it can be used in the routine procedure.

  9. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae).

    PubMed

    Starr, Julian R; Naczi, Robert F C; Chouinard, Brianna N

    2009-05-01

    We investigate the species discriminatory power of a subset of the proposed plant barcoding loci (matK, rbcL, rpoC1, rpoB, trnH-psbA) in Carex, a cosmopolitan genus that represents one of the three largest plant genera on earth (c. 2000 species). To assess the ability of barcoding loci to resolve Carex species, we focused our sampling on three of the taxonomically best-known groups in the genus, sections Deweyanae (6/8 species sampled), Griseae (18/21 species sampled), and Phyllostachyae (10/10 species sampled). Each group represents one of three major phylogenetic lineages previously identified in Carex and its tribe Cariceae, thus permitting us to evaluate the potential of DNA barcodes to broadly identify species across the tribe and to differentiate closely related sister species. Unlike some previous studies that have suggested that plant barcoding could achieve species identification rates around 90%, our results suggest that no single locus or multilocus barcode examined will resolve much greater than 60% of Carex species. In fact, no multilocus combination can significantly increase the resolution and statistical support (i.e., ≥ 70% bootstrap) for species than matK alone, even combinations involving the second most variable region, trnH-psbA. Results suggest that a matK barcode could help with species discovery as 47% of Carex taxa recently named or resolved within cryptic complexes in the past 25 years also formed unique species clusters in upgma trees. Comparisons between the nrDNA internal transcribed spacer region (ITS) and matK in sect. Phyllostachyae suggest that matK not only discriminates more species (50-60% vs. 25%), but it provides more resolved phylogenies than ITS. Given the low levels of species resolution in rpoC1 and rpoB (0-13%), and difficulties with polymerase chain reaction amplification and DNA sequencing in rbcL and trnH-psbA (alignment included), we strongly advocate that matK should be part of a universal plant barcoding system

  10. Denture bar-coding: An innovative technique in forensic dentistry

    PubMed Central

    Dineshshankar, Janardhanam; Venkateshwaran, Rajendran; Vidhya, J.; Anuradha, R.; Mary, Gold Pealin; Pradeep, R.; Senthileagappan, A. R.

    2015-01-01

    Denture markers play an important role in forensic odontology and also in identifying a person. A number of methods are there for identifying dentures from a less expensive technique to a more expensive technique. Out of different denture markers, the bar-coding system is a way of collecting data from the mobile. Even a huge amount of data can be stored in that. It can be easily incorporated during acrylization of the denture and thus could be helpful in identification. This article reviews the strengths of bar-coding and how easily it can be used in the routine procedure. PMID:26538876

  11. Fully automated 2D-3D registration and verification.

    PubMed

    Varnavas, Andreas; Carrell, Tom; Penney, Graeme

    2015-12-01

    Clinical application of 2D-3D registration technology often requires a significant amount of human interaction during initialisation and result verification. This is one of the main barriers to more widespread clinical use of this technology. We propose novel techniques for automated initial pose estimation of the 3D data and verification of the registration result, and show how these techniques can be combined to enable fully automated 2D-3D registration, particularly in the case of a vertebra based system. The initialisation method is based on preoperative computation of 2D templates over a wide range of 3D poses. These templates are used to apply the Generalised Hough Transform to the intraoperative 2D image and the sought 3D pose is selected with the combined use of the generated accumulator arrays and a Gradient Difference Similarity Measure. On the verification side, two algorithms are proposed: one using normalised features based on the similarity value and the other based on the pose agreement between multiple vertebra based registrations. The proposed methods are employed here for CT to fluoroscopy registration and are trained and tested with data from 31 clinical procedures with 417 low dose, i.e. low quality, high noise interventional fluoroscopy images. When similarity value based verification is used, the fully automated system achieves a 95.73% correct registration rate, whereas a no registration result is produced for the remaining 4.27% of cases (i.e. incorrect registration rate is 0%). The system also automatically detects input images outside its operating range.

  12. Effects of 22 CYP2D6 Genetic Variations Newly Identified in Chinese Population on Olanzapine Metabolism in vitro.

    PubMed

    Zhou, Hong-Yu; Gu, Er-Min; Chen, Qiu-Lei; Zhan, Yun-Yun; Wang, Shuang-Hu; Liang, Bing-Qing; Dai, Da-Peng; Cai, Jian-Ping; Hu, Guo-Xin

    2016-01-01

    The objective of this study was to assess the catalytic activity of 22 novel CYP2D6 allelic variants (2D6*87-*98, R25Q, F164L, E215K, F219S, V327M, D336N, V342M, R344Q, R440C and R497C) to olanzapine in vitro. Their protein products expressed in Spodoptera frugiperda 21 (Sf21) insect cells were incubated with olanzapine 100-2,000 μmol/l for 30 min. The kinetic parameters of Km, Vmax and intrinsic clearance were determined by 2-hydroxymethylolanzapine, the metabolite of olanzapine mediated by CYP2D6, using ultra-performance liquid chromatography tandem mass spectrometry. Results showed that the kinetic parameters of 2 alleles, CYP2D6*92 and 2D6*96, could not be detected; 17 allelic variants, CYP2D6*87-*88, 2D6*90-*91, 2D6*93-*95, 2D6*97, R25Q, F164L, E215K, F219S, V327M, V342M, R344Q, R440C and R497C, significantly reduced the intrinsic clearance of olanzapine; 2 variants, CYP2D6*89 and 2D6*98, increased the intrinsic clearance of olanzapine; no difference was found in intrinsic clearance of D336N. Furthermore, 6 alleles, CYP2D6*87, 2D6*88, 2D6*91, 2D6*93, 2D6*97 and R497C, exhibited higher Km values in a range of 120.80-217.56% relative to wild-type CYP2D6*1. The research demonstrated the metabolic phenotype of the 22 novel CYP2D6 variants for olanzapine that were different from probe drugs we used previously and might provide beneficial information to the personalized medicine of olanzapine.

  13. Flexible and Scalable Full‐Length CYP2D6 Long Amplicon PacBio Sequencing

    PubMed Central

    Vossen, Rolf H.A.M.; Anvar, Seyed Yahya; Allard, William G.; Guchelaar, Henk‐Jan; White, Stefan J.; den Dunnen, Johan T.; Swen, Jesse J.; van der Straaten, Tahar

    2017-01-01

    ABSTRACT Cytochrome P450 2D6 (CYP2D6) is among the most important genes involved in drug metabolism. Specific variants are associated with changes in the enzyme's amount and activity. Multiple technologies exist to determine these variants, like the AmpliChip CYP450 test, Taqman qPCR, or Second‐Generation Sequencing, however, sequence homology between cytochrome P450 genes and pseudogene CYP2D7 impairs reliable CYP2D6 genotyping, and variant phasing cannot accurately be determined using these assays. To circumvent this, we sequenced CYP2D6 using the Pacific Biosciences RSII and obtained high‐quality, full‐length, phased CYP2D6 sequences, enabling accurate variant calling and haplotyping of the entire gene‐locus including exonic, intronic, and upstream and downstream regions. Unphased diplotypes (Roche AmpliChip CYP450 test) were confirmed for 24 of the 25 samples, including gene duplications. Cases with gene deletions required additional specific assays to resolve. In total, 61 unique variants were detected, including variants that had not previously been associated with specific haplotypes. To further aid genomic analysis using standard reference sequences, we have established an LOVD‐powered CYP2D6 gene‐variant database, and added all reference haplotypes and data reported here. We conclude that our CYP2D6 genotyping approach produces reliable CYP2D6 diplotypes and reveals information about additional variants, including phasing and copy‐number variation. PMID:28044414

  14. A selective role of NKG2D in inflammatory and autoimmune diseases.

    PubMed

    Guerra, Nadia; Pestal, Kathleen; Juarez, Tiffany; Beck, Jennifer; Tkach, Karen; Wang, Lin; Raulet, David H

    2013-12-01

    The NKG2D activating receptor has been implicated in numerous autoimmune diseases. We tested the role of NKG2D in models of autoimmunity and inflammation using NKG2D knockout mice and antibody blockade experiments. The severity of experimental autoimmune encephalitis (EAE) was decreased in NKG2D-deficient mice when the disease was induced with a limiting antigen dose, but unchanged with an optimal antigen dose. Surprisingly, however, NKG2D deficiency had no detectable effect in several other models, including two models of type 1 diabetes, and a model of intestinal inflammation induced by poly(I:C). NKG2D antibody blockade in normal mice also failed to inhibit disease in the NOD diabetes model or the intestinal inflammation model. Published evidence using NKG2D knockout mice demonstrated a role for NKG2D in mouse models of atherosclerosis and liver inflammation, as well as in chronic obstructive pulmonary disease. Therefore, our results suggest that NKG2D plays selective roles in inflammatory diseases.

  15. Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

    PubMed Central

    Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

    2017-01-01

    Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing. PMID:28290550

  16. Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

    NASA Astrophysics Data System (ADS)

    Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

    2017-03-01

    Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

  17. Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding.

    PubMed

    Shahi, Payam; Kim, Samuel C; Haliburton, John R; Gartner, Zev J; Abate, Adam R

    2017-03-14

    Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

  18. Periodically sheared 2D Yukawa systems

    SciTech Connect

    Kovács, Anikó Zsuzsa; Hartmann, Peter; Donkó, Zoltán

    2015-10-15

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates.

  19. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

    The equilibrium states of 2D non-coarsening fluid foams, which consist of bubbles with fixed areas, correspond to local minima of the total perimeter. (1) The authors find an approximate value of the global minimum, and determine directly from an image how far a foam is from its ground state. (2) For (small) area disorder, small bubbles tend to sort inwards and large bubbles outwards. (3) Topological charges of the same sign repel while charges of opposite sign attract. (4) They discuss boundary conditions and the uniqueness of the pattern for fixed topology.

  20. Codon Constraints on Closed 2D Shapes,

    DTIC Science & Technology

    2014-09-26

    19843$ CODON CONSTRAINTS ON CLOSED 2D SHAPES Go Whitman Richards "I Donald D. Hoffman’ D T 18 Abstract: Codons are simple primitives for describing plane...RSONAL AUT"ORtIS) Richards, Whitman & Hoffman, Donald D. 13&. TYPE OF REPORT 13b. TIME COVERED N/A P8 AT F RRrT t~r. Ago..D,) is, PlE COUNT Reprint...outlines, if figure and ground are ignored. Later, we will address the problem of indexing identical codon descriptors that have different figure

  1. DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species.

    PubMed

    Saarela, Jeffery M; Sokoloff, Paul C; Gillespie, Lynn J; Consaul, Laurie L; Bull, Roger D

    2013-01-01

    Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.

  2. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    PubMed

    Sass, Chodon; Little, Damon P; Stevenson, Dennis Wm; Specht, Chelsea D

    2007-11-07

    Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  3. Quantum-dot-encoded microbeads for multiplexed genetic detection of non-amplified DNA samples.

    PubMed

    Gao, Yali; Stanford, William L; Chan, Warren C W

    2011-01-03

    Barcoding technologies have become the basis for a new generation of molecular diagnostic platforms for measuring biomarkers in a high-throughput, rapid, and sensitive manner. Thus far, researchers have mainly focused on preparing different types of barcodes but, in order to use them optimally in genomic- and proteomic-based applications, there is a need to understand the effect of barcode and assay parameters on their performance. Herein, quantum-dot barcodes are systematically characterized for the detection of non-amplified DNA sequences. The effect of capture probes, reporter probes, and target DNA sequence lengths are studied, as well as the effect of the amount of noncomplementary sequences on the hybridization kinetics and efficiency. From DNA denaturation to signal detection, quantum-dot-barcode assays require less than one hour to detect a target DNA sequence with a linear dynamic range of 0.02-100 fmol. Three optically distinct quantum-dot barcodes are used to demonstrate the multiplexing capability of these barcodes for genomic detection. These results suggest that quantum-dot barcodes are an excellent platform for multiplex, rapid, and sensitive genetic detection.

  4. DNA Barcoding Reveals Cryptic Diversity within Commercially Exploited Indo-Malay Carangidae (Teleosteii: Perciformes)

    PubMed Central

    Mat Jaafar, Tun Nurul Aimi; Taylor, Martin I.; Mohd Nor, Siti Azizah; de Bruyn, Mark; Carvalho, Gary R.

    2012-01-01

    Background DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library. Methodology/Principal Findings Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32–4.82%) than mean estimates (0.24–0.39%), indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P) distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata. Conclusion/Significance This study confirms

  5. Remarks on thermalization in 2D CFT

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Engelhardt, Dalit

    2016-12-01

    We revisit certain aspects of thermalization in 2D conformal field theory (CFT). In particular, we consider similarities and differences between the time dependence of correlation functions in various states in rational and non-rational CFTs. We also consider the distinction between global and local thermalization and explain how states obtained by acting with a diffeomorphism on the ground state can appear locally thermal, and we review why the time-dependent expectation value of the energy-momentum tensor is generally a poor diagnostic of global thermalization. Since all 2D CFTs have an infinite set of commuting conserved charges, generic initial states might be expected to give rise to a generalized Gibbs ensemble rather than a pure thermal ensemble at late times. We construct the holographic dual of the generalized Gibbs ensemble and show that, to leading order, it is still described by a Banados-Teitelboim-Zanelli black hole. The extra conserved charges, while rendering c <1 theories essentially integrable, therefore seem to have little effect on large-c conformal field theories.

  6. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

    Two-dimensional materials have emerged as extremely important materials with applications ranging from energy and environmental science to electronics and biology. Here we report our discovery of a universal, ultrafast, green, solvo-thermal technology for producing excellent-quality, few-layered nanosheets in liquid phase from well-known 2D materials such as such hexagonal boron nitride (h-BN), graphite, and MoS2. We start by mixing the uniform bulk-layered material with a common organic solvent that matches its surface energy to reduce the van der Waals attractive interactions between the layers; next, the solutions are heated in a commercial microwave oven to overcome the energy barrier between bulk and few-layers states. We discovered the minutes-long rapid exfoliation process is highly temperature dependent, which requires precise thermal management to obtain high-quality inks. We hypothesize a possible mechanism of this proposed solvo-thermal process; our theory confirms the basis of this novel technique for exfoliation of high-quality, layered 2D materials by using an as yet unknown role of the solvent.

  7. Effect of CYP2D6 variants on venlafaxine metabolism in vitro.

    PubMed

    Zhan, Yun-Yun; Liang, Bing-Qing; Wang, Hao; Wang, Zhen-He; Weng, Qing-Hua; Dai, Da-Peng; Cai, Jian-Ping; Hu, Guo-Xin

    2016-01-01

    1. CYP2D6 is an important member of the cytochrome P450 (CYP450) enzyme superfamily, we recently identified 22 CYP2D6 alleles in the Han Chinese population. The aim of this study was to assess the catalytic activities of these allelic isoforms and their effects on the metabolism of venlafaxine in vitro. 2. The wild-type and 24 CYP2D6 variants were expressed in insect cells, and each variant was characterized using venlafaxine as the substrate. Reactions were performed at 37 °C with 5-500 μM substrate (three variants was adjusted to 1000 μM) for 50 min. By using high-performance liquid chromatography to detect the products, the kinetic parameters Km, Vmax, and intrinsic clearance (Vmax/Km) of O-desmethylvenlafaxine were determined. 3. Among the 22 CYP2D6 variants, the intrinsic clearance (Vmax/Km) values of all variants were significantly decreased (from 0.2% to 84.5%) compared with wild-type CYP2D6*1. In addition, the kinetic parameters of two CYP2D6 variants could not be detected because they have no detectable enzyme activity. 4. The comprehensive in vitro assessment of CYP2D6 variants provides significant insights into allele-specific activity towards venlafaxine in vivo.

  8. Medicinal plants recommended by the world health organization: DNA barcode identification associated with chemical analyses guarantees their quality.

    PubMed

    Palhares, Rafael Melo; Gonçalves Drummond, Marcela; Dos Santos Alves Figueiredo Brasil, Bruno; Pereira Cosenza, Gustavo; das Graças Lins Brandão, Maria; Oliveira, Guilherme

    2015-01-01

    Medicinal plants are used throughout the world, and the regulations defining their proper use, such as identification of the correct species and verification of the presence, purity and concentration of the required chemical compounds, are widely recognized. Herbal medicines are made from vegetal drugs, the processed products of medicinal species. These processed materials present a number of challenges in terms of botanical identification, and according to the World Health Organization (WHO), the use of incorrect species is a threat to consumer safety. The samples used in this study consisted of the dried leaves, flowers and roots of 257 samples from 8 distinct species approved by the WHO for the production of medicinal herbs and sold in Brazilian markets. Identification of the samples in this study using DNA barcoding (matK, rbcL and ITS2 regions) revealed that the level of substitutions may be as high as 71%. Using qualitative and quantitative chemical analyses, this study identified situations in which the correct species was being sold, but the chemical compounds were not present. Even more troubling, some samples identified as substitutions using DNA barcoding contained the chemical compounds from the correct species at the minimum required concentration. This last situation may lead to the use of unknown species or species whose safety for human consumption remains unknown. This study concludes that DNA barcoding should be used in a complementary manner for species identification with chemical analyses to detect and quantify the required chemical compounds, thus improving the quality of this class of medicines.

  9. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

  10. Epitope spreading of the anti-CYP2D6 antibody response in patients with autoimmune hepatitis and in the CYP2D6 mouse model.

    PubMed

    Hintermann, Edith; Holdener, Martin; Bayer, Monika; Loges, Stephanie; Pfeilschifter, Josef M; Granier, Claude; Manns, Michael P; Christen, Urs

    2011-11-01

    Autoimmune hepatitis (AIH) is a serious chronic inflammatory disease of the liver with yet unknown etiology and largely uncertain immunopathology. The hallmark of type 2 AIH is the generation of liver kidney microsomal-1 (LKM-1) autoantibodies, which predominantly react to cytochrome P450 2D6 (CYP2D6). The identification of disease initiating factors has been hampered in the past, since antibody epitope mapping was mostly performed using serum samples collected late during disease resulting in the identification of immunodominant epitopes not necessarily representing those involved in disease initiation. In order to identify possible environmental triggers for AIH, we analyzed for the first time the spreading of the anti-CYP2D6 antibody response over a prolonged period of time in AIH patients and in the CYP2D6 mouse model, in which mice infected with Adenovirus-human CYP2D6 (Ad-h2D6) develop antibodies with a similar specificity than AIH patients. Epitope spreading was analyzed in six AIH-2-patients and in the CYP2D6 mouse model using SPOTs membranes containing peptides covering the entire CYP2D6 protein. Despite of a considerable variation, both mice and AIH patients largely focus their humoral immune response on an immunodominant epitope early after infection (mice) or diagnosis (patients). The CYP2D6 mouse model revealed that epitope spreading is initiated at the immunodominant epitope and later expands to neighboring and remote regions. Sequence homologies to human pathogens have been detected for all identified epitopes. Our study demonstrates that epitope spreading does indeed occur during the pathogenesis of AIH and supports the concept of molecular mimicry as a possible initiating mechanism for AIH.

  11. DNA barcoding of medicinal plant material for identification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because of the increasing demand for herbal remedies and for authentication of the source material, it is vital to provide a single database containing information about authentic plant materials and their potential adulterants. The database should provide DNA barcodes for data retrieval and similar...

  12. Use of DNA barcodes to identify flowering plants.

    PubMed

    Kress, W John; Wurdack, Kenneth J; Zimmer, Elizabeth A; Weigt, Lee A; Janzen, Daniel H

    2005-06-07

    Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

  13. Telling plant species apart with DNA: from barcodes to genomes.

    PubMed

    Hollingsworth, Peter M; Li, De-Zhu; van der Bank, Michelle; Twyford, Alex D

    2016-09-05

    Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.

  14. Identification of Rays through DNA Barcoding: An Application for Ecologists

    PubMed Central

    Cerutti-Pereyra, Florencia; Meekan, Mark G.; Wei, Nu-Wei V.; O'Shea, Owen; Bradshaw, Corey J. A.; Austin, Chris M.

    2012-01-01

    DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data. PMID:22701556

  15. Improving Warehouse Inventory Management Through Rfid, Barcoding and Robotics Technologies

    DTIC Science & Technology

    2014-12-01

    NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA MBA PROFESSIONAL REPORT IMPROVING WAREHOUSE INVENTORY MANAGEMENT THROUGH RFID ...INVENTORY MANAGEMENT THROUGH RFID , BARCO DING AND ROBOTICS TECHNOLOGIES 6. AUTHOR(S) Eric M. Bw·ke and Danny L. Ewing, Jr. 7. PERFORMING ORGANIZATION...solution. A cost- benefit analysis is included to determine the affordability of efficiencies that RFID and barcoding bring to warehouse operations . This

  16. Assembly of barcode-like nucleic acid nanostructures.

    PubMed

    Wang, Pengfei; Tian, Cheng; Li, Xiang; Mao, Chengde

    2014-10-15

    Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach.

  17. Looking back on a decade of barcoding crustaceans

    PubMed Central

    Raupach, Michael J.; Radulovici, Adriana E.

    2015-01-01

    Abstract Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication. PMID:26798245

  18. DNA barcoding and phylogenetic relationships of Ardeidae (Aves: Ciconiiformes).

    PubMed

    Huang, Z H; Li, M F; Qin, J W

    2016-08-19

    The avian family Ardeidae comprises long-legged freshwater and coastal birds. There has been considerable disagreement concerning the intrafamilial relationships of Ardeidae. Mitochondrial cytochrome c oxidase subunit I (COI) was used as a marker for the identification and phylogenetic analysis of avian species. In the present study, we analyzed the COI barcodes of 32 species from 17 genera belonging to the family Ardeidae. Each bird species possessed a barcode distinct from that of other bird species except for Egretta thula and E. garzetta, which shared one barcoding sequence. Kimura two-parameter distances were calculated between barcodes. The average genetic distance between species was 34-fold higher than the average genetic distance within species. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. Most species could be discriminated by their distinct clades in the phylogenetic tree. Both methods of phylogenetic reconstruction suggested that Zebrilus, Tigrisoma, and Cochlearius were an offshoot of the primitive herons. COI gene analysis suggested that the other herons could be divided into two clades: Botaurinae and Ardeinae. Our results support the Great Egret and Intermediate Egret being in separate genera, Casmerodius and Mesophoyx, respectively.

  19. DNA barcoding of parasitic nematodes: is it kosher?

    PubMed

    Siddall, Mark E; Kvist, Sebastion; Phillips, Anna; Oceguera-Figuero, Alejandro

    2012-06-01

    Nematode parasites were encountered in kosher-certified fish meat and roe, and the question was raised as to whether or not these food products were kosher as concerns food preparation standards-a matter that pertains to the identity and, by extension, the life cycle of the parasites. To ascertain the identities of parasitic nematodes, given the distorted or damaged nature of the specimens, molecular techniques were applied in the form of DNA barcoding. To our knowledge, this is the first application of this technique to an obviously cultural concern as opposed to one of health or economic significance. Results, based both on cytochrome c oxidase subunits I and II, suggested that the parasite species found in the fish products are anisakine species that do not inhabit the intestinal lumen of the fish hosts examined. Thus, there was no evidence of failure to adhere to food preparation practices consistent with the proscriptions of Orthodox Judaism. Notwithstanding the success of DNA barcoding in determining at least the higher taxonomic identities of the parasites, some shortcomings of the DNA barcoding pipeline as it pertains to nematode parasites were encountered; specifically, the paucity of data available for the DNA barcoding locus, even for very common nematode taxa.

  20. Telling plant species apart with DNA: from barcodes to genomes

    PubMed Central

    Li, De-Zhu; van der Bank, Michelle

    2016-01-01

    Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity—yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481790

  1. DNA Barcode Authentication of Saw Palmetto Herbal Dietary Supplements

    PubMed Central

    Little, Damon P.; Jeanson, Marc L.

    2013-01-01

    Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini–barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74–1.00); sensitivity = 1.00 (95% confidence interval = 0.66–1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini–barcodes were used to estimate the frequency of mislabeled saw palmetto herbal dietary supplements on the market in the United States of America. Of the 37 supplements examined, amplifiable DNA could be extracted from 34 (92%). Mini–barcode analysis of these supplements demonstrated that 29 (85%) contain saw palmetto and that 2 (6%) supplements contain related species that cannot be legally sold as herbal dietary supplements in the United States of America. The identity of 3 (9%) supplements could not be conclusively determined. PMID:24343362

  2. Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes.

    PubMed

    Boyle, Elizabeth E; Adamowicz, Sarah J

    2015-01-01

    Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel's λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.

  3. An integrative approach to species discovery in odonates: from character-based DNA barcoding to ecology.

    PubMed

    Damm, Sandra; Schierwater, Bernd; Hadrys, Heike

    2010-09-01

    Modern taxonomy requires an analytical approach incorporating all lines of evidence into decision-making. Such an approach can enhance both species identification and species discovery. The character-based DNA barcode method provides a molecular data set that can be incorporated into classical taxonomic data such that the discovery of new species can be made in an analytical framework that includes multiple sources of data. We here illustrate such a corroborative framework in a dragonfly model system that permits the discovery of two new, but visually cryptic species. In the African dragonfly genus Trithemis three distinct genetic clusters can be detected which could not be identified by using classical taxonomic characters. In order to test the hypothesis of two new species, DNA-barcodes from different sequence markers (ND1 and COI) were combined with morphological, ecological and biogeographic data sets. Phylogenetic analyses and incorporation of all data sets into a scheme called taxonomic circle highly supports the hypothesis of two new species. Our case study suggests an analytical approach to modern taxonomy that integrates data sets from different disciplines, thereby increasing the ease and reliability of both species discovery and species assignment.

  4. DNA Barcode Identification of Freshwater Snails in the Family Bithyniidae from Thailand

    PubMed Central

    Kulsantiwong, Jutharat; Prasopdee, Sattrachai; Ruangsittichai, Jiraporn; Ruangjirachuporn, Wipaporn; Boonmars, Thidarut; Viyanant, Vithoon; Pierossi, Paola; Hebert, Paul D. N.; Tesana, Smarn

    2013-01-01

    Freshwater snails in the family Bithyniidae are the first intermediate host for Southeast Asian liver fluke (Opisthorchis viverrini), the causative agent of opisthorchiasis. Unfortunately, the subtle morphological characters that differentiate species in this group are not easily discerned by non-specialists. This is a serious matter because the identification of bithyniid species is a fundamental prerequisite for better understanding of the epidemiology of this disease. Because DNA barcoding, the analysis of sequence diversity in the 5’ region of the mitochondrial COI gene, has shown strong performance in other taxonomic groups, we decided to test its capacity to resolve 10 species/ subspecies of bithyniids from Thailand. Our analysis of 217 specimens indicated that COI sequences delivered species-level identification for 9 of 10 currently recognized species. The mean intraspecific divergence of COI was 2.3% (range 0-9.2 %), whereas sequence divergences between congeneric species averaged 8.7% (range 0-22.2 %). Although our results indicate that DNA barcoding can differentiate species of these medically-important snails, we also detected evidence for the presence of one overlooked species and one possible case of synonymy. PMID:24223896

  5. DNA barcode identification of freshwater snails in the family Bithyniidae from Thailand.

    PubMed

    Kulsantiwong, Jutharat; Prasopdee, Sattrachai; Ruangsittichai, Jiraporn; Ruangjirachuporn, Wipaporn; Boonmars, Thidarut; Viyanant, Vithoon; Pierossi, Paola; Hebert, Paul D N; Tesana, Smarn

    2013-01-01

    Freshwater snails in the family Bithyniidae are the first intermediate host for Southeast Asian liver fluke (Opisthorchis viverrini), the causative agent of opisthorchiasis. Unfortunately, the subtle morphological characters that differentiate species in this group are not easily discerned by non-specialists. This is a serious matter because the identification of bithyniid species is a fundamental prerequisite for better understanding of the epidemiology of this disease. Because DNA barcoding, the analysis of sequence diversity in the 5' region of the mitochondrial COI gene, has shown strong performance in other taxonomic groups, we decided to test its capacity to resolve 10 species/ subspecies of bithyniids from Thailand. Our analysis of 217 specimens indicated that COI sequences delivered species-level identification for 9 of 10 currently recognized species. The mean intraspecific divergence of COI was 2.3% (range 0-9.2 %), whereas sequence divergences between congeneric species averaged 8.7% (range 0-22.2 %). Although our results indicate that DNA barcoding can differentiate species of these medically-important snails, we also detected evidence for the presence of one overlooked species and one possible case of synonymy.

  6. Transition to turbulence: 2D directed percolation

    NASA Astrophysics Data System (ADS)

    Chantry, Matthew; Tuckerman, Laurette; Barkley, Dwight

    2016-11-01

    The transition to turbulence in simple shear flows has been studied for well over a century, yet in the last few years has seen major leaps forward. In pipe flow, this transition shows the hallmarks of (1 + 1) D directed percolation, a universality class of continuous phase transitions. In spanwisely confined Taylor-Couette flow the same class is found, suggesting the phenomenon is generic to shear flows. However in plane Couette flow the largest simulations and experiments to-date find evidence for a discrete transition. Here we study a planar shear flow, called Waleffe flow, devoid of walls yet showing the fundamentals of planar transition to turbulence. Working with a quasi-2D yet Navier-Stokes derived model of this flow we are able to attack the (2 + 1) D transition problem. Going beyond the system sizes previously possible we find all of the required scalings of directed percolation and thus establish planar shears flow in this class.

  7. 2D quantum gravity from quantum entanglement.

    PubMed

    Gliozzi, F

    2011-01-21

    In quantum systems with many degrees of freedom the replica method is a useful tool to study the entanglement of arbitrary spatial regions. We apply it in a way that allows them to backreact. As a consequence, they become dynamical subsystems whose position, form, and extension are determined by their interaction with the whole system. We analyze, in particular, quantum spin chains described at criticality by a conformal field theory. Its coupling to the Gibbs' ensemble of all possible subsystems is relevant and drives the system into a new fixed point which is argued to be that of the 2D quantum gravity coupled to this system. Numerical experiments on the critical Ising model show that the new critical exponents agree with those predicted by the formula of Knizhnik, Polyakov, and Zamolodchikov.

  8. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse.

  9. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Jones, Justin S.; Kelly, Daniel P.; Zheng, Yun; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    An electrostatically actuated microshutter array consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutter arrays demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  10. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  11. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

    Child, R. D.; Henderson, W. P.

    1978-01-01

    A closely-coupled canard fighter with vectorable two-dimensional nozzle was designed for enhanced transonic maneuvering. The HiMAT maneuver goal of a sustained 8g turn at a free-stream Mach number of 0.9 and 30,000 feet was the primary design consideration. The aerodynamic design process was initiated with a linear theory optimization minimizing the zero percent suction drag including jet effects and refined with three-dimensional nonlinear potential flow techniques. Allowances were made for mutual interference and viscous effects. The design process to arrive at the resultant configuration is described, and the design of a powered 2-D nozzle model to be tested in the LRC 16-foot Propulsion Wind Tunnel is shown.

  12. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

    A ground state is defined as the positive radial solution of the multidimensional nonlinear problem \\varepsilon propto k_ bot 1 - ξ with the function f being either f(u) =a|u|p-1u or f(u) =a|u|pu+b|u|2pu. The numerical evaluation of ground states is based on the shooting method applied to an equivalent dynamical system. A combination of fourth order Runge-Kutta method and Hermite extrapolation formula is applied to solving the resulting initial value problem. The efficiency of this procedure is demonstrated in the 1D case, where the maximal difference between the exact and numerical solution is ≈ 10-11 for a discretization step 0:00025. As a major application, we evaluate numerically the critical energy constant. This constant is defined as a functional of the ground state and is used in the study of the 2D Boussinesq equations.

  13. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  14. DNA barcoding reveals high levels of genetic diversity in the fishes of the Itapecuru Basin in Maranhão, Brazil.

    PubMed

    Nascimento, M H S; Almeida, M S; Veira, M N S; Limeira Filho, D; Lima, R C; Barros, M C; Fraga, E C

    2016-08-29

    DNA barcoding is a useful complementary tool for use in traditional taxonomic studies due to its ability to detect cryptic species, and may be particularly efficient in the identification of fish species. The fish fauna of the Itapecuru River represents an important fishery resource in the Brazilian State of Maranhão, although it is currently suffering increasing degradation as a result of anthropogenic impacts. Therefore, DNA barcoding was used in the present study to identify fish species and establish a database of the rich freshwater fish fauna of Maranhão. A total of 440 specimens were analyzed, corresponding to 64 species belonging to 59 genera, 31 families, and 10 orders. Overall, 92.19% of these species could be identified by DNA barcoding, and were characterized by low levels (average 0.80%) of intra-specific divergence. However, five species (Anableps anableps, Gymnotus carapo, Sciades couma, Pseudauchenipterus nodosus, and Leporinus piau) presented values of mean genetic divergence above 3%, indicating the existence of cryptic diversity in these fishes. The DNA barcoding approach permitted the analysis of a large number of specimens and facilitated the discrimination and identification of closely related fish species in the Itapecuru Basin.

  15. Building a DNA barcode library of Alaska's non-marine arthropods.

    PubMed

    Sikes, Derek S; Bowser, Matthew; Morton, John M; Bickford, Casey; Meierotto, Sarah; Hildebrandt, Kyndall

    2017-03-01

    Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska - i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.

  16. Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera

    PubMed Central

    Xiang, Xiao-Guo; Huang, Lu-Qi; Jin, Xiao-Hua

    2017-01-01

    DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera. PMID:28182623

  17. Species-Specific Identification from Incomplete Sampling: Applying DNA Barcodes to Monitoring Invasive Solanum Plants

    PubMed Central

    Zhang, Wei; Fan, Xiaohong; Zhu, Shuifang; Zhao, Hong; Fu, Lianzhong

    2013-01-01

    Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling–through this, DNA barcoding will greatly benefit the current fields of its application. PMID:23409092

  18. A test of seven candidate barcode regions from the plastome in Picea (Pinaceae).

    PubMed

    Ran, Jin-Hua; Wang, Pei-Pei; Zhao, Hui-Juan; Wang, Xiao-Quan

    2010-12-01

    DNA barcoding, as a tool for species discrimination, has been used efficiently in animals, algae and fungi, but there are still debates on which DNA region(s) can be used as the standard barcode(s) for land plants. Gymnosperms, especially conifers, are important components of forests, and there is an urgent need for them to be identified through DNA barcoding because of their high frequency of collection in the field. However, the feasibility of DNA barcoding in gymnosperms has not been examined based on a dense species sampling. Here we selected seven candidate DNA barcodes from the plastome (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbA-trnH, and psbK-psbI) to evaluate their suitability in Picea (spruce). The results showed that none of them or their different combinations has sufficient resolution for spruce species, although matK+rbcL might be used as a two-locus barcode. The low efficiency of these candidate barcodes in Picea might be caused by the paternal inheritance of the chloroplast genome, long generation time, recent radiation, and frequent inter-specific hybridization aided by wind pollination. Some of these factors could also be responsible for the difficulties in barcoding other plant groups. Furthermore, the potential of the nuclear LEAFY gene as a land plant barcode was discussed.

  19. Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding

    PubMed Central

    Janzen, Daniel H; Hajibabaei, Mehrdad; Burns, John M; Hallwachs, Winnie; Remigio, Ed; Hebert, Paul D.N

    2005-01-01

    By facilitating bioliteracy, DNA barcoding has the potential to improve the way the world relates to wild biodiversity. Here we describe the early stages of the use of cox1 barcoding to supplement and strengthen the taxonomic platform underpinning the inventory of thousands of sympatric species of caterpillars in tropical dry forest, cloud forest and rain forest in northwestern Costa Rica. The results show that barcoding a biologically complex biota unambiguously distinguishes among 97% of more than 1000 species of reared Lepidoptera. Those few species whose barcodes overlap are closely related and not confused with other species. Barcoding also has revealed a substantial number of cryptic species among morphologically defined species, associated sexes, and reinforced identification of species that are difficult to distinguish morphologically. For barcoding to achieve its full potential, (i) ability to rapidly and cheaply barcode older museum specimens is urgent, (ii) museums need to address the opportunity and responsibility for housing large numbers of barcode voucher specimens, (iii) substantial resources need be mustered to support the taxonomic side of the partnership with barcoding, and (iv) hand-held field-friendly barcorder must emerge as a mutualism with the taxasphere and the barcoding initiative, in a manner such that its use generates a resource base for the taxonomic process as well as a tool for the user. PMID:16214742

  20. The changing epitome of species identification – DNA barcoding

    PubMed Central

    Ajmal Ali, M.; Gyulai, Gábor; Hidvégi, Norbert; Kerti, Balázs; Al Hemaid, Fahad M.A.; Pandey, Arun K.; Lee, Joongku

    2014-01-01

    The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The ‘DNA barcodes’ show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more. PMID:24955007

  1. When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.

    PubMed

    Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Opler, Paul A; Otwinowski, Zbyszek; Grishin, Nick V

    2017-02-08

    Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.

  2. Deciphering amphibian diversity through DNA barcoding: chances and challenges.

    PubMed

    Vences, Miguel; Thomas, Meike; Bonett, Ronald M; Vieites, David R

    2005-10-29

    Amphibians globally are in decline, yet there is still a tremendous amount of unrecognized diversity, calling for an acceleration of taxonomic exploration. This process will be greatly facilitated by a DNA barcoding system; however, the mitochondrial population structure of many amphibian species presents numerous challenges to such a standardized, single locus, approach. Here we analyse intra- and interspecific patterns of mitochondrial variation in two distantly related groups of amphibians, mantellid frogs and salamanders, to determine the promise of DNA barcoding with cytochrome oxidase subunit I (cox1) sequences in this taxon. High intraspecific cox1 divergences of 7-14% were observed (18% in one case) within the whole set of amphibian sequences analysed. These high values are not caused by particularly high substitution rates of this gene but by generally deep mitochondrial divergences within and among amphibian species. Despite these high divergences, cox1 sequences were able to correctly identify species including disparate geographic variants. The main problems with cox1 barcoding of amphibians are (i) the high variability of priming sites that hinder the application of universal primers to all species and (ii) the observed distinct overlap of intraspecific and interspecific divergence values, which implies difficulties in the definition of threshold values to identify candidate species. Common discordances between geographical signatures of mitochondrial and nuclear markers in amphibians indicate that a single-locus approach can be problematic when high accuracy of DNA barcoding is required. We suggest that a number of mitochondrial and nuclear genes may be used as DNA barcoding markers to complement cox1.

  3. Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan

    PubMed Central

    Akhtar, Saleem; Rafi, Muhammad Athar; Mansoor, Shahid; Hebert, Paul D. N.

    2017-01-01

    Sequences from the DNA barcode region of the mitochondrial COI gene are an effective tool for specimen identification and for the discovery of new species. The Barcode of Life Data Systems (BOLD) (www.boldsystems.org) currently hosts 4.5 million records from animals which have been assigned to more than 490,000 different Barcode Index Numbers (BINs), which serve as a proxy for species. Because a fourth of these BINs derive from Lepidoptera, BOLD has a strong capability to both identify specimens in this order and to support studies of faunal overlap. DNA barcode sequences were obtained from 4503 moths from 329 sites across Pakistan, specimens that represented 981 BINs from 52 families. Among 379 species with a Linnaean name assignment, all were represented by a single BIN excepting five species that showed a BIN split. Less than half (44%) of the 981 BINs had counterparts in other countries; the remaining BINs were unique to Pakistan. Another 218 BINs of Lepidoptera from Pakistan were coupled with the 981 from this study before being compared with all 116,768 BINs for this order. As expected, faunal overlap was highest with India (21%), Sri Lanka (21%), United Arab Emirates (20%) and with other Asian nations (2.1%), but it was very low with other continents including Africa (0.6%), Europe (1.3%), Australia (0.6%), Oceania (1.0%), North America (0.1%), and South America (0.1%). This study indicates the way in which DNA barcoding facilitates measures of faunal overlap even when taxa have not been assigned to a Linnean species. PMID:28339501

  4. DNA Barcoding of Sigmodontine Rodents: Identifying Wildlife Reservoirs of Zoonoses

    PubMed Central

    Müller, Lívia; Gonçalves, Gislene L.; Cordeiro-Estrela, Pedro; Marinho, Jorge R.; Althoff, Sérgio L.; Testoni, André. F.; González, Enrique M.; Freitas, Thales R. O.

    2013-01-01

    Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments. PMID:24244670

  5. 2D to 3D transition of polymeric carbon nitride nanosheets

    SciTech Connect

    Chamorro-Posada, Pedro; Vázquez-Cabo, José; Martín-Ramos, Pablo; Martín-Gil, Jesús; Navas-Gracia, Luis M.; Dante, Roberto C.

    2014-11-15

    The transition from a prevalent turbostratic arrangement with low planar interactions (2D) to an array of polymeric carbon nitride nanosheets with stronger interplanar interactions (3D), occurring for samples treated above 650 °C, was detected by terahertz-time domain spectroscopy (THz-TDS). The simulated 3D material made of stacks of shifted quasi planar sheets composed of zigzagged polymer ribbons, delivered a XRD simulated pattern in relatively good agreement with the experimental one. The 2D to 3D transition was also supported by the simulation of THz-TDS spectra obtained from quantum chemistry calculations, in which the same broad bands around 2 THz and 1.5 THz were found for 2D and 3D arrays, respectively. This transition was also in accordance with the tightening of the interplanar distance probably due to an interplanar π bond contribution, as evidenced also by a broad absorption around 2.6 eV in the UV–vis spectrum, which appeared in the sample treated at 650 °C, and increased in the sample treated at 700 °C. The band gap was calculated for 1D and 2D cases. The value of 3.374 eV for the 2D case is, within the model accuracy and precision, in a relative good agreement with the value of 3.055 eV obtained from the experimental results. - Graphical abstract: 2D lattice mode vibrations and structural changes correlated with the so called “2D to 3D transition”. - Highlights: • A 2D to 3D transition has been detected for polymeric carbon nitride. • THz-TDS allowed us to discover and detect the 2D to 3D transition of polymeric carbon nitride. • We propose a structure for polymeric carbon nitride confirming it with THz-TDS.

  6. In vitro functional assessment of 22 newly identified CYP2D6 allelic variants in the Chinese population.

    PubMed

    Dai, Da-Peng; Geng, Pei-Wu; Wang, Shuang-Hu; Cai, Jie; Hu, Li-Ming; Nie, Jing-Jing; Hu, Ji-Hong; Hu, Guo-Xin; Cai, Jian-Ping

    2015-07-01

    Cytochrome P450 2D6 (CYP2D6) is one of the most widely investigated CYPs related to genetic polymorphisms and is responsible for one-quarter of the currently used clinical drugs. We previously detected 22 novel, non-synonymous, mutated sites in the Chinese population, but nothing is known about the functional effects of these mutations in terms of specific CYP2D6 substrates. In this study, wild-type CYP2D6, two common allelic variants and 22 newly reported CYP2D6 isoforms were transiently expressed in 293FT cells, and the enzymatic activities of these variants were systematically assessed using dextromethorphan and bufuralol as the probing substrates. Consequently, 19 and 21 allelic variants were found to exhibit significantly decreased enzymatic activities for dextromethorphan and bufuralol, respectively. Of 22 novel CYP2D6 variants, six allelic isoforms (CYP2D6.89, CYP2D6.92, CYP2D6.93, CYP2D6.96, E215K and R440C) exhibited absent or extremely reduced metabolic activities compared with those observed for the wild-type enzyme. Our in vitro functional data can be useful for CYP2D6 phenotype prediction and provide valuable information for the study of clinical impact of these newly found CYP2D6 variants in China.

  7. Long-lived magnetoexcitons in 2D-fermion system

    NASA Astrophysics Data System (ADS)

    Kulik, L. V.; Zhuravlev, A. S.; Gorbunov, A. V.; Timofeev, V. B.; Kukushkin, I. V.

    2017-01-01

    The paper addresses the experimental technique that, when applied to a 2D-electron system in the integer quantum Hall regime with filling factor ν = 2 (the Hall insulating state), allows resonant excitation of magnetoexcitons, their detection, control of an ensemble of long-lived triplet excitons and investigation of their radiationless decay related to exciton spin relaxation into the ground state. The technique proposed enables independent control of photoexcited electrons and Fermi-holes using photoinduced resonance reflection spectra as well as estimate with a reasonable degree of accuracy the resulting density of photoinduced electron-hole pairs bound into magnetoexcitons. The mere existence of triplet excitons was directly established by inelastic light scattering spectra which were analyzed to determine the value of singlet-triplet exciton splitting. It was found that the lifetimes of triplet excitons conditioned by electron spin relaxation in highly perfect GaAs/AlGaAs heterostructures with highly mobile 2D electrons are extremely long exceeding 100 μs at T < 1 K. The paper presents a qualitative explanation of the long-spin relaxation lifetimes which are unprecedented for translation-invariant 2D systems. This enabled us to create sufficiently high concentrations of triplet magnetoexcitons, electrically neutral excitations following Bose-Einstein statistics, in a Fermi electron system and investigate their collective properties. At sufficiently high densities of triplet magnetoexcitons and low temperatures, T < 1 K, the degenerate magnetofermionic system exhibits condensation of the triplet magnetoexcitons into a qualitatively new collective state with unusual properties which occurs in the space of generalized moments (magnetic translation vectors). The occurrence of a condensed phase is accompanied with a significant decrease in the viscosity of the photoexcited system, which is responsible for electron spin transport at macroscopic distances, as well

  8. Search for H2D(+) at 372 GHz in dense interstellar clouds

    NASA Technical Reports Server (NTRS)

    Pagani, L.; Wannier, P. G.; Frerking, M. A.; Kuiper, T. B. H.; Gulkis, S.; Zimmermann, P.; Encrenaz, P. J.; Whiteoak, J. B.; Destombes, J. L.; Pickett, H. M.

    1992-01-01

    The 1(10)-1(11) transition of ortho-H2D(+) at 372 GHz has been sought in several dark clouds. The transition was not detected; the best upper limits obtained are about 0.3 K (3 sigma). We derive upper limits for the ortho-H2D(+) column density and briefly discuss their meaning in comparison with a simple chemical model we have developed (Pagani et al., 1992).

  9. Project description: DNA barcodes of bird species in the national museum of natural history, smithsonian institution, USA.

    PubMed

    Schindel, David E; Stoeckle, Mark Y; Milensky, Chris; Trizna, Michael; Schmidt, Brian; Gebhard, Christina; Graves, Gary

    2011-01-01

    The Division of Birds, National Museum of Natural History, Smithsonian Institution in Washington, DC, has obtained and released DNA barcodes for 2808 frozen tissue samples. Of the 1,403 species represented by these samples, 1,147 species have not been barcoded previously. This data release increases the number of bird species with standard barcodes by 91%. These records meet the data standard of the Consortium for the Barcode of Life and they have the reserved keyword BARCODE in GenBank. The data are now available on GenBank and the Barcode of Life Data Systems.

  10. Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead.

    PubMed

    Joly, Simon; Davies, T Jonathan; Archambault, Annie; Bruneau, Anne; Derry, Alison; Kembel, Steven W; Peres-Neto, Pedro; Vamosi, Jana; Wheeler, Terry A

    2014-03-01

    Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion,