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Sample records for dna fiber mapping

  1. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  2. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas

    2009-09-18

    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.

  3. Time of flight Laue fiber diffraction studies of perdeuterated DNA

    Energy Technology Data Exchange (ETDEWEB)

    Forsyth, V.T.; Whalley, M.A.; Mahendrasingam, A.; Fuller, W. [Keele Univ. (United Kingdom)] [and others

    1994-12-31

    The diffractometer SXD at the Rutherford Appleton Laboratory ISIS pulsed neutron source has been used to record high resolution time-of-flight Laue fiber diffraction data from DNA. These experiments, which are the first of their kind, were undertaken using fibers of DNA in the A conformation and prepared using deuterated DNA in order to minimis incoherent background scattering. These studies complement previous experiments on instrument D19 at the Institute Laue Langevin using monochromatic neutrons. Sample preparation involved drawing large numbers of these deuterated DNA fibers and mounting them in a parallel array. The strategy of data collection is discussed in terms of camera design, sample environment and data collection. The methods used to correct the recorded time-of-flight data and map it into the final reciprocal space fiber diffraction dataset are also discussed. Difference Fourier maps showing the distribution of water around A-DNA calculated on the basis of these data are compared with results obtained using data recorded from hydrogenated A-DNA on D19. Since the methods used for sample preparation, data collection and data processing are fundamentally different for the monochromatic and Laue techniques, the results of these experiments also afford a valuable opportunity to independently test the data reduction and analysis techniques used in the two methods.

  4. High resolution optical DNA mapping

    Science.gov (United States)

    Baday, Murat

    Many types of diseases including cancer and autism are associated with copy-number variations in the genome. Most of these variations could not be identified with existing sequencing and optical DNA mapping methods. We have developed Multi-color Super-resolution technique, with potential for high throughput and low cost, which can allow us to recognize more of these variations. Our technique has made 10--fold improvement in the resolution of optical DNA mapping. Using a 180 kb BAC clone as a model system, we resolved dense patterns from 108 fluorescent labels of two different colors representing two different sequence-motifs. Overall, a detailed DNA map with 100 bp resolution was achieved, which has the potential to reveal detailed information about genetic variance and to facilitate medical diagnosis of genetic disease.

  5. DNA hydration studied by neutron fiber diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J. [Keele Univ. (United Kingdom)] [and others

    1994-12-31

    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix.

  6. DNA hydration studied by neutron fiber diffraction

    International Nuclear Information System (INIS)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J.

    1994-01-01

    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix

  7. FIBER OPTIC BIOSENSOR FOR DNA DAMAGE

    Science.gov (United States)

    This paper describes a fiber optic biosensor for the rapid and sensitive detection of radiation-induced or chemically-induced oxidative DNA damage. The assay is based on the hybridization and temperature-induced dissociation (melting curves) of synthetic oligonucleotides. The...

  8. Sensitive Leptospira DNA detection using tapered optical fiber sensor.

    Science.gov (United States)

    Zainuddin, Nurul H; Chee, Hui Y; Ahmad, Muhammad Z; Mahdi, Mohd A; Abu Bakar, Muhammad H; Yaacob, Mohd H

    2018-03-23

    This paper presents the development of tapered optical fiber sensor to detect a specific Leptospira bacteria DNA. The bacteria causes Leptospirosis, a deadly disease but with common early flu-like symptoms. Optical single mode fiber (SMF) of 125 μm diameter is tapered to produce 12 μm waist diameter and 15 cm length. The novel DNA-based optical fiber sensor is functionalized by incubating the tapered region with sodium hydroxide (NaOH), (3-Aminopropyl) triethoxysilane and glutaraldehyde. Probe DNA is immobilized onto the tapered region and subsequently hybridized by its complementary DNA (cDNA). The transmission spectra of the DNA-based optical fiber sensor are measured in the 1500 to 1600 nm wavelength range. It is discovered that the shift of the wavelength in the SMF sensor is linearly proportional with the increase in the cDNA concentrations from 0.1 to 1.0 nM. The sensitivity of the sensor toward DNA is measured to be 1.2862 nm/nM and able to detect as low as 0.1 fM. The sensor indicates high specificity when only minimal shift is detected for non-cDNA testing. The developed sensor is able to distinguish between actual DNA of Leptospira serovars (Canicola and Copenhageni) against Clostridium difficile (control sample) at very low (femtomolar) target concentrations. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Axon diameter mapping in crossing fibers with diffusion MRI

    DEFF Research Database (Denmark)

    Zhang, Hui; Dyrby, Tim B; Alexander, Daniel C

    2011-01-01

    This paper proposes a technique for a previously unaddressed problem, namely, mapping axon diameter in crossing fiber regions, using diffusion MRI. Direct measurement of tissue microstructure of this kind using diffusion MRI offers a new class of biomarkers that give more specific information about...... tissue than measures derived from diffusion tensor imaging. Most existing techniques for axon diameter mapping assume a single axon orientation in the tissue model, which limits their application to only the most coherently oriented brain white matter, such as the corpus callosum, where the single...... model to enable axon diameter mapping in voxels with crossing fibers. We show in simulation that the technique can provide robust axon diameter estimates in a two-fiber crossing with the crossing angle as small as 45 degrees. Using ex vivo imaging data, we further demonstrate the feasibility...

  10. DNA origami nanorobot fiber optic genosensor to TMV.

    Science.gov (United States)

    Torelli, Emanuela; Manzano, Marisa; Srivastava, Sachin K; Marks, Robert S

    2018-01-15

    In the quest of greater sensitivity and specificity of diagnostic systems, one continually searches for alternative DNA hybridization methods, enabling greater versatility and where possible field-enabled detection of target analytes. We present, herein, a hybrid molecular self-assembled scaffolded DNA origami entity, intimately immobilized via capture probes linked to aminopropyltriethoxysilane, onto a glass optical fiber end-face transducer, thus producing a novel biosensor. Immobilized DNA nanorobots with a switchable flap can then be actuated by a specific target DNA present in a sample, by exposing a hemin/G-quadruplex DNAzyme, which then catalyzes the generation of chemiluminescence, once the specific fiber probes are immersed in a luminol-based solution. Integrating organic nanorobots to inorganic fiber optics creates a hybrid system that we demonstrate as a proof-of-principle can be utilized in specific DNA sequence detection. This system has potential applications in a wide range of fields, including point-of-care diagnostics or cellular in vivo biosensing when using ultrathin fiber optic probes for research purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Fiber optic chemical sensors: The evolution of high- density fiber-optic DNA microarrays

    Science.gov (United States)

    Ferguson, Jane A.

    2001-06-01

    Sensors were developed for multianalyte monitoring, fermentation monitoring, lactate analysis, remote oxygen detection for use in bioremediation monitoring and in a fuel spill clean-up project, heavy metal analysis, and high density DNA microarrays. The major focus of this thesis involved creating and improving high-density DNA gene arrays. Fiber optic sensors are created using fluorescent indicators, polymeric supports, and optical fiber substrates. The fluorescent indicator is entrapped in a polymer layer and attached to the tip of the optical fiber. The tip of the fiber bearing the sensing layer (the distal end) is placed in the sample of interest while the other end of the fiber (the proximal end) is connected to an analysis system. Any length of fiber can be used without compromising the integrity or sensitivity of the system. A fiber optic oxygen sensor was designed incorporating an oxygen sensitive fluorescent dye and a gas permeable polymer attached to an optical fiber. The construction simplicity and ruggedness of the sensor enabled its deployment for in situ chemical oxidation and bioremediation studies. Optical fibers were also used as the substrate to detect biomolecules in solution. To monitor bioprocesses, the production of the analyte of interest must be coupled with a species that is optically measurable. For example, oxygen is consumed in many metabolic functions. The fiber optic oxygen sensor is equipped with an additional sensing layer. Upon contact with a specific biochemical in the sample, a reaction occurs in the additional sensing layer that either consumes or produces oxygen. This dual layer system was used to monitor the presence of lactate, an important metabolite for clinical and bioprocess analysis. In many biological and environmental systems, the generation of one species occurs coincidentally with the generation or consumption of another species. A multianalyte sensor was prepared that can monitor the simultaneous activity of pH, CO2

  12. Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

    DEFF Research Database (Denmark)

    Vranken, Charlotte; Deen, Jochem; Dirix, Lieve

    2014-01-01

    We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore...... to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay...... the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes...

  13. Selective detection of labeled DNA using an air-clad photonic crystal fiber

    DEFF Research Database (Denmark)

    Jensen, Jesper Bo Damm; Hoiby, P.E.; Pedersen, L.H.

    2004-01-01

    Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core.......Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core....

  14. Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.

    Science.gov (United States)

    Vitelli, Valerio; Galbiati, Alessandro; Iannelli, Fabio; Pessina, Fabio; Sharma, Sheetal; d'Adda di Fagagna, Fabrizio

    2017-08-31

    Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

  15. Genome-wide mapping of DNA strand breaks.

    Directory of Open Access Journals (Sweden)

    Frédéric Leduc

    Full Text Available Determination of cellular DNA damage has so far been limited to global assessment of genome integrity whereas nucleotide-level mapping has been restricted to specific loci by the use of specific primers. Therefore, only limited DNA sequences can be studied and novel regions of genomic instability can hardly be discovered. Using a well-characterized yeast model, we describe a straightforward strategy to map genome-wide DNA strand breaks without compromising nucleotide-level resolution. This technique, termed "damaged DNA immunoprecipitation" (dDIP, uses immunoprecipitation and the terminal deoxynucleotidyl transferase-mediated dUTP-biotin end-labeling (TUNEL to capture DNA at break sites. When used in combination with microarray or next-generation sequencing technologies, dDIP will allow researchers to map genome-wide DNA strand breaks as well as other types of DNA damage and to establish a clear profiling of altered genes and/or intergenic sequences in various experimental conditions. This mapping technique could find several applications for instance in the study of aging, genotoxic drug screening, cancer, meiosis, radiation and oxidative DNA damage.

  16. Environmental DNA mapping of Zebra Mussel populations

    Science.gov (United States)

    Amberg, Jon J.; Merkes, Christopher

    2016-01-01

    Environmental DNA (eDNA) has become a popular tool for detecting aquatic invasive species, but advancements have made it possible to potentially answer other questions like reproduction, movement, and abundance of the targeted organism. In this study we developed a Zebra Mussel (Dreissena polymorpha) eDNA protocol. We then determined if this assay could be used to help determine Zebra Mussel biomass in a lake with a well-established population of Zebra Mussels and a lake with an emerging population of mussels. Our eDNA assay detected DNA of Zebra Mussels but not DNA from more than 20 other species of fish and mussels, many commonly found in Minnesota waters. Our assay did not predict biomass. We did find that DNA from Zebra Mussels accumulated in softer substrates in both lakes, even though the mussels were predominately on the harder substrates. Therefore, we concluded that eDNA may be useful to detect the presence of Zebra Mussels in these lakes but our assay/approach could not predict biomass.

  17. A Novel Audio Cryptosystem Using Chaotic Maps and DNA Encoding

    Directory of Open Access Journals (Sweden)

    S. J. Sheela

    2017-01-01

    Full Text Available Chaotic maps have good potential in security applications due to their inherent characteristics relevant to cryptography. This paper introduces a new audio cryptosystem based on chaotic maps, hybrid chaotic shift transform (HCST, and deoxyribonucleic acid (DNA encoding rules. The scheme uses chaotic maps such as two-dimensional modified Henon map (2D-MHM and standard map. The 2D-MHM which has sophisticated chaotic behavior for an extensive range of control parameters is used to perform HCST. DNA encoding technology is used as an auxiliary tool which enhances the security of the cryptosystem. The performance of the algorithm is evaluated for various speech signals using different encryption/decryption quality metrics. The simulation and comparison results show that the algorithm can achieve good encryption results and is able to resist several cryptographic attacks. The various types of analysis revealed that the algorithm is suitable for narrow band radio communication and real-time speech encryption applications.

  18. Optical Fiber Nanotips Coated with Molecular Beacons for DNA Detection

    Directory of Open Access Journals (Sweden)

    Ambra Giannetti

    2015-04-01

    Full Text Available Optical fiber sensors, thanks to their compactness, fast response and real-time measurements, have a large impact in the fields of life science research, drug discovery and medical diagnostics. In recent years, advances in nanotechnology have resulted in the development of nanotools, capable of entering the single cell, resulting in new nanobiosensors useful for the detection of biomolecules inside living cells. In this paper, we provide an application of a nanotip coupled with molecular beacons (MBs for the detection of DNA. The MBs were characterized by hybridization studies with a complementary target to prove their functionality both free in solution and immobilized onto a solid support. The solid support chosen as substrate for the immobilization of the MBs was a 30 nm tapered tip of an optical fiber, fabricated by chemical etching. With this set-up promising results were obtained and a limit of detection (LOD of 0.57 nM was reached, opening up the possibility of using the proposed nanotip to detect mRNAs inside the cytoplasm of living cells.

  19. Linkage map of the fragments of herpesvirus papio DNA.

    Science.gov (United States)

    Lee, Y S; Tanaka, A; Lau, R Y; Nonoyama, M; Rabin, H

    1981-01-01

    Herpesvirus papio (HVP), an Epstein-Barr-like virus, causes lymphoblastoid disease in baboons. The physical map of HVP DNA was constructed for the fragments produced by cleavage of HVP DNA with restriction endonucleases EcoRI, HindIII, SalI, and PvuI, which produced 12, 12, 10, and 4 fragments, respectively. The total molecular size of HVP DNA was calculated as close to 110 megadaltons. The following methods were used for construction of the map; (i) fragments near the ends of HVP DNA were identified by treating viral DNA with lambda exonuclease before restriction enzyme digestion; (ii) fragments containing nucleotide sequences in common with fragments from the second enzyme digest of HVP DNA were examined by Southern blot hybridization; and (iii) the location of some fragments was determined by isolating individual fragments from agarose gels and redigesting the isolated fragments with a second restriction enzyme. Terminal heterogeneity and internal repeats were found to be unique features of HVP DNA molecule. One to five repeats of 0.8 megadaltons were found at both terminal ends. Although the repeats of both ends shared a certain degree of homology, it was not determined whether they were identical repeats. The internal repeat sequence of HVP DNA was found in the EcoRI-C region, which extended from 8.4 to 23 megadaltons from the left end of the molecule. The average number of the repeats was calculated to be seven, and the molecular size was determined to be 1.8 megadaltons. Similar unique features have been reported in EBV DNA (D. Given and E. Kieff, J. Virol. 28:524-542, 1978). Images PMID:6261015

  20. Mapping misoriented fibers using X-ray dark field tomography

    DEFF Research Database (Denmark)

    Lauridsen, Torsten; Lauridsen, Erik Mejdal; Feidenhans’l, Robert

    2014-01-01

    such tomograms on a highly nonisotropic sample, i.e. a five layer “sandwich” of oriented carbon fibers. The fibers are parallel within the individual sandwich layers, but perpendicular to the fibers in the adjacent layers. We show that by choosing a rotation axis parallel to the grating stepping direction (i.......e. a horizontal rotation axis in most setup configurations) it is possible to produce a darkfield tomogram where fibers parallel to the probed scattering direction appear to have no dark field signal. The method produces a tomogram in the form of a scalar field of dark field scattering values....

  1. Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Giulia Menconi

    2015-04-01

    Full Text Available In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3'UTR, a region affecting mRNA translation, localization and stability. (TAn repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TAn repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3'-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in

  2. Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.

    Science.gov (United States)

    Menconi, Giulia; Bedini, Andrea; Barale, Roberto; Sbrana, Isabella

    2015-04-01

    In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3'UTR, a region affecting mRNA translation, localization and stability. (TA)n repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE) signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TA)n repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3'-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in genomes and a

  3. Genetic maps of polymorphic DNA loci on rat chromosome 1

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Yan-Ping; Remmers, E.F.; Longman, R.E. [National Institutes of Health, Bethesda, MD (United States)] [and others

    1996-09-01

    Genetic linkage maps of loci defined by polymorphic DNA markers on rat chromosome 1 were constructed by genotyping F2 progeny of F344/N x LEW/N, BN/SsN x LEW/N, and DA/Bkl x F344/Hsd inbred rat strains. In total, 43 markers were mapped, of which 3 were restriction fragment length polymorphisms and the others were simple sequence length polymorphisms. Nineteen of these markers were associated with genes. Six markers for five genes, {gamma}-aminobutyric acid receptor {beta}3 (Gabrb3), syntaxin 2 (Stx2), adrenergic receptor {beta}3 (Gabrb3), syntaxin 2 (Stx2), adrenergic receptor {beta}1 (Adrb1), carcinoembryonic antigen gene family member 1 (Cgm1), and lipogenic protein S14 (Lpgp), and 20 anonymous loci were not previously reported. Thirteen gene loci (Myl2, Aldoa, Tnt, Igf2, Prkcg, Cgm4, Calm3, Cgm3, Psbp1, Sa, Hbb, Ins1, and Tcp1) were previously mapped. Comparative mapping analysis indicated that the large portion of rat chromosome 1 is homologous to mouse chromosome 7, although the homologous to mouse chromosome 7, although the homologs of two rat genes are located on mouse chromosomes 17 and 19. Homologs of the rat chromosome 1 genes that we mapped are located on human chromosomes 6, 10, 11, 12, 15, 16, and 19. 38 refs., 1 fig., 3 tabs.

  4. Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.

    Science.gov (United States)

    Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S

    2016-09-26

    In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

    2008-12-16

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  6. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-12-04

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  7. Association mapping and favorable QTL alleles for fiber quality traits ...

    Indian Academy of Sciences (India)

    A total of 201 markers were polymorphic and generated 394 ... identified favorable QTL alleles and typical accessions for fiber quality are excellent genetic resources for future cotton .... Field management followed respective local practices.

  8. Single-molecule denaturation mapping of DNA in nanofluidic channels

    DEFF Research Database (Denmark)

    Reisner, Walter; Larsen, Niels Bent; Silahtaroglu, Asli

    2010-01-01

    Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips...... and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence...

  9. A MapReduce Framework for DNA Sequencing Data Processing

    Directory of Open Access Journals (Sweden)

    Samy Ghoneimy

    2016-12-01

    Full Text Available Genomics and Next Generation Sequencers (NGS like Illumina Hiseq produce data in the order of ‎‎200 billion base pairs in a single one-week run for a 60x human genome coverage, which ‎requires modern high-throughput experimental technologies that can ‎only be tackled with high performance computing (HPC and specialized software algorithms called ‎‎“short read aligners”. This paper focuses on the implementation of the DNA sequencing as a set of MapReduce programs that will accept a DNA data set as a FASTQ file and finally generate a VCF (variant call format file, which has variants for a given DNA data set. In this paper MapReduce/Hadoop along with Burrows-Wheeler Aligner (BWA, Sequence Alignment/Map (SAM ‎tools, are fully utilized to provide various utilities for manipulating alignments, including sorting, merging, indexing, ‎and generating alignments. The Map-Sort-Reduce process is designed to be suited for a Hadoop framework in ‎which each cluster is a traditional N-node Hadoop cluster to utilize all of the Hadoop features like HDFS, program ‎management and fault tolerance. The Map step performs multiple instances of the short read alignment algorithm ‎‎(BoWTie that run in parallel in Hadoop. The ordered list of the sequence reads are used as input tuples and the ‎output tuples are the alignments of the short reads. In the Reduce step many parallel instances of the Short ‎Oligonucleotide Analysis Package for SNP (SOAPsnp algorithm run in the cluster. Input tuples are sorted ‎alignments for a partition and the output tuples are SNP calls. Results are stored via HDFS, and then archived in ‎SOAPsnp format. ‎ The proposed framework enables extremely fast discovering somatic mutations, inferring population genetical ‎parameters, and performing association tests directly based on sequencing data without explicit genotyping or ‎linkage-based imputation. It also demonstrate that this method achieves comparable

  10. White matter fiber-based analysis of T1w/T2w ratio map

    Science.gov (United States)

    Chen, Haiwei; Budin, Francois; Noel, Jean; Prieto, Juan Carlos; Gilmore, John; Rasmussen, Jerod; Wadhwa, Pathik D.; Entringer, Sonja; Buss, Claudia; Styner, Martin

    2017-02-01

    Purpose: To develop, test, evaluate and apply a novel tool for the white matter fiber-based analysis of T1w/T2w ratio maps quantifying myelin content. Background: The cerebral white matter in the human brain develops from a mostly non-myelinated state to a nearly fully mature white matter myelination within the first few years of life. High resolution T1w/T2w ratio maps are believed to be effective in quantitatively estimating myelin content on a voxel-wise basis. We propose the use of a fiber-tract-based analysis of such T1w/T2w ratio data, as it allows us to separate fiber bundles that a common regional analysis imprecisely groups together, and to associate effects to specific tracts rather than large, broad regions. Methods: We developed an intuitive, open source tool to facilitate such fiber-based studies of T1w/T2w ratio maps. Via its Graphical User Interface (GUI) the tool is accessible to non-technical users. The framework uses calibrated T1w/T2w ratio maps and a prior fiber atlas as an input to generate profiles of T1w/T2w values. The resulting fiber profiles are used in a statistical analysis that performs along-tract functional statistical analysis. We applied this approach to a preliminary study of early brain development in neonates. Results: We developed an open-source tool for the fiber based analysis of T1w/T2w ratio maps and tested it in a study of brain development.

  11. White Matter Fiber-based Analysis of T1w/T2w Ratio Map.

    Science.gov (United States)

    Chen, Haiwei; Budin, Francois; Noel, Jean; Prieto, Juan Carlos; Gilmore, John; Rasmussen, Jerod; Wadhwa, Pathik D; Entringer, Sonja; Buss, Claudia; Styner, Martin

    2017-02-01

    To develop, test, evaluate and apply a novel tool for the white matter fiber-based analysis of T1w/T2w ratio maps quantifying myelin content. The cerebral white matter in the human brain develops from a mostly non-myelinated state to a nearly fully mature white matter myelination within the first few years of life. High resolution T1w/T2w ratio maps are believed to be effective in quantitatively estimating myelin content on a voxel-wise basis. We propose the use of a fiber-tract-based analysis of such T1w/T2w ratio data, as it allows us to separate fiber bundles that a common regional analysis imprecisely groups together, and to associate effects to specific tracts rather than large, broad regions. We developed an intuitive, open source tool to facilitate such fiber-based studies of T1w/T2w ratio maps. Via its Graphical User Interface (GUI) the tool is accessible to non-technical users. The framework uses calibrated T1w/T2w ratio maps and a prior fiber atlas as an input to generate profiles of T1w/T2w values. The resulting fiber profiles are used in a statistical analysis that performs along-tract functional statistical analysis. We applied this approach to a preliminary study of early brain development in neonates. We developed an open-source tool for the fiber based analysis of T1w/T2w ratio maps and tested it in a study of brain development.

  12. Satellites vs. fiber optics based networks and services - Road map to strategic planning

    Science.gov (United States)

    Marandi, James H. R.

    An overview of a generic telecommunications network and its components is presented, and the current developments in satellite and fiber optics technologies are discussed with an eye on the trends in industry. A baseline model is proposed, and a cost comparison of fiber- vs satellite-based networks is made. A step-by-step 'road map' to the successful strategic planning of telecommunications services and facilities is presented. This road map provides for optimization of the current and future networks and services through effective utilization of both satellites and fiber optics. The road map is then applied to different segments of the telecommunications industry and market place, to show its effectiveness for the strategic planning of executives of three types: (1) those heading telecommunications manufacturing concerns, (2) those leading communication service companies, and (3) managers of telecommunication/MIS departments of major corporations. Future networking issues, such as developments in integrated-services digital network standards and technologies, are addressed.

  13. Dietary Fiber and the Human Gut Microbiota: Application of Evidence Mapping Methodology

    Directory of Open Access Journals (Sweden)

    Caleigh M. Sawicki

    2017-02-01

    Full Text Available Interest is rapidly growing around the role of the human gut microbiota in facilitating beneficial health effects associated with consumption of dietary fiber. An evidence map of current research activity in this area was created using a newly developed database of dietary fiber intervention studies in humans to identify studies with the following broad outcomes: (1 modulation of colonic microflora; and/or (2 colonic fermentation/short-chain fatty acid concentration. Study design characteristics, fiber exposures, and outcome categories were summarized. A sub-analysis described oligosaccharides and bacterial composition in greater detail. One hundred eighty-eight relevant studies were identified. The fiber categories represented by the most studies were oligosaccharides (20%, resistant starch (16%, and chemically synthesized fibers (15%. Short-chain fatty acid concentration (47% and bacterial composition (88% were the most frequently studied outcomes. Whole-diet interventions, measures of bacterial activity, and studies in metabolically at-risk subjects were identified as potential gaps in the evidence. This evidence map efficiently captured the variability in characteristics of expanding research on dietary fiber, gut microbiota, and physiological health benefits, and identified areas that may benefit from further research. We hope that this evidence map will provide a resource for researchers to direct new intervention studies and meta-analyses.

  14. Pontryagin-Thom-Szucs type construction for non-positive codimensional singular maps with prescribed singular fibers

    OpenAIRE

    Kalmar, Boldizsar

    2006-01-01

    We give a Pontryagin-Thom-Szucs type construction for non-positive codimensional singular maps, and obtain results about cobordism and bordism groups of -1 codimensional stable maps with prescribed singular fibers.

  15. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Michael A. Gore

    2014-03-01

    Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

  16. Enzyme-enhanced fluorescence detection of DNA on etched optical fibers.

    Science.gov (United States)

    Niu, Shu-yan; Li, Quan-yi; Ren, Rui; Zhang, Shu-sheng

    2009-05-15

    A novel DNA biosensor based on enzyme-enhanced fluorescence detection on etched optical fibers was developed. The hybridization complex of DNA probe and biotinylated target was formed on the etched optical fiber, and was then bound with streptavidin labeled horseradish peroxidase (streptavidin-HRP). The target DNA was quantified through the fluorescent detection of bi-p,p'-4-hydroxyphenylacetic acid (DBDA) generated from the substrate 4-hydroxyphenylacetic acid (p-HPA) under the catalysis of HRP, with a detection limit of 1 pM and a linear range from 1.69 pM to 169 pM. It is facile to regenerate this sensor through surface treatment with concentrated urea solution. It was discovered that the sensor can retain 70% of its original activity after three detection-regeneration cycles.

  17. Mapped DNA probes from Ioblolly pine can be used for restriction fragment length polymorphism mapping in other conifers

    Science.gov (United States)

    M.R. Ahuja; M.E. Devey; A.T. Groover; K.D. Jermstad; D.B Neale

    1994-01-01

    A high-density genetic map based on restriction fragment length polymorphisms (RFLPs) is being constructed for loblolly pine (Pinus taeda L.). Consequently, a large number of DNA probes from loblolly pine are potentially available for use in other species. We have used some of these DNA probes to detect RFLPs in 12 conifers and an angiosperm....

  18. Thermo-optic characteristic of DNA thin solid film and its application as a biocompatible optical fiber temperature sensor.

    Science.gov (United States)

    Hong, Seongjin; Jung, Woohyun; Nazari, Tavakol; Song, Sanggwon; Kim, Taeoh; Quan, Chai; Oh, Kyunghwan

    2017-05-15

    We report unique thermo-optical characteristics of DNA-Cetyl tri-methyl ammonium (DNA-CTMA) thin solid film with a large negative thermo-optical coefficient of -3.4×10-4/°C in the temperature range from 20°C to 70°C without any observable thermal hysteresis. By combining this thermo-optic DNA film and fiber optic multimode interference (MMI) device, we experimentally demonstrated a highly sensitive compact temperature sensor with a large spectral shift of 0.15 nm/°C. The fiber optic MMI device was a concatenated structure with single-mode fiber (SMF)-coreless silica fiber (CSF)-single mode fiber (SMF) and the DNA-CTMA film was deposited on the CSF. The spectral shifts of the device in experiments were compared with the beam propagation method, which showed a good agreement.

  19. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  20. Magnetic resonance fiber density mapping of age-related white matter changes

    International Nuclear Information System (INIS)

    Stadlbauer, Andreas; Ganslandt, Oliver; Salomonowitz, Erich; Buchfelder, Michael; Hammen, Thilo; Bachmair, Johanna; Eberhardt, Knut

    2012-01-01

    Objectives: To introduce fiber density mapping (FDM) for investigation of age-related white matter (WM) changes and to compare its capabilities with conventional diffusion tensor imaging (DTI) post-processing. Methods: DTI data with 1.9 mm 3 isotropic voxels were acquired from 44 healthy volunteers (18–88 years) at 3 T. FDM is a 3-step approach which includes diagonalization of the diffusion tensor, fiber reconstruction for the whole brain, and calculation of fiber density (FD) values. Maps of fractional anisotropy (FA) and mean diffusivity (MD) were additionally calculated. Voxel-based analyses were performed to determine volume clusters of significant correlation with age. Bivariate linear regression models and Hotelling–Williams tests were used to detect significant differences between correlations. Results: FDM detected a larger WM volume affected by age-related changes concomitant with fewer significant clusters compared to FA and MD. This indicates that WM alterations due to normal aging occur rather globally than locally. FD values showed a significant stronger correlation with age in frontal lobes (prefrontal and precentral gyrus), limbic lobes (cingulate and parahippocampal gyrus), the corpus callosum (genu) and temporal lobes. Conclusions: FDM shows higher sensitivity for detection of age-related WM changes because it includes all surrounding fiber structures into the evaluation of each DTI data voxel.

  1. Magnetic resonance fiber density mapping of age-related white matter changes

    Energy Technology Data Exchange (ETDEWEB)

    Stadlbauer, Andreas, E-mail: andi@nmr.at [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, A-3100 St. Poelten (Austria); Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany); Ganslandt, Oliver [Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany); Salomonowitz, Erich [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, A-3100 St. Poelten (Austria); Buchfelder, Michael [Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany); Hammen, Thilo [Department of Neurology, Epilepsy Center, University of Erlangen-Nuremberg, Schwabachanlage 6, D-90429 Erlangen (Germany); Bachmair, Johanna [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, A-3100 St. Poelten (Austria); Eberhardt, Knut [Krankenhaus Schloss Werneck, MRT-Kompetenzzentrum, Balthasar-Neumann-Platz 1, D-97440 Werneck (Germany)

    2012-12-15

    Objectives: To introduce fiber density mapping (FDM) for investigation of age-related white matter (WM) changes and to compare its capabilities with conventional diffusion tensor imaging (DTI) post-processing. Methods: DTI data with 1.9 mm{sup 3} isotropic voxels were acquired from 44 healthy volunteers (18–88 years) at 3 T. FDM is a 3-step approach which includes diagonalization of the diffusion tensor, fiber reconstruction for the whole brain, and calculation of fiber density (FD) values. Maps of fractional anisotropy (FA) and mean diffusivity (MD) were additionally calculated. Voxel-based analyses were performed to determine volume clusters of significant correlation with age. Bivariate linear regression models and Hotelling–Williams tests were used to detect significant differences between correlations. Results: FDM detected a larger WM volume affected by age-related changes concomitant with fewer significant clusters compared to FA and MD. This indicates that WM alterations due to normal aging occur rather globally than locally. FD values showed a significant stronger correlation with age in frontal lobes (prefrontal and precentral gyrus), limbic lobes (cingulate and parahippocampal gyrus), the corpus callosum (genu) and temporal lobes. Conclusions: FDM shows higher sensitivity for detection of age-related WM changes because it includes all surrounding fiber structures into the evaluation of each DTI data voxel.

  2. Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.

    Science.gov (United States)

    Rudd, K E; Miller, W; Ostell, J; Benson, D A

    1990-01-25

    We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.

  3. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Science.gov (United States)

    Craig S. Echt; Surya Saha; Konstantin V. Krutovsky; Kokulapalan Wimalanathan; John E. Erpelding; Chun Liang; C Dana Nelson

    2011-01-01

    Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety...

  4. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Science.gov (United States)

    Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective o...

  5. Human cDNA mapping using fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-03-04

    Genetic mapping is approached using the techniques of high resolution fluorescence in situ hybridization (FISH). This technology and the results of its application are designed to rapidly generate whole genome as tool box of expressed sequence to speed the identification of human disease genes. The results of this study are intended to dovetail with and to link the results of existing technologies for creating backbone YAC and genetic maps. In the first eight months, this approach generated 60--80% of the expressed sequence map, the remainder expected to be derived through more long-term, labor-intensive, regional chromosomal gene searches or sequencing. The laboratory has made significant progress in the set-up phase, in mapping fetal and adult brain and other cDNAs, in testing a model system for directly linking genetic and physical maps using FISH with small fragments, in setting up a database, and in establishing the validity and throughput of the system.

  6. Mapping Base Modifications in DNA by Transverse-Current Sequencing

    Science.gov (United States)

    Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

    2018-02-01

    Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

  7. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

    Directory of Open Access Journals (Sweden)

    Bartoš Jan

    2008-06-01

    Full Text Available Abstract Background Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification. Results Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA. Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H. Conclusion The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which

  8. Algorithms for mapping high-throughput DNA sequences

    DEFF Research Database (Denmark)

    Frellsen, Jes; Menzel, Peter; Krogh, Anders

    2014-01-01

    of data generation, new bioinformatics approaches have been developed to cope with the large amount of sequencing reads obtained in these experiments. In this chapter, we first introduce HTS technologies and their usage in molecular biology and discuss the problem of mapping sequencing reads...... to their genomic origin. We then in detail describe two approaches that offer very fast heuristics to solve the mapping problem in a feasible runtime. In particular, we describe the BLAT algorithm, and we give an introduction to the Burrows-Wheeler Transform and the mapping algorithms based on this transformation....

  9. Development and production of Lab-on-Chip systems for DNA mapping

    DEFF Research Database (Denmark)

    Østergaard, Peter Friis

    as low as 1:200. The developed polymer systems are tested by conducting two different experiments on DNA. Since such experiments are highly sensitive, efforts have been taken in order to lower the autofluorescence of the devices, resulting in a decrease of the background signal to roughly half...... several nanochannels can be placed parallel to each other, a large number of DNA molecules can be investigated. In the second experiment, mapping is performed on human DNA in nanoslit devices. A fluorescent profile is created by heating the sample up to a temperature, where the DNA is partially denatured....... The fluorescent dye will diffuse away from the denatured regions, and by analysing these black areas, the DNA molecule can be identified and potential mutations can be found. In the nanoslits, the DNA is stretched out via a shear flow, resulting in a stretching of more than 95% of the contour length meaning...

  10. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Directory of Open Access Journals (Sweden)

    Wimalanathan Kokulapalan

    2011-01-01

    Full Text Available Abstract Background Previous loblolly pine (Pinus taeda L. genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats, also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs and 149 were from non-transcribed genomic sequences (genomic-SSRs. Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO terms. Duplicate (i.e., redundant accessory and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped

  11. Pulsed single-photon spectrometer by frequency-to-time mapping using chirped fiber Bragg gratings.

    Science.gov (United States)

    Davis, Alex O C; Saulnier, Paul M; Karpiński, Michał; Smith, Brian J

    2017-05-29

    A fiber-integrated spectrometer for single-photon pulses outside the telecommunications wavelength range based upon frequency-to-time mapping, implemented by chromatic group delay dispersion (GDD), and precise temporally-resolved single-photon counting, is presented. A chirped fiber Bragg grating provides low-loss GDD, mapping the frequency distribution of an input pulse onto the temporal envelope of the output pulse. Time-resolved detection with fast single-photon-counting modules enables monitoring of a wavelength range from 825 nm to 835 nm with nearly uniform efficiency at 55 pm resolution (24 GHz at 830 nm). To demonstrate the versatility of this technique, spectral interference of heralded single photons and the joint spectral intensity distribution of a photon-pair source are measured. This approach to single-photon-level spectral measurements provides a route to realize applications of time-frequency quantum optics at visible and near-infrared wavelengths, where multiple spectral channels must be simultaneously monitored.

  12. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

    OpenAIRE

    Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

    2012-01-01

    DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it possible to map SCEs at orders-of-magnitude greater resolution than was previously possible. On average, murine embryonic stem (mES) cells exhibit eight SCEs, which are detected at a resolution of up...

  13. Color Image Encryption Using Three-Dimensional Sine ICMIC Modulation Map and DNA Sequence Operations

    Science.gov (United States)

    Liu, Wenhao; Sun, Kehui; He, Yi; Yu, Mengyao

    Derived from Sine map and iterative chaotic map with infinite collapse (ICMIC), a three-dimensional hyperchaotic Sine ICMIC modulation map (3D-SIMM) is proposed based on a close-loop modulation coupling (CMC) method. Based on this map, a novel color image encryption algorithm is designed by employing a hybrid model of multidirectional circular permutation and deoxyribonucleic acid (DNA) masking. In this scheme, the pixel positions of image are scrambled by multidirectional circular permutation, and the pixel values are substituted by DNA sequence operations. The simulation results and security analysis show that the algorithm has good encryption effect and strong key sensitivity, and can resist brute-force, statistical, differential, known-plaintext and chosen-plaintext attacks.

  14. Mode-selective mapping and control of vectorial nonlinear-optical processes in multimode photonic-crystal fibers.

    Science.gov (United States)

    Hu, Ming-Lie; Wang, Ching-Yue; Song, You-Jian; Li, Yan-Feng; Chai, Lu; Serebryannikov, Evgenii; Zheltikov, Aleksei

    2006-02-06

    We demonstrate an experimental technique that allows a mapping of vectorial nonlinear-optical processes in multimode photonic-crystal fibers (PCFs). Spatial and polarization modes of PCFs are selectively excited in this technique by varying the tilt angle of the input beam and rotating the polarization of the input field. Intensity spectra of the PCF output plotted as a function of the input field power and polarization then yield mode-resolved maps of nonlinear-optical interactions in multimode PCFs, facilitating the analysis and control of nonlinear-optical transformations of ultrashort laser pulses in such fibers.

  15. Cloning and restriction enzyme mapping of ribosomal DNA of Giardia duodenalis, Giardia ardeae and Giardia muris.

    Science.gov (United States)

    van Keulen, H; Campbell, S R; Erlandsen, S L; Jarroll, E L

    1991-06-01

    In an attempt to study Giardia at the DNA sequence level, the rRNA genes of three species, Giardia duodenalis, Giardia ardeae and Giardia muris were cloned and restriction enzyme maps were constructed. The rDNA repeats of these Giardia show completely different restriction enzyme recognition patterns. The size of the rDNA repeat ranges from approximately 5.6 kb in G. duodenalis to 7.6 kb in both G. muris and G. ardeae. These size differences are mainly attributable to the variation in length of the spacer. Minor differences exist among these Giardia in the sizes of their small subunit rRNA and the internal transcribed spacer between small and large subunit rRNA. The genetic maps were constructed by sequence analysis of the DNA around the 5' and 3' ends of the mature rRNA genes and between the rRNA covering the 5.8S rRNA gene and internal transcribed spacer. Comparison of the 5.8S rDNA and 3' end of large subunit rDNA from these three Giardia species showed considerable sequence variation, but the rDNA sequences of G. duodenalis and G. ardeae appear more closely related to each other than to G. muris.

  16. Presence of intestinal Mycobacterium avium subspecies paratuberculosis (MAP DNA is not associated with altered MMP expression in ulcerative colitis

    Directory of Open Access Journals (Sweden)

    Halwe Jörg M

    2011-04-01

    Full Text Available Abstract Background Mycobacterium avium subspecies paratuberculosis (MAP is suspected to be a causative agent in human Crohn's disease (CD. Recent evidence suggests that pathogenic mycobacteria and MAP can induce the expression of Matrix Metalloproteinases (MMP, which are the main proteases in the pathogenesis of mucosal ulcerations in inflammatory bowel disease (IBD. Within this study we assessed the prevalence of intestinal MAP specific DNA in patients with Crohn's disease, ulcerative colitis (UC, and healthy controls. We further analysed regulation patterns of MMPs in mucosal tissues of UC patients with and without intestinal MAP DNA detection. Methods Colonic biopsy samples were obtained from 63 Norwegian and German IBD patients and 21 healthy controls. RNA was quantified by quantitative real-time polymerase chain reaction (PCR to study MMP gene expression in both pathological and healthy mucosal specimens. The presence of MAP DNA in colonic mucosa was examined using MAP specific PCR. Results MAP DNA was detected in 20% of UC patients and 33% of healthy controls but only in 7% of patients with CD. UC patients treated with corticosteroids exhibited a significantly increased frequency of intestinal MAP DNA compared to those not receiving corticosteroids. Expression of MMP-1, -2, -7, -9, -13, -19, -28 and TNF-α did not differ between UC patients with presence of intestinal MAP DNA compared to those without. MMP-2, MMP-9 and MMP-13 were significantly decreased in UC patients receiving corticosteroids. Conclusions The presence of intestinal MAP specific DNA is not associated with altered MMP expression in UC in vivo. Corticosteroids are associated with increased detection of intestinal MAP DNA and decreased expression of certain MMPs. Frequent detection of MAP DNA in healthy controls might be attributable to the wide environmental distribution of MAP and its presence in the food-chain.

  17. Extensive mapping of PPAR binding to genomic DNA

    DEFF Research Database (Denmark)

    Nielsen, Ronni; Pedersen, Thomas Åskov; Trindade, Luisa

    processes such as adaptation to fasting and cold, muscle isotype switching and adipogenesis, underscoring the metabolic importance of these transcription factors. Although the PPARs have been subject to intensive studies for almost two decades, far from all PPAR target genes are known. In addition, only few...... analysis of the regulatory networks controlled by PPAR transcription factors, thereby allowing for a better understanding of PPAR biology. - Adenoviral expression PPARg2 and RXR induce transcription from a wide range of hepatocyte as well as non-hepatocyte PPAR target genes in the murine AML-12 hepatoma...... cell line. Only very few PPAR target genes are not induced by PPARg2/RXR. - ChIP-on-chip analysis shows ~1200 peaks on chr. 7 & 8 by peak detection software. 80% of selected peaks were positive in single ChIP experiments.   - PPARg2/RXR are recruited to DNA elements near several genes on chr. 7 & 8...

  18. Updating rDNA restriction enzyme maps of Tetrahymena reveals four new intron-containing species

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Simon, E M; Engberg, J

    1985-01-01

    an intron in the 26s rRNA coding region. The evolutionary relationship among the species of the T. pyriformis complex was examined on the basis of the rDNA maps with emphasis on similarities between two of the new species and the widely studied T. thermophila and T. pigmentosa. Examination of a large number...

  19. Mapping yeast origins of replication via single-stranded DNA detection.

    Science.gov (United States)

    Feng, Wenyi; Raghuraman, M K; Brewer, Bonita J

    2007-02-01

    Studies in th Saccharomyces cerevisiae have provided a framework for understanding how eukaryotic cells replicate their chromosomal DNA to ensure faithful transmission of genetic information to their daughter cells. In particular, S. cerevisiae is the first eukaryote to have its origins of replication mapped on a genomic scale, by three independent groups using three different microarray-based approaches. Here we describe a new technique of origin mapping via detection of single-stranded DNA in yeast. This method not only identified the majority of previously discovered origins, but also detected new ones. We have also shown that this technique can identify origins in Schizosaccharomyces pombe, illustrating the utility of this method for origin mapping in other eukaryotes.

  20. Nonlinear microrheology and molecular imaging to map microscale deformations of entangled DNA networks

    Science.gov (United States)

    Wu, Tsai-Chin; Anderson, Rae

    We use active microrheology coupled to single-molecule fluorescence imaging to elucidate the microscale dynamics of entangled DNA. DNA naturally exists in a wide range of lengths and topologies, and is often confined in cell nucleui, forming highly concentrated and entangled biopolymer networks. Thus, DNA is the model polymer for understanding entangled polymer dynamics as well as the crowded environment of cells. These networks display complex viscoelastic properties that are not well understood, especially at the molecular-level and in response to nonlinear perturbations. Specifically, how microscopic stresses and strains propagate through entangled networks, and what molecular deformations lead to the network stress responses are unknown. To answer these important questions, we optically drive a microsphere through entangled DNA, perturbing the system far from equilibrium, while measuring the resistive force the DNA exerts on the bead during and after bead motion. We simultaneously image single fluorescent-labeled DNA molecules throughout the network to directly link the microscale stress response to molecular deformations. We characterize the deformation of the network from the molecular-level to the mesoscale, and map the stress propagation throughout the network. We further study the impact of DNA length (11 - 115 kbp) and topology (linear vs ring DNA) on deformation and propagation dynamics, exploring key nonlinear features such as tube dilation and power-law relaxation.

  1. Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication.

    Science.gov (United States)

    Feng, Wenyi; Collingwood, David; Boeck, Max E; Fox, Lindsay A; Alvino, Gina M; Fangman, Walton L; Raghuraman, Mosur K; Brewer, Bonita J

    2006-02-01

    During DNA replication one or both strands transiently become single stranded: first at the sites where initiation of DNA synthesis occurs (known as origins of replication) and subsequently on the lagging strands of replication forks as discontinuous Okazaki fragments are generated. We report a genome-wide analysis of single-stranded DNA (ssDNA) formation in the presence of hydroxyurea during DNA replication in wild-type and checkpoint-deficient rad53 Saccharomyces cerevisiae cells. In wild-type cells, ssDNA was first observed at a subset of replication origins and later 'migrated' bi-directionally, suggesting that ssDNA formation is associated with continuously moving replication forks. In rad53 cells, ssDNA was observed at virtually every known origin, but remained there over time, suggesting that replication forks stall. Telomeric regions seemed to be particularly sensitive to the loss of Rad53 checkpoint function. Replication origins in Schizosaccharomyces pombe were also mapped using our method.

  2. DNA adduct profiling of in vitro colonic meat digests to map red vs. white meat genotoxicity.

    Science.gov (United States)

    Hemeryck, Lieselot Y; Rombouts, Caroline; De Paepe, Ellen; Vanhaecke, Lynn

    2018-05-01

    The consumption of red meat has been linked to an increased colorectal cancer (CRC) risk. One of the major hypotheses states that heme iron (present in red meat) stimulates the formation of genotoxic N-nitroso compounds (NOCs) and lipid peroxidation products (LPOs). By means of DNA adductomics, chemically induced DNA adduct formation can be mapped in relation to e.g. dietary exposures. In this study, this state-of-the-art methodology was used to investigate alkylation and (lipid per)oxidation induced DNA adduct formation in in vitro red vs. white meat digests. In doing so, 90 alkylation and (lipid per)oxidation induced DNA adduct types could be (tentatively) identified. Overall, 12 NOC- and/or LPO-related DNA adduct types, i.e. dimethyl-T (or ethyl-T), hydroxymethyl-T, tetramethyl-T, methylguanine (MeG), guanidinohydantoin, hydroxybutyl-C, hydroxymethylhydantoin, malondialdehyde-x3-C, O 6 -carboxymethylguanine, hydroxyethyl-T, carboxyethyl-T and 3,N 4 -etheno-C were singled out as potential heme-rich meat digestion markers. The retrieval of these DNA adduct markers is in support of the heme, NOC and LPO hypotheses, suggesting that DNA adduct formation may indeed contribute to red meat related CRC risk. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Single-shot T1 mapping of the corpus callosum: A rapid characterization of fiber bundle anatomy

    Directory of Open Access Journals (Sweden)

    Sabine eHofer

    2015-05-01

    Full Text Available Using diffusion-tensor MRI and fiber tractography the topographic organization of the corpus callosum (CC has been described to comprise 5 segments with fibers projecting into prefrontal (I, premotor and supplementary motor (II, primary motor (III, and primary sensory areas (IV, as well as into parietal, temporal, and occipital cortical areas (V. In order to more rapidly characterize the underlying anatomy of these segments, this study used a novel single-shot T1 mapping method to quantitatively determine T1 relaxation times in the human CC. A region-of-interest analysis revealed a tendency for the lowest T1 relaxation times in the genu and the highest T1 relaxation times in the somatomotor region of the CC. This observation separates regions dominated by myelinated fibers with large diameters (somatomotor area from densely packed smaller axonal bundles (genu with less myelin. The results indicate that characteristic T1 relaxation times in callosal profiles provide an additional means to monitor differences in fiber anatomy, fiber density, and gray matter in respective neocortical areas. In conclusion, rapid T1 mapping allows for a characterization of the axonal architecture in an individual CC in less than 10 s. The approach emerges as a valuable means for studying neocortical brain anatomy with possible implications for the diagnosis of neurodegenerative processes.

  4. Mapping of rDNA on the chromosomes of Eleusine species by fluorescence in situ hybridization.

    Science.gov (United States)

    Bisht, M S; Mukai, Y

    2000-12-01

    Mapping of rDNA sites on the chromosomes of four diploid and two tetraploid species of Eleusine has provided valuable information on genome relationship between the species. Presence of 18S-5.8S-26S rDNA on the largest pair of the chromosomes, location of 5S rDNA at four sites on two pairs of chromosomes and presence of 18S-5.8S-26S and 5S rDNA at same location on one pair of chromosomes have clearly differentiated E. multiflora from rest of the species of Eleusine. The two tetraploid species, E. coracana and E. africana have the same number of 18S-5.8S-26S and 5S rDNA sites and located at similar position on the chromosomes. Diploid species, E. indica, E. floccifolia and E. tristachya have the same 18S-5.8S-26S sites and location on the chromosomes which also resembled with the two pairs of 18S-5.8S-26S rDNA locations in tetraploid species, E. coracana and E. africana. The 5S rDNA sites on chromosomes of E. indica and E. floccifolia were also comparable to the 5S rDNA sites of E. africana and E. coracana. The similarity of the rDNA sites and their location on chromosomes in the three diploid and two polyploid species also supports the view that genome donors to tetraploid species may be from these diploid species.

  5. Mapping of gene transcripts by nuclease protection assays and cDNA primer extension

    International Nuclear Information System (INIS)

    Calzone, F.J.; Britten, R.J.; Davidson, E.J.

    1987-01-01

    An important problem often faced in the molecular characterization of genes is the precise mapping of those genomic sequences transcribed into RNA. This requires identification of the genomic site initiating gene transcription, the location of genomic sequences removed from the primary gene transcript during RNA processing, and knowledge of sequences terminating the processed gene transcript. The objective of the protocols described here is the generation of transcription maps utilizing relatively uncharacterized gene fragments. The basic approach is hybridization of a single-stranded DNA probe with cellular RNA, followed by treatment with a single-strand-specific nuclease that does not attack DNA-RNA hybrids, in order to destroy any unreacted probe sequences. Thus the probe sequences included in the hybrid duplexes are protected from nuclease digestion. The sizes of the protected probe fragments determined by gel electrophoresis correspond to the lengths of the hybridized sequence elements

  6. The impact of white matter fiber orientation in single-acquisition quantitative susceptibility mapping.

    Science.gov (United States)

    Lancione, Marta; Tosetti, Michela; Donatelli, Graziella; Cosottini, Mirco; Costagli, Mauro

    2017-11-01

    The aim of this work was to assess the impact of tissue structural orientation on quantitative susceptibility mapping (QSM) reliability, and to provide a criterion to identify voxels in which measures of magnetic susceptibility (χ) are most affected by spatial orientation effects. Four healthy volunteers underwent 7-T magnetic resonance imaging (MRI). Multi-echo, gradient-echo sequences were used to obtain quantitative maps of frequency shift (FS) and χ. Information from diffusion tensor imaging (DTI) was used to investigate the relationship between tissue orientation and FS measures and QSM. After sorting voxels on the basis of their fractional anisotropy (FA), the variations in FS and χ values over tissue orientation were measured. Using a K-means clustering algorithm, voxels were separated into two groups depending on the variability of measures within each FA interval. The consistency of FS and QSM values, observed at low FA, was disrupted for FA > 0.6. The standard deviation of χ measured at high FA (0.0103 ppm) was nearly five times that at low FA (0.0022 ppm). This result was consistent through data across different head positions and for different brain regions considered separately, which confirmed that such behavior does not depend on structures with different bulk susceptibility oriented along particular angles. The reliability of single-orientation QSM anticorrelates with local FA. QSM provides replicable values with little variability in brain regions with FA < 0.6, but QSM should be interpreted cautiously in major and coherent fiber bundles, which are strongly affected by structural anisotropy and magnetic susceptibility anisotropy. Copyright © 2017 John Wiley & Sons, Ltd.

  7. Fiber

    Science.gov (United States)

    ... meals instead of white rice. Add beans (kidney, black, navy, and pinto) to rice dishes for even more fiber. Spice up salads with berries and almonds, chickpeas, cooked artichokes, and beans (kidney, black, navy, or pinto). Use whole-grain (corn or ...

  8. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN

    Energy Technology Data Exchange (ETDEWEB)

    Rangaraj, K.; Cooper, P.K.; Trego, K.S.

    2009-01-01

    The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of

  9. Polarized light microscopy for 3-dimensional mapping of collagen fiber architecture in ocular tissues.

    Science.gov (United States)

    Yang, Bin; Jan, Ning-Jiun; Brazile, Bryn; Voorhees, Andrew; Lathrop, Kira L; Sigal, Ian A

    2018-04-06

    Collagen fibers play a central role in normal eye mechanics and pathology. In ocular tissues, collagen fibers exhibit a complex 3-dimensional (3D) fiber orientation, with both in-plane (IP) and out-of-plane (OP) orientations. Imaging techniques traditionally applied to the study of ocular tissues only quantify IP fiber orientation, providing little information on OP fiber orientation. Accurate description of the complex 3D fiber microstructures of the eye requires quantifying full 3D fiber orientation. Herein, we present 3dPLM, a technique based on polarized light microscopy developed to quantify both IP and OP collagen fiber orientations of ocular tissues. The performance of 3dPLM was examined by simulation and experimental verification and validation. The experiments demonstrated an excellent agreement between extracted and true 3D fiber orientation. Both IP and OP fiber orientations can be extracted from the sclera and the cornea, providing previously unavailable quantitative 3D measures and insight into the tissue microarchitecture. Together, the results demonstrate that 3dPLM is a powerful imaging technique for the analysis of ocular tissues. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing

    DEFF Research Database (Denmark)

    Łopacińska-Jørgensen, Joanna M; Pedersen, Jonas Nyvold; Bak, Mads

    2017-01-01

    Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so...

  11. Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics.

    Science.gov (United States)

    Díaz-Mejía, J Javier; Celaj, Albi; Mellor, Joseph C; Coté, Atina; Balint, Attila; Ho, Brandon; Bansal, Pritpal; Shaeri, Fatemeh; Gebbia, Marinella; Weile, Jochen; Verby, Marta; Karkhanina, Anna; Zhang, YiFan; Wong, Cassandra; Rich, Justin; Prendergast, D'Arcy; Gupta, Gaurav; Öztürk, Sedide; Durocher, Daniel; Brown, Grant W; Roth, Frederick P

    2018-05-28

    Condition-dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State-of-the-art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double-mutant strains, does not scale readily to multi-condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG-GI), by which double-mutant strains generated via en masse "party" mating can also be monitored en masse for growth to detect genetic interactions. By using site-specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG-GI enables multiplexed quantitative tracking of double mutants via next-generation sequencing. We applied BFG-GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (4NQO), bleomycin, zeocin, and three other DNA-damaging environments. BFG-GI recapitulated known genetic interactions and yielded new condition-dependent genetic interactions. We validated and further explored a subnetwork of condition-dependent genetic interactions involving MAG1 , SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  12. Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe.

    Science.gov (United States)

    Horn, Susanne; Prost, Stefan; Stiller, Mathias; Makowiecki, Daniel; Kuznetsova, Tatiana; Benecke, Norbert; Pucher, Erich; Hufthammer, Anne K; Schouwenburg, Charles; Shapiro, Beth; Hofreiter, Michael

    2014-04-01

    After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.

  13. Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing.

    Science.gov (United States)

    Senkevich, Tatiana G; Bruno, Daniel; Martens, Craig; Porcella, Stephen F; Wolf, Yuri I; Moss, Bernard

    2015-09-01

    Poxviruses reproduce in the host cytoplasm and encode most or all of the enzymes and factors needed for expression and synthesis of their double-stranded DNA genomes. Nevertheless, the mode of poxvirus DNA replication and the nature and location of the replication origins remain unknown. A current but unsubstantiated model posits only leading strand synthesis starting at a nick near one covalently closed end of the genome and continuing around the other end to generate a concatemer that is subsequently resolved into unit genomes. The existence of specific origins has been questioned because any plasmid can replicate in cells infected by vaccinia virus (VACV), the prototype poxvirus. We applied directional deep sequencing of short single-stranded DNA fragments enriched for RNA-primed nascent strands isolated from the cytoplasm of VACV-infected cells to pinpoint replication origins. The origins were identified as the switching points of the fragment directions, which correspond to the transition from continuous to discontinuous DNA synthesis. Origins containing a prominent initiation point mapped to a sequence within the hairpin loop at one end of the VACV genome and to the same sequence within the concatemeric junction of replication intermediates. These findings support a model for poxvirus genome replication that involves leading and lagging strand synthesis and is consistent with the requirements for primase and ligase activities as well as earlier electron microscopic and biochemical studies implicating a replication origin at the end of the VACV genome.

  14. Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA.

    Science.gov (United States)

    Marr, Melissa M; Brace, Selina; Schreve, Danielle C; Barnes, Ian

    2018-02-09

    Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.

  15. Analysis and Design of a Fiber-optic Probe for DNA Sensors Final Report CRADA No. TSB-1147-95

    Energy Technology Data Exchange (ETDEWEB)

    Molau, Nicole [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vail, Curtis [Accu.Photonics, Inc., Ann Arbor, MI (United States)

    2018-01-24

    In 1995, a challenge in the field of genetics dealt with the acquisition of efficient DNA sequencing techniques for reading the 3 billion base-pairs that comprised the human genome. AccuPhotonics, Inc. proposed to develop and manufacture a state-of-the-art near-field scanning optical microscopy (NSOM) fiber-optic probe that was expected to increase probe efficiency by two orders of magnitude over the existing state-of-the-art and to improve resolution to 10Å. The detailed design calculation and optimization of electrical properties of the fiber-optic probe tip geometry would be performed at LLNL, using existing finite-difference time-domain (FDTD) electromagnetic (EM) codes.

  16. Fibered confocal fluorescence microscopy for imaging apoptotic DNA fragmentation at the single-cell level in vivo

    International Nuclear Information System (INIS)

    Al-Gubory, Kais H.

    2005-01-01

    The major characteristic of cell death by apoptosis is the loss of nuclear DNA integrity by endonucleases, resulting in the formation of small DNA fragments. The application of confocal imaging to in vivo monitoring of dynamic cellular events, like apoptosis, within internal organs and tissues has been limited by the accessibility to these sites. Therefore, the aim of the present study was to test the feasibility of fibered confocal fluorescence microscopy (FCFM) to image in situ apoptotic DNA fragmentation in surgically exteriorized sheep corpus luteum in the living animal. Following intra-luteal administration of a fluorescent DNA-staining dye, YO-PRO-1, DNA cleavage within nuclei of apoptotic cells was serially imaged at the single-cell level by FCFM. This imaging technology is sufficiently simple and rapid to allow time series in situ detection and visualization of cells undergoing apoptosis in the intact animal. Combined with endoscope, this approach can be used for minimally invasive detection of fluorescent signals and visualization of cellular events within internal organs and tissues and thereby provides the opportunity to study biological processes in the natural physiological environment of the cell in living animals

  17. Cloning and comparative mapping of a human chromosome 4-specific alpha satellite DNA sequence

    Energy Technology Data Exchange (ETDEWEB)

    D' Aiuto, L.; Marzella, R.; Archidiacono, N.; Rocchi, M. (Universita di Bari (Italy)); Antonacci, R. (Instituto Anatomia Umana Normale, Modena (Italy))

    1993-11-01

    The authors have isolated and characterized two human alphoid DNA clones: p4n1/4 and pZ4.1. Clone p4n1/4 identifies specifically the centromeric region of chromosome 4; pZ4.1 recognizes a subset of alphoid DNA shared by chromosomes 4 and 9. The specificity was determined using fluorescence in situ hybridization experiments on metaphase spreads and Southern blotting analysis of human-hamster somatic cell hybrids. The genomic organization of both subsets was also investigated. Comparative mapping on chimpanzee and gorilla chromosomes was performed. p4n1/4 hybridizes to chimpanzee chromosomes 11 and 13, homologs of human chromosomes 9 and 2q, respectively. On gorilla metaphase spreads, p4n1/4 hybridizes exclusively to the centromeric region of chromosome 19, partially homologous to human chromosome 17. No hybridization signal was detected on chromosome 3 of both chimpanzee and gorilla, in both species homolog of human chromosome 4. Identical comparative mapping results were obtained using pZ4.1 probe, although the latter recognizes an alphoid subset distinct from the one recognized by p4n1/4. The implications of these results in the evolution of centromeric regions of primate chromosomes are discussed. 33 refs., 4 figs.

  18. Mapping DNA methylation by transverse current sequencing: Reduction of noise from neighboring nucleotides

    Science.gov (United States)

    Alvarez, Jose; Massey, Steven; Kalitsov, Alan; Velev, Julian

    Nanopore sequencing via transverse current has emerged as a competitive candidate for mapping DNA methylation without needed bisulfite-treatment, fluorescent tag, or PCR amplification. By eliminating the error producing amplification step, long read lengths become feasible, which greatly simplifies the assembly process and reduces the time and the cost inherent in current technologies. However, due to the large error rates of nanopore sequencing, single base resolution has not been reached. A very important source of noise is the intrinsic structural noise in the electric signature of the nucleotide arising from the influence of neighboring nucleotides. In this work we perform calculations of the tunneling current through DNA molecules in nanopores using the non-equilibrium electron transport method within an effective multi-orbital tight-binding model derived from first-principles calculations. We develop a base-calling algorithm accounting for the correlations of the current through neighboring bases, which in principle can reduce the error rate below any desired precision. Using this method we show that we can clearly distinguish DNA methylation and other base modifications based on the reading of the tunneling current.

  19. Hight Energy Fiber Laser Based Lidar Transmitter for Topographic Mapping, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR will develop core Yb laser technology that is higher than 50% optical to optical efficient with pulse energies up to 300uJ/pulse in the all fiber version...

  20. Fiber-optic fluorometer for microscale mapping of photosynthetic pigments in microbial communities

    DEFF Research Database (Denmark)

    Thar, Roland Matthias; Kühl, Michael; Holst, Gerhard

    2001-01-01

    Microscale fluorescence measurements were performed in photosynthetic biofilms at a spatial resolution of 100 to 200 µm with a new fiber-optic fluorometer which allowed four different excitation and emission wavelengths and was configured for measuring phycobiliproteins, chlorophylls, and bacteri......Microscale fluorescence measurements were performed in photosynthetic biofilms at a spatial resolution of 100 to 200 µm with a new fiber-optic fluorometer which allowed four different excitation and emission wavelengths and was configured for measuring phycobiliproteins, chlorophylls...

  1. All-fiber incoherent frequency-to-time mapping method for microwave signal generation with baseband transmission and multicasting support

    DEFF Research Database (Denmark)

    Company Torres, Victor; Tafur Monroy, Idelfonso; Lancis, Jesus

    2008-01-01

    We present a proof-of-principle experiment for achieving simultaneous distribution of baseband radio-frequency data and up-conversion with broadcasting support over a passive optical network. The technique is based on an incoherent frequency-to-time mapping method for pulse shaping. Specifically...... resembles the shape of the incoherent source. The photodetected signal contains both the baseband data and an up-frequency converted copy with central wavelength for the microwave carrier into the ultra-wideband range and tuning capability by selection of the fiber length. (c) 2008 Elsevier B.V. All rights...

  2. High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L..

    Directory of Open Access Journals (Sweden)

    Zhen Zhang

    Full Text Available Cotton (Gossypium hirsutum L. is an important agricultural crop that provides renewable natural fiber resources for the global textile industry. Technological developments in the textile industry and improvements in human living standards have increased the requirement for supplies and better quality cotton. Upland cotton 0-153 is an elite cultivar harboring strong fiber strength genes. To conduct quantitative trait locus (QTL mapping for fiber quality in 0-153, we developed a population of 196 recombinant inbred lines (RILs from a cross between 0-153 and sGK9708. The fiber quality traits in 11 environments were measured and a genetic linkage map of chromosome 25 comprising 210 loci was constructed using this RIL population, mainly using simple sequence repeat markers and single nucleotide polymorphism markers. QTLs were identified across diverse environments using the composite interval mapping method. A total of 37 QTLs for fiber quality traits were identified on chromosome 25, of which 17 were stably expressed in at least in two environments. A stable fiber strength QTL, qFS-chr25-4, which was detected in seven environments and was located in the marker interval between CRI-SNP120491 and BNL2572, could explain 6.53%-11.83% of the observed phenotypic variations. Meta-analysis also confirmed the above QTLs with previous reports. Application of these QTLs could contribute to improving fiber quality and provide information for marker-assisted selection.

  3. High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Zhang, Zhen; Li, Junwen; Muhammad, Jamshed; Cai, Juan; Jia, Fei; Shi, Yuzhen; Gong, Juwu; Shang, Haihong; Liu, Aiying; Chen, Tingting; Ge, Qun; Palanga, Koffi Kibalou; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Li, Wei; Sun, Linyang; Gong, Wankui; Yuan, Youlu

    2015-01-01

    Cotton (Gossypium hirsutum L.) is an important agricultural crop that provides renewable natural fiber resources for the global textile industry. Technological developments in the textile industry and improvements in human living standards have increased the requirement for supplies and better quality cotton. Upland cotton 0-153 is an elite cultivar harboring strong fiber strength genes. To conduct quantitative trait locus (QTL) mapping for fiber quality in 0-153, we developed a population of 196 recombinant inbred lines (RILs) from a cross between 0-153 and sGK9708. The fiber quality traits in 11 environments were measured and a genetic linkage map of chromosome 25 comprising 210 loci was constructed using this RIL population, mainly using simple sequence repeat markers and single nucleotide polymorphism markers. QTLs were identified across diverse environments using the composite interval mapping method. A total of 37 QTLs for fiber quality traits were identified on chromosome 25, of which 17 were stably expressed in at least in two environments. A stable fiber strength QTL, qFS-chr25-4, which was detected in seven environments and was located in the marker interval between CRI-SNP120491 and BNL2572, could explain 6.53%-11.83% of the observed phenotypic variations. Meta-analysis also confirmed the above QTLs with previous reports. Application of these QTLs could contribute to improving fiber quality and provide information for marker-assisted selection.

  4. Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing

    DEFF Research Database (Denmark)

    Łopacińska-Jørgensen, Joanna M; Pedersen, Jonas Nyvold; Bak, Mads

    2017-01-01

    Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so......-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We...... demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our...

  5. Statistical mapping of zones of focused groundwater/surface-water exchange using fiber-optic distributed temperature sensing

    Science.gov (United States)

    Mwakanyamale, Kisa; Day-Lewis, Frederick D.; Slater, Lee D.

    2013-01-01

    Fiber-optic distributed temperature sensing (FO-DTS) increasingly is used to map zones of focused groundwater/surface-water exchange (GWSWE). Previous studies of GWSWE using FO-DTS involved identification of zones of focused GWSWE based on arbitrary cutoffs of FO-DTS time-series statistics (e.g., variance, cross-correlation between temperature and stage, or spectral power). New approaches are needed to extract more quantitative information from large, complex FO-DTS data sets while concurrently providing an assessment of uncertainty associated with mapping zones of focused GSWSE. Toward this end, we present a strategy combining discriminant analysis (DA) and spectral analysis (SA). We demonstrate the approach using field experimental data from a reach of the Columbia River adjacent to the Hanford 300 Area site. Results of the combined SA/DA approach are shown to be superior to previous results from qualitative interpretation of FO-DTS spectra alone.

  6. Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami

    Science.gov (United States)

    Chikkaraddy, Rohit; Turek, V. A.; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F.; Baumberg, Jeremy J.

    2018-01-01

    Fabricating nanocavities in which optically-active single quantum emitters are precisely positioned, is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore, and obtain enhancements of $\\geq4\\times10^3$ with high quantum yield ($\\geq50$%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of $\\pm1.5$ nm. Our approach introduces a straightforward non-invasive way to measure and quantify confined optical modes on the nanoscale.

  7. Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami.

    Science.gov (United States)

    Chikkaraddy, Rohit; Turek, V A; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F; Baumberg, Jeremy J

    2018-01-10

    Fabricating nanocavities in which optically active single quantum emitters are precisely positioned is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5 nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore and obtain enhancements of ≥4 × 10 3 with high quantum yield (≥50%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of ±1.5 nm. Our approach introduces a straightforward noninvasive way to measure and quantify confined optical modes on the nanoscale.

  8. Detection and Mapping of the September 2017 Mexico Earthquakes Using DAS Fiber-Optic Infrastructure Arrays

    Science.gov (United States)

    Karrenbach, M. H.; Cole, S.; Williams, J. J.; Biondi, B. C.; McMurtry, T.; Martin, E. R.; Yuan, S.

    2017-12-01

    Fiber-optic distributed acoustic sensing (DAS) uses conventional telecom fibers for a wide variety of monitoring purposes. Fiber-optic arrays can be located along pipelines for leak detection; along borders and perimeters to detect and locate intruders, or along railways and roadways to monitor traffic and identify and manage incidents. DAS can also be used to monitor oil and gas reservoirs and to detect earthquakes. Because thousands of such arrays are deployed worldwide and acquiring data continuously, they can be a valuable source of data for earthquake detection and location, and could potentially provide important information to earthquake early-warning systems. In this presentation, we show that DAS arrays in Mexico and the United States detected the M8.1 and M7.2 Mexico earthquakes in September 2017. At Stanford University, we have deployed a 2.4 km fiber-optic DAS array in a figure-eight pattern, with 600 channels spaced 4 meters apart. Data have been recorded continuously since September 2016. Over 800 earthquakes from across California have been detected and catalogued. Distant teleseismic events have also been recorded, including the two Mexican earthquakes. In Mexico, fiber-optic arrays attached to pipelines also detected these two events. Because of the length of these arrays and their proximity to the event locations, we can not only detect the earthquakes but also make location estimates, potentially in near real time. In this presentation, we review the data recorded for these two events recorded at Stanford and in Mexico. We compare the waveforms recorded by the DAS arrays to those recorded by traditional earthquake sensor networks. Using the wide coverage provided by the pipeline arrays, we estimate the event locations. Such fiber-optic DAS networks can potentially play a role in earthquake early-warning systems, allowing actions to be taken to minimize the impact of an earthquake on critical infrastructure components. While many such fiber

  9. Empirical evaluation of selective DNA pooling to map QTL in dairy cattle using a half-sib design by comparison to individual genotyping and interval mapping

    Directory of Open Access Journals (Sweden)

    Robinson Nicholas

    2007-04-01

    Full Text Available Abstract This study represents the first attempt at an empirical evaluation of the DNA pooling methodology by comparing it to individual genotyping and interval mapping to detect QTL in a dairy half-sib design. The findings indicated that the use of peak heights from the pool electropherograms without correction for stutter (shadow product and preferential amplification performed as well as corrected estimates of frequencies. However, errors were found to decrease the power of the experiment at every stage of the pooling and analysis. The main sources of errors include technical errors from DNA quantification, pool construction, inconsistent differential amplification, and from the prevalence of sire alleles in the dams. Additionally, interval mapping using individual genotyping gains information from phenotypic differences between individuals in the same pool and from neighbouring markers, which is lost in a DNA pooling design. These errors cause some differences between the markers detected as significant by pooling and those found significant by interval mapping based on individual selective genotyping. Therefore, it is recommended that pooled genotyping only be used as part of an initial screen with significant results to be confirmed by individual genotyping. Strategies for improving the efficiency of the DNA pooling design are also presented.

  10. ‘‘Blind'' mapping of genic DNA sequence polymorphisms in Lolium perenne L. by high resolution melting curve analysis

    DEFF Research Database (Denmark)

    Studer, Bruno; Jensen, Louise Bach; Fiil, Alice

    2009-01-01

    High resolution melting curve analysis (HRM) measures dissociation of double stranded DNA of a PCR product amplified in the presence of a saturating fluorescence dye. Recently, HRM proved successful to genotype DNA sequence polymorphisms such as SSRs and SNPs based on the shape of the melting...... curves. In this study, HRM was used for simultaneous screening and genotyping of genic DNA sequence polymorphisms identified in the Lolium perenne F2 mapping population VrnA. Melting profiles of PCR products amplified from previously published gene loci and from a novel gene putatively involved...

  11. Retinal nerve fiber layer thickness map determined from optical coherence tomography images

    NARCIS (Netherlands)

    Mujat, M.; Chan, R. C.; Cense, B.; Park, B.H.; Joo, C.; Akkin, T.; Chen, TC; de Boer, JF

    2005-01-01

    We introduce a method to determine the retinal nerve fiber layer (RNFL) thickness in OCT images based on anisotropic noise suppression and deformable splines. Spectral-Domain Optical Coherence Tomography (SDOCT) data was acquired at 29 kHz A-line rate with a depth resolution of 2.6 mum and a depth

  12. Observing dynamics of chromatin fibers in Xenopus egg extracts by single DNA manipulation using a transverse magnetic tweezer setup

    Science.gov (United States)

    Yan, Jie; Skoko, Dunja; Marko, John; Maresca, Tom; Heald, Rebecca

    2005-03-01

    We have studied assembly of chromatin on single DNAs using Xenopus egg extracts and a specially designed magnetic tweezer setup which generates controlled force in the focal plane of the objective, allowing us to visualize and measure DNA extension under a wide range of constant tensions. We found, in the absence of ATP, interphase extracts assembled nucleosomes against DNA tensions of up to 3.5 piconewtons (pN). We observed force-induced disassembly and opening-closing fluctuations indicating our experiments were in mechano-chemical equilibrium. We found that the ATP-depleted reaction can do mechanical work of 27 kcal/mol per nucleosome, providing a measurement of the free energy difference between core histone octamers on and off DNA. Addition of ATP leads to highly dynamic behavior: time courses show processive runs of assembly and disassembly of not observed in the -ATP case, with forces of 2 pN leading to nearly complete fiber disassembly. Our study shows that ATP hydrolysis plays a major role in nucleosome rearrangement and removal, and suggests that chromatin in vivo may be subject to continual assembly and disassembly.

  13. Analysis of correlations between the occurrence of anti-MAP antibodies in blood serum and the presence of DNA-MAP in milk.

    Science.gov (United States)

    Wiszniewska-Łaszczych, A; Szteyn, J; Smolińska, A

    2009-01-01

    Paratuberculosis (Johne's disease) is a chronic, infectious enteritis of both domestic and wild ruminants. Unfortunately, the problem of MAP infections is not linked only with the health status of animals and potential direct and indirect economic losses in bovine herds (of dairy cattle in particular). MAP bacilli present in food of animal origin (milk in particular) are likely to lead to the development of the disease in humans. Fast and effective diagnosis of the disease in animals, especially of its subclinical form, may prevent the transmission of the germ to humans. The study was aimed at analyzing the correlations between the occurance of seropositive and serodoubtful reaction in the ELISA test and the presence of DNA-MAP in udder milk. The results suggest that half of the population of animals with positive and doubtful serological responces against John's disease are likely to be a potential source of germ transmission into humans. The fact of detecting DNA-MAP in 1/3 of all milk samples points to the likelihood of occurrence of MAP bacilli in milk of animals not displaying seropositive or serodoubtful responses.

  14. Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

    Science.gov (United States)

    Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

    2014-01-01

    For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information. PMID:25914583

  15. Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations

    Science.gov (United States)

    van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D.

    2015-01-01

    The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1–2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand breaks are introduced at random wherever two translocating enzymes form a so-called collision complex following long-range communication between a pair of target sites in inverted (head-to-head) repeat. Paradoxically, structural models for collision suggest that the nuclease domains are too far apart (>30 bp) to dimerise and produce a double-strand DNA break using just two strand-cleavage events. Here, we examined the organisation of different collision complexes and how these lead to nuclease activation. We mapped DNA cleavage when a translocating enzyme collides with a static enzyme bound to its site. By following communication between sites in both head-to-head and head-to-tail orientations, we could show that motor activity leads to activation of the nuclease domains via distant interactions of the helicase or MTase-TRD. Direct nuclease dimerization is not required. To help explain the observed cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP domains can swing off the DNA. This study lends further support to a model where DNA breaks are generated by multiple random nicks due to mobility of a collision complex with an overall DNA-binding footprint of ∼30 bp. PMID:26507855

  16. High-resolution low-frequency fluctuation map of a multimode laser diode subject to filtered optical feedback via a fiber Bragg grating.

    Science.gov (United States)

    Baladi, Fadwa; Lee, Min Won; Burie, Jean-René; Bettiati, Mauro A; Boudrioua, Azzedine; Fischer, Alexis P A

    2016-07-01

    A highly detailed and extended map of low-frequency fluctuations is established for a high-power multi-mode 980 nm laser diode subject to filtered optical feedback from a fiber Bragg grating. The low-frequency fluctuations limits and substructures exhibit substantial differences with previous works.

  17. Mapping of histone modifications in episomal HBV cccDNA uncovers an unusual chromatin organization amenable to epigenetic manipulation

    Science.gov (United States)

    Tropberger, Philipp; Mercier, Alexandre; Robinson, Margaret; Zhong, Weidong; Ganem, Don E.; Holdorf, Meghan

    2015-01-01

    Chronic hepatitis B virus (HBV) infection affects 240 million people worldwide and is a major risk factor for liver failure and hepatocellular carcinoma. Current antiviral therapy inhibits cytoplasmic HBV genomic replication, but is not curative because it does not directly affect nuclear HBV closed circular DNA (cccDNA), the genomic form that templates viral transcription and sustains viral persistence. Novel approaches that directly target cccDNA regulation would therefore be highly desirable. cccDNA is assembled with cellular histone proteins into chromatin, but little is known about the regulation of HBV chromatin by histone posttranslational modifications (PTMs). Here, using a new cccDNA ChIP-Seq approach, we report, to our knowledge, the first genome-wide maps of PTMs in cccDNA-containing chromatin from de novo infected HepG2 cells, primary human hepatocytes, and from HBV-infected liver tissue. We find high levels of PTMs associated with active transcription enriched at specific sites within the HBV genome and, surprisingly, very low levels of PTMs linked to transcriptional repression even at silent HBV promoters. We show that transcription and active PTMs in HBV chromatin are reduced by the activation of an innate immunity pathway, and that this effect can be recapitulated with a small molecule epigenetic modifying agent, opening the possibility that chromatin-based regulation of cccDNA transcription could be a new therapeutic approach to chronic HBV infection. PMID:26438841

  18. A map of brain neuropils and fiber systems in the ant Cardiocondyla obscurior

    Directory of Open Access Journals (Sweden)

    Joris eBressan

    2015-02-01

    Full Text Available A wide spectrum of occupied ecological niches and spectacular morphological adaptations make social insects a prime object for comparative neuroanatomical studies. Eusocial insects have evolved complex societies based on caste polyphenism. A diverse behavioral repertoire of morphologically distinct castes of the same species requires a high degree of plasticity in the central nervous system. We have analyzed the central brain neuropils and fiber tract systems of the worker of the ant Cardiocondyla obscurior, a model for the study of social traits. Our analysis is based on whole mount preparations of adult brains labeled with an antibody against Drosophila-Synapsin, which cross-reacts strongly with synapses in Cardiocondyla. Neuropil compartments stand out as domains with a certain texture and intensity of the anti-Synapsin signal. By contrast, fiber tracts, which are composed of bundles of axons accompanied by glia and are devoid of synapses, appear as channels or sheaths with low anti-Synapsin signal. We have generated a digital 3D atlas of the Cardiocondyla brain neuropil. The atlas provides a reference for future studies of brain polymorphisms in distinct castes, brain development or localization of neurotransmitter systems.

  19. A map of brain neuropils and fiber systems in the ant Cardiocondyla obscurior.

    Science.gov (United States)

    Bressan, Joris M A; Benz, Martin; Oettler, Jan; Heinze, Jürgen; Hartenstein, Volker; Sprecher, Simon G

    2014-01-01

    A wide spectrum of occupied ecological niches and spectacular morphological adaptations make social insects a prime object for comparative neuroanatomical studies. Eusocial insects have evolved complex societies based on caste polyphenism. A diverse behavioral repertoire of morphologically distinct castes of the same species requires a high degree of plasticity in the central nervous system. We have analyzed the central brain neuropils and fiber tract systems of the worker of the ant Cardiocondyla obscurior, a model for the study of social traits. Our analysis is based on whole mount preparations of adult brains labeled with an antibody against Drosophila-Synapsin, which cross-reacts strongly with synapses in Cardiocondyla. Neuropil compartments stand out as domains with a certain texture and intensity of the anti-Synapsin signal. By contrast, fiber tracts, which are composed of bundles of axons accompanied by glia and are devoid of synapses, appear as channels or sheaths with low anti-Synapsin signal. We have generated a digital 3D atlas of the Cardiocondyla brain neuropil. The atlas provides a reference for future studies of brain polymorphisms in distinct castes, brain development or localization of neurotransmitter systems.

  20. Mitochondrial DNA mapping of social-biological interactions in Brazilian Amazonian African-descendant populations

    Directory of Open Access Journals (Sweden)

    Bruno Maia Carvalho

    2008-01-01

    Full Text Available The formation of the Brazilian Amazonian population has historically involved three main ethnic groups, Amerindian, African and European. This has resulted in genetic investigations having been carried out using classical polymorphisms and molecular markers. To better understand the genetic variability and the micro-evolutionary processes acting in human groups in the Brazilian Amazon region we used mitochondrial DNA to investigate 159 maternally unrelated individuals from five Amazonian African-descendant communities. The mitochondrial lineage distribution indicated a contribution of 50.2% from Africans (L0, L1, L2, and L3, 46.6% from Amerindians (haplogroups A, B, C and D and a small European contribution of 1.3%. These results indicated high genetic diversity in the Amerindian and African lineage groups, suggesting that the Brazilian Amazonian African-descendant populations reflect a possible population amalgamation of Amerindian women from different Amazonian indigenous tribes and African women from different geographic regions of Africa who had been brought to Brazil as slaves. The present study partially mapped the historical biological and social interactions that had occurred during the formation and expansion of Amazonian African-descendant communities.

  1. DNA detection on ultrahigh-density optical fiber-based nanoarrays.

    Science.gov (United States)

    Tam, Jenny M; Song, Linan; Walt, David R

    2009-04-15

    Nanoarrays for DNA detection were fabricated on etched nanofiber bundles based on recently developed techniques for microscale arrays. Two different-sized nanoarrays were created: one with 700 nm feature sizes and a 1 microm center-to-center pitch (approximately 1x10(6) array elements/mm(2)) and one with 300 nm feature sizes and a 500 nm center-to-center pitch (4.6x10(6) array elements/mm(2)). A random, multiplexed array composed of oligonucleotide-functionalized nanospheres was constructed and used for parallel detection and analysis of fluorescently labeled DNA targets. We have used these arrays to detect a variety of target sequences including Bacillus thuringiensis kurstaki and vaccina virus sequences, two potential biowarfare agents, as well as interleukin-2 sequences, an immune system modulator that has been used for the diagnosis of HIV.

  2. Restriction map of the single-stranded DNA genome of Kilham rat virus strain 171, a nondefective parvovirus

    International Nuclear Information System (INIS)

    Banerjee, P.T.; Rathrock, R.; Mitra, S.

    1981-01-01

    A physical map of Kilham rat virus strain 171 DNA was constructed by analyzing the sizes and locations of restriction endonuclease-generated fragments of the replicative-form viral DNA synthesized in vitro. BglI, KpnI, BamHI, SmaI, XhoI, and XorII did not appear to have any cleavage sites, whereas 11 other enzymes cleaved the genome at one to eight sites, and AluI generated more than 12 distinct fragments. The 30 restriction sites that were mapped were distributed randomly in the viral genome. A comparison of the restriction fragments of in vivo- and in vitro-replicated replicative-form DNAs showed that these DNAs were identical except in the size or configuration of the terminal fragments

  3. Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

    Directory of Open Access Journals (Sweden)

    Yingliang Liu

    2017-07-01

    Full Text Available Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm–1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

  4. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    Directory of Open Access Journals (Sweden)

    Wang Nian

    2012-08-01

    Full Text Available Abstract Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

  5. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.

    Directory of Open Access Journals (Sweden)

    Kouji Satoh

    Full Text Available Rice (Oryza sativa L. is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE genes, 33K annotated non-expressed (ANE genes, and 5.5K non-annotated expressed (NAE genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.

  6. Human cDNA mapping using fluorescence in situ hybridization. Progress report, April 1--December 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-12-31

    The ultimate goal of this proposal is to create a cDNA map of the human genome. Mapping is approached using the techniques of high resolution fluorescence in situ hybridization (FISH). This technology and the results of its application are designed to rapidly generate whole genome as tool box of expressed sequence to speed the identification of human disease genes. The results of this study are intended to dovetail with and to link the results of existing technologies for creating backbone YAC and genetic maps. In the first eight months, this approach will generate 60--80% of the expressed sequence map, the remainder expected to be derived through more long-term, labor-intensive, regional chromosomal gene searches or sequencing. The laboratory has made significant progress in the set-up phase, in mapping fetal and adult brain and other cDNAs, in testing a model system for directly linking genetic and physical maps using FISH with small fragments, in setting up a database, and in establishing the validity and throughput of the system.

  7. FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae).

    Science.gov (United States)

    Aguilera, Patricia M; Debat, Humberto J; Scaldaferro, Marisel A; Martí, Dardo A; Grabiele, Mauro

    2016-03-01

    We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus.

  8. Physical mapping of 5S and 18S ribosomal DNA in three species of Agave (Asparagales, Asparagaceae

    Directory of Open Access Journals (Sweden)

    Victor Manuel Gomez-Rodriguez

    2013-08-01

    Full Text Available Agave Linnaeus, 1753 is endemic of America and is considered one of the most important crops in Mexico due to its key role in the country’s economy. Cytogenetic analysis was carried out in A. tequilana Weber, 1902 ‘Azul’, A. cupreata Trelease et Berger, 1915 and A. angustifolia Haworth, 1812. The analysis showed that in all species the diploid chromosome number was 2n = 60, with bimodal karyotypes composed of five pairs of large chromosomes and 25 pairs of small chromosomes. Furthermore, different karyotypical formulae as well as a secondary constriction in a large chromosome pair were found in all species. Fluorescent in situ hybridization (FISH was used for physical mapping of 5S and 18S ribosomal DNA (rDNA. All species analyzed showed that 5S rDNA was located in both arms of a small chromosome pair, while 18S rDNA was associated with the secondary constriction of a large chromosome pair. Data of FISH analysis provides new information about the position and number of rDNA loci and helps for detection of hybrids in breeding programs as well as evolutionary studies.

  9. Physical mapping of 5S and 18S ribosomal DNA in three species of Agave (Asparagales, Asparagaceae).

    Science.gov (United States)

    Gomez-Rodriguez, Victor Manuel; Rodriguez-Garay, Benjamin; Palomino, Guadalupe; Martínez, Javier; Barba-Gonzalez, Rodrigo

    2013-01-01

    Agave Linnaeus, 1753 is endemic of America and is considered one of the most important crops in Mexico due to its key role in the country's economy. Cytogenetic analysis was carried out in Agave tequilana Weber, 1902 'Azul', Agave cupreata Trelease et Berger, 1915 and Agave angustifolia Haworth, 1812. The analysis showed that in all species the diploid chromosome number was 2n = 60, with bimodal karyotypes composed of five pairs of large chromosomes and 25 pairs of small chromosomes. Furthermore, different karyotypical formulae as well as a secondary constriction in a large chromosome pair were found in all species. Fluorescent in situ hybridization (FISH) was used for physical mapping of 5S and 18S ribosomal DNA (rDNA). All species analyzed showed that 5S rDNA was located in both arms of a small chromosome pair, while 18S rDNA was associated with the secondary constriction of a large chromosome pair. Data of FISH analysis provides new information about the position and number of rDNA loci and helps for detection of hybrids in breeding programs as well as evolutionary studies.

  10. Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

    Directory of Open Access Journals (Sweden)

    Suryani Lukman

    Full Text Available The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD. In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs. Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3. Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart. Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1 a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2 possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.

  11. Phylogenetic analysis of the kenaf fiber microbial retting community by semiconductor sequencing of 16S rDNA amplicons

    Science.gov (United States)

    Kenaf, hemp, and jute have been used for cordage and fiber production since prehistory. To obtain the fibers, harvested plants are soaked in ponds where indigenous microflora digests pectins and other heteropolysaccharides, releasing fibers in a process called retting. Renewed interest in “green” ...

  12. MAP kinase-signaling controls nuclear translocation of tripeptidyl-peptidase II in response to DNA damage and oxidative stress

    Energy Technology Data Exchange (ETDEWEB)

    Preta, Giulio; Klark, Rainier de; Chakraborti, Shankhamala [Center for Molecular Medicine (CMM), Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 171 76 Stockholm (Sweden); Glas, Rickard, E-mail: rickard.glas@ki.se [Center for Molecular Medicine (CMM), Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 171 76 Stockholm (Sweden)

    2010-08-27

    Research highlights: {yields} Nuclear translocation of TPPII occurs in response to different DNA damage inducers. {yields} Nuclear accumulation of TPPII is linked to ROS and anti-oxidant enzyme levels. {yields} MAPKs control nuclear accumulation of TPPII. {yields} Inhibited nuclear accumulation of TPPII decreases DNA damage-induced {gamma}-H2AX expression. -- Abstract: Reactive oxygen species (ROS) are a continuous hazard in eukaroytic cells by their ability to cause damage to biomolecules, in particular to DNA. Previous data indicated that the cytosolic serine peptidase tripeptidyl-peptidase II (TPPII) translocates into the nucleus of most tumor cell lines in response to {gamma}-irradiation and ROS production; an event that promoted p53 expression as well as caspase-activation. We here observed that nuclear translocation of TPPII was dependent on signaling by MAP kinases, including p38MAPK. Further, this was caused by several types of DNA-damaging drugs, a DNA cross-linker (cisplatinum), an inhibitor of topoisomerase II (etoposide), and to some extent also by nucleoside-analogues (5-fluorouracil, hydroxyurea). In the minority of tumor cell lines where TPPII was not translocated into the nucleus in response to DNA damage we observed reduced intracellular ROS levels, and the expression levels of redox defense systems were increased. Further, treatment with the ROS-inducer {gamma}-hexa-chloro-cyclohexane ({gamma}-HCH, lindane), an inhibitor of GAP junctions, restored nuclear translocation of TPPII in these cell lines upon {gamma}-irradiation. Moreover, blocking nuclear translocation of TPPII in etoposide-treated cells, by using a peptide-derived inhibitor (Z-Gly-Leu-Ala-OH), attenuated expression of {gamma}-H2AX in {gamma}-irradiated melanoma cells. Our results indicated a role for TPPII in MAPK-dependent DNA damage signaling.

  13. Mapa de preferência de sorvetes ricos em fibras Preference map of high-fiber ice cream

    Directory of Open Access Journals (Sweden)

    Regiane Lopes de Sales

    2008-12-01

    Full Text Available Quatro amostras de sorvete foram preparadas adicionando-se diferentes concentrações de granola e Frutooligossacarídeo (FOS. Foi avaliado o teor de fibras segundo método AOAC. A avaliação da aceitabilidade sensorial foi realizada por 78 consumidores, com idade entre 15 e 25 anos. Estes avaliaram a aceitação global das formulações, utilizando a escala hedônica de nove pontos, em uma única seção, de forma monádica. O experimento foi estruturado segundo delineamento em blocos inteiramente casualizados. Os resultados foram submetidos à análise de variância, ao teste de médias de Tuckey e à metodologia do Mapa de Preferência interno para análise dos componentes principais. As amostras controle e as adicionadas de FOS tiveram melhor aceitação. A amostra contendo somente FOS foi a que mais se aproximou do produto tradicional, não diferindo significativamente quanto à aceitação global. A granola distinguiu-se estatisticamente do produto tradicional. O teor de fibras analisado foi superior ao fornecido pelo fabricante da granola. As concentrações de fibras nos sorvetes variaram de 0,9 a 5,45 g.100 g-1 de sorvete, com a maior concentração de fibras provenientes do FOS. Esse resultado permite concluir que o FOS é um ingrediente promissor no desenvolvimento de produtos ricos em fibras.Four samples of ice cream were prepared with four different concentrations of granola and fructooligosaccharide (FOS. The concentration of fiber was evaluated using the AOAC method. The acceptance evaluation was conducted by 78 consumers between 15 and 25 years of age. The consumers evaluated the global acceptance of the formulations through the structured 9-point hedonic scale, in a single section, in a monadic form. The experiment was structured by a Randomized Complete Block Design. The results were submitted to the analysis of variance, Tukey test, and to the preference mapping technique for principal component analysis. The control samples

  14. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

    DEFF Research Database (Denmark)

    Li, Xin; Zhu, Jingde; Hu, Fengyi

    2012-01-01

    DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild rela...

  15. A DNA minor groove electronegative potential genome map based on photo-chemical probing

    DEFF Research Database (Denmark)

    Lindemose, Søren; Nielsen, Peter Eigil; Hansen, Morten

    2011-01-01

    The double-stranded DNA of the genome contains both sequence information directly relating to the protein and RNA coding as well as functional and structural information relating to protein recognition. Only recently is the importance of DNA shape in this recognition process being fully appreciat...

  16. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

    NARCIS (Netherlands)

    Falconer, Ester; Hills, Mark; Naumann, Ulrike; Poon, Steven S. S.; Chavez, Elizabeth A.; Sanders, Ashley D.; Zhao, Yongjun; Hirst, Martin; Lansdorp, Peter M.

    DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it

  17. DNA Mapping Made Simple: An Intellectual Activity about the Genetic Modification of Organisms

    Science.gov (United States)

    Marques, Miguel; Arrabaca, Joao; Chagas, Isabel

    2004-01-01

    Since the discovery of the DNA double helix (in 1953 by Watson and Crick), technologies have been developed that allow scientists to manipulate the genome of bacteria to produce human hormones, as well as the genome of crop plants to achieve high yield and enhanced flavor. The universality of the genetic code has allowed DNA isolated from a…

  18. Full-length cDNA sequences from Rhesus monkey placenta tissue: analysis and utility for comparative mapping

    Directory of Open Access Journals (Sweden)

    Lee Sang-Rae

    2010-07-01

    Full Text Available Abstract Background Rhesus monkeys (Macaca mulatta are widely-used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as cynomolgus monkeys (Macaca fascicularis, and to humans, sharing a last common ancestor from about 25 million years ago. Although rhesus monkeys have been studied extensively under field and laboratory conditions, research has been limited by the lack of genetic resources. The present study generated placenta full-length cDNA libraries, characterized the resulting expressed sequence tags, and described their utility for comparative mapping with human RefSeq mRNA transcripts. Results From rhesus monkey placenta full-length cDNA libraries, 2000 full-length cDNA sequences were determined and 1835 rhesus placenta cDNA sequences longer than 100 bp were collected. These sequences were annotated based on homology to human genes. Homology search against human RefSeq mRNAs revealed that our collection included the sequences of 1462 putative rhesus monkey genes. Moreover, we identified 207 genes containing exon alterations in the coding region and the untranslated region of rhesus monkey transcripts, despite the highly conserved structure of the coding regions. Approximately 10% (187 of all full-length cDNA sequences did not represent any public human RefSeq mRNAs. Intriguingly, two rhesus monkey specific exons derived from the transposable elements of AluYRa2 (SINE family and MER11B (LTR family were also identified. Conclusion The 1835 rhesus monkey placenta full-length cDNA sequences described here could expand genomic resources and information of rhesus monkeys. This increased genomic information will greatly contribute to the development of evolutionary biology and biomedical research.

  19. Fine resolution mapping of double-strand break sites for human ribosomal DNA units

    Directory of Open Access Journals (Sweden)

    Bernard J. Pope

    2016-12-01

    Full Text Available DNA breakage arises during a variety of biological processes, including transcription, replication and genome rearrangements. In the context of disease, extensive fragmentation of DNA has been described in cancer cells and during early stages of neurodegeneration (Stephens et al., 2011 Stephens et al. (2011 [5]; Blondet et al., 2001 Blondet et al. (2001 [1]. Stults et al. (2009 Stults et al. (2009 [6] reported that human rDNA gene clusters are hotspots for recombination and that rDNA restructuring is among the most common chromosomal alterations in adult solid tumours. As such, analysis of rDNA regions is likely to have significant prognostic and predictive value, clinically. Tchurikov et al. (2015a, 2016 Tchurikov et al. (2015a, 2016 [7,9] have made major advances in this direction, reporting that sites of human genome double-strand breaks (DSBs occur frequently at sites in rDNA that are tightly linked with active transcription - the authors used a RAFT (rapid amplification of forum termini protocol that selects for blunt-ended sites. They reported the relative frequency of these rDNA DSBs within defined co-ordinate ‘windows’ of varying size and made these data (as well as the relevant ‘raw’ sequencing information available to the public (Tchurikov et al., 2015b. Assay designs targeting rDNA DSB hotspots will benefit greatly from the publication of break sites at greater resolution. Here, we re-analyse public RAFT data and make available rDNA DSB co-ordinates to the single-nucleotide level.

  20. DNA Physical Mapping via the Controlled Translocation of Single Molecules through a 5-10nm Silicon Nitride Nanopore

    Science.gov (United States)

    Stein, Derek; Reisner, Walter; Jiang, Zhijun; Hagerty, Nick; Wood, Charles; Chan, Jason

    2009-03-01

    The ability to map the binding position of sequence-specific markers, including transcription-factors, protein-nucleic acids (PNAs) or deactivated restriction enzymes, along a single DNA molecule in a nanofluidic device would be of key importance for the life-sciences. Such markers could give an indication of the active genes at particular stage in a cell's transcriptional cycle, pinpoint the location of mutations or even provide a DNA barcode that could aid in genomics applications. We have developed a setup consisting of a 5-10 nm nanopore in a 20nm thick silicon nitride film coupled to an optical tweezer setup. The translocation of DNA across the nanopore can be detected via blockades in the electrical current through the pore. By anchoring one end of the translocating DNA to an optically trapped microsphere, we hope to stretch out the molecule in the nanopore and control the translocation speed, enabling us to slowly scan across the genome and detect changes in the baseline current due to the presence of bound markers.

  1. Clustering self-organizing maps (SOM) method for human papillomavirus (HPV) DNA as the main cause of cervical cancer disease

    Science.gov (United States)

    Bustamam, A.; Aldila, D.; Fatimah, Arimbi, M. D.

    2017-07-01

    One of the most widely used clustering method, since it has advantage on its robustness, is Self-Organizing Maps (SOM) method. This paper discusses the application of SOM method on Human Papillomavirus (HPV) DNA which is the main cause of cervical cancer disease, the most dangerous cancer in developing countries. We use 18 types of HPV DNA-based on the newest complete genome. By using open-source-based program R, clustering process can separate 18 types of HPV into two different clusters. There are two types of HPV in the first cluster while 16 others in the second cluster. The analyzing result of 18 types HPV based on the malignancy of the virus (the difficultness to cure). Two of HPV types the first cluster can be classified as tame HPV, while 16 others in the second cluster are classified as vicious HPV.

  2. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification.

    Science.gov (United States)

    Liu, Jie; Milne, Richard I; Möller, Michael; Zhu, Guang-Fu; Ye, Lin-Jiang; Luo, Ya-Huang; Yang, Jun-Bo; Wambulwa, Moses Cheloti; Wang, Chun-Neng; Li, De-Zhu; Gao, Lian-Ming

    2018-05-22

    Rapid and accurate identification of endangered species is a critical component of bio-surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre-processed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa. Here we construct a comprehensive DNA barcode reference library, and generate distribution maps using species distribution modeling (SDM), for all 15 Taxus species worldwide. We find that trnL-trnF is the ideal barcode for Taxus: it can distinguish all Taxus species, and in combination with ITS identify hybrids. Among five analysis methods tested, NJ was the most effective. Among 4151 individuals screened for trnL-trnF, 73 haplotypes were detected, all species-specific and some population private. Taxonomical, geographical and genetic dimensions of sampling strategy were all found to affect the comprehensiveness of the resulting DNA barcode library. Maps from SDM showed that most species had allopatric distributions, except three in the Sino-Himalayan region. Using the barcode library and distribution map data, two unknown forensic samples were identified to species (and in one case, population) level, and another was determined as a putative interspecific hybrid. This integrated species identification system for Taxus can be used for bio-surveillance, conservation management and to monitor and prosecute illegal trade. Similar identification systems are recommended for other IUCN- and -CITES listed taxa. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  3. Mouse tetranectin: cDNA sequence, tissue-specific expression, and chromosomal mapping

    DEFF Research Database (Denmark)

    Ibaraki, K; Kozak, C A; Wewer, U M

    1995-01-01

    regulation, mouse tetranectin cDNA was cloned from a 16-day-old mouse embryo library. Sequence analysis revealed a 992-bp cDNA with an open reading frame of 606 bp, which is identical in length to the human tetranectin cDNA. The deduced amino acid sequence showed high homology to the human cDNA with 76......(s) of tetranectin. The sequence analysis revealed a difference in both sequence and size of the noncoding regions between mouse and human cDNAs. Northern analysis of the various tissues from mouse, rat, and cow showed the major transcript(s) to be approximately 1 kb, which is similar in size to that observed...

  4. Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing

    DEFF Research Database (Denmark)

    Børglum, Anders; Nyegaard, Mette; Kvistgaard, AB

    1997-01-01

    Two-dimensional (2-D) DNA typing is based on electrophoretic separation of genomic DNA fragments in two dimensions according to independent criteria (size and base-pair sequence), followed by hybridization analysis using multilocus probes. The technique allows simultaneous visualization of several...... could be deduced, showing no evidence of clustering. In the analysis of spot patterns, use was made of a computerized image analysis system specifically designed for 2-D DNA typing. Since experimental variations between different separation patterns were automatically corrected for with this program......, rapid and reliable scorings could be obtained. The results presented demonstrate the availability of reliable genetic information throughout the 2-D separation pattern. Adding the use of semiautomated computerized pattern analysis, this study further substantiates the applicability of 2-D DNA typing...

  5. Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

    Czech Academy of Sciences Publication Activity Database

    Koo, D.H.; Tiwari, V.K.; Hřibová, Eva; Doležel, Jaroslav; Friebe, B.; Gill, B.S.

    2016-01-01

    Roč. 148, č. 4 (2016), s. 314-321 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : in-situ hybridization * chromosome addition lines * resistance genes lr57 * repetitive dna * triticum-ovatum * powdery mildew * plant genome * bread wheat * leaf rust * identification * Aegilops geniculata * Chromosome identification * Fluorescence in situ hybridization * Satellite DNA * Wheat Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

  6. Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Liu, Xueying; Teng, Zhonghua; Wang, Jinxia; Wu, Tiantian; Zhang, Zhiqin; Deng, Xianping; Fang, Xiaomei; Tan, Zhaoyun; Ali, Iftikhar; Liu, Dexin; Zhang, Jian; Liu, Dajun; Liu, Fang; Zhang, Zhengsheng

    2017-12-01

    Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.

  7. Hydration forces between aligned DNA helices undergoing B to A conformational change: In-situ X-ray fiber diffraction studies in a humidity and temperature controlled environment.

    Science.gov (United States)

    Case, Ryan; Schollmeyer, Hauke; Kohl, Phillip; Sirota, Eric B; Pynn, Roger; Ewert, Kai E; Safinya, Cyrus R; Li, Youli

    2017-12-01

    Hydration forces between DNA molecules in the A- and B-Form were studied using a newly developed technique enabling simultaneous in situ control of temperature and relative humidity. X-ray diffraction data were collected from oriented calf-thymus DNA fibers in the relative humidity range of 98%-70%, during which DNA undergoes the B- to A-form transition. Coexistence of both forms was observed over a finite humidity range at the transition. The change in DNA separation in response to variation in humidity, i.e. change of chemical potential, led to the derivation of a force-distance curve with a characteristic exponential decay constant of∼2Å for both A- and B-DNA. While previous osmotic stress measurements had yielded similar force-decay constants, they were limited to B-DNA with a surface separation (wall-to-wall distance) typically>5Å. The current investigation confirms that the hydration force remains dominant even in the dry A-DNA state and at surface separation down to∼1.5Å, within the first hydration shell. It is shown that the observed chemical potential difference between the A and B states could be attributed to the water layer inside the major and minor grooves of the A-DNA double helices, which can partially interpenetrate each other in the tightly packed A phase. The humidity-controlled X-ray diffraction method described here can be employed to perform direct force measurements on a broad range of biological structures such as membranes and filamentous protein networks. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.

    Science.gov (United States)

    Croce, Olivier; Chevenet, François; Christen, Richard

    2008-07-01

    The efficiency of molecular methods involving DNA/DNA hybridizations depends on the accurate prediction of the melting temperature (T(m)) of the duplex. Many softwares are available for T(m) calculations, but difficulties arise when one wishes to check if a given oligomer (PCR primer or probe) hybridizes well or not on more than a single sequence. Moreover, the presence of mismatches within the duplex is not sufficient to estimate specificity as it does not always significantly decrease the T(m). OHM (OligoHeatMap) is an online tool able to provide estimates of T(m) for a set of oligomers and a set of aligned sequences, not only as text files of complete results but also in a graphical way: T(m) values are translated into colors and displayed as a heat map image, either stand alone or to be used by softwares such as TreeDyn to be included in a phylogenetic tree. OHM is freely available at http://bioinfo.unice.fr/ohm/, with links to the full source code and online help.

  9. Quantification and genome-wide mapping of DNA double-strand breaks.

    Science.gov (United States)

    Grégoire, Marie-Chantal; Massonneau, Julien; Leduc, Frédéric; Arguin, Mélina; Brazeau, Marc-André; Boissonneault, Guylain

    2016-12-01

    DNA double-strand breaks (DSBs) represent a major threat to the genetic integrity of the cell. Knowing both their genome-wide distribution and number is important for a better assessment of genotoxicity at a molecular level. Available methods may have underestimated the extent of DSBs as they are based on markers specific to those undergoing active repair or may not be adapted for the large diversity of naturally occurring DNA ends. We have established conditions for an efficient first step of DNA nick and gap repair (NGR) allowing specific determination of DSBs by end labeling with terminal transferase. We used DNA extracted from HeLa cells harboring an I-SceI cassette to induce a targeted nick or DSB and demonstrated by immunocapture of 3'-OH that a prior step of NGR allows specific determination of loci-specific or genome wide DSBs. This method can be applied to the global determination of DSBs using radioactive end labeling and can find several applications aimed at understanding the distribution and kinetics of DSBs formation and repair. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Identification of two new repetitive elements and chromosomal mapping of repetitive DNA sequences in the fish Gymnothorax unicolor (Anguilliformes: Muraenidae

    Directory of Open Access Journals (Sweden)

    E. Coluccia

    2011-05-01

    Full Text Available Muraenidae is a species-rich family, with relationships among genera and species and taxonomy that have not been completely clarified. Few cytogenetic studies have been conducted on this family, and all of them showed the same diploid chromosome number (2n=42 but with conspicuous karyotypic variation among species. The Mediterranean moray eel Gymnothorax unicolor was previously cytogenetically studied using classical techniques that allowed the characterization of its karyotype structure and the constitutive heterochromatin and argyrophilic nucleolar organizer regions (Ag-NORs distribution pattern. In the present study, we describe two new repetitive elements (called GuMboI and GuDdeI obtained from restricted genomic DNA of G. unicolor that were characterized by Southern blot and physically localized by in situ hybridization on metaphase chromosomes. As they are highly repetitive DNA sequences, they map in heterochromatic regions. However, while GuDdeI was localized in the centromeric regions, the GuMboI fraction was distributed on some centromeres and was co-localized with the nucleolus organizer region (NOR. Comparative analysis with other Mediterranean species such as Muraena helena pointed out that these DNA fractions are species-specific and could potentially be used for species discrimination. As a new contribution to the karyotype of this species, we found that the major ribosomal genes are localized on acrocentric chromosome 9 and that the telomeres of each chromosome are composed of a tandem repeat derived from a poly-TTAGGG DNA sequence, as it occurs in most vertebrate species. The results obtained add new information useful in comparative genomics at the chromosomal level and contribute to the cytogenetic knowledge regarding this fish family, which has not been extensively studied.

  11. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

    Czech Academy of Sciences Publication Activity Database

    Šimková, Hana; Svensson, J.T.; Condamine, P.; Hřibová, Eva; Suchánková, Pavla; Bhat, P.R.; Bartoš, Jan; Šafář, Jan; Close, T.J.; Doležel, Jaroslav

    2008-01-01

    Roč. 9, č. 294 (2008), s. 1-9 ISSN 1471-2164 R&D Projects: GA ČR GD521/05/H013; GA MŠk ME 884; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : Flow cytometry * DNA amplification * Hordeum vulgare L. Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.926, year: 2008

  12. GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

    Science.gov (United States)

    Kim, Jeremie S; Senol Cali, Damla; Xin, Hongyi; Lee, Donghyuk; Ghose, Saugata; Alser, Mohammed; Hassan, Hasan; Ergin, Oguz; Alkan, Can; Mutlu, Onur

    2018-05-09

    Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i.e., sequence alignment) to determine the origin of the read. A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments. We propose a novel seed location filtering algorithm, GRIM-Filter, optimized to exploit 3D-stacked memory systems that integrate computation within a logic layer stacked under memory layers, to perform processing-in-memory (PIM). GRIM-Filter quickly filters seed locations by 1) introducing a new representation of coarse-grained segments of the reference genome, and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for a sequence alignment error tolerance of 0.05, GRIM-Filter 1) reduces the false negative rate of filtering by 5.59x-6.41x, and 2) provides an end-to-end read mapper speedup of 1.81x-3.65x, compared to a state-of-the-art read mapper employing the best previous seed location filtering algorithm. GRIM-Filter exploits 3D-stacked memory, which enables the efficient use of processing-in-memory, to overcome the memory bandwidth bottleneck in seed location filtering. We show that GRIM-Filter significantly improves the performance of a state-of-the-art read mapper. GRIM-Filter is a universal seed location filter that can be

  13. Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons

    2009-01-01

    , but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943-1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pair-wise F-ST of 0.047 and 0.053). By analysing...... a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals...... nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor...

  14. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

    Directory of Open Access Journals (Sweden)

    Bharti Arvind K

    2008-12-01

    Full Text Available Abstract Background Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR and methylation spanning linker libraries (MSLL. These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends. Results A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the SalI MSLL libraries being the most highly enriched (31% align to an EST contig, while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%. These two techniques were compared with other gene-enrichment methods, and shown to be complementary. Conclusion MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of

  15. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  16. Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding.

    Science.gov (United States)

    Shapcott, Alison; Forster, Paul I; Guymer, Gordon P; McDonald, William J F; Faith, Daniel P; Erickson, David; Kress, W John

    2015-01-01

    Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.

  17. Mapping Biodiversity and Setting Conservation Priorities for SE Queensland’s Rainforests Using DNA Barcoding

    Science.gov (United States)

    Shapcott, Alison; Forster, Paul I.; Guymer, Gordon P.; McDonald, William J. F.; Faith, Daniel P.; Erickson, David; Kress, W. John

    2015-01-01

    Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions. PMID:25803607

  18. Differences in replicon behavior between x-irradiation-sensitive L5178Y mouse lymphoma cells and A-T fibroblasts using DNA fiber autoradiography

    International Nuclear Information System (INIS)

    Ockey, C.H.

    1983-01-01

    Replicon behavior in radiosensitive Ataxia telangiectasia (A-T) fibroblasts and mouse lymphoma L5178Y (LS) cells was studied by DNA fiber autoradiography. LS cells, irradiated at 13 Gy, showed a similar reduction in rate of DNA chain growth and initiation of replicons as did resistant (LR) cells. A progressive increase in the intensity of [ 3 H]TdR labeling of many replicons was observed after irradition in the LS cells, but not in LR cells. This indicated a reduced or absent endogenous dTTP supply after irradiation in the LS cells, implicating a defect in nucleoside precursor production. Irradiated normal human and A-T cells did not show this effect. After 2 Gy, the frequency of initiation of replicons into synthesis was temporarily reduced in the normal human but not in the A-T cells. After 20 Gy, the rate of DNA chain growth was preferentially reduced in the normal human cells, but an increase was observed in the A-T cells. This increased rate could be explained in terms of a normal supply of complexes involved in chain elongation being distributed over a reduced number of initiated replicon clusters in the A-T cells

  19. Karyotypes, heterochromatin, and physical mapping of 18S-26S rDNA in Cactaceae.

    Science.gov (United States)

    Las Peñas, M L; Urdampilleta, J D; Bernardello, G; Forni-Martins, E R

    2009-01-01

    Karyotype analyses in members of the four Cactaceae subfamilies were performed. Numbers and karyotype formula obtained were: Pereskioideae = Pereskiaaculeata(2n = 22; 10 m + 1 sm), Maihuenioideae = Maihuenia patagonica (2n = 22, 9 m + 2 sm; 2n = 44, 18 m + 4 sm), Opuntioideae = Cumulopuntia recurvata(2n = 44; 20 m + 2 sm), Cactoideae = Acanthocalycium spiniflorum (2n = 22; 10 m + 1 sm),Echinopsis tubiflora (2n = 22; 10 m + 1 sm), Trichocereus candicans (2n = 22, 22 m). Chromosomes were small, the average chromosome length was 2.3 mum. Diploid species and the tetraploid C. recurvata had one terminal satellite, whereas the remaining tetraploid species showed four satellited chromosomes. Karyotypes were symmetrical. No CMA(-)/DAPI(+) bands were detected, but CMA(+)/DAPI(-) bands associated with NOR were always found. Pericentromeric heterochromatin was found in C. recurvata, A. spiniflorum, and the tetraploid cytotype of M. patagonica. The locations of the 18S-26S rDNA sites in all species coincided with CMA(+)/DAPI(-) bands; the same occurred with the sizes and numbers of signals for each species. This technique was applied for the first time in metaphase chromosomes in cacti. NOR-bearing pair no.1 may be homeologous in all species examined. In Cactaceae, the 18S-26S loci seem to be highly conserved. Copyright 2009 S. Karger AG, Basel.

  20. Discovery of possible gene relationships through the application of self-organizing maps to DNA microarray databases.

    Science.gov (United States)

    Chavez-Alvarez, Rocio; Chavoya, Arturo; Mendez-Vazquez, Andres

    2014-01-01

    DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques--an unsupervised artificial neural network called a Self-Organizing Map (SOM)-which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis. As a test bed for the use of SOMs in finding possible relationships among genes and their possible contribution in some biological processes, we selected 282 S. cerevisiae genes that have been shown through biological experiments to have an activity during the cell cycle. The expression level of these genes was analyzed in five of the most cited time series DNA microarray databases used in the study of the cell cycle of this organism. With the use of SOM, it was possible to find clusters of genes with similar behavior in the five databases along two cell cycles. This result suggested that some of these genes might be biologically related or might have a regulatory relationship, as was corroborated by comparing some of the clusters obtained with SOMs against a previously reported regulatory network that was generated using biological knowledge, such as protein-protein interactions, gene expression levels, metabolism dynamics, promoter binding, and modification, regulation and transport of proteins. The methodology described in this paper could be applied to the study of gene relationships of other biological processes in different organisms.

  1. GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

    Science.gov (United States)

    Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oguz; Mutlu, Onur; Alkan, Can

    2017-11-01

    High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10. https://github.com/BilkentCompGen/GateKeeper. mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press

  2. Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types.

    Science.gov (United States)

    Soto-Cerda, Braulio J; Diederichsen, Axel; Ragupathy, Raja; Cloutier, Sylvie

    2013-05-06

    Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (F(ST) = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r²) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a

  3. XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

    Directory of Open Access Journals (Sweden)

    Giegerich Robert

    2005-09-01

    Full Text Available Abstract Background Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems. Description Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and ~67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined. Conclusion The results of the analysis have been stored in a publicly available database XenDB http://bibiserv.techfak.uni-bielefeld.de/xendb/. A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches. Supplementary material can be found at http://bibiserv.techfak.uni-bielefeld.de/xendb/.

  4. Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake

    Science.gov (United States)

    2012-01-01

    Background Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC3) of the genes and the size of chromosomes on which the genes were localized. Results Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 < 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 ≥ 50%). Conclusion Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution. PMID:23140509

  5. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    Energy Technology Data Exchange (ETDEWEB)

    Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Waleń, Tomasz [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); University of Warsaw, Banacha 2, 02-097 Warsaw (Poland); Piątkowski, Paweł; Potrzebowski, Wojciech [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Bujnicki, Janusz M. [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Adam Mickiewicz University, Umultowska 89, 61-614 Poznan (Poland)

    2015-03-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

  6. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    International Nuclear Information System (INIS)

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-01-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx

  7. Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations

    OpenAIRE

    van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D

    2015-01-01

    The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1-2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand brea...

  8. Amplitude-modulated fiber-ring laser

    DEFF Research Database (Denmark)

    Caputo, J. G.; Clausen, Carl A. Balslev; Sørensen, Mads Peter

    2000-01-01

    Soliton pulses generated by a fiber-ring laser are investigated by numerical simulation and perturbation methods. The mathematical modeling is based on the nonlinear Schrödinger equation with perturbative terms. We show that active mode locking with an amplitude modulator leads to a self......-starting of stable solitonic pulses from small random noise, provided the modulation depth is small. The perturbative analysis leads to a nonlinear coupled return map for the amplitude, phase, and position of the soliton pulses circulating in the fiber-ring laser. We established the validity of this approach...

  9. Cloning of the cDNA for a human homologue of the Drosophila white gene and mapping to chromosome 21q22.3.

    OpenAIRE

    Chen, H.; Rossier, C.; Lalioti, M. D.; Lynn, A.; Chakravarti, A.; Perrin, G.; Antonarakis, S. E.

    1996-01-01

    In an effort to contribute to the transcript map of human chromosome 21 and the understanding of the pathophysiology of trisomy 21, we have used exon trapping to identify fragments of chromosome 21 genes. Two trapped exons, from pools of chromosome 21-specific cosmids, showed homology to the Drosophila white (w) gene. We subsequently cloned the corresponding cDNA for a human homologue of the Drosophila w gene (hW) from human retina and fetal brain cDNA libraries. The gene belongs to the ATP-b...

  10. High resolution temperature mapping of gas turbine combustor simulator exhaust with femtosecond laser induced fiber Bragg gratings

    Science.gov (United States)

    Walker, Robert B.; Yun, Sangsig; Ding, Huimin; Charbonneau, Michel; Coulas, David; Lu, Ping; Mihailov, Stephen J.; Ramachandran, Nanthan

    2017-04-01

    Femtosecond infrared (fs-IR) laser written fiber Bragg gratings (FBGs), have demonstrated great potential for extreme sensing. Such conditions are inherent in advanced gas turbine engines under development to reduce greenhouse gas emissions; and the ability to measure temperature gradients in these harsh environments is currently limited by the lack of sensors and controls capable of withstanding the high temperature, pressure and corrosive conditions present. This paper discusses fabrication and deployment of several fs-IR written FBG arrays, for monitoring exhaust temperature gradients of a gas turbine combustor simulator. Results include: contour plots of measured temperature gradients, contrast with thermocouple data.

  11. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

    Directory of Open Access Journals (Sweden)

    Li Xin

    2012-07-01

    Full Text Available Abstract Background DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. Results The overall methylation level of rice genomes is four times higher than that of Arabidopsis. Consistent with the results reported for Arabidopsis, methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression. Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice. Conclusions The single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice.

  12. High-resolution fast temperature mapping of a gas turbine combustor simulator with femtosecond infrared laser written fiber Bragg gratings

    Science.gov (United States)

    Walker, Robert B.; Yun, Sangsig; Ding, Huimin; Charbonneau, Michel; Coulas, David; Ramachandran, Nanthan; Mihailov, Stephen J.

    2017-02-01

    Femtosecond infrared (fs-IR) written fiber Bragg gratings (FBGs), have demonstrated great potential for extreme sensing. Such conditions are inherent to the advanced gas turbine engines under development to reduce greenhouse gas emissions; and the ability to measure temperature gradients in these harsh environments is currently limited by the lack of sensors and controls capable of withstanding the high temperature, pressure and corrosive conditions present. This paper discusses fabrication and deployment of several fs-IR written FBG arrays, for monitoring the sidewall and exhaust temperature gradients of a gas turbine combustor simulator. Results include: contour plots of measured temperature gradients contrasted with thermocouple data, discussion of deployment strategies and comments on reliability.

  13. Novel p38α MAP kinase inhibitors identified from yoctoReactor DNA-encoded small molecule library

    DEFF Research Database (Denmark)

    Petersen, L. K.; Blakskjær, P.; Chaikuad, A.

    2016-01-01

    A highly specific and potent (7 nM cellular IC50) inhibitor of p38α kinase was identified directly from a 12.6 million membered DNA-encoded small molecule library. This was achieved using the high fidelity yoctoReactor technology (yR) for preparing the DNA-encoded library, and a homogeneous...... interactions. Moreover, the crystal structure showed, that although buried in the p38α active site, the original DNA attachment point of the compound was accessible through a channel created by the distorted P-loop conformation. This study demonstrates the usability of DNA-encoded library technologies...

  14. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José

    2016-11-03

    The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

  15. Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

    Directory of Open Access Journals (Sweden)

    Santos Carlos A.F.

    2002-01-01

    Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

  16. Human cDNA mapping using fluorescence in situ hybridization. Progress report, April 1, 1992--December 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-03-04

    Genetic mapping is approached using the techniques of high resolution fluorescence in situ hybridization (FISH). This technology and the results of its application are designed to rapidly generate whole genome as tool box of expressed sequence to speed the identification of human disease genes. The results of this study are intended to dovetail with and to link the results of existing technologies for creating backbone YAC and genetic maps. In the first eight months, this approach generated 60--80% of the expressed sequence map, the remainder expected to be derived through more long-term, labor-intensive, regional chromosomal gene searches or sequencing. The laboratory has made significant progress in the set-up phase, in mapping fetal and adult brain and other cDNAs, in testing a model system for directly linking genetic and physical maps using FISH with small fragments, in setting up a database, and in establishing the validity and throughput of the system.

  17. Human cDNA mapping using fluorescence in situ hybridization. Final progress report, April 1, 1994--July 31, 1997

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1997-12-31

    The ultimate goal of this research is to generate and apply novel technologies to speed completion and integration of the human genome map and sequence with biomedical problems. To do this, techniques were developed and genome-wide resources generated. This includes a genome-wide Mapped and Integrated BAC/PAC Resource that has been used for gene finding, map completion and anchoring, breakpoint definition and sequencing. In the last period of the grant, the Human Mapped BAC/PAC Resource was also applied to determine regions of human variation and to develop a novel paradigm of primate evolution through to humans. Further, in order to more rapidly evaluate animal models of human disease, a BAC Map of the mouse was generated in collaboration with the MTI Genome Center, Dr. Bruce Birren.

  18. Robust fiber clustering of cerebral fiber bundles in white matter

    Science.gov (United States)

    Yao, Xufeng; Wang, Yongxiong; Zhuang, Songlin

    2014-11-01

    Diffusion tensor imaging fiber tracking (DTI-FT) has been widely accepted in the diagnosis and treatment of brain diseases. During the rendering pipeline of specific fiber tracts, the image noise and low resolution of DTI would lead to false propagations. In this paper, we propose a robust fiber clustering (FC) approach to diminish false fibers from one fiber tract. Our algorithm consists of three steps. Firstly, the optimized fiber assignment continuous tracking (FACT) is implemented to reconstruct one fiber tract; and then each curved fiber in the fiber tract is mapped to a point by kernel principal component analysis (KPCA); finally, the point clouds of fiber tract are clustered by hierarchical clustering which could distinguish false fibers from true fibers in one tract. In our experiment, the corticospinal tract (CST) in one case of human data in vivo was used to validate our method. Our method showed reliable capability in decreasing the false fibers in one tract. In conclusion, our method could effectively optimize the visualization of fiber bundles and would help a lot in the field of fiber evaluation.

  19. Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, S.V.; Nadeau, J.H.; Tanzi, R.E.; Watkins, P.C.; Jagadesh, J.; Taylor, B.A.; Haines, J.L.; Sacchi, N.; Gusella, J.F. (Harvard Medical School, Boston, MA (USA))

    1988-08-01

    Mouse trisomy 16 has been proposed as an animal model of Down syndrome (DS), since this chromosome contains homologues of several loci from the q22 band of human chromosome 21. The recent mapping of the defect causing familial Alzheimer disease (FAD) and the locus encoding the Alzheimer amyloid {beta} precursor protein (APP) to human chromosome 21 has prompted a more detailed examination of the extent of conservation of this linkage group between the two species. Using anonymous DNA probes and cloned genes from human chromosome 21 in a combination of recombinant inbred and interspecific mouse backcross analyses, the authors have established that the linkage group shared by mouse chromosome 16 includes not only the critical DS region of human chromosome 21 but also the APP gene and FAD-linked markers. Extending from the anonymous DNA locus D21S52 to ETS2, the linkage map of six loci spans 39% recombination in man but only 6.4% recombination in the mouse. A break in synteny occurs distal to ETS2, with the homologue of the human marker D21S56 mapping to mouse chromosome 17. Conservation of the linkage relationships of markers in the FAD region suggests that the murine homologue of the FAD locus probably maps to chromosome 16 and that detailed comparison of the corresponding region in both species could facilitate identification of the primary defect in this disorder. The break in synteny between the terminal portion of human chromosome 21 and mouse chromosome 16 indicates, however, that mouse trisomy 16 may not represent a complete model of DS.

  20. Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17

    International Nuclear Information System (INIS)

    Cheng, S.V.; Nadeau, J.H.; Tanzi, R.E.; Watkins, P.C.; Jagadesh, J.; Taylor, B.A.; Haines, J.L.; Sacchi, N.; Gusella, J.F.

    1988-01-01

    Mouse trisomy 16 has been proposed as an animal model of Down syndrome (DS), since this chromosome contains homologues of several loci from the q22 band of human chromosome 21. The recent mapping of the defect causing familial Alzheimer disease (FAD) and the locus encoding the Alzheimer amyloid β precursor protein (APP) to human chromosome 21 has prompted a more detailed examination of the extent of conservation of this linkage group between the two species. Using anonymous DNA probes and cloned genes from human chromosome 21 in a combination of recombinant inbred and interspecific mouse backcross analyses, the authors have established that the linkage group shared by mouse chromosome 16 includes not only the critical DS region of human chromosome 21 but also the APP gene and FAD-linked markers. Extending from the anonymous DNA locus D21S52 to ETS2, the linkage map of six loci spans 39% recombination in man but only 6.4% recombination in the mouse. A break in synteny occurs distal to ETS2, with the homologue of the human marker D21S56 mapping to mouse chromosome 17. Conservation of the linkage relationships of markers in the FAD region suggests that the murine homologue of the FAD locus probably maps to chromosome 16 and that detailed comparison of the corresponding region in both species could facilitate identification of the primary defect in this disorder. The break in synteny between the terminal portion of human chromosome 21 and mouse chromosome 16 indicates, however, that mouse trisomy 16 may not represent a complete model of DS

  1. Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.).

    Science.gov (United States)

    Schönhals, E M; Ortega, F; Barandalla, L; Aragones, A; Ruiz de Galarreta, J I; Liao, J-C; Sanetomo, R; Walkemeier, B; Tacke, E; Ritter, E; Gebhardt, C

    2016-04-01

    SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker-trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker-trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.

  2. Fiber webs

    Science.gov (United States)

    Roger M. Rowell; James S. Han; Von L. Byrd

    2005-01-01

    Wood fibers can be used to produce a wide variety of low-density three-dimensional webs, mats, and fiber-molded products. Short wood fibers blended with long fibers can be formed into flexible fiber mats, which can be made by physical entanglement, nonwoven needling, or thermoplastic fiber melt matrix technologies. The most common types of flexible mats are carded, air...

  3. Comparative physical mapping of 18S rDNA in the karyotypes of six leafcutter ant species of the genera Atta and Acromyrmex (Formicidae: Myrmicinae).

    Science.gov (United States)

    Teixeira, Gisele Amaro; Barros, Luísa Antônia Campos; de Aguiar, Hilton Jeferson Alves Cardoso; das Graças Pompolo, Silvia

    2017-10-01

    Leafcutter ants of the Atta and Acromyrmex genera are important plagues in different cultures. Cytogenetic data on chromosome number, morphology, and chromosomal banding pattern are only available for 17 species of leafcutter ants. Molecular cytogenetic data for the detection of ribosomal genes by the FISH technique are scarce, and only 15 Neotropical ant species have been studied. This study aimed to physically map the 18S ribosomal RNA genes (rDNA) of six leafcutter ants belonging to the genera Atta and Acromyrmex using FISH. The results were compared with data on the fluorochrome CMA 3 currently available for these species. All analyzed species presented the 18S rDNA on one pair of chromosomes. In Acromyrmex subterraneus molestans and Ac. aspersus, FISH signals were observed in the terminal region of the short arm of the largest subtelocentric pair, while in Atta bisphaerica, A. laevigata, and A. sexdens, FISH signals were observed in the interstitial region of the long arm of the fourth metacentric pair. In Acromyrmex striatus, 18S rDNA was located in the interstitial region of the second metacentric pair. The karyotypic formula for Ac. aspersus was 2n = 38 (8m + 10sm + 16st + 4a), representing the first report in this species. The observed 18S rDNA regions in A. laevigata, A. sexdens, A. bisphaerica, Ac. aspersus, and Ac. subterraneus molestans corresponded to the CMA 3 + bands, while in Ac. striatus, several GC-rich bands and one pair of 18S rDNA bands were observed. No differential bands were visible using the DAPI fluorochrome. Karyotype uniformity with previously studied Atta spp. was also observed at the level of molecular cytogenetics using 18S rDNA FISH. A difference in the size of the chromosomal pair carrying the 18S rDNA gene was observed in Ac. striatus (2n = 22) and Atta spp. (2n = 22) highlighting the dissimilarity between these species. The results from the present study contribute to the description of 18S rDNA clusters

  4. Generation of an induced pluripotent stem cell (iPSC line from a 40-year-old patient with the A8344G mutation of mitochondrial DNA and MERRF (myoclonic epilepsy with ragged red fibers syndrome

    Directory of Open Access Journals (Sweden)

    Yu-Ting Wu

    2018-03-01

    Full Text Available Mitochondrial defects are associated with clinical manifestations from common diseases to rare genetic disorders. Myoclonus epilepsy associated with ragged-red fibers (MERRF syndrome results from an A to G transition at nucleotide position 8344 in the tRNALys gene of mitochondrial DNA (mtDNA and is characterized by myoclonus, myopathy and severe neurological symptoms. In this study, Sendai reprogramming method was used to generate an iPS cell line carrying the A8344G mutation of mtDNA from a MERRF patient. This patient-specific iPSC line expressed pluripotent stem cell markers, possessed normal karyotype, and displayed the capability to differentiate into mature cells in three germ layers.

  5. The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes

    Directory of Open Access Journals (Sweden)

    Claude Pasquier

    2017-07-01

    Full Text Available Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson–Crick duplex. The “triplex-forming oligonucleotide” (TFO can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the “triplex-forming oligonucleotide” in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster. These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The refined analysis by Gene Ontology enrichment demonstrates that some individual TFOs present genome-wide scale matches that are located in numerous genes and regulatory sequences. The triplex DNA:RNA computational mapping at the genome-wide scale suggests broad interference in the regulatory process of the gene networks orchestrated by TFO RNAs acting in association simultaneously at multiple sites.

  6. Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping

    Science.gov (United States)

    Müller, Vilhelm; Rajer, Fredrika; Frykholm, Karolin; Nyberg, Lena K.; Quaderi, Saair; Fritzsche, Joachim; Kristiansson, Erik; Ambjörnsson, Tobias; Sandegren, Linus; Westerlund, Fredrik

    2016-12-01

    Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.

  7. A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq).

    Science.gov (United States)

    Recknagel, Hans; Elmer, Kathryn R; Meyer, Axel

    2013-01-01

    Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F(2) hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F(2) offspring, we calculated a genome-wide mutation rate of 6.6 × 10(-8) mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.

  8. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes.

    Directory of Open Access Journals (Sweden)

    Duílio M Z de A Silva

    Full Text Available Supernumerary (B chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.

  9. Surface-enhanced Raman spectroscopic study of DNA and 6-mercapto-1-hexanol interactions using large area mapping

    DEFF Research Database (Denmark)

    Frøhling, Kasper Bayer; Alstrøm, Tommy Sonne; Bache, Michael

    2016-01-01

    intensities and peak positions it is possible to directly inspect the interplay between DNA and 6-mercapto-1-hexanol on gold covered nanopillars. It is demonstrated that optimised functionalization parameters can be extracted from the Raman spectra directly. Using the peak-fitting approach it is possible...

  10. rDNA mapping, heterochromatin characterization and AT/GC content of Agapanthus africanus (L. Hoffmanns (Agapanthaceae

    Directory of Open Access Journals (Sweden)

    ARYANE C. REIS

    2016-01-01

    Full Text Available ABSTRACT Agapanthus (Agapanthaceae has 10 species described. However, most taxonomists differ respect to this number because the great phenotypic plasticity of the species. The cytogenetic has been an important tool to aid the plant taxon identification, and to date, all taxa of Agapanthus L'Héritier studied cytologically, presented 2n = 30. Although the species possess large chromosomes, the group is karyologically little explored. This work aimed to increase the cytogenetic knowledge of Agapanthus africanus (L. Hoffmanns by utilization of chromosome banding techniques with DAPI / CMA3 and Fluorescent in situ Hybridization (FISH. In addition, flow cytometry was used for determination of DNA content and the percentage of AT / GC nitrogenous bases. Plants studied showed 2n = 30 chromosomes, ranging from 4.34 - 8.55 µm, with the karyotype formulae (KF = 10m + 5sm. Through FISH, one 45S rDNA signal was observed proximally to centromere of the chromosome 7, while for 5S rDNA sites we observed one signal proximally to centromere of chromosome 9. The 2C DNA content estimated for the species was 2C = 24.4 with 59% of AT and 41% of GC. Our data allowed important upgrade for biology and cytotaxonomy of Agapanthus africanus (L. Hoffmanns.

  11. Human thyroid peroxidase: complete cDNA and protein sequence, chromosome mapping, and identification of two alternately spliced mRNAs

    International Nuclear Information System (INIS)

    Kimura, S.; Kotani, T.; McBride, O.W.; Umeki, K.; Hirai, K.; Nakayama, T.; Ohtaki, S.

    1987-01-01

    Two forms of human thyroid peroxidase cDNAs were isolated from a λgt11 cDNA library, prepared from Graves disease thyroid tissue mRNA, by use of oligonucleotides. The longest complete cDNA, designated phTPO-1, has 3048 nucleotides and an open reading frame consisting of 933 amino acids, which would encode a protein with a molecular weight of 103,026. Five potential asparagine-linked glycosylation sites are found in the deduced amino acid sequence. The second peroxidase cDNA, designated phTPO-2, is almost identical to phTPO-1 beginning 605 base pairs downstream except that it contains 1-base-pair difference and lacks 171 base pairs in the middle of the sequence. This results in a loss of 57 amino acids corresponding to a molecular weight of 6282. Interestingly, this 171-nucleotide sequence has GT and AG at its 5' and 3' boundaries, respectively, that are in good agreement with donor and acceptor splice site consensus sequences. Using specific oligonucleotide probes for the mRNAs derived from the cDNA sequences hTOP-1 and hTOP-2, the authors show that both are expressed in all thyroid tissues examined and the relative level of two mRNAs is different in each sample. The results suggest that two thyroid peroxidase proteins might be generated through alternate splicing of the same gene. By using somatic cell hybrid lines, the thyroid peroxidase gene was mapped to the short arm of human chromosome 2

  12. A first linkage map and downy mildew resistance QTL discovery for sweet basil (Ocimum basilicum) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq).

    Science.gov (United States)

    Pyne, Robert; Honig, Josh; Vaiciunas, Jennifer; Koroch, Adolfina; Wyenandt, Christian; Bonos, Stacy; Simon, James

    2017-01-01

    Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an O. basilicum allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37-55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, dm11.1 explained 21-28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL dm9.1 and dm14.1 explained 5-16% and 4-18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL dm11.1 increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome.

  13. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers.

    Science.gov (United States)

    Umeyama, Taichi; Ito, Takashi

    2017-10-03

    Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Genomic Mapping of Human DNA provides Evidence of Difference in Stretch between AT and GC rich regions

    Science.gov (United States)

    Reifenberger, Jeffrey; Dorfman, Kevin; Cao, Han

    Human DNA is a not a polymer consisting of a uniform distribution of all 4 nucleic acids, but rather contains regions of high AT and high GC content. When confined, these regions could have different stretch due to the extra hydrogen bond present in the GC basepair. To measure this potential difference, human genomic DNA was nicked with NtBspQI, labeled with a cy3 like fluorophore at the nick site, stained with YOYO, loaded into a device containing an array of nanochannels, and imaged. Over 473,000 individual molecules of DNA, corresponding to roughly 30x coverage of a human genome, were collected and aligned to the human reference. Based on the known AT/GC content between aligned pairs of labels, the stretch was measured for regions of similar size but different AT/GC content. We found that regions of high GC content were consistently more stretched than regions of high AT content between pairs of labels varying in size between 2.5 kbp and 500 kbp. We measured that for every 1% increase in GC content there was roughly a 0.06% increase in stretch. While this effect is small, it is important to take into account differences in stretch between AT and GC rich regions to improve the sensitivity of detection of structural variations from genomic variations. NIH Grant: R01-HG006851.

  15. Photorefractive Fibers

    National Research Council Canada - National Science Library

    Kuzyk, Mark G

    2003-01-01

    ... scope of the project. In addition to our work in optical limiting fibers, spillover results included making fiber-based light-sources, writing holograms in fibers, and developing the theory of the limits of the nonlinear...

  16. DNA methylation map in circulating leukocytes mirrors subcutaneous adipose tissue methylation pattern: a genome-wide analysis from non-obese and obese patients

    Science.gov (United States)

    Crujeiras, A. B.; Diaz-Lagares, A.; Sandoval, J.; Milagro, F. I.; Navas-Carretero, S.; Carreira, M. C.; Gomez, A.; Hervas, D.; Monteiro, M. P.; Casanueva, F. F.; Esteller, M.; Martinez, J. A.

    2017-01-01

    The characterization of the epigenetic changes within the obesity-related adipose tissue will provide new insights to understand this metabolic disorder, but adipose tissue is not easy to sample in population-based studies. We aimed to evaluate the capacity of circulating leukocytes to reflect the adipose tissue-specific DNA methylation status of obesity susceptibility. DNA samples isolated from subcutaneous adipose tissue and circulating leukocytes were hybridized in the Infinium HumanMethylation 450 BeadChip. Data were compared between samples from obese (n = 45) and non-obese (n = 8–10) patients by Wilcoxon-rank test, unadjusted for cell type distributions. A global hypomethylation of the differentially methylated CpG sites (DMCpGs) was observed in the obese subcutaneous adipose tissue and leukocytes. The overlap analysis yielded a number of genes mapped by the common DMCpGs that were identified to reflect the obesity state in the leukocytes. Specifically, the methylation levels of FGFRL1, NCAPH2, PNKD and SMAD3 exhibited excellent and statistically significant efficiencies in the discrimination of obesity from non-obesity status (AUC > 0.80; p obesity-related adipose tissue pathogenesis through peripheral blood analysis, an easily accessible and minimally invasive biological material instead of adipose tissue. PMID:28211912

  17. Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology.

    Science.gov (United States)

    Liu, Ying; Lu, Zheming; Xu, Ruiping; Ke, Yang

    2016-02-02

    Integration of human papillomavirus (HPV) DNA into the host genome can be a driver mutation in cervical carcinoma. Identification of HPV integration at base resolution has been a longstanding technical challenge, largely due to sensitivity masking by HPV in episomes or concatenated forms. The aim was to enhance the understanding of the precise localization of HPV integration sites using an innovative strategy. Using HPV capture technology combined with next generation sequencing, HPV prevalence and the exact integration sites of the HPV DNA in 47 primary cervical cancer samples and 2 cell lines were investigated. A total of 117 unique HPV integration sites were identified, including HPV16 (n = 101), HPV18 (n = 7), and HPV58 (n = 9). We observed that the HPV16 integration sites were broadly located across the whole viral genome. In addition, either single or multiple integration events could occur frequently for HPV16, ranging from 1 to 19 per sample. The viral integration sites were distributed across almost all the chromosomes, except chromosome 22. All the cervical cancer cases harboring more than four HPV16 integration sites showed clinical diagnosis of stage III carcinoma. A significant enrichment of overlapping nucleotides shared between the human genome and HPV genome at integration breakpoints was observed, indicating that it may play an important role in the HPV integration process. The results expand on knowledge from previous findings on HPV16 and HPV18 integration sites and allow a better understanding of the molecular basis of the pathogenesis of cervical carcinoma.

  18. Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing.

    Directory of Open Access Journals (Sweden)

    Jeong-Hyeon Choi

    Full Text Available BACKGROUND: Follicular lymphoma (FL is a form of non-Hodgkin's lymphoma (NHL that arises from germinal center (GC B-cells. Despite the significant advances in immunotherapy, FL is still not curable. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and therefore identify novel mechanisms and targets for successful prevention and treatment of FL. METHODOLOGY/PRINCIPAL FINDINGS: We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19(+ B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19(+ B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs were identified respectively. The genome-wide distribution of these MRIs displayed significant differences between FL and normal B-cells. A reverse trend in the distribution of MRIs between the promoter and the gene body was observed in FL and CD19(+ B-cells. The MRIs identified in FL cells also correlated well with transcriptomic data and ChIP-on-Chip analyses of genome-wide histone modifications such as tri-methyl-H3K27, and tri-methyl-H3K4, indicating a concerted epigenetic alteration in FL cells. CONCLUSIONS/SIGNIFICANCE: This study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. These integrated approaches have led to the discovery of novel and frequent targets of aberrant epigenetic alterations. The genome-wide bisulfite sequencing approach developed here can be a useful tool for profiling DNA methylation in clinical samples.

  19. Fiber dielectrophoresis

    International Nuclear Information System (INIS)

    Lipowicz, P.J.; Yeh, H.C.

    1988-01-01

    Dielectrophoresis is the motion of uncharged particles in nonuniform electric fields. We find that the theoretical dielectrophoretic velocity of a conducting fiber in an insulating medium is proportional to the square of the fiber length, and is virtually independent of fiber diameter. This prediction has been verified experimentally. The results point to the development of a fiber length classifier based on dielectrophoresis. (author)

  20. HapMap-based study of the DNA repair gene ERCC2 and lung cancer susceptibility in a Chinese population

    DEFF Research Database (Denmark)

    Yin, Jiaoyang; Vogel, Ulla Birgitte; Ma, Yegang

    2009-01-01

    -nucleotide polymorphisms (htSNPs) (rs238403, rs50871, rs3916840, rs238415, rs3916874 and rs1799787) from HapMap database were analyzed, which provide an almost complete coverage of the genetic variations in the ERCC2 gene. Although none of the six htSNPs was individually associated with lung cancer risk, we found that two...... ratio, OR (95% confidence interval, CI) = 2.62 (1.53–4.50), P = 0.0003 for hap4; OR (95% CI) = 3.01 (1.36–6.63), P = 0.004 for hap7]. Furthermore, diplotype analyses also strengthened the significant associations of risk haplotype 4 [OR (95% CI) = 3.56 (2.12–5.87), P

  1. Fiber Amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten

    2017-01-01

    The chapter provides a discussion of optical fiber amplifiers and through three sections provides a detailed treatment of three types of optical fiber amplifiers, erbium doped fiber amplifiers (EDFA), Raman amplifiers, and parametric amplifiers. Each section comprises the fundamentals including...... the basic physics and relevant in-depth theoretical modeling, amplifiers characteristics and performance data as a function of specific operation parameters. Typical applications in fiber optic communication systems and the improvement achievable through the use of fiber amplifiers are illustrated....

  2. Functional mapping of the fission yeast DNA polymerase δ B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis

    Directory of Open Access Journals (Sweden)

    Gray Fiona C

    2009-08-01

    Full Text Available Abstract Background DNA polymerase δ plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol δ is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol δ comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively. Results To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1. Conclusion In the absence of a three-dimensional structure of the entire Pol δ complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.

  3. Mapping recessive ophthalmic diseases: linkage of the locus for Usher syndrome type II to a DNA marker on chromosome 1q.

    Science.gov (United States)

    Lewis, R A; Otterud, B; Stauffer, D; Lalouel, J M; Leppert, M

    1990-06-01

    Usher syndrome is a heterogeneous group of autosomal recessive disorders that combines variably severe congenital neurosensory hearing impairment with progressive night-blindness and visual loss similar to that in retinitis pigmentosa. Usher syndrome type I is distinguished by profound congenital (preverbal) deafness and retinal disease with onset in the first decade of life. Usher syndrome type II is characterized by partial hearing impairment and retinal dystrophy that occurs in late adolescence or early adulthood. The chromosomal assignment and the regional localization of the genetic mutation(s) causing the Usher syndromes are unknown. We analyzed a panel of polymorphic genomic markers for linkage to the disease gene among six families with Usher syndrome type I and 22 families with Usher syndrome type II. Significant linkage was established between Usher syndrome type II and the DNA marker locus THH33 (D1S81), which maps to chromosome 1q. The most likely location of the disease gene is at a map distance of 9 cM from THH33 (lod score 6.5). The same marker failed to show linkage in families segregating an allele for Usher syndrome type I. These data confirm the provisional assignment of the locus for Usher syndrome type II to the distal end of chromosome 1q and demonstrate that the clinical heterogeneity between Usher types I and II is caused by mutational events at different genetic loci. Regional localization has the potential to improve carrier detection and to provide antenatal diagnosis in families at risk for the disease.

  4. Fiber optic-based biosensor

    Science.gov (United States)

    Ligler, Frances S.

    1991-01-01

    The NRL fiber optic biosensor is a device which measures the formation of a fluorescent complex at the surface of an optical fiber. Antibodies and DNA binding proteins provide the mechanism for recognizing an analyze and immobilizing a fluorescent complex on the fiber surface. The fiber optic biosensor is fast, sensitive, and permits analysis of hazardous materials remote from the instrumentation. The fiber optic biosensor is described in terms of the device configuration, chemistry for protein immobilization, and assay development. A lab version is being used for assay development and performance characterization while a portable device is under development. Antibodies coated on the fiber are stable for up to two years of storage prior to use. The fiber optic biosensor was used to measure concentration of toxins in the parts per billion (ng/ml) range in under a minute. Immunoassays for small molecules and whole bacteria are under development. Assays using DNA probes as the detection element can also be used with the fiber optic sensor, which is currently being developed to detect biological warfare agents, explosives, pathogens, and toxic materials which pollute the environment.

  5. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq).

    Science.gov (United States)

    Yu, Hui; You, Xinxin; Li, Jia; Liu, Hankui; Meng, Zining; Xiao, Ling; Zhang, Haifa; Lin, Hao-Ran; Zhang, Yong; Shi, Qiong

    2016-04-06

    Mapping of quantitative trait loci (QTL) is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms) by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides) using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs) spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1) including three (tert, ftz-f1 and notch1) that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS) efforts to improve growth-related traits in this economically important fish.

  6. Dna fingerprinting - review paper

    OpenAIRE

    Blundell, Renald

    2006-01-01

    Before the Polymerase Chain Reaction (PCR) was established, DNA fingerprinting technology has relied for years on Restriction Fragment Length Polymorphism (RFLP) and Variable Number of Tandom Repeats (VNTR) analysis, a very efficient technique but quite laborious and not suitable for high throughput mapping. Since its, development, PCR has provided a new and powerful tool for DNA fingerprinting.

  7. Two Fiber Optical Fiber Thermometry

    Science.gov (United States)

    Jones, Mathew R.; Farmer, Jeffery T.; Breeding, Shawn P.

    2000-01-01

    An optical fiber thermometer consists of an optical fiber whose sensing tip is given a metallic coating. The sensing tip of the fiber is essentially an isothermal cavity, so the emission from this cavity will be approximately equal to the emission from a blackbody. Temperature readings are obtained by measuring the spectral radiative heat flux at the end of the fiber at two wavelengths. The ratio of these measurements and Planck's Law are used to infer the temperature at the sensing tip. Optical fiber thermometers have high accuracy, excellent long-term stability and are immune to electromagnetic interference. In addition, they can be operated for extended periods without requiring re-calibration. For these reasons. it is desirable to use optical fiber thermometers in environments such as the International Space Station. However, it has recently been shown that temperature readings are corrupted by emission from the fiber when extended portions of the probe are exposed to elevated temperatures. This paper will describe several ways in which the reading from a second fiber can be used to correct the corrupted temperature measurements. The accuracy and sensitivity to measurement uncertainty will be presented for each method.

  8. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  9. Chromosomal DNA replication of Vicia faba cells

    International Nuclear Information System (INIS)

    Ikushima, Takaji

    1976-01-01

    The chromosomal DNA replication of higher plant cells has been investigated by DNA fiber autoradiography. The nuclear DNA fibers of Vicia root meristematic cells are organized into many tandem arrays of replication units or replicons which exist as clusters with respect to replication. DNA is replicated bidirectionally from the initiation points at the average rate of 0.15 μm/min at 20 0 C, and the average interinitiation interval is about 16 μm. The manner of chromosomal DNA replication in this higher plant is similar to that found in other eukaryotic cells at a subchromosomal level. (auth.)

  10. Human Genome Research: Decoding DNA

    Science.gov (United States)

    dropdown arrow Site Map A-Z Index Menu Synopsis Human Genome Research: Decoding DNA Resources with of the DNA double helix during April 2003. James D. Watson, Francis Crick, and Maurice Wilkins were company Celera announced the completion of a "working draft" reference DNA sequence of the human

  11. Deposition of carbon nanotubes onto aramid fibers using as-received and chemically modified fibers

    International Nuclear Information System (INIS)

    Rodríguez-Uicab, O.; Avilés, F.; Gonzalez-Chi, P.I; Canché-Escamilla, G.; Duarte-Aranda, S.; Yazdani-Pedram, M.; Toro, P.; Gamboa, F.; Mazo, M.A.; Nistal, A.; Rubio, J.

    2016-01-01

    Highlights: • The surface of aramid fibers was functionalized by two acid treatments. • The treatment based on HNO_3/H_2SO_4 reduced the mechanical properties of the fibers. • CNTs were deposited on the aramid fibers, reaching electrical conductivity. • Homogeneous CNT distribution was achieved by using pristine fibers or chlorosulfonic acid. - Abstract: Multiwall carbon nanotubes (MWCNTs) oxidized by an acid treatment were deposited on the surface of as-received commercial aramid fibers containing a surface coating (“sizing”), and fibers modified by either a chlorosulfonic treatment or a mixture of nitric and sulfuric acids. The surface of the aramid fiber activated by the chemical treatments presents increasing density of CO, COOH and OH functional groups. However, these chemical treatments reduced the tensile mechanical properties of the fibers, especially when the nitric and sulfuric acid mixture was used. Characterization of the MWCNTs deposited on the fiber surface was conducted by scanning electron microscopy, Raman spectroscopy mapping and X-ray photoelectron spectroscopy. These characterizations showed higher areal concentration and more homogeneous distribution of MWCNTs over the aramid fibers for as-received fibers and for those modified with chlorosulfonic acid, suggesting the existence of interaction between the oxidized MWCNTs and the fiber coating. The electrical resistance of the MWCNT-modified aramid yarns comprising ∼1000 individual fibers was in the order of MΩ/cm, which renders multifunctional properties.

  12. Deposition of carbon nanotubes onto aramid fibers using as-received and chemically modified fibers

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez-Uicab, O. [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburna de Hidalgo, C.P. 97200 Mérida, Yucatán (Mexico); Avilés, F., E-mail: faviles@cicy.mx [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburna de Hidalgo, C.P. 97200 Mérida, Yucatán (Mexico); Gonzalez-Chi, P.I; Canché-Escamilla, G.; Duarte-Aranda, S. [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburna de Hidalgo, C.P. 97200 Mérida, Yucatán (Mexico); Yazdani-Pedram, M. [Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, S. Livingstone 1007, Independencia, Santiago (Chile); Toro, P. [Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Av. Beauchef 850, Santiago (Chile); Gamboa, F. [Centro de Investigacion y de Estudios Avanzados del IPN, Unidad Mérida, Depto. de Física Aplicada, Km. 6 Antigua Carretera a Progreso, 97310 Mérida, Yucatán (Mexico); Mazo, M.A.; Nistal, A.; Rubio, J. [Instituto de Cerámica y Vidrio (ICV-CSIC), Kelsen 5, 28049 Madrid (Spain)

    2016-11-01

    Highlights: • The surface of aramid fibers was functionalized by two acid treatments. • The treatment based on HNO{sub 3}/H{sub 2}SO{sub 4} reduced the mechanical properties of the fibers. • CNTs were deposited on the aramid fibers, reaching electrical conductivity. • Homogeneous CNT distribution was achieved by using pristine fibers or chlorosulfonic acid. - Abstract: Multiwall carbon nanotubes (MWCNTs) oxidized by an acid treatment were deposited on the surface of as-received commercial aramid fibers containing a surface coating (“sizing”), and fibers modified by either a chlorosulfonic treatment or a mixture of nitric and sulfuric acids. The surface of the aramid fiber activated by the chemical treatments presents increasing density of CO, COOH and OH functional groups. However, these chemical treatments reduced the tensile mechanical properties of the fibers, especially when the nitric and sulfuric acid mixture was used. Characterization of the MWCNTs deposited on the fiber surface was conducted by scanning electron microscopy, Raman spectroscopy mapping and X-ray photoelectron spectroscopy. These characterizations showed higher areal concentration and more homogeneous distribution of MWCNTs over the aramid fibers for as-received fibers and for those modified with chlorosulfonic acid, suggesting the existence of interaction between the oxidized MWCNTs and the fiber coating. The electrical resistance of the MWCNT-modified aramid yarns comprising ∼1000 individual fibers was in the order of MΩ/cm, which renders multifunctional properties.

  13. Mapping out Map Libraries

    Directory of Open Access Journals (Sweden)

    Ferjan Ormeling

    2008-09-01

    Full Text Available Discussing the requirements for map data quality, map users and their library/archives environment, the paper focuses on the metadata the user would need for a correct and efficient interpretation of the map data. For such a correct interpretation, knowledge of the rules and guidelines according to which the topographers/cartographers work (such as the kind of data categories to be collected, and the degree to which these rules and guidelines were indeed followed are essential. This is not only valid for the old maps stored in our libraries and archives, but perhaps even more so for the new digital files as the format in which we now have to access our geospatial data. As this would be too much to ask from map librarians/curators, some sort of web 2.0 environment is sought where comments about data quality, completeness and up-to-dateness from knowledgeable map users regarding the specific maps or map series studied can be collected and tagged to scanned versions of these maps on the web. In order not to be subject to the same disadvantages as Wikipedia, where the ‘communis opinio’ rather than scholarship, seems to be decisive, some checking by map curators of this tagged map use information would still be needed. Cooperation between map curators and the International Cartographic Association ( ICA map and spatial data use commission to this end is suggested.

  14. All-Silica Hollow-Core Microstructured Bragg Fibers for Biosensor Application

    DEFF Research Database (Denmark)

    Passaro, Davide; Foroni, Matteo; Poli, Federica

    2008-01-01

    The possibility to exploit all-silica hollow-core-microstructured Bragg fibers to realize a biosensor useful to detect the DNA hybridization process has been investigated. A Bragg fiber recently fabricated has been considered for the analysis performed by means of a full-vector modal solver based...... layer on the inner surface of the fiber holes can modify the fundamental mode properties. The numerical analysis results have successfully demonstrated the DNA bio-sensor feasibility in hollow-core Bragg fibers....

  15. Low-fiber diet

    Science.gov (United States)

    ... residue; Low-fiber diet; Fiber restricted diet; Crohn disease - low fiber diet; Ulcerative colitis - low fiber diet; ... them if they do not contain seeds or pulp: Yellow squash (without seeds) Spinach Pumpkin Eggplant Potatoes, ...

  16. Photovoltaic fibers

    Science.gov (United States)

    Gaudiana, Russell; Eckert, Robert; Cardone, John; Ryan, James; Montello, Alan

    2006-08-01

    It was realized early in the history of Konarka that the ability to produce fibers that generate power from solar energy could be applied to a wide variety of applications where fabrics are utilized currently. These applications include personal items such as jackets, shirts and hats, to architectural uses such as awnings, tents, large covers for cars, trucks and even doomed stadiums, to indoor furnishings such as window blinds, shades and drapes. They may also be used as small fabric patches or fiber bundles for powering or recharging batteries in small sensors. Power generating fabrics for clothing is of particular interest to the military where they would be used in uniforms and body armor where portable power is vital to field operations. In strong sunlight these power generating fabrics could be used as a primary source of energy, or they can be used in either direct sunlight or low light conditions to recharge batteries. Early in 2002, Konarka performed a series of proof-of-concept experiments to demonstrate the feasibility of building a photovoltaic cell using dye-sensitized titania and electrolyte on a metal wire core. The approach taken was based on the sequential coating processes used in making fiber optics, namely, a fiber core, e.g., a metal wire serving as the primary electrode, is passed through a series of vertically aligned coating cups. Each of the cups contains a coating fluid that has a specific function in the photocell. A second wire, used as the counter electrode, is brought into the process prior to entering the final coating cup. The latter contains a photopolymerizable, transparent cladding which hardens when passed through a UV chamber. Upon exiting the UV chamber, the finished PV fiber is spooled. Two hundred of foot lengths of PV fiber have been made using this process. When the fiber is exposed to visible radiation, it generates electrical power. The best efficiency exhibited by these fibers is 6% with an average value in the 4

  17. Use of reiterative primer extension methodology to map UV-induced photoproducts at the nucleotide level in the laci gene from genomic DNA

    International Nuclear Information System (INIS)

    Chandrasekhar, D.; Houten, B. Van

    1994-01-01

    A newly developed reiterative primer extension assay has been employed to examine photoproduct formation and repair at the nucleotide level. Analysis of UV-induced DNA photoproduct hotspots in the first 184 base pairs of the laci genes of genomic E. coli DNA has revealed that photoproducts are formed linearly with dose and display a sequence-dependent increase. Generally, pyrimdine dimers were twice as frequent as all other UV-induced photoproducts. However, specific sites showed differing distributions. A post-irradiation recovery period revealed differences in the repair efficiency at individual nucleotides. Repair of photoproducts on the transcribed strand was generally twice as efficient as repair of photoproducts on the nontranscribed strand, indicating that strand-specific DNA repair occurs in the constitutively transcribed laci gene of E. coli. The UV-induced DNA photoproduct distribution following repair was well correlated with an established UV-induced mutation spectrum for wild-type E. coli cells. This analysis revealed that photoproduct hotspots on the efficiently repaired transcribed strand did not correlate with mutagenic hotspots. These data strongly support the hypothesis that mutations arise at inefficiently repaired sites on the nontranscribed strand

  18. Gene mapping of 28S and 5S rDNA sites in chromosomes of two Barbus species and their F1 hybrids (Teleostei, Cyprinidae

    Directory of Open Access Journals (Sweden)

    Aneta Spoz

    2015-11-01

    Chromosomal location of ribosomal DNA sequences is useful for comparative cytogenetic fish studies due to their relatively fast rate of evolution. The results of species from the family Barbinae comparatively presented here for the first time, and they may support further taxonomical studies of the Barbus species.

  19. In silico analysis, mapping of regulatory elements and corresponding dna-protein interaction in polyphenol oxidase gene promoter from different rice varieties

    International Nuclear Information System (INIS)

    Mahmood, T.; Rehman, M.; Aziz, E.

    2015-01-01

    Polyphenol oxidase (PPO) is an important enzyme that has positive impact regarding plant resistance against different biotic and abiotic stresses. In the present study PPO promoter from six different rice varieties was amplified and then analyzed for cis- and trans-acting elements. The study revealed a total of 79 different cis-acting regulatory elements including 11 elements restricted to only one or other variety. Among six varieties Pakhal-Basmati had highest number (5) of these elements, whereas C-622 and Rachna-Basmati have no such sequences. Rachna-Basmati, IR-36-Basmati and Kashmir- Basmati had 1, 2 and 3 unique elements, respectively. Different elementsrelated to pathogen, salt and water stresses were found, which may be helpful in controlling PPO activity according to changing environment. Moreover, HADDOCK was used to understand molecular mechanism of PPO regulation and it was found that DNA-protein interactions are stabilized by many potential hydrogen bonds. Adenine and arginine were the most reactive residues in DNA and proteins respectively.Structural comparison of different protein-DNA complexes show that even a highly conserved transcriptional factor can adopt different conformations when they contact a different DNA binding sequence, however their stable interactions depend on the number of hydrogen bonds formed and distance. (author)

  20. Towards biochips using microstructured optical fiber sensors

    DEFF Research Database (Denmark)

    Rindorf, Lars Henning; Hoiby, Poul Erik; Jensen, Jesper Bo

    2006-01-01

    In this paper we present the first incorporation of a microstructured optical fiber (MOF) into biochip applications. A 16-mm-long piece of MOF is incorporated into an optic-fluidic coupler chip, which is fabricated in PMMA polymer using a CO2 laser. The developed chip configuration allows...... the continuous control of liquid flow through the MOF and simultaneous optical characterization. While integrated in the chip, the MOF is functionalized towards the capture of a specific single-stranded DNA string by immobilizing a sensing layer on the microstructured internal surfaces of the fiber. The sensing...... layer contains the DNA string complementary to the target DNA sequence and thus operates through the highly selective DNA hybridization process. Optical detection of the captured DNA was carried out using the evanescent-wave-sensing principle. Owing to the small size of the chip, the presented technique...

  1. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

    Directory of Open Access Journals (Sweden)

    De Marzo Angelo M

    2011-06-01

    Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

  2. Mitochondrial DNA copy number threshold in mtDNA depletion myopathy.

    Science.gov (United States)

    Durham, S E; Bonilla, E; Samuels, D C; DiMauro, S; Chinnery, P F

    2005-08-09

    The authors measured the absolute amount of mitochondrial DNA (mtDNA) within single muscle fibers from two patients with thymidine kinase 2 (TK2) deficiency and two healthy controls. TK2 deficient fibers containing more than 0.01 mtDNA/microm3 had residual cytochrome c oxidase (COX) activity. This defines the minimum amount of wild-type mtDNA molecules required to maintain COX activity in skeletal muscle and provides an explanation for the mosaic histochemical pattern seen in patients with mtDNA depletion syndrome.

  3. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.

    Science.gov (United States)

    Chèneby, Jeanne; Gheorghe, Marius; Artufel, Marie; Mathelier, Anthony; Ballester, Benoit

    2018-01-04

    With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Karyotypes, male meiosis and comparative FISH mapping of 18S ribosomal DNA and telomeric (TTAGGn repeat in eight species of true bugs (Hemiptera, Heteroptera

    Directory of Open Access Journals (Sweden)

    Snejana Grozeva

    2011-11-01

    Full Text Available Eight species belonging to five true bug families were analyzed using DAPI/CMA3-staining and fluorescence in situ hybridization (FISH with telomeric (TTAGGn and 18S rDNA probes. Standard chromosomal complements are reported for the first time for Deraeocoris rutilus (Herrich-Schäffer, 1838 (2n=30+2m+XY and D. ruber (Linnaeus, 1758 (2n=30+2m+XY from the family Miridae. Using FISH, the location of a 18S rDNA cluster was detected in these species and in five more species: Megaloceroea recticornis (Geoffroy, 1785 (2n=30+XY from the Miridae; Oxycarenus lavaterae (Fabricius, 1787 (2n=14+2m+XY from the Lygaeidae s.l.; Pyrrhocoris apterus (Linnaeus, 1758 (2n=22+X from the Pyrrhocoridae; Eurydema oleracea (Linnaeus, 1758 (2n=12+XY and Graphosoma lineatum (Linnaeus, 1758 (2n=12+XY from the Pentatomidae. The species were found to differ with respect to location of a 18S rRNA gene cluster which resides on autosomes in O. lavaterae and P. apterus, whereas it locates on sex chromosomes in other five species. The 18S rDNA location provides the first physical landmark of the genomes of the species studied. The insect consensus telomeric pentanucleotide (TTAGGn was demonstrated to be absent in all the species studied in this respect, D. rutilus, M. recticornis, Cimex lectularius Linnaeus, 1758 (Cimicidae, E. oleracea, and G. lineatum, supporting the hypothesis that this motif was lost in early evolution of the Heteroptera and secondarily replaced with another motif (yet unknown or the alternative telomerase-independent mechanisms of telomere maintenance. Dot-blot hybridization analysis of the genomic DNA from C. lectularius, Nabis sp. and O. lavaterae with (TTAGGn and six other telomeric probes likewise provided a negative result.

  5. Application Specific Optical Fibers

    OpenAIRE

    Pal, Bishnu P.

    2010-01-01

    In this chapter we have attempted to provide a unified summary description of the most important propagation characteristics of an optical fiber followed by discussion on several variety of special fibers for realizing fiber amplifiers, dispersion compensating fibers, microstructured optical fibers, and so on. Even though huge progress has been made on development of optical fibers for telecom application, a need for developing special fibers, not necessarily for telecom alone, has arisen. Th...

  6. Mass and charge distributions of amyloid fibers involved in neurodegenerative diseases: mapping heterogeneity and polymorphism† †Electronic supplementary information (ESI) available: Experimental section and supplementary figures. See DOI: 10.1039/c7sc04542e

    Science.gov (United States)

    Pansieri, Jonathan; Halim, Mohammad A.; Vendrely, Charlotte; Dumoulin, Mireille; Legrand, François; Sallanon, Marcelle Moulin; Chierici, Sabine; Denti, Simona; Dagany, Xavier; Dugourd, Philippe; Marquette, Christel

    2018-01-01

    Heterogeneity and polymorphism are generic features of amyloid fibers with some important effects on the related disease development. We report here the characterization, by charge detection mass spectrometry, of amyloid fibers made of three polypeptides involved in neurodegenerative diseases: Aβ1–42 peptide, tau and α-synuclein. Beside the mass of individual fibers, this technique enables to characterize the heterogeneity and the polymorphism of the population. In the case of Aβ1–42 peptide and tau protein, several coexisting species could be distinguished and characterized. In the case of α-synuclein, we show how the polymorphism affects the mass and charge distributions. PMID:29732065

  7. Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon.

    Science.gov (United States)

    Gomes Júnior, Renan Gabriel; Schneider, Carlos Henrique; de Lira, Thatianna; Carvalho, Natália Dayane Moura; Feldberg, Eliana; da Silva, Maria Nazareth Ferreira; Gross, Maria Claudia

    2016-01-01

    Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939), Oecomys bicolor (Tomes, 1860) and Oecomys rutilus (Anthony, 1921). COI sequence analysis grouped Oecomys auyantepui , Oecomys bicolor and Oecomys rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for Oecomys auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while Oecomys bicolor exhibited 2n=80/NFa=142 and Oecomys rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in Oecomys auyantepui . The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.

  8. Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae: comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Renan Gabriel Gomes Junior

    2016-09-01

    Full Text Available Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939, O. bicolor (Tomes, 1860 and O. rutilus (Anthony, 1921. COI sequence analysis grouped O. auyantepui, O. bicolor and O. rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for O. auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while O. bicolor exhibited 2n=80/NFa=142 and O. rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in O. auyantepui. The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.

  9. Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA Genes in Flax (Linum usitatissimum L.

    Directory of Open Access Journals (Sweden)

    Olga Y. Yurkevich

    2017-08-01

    Full Text Available Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH-based chromosomal localization of the CesA conserved fragment (KF011584.1, 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

  10. Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.).

    Science.gov (United States)

    Yurkevich, Olga Y; Kirov, Ilya V; Bolsheva, Nadezhda L; Rachinskaya, Olga A; Grushetskaya, Zoya E; Zoschuk, Svyatoslav A; Samatadze, Tatiana E; Bogdanova, Marina V; Lemesh, Valentina A; Amosova, Alexandra V; Muravenko, Olga V

    2017-01-01

    Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase ( CesA ) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum . Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

  11. cDNA cloning and characterization of the human THRAP2 gene which maps to chromosome 12q24, and its mouse ortholog Thrap2.

    Science.gov (United States)

    Musante, Luciana; Bartsch, Oliver; Ropers, Hans-Hilger; Kalscheuer, Vera M

    2004-05-12

    Characterization of a balanced t(2;12)(q37;q24) translocation in a patient with suspicion of Noonan syndrome revealed that the chromosome 12 breakpoint lies in the vicinity of a novel human gene, thyroid hormone receptor-associated protein 2 (THRAP2). We therefore characterized this gene and its mouse counterpart in more detail. Human and mouse THRAP2/Thrap2 span a genomic region of about 310 and >170 kilobases (kb), and both contain 31 exons. Corresponding transcripts are approximately 9.5 kb long. Their open reading frames code for proteins of 2210 and 2203 amino acids, which are 93% identical. By northern blot analysis, human and mouse THRAP2/Thrap2 genes showed ubiquitous expression. Transcripts were most abundant in human skeletal muscle and in mouse heart. THRAP2 protein is 56% identical to human TRAP240, which belongs to the thyroid hormone receptor associated protein (TRAP) complex and is evolutionary conserved up to yeast. This complex is involved in transcriptional regulation and is believed to serve as adapting interface between regulatory proteins bound to specific DNA sequences and RNA polymerase II.

  12. Scintillating Optical Fiber Imagers for biology

    International Nuclear Information System (INIS)

    Mastrippolito, R.

    1990-01-01

    S.O.F.I (Scintillating Optical Fiber Imager) is a detector developed to replace the autoradiographic films used in molecular biology for the location of radiolabelled ( 32 P) DNA molecules in blotting experiments. It analyses samples on a 25 x 25 cm 2 square area still 25 times faster than autoradiographic films, with a 1.75 and 3 mm resolution for two orthogonal directions. This device performs numerised images with a dynamic upper than 100 which allows the direct quantitation of the analysed samples. First, this thesis describes the S.O.F.I. development (Scintillating Optical Fibers, coding of these fibers and specific electronic for the treatment of the Multi-Anode Photo-Multiplier signals) and experiments made in collaboration with molecular biology laboratories. In a second place, we prove the feasibility of an automatic DNA sequencer issued from S.O.F.I [fr

  13. Comparative mapping of DNA probes derived from the V{sub k} immunoglobulin gene regions on human and great ape chromosomes by fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, N.; Wienberg, J.; Ermert, K. [Universitaet Muenchen (Germany)] [and others

    1995-03-01

    Fluorescence in situ hybridization (FISH) of cosmid clones of human V{sub K} gene regions to human and primate chromosomes contributed to the dating of chromosome reorganizations in evolution. A clone from the K locus at 2p11-p12 (cos 106) hybridized to the assumed homologous chromosome bands in the chimpanzees Pan troglodytes (PTR) and P. paniscus (PPA), the Gorilla gorilla (GGO), and the orangutan Pongo Pygmaeus (PPY). Human and both chimpanzees differed from gorilla and orangutan by the mapping of cos 170, a clone derived from chromosome 2cen-q11.2; the transposition of this orphon to the other side of the centromere can, therefore, be dated after the human/chimpanzee and gorilla divergence. Hybridization to homologous bands was also found with a cosmid clone containing a V{sub K}I orphon located on chromosome 1 (cos 115, main signal at 1q31-q32), although the probe is not fully unique. Also, a clone derived from the orphon V{sub K} region on chromosome 22q11 (cos 121) hybridized to the homologous bands in the great apes. This indicates that the orphons on human chromosomes 1 and 22 had been translocated early in primate evolution. 18 refs., 2 figs.

  14. Spectral staining of tumor tissue by fiber optic FTIR spectroscopy

    Science.gov (United States)

    Salzer, Reiner; Steiner, Gerald; Kano, Angelique; Richter, Tom; Bergmann, Ralf; Rodig, Heike; Johannsen, Bernd; Kobelke, Jens

    2003-07-01

    Infrared (IR) optical fiber have aroused great interest in recent years because of their potential in in-vivo spectroscopy. This potential includes the ability to be flexible, small and to guide IR light in a very large range of wavelengths. Two types - silver halide and chalcogenide - infrared transmitting fibers are investigated in the detection of a malignant tumor. As a test sample for all types of fibers we used a thin section of an entire rat brain with glioblastoma. The fibers were connected with a common infrared microscope. Maps across the whole tissue section with more than 200 spectra were recorded by moving the sample with an XY stage. Data evaluation was performed using fuzzy c-means cluster analysis (FCM). The silver halide fibers provided excellent results. The tumor was clearly discernible from healthy tissue. Chalcogenide fibers are not suitable to distinguish tumor from normal tissue because the fiber has a very low transmittance in the important fingerprint region.

  15. Cloning of a cDNA encoding the rat high molecular weight neurofilament peptide (NF-H): Developmental and tissue expression in the rat, and mapping of its human homologue to chromosomes 1 and 22

    International Nuclear Information System (INIS)

    Lieberburg, I.; Spinner, N.; Snyder, S.

    1989-01-01

    Neurofilaments (NFs) are the intermediate filaments specific to nervous tissue. Three peptides with apparent molecular masses of approximately 68 (NF-L), 145 (NF-M), and 200 (NF-H) kDa appear to be the major components of NF. The expression of these peptides is specific to nervous tissue and is developmentally regulated. Recently, complete cDNAs encoding NF-L and NF-M, and partial cDNAs encoding NF-H, have been described. To better understand the normal pathophysiology of NFs the authors chose to clone the cDNA encoding the rat NF-H peptide. Using monoclonal antibodies that recognized NF-H, they screened a rat brain λgt11 library and identified a clone that contained a 2,100-nucleotide cDNA insert representing the carboxyl-terminal portion of the NF-H protein. Levels of NF-H mRNA varied 20-fold among brain regions, with highest levels in pons/medulla, spinal cord, and cerebellum, and lowest levels in olfactory bulb and hypothalamus. Based on these results, the authors infer that half of the developmental increase and most of the interregional variation in the levels of the NF-H mRNA are mediated through message stabilization. Sequence information revealed that the carboxyl-terminal region of the NF-H peptide contained a unique serine-, proline-, alanine-, glutamic acid-, and lysine-rich repeat. Genomic blots revealed a single copy of the gene in the rat genome and two copies in the human genome. In situ hybridizations performed on human chromosomes mapped the NF-H gene to chromosomes 1 and 22

  16. Development of eddy current probe for fiber orientation assessment in carbon fiber composites

    Science.gov (United States)

    Wincheski, Russell A.; Zhao, Selina

    2018-04-01

    Measurement of the fiber orientation in a carbon fiber composite material is crucial in understanding the load carrying capability of the structure. As manufacturing conditions including resin flow and molding pressures can alter fiber orientation, verification of the as-designed fiber layup is necessary to ensure optimal performance of the structure. In this work, the development of an eddy current probe and data processing technique for analysis of fiber orientation in carbon fiber composites is presented. A proposed directional eddy current probe is modeled and its response to an anisotropic multi-layer conductor simulated. The modeling results are then used to finalize specifications of the eddy current probe. Experimental testing of the fabricated probe is presented for several samples including a truncated pyramid part with complex fiber orientation draped to the geometry for resin transfer molding. The inductively coupled single sided measurement enables fiber orientation characterization through the thickness of the part. The fast and cost-effective technique can be applied as a spot check or as a surface map of the fiber orientations across the structure. This paper will detail the results of the probe design, computer simulations, and experimental results.

  17. BAC-HAPPY mapping (BAP mapping: a new and efficient protocol for physical mapping.

    Directory of Open Access Journals (Sweden)

    Giang T H Vu

    2010-02-01

    Full Text Available Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping, that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS markers spanning approximately 10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual "BAC-HAPPY-mapping" to convert BAC landing data into BAC linkage contigs is possible.

  18. Circle diffeomorphisms forced by expanding circle maps

    NARCIS (Netherlands)

    Homburg, A.J.

    2012-01-01

    We discuss the dynamics of skew product maps defined by circle diffeomorphisms forced by expanding circle maps. We construct an open class of such systems that are robustly topologically mixing and for which almost all points in the same fiber converge under iteration. This property follows from the

  19. Fibered F-Algebra

    OpenAIRE

    Kleyn, Aleks

    2007-01-01

    The concept of F-algebra and its representation can be extended to an arbitrary bundle. We define operations of fibered F-algebra in fiber. The paper presents the representation theory of of fibered F-algebra as well as a comparison of representation of F-algebra and of representation of fibered F-algebra.

  20. Photonic crystal fibers

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper; Hansen, K P; Nielsen, M D

    2003-01-01

    Photonic crystal fibers having a complex microstructure in the transverse plane constitute a new and promising class of optical fibers. Such fibers can either guide light through total internal reflection or the photonic bandgap effect, In this paper, we review the different types and applications...... of photonic crystal fibers with particular emphasis on recent advances in the field....

  1. Photonic crystal fibers -

    DEFF Research Database (Denmark)

    Libori, Stig E. Barkou

    2002-01-01

    . Such micro-structured fibers are the ones most often trated in literature concerning micro-structured fibers. These micro-structured fibers offer a whole range of novel wave guiding characteristics, including the possibility of fibers that guide only one mode irrespective of the frequency of light...

  2. Fiber optic connector

    Science.gov (United States)

    Rajic, Slobodan; Muhs, Jeffrey D.

    1996-01-01

    A fiber optic connector and method for connecting composite materials within which optical fibers are imbedded. The fiber optic connector includes a capillary tube for receiving optical fibers at opposing ends. The method involves inserting a first optical fiber into the capillary tube and imbedding the unit in the end of a softened composite material. The capillary tube is injected with a coupling medium which subsequently solidifies. The composite material is machined to a desired configuration. An external optical fiber is then inserted into the capillary tube after fluidizing the coupling medium, whereby the optical fibers are coupled.

  3. Computer simulation of the 30-nanometer chromatin fiber.

    Science.gov (United States)

    Wedemann, Gero; Langowski, Jörg

    2002-06-01

    A new Monte Carlo model for the structure of chromatin is presented here. Based on our previous work on superhelical DNA and polynucleosomes, it reintegrates aspects of the "solenoid" and the "zig-zag" models. The DNA is modeled as a flexible elastic polymer chain, consisting of segments connected by elastic bending, torsional, and stretching springs. The electrostatic interaction between the DNA segments is described by the Debye-Hückel approximation. Nucleosome core particles are represented by oblate ellipsoids; their interaction potential has been parameterized by a comparison with data from liquid crystals of nucleosome solutions. DNA and chromatosomes are linked either at the surface of the chromatosome or through a rigid nucleosome stem. Equilibrium ensembles of 100-nucleosome chains at physiological ionic strength were generated by a Metropolis-Monte Carlo algorithm. For a DNA linked at the nucleosome stem and a nucleosome repeat of 200 bp, the simulated fiber diameter of 32 nm and the mass density of 6.1 nucleosomes per 11 nm fiber length are in excellent agreement with experimental values from the literature. The experimental value of the inclination of DNA and nucleosomes to the fiber axis could also be reproduced. Whereas the linker DNA connects chromatosomes on opposite sides of the fiber, the overall packing of the nucleosomes leads to a helical aspect of the structure. The persistence length of the simulated fibers is 265 nm. For more random fibers where the tilt angles between two nucleosomes are chosen according to a Gaussian distribution along the fiber, the persistence length decreases to 30 nm with increasing width of the distribution, whereas the other observable parameters such as the mass density remain unchanged. Polynucleosomes with repeat lengths of 212 bp also form fibers with the expected experimental properties. Systems with larger repeat length form fibers, but the mass density is significantly lower than the measured value. The

  4. DNA Protecting Activities of Nymphaea nouchali (Burm. f Flower Extract Attenuate t-BHP-Induced Oxidative Stress Cell Death through Nrf2-Mediated Induction of Heme Oxygenase-1 Expression by Activating MAP-Kinases

    Directory of Open Access Journals (Sweden)

    Md Badrul Alam

    2017-09-01

    Full Text Available This study was performed to investigate the antioxidant activities of Nymphaea nouchali flower (NNF extract and the underlying mechanism using RAW 264.7 cells. The presence of gallic acid, catechin, epicatechin, epigallocatechin, epicatechin gallate, caffeic acid, quercetin, and apigenin in the NNF was confirmed by high-performance liquid chromatography (HPLC. The extract had a very potent capacity to scavenge numerous free radicals. NNF extract was also able to prevent DNA damage and quench cellular reactive oxygen species (ROS generation induced by tert-Butyl hydroperoxide (t-BHP with no signs of toxicity. The NNF extract was able to augment the expression of both primary and phase II detoxifying enzyme, resulting in combat the oxidative stress. This is accomplished by phosphorylation of mitogen-activated protein kinase (MAP kinase (p38 kinase and extracellular signal-regulated kinase (ERK followed by enhancing the nuclear translocation of the nuclear factor erythroid 2-related factor 2 (Nrf2. This attenuates cellular ROS generation and confers protection from cell death. Altogether, the results of current study revealed that Nymphaea nouchali flower could be a source of natural phytochemicals that could lead to the development of new therapeutic agents for preventing oxidative stress associated diseases and attenuating disease progression.

  5. In-Situ Single DNA Manipulation with phi 20nm Electron-Beam-Deposited Probe

    National Research Council Canada - National Science Library

    Fujioka, Sota

    2001-01-01

    .... In this method full-time observation of the manipulation is provided for the purpose of keeping the information about where the isolated DNA fragment used to he located in the original DNA fiber...

  6. Capturing Structural Heterogeneity in Chromatin Fibers.

    Science.gov (United States)

    Ekundayo, Babatunde; Richmond, Timothy J; Schalch, Thomas

    2017-10-13

    Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Nonlinear Photonic Crystal Fibers

    DEFF Research Database (Denmark)

    Hansen, Kim Per

    2004-01-01

    Despite the general recession in the global economy and the collapse of the optical telecommunication market, research within specialty fibers is thriving. This is, more than anything else, due to the technology transition from standard all-glass fibers to photonic crystal fibers, which, instead....... The freedom to design the dispersion profile of the fibers is much larger and it is possible to create fibers, which support only a single spatial mode, regardless of wavelength. In comparison, the standard dispersion-shifted fibers are limited by a much lower index-contrast between the core and the cladding...... in 1996, and are today on their way to become the dominating technology within the specialty fiber field. Whether they will replace the standard fiber in the more traditional areas like telecommunication transmission, is not yet clear, but the nonlinear photonic crystal fibers are here to stay....

  8. Optical Fiber Fusion Splicing

    CERN Document Server

    Yablon, Andrew D

    2005-01-01

    This book is an up-to-date treatment of optical fiber fusion splicing incorporating all the recent innovations in the field. It provides a toolbox of general strategies and specific techniques that the reader can apply when optimizing fusion splices between novel fibers. It specifically addresses considerations important for fusion splicing of contemporary specialty fibers including dispersion compensating fiber, erbium-doped gain fiber, polarization maintaining fiber, and microstructured fiber. Finally, it discusses the future of optical fiber fusion splicing including silica and non-silica based optical fibers as well as the trend toward increasing automation. Whilst serving as a self-contained reference work, abundant citations from the technical literature will enable readers to readily locate primary sources.

  9. Using AFM to probe the complexation of DNA with anionic lipids mediated by Ca(2+): the role of surface pressure.

    Science.gov (United States)

    Luque-Caballero, Germán; Martín-Molina, Alberto; Sánchez-Treviño, Alda Yadira; Rodríguez-Valverde, Miguel A; Cabrerizo-Vílchez, Miguel A; Maldonado-Valderrama, Julia

    2014-04-28

    Complexation of DNA with lipids is currently being developed as an alternative to classical vectors based on viruses. Most of the research to date focuses on cationic lipids owing to their spontaneous complexation with DNA. Nonetheless, recent investigations have revealed that cationic lipids induce a large number of adverse effects on DNA delivery. Precisely, the lower cytotoxicity of anionic lipids accounts for their use as a promising alternative. However, the complexation of DNA with anionic lipids (mediated by cations) is still in early stages and is not yet well understood. In order to explore the molecular mechanisms underlying the complexation of anionic lipids and DNA we proposed a combined methodology based on the surface pressure-area isotherms, Gibbs elasticity and Atomic Force Microscopy (AFM). These techniques allow elucidation of the role of the surface pressure in the complexation and visualization of the interfacial aggregates for the first time. We demonstrate that the DNA complexes with negatively charged model monolayers (DPPC/DPPS 4 : 1) only in the presence of Ca(2+), but is expelled at very high surface pressures. Also, according to the Gibbs elasticity plot, the complexation of lipids and DNA implies a whole fluidisation of the monolayer and a completely different phase transition map in the presence of DNA and Ca(2+). AFM imaging allows identification for the first time of specific morphologies associated with different packing densities. At low surface coverage, a branched net like structure is observed whereas at high surface pressure fibers formed of interfacial aggregates appear. In summary, Ca(2+) mediates the interaction between DNA and negatively charged lipids and also the conformation of the ternary system depends on the surface pressure. Such observations are important new generic features of the interaction between DNA and anionic lipids.

  10. Single Molecule Scanning of DNA Radiation Oxidative Damage, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This proposal will develop an assay to map genomic DNA, at the single molecule level and in a nanodevice, for oxidative DNA damage arising from radiation exposure;...

  11. Ceramic fiber reinforced filter

    Science.gov (United States)

    Stinton, David P.; McLaughlin, Jerry C.; Lowden, Richard A.

    1991-01-01

    A filter for removing particulate matter from high temperature flowing fluids, and in particular gases, that is reinforced with ceramic fibers. The filter has a ceramic base fiber material in the form of a fabric, felt, paper of the like, with the refractory fibers thereof coated with a thin layer of a protective and bonding refractory applied by chemical vapor deposition techniques. This coating causes each fiber to be physically joined to adjoining fibers so as to prevent movement of the fibers during use and to increase the strength and toughness of the composite filter. Further, the coating can be selected to minimize any reactions between the constituents of the fluids and the fibers. A description is given of the formation of a composite filter using a felt preform of commercial silicon carbide fibers together with the coating of these fibers with pure silicon carbide. Filter efficiency approaching 100% has been demonstrated with these filters. The fiber base material is alternately made from aluminosilicate fibers, zirconia fibers and alumina fibers. Coating with Al.sub.2 O.sub.3 is also described. Advanced configurations for the composite filter are suggested.

  12. Steel fiber reinforced concrete

    International Nuclear Information System (INIS)

    Baloch, S.U.

    2005-01-01

    Steel-Fiber Reinforced Concrete is constructed by adding short fibers of small cross-sectional size .to the fresh concrete. These fibers reinforce the concrete in all directions, as they are randomly oriented. The improved mechanical properties of concrete include ductility, impact-resistance, compressive, tensile and flexural strength and abrasion-resistance. These uniqlte properties of the fiber- reinforcement can be exploited to great advantage in concrete structural members containing both conventional bar-reinforcement and steel fibers. The improvements in mechanical properties of cementitious materials resulting from steel-fiber reinforcement depend on the type, geometry, volume fraction and material-properties of fibers, the matrix mix proportions and the fiber-matrix interfacial bond characteristics. Effects of steel fibers on the mechanical properties of concrete have been investigated in this paper through a comprehensive testing-programme, by varying the fiber volume fraction and the aspect-ratio (Lid) of fibers. Significant improvements are observed in compressive, tensile, flexural strength and impact-resistance of concrete, accompanied by marked improvement in ductility. optimum fiber-volume fraction and aspect-ratio of steel fibers is identified. Test results are analyzed in details and relevant conclusions drawn. The research is finally concluded with future research needs. (author)

  13. Fiber optics in adverse environments

    International Nuclear Information System (INIS)

    Lyous, P.B.

    1982-01-01

    Radiation effects in optical fibers are considered, taking into account recent progress in the investigation of radiation resistant optical fibers, radiation damage in optical fibers, radiation-induced transient absorption in optical fibers, X-ray-induced transient attenuation at low temperatures in polymer clad silica (PCS) fibers, optical fiber composition and radiation hardness, the response of irradiated optical waveguides at low temperatures, and the effect of ionizing radiation on fiber-optic waveguides. Other topics explored are related to environmental effects on components of fiber optic systems, and radiation detection systems using optical fibers. Fiber optic systems in adverse environments are also discussed, giving attention to the survivability of Army fiber optics systems, space application of fiber optics systems, fiber optic wavelength multiplexing for civil aviation applications, a new fiber optic data bus topology, fiber optics for aircraft engine/inlet control, and application of fiber optics in high voltage substations

  14. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  15. Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Linskens, Maarten H.K.; Huberman, Joel A.

    1988-01-01

    Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the

  16. Fiber Optics Technology.

    Science.gov (United States)

    Burns, William E.

    1986-01-01

    Discusses various applications of fiber optics technology: information systems, industrial robots, medicine, television, transportation, and training. Types of jobs that will be available with fiber optics training (such as electricians and telephone cable installers and splicers) are examined. (CT)

  17. Fiber Optics Instrumentation Development

    Science.gov (United States)

    Chan, Patrick Hon Man; Parker, Allen R., Jr.; Richards, W. Lance

    2010-01-01

    This is a general presentation of fiber optics instrumentation development work being conducted at NASA Dryden for the past 10 years and recent achievements in the field of fiber optics strain sensors.

  18. Shaped fiber composites

    Science.gov (United States)

    Kinnan, Mark K.; Roach, Dennis P.

    2017-12-05

    A composite article is disclosed that has non-circular fibers embedded in a polymer matrix. The composite article has improved damage tolerance, toughness, bending, and impact resistance compared to composites having traditional round fibers.

  19. Advances in Fiber Lasers

    National Research Council Canada - National Science Library

    Morse, T

    1999-01-01

    Most of the time of this contract has been devoted toward improvements in optical fiber lasers and toward gathering experience to improve our program in high power, cladding pumped optical fiber lasers...

  20. A fiber orientation-adapted integration scheme for computing the hyperelastic Tucker average for short fiber reinforced composites

    Science.gov (United States)

    Goldberg, Niels; Ospald, Felix; Schneider, Matti

    2017-10-01

    In this article we introduce a fiber orientation-adapted integration scheme for Tucker's orientation averaging procedure applied to non-linear material laws, based on angular central Gaussian fiber orientation distributions. This method is stable w.r.t. fiber orientations degenerating into planar states and enables the construction of orthotropic hyperelastic energies for truly orthotropic fiber orientation states. We establish a reference scenario for fitting the Tucker average of a transversely isotropic hyperelastic energy, corresponding to a uni-directional fiber orientation, to microstructural simulations, obtained by FFT-based computational homogenization of neo-Hookean constituents. We carefully discuss ideas for accelerating the identification process, leading to a tremendous speed-up compared to a naive approach. The resulting hyperelastic material map turns out to be surprisingly accurate, simple to integrate in commercial finite element codes and fast in its execution. We demonstrate the capabilities of the extracted model by a finite element analysis of a fiber reinforced chain link.

  1. Hierarchically Structured Electrospun Fibers

    Science.gov (United States)

    2013-01-07

    in the natural lotus and silver ragwort leaves. Figure 4. Examples of electrospun bio-mimics of natural hierarchical structures. (A) Lotus leaf...B) pillared poly(methyl methacrylate) (PMMA) electrospun fiber mimic; (C) silver ragwort leaf; (D) electrospun fiber mimic made from nylon 6 and...domains containing the protein in the surrounding EVA fibers [115]. A wide variety of core-shell fibers have been generated, including PCL/ gelatin

  2. Superlattice Microstructured Optical Fiber

    Science.gov (United States)

    Tse, Ming-Leung Vincent; Liu, Zhengyong; Cho, Lok-Hin; Lu, Chao; Wai, Ping-Kong Alex; Tam, Hwa-Yaw

    2014-01-01

    A generic three-stage stack-and-draw method is demonstrated for the fabrication of complex-microstructured optical fibers. We report the fabrication and characterization of a silica superlattice microstructured fiber with more than 800 rhomboidally arranged air-holes. A polarization-maintaining fiber with a birefringence of 8.5 × 10−4 is demonstrated. The birefringent property of the fiber is found to be highly insensitive to external environmental effects, such as pressure. PMID:28788693

  3. High-fiber foods

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/patientinstructions/000193.htm High-fiber foods To use the sharing features on this page, ... Read food labels carefully to see how much fiber they have. Choose foods that have higher amounts of fiber, such as ...

  4. Resonant filtered fiber amplifiers

    DEFF Research Database (Denmark)

    Alkeskjold, Thomas Tanggaard; Laurila, Marko; Olausson, Christina Bjarnal Thulin

    2013-01-01

    In this paper we present our recent result on utilizing resonant/bandgap fiber designs to achieve high performance ytterbium doped fiber amplifers for achieving diffraction limited beam quality in large mode area fibers, robust bending performance and gain shaping for long wavelength operation...

  5. Fiber Singular Optics

    OpenAIRE

    A. V. Volyar

    2002-01-01

    The present review is devoted to the optical vortex behavior both in free space and optical fibers. The processes of the vortex transformations in perturbed optical fibers are analyzed on the base of the operator of the spin – orbit interaction in order to forecast the possible ways of manufacturing the vortex preserving fibers and their applications in supersensitive optical devices.

  6. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  7. DETECTION OF DNA DAMAGE USING A FIBEROPTIC BIOSENSOR

    Science.gov (United States)

    A rapid and sensitive fiber optic biosensor assay for radiation-induced DNA damage is reported. For this assay, a biotin-labeled capture oligonucleotide (38 mer) was immobilized to an avidin-coated quartz fiber. Hybridization of a dye-labeled complementary sequence was observed...

  8. Hole-assisted fiber based fiber fuse terminator supporting 22 W input

    Science.gov (United States)

    Tsujikawa, Kyozo; Kurokawa, Kenji; Hanzawa, Nobutomo; Nozoe, Saki; Matsui, Takashi; Nakajima, Kazuhide

    2018-05-01

    We investigated the air hole structure in hole-assisted fiber (HAF) with the aim of terminating fiber fuse propagation. We focused on two structural parameters c/MFD and S1/S2, which are related respectively to the position and area of the air holes, and mapped their appropriate values for terminating fiber fuse propagation. Here, MFD is the mode field diameter, c is the diameter of an inscribed circle linking the air holes, S1 is the total area of the air holes, and S2 is the area of a circumscribed circle linking the air holes. On the basis of these results, we successfully realized a compact fiber fuse terminator consisting of a 1.35 mm-long HAF, which can terminate fiber fuse propagation even with a 22 W input. In addition, we observed fiber fuse termination using a high-speed camera. We additionally confirmed that the HAF-based fiber fuse terminator is effective under various input power conditions. The penetration length of the optical discharge in the HAF was only less than 300 μm when the input power was from 2 to 22 W.

  9. Superconducting tin core fiber

    International Nuclear Information System (INIS)

    Homa, Daniel; Liang, Yongxuan; Hill, Cary; Kaur, Gurbinder; Pickrell, Gary

    2015-01-01

    In this study, we demonstrated superconductivity in a fiber with a tin core and fused silica cladding. The fibers were fabricated via a modified melt-draw technique and maintained core diameters ranging from 50-300 microns and overall diameters of 125-800 microns. Superconductivity of this fiber design was validated via the traditional four-probe test method in a bath of liquid helium at temperatures on the order of 3.8 K. The synthesis route and fiber design are perquisites to ongoing research dedicated all-fiber optoelectronics and the relationships between superconductivity and the material structures, as well as corresponding fabrication techniques. (orig.)

  10. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

  11. Airclad fiber laser technology

    DEFF Research Database (Denmark)

    Hansen, Kim P.; Olausson, Christina Bjarnal Thulin; Broeng, Jes

    2011-01-01

    High-power fiber lasers and amplifiers have gained tremendous momentum in the last 5 years. Many of the traditional manufacturers of gas and solid-state lasers are now pursuing the fiber-based systems, which are displacing the conventional technology in many areas. High-power fiber laser systems...... require reliable fibers with large cores, stable mode quality, and good power handling capabilities-requirements that are all met by the airclad fiber technology. In the present paper we go through many of the building blocks needed to build high-power systems and we show an example of a complete airclad...... laser system. We present the latest advancements within airclad fiber technology including a new 100 m single-mode polarization-maintaining rod-type fiber capable of amplifying to megawatt power levels. Furthermore, we describe the novel airclad-based pump combiners and their use in a completely...

  12. Airclad fiber laser technology

    DEFF Research Database (Denmark)

    Hansen, Kim P.; Olausson, Christina Bjarnal Thulin; Broeng, Jes

    2008-01-01

    High-power fiber lasers and amplifiers have gained tremendous momentum in the last five years, and many of the traditional manufactures of gas and solid-state lasers are pursuing the attractive fiber-based systems, which are now displacing the old technology in many areas. High-power fiber laser...... systems require specially designed fibers with large cores and good power handling capabilities - requirements that are all met by the airclad fiber technology. In the present paper we go through many of the building blocks needed to build high-power systems and we show an example of a complete airclad...... laser system. We present the latest advancements within airclad fiber technology including a new 70 μm single-mode polarization-maintaining rod-type fiber capable of amplifying to MW power levels. Furthermore we describe the novel airclad based pump combiners and their use in a completely monolithic 350...

  13. Physical mapping of the 5S and 18S rDNA in ten species of Hypostomus Lacépède 1803 (Siluriformes: Loricariidae): evolutionary tendencies in the genus.

    Science.gov (United States)

    Bueno, Vanessa; Venere, Paulo César; Thums Konerat, Jocicléia; Zawadzki, Cláudio Henrique; Vicari, Marcelo Ricardo; Margarido, Vladimir Pavan

    2014-01-01

    Hypostomus is a diverse group with unclear aspects regarding its biology, including the mechanisms that led to chromosome diversification within the group. Fluorescence in situ hybridization (FISH) with 5S and 18S rDNA probes was performed on ten Hypostomini species. Hypostomus faveolus, H. cochliodon, H. albopunctatus, H. aff. paulinus, and H. topavae had only one chromosome pair with 18S rDNA sites, while H. ancistroides, H. commersoni, H. hermanni, H. regani, and H. strigaticeps had multiple 18S rDNA sites. Regarding the 5S rDNA genes, H. ancistroides, H. regani, H. albopunctatus, H. aff. paulinus, and H. topavae had 5S rDNA sites on only one chromosome pair and H. faveolus, H. cochliodon, H. commersoni, H. hermanni, and H. strigaticeps had multiple 5S rDNA sites. Most species had 18S rDNA sites in the telomeric region of the chromosomes. All species but H. cochliodon had 5S rDNA in the centromeric/pericentromeric region of one metacentric pair. Obtained results are discussed based on existent phylogenies for the genus, with comments on possible dispersion mechanisms to justify the variability of the rDNA sites in Hypostomus.

  14. Physical Mapping of the 5S and 18S rDNA in Ten Species of Hypostomus Lacépède 1803 (Siluriformes: Loricariidae: Evolutionary Tendencies in the Genus

    Directory of Open Access Journals (Sweden)

    Vanessa Bueno

    2014-01-01

    Full Text Available Hypostomus is a diverse group with unclear aspects regarding its biology, including the mechanisms that led to chromosome diversification within the group. Fluorescence in situ hybridization (FISH with 5S and 18S rDNA probes was performed on ten Hypostomini species. Hypostomus faveolus, H. cochliodon, H. albopunctatus, H. aff. paulinus, and H. topavae had only one chromosome pair with 18S rDNA sites, while H. ancistroides, H. commersoni, H. hermanni, H. regani, and H. strigaticeps had multiple 18S rDNA sites. Regarding the 5S rDNA genes, H. ancistroides, H. regani, H. albopunctatus, H. aff. paulinus, and H. topavae had 5S rDNA sites on only one chromosome pair and H. faveolus, H. cochliodon, H. commersoni, H. hermanni, and H. strigaticeps had multiple 5S rDNA sites. Most species had 18S rDNA sites in the telomeric region of the chromosomes. All species but H. cochliodon had 5S rDNA in the centromeric/pericentromeric region of one metacentric pair. Obtained results are discussed based on existent phylogenies for the genus, with comments on possible dispersion mechanisms to justify the variability of the rDNA sites in Hypostomus.

  15. Hot Springs-Garrison Fiber Optic Project

    International Nuclear Information System (INIS)

    1994-10-01

    Bonneville Power Administration (BPA) is proposing to upgrade its operational telecommunications system between the Hot Springs Substation and the Garrison Substation using a fiber optic system. The project would primarily involve installing 190 kilometers (120 miles) of fiber optic cable on existing transmission structures and installing new fiber optic equipment in BPA's substation yards and control houses. BPA prepared an environmental assessment (EA) evaluating the proposed action. This EA was published in October 1994. The EA identifies a number of minor impacts that might occur as a result of the proposed action, as well as some recommended mitigation measures. This Mitigation Action Plan (MAP) identifies specific measures to avoid, minimize, or compensate for impacts identified in the EA

  16. Hot Springs-Garrison Fiber Optic Project

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-01

    Bonneville Power Administration (BPA) is proposing to upgrade its operational telecommunications system between the Hot Springs Substation and the Garrison Substation using a fiber optic system. The project would primarily involve installing 190 kilometers (120 miles) of fiber optic cable on existing transmission structures and installing new fiber optic equipment in BPA`s substation yards and control houses. BPA prepared an environmental assessment (EA) evaluating the proposed action. This EA was published in October 1994. The EA identifies a number of minor impacts that might occur as a result of the proposed action, as well as some recommended mitigation measures. This Mitigation Action Plan (MAP) identifies specific measures to avoid, minimize, or compensate for impacts identified in the EA.

  17. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  18. Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles

    Directory of Open Access Journals (Sweden)

    Boussaha Mekki

    2006-05-01

    Full Text Available Abstract Background The Fragile Histidine Triad gene (FHIT is an oncosuppressor implicated in many human cancers, including vesical tumors. FHIT is frequently hit by deletions caused by fragility at FRA3B, the most active of human common fragile sites, where FHIT lays. Vesical tumors affect also cattle, including animals grazing in the wild on bracken fern; compounds released by the fern are known to induce chromosome fragility and may trigger cancer with the interplay of latent Papilloma virus. Results The bovine FHIT was characterized by assembling a contig of 78 BACs. Sequence tags were designed on human exons and introns and used directly to select bovine BACs, or compared with sequence data in the bovine genome database or in the trace archive of the bovine genome sequencing project, and adapted before use. FHIT is split in ten exons like in man, with exons 5 to 9 coding for a 149 amino acids protein. VISTA global alignments between bovine genomic contigs retrieved from the bovine genome database and the human FHIT region were performed. Conservation was extremely high over a 2 Mb region spanning the whole FHIT locus, including the size of introns. Thus, the bovine FHIT covers about 1.6 Mb compared to 1.5 Mb in man. Expression was analyzed by RT-PCR and Northern blot, and was found to be ubiquitous. Four cDNA isoforms were isolated and sequenced, that originate from an alternative usage of three variants of exon 4, revealing a size very close to the major human FHIT cDNAs. Conclusion A comparative genomic approach allowed to assemble a contig of 78 BACs and to completely annotate a 1.6 Mb region spanning the bovine FHIT gene. The findings confirmed the very high level of conservation between human and bovine genomes and the importance of comparative mapping to speed the annotation process of the recently sequenced bovine genome. The detailed knowledge of the genomic FHIT region will allow to study the role of FHIT in bovine cancerogenesis

  19. Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

    Science.gov (United States)

    Uboldi, Cristina; Guidi, Elena; Roperto, Sante; Russo, Valeria; Roperto, Franco; Di Meo, Giulia Pia; Iannuzzi, Leopoldo; Floriot, Sandrine; Boussaha, Mekki; Eggen, André; Ferretti, Luca

    2006-05-23

    The Fragile Histidine Triad gene (FHIT) is an oncosuppressor implicated in many human cancers, including vesical tumors. FHIT is frequently hit by deletions caused by fragility at FRA3B, the most active of human common fragile sites, where FHIT lays. Vesical tumors affect also cattle, including animals grazing in the wild on bracken fern; compounds released by the fern are known to induce chromosome fragility and may trigger cancer with the interplay of latent Papilloma virus. The bovine FHIT was characterized by assembling a contig of 78 BACs. Sequence tags were designed on human exons and introns and used directly to select bovine BACs, or compared with sequence data in the bovine genome database or in the trace archive of the bovine genome sequencing project, and adapted before use. FHIT is split in ten exons like in man, with exons 5 to 9 coding for a 149 amino acids protein. VISTA global alignments between bovine genomic contigs retrieved from the bovine genome database and the human FHIT region were performed. Conservation was extremely high over a 2 Mb region spanning the whole FHIT locus, including the size of introns. Thus, the bovine FHIT covers about 1.6 Mb compared to 1.5 Mb in man. Expression was analyzed by RT-PCR and Northern blot, and was found to be ubiquitous. Four cDNA isoforms were isolated and sequenced, that originate from an alternative usage of three variants of exon 4, revealing a size very close to the major human FHIT cDNAs. A comparative genomic approach allowed to assemble a contig of 78 BACs and to completely annotate a 1.6 Mb region spanning the bovine FHIT gene. The findings confirmed the very high level of conservation between human and bovine genomes and the importance of comparative mapping to speed the annotation process of the recently sequenced bovine genome. The detailed knowledge of the genomic FHIT region will allow to study the role of FHIT in bovine cancerogenesis, especially of vesical papillomavirus-associated cancers of

  20. Hierarchically Structured Electrospun Fibers

    Directory of Open Access Journals (Sweden)

    Nicole E. Zander

    2013-01-01

    Full Text Available Traditional electrospun nanofibers have a myriad of applications ranging from scaffolds for tissue engineering to components of biosensors and energy harvesting devices. The generally smooth one-dimensional structure of the fibers has stood as a limitation to several interesting novel applications. Control of fiber diameter, porosity and collector geometry will be briefly discussed, as will more traditional methods for controlling fiber morphology and fiber mat architecture. The remainder of the review will focus on new techniques to prepare hierarchically structured fibers. Fibers with hierarchical primary structures—including helical, buckled, and beads-on-a-string fibers, as well as fibers with secondary structures, such as nanopores, nanopillars, nanorods, and internally structured fibers and their applications—will be discussed. These new materials with helical/buckled morphology are expected to possess unique optical and mechanical properties with possible applications for negative refractive index materials, highly stretchable/high-tensile-strength materials, and components in microelectromechanical devices. Core-shell type fibers enable a much wider variety of materials to be electrospun and are expected to be widely applied in the sensing, drug delivery/controlled release fields, and in the encapsulation of live cells for biological applications. Materials with a hierarchical secondary structure are expected to provide new superhydrophobic and self-cleaning materials.

  1. Participatory Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    2016-01-01

    practice. In particular, mapping environmental damage, endangered species, and human-made disasters has become one focal point for environmental knowledge production. This type of digital map has been highlighted as a processual turn in critical cartography, whereas in related computational journalism...... of a geo-visualization within information mapping that enhances embodiment in the experience of the information. InfoAmazonia is defined as a digitally created map-space within which journalistic practice can be seen as dynamic, performative interactions between journalists, ecosystems, space, and species...

  2. Selective muscle fiber loss and molecular compensation in mitochondrial myopathy due to TK2 deficiency.

    Science.gov (United States)

    Vilà, Maya R; Villarroya, Joan; García-Arumí, Elena; Castellote, Amparo; Meseguer, Anna; Hirano, Michio; Roig, Manuel

    2008-04-15

    A 12-year-old patient with mitochondrial DNA (mtDNA) depletion syndrome due to TK2 gene mutations has been evaluated serially over the last 10 years. We observed progressive muscle atrophy with selective loss of type 2 muscle fibers and, despite severe depletion of mtDNA, normal activities of respiratory chain (RC) complexes and levels of COX II mitochondrial protein in the remaining muscle fibers. These results indicate that compensatory mechanisms account for the slow progression of the disease. Identification of factors that ameliorate mtDNA depletion may reveal new therapeutic targets for these devastating disorders.

  3. Microbial genome sequencing using optical mapping and Illumina sequencing

    Science.gov (United States)

    Introduction Optical mapping is a technique in which strands of genomic DNA are digested with one or more restriction enzymes, and a physical map of the genome constructed from the resulting image. In outline, genomic DNA is extracted from a pure culture, linearly arrayed on a specialized glass sli...

  4. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  5. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  6. Fiber optics in SHIVA

    International Nuclear Information System (INIS)

    Severyn, J.; Parker, J.

    1978-01-01

    SHIVA is a twenty arm laser which is controlled with a network of fifty computers, interconnected with digital fiber optic links. Three different fiber optic systems employed on the Shiva laser will be described. Two of the systems are for digital communications, one at 9600 baud and the other at 1 megabaud. The third system uses fiber optics to distribute diagnostic triggers with subnanosecond jitter

  7. Continuous Fiber Ceramic Composites

    Energy Technology Data Exchange (ETDEWEB)

    Fareed, Ali [Honeywell Advanced Composites Inc. (HACI), Newark, DE (United States); Craig, Phillip A. [Honeywell Advanced Composites Inc. (HACI), Newark, DE (United States)

    2002-09-01

    Fiber-reinforced ceramic composites demonstrate the high-temperature stability of ceramics--with an increased fracture toughness resulting from the fiber reinforcement of the composite. The material optimization performed under the continuous fiber ceramic composites (CFCC) included a series of systematic optimizations. The overall goals were to define the processing window, to increase the robustinous of the process, to increase process yield while reducing costs, and to define the complexity of parts that could be fabricated.

  8. Stochastic phenomena in a fiber Raman amplifier

    Energy Technology Data Exchange (ETDEWEB)

    Kalashnikov, Vladimir [Aston Institute of Photonic Technologies, Aston University, Birmingham (United Kingdom); Institute of Photonics, Vienna University of Technology (Austria); Sergeyev, Sergey V. [Aston Institute of Photonic Technologies, Aston University, Birmingham (United Kingdom); Ania-Castanon, Juan Diego [Instituto de Optica CSIC, Madrid (Spain); Jacobsen, Gunnar [Acreo, Kista (Sweden); Popov, Sergei [Royal Institute of Technology (KTH), Stockholm (Sweden)

    2017-01-15

    The interplay of such cornerstones of modern nonlinear fiber optics as a nonlinearity, stochasticity and polarization leads to variety of the noise induced instabilities including polarization attraction and escape phenomena harnessing of which is a key to unlocking the fiber optic systems specifications required in high resolution spectroscopy, metrology, biomedicine and telecommunications. Here, by using direct stochastic modeling, the mapping of interplay of the Raman scattering-based nonlinearity, the random birefringence of a fiber, and the pump-to-signal intensity noise transfer has been done in terms of the fiber Raman amplifier parameters, namely polarization mode dispersion, the relative intensity noise of the pump laser, fiber length, and the signal power. The obtained results reveal conditions for emergence of the random birefringence-induced resonance-like enhancement of the gain fluctuations (stochastic anti-resonance) accompanied by pulse broadening and rare events in the form of low power output signals having probability heavily deviated from the Gaussian distribution. (copyright 2016 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Agave Americana Leaf Fibers

    Directory of Open Access Journals (Sweden)

    Ashish Hulle

    2015-02-01

    Full Text Available The growing environmental problems, the problem of waste disposal and the depletion of non-renewable resources have stimulated the use of green materials compatible with the environment to reduce environmental impacts. Therefore, there is a need to design products by using natural resources. Natural fibers seem to be a good alternative since they are abundantly available and there are a number of possibilities to use all the components of a fiber-yielding crop; one such fiber-yielding plant is Agave Americana. The leaves of this plant yield fibers and all the parts of this plant can be utilized in many applications. The “zero-waste” utilization of the plant would enable its production and processing to be translated into a viable and sustainable industry. Agave Americana fibers are characterized by low density, high tenacity and high moisture absorbency in comparison with other leaf fibers. These fibers are long and biodegradable. Therefore, we can look this fiber as a sustainable resource for manufacturing and technical applications. Detailed discussion is carried out on extraction, characterization and applications of Agave Americana fiber in this paper.

  10. Concept Mapping

    Science.gov (United States)

    Technology & Learning, 2005

    2005-01-01

    Concept maps are graphical ways of working with ideas and presenting information. They reveal patterns and relationships and help students to clarify their thinking, and to process, organize and prioritize. Displaying information visually--in concept maps, word webs, or diagrams--stimulates creativity. Being able to think logically teaches…

  11. DNA adducts in senescent cells

    International Nuclear Information System (INIS)

    Gaubatz, J.W.

    1987-01-01

    Perturbations in DNA repair and other metabolic processes during development and aging might affect the steady-state level of genomic damage. The persistence or accumulation of DNA lesions in postmitotic cells could have a significant impact on proper cellular function, interfering with gene regulation for example. To test the notion that DNA damage increases as a function of age in non-dividing cells, DNA was purified from heart tissue of C57BL/6Nia mice at different ages and analyzed by post labeling techniques to detect DNA adducts. In the present experiments, four-dimensional, thin-layer chromatography was used to isolate aromatic adducts that were labeled with carrier-free (γ- 32 P) ATP under DNA-P excess conditions. The complexity and frequency of aromatic adducts varied between DNA samples. Several adducts were present in all preparations and were clearly more abundant in nucleotide maps of mature and old heart DNA. However, a direct correlation with age was not observed. In contrast, experiments in which aromatic adducts were first isolated by phase-transfer to 1-butanol, then labeled with excess (γ- 32 P)ATP indicated that there was an age-related increase in these adducts. The results are consistent with their earlier studies that showed alkyl adducts increased during aging of mouse myocardium and suggest that a common repair pathway might be involved

  12. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  13. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  14. Geometric phases in singlemode fiber lightguides and fiber ring interferometers

    International Nuclear Information System (INIS)

    Malykin, Grigorii B; Pozdnyakova, Vera I

    2004-01-01

    We consider various geometric phases (GPs) in singlemode fiber lightguides (SMFs) and in fiber ring interferometers (FRIs): the Pancharatnam phase stemming from the cyclic evolution of the polarization state of radiation (RP state) in SMF, the Rytov-Vladimirskii phase (RV phase) stemming from the Rytov effect (specifically, rotation of the polarization plane due to noncoplanar winding of SMFs), as well as the nonreciprocal phase difference of counterpropagating waves (NPDCW) and nonreciprocal geometric phase of counterpropagating waves (NGPCW), which are caused by polarization nonreciprocity (PN) in FRIs. We show that in the general case, the Pancharatnam phase for an arbitrary RP state is inconsistent with the real phase change of light fluctuations in media that possess not only circular but also linear birefringence. We show that the RV phase, having a geometric origin, can in principle be considered as a dynamic phase (DP). We also show that the NGPCW can be considered as an effect of the evolution of the RP state mapped on the Poincare sphere in Ginzburg's orthogonal screw polarization modes (GSPMs) of SMFs in the FRI contour. We analyze a number of experiments in which geometric phases were detected in FRIs: changing the RV phase and Rytov's angle (RA) in response to change of the pitch of helicoidal winding of SMFs. (methodological notes)

  15. USDA Flax fiber utilization research

    Science.gov (United States)

    The United States is pursuing natural fibers as sustainable, environmentally friendly sources for a variety of industrial applications. Flax (Linum usitatissimum L.) fiber offers many possibilities towards this goal. Research on flax fiber production, processing, and standards development is urgen...

  16. Ultrafine PBI fibers and yarns

    Science.gov (United States)

    Leal, J. R.; Tan, M.

    1979-01-01

    Gentle precisely controlled process is used to draw polybenzimidazole (PBI) fibers to denier as low as 0.17 per fiber. Yarns of lightweight fibers could be useful in applications where lightweight textiles must withstand high temperatures, corrosion, or radiation.

  17. Directed Formation of DNA Nanoarrays through Orthogonal Self-Assembly

    Directory of Open Access Journals (Sweden)

    Eugen Stulz

    2011-06-01

    Full Text Available We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II and Ni(II induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.

  18. Applications of nonlinear fiber optics

    CERN Document Server

    Agrawal, Govind

    2008-01-01

    * The only book describing applications of nonlinear fiber optics * Two new chapters on the latest developments: highly nonlinear fibers and quantum applications* Coverage of biomedical applications* Problems provided at the end of each chapterThe development of new highly nonlinear fibers - referred to as microstructured fibers, holey fibers and photonic crystal fibers - is the next generation technology for all-optical signal processing and biomedical applications. This new edition has been thoroughly updated to incorporate these key technology developments.The bo

  19. Inhibition of DNA replication by ultraviolet light

    International Nuclear Information System (INIS)

    Edenberg, H.J.

    1976-01-01

    DNA replication in ultraviolet-irradiated HeLa cells was studied by two different techniques: measurements of the kinetics of semiconservative DNA synthesis, and DNA fiber autoradiography. In examining the kinetics of semiconservative DNA synthesis, density label was used to avoid measuring the incorporation due to repair replication. The extent of inhibition varied with time. After doses of less than 10 J/m 2 the rate was initially depressed but later showed some recovery. After higher doses, a constant, low rate of synthesis was seen for at least the initial 6 h. An analysis of these data indicated that the inhibition of DNA synthesis could be explained by replication forks halting at pyrimidine dimers. DNA fiber autoradiography was used to further characterize replication after ultraviolet irradiation. The average length of labeled segments in irradiated cells increased in the time immediately after irradiation, and then leveled off. This is the predicted pattern if DNA synthesis in each replicon continued at its previous rate until a lesion is reached, and then halted. The frequency of lesions that block synthesis is approximately the same as the frequency of pyrimidine dimers

  20. Mapping racism.

    Science.gov (United States)

    Moss, Donald B

    2006-01-01

    The author uses the metaphor of mapping to illuminate a structural feature of racist thought, locating the degraded object along vertical and horizontal axes. These axes establish coordinates of hierarchy and of distance. With the coordinates in place, racist thought begins to seem grounded in natural processes. The other's identity becomes consolidated, and parochialism results. The use of this kind of mapping is illustrated via two patient vignettes. The author presents Freud's (1905, 1927) views in relation to such a "mapping" process, as well as Adorno's (1951) and Baldwin's (1965). Finally, the author conceptualizes the crucial status of primitivity in the workings of racist thought.

  1. Multimode optical fiber

    Science.gov (United States)

    Bigot-Astruc, Marianne; Molin, Denis; Sillard, Pierre

    2014-11-04

    A depressed graded-index multimode optical fiber includes a central core, an inner depressed cladding, a depressed trench, an outer depressed cladding, and an outer cladding. The central core has an alpha-index profile. The depressed claddings limit the impact of leaky modes on optical-fiber performance characteristics (e.g., bandwidth, core size, and/or numerical aperture).

  2. Fiber Lasers V

    DEFF Research Database (Denmark)

    Hansen, Kim P.; Olausson, Christina Bjarnal Thulin; Broeng, Jes

    2008-01-01

    laser system. We present the latest advancements within airclad fiber technology including a new 70 μm single-mode polarization-maintaining rod-type fiber capable of amplifying to MW power levels. Furthermore we describe the novel airclad based pump combiners and their use in a completely monolithic 350...

  3. Fiber Sensor Technology Today

    Science.gov (United States)

    Hotate, Kazuo

    2006-08-01

    Fiber sensor technologies are overviewed. Since the early 1970s, this field has been developed, on the basis of the same devices and photonic principles as fiber communication technologies. Besides simple configurations, in which the fiber acts only as a data transmission line, sophisticated configurations have also been developed, in which the fiber is used as a device to realize unique sensing mechanisms. The fiber optic gyroscope (FOG) is a good example, and has been developed as an absolute rotation sensor used, for example, for navigation and/or attitude control applications. Compared with traditional spinning-mass gyroscopes, the FOG has advantages, such as a short warming-up time, a light weight, and easy handling. A Japanese satellite, which was launched in August 2005 with a mission to observe the aurora, is controlled with a FOG. The FOG has also been used in consumer applications, such as the camera stabilizer, radio-controlled (RC) helicopter navigation, and the control of humanoid robots. Recently, distributed and multiplexed sensing schemes, in particular, have been studied and developed, in which a long fiber acts like a “nerve” for feeling the strain and/or the temperature distribution along the fiber. Performances of artificial nerve systems have markedly improved within the last couple of years, in spatial resolution and measurement speed. By embedding the “fiber-optic nerve system” in aircraft wings, bridges and tall buildings, these materials and structures can sense damage to prevent disasters.

  4. Ways to Boost Fiber

    Science.gov (United States)

    ... can help to lower cholesterol. Third, it helps prevent constipation and diverticulosis. And fourth, adequate fiber from food ... is similar to a new sponge; it needs water to plump up pass smoothly. If you ... or constipation. Before you reach for the fiber supplements, consider ...

  5. Quartz fiber calorimeter

    International Nuclear Information System (INIS)

    Akchurin, N.; Doulas, S.; Ganel, O.; Gershtein, Y.; Gavrilov, V.; Kolosov, V.; Kuleshov, S.; Litvinsev, D.; Merlo, J.-P.; Onel, Y.; Osborne, D.; Rosowsky, A.; Stolin, V.; Sulak, L.; Sullivan, J.; Ulyanov, A.; Wigmans, R.; Winn, D.

    1996-01-01

    A calorimeter with optical quartz fibers embedded into an absorber matrix was proposed for the small angle region of the CMS detector at LHC (CERN). This type of calorimeter is expected to be radiation hard and to produce extremely fast signal. Some results from beam tests of the quartz fiber calorimeter prototype are presented. (orig.)

  6. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  7. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  8. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  9. High-density multicore fibers

    DEFF Research Database (Denmark)

    Takenaga, K.; Matsuo, S.; Saitoh, K.

    2016-01-01

    High-density single-mode multicore fibers were designed and fabricated. A heterogeneous 30-core fiber realized a low crosstalk of −55 dB. A quasi-single-mode homogeneous 31-core fiber attained the highest core count as a single-mode multicore fiber.......High-density single-mode multicore fibers were designed and fabricated. A heterogeneous 30-core fiber realized a low crosstalk of −55 dB. A quasi-single-mode homogeneous 31-core fiber attained the highest core count as a single-mode multicore fiber....

  10. Automated characterization of nerve fibers labeled fluorescently: determination of size, class and spatial distribution.

    Science.gov (United States)

    Prodanov, Dimiter; Feirabend, Hans K P

    2008-10-03

    Morphological classification of nerve fibers could help interpret the assessment of neural regeneration and the understanding of selectivity of nerve stimulation. Specific populations of myelinated nerve fibers can be investigated by retrograde tracing from a muscle followed by microscopic measurements of the labeled fibers at different anatomical levels. Gastrocnemius muscles of adult rats were injected with the retrograde tracer Fluoro-Gold. After a survival period of 3 days, cross-sections of spinal cords, ventral roots, sciatic, and tibial nerves were collected and imaged on a fluorescence microscope. Nerve fibers were classified using a variation-based criterion acting on the distribution of their equivalent diameters. The same criterion was used to classify the labeled axons using the size of the fluorescent marker. Measurements of the axons were paired to those of the entire fibers (axons+myelin sheaths) in order to establish the correspondence between so-established axonal and fiber classifications. It was found that nerve fibers in L6 ventral roots could be classified into four populations comprising two classes of Aalpha (denoted Aalpha1 and Aalpha2), Agamma, and an additional class of Agammaalpha fibers. Cut-off borders between Agamma and Agammaalpha fiber classes were estimated to be 5.00+/-0.09 microm (SEM); between Agammaalpha and Aalpha1 fiber classes to be 6.86+/-0.11 microm (SEM); and between Aalpha1 and Aalpha2 fiber classes to be 8.66+/-0.16 microm (SEM). Topographical maps of the nerve fibers that innervate the gastrocnemius muscles were constructed per fiber class for the spinal root L6. The major advantage of the presented approach consists of the combined indirect classification of nerve fiber types and the construction of topographical maps of so-identified fiber classes.

  11. Sorting fluorescent nanocrystals with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Gerion, Daniele; Parak, Wolfgang J.; Williams, Shara C.; Zanchet, Daniela; Micheel, Christine M.; Alivisatos, A. Paul

    2001-12-10

    Semiconductor nanocrystals with narrow and tunable fluorescence are covalently linked to oligonucleotides. These biocompounds retain the properties of both nanocrystals and DNA. Therefore, different sequences of DNA can be coded with nanocrystals and still preserve their ability to hybridize to their complements. We report the case where four different sequences of DNA are linked to four nanocrystal samples having different colors of emission in the range of 530-640 nm. When the DNA-nanocrystal conjugates are mixed together, it is possible to sort each type of nanoparticle using hybridization on a defined micrometer -size surface containing the complementary oligonucleotide. Detection of sorting requires only a single excitation source and an epifluorescence microscope. The possibility of directing fluorescent nanocrystals towards specific biological targets and detecting them, combined with their superior photo-stability compared to organic dyes, opens the way to improved biolabeling experiments, such as gene mapping on a nanometer scale or multicolor microarray analysis.

  12. Green insulation: hemp fibers

    Energy Technology Data Exchange (ETDEWEB)

    Anon,

    2011-09-15

    Indian hemp (Cannabis indica) is known for its psychotropic values and it is banned in most countries. However, industrial hemp (Cannabis sativa) is known for its tough fibers. Several manufactures in Europe including, small niche players, have been marketing hemp insulation products for several years. Hemp is a low environmental impact material. Neither herbicide nor pesticide is used during the growth of hemp. The fibers are extracted in a waste-free and chemical-free mechanical process. Hemp can consume CO2 during its growth. In addition, hemp fiber can be disposed of harmlessly by composting or incineration at the end of its life. Hemp fibers are processed and treated only minimally to resist rot and fungal activity. There is little health risk when producing and installing the insulation, thanks to the absence of toxic additive. Its thermal resistance is comparable to mineral wool. But the development and marketing of hemp fibers may be restricted in North America.

  13. Raman fiber lasers

    CERN Document Server

    2017-01-01

    This book serves as a comprehensive, up-to-date reference about this cutting-edge laser technology and its many new and interesting developments. Various aspects and trends of Raman fiber lasers are described in detail by experts in their fields. Raman fiber lasers have progressed quickly in the past decade, and have emerged as a versatile laser technology for generating high power light sources covering a spectral range from visible to mid-infrared. The technology is already being applied in the fields of telecommunication, astronomy, cold atom physics, laser spectroscopy, environmental sensing, and laser medicine. This book covers various topics relating to Raman fiber laser research, including power scaling, cladding and diode pumping, cascade Raman shifting, single frequency operation and power amplification, mid-infrared laser generation, specialty optical fibers, and random distributed feedback Raman fiber lasers. The book will appeal to scientists, students, and technicians seeking to understand the re...

  14. Birefringent hollow core fibers

    DEFF Research Database (Denmark)

    Roberts, John

    2007-01-01

    Hollow core photonic crystal fiber (HC-PCF), fabricated according to a nominally non-birefringent design, shows a degree of un-controlled birefringence or polarization mode dispersion far in excess of conventional non polarization maintaining fibers. This can degrade the output pulse in many...... applications, and places emphasis on the development of polarization maintaining (PM) HC-PCF. The polarization cross-coupling characteristics of PM HC-PCF are very different from those of conventional PM fibers. The former fibers have the advantage of suffering far less from stress-field fluctuations...... and an increased overlap between the polarization modes at the glass interfaces. The interplay between these effects leads to a wavelength for optimum polarization maintenance, lambda(PM), which is detuned from the wavelength of highest birefringence. By a suitable fiber design involving antiresonance of the core...

  15. Fiber optic hydrophone

    Science.gov (United States)

    Kuzmenko, Paul J.; Davis, Donald T.

    1994-01-01

    A miniature fiber optic hydrophone based on the principles of a Fabry-Perot interferometer. The hydrophone, in one embodiment, includes a body having a shaped flexible bladder at one end which defines a volume containing air or suitable gas, and including a membrane disposed adjacent a vent. An optic fiber extends into the body with one end terminating in spaced relation to the membrane. Acoustic waves in the water that impinge on the bladder cause the pressure of the volume therein to vary causing the membrane to deflect and modulate the reflectivity of the Fabry-Perot cavity formed by the membrane surface and the cleaved end of the optical fiber disposed adjacent to the membrane. When the light is transmitted down the optical fiber, the reflected signal is amplitude modulated by the incident acoustic wave. Another embodiment utilizes a fluid filled volume within which the fiber optic extends.

  16. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  17. Genetic Mapping

    Science.gov (United States)

    ... greatly advanced genetics research. The improved quality of genetic data has reduced the time required to identify a ... cases, a matter of months or even weeks. Genetic mapping data generated by the HGP's laboratories is freely accessible ...

  18. From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions.

    Directory of Open Access Journals (Sweden)

    Mu Gao

    2009-03-01

    Full Text Available DNA-protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA-protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA-protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA-protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA-protein interaction modes exhibit some similarity to specific DNA-protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Calpha deviation from native is up to 5 A from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA-protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein.

  19. Method for the preparation of carbon fiber from polyolefin fiber precursor, and carbon fibers made thereby

    Science.gov (United States)

    Naskar, Amit Kumar; Hunt, Marcus Andrew; Saito, Tomonori

    2015-08-04

    Methods for the preparation of carbon fiber from polyolefin fiber precursor, wherein the polyolefin fiber precursor is partially sulfonated and then carbonized to produce carbon fiber. Methods for producing hollow carbon fibers, wherein the hollow core is circular- or complex-shaped, are also described. Methods for producing carbon fibers possessing a circular- or complex-shaped outer surface, which may be solid or hollow, are also described.

  20. Two potential Petunia hybrida mitochondrial DNA replication origins show structural and in vitro functional homology with the animal mitochondrial DNA heavy and light strand replication origins

    NARCIS (Netherlands)

    Haas, Jan M. de; Hille, Jacques; Kors, Frank; Meer, Bert van der; Kool, Ad J.; Folkerts, Otto; Nijkamp, H. John J.

    1991-01-01

    Four Petunia hybrida mitochondrial (mt) DNA fragments have been isolated, sequenced, localized on the physical map and analyzed for their ability to initiate specific DNA synthesis. When all four mtDNA fragments were tested as templates in an in vitro DNA synthesizing lysate system, developed from

  1. A Probabilistic Approach for Improved Sequence Mapping in Metatranscriptomic Studies

    Science.gov (United States)

    Mapping millions of short DNA sequences a reference genome is a necessary step in many experiments designed to investigate the expression of genes involved in disease resistance. This is a difficult task in which several challenges often arise resulting in a suboptimal mapping. This mapping process ...

  2. Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers

    NARCIS (Netherlands)

    Atienza, S.G.; Satovic, Z.; Petersen, K.K.; Dolstra, O.; Martin, A.

    2002-01-01

    We have used an "offspring cross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct the first genetic map of the species Miscanthus sinensis (2n = 2x = 38). This map is based on an outbred population of 89 individuals resulting from the cross between

  3. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2003-01-01

    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

  4. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  5. Molecular mechanisms of DNA photodamage

    Energy Technology Data Exchange (ETDEWEB)

    Starrs, S.M

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA){sub n} and (GA){sub n}, and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a

  6. Molecular mechanisms of DNA photodamage

    International Nuclear Information System (INIS)

    Starrs, S.M.

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA) n and (GA) n , and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a dimeric

  7. Fiber Pulling Apparatus

    Science.gov (United States)

    Workman, Gary L.; Smith, Guy A.; OBrien, Sue; Adcock, Leonard

    1998-01-01

    The fiber optics industry has grown into a multi-billion marketplace that will continue to grow into the 21st century. Optical fiber communications is currently dominated by silica glass technology. Successful efforts to improve upon the low loss transmission characteristics of silica fibers have propelled the technology into the forefront of the communications industry. However, reaching the theoretical transmission capability of silica fiber through improved processing has still left a few application areas in which other fiber systems can provide an influential role due to specific characteristics of high theoretical transmission in the 2 - 3 micron wavelength region. One of the other major materials used for optical fibers is the systems based upon Heavy Metal Fluoride Glass (HMFG). Commercial interest is driven primarily by the potential for low loss repeaterless infrared fibers. An example of the major communications marketplace which would benefit from the long distance repeaterless capability of infrared fibers is the submarine cables which link the continents. When considering commercial interests, optical fiber systems provide a healthy industrial position which continues to expand. Major investments in the systems used for optical fiber communications have continued to increase each year and are predicted to continue well into the next century. Estimates of 8.5% compounded annually are predicted through 1999 for the North American market and 1 1 % worldwide. The growth for the optical fiber cable itself is expected to continue between 44 and 50 per cent of the optical fiber communications budget through 1999. The total budget in 1999 world-wide is expected to be in the neighborhood of $9 billion. Another survey predicts that long haul telecommunications represents 15% of a world-wide fiber optics market in 1998. The actual amount allotted to cable was not specified. However, another market research had predicted that the cable costs alone represents more

  8. Fiber Optic Microphone

    Science.gov (United States)

    Cho, Y. C.; George, Thomas; Norvig, Peter (Technical Monitor)

    1999-01-01

    Research into advanced pressure sensors using fiber-optic technology is aimed at developing compact size microphones. Fiber optic sensors are inherently immune to electromagnetic noise, and are very sensitive, light weight, and highly flexible. In FY 98, NASA researchers successfully designed and assembled a prototype fiber-optic microphone. The sensing technique employed was fiber optic Fabry-Perot interferometry. The sensing head is composed of an optical fiber terminated in a miniature ferrule with a thin, silicon-microfabricated diaphragm mounted on it. The optical fiber is a single mode fiber with a core diameter of 8 micron, with the cleaved end positioned 50 micron from the diaphragm surface. The diaphragm is made up of a 0.2 micron thick silicon nitride membrane whose inner surface is metallized with layers of 30 nm titanium, 30 nm platinum, and 0.2 micron gold for efficient reflection. The active sensing area is approximately 1.5 mm in diameter. The measured differential pressure tolerance of this diaphragm is more than 1 bar, yielding a dynamic range of more than 100 dB.

  9. Applications of fiber-optics-based nanosensors to drug discovery.

    Science.gov (United States)

    Vo-Dinh, Tuan; Scaffidi, Jonathan; Gregas, Molly; Zhang, Yan; Seewaldt, Victoria

    2009-08-01

    Fiber-optic nanosensors are fabricated by heating and pulling optical fibers to yield sub-micron diameter tips and have been used for in vitro analysis of individual living mammalian cells. Immobilization of bioreceptors (e.g., antibodies, peptides, DNA) selective to targeting analyte molecules of interest provides molecular specificity. Excitation light can be launched into the fiber, and the resulting evanescent field at the tip of the nanofiber can be used to excite target molecules bound to the bioreceptor molecules. The fluorescence or surface-enhanced Raman scattering produced by the analyte molecules is detected using an ultra-sensitive photodetector. This article provides an overview of the development and application of fiber-optic nanosensors for drug discovery. The nanosensors provide minimally invasive tools to probe subcellular compartments inside single living cells for health effect studies (e.g., detection of benzopyrene adducts) and medical applications (e.g., monitoring of apoptosis in cells treated with anticancer drugs).

  10. Optical fiber spectrophotometer

    International Nuclear Information System (INIS)

    Zhuang Weixin; Tian Guocheng; Ye Guoan; Zhou Zhihong; Cheng Weiwei; Huang Lifeng; Liu Suying; Tang Yanji; Hu Jingxin; Zhao Yonggang

    1998-12-01

    A method called 'Two Arm's Photo out and Electricity Send-back' is introduced. UV-365 UV/VIS/NIR spectrophotometer has been reequipped by this way with 5 meters long optical fiber. Another method called 'One Arm's Photo out and Photo Send-back' is also introduced. λ 19 UV/VIS/NIR spectrophotometer has been reequipped by this way with 10 meters long optical fiber. Optical fiber spectrophotometer can work as its main set. So it is particularly applicable to radio activity work

  11. Chemistry Research of Optical Fibers.

    Science.gov (United States)

    1982-09-27

    BROADENING IN OPTICAL FIBERS Herbert B. Rosenstock* Naval Research Laboratory Washington, DC 20375 ABSTRACT A light pulse transmitted through a fiber...Marcatili, Marcuse , and Personick, "Dispersion Properties of Fibers" (Ch. 4 in "Optical Fiber Telecommunications," S. E. Miller and A. C. Chynoweth, eds

  12. Semiconductor and ceramic microstructure made by single mode fiber laser

    International Nuclear Information System (INIS)

    Pawlak, R; Tomczyk, M; Walczak, M; Domagalski, P

    2014-01-01

    In the paper the results of micromachining of 3D microstructures of microsystems made from silicon and alumina ceramic using a single mode fiber laser (1064 nm) are presented. The quality of obtained structures and its smallest dimensions with acceptable maintained quality were examined. The influence of variable parameters of laser processing with changing of mapping scale on geometrical features of structures was identified.

  13. The structure of DNA by direct imaging

    KAUST Repository

    Marini, Monica; Falqui, Andrea; Moretti, Manola; Limongi, Tania; Allione, Marco; Genovese, Alessandro; Lopatin, Sergei; Tirinato, Luca; Das, Gobind; Torre, Bruno; Giugni, Andrea; Gentile, Francesco; Candeloro, Patrizio; Di Fabrizio, Enzo M.

    2015-01-01

    The structure of DNA was determined in 1953 by x-ray fiber diffraction. Several attempts have been made to obtain a direct image of DNA with alternative techniques. The direct image is intended to allow a quantitative evaluation of all relevant characteristic lengths present in a molecule. A direct image of DNA, which is different from diffraction in the reciprocal space, is difficult to obtain for two main reasons: the intrinsic very low contrast of the elements that form the molecule and the difficulty of preparing the sample while preserving its pristine shape and size. We show that through a preparation procedure compatible with the DNA physiological conditions, a direct image of a single suspended DNA molecule can be obtained. In the image, all relevant lengths of A-form DNA are measurable. A high-resolution transmission electron microscope that operates at 80 keV with an ultimate resolution of 1.5 Å was used for this experiment. Direct imaging of a single molecule can be used as a method to address biological problems that require knowledge at the single-molecule level, given that the average information obtained by x-ray diffraction of crystals or fibers is not sufficient for detailed structure determination, or when crystals cannot be obtained from biological molecules or are not sufficient in understanding multiple protein configurations.

  14. The structure of DNA by direct imaging

    KAUST Repository

    Marini, Monica

    2015-08-28

    The structure of DNA was determined in 1953 by x-ray fiber diffraction. Several attempts have been made to obtain a direct image of DNA with alternative techniques. The direct image is intended to allow a quantitative evaluation of all relevant characteristic lengths present in a molecule. A direct image of DNA, which is different from diffraction in the reciprocal space, is difficult to obtain for two main reasons: the intrinsic very low contrast of the elements that form the molecule and the difficulty of preparing the sample while preserving its pristine shape and size. We show that through a preparation procedure compatible with the DNA physiological conditions, a direct image of a single suspended DNA molecule can be obtained. In the image, all relevant lengths of A-form DNA are measurable. A high-resolution transmission electron microscope that operates at 80 keV with an ultimate resolution of 1.5 Å was used for this experiment. Direct imaging of a single molecule can be used as a method to address biological problems that require knowledge at the single-molecule level, given that the average information obtained by x-ray diffraction of crystals or fibers is not sufficient for detailed structure determination, or when crystals cannot be obtained from biological molecules or are not sufficient in understanding multiple protein configurations.

  15. Projective mapping

    DEFF Research Database (Denmark)

    Dehlholm, Christian; Brockhoff, Per B.; Bredie, Wender Laurentius Petrus

    2012-01-01

    by the practical testing environment. As a result of the changes, a reasonable assumption would be to question the consequences caused by the variations in method procedures. Here, the aim is to highlight the proven or hypothetic consequences of variations of Projective Mapping. Presented variations will include...... instructions and influence heavily the product placements and the descriptive vocabulary (Dehlholm et.al., 2012b). The type of assessors performing the method influences results with an extra aspect in Projective Mapping compared to more analytical tests, as the given spontaneous perceptions are much dependent......Projective Mapping (Risvik et.al., 1994) and its Napping (Pagès, 2003) variations have become increasingly popular in the sensory field for rapid collection of spontaneous product perceptions. It has been applied in variations which sometimes are caused by the purpose of the analysis and sometimes...

  16. DNA AND ITS METAPHORES

    Directory of Open Access Journals (Sweden)

    Jan Domaradzki

    2015-04-01

    Full Text Available The aim of the present paper is to describe the main metaphors presented in genetic discourse: DNA as text, information, language, book, code, project/blueprint, map, computer, music, and cooking. It also analyses the social implication of these metaphors. The author of this article argues that metaphors are double-edged swords: while they brighten difficult and abstract genetic concepts, they also lead to the misunderstanding and misinterpretation of the reality. The reason for this is that most of these metaphors are of deterministic, reductionist, and fatalistic character. Consequently, they shift the attention from complexity of genetic processes. Moreover, as they appeal to emotions, ascetics, and morality they may involve exaggeration: while they bring hope, they also create an atmosphere of fear over the misuse of genetic knowledge. The author of this article states that the genetic metaphors do not simply reflect the social ideas on DNA, but also shape our understanding of genetics and imagination on the social application of genetic knowledge. Due to this reason, DNA should be understood not only as a biological code, but as a cultural as well.

  17. Mapping the space of genomic signatures.

    Directory of Open Access Journals (Sweden)

    Lila Kari

    Full Text Available We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR, is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM, implicitly compares the occurrences of oligomers of length up to k (herein k = 9 in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (superkingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal

  18. Fiber optics standard dictionary

    CERN Document Server

    Weik, Martin H

    1997-01-01

    Fiber Optics Vocabulary Development In 1979, the National Communications System published Technical InfonnationBulle­ tin TB 79-1, Vocabulary for Fiber Optics and Lightwave Communications, written by this author. Based on a draft prepared by this author, the National Communications System published Federal Standard FED-STD-1037, Glossary of Telecommunications Terms, in 1980 with no fiber optics tenns. In 1981, the first edition of this dictionary was published under the title Fiber Optics and Lightwave Communications Standard Dictionary. In 1982, the then National Bureau of Standards, now the National Institute of Standards and Technology, published NBS Handbook 140, Optical Waveguide Communications Glossary, which was also published by the General Services Admin­ istration as PB82-166257 under the same title. Also in 1982, Dynamic Systems, Inc. , Fiberoptic Sensor Technology Handbook, co-authored and edited by published the this author, with an extensive Fiberoptic Sensors Glossary. In 1989, the handbook w...

  19. Fiber Optics: No Illusion.

    Science.gov (United States)

    American School and University, 1983

    1983-01-01

    A campus computer center at Hofstra University (New York) that holds 70 terminals for student use was first a gymnasium, then a language laboratory. Strands of fiber optics are used for the necessary wiring. (MLF)

  20. Fiber optic gas sensor

    Science.gov (United States)

    Chen, Peng (Inventor); Buric, Michael P. (Inventor); Swinehart, Philip R. (Inventor); Maklad, Mokhtar S. (Inventor)

    2010-01-01

    A gas sensor includes an in-fiber resonant wavelength device provided in a fiber core at a first location. The fiber propagates a sensing light and a power light. A layer of a material is attached to the fiber at the first location. The material is able to absorb the gas at a temperature dependent gas absorption rate. The power light is used to heat the material and increases the gas absorption rate, thereby increasing sensor performance, especially at low temperatures. Further, a method is described of flash heating the gas sensor to absorb more of the gas, allowing the sensor to cool, thereby locking in the gas content of the sensor material, and taking the difference between the starting and ending resonant wavelengths as an indication of the concentration of the gas in the ambient atmosphere.

  1. Photonic Crystal Fibers

    National Research Council Canada - National Science Library

    Kristiansen, Rene E

    2005-01-01

    This report results from a contract tasking Crystal Fibre A/S as follows: Crystal Fibre will conduct research and development of large mode area, dual clad multi-core Yb-doped photonic crystal fiber...

  2. Fiber Laser Array

    National Research Council Canada - National Science Library

    Simpson, Thomas

    2002-01-01

    ...., field-dependent, loss within the coupled laser array. During this program, Jaycor focused on the construction and use of an experimental apparatus that can be used to investigate the coherent combination of an array of fiber lasers...

  3. Robust Fiber Coatings

    National Research Council Canada - National Science Library

    Goettler, Richard

    2002-01-01

    The highly desired ceramic matrix composite is the one in which the high strength and strain-to-failure is achieved through judicious selection of a fiber coating that can survive the high-temperature...

  4. Fiber Optic Bragg Gratings

    National Research Council Canada - National Science Library

    Battiato, James

    1998-01-01

    Coupled mode theory was used to model reflection fiber gratings. The effects of experimental parameters on grating characteristics were modeled for both uniform and non-uniform grating profiles using this approach...

  5. Cerenkov fiber sampling calorimeters

    International Nuclear Information System (INIS)

    Arrington, K.; Kefford, D.; Kennedy, J.; Pisani, R.; Sanzeni, C.; Segall, K.; Wall, D.; Winn, D.R.; Carey, R.; Dye, S.; Miller, J.; Sulak, L.; Worstell, W.; Efremenko, Y.; Kamyshkov, Y.; Savin, A.; Shmakov, K.; Tarkovsky, E.

    1994-01-01

    Clear optical fibers were used as a Cerenkov sampling media in Pb (electromagnetic) and Cu (hadron) absorbers in spaghetti calorimeters, for high rate and high radiation dose experiments, such as the forward region of high energy colliders. The fiber axes were aligned close to the direction of the incident particles (1 degree--7 degree). The 7 λ deep hadron tower contained 2.8% by volume 1.5 mm diameter core clear plastic fibers. The 27 radiation length deep electromagnetic towers had packing fractions of 6.8% and 7.2% of 1 mm diameter core quartz fibers as the active Cerenkov sampling medium. The energy resolution on electrons and pions, energy response, pulse shapes and angular studies are presented

  6. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    . In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-humangeographies’ practices include notions of species, space and territory, and movement towards a new political ecology. This type...... of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper looks at computer-assisted cartography as part...

  7. Investigating the real translucency of the endodontic fiber posts

    Science.gov (United States)

    Camilotti, Fernando; Bonardi, Cláudia; Somer, Aloisi; Novatski, Andressa; Szesz, Anna Luiza; Loguércio, Alessandro Dourado; Kniphoff da Cruz, Gerson

    2018-02-01

    Researchers have been investigating the light intensity scattered by a translucent fiber post with application in dentistry by different methods. In this work, we introduce a new system capable to record a light scattered profile, step-by-step, as a function of the length of the translucent fiber post. To support our studies, an extensive characterization of the system was carried out and this is presented and discussed here. The system was implemented using the phase sensitive detection. The equipment measures the light scattered without the need of any preparing parts and the fiber post is fixed directly in the fiber post holder becoming ready for measurement. Measures can be recorded with a spatial resolution smaller than 0.01 mm throughout the length of the fiber post being investigated. The system was implemented by using a photomultiplier tube that improves sensitivity for the optical detection. The recorded result is a signal directly proportional to the scattered light and it allows us to obtain a normalized profile that can be used as a map of the scattered light of the fiber post in study. Furthermore, we are able to demonstrate a low intensity of light in the tip region of the fiber post, along with the dependency of the light attenuation with the fiber post body volume and shape. This new system will certainly contribute to achieve better results in fiber post designing and in restoration of endodontic treated teeth because it provides a more well-founded choice of the fiber post to be used, and of the time of exposure to the curing light.

  8. Investigating the real translucency of the endodontic fiber posts

    Directory of Open Access Journals (Sweden)

    Fernando Camilotti

    2018-02-01

    Full Text Available Researchers have been investigating the light intensity scattered by a translucent fiber post with application in dentistry by different methods. In this work, we introduce a new system capable to record a light scattered profile, step-by-step, as a function of the length of the translucent fiber post. To support our studies, an extensive characterization of the system was carried out and this is presented and discussed here. The system was implemented using the phase sensitive detection. The equipment measures the light scattered without the need of any preparing parts and the fiber post is fixed directly in the fiber post holder becoming ready for measurement. Measures can be recorded with a spatial resolution smaller than 0.01 mm throughout the length of the fiber post being investigated. The system was implemented by using a photomultiplier tube that improves sensitivity for the optical detection. The recorded result is a signal directly proportional to the scattered light and it allows us to obtain a normalized profile that can be used as a map of the scattered light of the fiber post in study. Furthermore, we are able to demonstrate a low intensity of light in the tip region of the fiber post, along with the dependency of the light attenuation with the fiber post body volume and shape. This new system will certainly contribute to achieve better results in fiber post designing and in restoration of endodontic treated teeth because it provides a more well-founded choice of the fiber post to be used, and of the time of exposure to the curing light.

  9. CUDA-Accelerated Geodesic Ray-Tracing for Fiber Tracking

    Directory of Open Access Journals (Sweden)

    Evert van Aart

    2011-01-01

    Full Text Available Diffusion Tensor Imaging (DTI allows to noninvasively measure the diffusion of water in fibrous tissue. By reconstructing the fibers from DTI data using a fiber-tracking algorithm, we can deduce the structure of the tissue. In this paper, we outline an approach to accelerating such a fiber-tracking algorithm using a Graphics Processing Unit (GPU. This algorithm, which is based on the calculation of geodesics, has shown promising results for both synthetic and real data, but is limited in its applicability by its high computational requirements. We present a solution which uses the parallelism offered by modern GPUs, in combination with the CUDA platform by NVIDIA, to significantly reduce the execution time of the fiber-tracking algorithm. Compared to a multithreaded CPU implementation of the same algorithm, our GPU mapping achieves a speedup factor of up to 40 times.

  10. Fiber optics welder

    Science.gov (United States)

    Higgins, R.W.; Robichaud, R.E.

    A system is described for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45/sup 0/ angle to the optical axis of a stereomicroscope mounted for viewing the junction of the ends provides two orthogonal views of the interface during the alignment operation.

  11. FIBER OPTIC LIGHTING SYSTEMS

    Directory of Open Access Journals (Sweden)

    Munir BATUR

    2013-01-01

    Full Text Available Recently there have been many important and valuable developments in the communication industry. The huge increase in the sound, data and visual communications has caused a parallel increase in the demand for systems with wider capacity, higher speed and higher quality. Communication systems that use light to transfer data are immensely increased. There have recently many systems in which glass or plastic fiber cables were developed for light wave to be transmitted from a source to a target place. Fiber optic systems, are nowadays widely used in energy transmission control systems, medicine, industry and lighting. The basics of the system is, movement of light from one point to another point in fiber cable with reflections. Fiber optic lighting systems are quite secure than other lighting systems and have flexibility for realizing many different designs. This situation makes fiber optics an alternative for other lighting systems. Fiber optic lighting systems usage is increasing day-by-day in our life. In this article, these systems are discussed in detail.

  12. Electrospun amplified fiber optics.

    Science.gov (United States)

    Morello, Giovanni; Camposeo, Andrea; Moffa, Maria; Pisignano, Dario

    2015-03-11

    All-optical signal processing is the focus of much research aiming to obtain effective alternatives to existing data transmission platforms. Amplification of light in fiber optics, such as in Erbium-doped fiber amplifiers, is especially important for efficient signal transmission. However, the complex fabrication methods involving high-temperature processes performed in a highly pure environment slow the fabrication process and make amplified components expensive with respect to an ideal, high-throughput, room temperature production. Here, we report on near-infrared polymer fiber amplifiers working over a band of ∼20 nm. The fibers are cheap, spun with a process entirely carried out at room temperature, and shown to have amplified spontaneous emission with good gain coefficients and low levels of optical losses (a few cm(-1)). The amplification process is favored by high fiber quality and low self-absorption. The found performance metrics appear to be suitable for short-distance operations, and the large variety of commercially available doping dyes might allow for effective multiwavelength operations by electrospun amplified fiber optics.

  13. DNA Vaccines

    Indian Academy of Sciences (India)

    diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL .... tein vaccines require expensive virus/protein purification tech- niques as ... sphere continue to remain major health hazards in developing nations. ... significance since it can be produced at a very low cost and can be stored ...

  14. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  15. Continuous Natural Fiber Reinforced Thermoplastic Composites by Fiber Surface Modification

    Directory of Open Access Journals (Sweden)

    Patcharat Wongsriraksa

    2013-01-01

    Full Text Available Continuous natural fiber reinforced thermoplastic materials are expected to replace inorganic fiber reinforced thermosetting materials. However, in the process of fabricating the composite, it is difficult to impregnate the thermoplastic resin into reinforcement fiber because of the high melt viscosity. Therefore, intermediate material, which allows high impregnation during molding, has been investigated for fabricating continuous fiber reinforced thermoplastic composite by aligning resin fiber alongside reinforcing fiber with braiding technique. This intermediate material has been called “microbraid yarn (MBY.” Moreover, it is well known that the interfacial properties between natural fiber and resin are low; therefore, surface treatment on continuous natural fiber was performed by using polyurethane (PU and flexible epoxy (FLEX to improve the interfacial properties. The effect of surface treatment on the mechanical properties of continuous natural fiber reinforced thermoplastic composites was examined. From these results, it was suggested that surface treatment by PU with low content could produce composites with better mechanical properties.

  16. Energetic map

    International Nuclear Information System (INIS)

    2012-01-01

    This report explains the energetic map of Uruguay as well as the different systems that delimits political frontiers in the region. The electrical system importance is due to the electricity, oil and derived , natural gas, potential study, biofuels, wind and solar energy

  17. Necklace maps

    NARCIS (Netherlands)

    Speckmann, B.; Verbeek, K.A.B.

    2010-01-01

    Statistical data associated with geographic regions is nowadays globally available in large amounts and hence automated methods to visually display these data are in high demand. There are several well-established thematic map types for quantitative data on the ratio-scale associated with regions:

  18. Participatory maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    towards a new political ecology. This type of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper...

  19. Thulium fiber laser lithotripsy using a muzzle brake fiber tip

    Science.gov (United States)

    Hutchens, Thomas C.; Gonzalez, David A.; Irby, Pierce B.; Fried, Nathaniel M.

    2017-02-01

    The Thulium fiber laser (TFL) is being explored as an alternative to Holmium:YAG laser for lithotripsy. TFL beam profile allows coupling of higher power into smaller fibers than multimode Holmium laser beam, without proximal fiber tip degradation. A smaller fiber provides more space in ureteroscope working channel for increased saline irrigation and allows maximum ureteroscope flexion. However, distal fiber tip burnback increases as fiber diameter decreases. Previous studies utilizing hollow steel sheaths around recessed distal fiber tips reduced fiber burnback, but increased retropulsion. In this study, a "fiber muzzle brake" was tested for reducing fiber burnback and stone retropulsion. TFL lithotripsy studies were performed at 1908 nm, 35 mJ, 500 μs, and 300 Hz using a 100-μm-core fiber. The optimal stainless steel muzzle brake tip tested consisted of a 1-cm-long, 560-μm-OD, 360-μm-ID tube with 275-μm thru hole located 250-μm from the distal end. The fiber tip was recessed a distance of 500 μm. Stone phantom retropulsion, fiber tip burnback, and calcium oxalate stone ablation studies were performed, ex vivo. Small stones with a mass of 40 +/- 4 mg and 4-mm-diameter were ablated over a 1.5-mm sieve in 25 +/- 4 s (n=10), without distal fiber tip burnback. Reduction in stone phantom retropulsion distance by 50% and 85% was observed when using muzzle brake tips versus 100-μm-core bare fibers and hollow steel tip fibers. The muzzle brake fiber tip provided efficient stone ablation, reduced stone retropulsion, and minimal fiber degradation during TFL lithotripsy.

  20. Somatic DNA recombination yielding circular DNA and deletion of a genomic region in embryonic brain

    International Nuclear Information System (INIS)

    Maeda, Toyoki; Chijiiwa, Yoshiharu; Tsuji, Hideo; Sakoda, Saburo; Tani, Kenzaburo; Suzuki, Tomokazu

    2004-01-01

    In this study, a mouse genomic region is identified that undergoes DNA rearrangement and yields circular DNA in brain during embryogenesis. External region-directed inverse polymerase chain reaction on circular DNA extracted from late embryonic brain tissue repeatedly detected DNA of this region containing recombination joints. Wide-range genomic PCR and digestion-circularization PCR analysis showed this region underwent recombination accompanied with deletion of intervening sequences, including the circularized regions. This region was mapped by fluorescence in situ hybridization to C1 on mouse chromosome 16, where no gene and no physiological DNA rearrangement had been identified. DNA sequence in the region has segmental homology to an orthologous region on human chromosome 3q.13. These observations demonstrated somatic DNA recombination yielding genomic deletions in brain during embryogenesis

  1. Cellulosic Fibers: Effect of Processing on Fiber Bundle Strength

    DEFF Research Database (Denmark)

    Thygesen, Anders; Madsen, Bo; Thomsen, Anne Belinda

    2011-01-01

    A range of differently processed cellulosic fibers from flax and hemp plants were investigated to study the relation between processing of cellulosic fibers and fiber bundle strength. The studied processing methods are applied for yarn production and include retting, scutching, carding, and cotto......A range of differently processed cellulosic fibers from flax and hemp plants were investigated to study the relation between processing of cellulosic fibers and fiber bundle strength. The studied processing methods are applied for yarn production and include retting, scutching, carding...

  2. Study on basalt fiber parameters affecting fiber-reinforced mortar

    Science.gov (United States)

    Orlov, A. A.; Chernykh, T. N.; Sashina, A. V.; Bogusevich, D. V.

    2015-01-01

    This article considers the effect of different dosages and diameters of basalt fibers on tensile strength increase during bending of fiberboard-reinforced mortar samples. The optimal dosages of fiber, providing maximum strength in bending are revealed. The durability of basalt fiber in an environment of cement, by means of microscopic analysis of samples of fibers and fiberboard-reinforced mortar long-term tests is examined. The article also compares the behavior of basalt fiber in the cement stone environment to a glass one and reveals that the basalt fiber is not subject to destruction.

  3. Radiation hybrid mapping of human chromosome 18

    International Nuclear Information System (INIS)

    Francke, U.; Moon, A.J.; Chang, E.; Foellmer, B.; Strauss, B.; Haschke, A.; Chihlin Hsieh; Geigl, E.M.; Welch, S.

    1990-01-01

    The authors have generated a Chinese hamster V79/380-6 HPRT minus x human leukocyte hybrid cell line (18/V79) with chromosome 18 as the only human chromosome that is retained at high frequency without specific selection. Hybrid cells were selected in HAT medium, and 164 individual colonies were isolated. Of 110 colonies screened for human DNA by PCR amplification using a primer specific for human Alu repeats 67 (61%) were positive. These were expanded in culture for large-scale DNA preparations. Retesting expanded clones by PCR with Alu and LINE primers has revealed unique patterns of amplification products. In situ hybridization of biotin labelled total human DNA to metaphase spreads from various hybrids revealed the presence of one or more human DNA fragments integrated in hamster chromosomes. The authors have generated a resource that should allow the construction of a radiation map, to be compared with the YAC contig map also under construction in their laboratory

  4. Optical fiber stripper positioning apparatus

    Science.gov (United States)

    Fyfe, Richard W.; Sanchez, Jr., Amadeo

    1990-01-01

    An optical fiber positioning apparatus for an optical fiber stripping device is disclosed which is capable of providing precise axial alignment between an optical fiber to be stripped of its outer jacket and the cutting blades of a stripping device. The apparatus includes a first bore having a width approximately equal to the diameter of an unstripped optical fiber and a counter bore axially aligned with the first bore and dimensioned to precisely receive a portion of the stripping device in axial alignment with notched cutting blades within the stripping device to thereby axially align the notched cutting blades of the stripping device with the axis of the optical fiber to permit the notched cutting blades to sever the jacket on the optical fiber without damaging the cladding on the optical fiber. In a preferred embodiment, the apparatus further includes a fiber stop which permits determination of the length of jacket to be removed from the optical fiber.

  5. Suppressors of DnaAATP imposed overinitiation in Escherichia coli

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Riber, Leise; Cohen, Malene

    2011-01-01

    Chromosome replication in Escherichia coli is limited by the supply of DnaA associated with ATP. Cells deficient in RIDA (Regulatory Inactivation of DnaA) due to a deletion of the hda gene accumulate suppressor mutations (hsm) to counteract the overinitiation caused by an elevated DnaAATP level....... Eight spontaneous hda suppressor mutations were identified by whole-genome sequencing, and three of these were analysed further. Two mutations (hsm-2 and hsm-4) mapped in the dnaA gene and led to a reduced ability to initiate replication from oriC. One mutation (hsm-1) mapped to the seqA promoter...

  6. Adenovirus 36 DNA in human adipose tissue.

    Science.gov (United States)

    Ponterio, E; Cangemi, R; Mariani, S; Casella, G; De Cesare, A; Trovato, F M; Garozzo, A; Gnessi, L

    2015-12-01

    Recent studies have suggested a possible correlation between obesity and adenovirus 36 (Adv36) infection in humans. As information on adenoviral DNA presence in human adipose tissue are limited, we evaluated the presence of Adv36 DNA in adipose tissue of 21 adult overweight or obese patients. Total DNA was extracted from adipose tissue biopsies. Virus detection was performed using PCR protocols with primers against specific Adv36 fiber protein and the viral oncogenic E4orf1 protein nucleotide sequences. Sequences were aligned with the NCBI database and phylogenetic analyses were carried out with MEGA6 software. Adv36 DNA was found in four samples (19%). This study indicates that some individuals carry Adv36 in the visceral adipose tissue. Further studies are needed to determine the specific effect of Adv36 infection on adipocytes, the prevalence of Adv36 infection and its relationship with obesity in the perspective of developing a vaccine that could potentially prevent or mitigate infection.

  7. Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.

    Science.gov (United States)

    Tobiasson, Magnus; Abdulkadir, Hani; Lennartsson, Andreas; Katayama, Shintaro; Marabita, Francesco; De Paepe, Ayla; Karimi, Mohsen; Krjutskov, Kaarel; Einarsdottir, Elisabet; Grövdal, Michael; Jansson, Monika; Ben Azenkoud, Asmaa; Corddedu, Lina; Lehmann, Sören; Ekwall, Karl; Kere, Juha; Hellström-Lindberg, Eva; Ungerstedt, Johanna

    2017-04-25

    Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the histone modifications H3K18ac and H3K9me3 (ChIP seq). Aza induced a general increase in gene expression with 924 significantly upregulated genes but this increase showed no correlation with changes in DNA methylation or H3K18ac, and only a weak association with changes in H3K9me3. Interestingly, we observed activation of transcripts containing 15 endogenous retroviruses (ERVs) confirming previous cell line studies. DNA methylation decreased moderately in 99% of all genes, with a median β-value reduction of 0.018; the most pronounced effects seen in heterochromatin. Aza-induced hypomethylation correlated significantly with change in H3K9me3. The pattern of H3K18ac and H3K9me3 displayed large differences between patients and healthy controls without any consistent pattern induced by Aza. We conclude that the marked induction of gene expression only partly could be explained by epigenetic changes, and propose that activation of ERVs may contribute to the clinical effects of Aza in MDS.

  8. DNA repair

    International Nuclear Information System (INIS)

    Setlow, R.

    1978-01-01

    Some topics discussed are as follows: difficulty in extrapolating data from E. coli to mammalian systems; mutations caused by UV-induced changes in DNA; mutants deficient in excision repair; other postreplication mechanisms; kinds of excision repair systems; detection of repair by biochemical or biophysical means; human mutants deficient in repair; mutagenic effects of UV on XP cells; and detection of UV-repair defects among XP individuals

  9. Genetic maps and physical units

    International Nuclear Information System (INIS)

    Karunakaran, V.; Holt, G.

    1976-01-01

    The relationships between physical and genetic units are examined. Genetic mapping involves the detection of linkage of genes and the measurement of recombination frequencies. The genetic distance is measured in map units and is proportional to the recombination frequencies between linked markers. Physical mapping of genophores, particularly the simple genomes of bacteriophages and bacterial plasmids can be achieved through heteroduplex analysis. Genetic distances are dependent on recombination frequencies and, therefore, can only be correlated accurately with physical unit lengths if the recombination frequency is constant throughout the entire genome. Methods are available to calculate the equivalent length of DNA per average map unit in different organisms. Such estimates indicate significant differences from one organism to another. Gene lengths can also be calculated from the number of amino acids in a specified polypeptide and relating this to the number of nucleotides required to code for such a polypeptide. Many attempts have been made to relate microdosimetric measurements to radiobiological data. For irradiation effects involving deletion of genetic material such a detailed correlation may be possible in systems where heteroduplex analysis or amino acid sequencing can be performed. The problems of DNA packaging and other functional associations within the cell in interpreting data is discussed

  10. Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression.

    Science.gov (United States)

    Aze, Antoine; Sannino, Vincenzo; Soffientini, Paolo; Bachi, Angela; Costanzo, Vincenzo

    2016-06-01

    Half of the human genome is made up of repetitive DNA. However, mechanisms underlying replication of chromosome regions containing repetitive DNA are poorly understood. We reconstituted replication of defined human chromosome segments using bacterial artificial chromosomes in Xenopus laevis egg extract. Using this approach we characterized the chromatin assembly and replication dynamics of centromeric alpha-satellite DNA. Proteomic analysis of centromeric chromatin revealed replication-dependent enrichment of a network of DNA repair factors including the MSH2-6 complex, which was required for efficient centromeric DNA replication. However, contrary to expectations, the ATR-dependent checkpoint monitoring DNA replication fork arrest could not be activated on highly repetitive DNA due to the inability of the single-stranded DNA binding protein RPA to accumulate on chromatin. Electron microscopy of centromeric DNA and supercoil mapping revealed the presence of topoisomerase I-dependent DNA loops embedded in a protein matrix enriched for SMC2-4 proteins. This arrangement suppressed ATR signalling by preventing RPA hyper-loading, facilitating replication of centromeric DNA. These findings have important implications for our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions.

  11. MAPPING INNOVATION

    DEFF Research Database (Denmark)

    Thuesen, Christian Langhoff; Koch, Christian

    2011-01-01

    By adopting a theoretical framework from strategic niche management research (SNM) this paper presents an analysis of the innovation system of the Danish Construction industry. The analysis shows a multifaceted landscape of innovation around an existing regime, built around existing ways of working...... and developed over generations. The regime is challenged from various niches and the socio-technical landscape through trends as globalization. Three niches (Lean Construction, BIM and System Deliveries) are subject to a detailed analysis showing partly incompatible rationales and various degrees of innovation...... potential. The paper further discusses how existing policymaking operates in a number of tensions one being between government and governance. Based on the concepts from SNM the paper introduces an innovation map in order to support the development of meta-governance policymaking. By mapping some...

  12. Mapping filmmaking

    DEFF Research Database (Denmark)

    Gilje, Øystein; Frølunde, Lisbeth; Lindstrand, Fredrik

    2010-01-01

    This chapter concerns mapping patterns in regards to how young filmmakers (age 15 – 20) in the Scandinavian countries learn about filmmaking. To uncover the patterns, we present portraits of four young filmmakers who participated in the Scandinavian research project Making a filmmaker. The focus ...... is on their learning practices and how they create ‘learning paths’ in relation to resources in diverse learning contexts, whether formal, non-formal and informal contexts.......This chapter concerns mapping patterns in regards to how young filmmakers (age 15 – 20) in the Scandinavian countries learn about filmmaking. To uncover the patterns, we present portraits of four young filmmakers who participated in the Scandinavian research project Making a filmmaker. The focus...

  13. Natural Fiber Composites: A Review

    Energy Technology Data Exchange (ETDEWEB)

    Westman, Matthew P.; Fifield, Leonard S.; Simmons, Kevin L.; Laddha, Sachin; Kafentzis, Tyler A.

    2010-03-07

    The need for renewable fiber reinforced composites has never been as prevalent as it currently is. Natural fibers offer both cost savings and a reduction in density when compared to glass fibers. Though the strength of natural fibers is not as great as glass, the specific properties are comparable. Currently natural fiber composites have two issues that need to be addressed: resin compatibility and water absorption. The following preliminary research has investigated the use of Kenaf, Hibiscus cannabinus, as a possible glass replacement in fiber reinforced composites.

  14. Enhanced radiation resistant fiber optics

    International Nuclear Information System (INIS)

    Lyons, P.B.; Looney, L.D.

    1993-01-01

    A process for producing an optical fiber having enhanced radiation resistance is provided, the process including maintaining an optical fiber within a hydrogen-containing atmosphere for sufficient time to yield a hydrogen-permeated optical fiber having an elevated internal hydrogen concentration, and irradiating the hydrogen-permeated optical fiber at a time while the optical fiber has an elevated internal hydrogen concentration with a source of ionizing radiation. The radiation source is typically a cobalt-60 source and the fiber is pre-irradiated with a dose level up to about 1000 kilorads of radiation. 4 figures

  15. Fiber-optic technology review

    International Nuclear Information System (INIS)

    Lyons, P.B.

    1980-01-01

    A history of fiber technology is presented. The advantages of fiber optics are discussed (bandwidth, cost, weight and size, nonmetallic construction and isolation). Some aspects of the disadvantages of fiber systems briefly discussed are fiber and cable availability, fiber components, radiation effects, receivers and transmitters, and material dispersion. Particular emphasis over the next several years will involve development of fibers and systems optimized for use at wavelengths near 1.3 μm and development of wavelengths multiplexers for simultaneous system operation at several wavelengths

  16. Enhanced radiation resistant fiber optics

    Science.gov (United States)

    Lyons, P.B.; Looney, L.D.

    1993-11-30

    A process for producing an optical fiber having enhanced radiation resistance is provided, the process including maintaining an optical fiber within a hydrogen-containing atmosphere for sufficient time to yield a hydrogen-permeated optical fiber having an elevated internal hydrogen concentration, and irradiating the hydrogen-permeated optical fiber at a time while the optical fiber has an elevated internal hydrogen concentration with a source of ionizing radiation. The radiation source is typically a cobalt-60 source and the fiber is pre-irradiated with a dose level up to about 1000 kilorads of radiation. 4 figures.

  17. Anisotropic elliptic optical fibers

    Science.gov (United States)

    Kang, Soon Ahm

    1991-05-01

    The exact characteristic equation for an anisotropic elliptic optical fiber is obtained for odd and even hybrid modes in terms of infinite determinants utilizing Mathieu and modified Mathieu functions. A simplified characteristic equation is obtained by applying the weakly guiding approximation such that the difference in the refractive indices of the core and the cladding is small. The simplified characteristic equation is used to compute the normalized guide wavelength for an elliptical fiber. When the anisotropic parameter is equal to unity, the results are compared with the previous research and they are in close agreement. For a fixed value normalized cross-section area or major axis, the normalized guide wavelength lambda/lambda(sub 0) for an anisotropic elliptic fiber is small for the larger value of anisotropy. This condition indicates that more energy is carried inside of the fiber. However, the geometry and anisotropy of the fiber have a smaller effect when the normalized cross-section area is very small or very large.

  18. Hybrid Fiber Layup and Fiber-Reinforced Polymeric Composites Produced Therefrom

    Science.gov (United States)

    Barnell, Thomas J. (Inventor); Garrigan, Sean P. (Inventor); Rauscher, Michael D. (Inventor); Dietsch, Benjamin A. (Inventor); Cupp, Gary N. (Inventor)

    2018-01-01

    Embodiments of a hybrid fiber layup used to form a fiber-reinforced polymeric composite, and a fiber-reinforced polymeric composite produced therefrom are disclosed. The hybrid fiber layup comprises one or more dry fiber strips and one or more prepreg fiber strips arranged side by side within each layer, wherein the prepreg fiber strips comprise fiber material impregnated with polymer resin and the dry fiber strips comprise fiber material without impregnated polymer resin.

  19. Graphene fiber: a new trend in carbon fibers

    OpenAIRE

    Zhen Xu; Chao Gao

    2015-01-01

    New fibers with increased strength and rich functionalities have been untiringly pursued by materials researchers. In recent years, graphene fiber has arisen as a new carbonaceous fiber with high expectations in terms of mechanical and functional performance. In this review, we elucidated the concept of sprouted graphene fibers, including strategies for their fabrication and their basic structural attributes. We examine the rapid advances in the promotion of mechanical/functional properties o...

  20. Optical fiber switch

    Science.gov (United States)

    Early, James W.; Lester, Charles S.

    2002-01-01

    Optical fiber switches operated by electrical activation of at least one laser light modulator through which laser light is directed into at least one polarizer are used for the sequential transport of laser light from a single laser into a plurality of optical fibers. In one embodiment of the invention, laser light from a single excitation laser is sequentially transported to a plurality of optical fibers which in turn transport the laser light to separate individual remotely located laser fuel ignitors. The invention can be operated electro-optically with no need for any mechanical or moving parts, or, alternatively, can be operated electro-mechanically. The invention can be used to switch either pulsed or continuous wave laser light.

  1. Fiber Optic Calorimetry

    International Nuclear Information System (INIS)

    Rudy, C.; Bayliss, S.; Bracken, D.; Bush, J.; Davis, P.

    1997-01-01

    A twin-bridge calorimeter using optical fiber as the sensor element was constructed and tested. This system demonstrates the principle and capability of using optical fibers for heat-flow measurements of special nuclear material. This calorimeter uses piezoelectric-generated phase-carrier modulation with subsequent electronic signal processes to allow phase shifts as small as 1 microradian (microrad) to be measured. The sensing element consists of 21-m lengths of single-mode optical fiber wrapped around sample and reference chambers. The sensitivity of the calorimeter was determined to be 74 radians (rad) of phase shift per milliwatt of thermal power. One milliwatt of thermal power is equivalent to 400 mg of plutonium (6% 240 Pu). The system noise base was about 0.2 rad, equivalent to about 1 mg of plutonium

  2. Femtosecond Fiber Lasers

    Science.gov (United States)

    Bock, Katherine J.

    This thesis focuses on research I have done on ytterbium-doped femtosecond fiber lasers. These lasers operate in the near infrared region, lasing at 1030 nm. This wavelength is particularly important in biomedical applications, which includes but is not limited to confocal microscopy and ablation for surgical incisions. Furthermore, fiber lasers are advantageous compared to solid state lasers in terms of their cost, form factor, and ease of use. Solid state lasers still dominate the market due to their comparatively high energy pulses. High energy pulse generation in fiber lasers is hindered by either optical wave breaking or by multipulsing. One of the main challenges for fiber lasers is to overcome these limitations to achieve high energy pulses. The motivation for the work done in this thesis is increasing the output pulse peak power and energy. The main idea of the work is that decreasing the nonlinearity that acts on the pulse inside the cavity will prevent optical wave breaking, and thus will generate higher energy pulses. By increasing the output energy, ytterbium-doped femtosecond fiber lasers can be competitive with solid state lasers which are used commonly in research. Although fiber lasers tend to lack the wavelength tuning ability of solid state lasers, many biomedical applications take advantage of the 1030 microm central wavelength of ytterbium-doped fiber lasers, so the major limiting factor of fiber lasers in this field is simply the output power. By increasing the output energy without resorting to external amplification, the cavity is optimized and cost can remain low and economical. During verification of the main idea, the cavity was examined for possible back-reflections and for components with narrow spectral bandwidths which may have contributed to the presence of multipulsing. Distinct cases of multipulsing, bound pulse and harmonic mode-locking, were observed and recorded as they may be of more interest in the future. The third

  3. Higher Order Mode Fibers

    DEFF Research Database (Denmark)

    Israelsen, Stine Møller

    This PhD thesis considers higher order modes (HOMs) in optical fibers. That includes their excitation and characteristics. Within the last decades, HOMs have been applied both for space multiplexing in optical communications, group velocity dispersion management and sensing among others......-radial polarization as opposed to the linear polarization of the LP0X modes. The effect is investigated numerically in a double cladding fiber with an outer aircladding using a full vectorial modesolver. Experimentally, the bowtie modes are excited using a long period grating and their free space characteristics...... and polarization state are investigated. For this fiber, the onset of the bowtie effect is shown numerically to be LP011. The characteristics usually associated with Bessel-likes modes such as long diffraction free length and selfhealing are shown to be conserved despite the lack of azimuthal symmetry...

  4. Fiber optic calorimetry

    International Nuclear Information System (INIS)

    Rudy, C.R.; Bayliss, S.C.; Bracken, D.S.; Bush, I.J.; Davis, P.G.

    1998-01-01

    A twin-bridge calorimeter using optical fiber as the sensor element was constructed and tested. This system demonstrates the principle and capability of using optical fibers for heat-flow measurements of special nuclear material. This calorimeter uses piezoelectric-generated phase-carrier modulation with subsequent electronic signal processing to allow phase shifts as small as 1 microrad to be measured. The sensing element consists of 21-m lengths of single-mode optical fiber wrapped around sample and reference chambers. The sensitivity of the calorimeter was determined to be 74 rad of phase shift per mW of thermal power. One milliwatt of thermal power is equivalent to 400 mg of plutonium (6% 240 Pu). The system noise base was about 0.2 rad, equivalent to about 1 mg of plutonium

  5. Fiber optic calorimetry

    International Nuclear Information System (INIS)

    Rudy, C.; Bayliss, S.; Bracken, D.; Bush, J.; Davis, P.

    1998-01-01

    A twin-bridge calorimeter using optical fiber as the sensor element was constructed and tested. This system demonstrates the principle and capability of using fiber for heat-flow measurements of special nuclear material. This calorimeter uses piezoelectric-generated phase-carrier modulation with subsequent electronic signal processing to allow phase shifts as small as 1 microradian (μrad) to be measured. The sensing element consists of 21-m lengths of single-mode optical fiber wrapped around sample and reference chambers. The sensitivity of the calorimeter was determined to be 74 radians (rad) of phase shift per milliwatt of thermal power. One milliwatt of thermal power is equivalent to 400 mg of plutonium (6% 240 Pu). The system noise base was about 0.2 rad, equivalent to about 1 mg of plutonium

  6. Multibeam fiber laser cutting

    DEFF Research Database (Denmark)

    Olsen, Flemming Ove; Hansen, Klaus Schütt; Nielsen, Jakob Skov

    2009-01-01

    The appearance of the high power high brilliance fiber laser has opened for new possibilities in laser materials processing. In laser cutting this laser has demonstrated high cutting performance compared to the dominating Cutting laser, the CO2 laser. However, quality problems in fiber......-laser cutting have until now limited its application to metal cutting. In this paper the first results of proof-of-principle Studies applying a new approach (patent pending) for laser cutting with high brightness and short wavelength lasers will be presented. In the approach, multibeam patterns are applied...... to control the melt flow out of the cut kerf resulting in improved cut quality in metal cutting. The beam patterns in this study are created by splitting up beams from two single mode fiber lasers and combining these beams into a pattern in the cut kerf. The results are obtained with a total of 550 W...

  7. Monolithic Yb-fiber femtosecond laser using photonic crystal fiber

    DEFF Research Database (Denmark)

    Liu, Xiaomin; Lægsgaard, Jesper; Turchinovich, Dmitry

    2008-01-01

    We demonstrate, both experimentally and theoretically, an environmentally stable monolithic all-PM modelocked femtosecond Yb-fiber laser, with laser output pulse compressed in a spliced-on low-loss hollow-core photonic crystal fiber. Our laser provides direct fiber-end delivery of 4 nJ pulses...

  8. K3-fibered Calabi-Yau threefolds II, singular fibers

    OpenAIRE

    Hunt, Bruce

    1999-01-01

    In part I of this paper we constructed certain fibered Calabi-Yaus by a quotient construction in the context of weighted hypersurfaces. In this paper look at the case of K3 fibrations more closely and study the singular fibers which occur. This differs from previous work since the fibrations we discuss have constant modulus, and the singular fibers have torsion monodromy.

  9. Single fiber pullout from hybrid fiber reinforced concrete

    NARCIS (Netherlands)

    Markovich, I.; Van Mier, J.G.M.; Walraven, J.C.

    2001-01-01

    Hybrid fiber reinforcement can be very efficient for improving the tensile response of the composite. In such materials, fibers of different geometries can act as bridging mechanisms over cracks of different widths. The fiber bridging efficiency depends on the interface properties, which makes

  10. Isolation and characterization of gene sequences expressed in cotton fiber

    Directory of Open Access Journals (Sweden)

    Taciana de Carvalho Coutinho

    2016-06-01

    Full Text Available ABSTRACT Cotton fiber are tubular cells which develop from the differentiation of ovule epidermis. In addition to being one of the most important natural fiber of the textile group, cotton fiber afford an excellent experimental system for studying the cell wall. The aim of this work was to isolate and characterise the genes expressed in cotton fiber (Gossypium hirsutum L. to be used in future work in cotton breeding. Fiber of the cotton cultivar CNPA ITA 90 II were used to extract RNA for the subsequent generation of a cDNA library. Seventeen sequences were obtained, of which 14 were already described in the NCBI database (National Centre for Biotechnology Information, such as those encoding the lipid transfer proteins (LTPs and arabinogalactans (AGP. However, other cDNAs such as the B05 clone, which displays homology with the glycosyltransferases, have still not been described for this crop. Nevertheless, results showed that several clones obtained in this study are associated with cell wall proteins, wall-modifying enzymes and lipid transfer proteins directly involved in fiber development.

  11. Fluoride glass fiber optics

    CERN Document Server

    Aggarwal, Ishwar D

    1991-01-01

    Fluoride Glass Fiber Optics reviews the fundamental aspects of fluoride glasses. This book is divided into nine chapters. Chapter 1 discusses the wide range of fluoride glasses with an emphasis on fluorozirconate-based compositions. The structure of simple fluoride systems, such as BaF2 binary glass is elaborated in Chapter 2. The third chapter covers the intrinsic transparency of fluoride glasses from the UV to the IR, with particular emphasis on the multiphonon edge and electronic edge. The next three chapters are devoted to ultra-low loss optical fibers, reviewing methods for purifying and

  12. Nonlinear fiber optics

    CERN Document Server

    Agrawal, Govind

    2012-01-01

    Since the 4e appeared, a fast evolution of the field has occurred. The 5e of this classic work provides an up-to-date account of the nonlinear phenomena occurring inside optical fibers, the basis of all our telecommunications infastructure as well as being used in the medical field. Reflecting the big developments in research, this new edition includes major new content: slow light effects, which offers a reduction in noise and power consumption and more ordered network traffic-stimulated Brillouin scattering; vectorial treatment of highly nonlinear fibers; and a brand new chapter o

  13. Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand.

    Science.gov (United States)

    Yasukawa, Takehiro; Reyes, Aurelio; Cluett, Tricia J; Yang, Ming-Yao; Bowmaker, Mark; Jacobs, Howard T; Holt, Ian J

    2006-11-15

    Using two-dimensional agarose gel electrophoresis, we show that mitochondrial DNA (mtDNA) replication of birds and mammals frequently entails ribonucleotide incorporation throughout the lagging strand (RITOLS). Based on a combination of two-dimensional agarose gel electrophoretic analysis and mapping of 5' ends of DNA, initiation of RITOLS replication occurs in the major non-coding region of vertebrate mtDNA and is effectively unidirectional. In some cases, conversion of nascent RNA strands to DNA starts at defined loci, the most prominent of which maps, in mammalian mtDNA, in the vicinity of the site known as the light-strand origin.

  14. Impact of operation conditions, foulant adsorption, and chemical cleaning on the nanomechanical properties of ultrafiltraion hollow fiber membranes

    KAUST Repository

    Gutierrez, Leonardo; Keucken, Alexander; Aubry, Cyril; Zaouri, Noor A.; Teychene, Benoit; Croue, Jean-Philippe

    2018-01-01

    This study analyzed the change in nanomechanical properties of ultrafiltration hollow fiber membranes harvested from pilot-scale units after twelve months of operation. Quantitative Nanomechanical Mapping technique was used to distinguish between

  15. Silicon photonics for multicore fiber communication

    DEFF Research Database (Denmark)

    Ding, Yunhong; Kamchevska, Valerija; Dalgaard, Kjeld

    2016-01-01

    We review our recent work on silicon photonics for multicore fiber communication, including multicore fiber fan-in/fan-out, multicore fiber switches towards reconfigurable optical add/drop multiplexers. We also present multicore fiber based quantum communication using silicon devices.......We review our recent work on silicon photonics for multicore fiber communication, including multicore fiber fan-in/fan-out, multicore fiber switches towards reconfigurable optical add/drop multiplexers. We also present multicore fiber based quantum communication using silicon devices....

  16. DNA repair

    International Nuclear Information System (INIS)

    Van Zeeland, A.A.

    1984-01-01

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  17. Fiber-optic seismic sensor

    International Nuclear Information System (INIS)

    Finch, G. W.; Udd, E.

    1985-01-01

    A vibration sensor is constructed by providing two preferably matched coils of fiber-optic material. When the sensor experiences vibration, a differential pressure is exerted on the two fiber coils. The differential pressure results in a variation in the relative optical path lengths between the two fibers so that light beams transmitted through the two fibers are differently delayed, the phase difference therebetween being a detectable indication of the vibration applied to the sensor

  18. Tunable femtosecond Cherenkov fiber laser

    DEFF Research Database (Denmark)

    Liu, Xiaomin; Svane, Ask Sebastian; Lægsgaard, Jesper

    2014-01-01

    We demonstrate electrically-tunable femtosecond Cherenkov fiber laser output at the visible range. Using an all-fiber, self-starting femtosecond Yb-doped fiber laser as the pump source and nonlinear photonic crystal fiber link as the wave-conversion medium, ultrafast, milliwatt-level, tunable...... and spectral isolated Cherenkov radiation at visible wavelengths are reported. Such a femtosecond Cherenkov laser source is promising for practical biophotonics applications....

  19. Mapping Resilience

    DEFF Research Database (Denmark)

    Carruth, Susan

    2015-01-01

    by planners when aiming to construct resilient energy plans. It concludes that a graphical language has the potential to be a significant tool, flexibly facilitating cross-disciplinary communication and decision-making, while emphasising that its role is to support imaginative, resilient planning rather than...... the relationship between resilience and energy planning, suggesting that planning in, and with, time is a core necessity in this domain. It then reviews four examples of graphically mapping with time, highlighting some of the key challenges, before tentatively proposing a graphical language to be employed...

  20. In-fiber integrated Michelson interferometer.

    Science.gov (United States)

    Yuan, Libo; Yang, Jun; Liu, Zhihai; Sun, Jiaxing

    2006-09-15

    A novel fiber-optic in-fiber integrated Michelson interferometer has been proposed and demonstrated. It consists of a segment of two-core fiber with a mirrored fiber end. The sensing characteristics based on the two-core fiber bending, corresponding to the shift of the phase of the two-core in-fiber integrated Michelson interferometer, are investigated.

  1. Mutagenic DNA repair in enterobacteria

    International Nuclear Information System (INIS)

    Sedgwick, S.G.; Chao Ho; Woodgate, R.

    1991-01-01

    Sixteen species of enterobacteria have been screened for mutagenic DNA repair activity. In Escherichia coli, mutagenic DNA repair is encoded by the umuDC operon. Synthesis of UmuD and UmuC proteins is induced as part of the SOS response to DNA damage, and after induction, the UmuD protein undergoes an autocatalytic cleavage to produce the carboxy-terminal UmuD' fragment needed for induced mutagenesis. The presence of a similar system in other species was examined by using a combined approach of inducible-mutagenesis assays, cross-reactivity to E. coli UmuD and UmuD' antibodies to test for induction and cleavage of UmuD-like proteins, and hybridization with E. coli and Salmonella typhimurium u mu DNA probes to map umu-like genes. The results indicate a more widespread distribution of mutagenic DNA repair in other species than was previously thought. They also show that umu loci can be more complex in other species than in E. coli. Differences in UV-induced mutability of more than 200-fold were seen between different species of enteric bacteria and even between multiple natural isolates of E. coli, and yet some of the species which display a poorly mutable phenotype still have umu-like genes and proteins. It is suggested that umuDC genes can be curtailed in their mutagenic activities but that they may still participate in some other, unknown process which provides the continued stimulus for their retention

  2. Transient attenuation in optical fibers

    International Nuclear Information System (INIS)

    Hopkins, A.A.; Kelly, R.E.; Looney, L.D.; Lyons, P.B.

    1984-01-01

    Low and high energy pulsed electron beams were used to generate radiation-induced transient attenuation in high-OH, Suprasil core, PCS fibers, demonstrating the energy dependence of the radiation damage and recovery mechanisms. A radiation resistant low-OH fiber was studied and its performance contrasted to that of high-OH materials. Several fibers with differing core compositions were also studied

  3. Fiber Optics and Library Technology.

    Science.gov (United States)

    Koenig, Michael

    1984-01-01

    This article examines fiber optic technology, explains some of the key terminology, and speculates about the way fiber optics will change our world. Applications of fiber optics to library systems in three major areas--linkage of a number of mainframe computers, local area networks, and main trunk communications--are highlighted. (EJS)

  4. Water-core Fresnel fiber

    NARCIS (Netherlands)

    Martelli, C.; Canning, J.; Lyytikainen, K.; Groothoff, N.

    2005-01-01

    A water core photonic crystal Fresnel fiber exploiting a hole distribution on zone plates of a cylindrical waveguide was developed and characterized. This fiber has similar guiding properties as the pristine air-hole guiding fiber although a large loss edge ~900nm is observed indicating that the

  5. Optical fibers for FTTH application

    Science.gov (United States)

    Guzowski, Bartlomiej; Tosik, Grzegorz; Lisik, Zbigniew; Bedyk, Michal; Kubiak, Andrzej

    2013-07-01

    In this paper the specifics of FTTH (Fiber To The Home) networks in terms of requirements for optical fibers has been presented. Optical fiber samples used in FTTH applications acquired from the worldwide leading manufacturers were subjected to small diameter mandrel wraps tests. The detailed procedures of performed tests and the measurement results has been presented.

  6. Photonic-crystal fibers gyroscope

    Directory of Open Access Journals (Sweden)

    Ali Muse Haider

    2015-01-01

    Full Text Available In this paper we proposed to use of a photonic crystal fiber with an inner hollow defect. The use of such fibers is not affected by a material medium on the propagation of optical radiation. Photonic crystal fibers present special properties and capabilities that lead to an outstanding potential for sensing applications

  7. Thermal properties of Fiber ropes

    DEFF Research Database (Denmark)

    Bossolini, Elena; Nielsen, Ole Wennerberg; Oland, Espen

    There is a trend within the oil and gas market to shift from steel wire ropes to fiber ropes for lifting, hoisting and mooring applications. The cost of fiber ropes is about 2-3 times that of steel wire ropes, but the natural buoyancy of fiber ropes reduces the overall weight resulting in smaller...

  8. Shedding Light on Fiber Optics.

    Science.gov (United States)

    Bunch, Robert M.

    1994-01-01

    Explains the principles of fiber optics as a medium for light-wave communication. Current uses of fiber systems on college campuses include voice, video, and local area network applications. A group of seven school districts in Minnesota are linked via fiber-optic cables. Other uses are discussed. (MLF)

  9. Fabrication of Optical Fiber Devices

    Science.gov (United States)

    Andres, Miguel V.

    In this paper we present the main research activities of the Laboratorio de Fibras Opticas del Instituto de Ciencia de los Materiales de la Universidad de Valencia. We show some of the main results obtained for devices based on tapered fibers, fiber Bragg gratings, acousto-optic effects and photonic crystal fibers.

  10. Microstructured Fibers: Design and Applications

    DEFF Research Database (Denmark)

    Bjarklev, Anders Overgaard; Broeng, Jes

    2006-01-01

    Holey fibers, in which airholes are introduced in the cladding region and extended in the axial direction of the fiber, have been known since the early days of silica waveguide research. Early work demonstrated the first low-loss fibers, which featured very small silica cores held in air by thin...

  11. Illustrative white matter fiber bundles

    NARCIS (Netherlands)

    Otten, R.J.G.; Vilanova, A.; Wetering, van de H.M.M.

    2010-01-01

    Diffusion Tensor Imaging (DTI) has made feasible the visualization of the fibrous structure of the brain whitematter. In the last decades, several fiber-tracking methods have been developed to reconstruct the fiber tracts fromDTI data. Usually these fiber tracts are shown individually based on some

  12. Bluebonnet Fiber Collages

    Science.gov (United States)

    Sterling, Joan

    2009-01-01

    This article presents a lesson that uses stitching and applique techniques to create a fiber collage in which every child is successful with high-quality work. This lesson was inspired by Tomie dePaola's "The Legend of the Bluebonnet." The back cover had a lovely illustration of the bluebonnet flower the author thought would translate easily to a…

  13. The dentate mossy fibers

    DEFF Research Database (Denmark)

    Blaabjerg, Morten; Zimmer, Jens

    2007-01-01

    Hippocampal mossy fibers are the axons of the dentate granule cells and project to hippocampal CA3 pyramidal cells and mossy cells of the dentate hilus (CA4) as well as a number of interneurons in the two areas. Besides their role in hippocampal function, studies of which are still evolving...

  14. Optical Fiber Protection

    Science.gov (United States)

    1999-01-01

    F&S Inc. developed and commercialized fiber optic and microelectromechanical systems- (MEMS) based instrumentation for harsh environments encountered in the aerospace industry. The NASA SBIR programs have provided F&S the funds and the technology to develop ruggedized coatings and coating techniques that are applied during the optical fiber draw process. The F&S optical fiber fabrication facility and developed coating methods enable F&S to manufacture specialty optical fiber with custom designed refractive index profiles and protective or active coatings. F&S has demonstrated sputtered coatings using metals and ceramics and combinations of each, and has also developed techniques to apply thin coatings of specialized polyimides formulated at NASA Langley Research Center. With these capabilities, F&S has produced cost-effective, reliable instrumentation and sensors capable of withstanding temperatures up to 800? C and continues building commercial sales with corporate partners and private funding. More recently, F&S has adapted the same sensing platforms to provide the rapid detection and identification of chemical and biological agents

  15. Optical Fiber Spectroscopy

    Science.gov (United States)

    Buoncristiani, A. M.

    1999-01-01

    This is the final report of work done on NASA Grant NAG-1-443. The work covers the period from July 1, 1992 to December 1, 1998. During this period several distinct but related research studies and work tasks were undertaken. These different subjects are enumerated below with a description of the work done on each of them. The focus of the research was the development of optical fibers for use as distributed temperature and stress sensors. The initial concept was to utilize the utilize the temperature and stress dependence of emission from rare earth and transition metal ions substitutionally doped into crystalline or glass fibers. During the course of investigating this it became clear that fiber Bragg gratings provided a alternative for making the desired measurements and there was a shift of research focus on to include the photo-refractive properties of germano-silicate glasses used for most gratings and to the possibility of developing fiber laser sources for an integrated optical sensor in the research effort. During the course of this work several students from Christopher Newport University and other universities participated in this effort. Their names are listed below. Their participation was an important part of their education.

  16. Fiber and Your Child

    Science.gov (United States)

    ... meals instead of white rice. Add beans (kidney, black, navy, and pinto) to rice dishes for even more fiber. Spice up salads with berries and almonds, chickpeas, artichoke hearts, and beans (kidney, black, navy, or pinto). Use whole-grain (corn or ...

  17. Mapping of

    Directory of Open Access Journals (Sweden)

    Sayed M. Arafat

    2014-06-01

    Full Text Available Land cover map of North Sinai was produced based on the FAO-Land Cover Classification System (LCCS of 2004. The standard FAO classification scheme provides a standardized system of classification that can be used to analyze spatial and temporal land cover variability in the study area. This approach also has the advantage of facilitating the integration of Sinai land cover mapping products to be included with the regional and global land cover datasets. The total study area is covering a total area of 20,310.4 km2 (203,104 hectare. The landscape classification was based on SPOT4 data acquired in 2011 using combined multispectral bands of 20 m spatial resolution. Geographic Information System (GIS was used to manipulate the attributed layers of classification in order to reach the maximum possible accuracy. GIS was also used to include all necessary information. The identified vegetative land cover classes of the study area are irrigated herbaceous crops, irrigated tree crops and rain fed tree crops. The non-vegetated land covers in the study area include bare rock, bare soils (stony, very stony and salt crusts, loose and shifting sands and sand dunes. The water bodies were classified as artificial perennial water bodies (fish ponds and irrigated canals and natural perennial water bodies as lakes (standing. The artificial surfaces include linear and non-linear features.

  18. Polymer-Derived Ceramic Fibers

    Science.gov (United States)

    Ichikawa, Hiroshi

    2016-07-01

    SiC-based ceramic fibers are derived from polycarbosilane or polymetallocarbosilane precursors and are classified into three groups according to their chemical composition, oxygen content, and C/Si atomic ratio. The first-generation fibers are Si-C-O (Nicalon) fibers and Si-Ti-C-O (Tyranno Lox M) fibers. Both fibers contain more than 10-wt% oxygen owing to oxidation during curing and lead to degradation in strength at temperatures exceeding 1,300°C. The maximum use temperature is 1,100°C. The second-generation fibers are SiC (Hi-Nicalon) fibers and Si-Zr-C-O (Tyranno ZMI) fibers. The oxygen content of these fibers is reduced to less than 1 wt% by electron beam irradiation curing in He. The thermal stability of these fibers is improved (they are stable up to 1,500°C), but their creep resistance is limited to a maximum of 1,150°C because their C/Si atomic ratio results in excess carbon. The third-generation fibers are stoichiometric SiC fibers, i.e., Hi-Nicalon Type S (hereafter Type S), Tyranno SA, and Sylramic™ fibers. They exhibit improved thermal stability and creep resistance up to 1,400°C. Stoichiometric SiC fibers meet many of the requirements for the use of ceramic matrix composites for high-temperature structural application. SiBN3C fibers derived from polyborosilazane also show promise for structural applications, remain in the amorphous state up to 1,800°C, and have good high-temperature creep resistance.

  19. Improved Optical Fiber Chemical Sensors

    Science.gov (United States)

    Egalon, Claudio O.; Rogowski, Robert S.

    1994-01-01

    Calculations, based on exact theory of optical fiber, have shown how to increase optical efficiency sensitivity of active-core, step-index-profile optical-fiber fluorosensor. Calculations result of efforts to improve efficiency of optical-fiber chemical sensor of previous concept described in "Making Optical-Fiber Chemical Sensors More Sensitive" (LAR-14525). Optical fiber chemical detector of enhanced sensitivity made in several configurations. Portion of fluorescence or chemiluminescence generated in core, and launched directly into bound electromagnetic modes that propagate along core to photodetector.

  20. Solid fiber Z-pinches

    International Nuclear Information System (INIS)

    Lindemuth, I.R.

    1989-01-01

    One- and two-dimensional magnetohydrodynamic computations have been performed to study the behavior of solid deuterium fiber Z-pinch experiments performed at Los Alamos and the Naval Research Laboratory. The computations use a tabulated atomic data base and ''cold-start'' initial conditions. The computations predict that the solid fiber persists longer in existing experiments than previously expected and that the discharge actually consists of a relatively low-density, hot plasma which has been ablated from the fiber. The computations exhibit m = 0 behavior in the hot, exterior plasma prior to complete ablation of the solid fiber. The m = 0 behavior enhances the fiber ablation rate. 10 refs., 5 figs

  1. Introduction to optical fiber sensors

    International Nuclear Information System (INIS)

    Moukdad, S.

    1991-01-01

    Optical fiber sensors have many advantages over other types of sensors, for example: Low weight, immunity from EMI, electrical isolation, chemical passivity, and high sensitivity. In this seminar, a brief explanation of the optical fiber sensors, their use, and their advantages will be given. After, a description of the main optical fiber sensor components will be presented. Principles of some kinds of optical fiber sensors will be presented, and the principle of the fiber-optic rotation sensor and its realization will be discussed in some details, as well as its main applications. (author). 5 refs, 8 figs, 2 tabs

  2. Bonding Properties of Basalt Fiber and Strength Reduction According to Fiber Orientation

    OpenAIRE

    Choi, Jeong-Il; Lee, Bang

    2015-01-01

    The basalt fiber is a promising reinforcing fiber because it has a relatively higher tensile strength and a density similar to that of a concrete matrix as well as no corrosion possibility. This study investigated experimentally the bonding properties of basalt fiber with cementitious material as well as the effect of fiber orientation on the tensile strength of basalt fiber for evaluating basalt fiber?s suitability as a reinforcing fiber. Single fiber pullout tests were performed and then th...

  3. Guiding Properties of Silica/Air Hollow-Core Bragg Fibers

    DEFF Research Database (Denmark)

    Foroni, Matteo; Passaro, Davide; Poli, Federica

    2008-01-01

    The guiding properties of realistic silica/air hollow-core Bragg fibers have been investigated by calculating the dispersion curves, the confinement loss spectrum and the field distribution of the guided modes through a full-vector modal solver based on the finite element method. In particular, t...... the different possible applications, the feasibility of a DNA bio-sensor based on a hollow-core Bragg fiber has been demonstrated....

  4. Fiber optics: A brief introduction

    International Nuclear Information System (INIS)

    Gruchalla, M.E.

    1989-01-01

    A basic introduction into the principles of fiber optics is presented. A review of both the underlying physical principles and the individual elements of typical fiber-optic systems are presented. The optical phenomenon of total internal reflection is reviewed. The basic construction of the optical fiber is presented. Both step-index and graded-index fiber designs are reviewed. Multimode and single-mode fiber constructions are considered and typical performance parameters given. Typical optical-fiber bandwidth and loss characteristics are compared to various common coaxial cables, waveguides, and air transmission. The constructions of optical-fiber cables are reviewed. Both loose-tube and tightly-buffered designs are considered. Several optical connection approaches are presented. Photographs of several representative optical connectors are included. Light Emitting Diode and Laser Diode emitters for fiber-optic applications are reviewed, and some advantages and shortcomings of each are considered. The phenomenon of modal noise is briefly explained. Both PIN and Avalanche photodetectors are reviewed and their performance parameters compared. Methods of data transmission over optical fiber are introduced. Principles of Wavelength, Frequency, and Time Division Multiplexing are briefly presented. The technology of fiber-optic sensors is briefly reviewed with basic principles introduced. The performance of a fiber-optic strain sensor is included as a practical example. 7 refs., 10 figs

  5. Close sequence identity between ribosomal DNA episomes of the ...

    Indian Academy of Sciences (India)

    Unknown

    The restriction map of the E. dispar rDNA circle showed close simi- larity to EhR1 .... for 30 cycles in a DNA Thermal cycler (MJ Research,. USA). 3. .... by asterisk. The gaps show the variation between E. dispar and E. histolytica sequences.

  6. 49. Brazilian congress on genetics. DNA double helix. Abstracts

    International Nuclear Information System (INIS)

    2003-01-01

    Use of radioisotopes and ionizing radiations in genetics is presented. Several aspects related to men, animals, plants and microorganisms are reported highlighting biological radiation effects, evolution, mutagenesis and genetic engineering. Genetic mapping, gene mutations, genetic diversity, DNA hybridization, DNA sequencing, plant cultivation and plant grow are studied as well

  7. Concentrating Genomic Length DNA in a Microfabricated Array

    DEFF Research Database (Denmark)

    Chen, Yu; Abrams, Ezra S.; Boles, T. Christian

    2015-01-01

    the DNA molecules to minimal coil size using polyethylene glycol (PEG) derived depletion forces. We map out the sweet spot, where concentration occurs, as a function of PEG concentration and flow speed using a combination of theoretical analysis and experiment. Purification of DNA from enzymatic reactions...

  8. Sequence finishing and mapping of Drosophila melanogasterheterochromatin

    Energy Technology Data Exchange (ETDEWEB)

    Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

    2007-06-15

    Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

  9. All-Fiber Raman Probe

    DEFF Research Database (Denmark)

    Brunetti, Anna Chiara

    by means of fiber components. Assuming the possibility to use a fiber laser with a fundamental radiation at 1064nm, in-fiber efficient second harmonic generation is achieved by optically poling the core of the waveguide delivering the excitation light to the sample. In this way, Raman spectroscopy...... in the visible range can be performed. The simultaneous delivery of the excitation light and collection of the Raman signal from the sample are achieved by means of a doubleclad fiber, whose core and inner cladding act as \\independent" transmission channels. A double-clad fiber coupler allows for the recovery...... of the collected Raman scattering from the inner-cladding region of the double-clad fiber, thus replacing the bulk dichroic component normally used to demultiplex the pump and Raman signal. A tunable Rayleigh-rejection filter based on a liquid filled-photonic bandgap fiber is also demonstrated in this work...

  10. The hunt for origins of DNA replication in multicellular eukaryotes

    DEFF Research Database (Denmark)

    Urban, J. M.; Foulk, M. S.; Casella, Cinzia

    2015-01-01

    Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope...... that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed....

  11. Interference, heterogeneity and disease gene mapping

    Energy Technology Data Exchange (ETDEWEB)

    Keats, B. [Louisiana State Univ. Medical Center, New Orleans, LA (United States)

    1996-12-31

    The Human Genome Project has had a major impact on genetic research over the past five years. The number of mapped genes is now over 3,000 compared with approximately 1,600 in 1989 and only about 260 ten years before that. The realization that extensive variation could be detected in anonymous DNA segments greatly enhanced the potential for mapping by linkage analysis. Previously, linkage studies had depended on polymorphisms that could be detected in red blood cell antigens, proteins (revealed by electrophoresis and isoelectric focusing), and cytogenetic heteromorphisms. The identification of thousands of polymorphic DNA markers throughout the human genome has led to the construction of high density genetic linkage maps. These maps provide the data necessary to test hypotheses concerning differences in recombination rates and levels of interference. They are also important for disease gene mapping because the existence of these genes must be inferred from the phenotype. Showing linkage of a disease gene to a DNA marker is the first step towards isolating the disease gene, determining its protein product, and developing effective therapies. However, interpretation of results is not always straightforward. Factors such as etiological heterogeneity and undetected irregular segregation can lead to confusing linkage results and incorrect conclusions about the locations of disease genes. This paper will discuss these phenomena and present examples that illustrate the problems, as well as approaches to dealing with them. 23 refs., 3 figs., 3 tabs.

  12. Capacity-Approaching Superposition Coding for Optical Fiber Links

    DEFF Research Database (Denmark)

    Estaran Tolosa, Jose Manuel; Zibar, Darko; Tafur Monroy, Idelfonso

    2014-01-01

    We report on the first experimental demonstration of superposition coded modulation (SCM) for polarization-multiplexed coherent-detection optical fiber links. The proposed coded modulation scheme is combined with phase-shifted bit-to-symbol mapping (PSM) in order to achieve geometric and passive......-SCM) is employed in the framework of bit-interleaved coded modulation with iterative decoding (BICM-ID) for forward error correction. The fiber transmission system is characterized in terms of signal-to-noise ratio for back-to-back case and correlated with simulated results for ideal transmission over additive...... white Gaussian noise channel. Thereafter, successful demodulation and decoding after dispersion-unmanaged transmission over 240-km standard single mode fiber of dual-polarization 6-Gbaud 16-, 32- and 64-ary SCM-PSM is experimentally demonstrated....

  13. Triaxial fiber optic magnetic field sensor for MRI applications

    Science.gov (United States)

    Filograno, Massimo L.; Pisco, Marco; Catalano, Angelo; Forte, Ernesto; Aiello, Marco; Soricelli, Andrea; Davino, Daniele; Visone, Ciro; Cutolo, Antonello; Cusano, Andrea

    2016-05-01

    In this paper, we report a fiber-optic triaxial magnetic field sensor, based on Fiber Bragg Gratings (FBGs) integrated with giant magnetostrictive material, the Terfenol-D. The realized sensor has been designed and engineered for Magnetic Resonance Imaging (MRI) applications. A full magneto-optical characterization of the triaxial sensing probe has been carried out, providing the complex relationship among the FBGs wavelength shift and the applied magnetostatic field vector. Finally, the developed fiber optic sensors have been arranged in a sensor network composed of 20 triaxial sensors for mapping the magnetic field distribution in a MRI-room at a diagnostic center in Naples (SDN), equipped with Positron emission tomography/magnetic resonance (PET/MR) instrumentation. Experimental results reveal that the proposed sensor network can be efficiently used in MRI centers for performing quality assurance tests, paving the way for novel integrated tools to measure the magnetic dose accumulated day by day by MRI operators.

  14. MaNGA: Mapping Nearby Galaxies at Apache Point Observatory

    Science.gov (United States)

    Weijmans, A.-M.; MaNGA Team

    2016-10-01

    MaNGA (Mapping Nearby Galaxies at APO) is a galaxy integral-field spectroscopic survey within the fourth generation Sloan Digital Sky Survey (SDSS-IV). It will be mapping the composition and kinematics of gas and stars in 10,000 nearby galaxies, using 17 differently sized fiber bundles. MaNGA's goal is to provide new insights in galaxy formation and evolution, and to deliver a local benchmark for current and future high-redshift studies.

  15. Myoclonic epilepsy with ragged-red fibers without increased lactate levels.

    Science.gov (United States)

    Kimura, Shigemi; Ozasa, Shiro; Nakamura, Kyoko; Nomura, Keiko; Kosuge, Hirofumi

    2009-07-01

    Myoclonic epilepsy associated with ragged-red fibers is one of the mitochondrial encephalomyopathies. Pathogenic mitochondrial DNA mutations have been identified in the mitochondrial transfer RNA (tRNA)(Lys) at positions 8344 and 8356. Characteristics of myoclonic epilepsy associated with ragged-red fibers include myoclonic epilepsy, generalized epilepsy, hearing loss, exercise intolerance, lactic acidosis, and ragged-red fibers. The elevated lactate level is one of the most important symptoms needed to make a diagnosis of mitochondrial encephalomyopathy. In the present case, however, myoclonic epilepsy was associated with ragged-red fibers but without increased lactate levels. Therefore, myoclonic epilepsy associated with ragged-red fibers should be suspected in a patient who has myoclonic epilepsy that is difficult to control with antiepileptic medications and who has other symptoms of mitochondrial disease, such as mental retardation, even if the patient's lactate level is normal.

  16. Chemically modified carbon fibers and their applications

    International Nuclear Information System (INIS)

    Ermolenko, I.N.; Lyubliner, I.P.; Gulko, N.V.

    1990-01-01

    This book gives a comprehensive review about chemically modified carbon fibers (e.g. by incorporation of other elements) and is structured as follows: 1. Types of carbon fibers, 2. Structure of carbon fibers, 3. Properties of carbon fibers, 4. The cellulose carbonization process, 5. Formation of element-carbon fiber materials, 6. Surface modification of carbon fibers, and 7. Applications of carbon fibers (e.g. adsorbents, catalysts, constituents of composites). (MM)

  17. Multispot fiber laser welding

    DEFF Research Database (Denmark)

    Schutt Hansen, Klaus

    This dissertation presents work and results achieved in the field of multi beam fiber laser welding. The project has had a practical approach, in which simulations and modelling have been kept at a minimum. Different methods to produce spot patterns with high power single mode fiber lasers have...... been examined and evaluated. It is found that both diamond turned DOE’s in zinc sulphide and multilevel etched DOE’s (Diffractive Optical Elements) in fused silica have a good performance. Welding with multiple beams in a butt joint configuration has been tested. Results are presented, showing it has...... been possible to control the welding width in incremental steps by adding more beams in a row. The laser power was used to independently control the keyhole and consequently the depth of fusion. An example of inline repair of a laser weld in butt joint configuration was examined. Zinc powder was placed...

  18. Fiber optic fluid detector

    Science.gov (United States)

    Angel, S.M.

    1987-02-27

    Particular gases or liquids are detected with a fiber optic element having a cladding or coating of a material which absorbs the fluid or fluids and which exhibits a change of an optical property, such as index of refraction, light transmissiveness or fluoresence emission, for example, in response to absorption of the fluid. The fluid is sensed by directing light into the fiber optic element and detecting changes in the light, such as exit angle changes for example, that result from the changed optical property of the coating material. The fluid detector may be used for such purposes as sensing toxic or explosive gases in the atmosphere, measuring ground water contamination or monitoring fluid flows in industrial processes, among other uses. 10 figs.

  19. Fiber optic fluid detector

    Science.gov (United States)

    Angel, S. Michael

    1989-01-01

    Particular gases or liquids are detected with a fiber optic element (11, 11a to 11j) having a cladding or coating of a material (23, 23a to 23j) which absorbs the fluid or fluids and which exhibits a change of an optical property, such as index of refraction, light transmissiveness or fluoresence emission, for example, in response to absorption of the fluid. The fluid is sensed by directing light into the fiber optic element and detecting changes in the light, such as exit angle changes for example, that result from the changed optical property of the coating material. The fluid detector (24, 24a to 24j) may be used for such purposes as sensing toxic or explosive gases in the atmosphere, measuring ground water contamination or monitoring fluid flows in industrial processes, among other uses.

  20. Optical fiber communications

    CERN Document Server

    Keiser, Gerd

    2008-01-01

    The fourth edition of this popular text and reference book presents the fundamental principles for understanding and applying optical fiber technology to sophisticated modern telecommunication systems. Optical-fiber-based telecommunication networks have become a major information-transmission-system, with high capacity links encircling the globe in both terrestrial and undersea installations. Numerous passive and active optical devices within these links perform complex transmission and networking functions in the optical domain, such as signal amplification, restoration, routing, and switching. Along with the need to understand the functions of these devices comes the necessity to measure both component and network performance, and to model and stimulate the complex behavior of reliable high-capacity networks.

  1. Cloning of Salmonella typhimurium DNA encoding mutagenic DNA repair

    International Nuclear Information System (INIS)

    Thomas, S.M.; Sedgwick, S.G.

    1989-01-01

    Mutagenic DNA repair in Escherichia coli is encoded by the umuDC operon. Salmonella typhimurium DNA which has homology with E. coli umuC and is able to complement E. coli umuC122::Tn5 and umuC36 mutations has been cloned. Complementation of umuD44 mutants and hybridization with E. coli umuD also occurred, but these activities were much weaker than with umuC. Restriction enzyme mapping indicated that the composition of the cloned fragment is different from the E. coli umuDC operon. Therefore, a umu-like function of S. typhimurium has been found; the phenotype of this function is weaker than that of its E. coli counterpart, which is consistent with the weak mutagenic response of S. typhimurium to UV compared with the response in E. coli

  2. Fiber Optic Surface Plasmon Resonance-Based Biosensor Technique: Fabrication, Advancement, and Application.

    Science.gov (United States)

    Liang, Gaoling; Luo, Zewei; Liu, Kunping; Wang, Yimin; Dai, Jianxiong; Duan, Yixiang

    2016-05-03

    Fiber optic-based biosensors with surface plasmon resonance (SPR) technology are advanced label-free optical biosensing methods. They have brought tremendous progress in the sensing of various chemical and biological species. This review summarizes four sensing configurations (prism, grating, waveguide, and fiber optic) with two ways, attenuated total reflection (ATR) and diffraction, to excite the surface plasmons. Meanwhile, the designs of different probes (U-bent, tapered, and other probes) are also described. Finally, four major types of biosensors, immunosensor, DNA biosensor, enzyme biosensor, and living cell biosensor, are discussed in detail for their sensing principles and applications. Future prospects of fiber optic-based SPR sensor technology are discussed.

  3. DNA Repair Systems

    Indian Academy of Sciences (India)

    DNA molecule which makes it ideal for storage and propagation of genetic information. ... of these errors are broadly referred to as DNA repair. DNA can ... changes occur in the human genome per day. ..... nails, frequent physical and mental.

  4. Stable fiber interferometer

    International Nuclear Information System (INIS)

    Izmajlov, G.N.; Nikolaev, F.A.; Ozolin, V.V.; Grigor'yants, V.V.; Chamorovskij, Yu.K.

    1989-01-01

    The problem of construction the long-base Michelson interferometer for gravitational wave detection is discussed. Possible sources of noise and instability are considered. It is shown that evacuation of fiber interferometer, the winding of its arms on the glass ceramic bases, stabilization of radiation source frequency and seismic isolation of the base allow one to reduce its instability to the level, typical of mirror interferometer with the comparable optical base. 10 refs.; 2 figs

  5. Deriving muscle fiber diameter from recorded single fiber potential.

    Science.gov (United States)

    Zalewska, Ewa

    2017-12-01

    The aim of the study was to estimate muscle fiber diameters through analysis of single muscle fiber potentials (SFPs) recorded in the frontalis muscle of a healthy subject. Our previously developed analytical and graphic method to derive fiber diameter from the analysis of the negative peak duration and the amplitude of SFP, was applied to a sample of ten SFPs recorded in vivo. Muscle fiber diameters derived from the simulation method for the sample of frontalis muscle SFPs are consistent with anatomical data for this muscle. The results confirm the utility of proposed simulation method. Outlying data could be considered as the result of a contribution of other fibers to the potential recorded using an SFEMG electrode. Our graphic tool provides a rapid estimation of muscle fiber diameter. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  6. Carbon fiber reinforced asphalt concrete

    International Nuclear Information System (INIS)

    Jahromi, Saeed G.

    2008-01-01

    Fibers are often used in the manufacture of other materials. For many years, they have been utilized extensively in numerous applications in civil engineering. Fiber-reinforcement refers to incorporating materials with desired properties within some other materials lacking those properties. Use of fibers is not a new phenomenon, as the technique of fiber-reinforced bitumen began early as 1950. In all industrialized countries today, nearly all concretes used in construction are reinforced. A multitude of fibers and fiber materials are being introduced in the market regularly. The present paper presents characteristics and properties of carbon fiber-reinforced asphalt mixtures, which improve the performance of pavements. To evaluate the effect of fiber contents on bituminous mixtures, laboratory investigations were carried out on the samples with and without fibers. During the course of this study, various tests were undertaken, applying Marshall Test indirect tensile test, creep test and resistance to fatigue cracking by using repeated load indirect tensile test. Carbon fiber exhibited consistency in results and as such it was observed that the addition of fiber does affect the properties of bituminous mixtures, i.e. an increase in its stability and decrease in the flow value as well as an increase in voids in the mix. Results indicate that fibers have the potential to resist structural distress in pavement, in the wake of growing traffic loads and thus improve fatigue by increasing resistance to cracks or permanent deformation. On the whole, the results show that the addition of carbon fiber will improve some of the mechanical properties like fatigue and deformation in the flexible pavement. (author)

  7. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  8. Thermoluminescence characteristics of Ge-doped optical fibers with different dimensions for radiation dosimetry

    International Nuclear Information System (INIS)

    Begum, Mahfuza; Rahman, A.K.M. Mizanur; Abdul-Rashid, H.A.; Yusoff, Z.; Begum, Mahbuba; Mat-Sharif, K.A.; Amin, Y.M.; Bradley, D.A.

    2015-01-01

    Important thermoluminescence (TL) properties of five (5) different core sizes Ge-doped optical fibers have been studied to develop new TL material with better response. These are drawn from same preform applying different speed and tension during drawing phase to produce Ge-doped optical fibers with five (5) different core sizes. The results of the investigations are also compared with most commonly used standard TLD-100 chips (LiF:Mg,Ti) and commercial multimode Ge-doped optical fiber (Yangtze Optical Fiber, China). Scanning Electron Microscope (SEM) and EDX analysis of the fibers are also performed to map Ge distribution across the deposited region. Standard Gamma radiation source in Secondary Standard Dosimetry Lab (SSDL) was used for irradiation covering dose range from 1 Gy to 10 Gy. The essential dosimetric parameters that have been studied are TL linearity, reproducibility and fading. Prior to irradiation all samples ∼0.5 cm length are annealed at temperature of 400 °C for 1 h period to standardize their sensitivities and background. Standard TLD-100 chips are also annealed for 1 h at 400 °C and subsequently 2 h at 100 °C to yield the highest sensitivity. TL responses of these fibers show linearity over a wide gamma radiation dose that is an important property for radiation dosimetry. Among all fibers used in this study, 100 μm core diameter fiber provides highest response that is 2.6 times than that of smallest core (20 μm core) optical fiber. These fiber-samples demonstrate better response than commercial multi-mode optical fiber and also provide low degree of fading about 20% over a period of fifteen days for gamma radiation. Effective atomic number (Z eff ) is found in the range (13.25–13.69) which is higher than soft tissue (7.5) however within the range of human-bone (11.6–13.8). All the fibers can also be re-used several times as a detector after annealing. TL properties of the Ge-doped optical fibers indicate promising applications in

  9. Monolithic femtosecond Yb-fiber laser with photonic crystal fibers

    DEFF Research Database (Denmark)

    Liu, Xiaomin; Lægsgaard, Jesper; Turchinovich, Dmitry

    We demonstrate a monolithic stable SESAM-modelocked self-starting Yb-fiber laser. A novel PM all-solid photonic bandgap fiber is used for intra-cavity of dispersion management. The ex-cavity final pulse compression is performed in a spliced-on PM hollow-core photonic crystal fiber. The laser...... directly delivers 9 nJ pulses of 275 fs duration with pulse repetition of 26.7MHz....

  10. Deep Into the Fibers! Postmortem Diffusion Tensor Imaging in Forensic Radiology.

    Science.gov (United States)

    Flach, Patricia Mildred; Schroth, Sarah; Schweitzer, Wolf; Ampanozi, Garyfalia; Slotboom, Johannes; Kiefer, Claus; Germerott, Tanja; Thali, Michael J; El-Koussy, Marwan

    2015-09-01

    In traumatic brain injury, diffusion-weighted and diffusion tensor imaging of the brain are essential techniques for determining the pathology sustained and the outcome. Postmortem cross-sectional imaging is an established adjunct to forensic autopsy in death investigation. The purpose of this prospective study was to evaluate postmortem diffusion tensor imaging in forensics for its feasibility, influencing factors and correlation to the cause of death compared with autopsy. Postmortem computed tomography, magnetic resonance imaging, and diffusion tensor imaging with fiber tracking were performed in 10 deceased subjects. The Likert scale grading of colored fractional anisotropy maps was correlated to the body temperature and intracranial pathology to assess the diagnostic feasibility of postmortem diffusion tensor imaging and fiber tracking. Optimal fiber tracking (>15,000 fiber tracts) was achieved with a body temperature at 10°C. Likert scale grading showed no linear correlation (P > 0.7) to fiber tract counts. No statistically significant correlation between total fiber count and postmortem interval could be observed (P = 0.122). Postmortem diffusion tensor imaging and fiber tracking allowed for radiological diagnosis in cases with shearing injuries but was impaired in cases with pneumencephalon and intracerebral mass hemorrhage. Postmortem diffusion tensor imaging with fiber tracking provides an exceptional in situ insight "deep into the fibers" of the brain with diagnostic benefit in traumatic brain injury and axonal injuries in the assessment of the underlying cause of death, considering influencing factors for optimal imaging technique.

  11. Nerve Fiber Flux Analysis Using Wide-Field Swept-Source Optical Coherence Tomography.

    Science.gov (United States)

    Tan, Ou; Liu, Liang; Liu, Li; Huang, David

    2018-02-01

    To devise a method to quantify nerve fibers over their arcuate courses over an extended peripapillary area using optical coherence tomography (OCT). Participants were imaged with 8 × 8-mm volumetric OCT scans centered at the optic disc. A new quantity, nerve fiber flux (NFF), represents the cross-sectional area transected perpendicular to the nerve fibers. The peripapillary area was divided into 64 tracks with equal flux. An iterative algorithm traced the trajectory of the tracks assuming that the relative distribution of the NFF was conserved with compensation for fiber connections to ganglion cells on the macular side. Average trajectory was averaged from normal eyes and use to calculate the NFF maps for glaucomatous eyes. The NFF maps were divided into eight sectors that correspond to visual field regions. There were 24 healthy and 10 glaucomatous eyes enrolled. The algorithm converged on similar patterns of NFL tracks for all healthy eyes. In glaucomatous eyes, NFF correlated with visual field sensitivity in the arcuate sectors (Spearman ρ = 0.53-0.62). Focal nerve fiber loss in glaucomatous eyes appeared as uniform tracks of NFF defects that followed the expected arcuate fiber trajectory. Using an algorithm based on the conservation of flux, we derived nerve fiber trajectories in the peripapillary area. The NFF map is useful for the visualization of focal defects and quantification of sector nerve fiber loss from wide-area volumetric OCT scans. NFF provides a cumulative measure of volumetric loss along nerve fiber tracks and could improve the detection of focal glaucoma damage.

  12. Human Mind Maps

    Science.gov (United States)

    Glass, Tom

    2016-01-01

    When students generate mind maps, or concept maps, the maps are usually on paper, computer screens, or a blackboard. Human Mind Maps require few resources and little preparation. The main requirements are space where students can move around and a little creativity and imagination. Mind maps can be used for a variety of purposes, and Human Mind…

  13. Homogenization of long fiber reinforced composites including fiber bending effects

    DEFF Research Database (Denmark)

    Poulios, Konstantinos; Niordson, Christian Frithiof

    2016-01-01

    This paper presents a homogenization method, which accounts for intrinsic size effects related to the fiber diameter in long fiber reinforced composite materials with two independent constitutive models for the matrix and fiber materials. A new choice of internal kinematic variables allows...... of the reinforcing fibers is captured by higher order strain terms, resulting in an accurate representation of the micro-mechanical behavior of the composite. Numerical examples show that the accuracy of the proposed model is very close to a non-homogenized finite-element model with an explicit discretization...

  14. The tensile strength of mechanical joint prototype of lontar fiber composite

    Science.gov (United States)

    Bale, Jefri; Adoe, Dominggus G. H.; Boimau, Kristomus; Sakera, Thomas

    2018-03-01

    In the present study, an experimental activity has been programmed to investigate the effect of joint prototype configuration on tensile strength of lontar (Borassus Flabellifer) fiber composite. To do so, a series of tests were conducted to establish the tensile strength of different joint prototype configuration specimen of lontar fiber composite. In addition, post observation of macroscope was used to map damage behavior. The analysis of lontar fiber composite is a challenge since the material has limited information than others natural fiber composites materials. The results shown that, under static tensile loading, the tensile strength of 13 MPa produced by single lap joint of lontar fiber composite is highest compare to 11 MPa of tensile strength generated by step lap joint and double lap joint where produced the lowest tensile strength of 6 MPa. It is concluded that the differences of tensile strength depend on the geometric dimensions of the cross-sectional area and stress distribution of each joint prototype configuration.

  15. Raman fiber distributed feedback lasers.

    Science.gov (United States)

    Westbrook, Paul S; Abedin, Kazi S; Nicholson, Jeffrey W; Kremp, Tristan; Porque, Jerome

    2011-08-01

    We demonstrate fiber distributed feedback (DFB) lasers using Raman gain in two germanosilicate fibers. Our DFB cavities were 124 mm uniform fiber Bragg gratings with a π phase shift offset from the grating center. Our pump was at 1480 nm and the DFB lasers operated on a single longitudinal mode near 1584 nm. In a commercial Raman gain fiber, the maximum output power, linewidth, and threshold were 150 mW, 7.5 MHz, and 39 W, respectively. In a commercial highly nonlinear fiber, these figures improved to 350 mW, 4 MHz, and 4.3 W, respectively. In both lasers, more than 75% of pump power was transmitted, allowing for the possibility of substantial amplification in subsequent Raman gain fiber. © 2011 Optical Society of America

  16. Molecular cloning and restriction analysis of EcoRI-fragments of Vicia faba rDNA

    International Nuclear Information System (INIS)

    Yakura, Kimitaka; Tanifuji, Shigeyuki.

    1983-01-01

    EcoRI-fragments of Vicia faba rDNA were cloned in plasmid pBR325. Southern blot hybridization of BamHI-digests of these cloned plasmids and Vicia genomic DNA led to the determination of relative positions of BamHI sites in the rDNA and the physical map that had been tentatively made is corrected. (author)

  17. Multi-color fluorescent DNA analysis in an integrated optofluidic lab-on-a-chip

    NARCIS (Netherlands)

    Dongre, C.; van Weerd, J.; van Weeghel, R.; Martinez-Vazquez, R.; Osellame, R.; Cerullo, G.; Besselink, G.A.J.; van den Vlekkert, H.H.; Hoekstra, Hugo; Pollnau, Markus

    Sorting and sizing of DNA molecules within the human genome project has enabled the genetic mapping of various illnesses. By employing tiny lab-on-a-chip devices for such DNA analysis, integrated DNA sequencing and genetic diagnostics have become feasible. However, such diagnostic chips typically

  18. Flexible optical fiber sensor based on polyurethane

    DEFF Research Database (Denmark)

    Kaysir, Md Rejvi; Stefani, Alessio; Lwin, Richard

    Polyurethane (PU) based hollow core fibers are investigated as optical sensors. The flexibility of PU fibers makes it suitable for sensing mechanical perturbations. We fabricated a PU fiber using the fiber drawing method, characterized the fiber and experimentally demonstrated a simple way...... to measure deformation, in the form of applied pressure....

  19. A fiber-optic polarimetric demonstration kit

    International Nuclear Information System (INIS)

    Eftimov, T; Dimitrova, T L; Ivanov, G

    2012-01-01

    A simple and multifunctional fiber-optic polarimetric kit on the basis of highly birefringent single-mode fibers is presented. The fiber-optic polarimetric kit allows us to perform the following laboratory exercises: (i) fiber excitation and the measurement of numerical aperture, (ii) polarization preservation and (iii) obtain polarization-sensitive fiberized interferometers.

  20. Dynamic drainage of froth with wood fibers

    Science.gov (United States)

    J.Y. Zhu; Freya Tan

    2005-01-01

    Understanding froth drainage with fibers (or simply called fiber drainage in froth) is important for improving fiber yield in the flotation deinking operation. In this study, the data of water and fiber mass in foams collected at different froth heights were used to reconstruct the time dependent and spatially resolved froth density and fiber volumetric concentration...

  1. Fiber optic sensor and method for making

    Science.gov (United States)

    Vartuli, James Scott; Bousman, Kenneth Sherwood; Deng, Kung-Li; McEvoy, Kevin Paul; Xia, Hua

    2010-05-18

    A fiber optic sensor including a fiber having a modified surface integral with the fiber wherein the modified surface includes an open pore network with optical agents dispersed within the open pores of the open pore network. Methods for preparing the fiber optic sensor are also provided. The fiber optic sensors can withstand high temperatures and harsh environments.

  2. Electrochromic fiber-shaped supercapacitors.

    Science.gov (United States)

    Chen, Xuli; Lin, Huijuan; Deng, Jue; Zhang, Ye; Sun, Xuemei; Chen, Peining; Fang, Xin; Zhang, Zhitao; Guan, Guozhen; Peng, Huisheng

    2014-12-23

    An electrochromic fiber-shaped super-capacitor is developed by winding aligned carbon nanotube/polyaniline composite sheets on an elastic fiber. The fiber-shaped supercapacitors demonstrate rapid and reversible chromatic transitions under different working states, which can be directly observed by the naked eye. They are also stretchable and flexible, and are woven into textiles to display designed signals in addition to storing energy. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. System for testing optical fibers

    Science.gov (United States)

    Golob, John E. [Olathe, KS; Looney, Larry D. [Los Alamos, NM; Lyons, Peter B. [Los Alamos, NM; Nelson, Melvin A. [Santa Barbara, CA; Davies, Terence J. [Santa Barbara, CA

    1980-07-15

    A system for measuring a combination of optical transmission properties of fiber optic waveguides. A polarized light pulse probe is injected into one end of the optical fiber. Reflections from discontinuities within the fiber are unpolarized whereas reflections of the probe pulse incident to its injection remain polarized. The polarized reflections are prevented from reaching a light detector whereas reflections from the discontinuities reaches the detector.

  4. Quantifying anisotropy and fiber orientation in human brain histological sections

    Directory of Open Access Journals (Sweden)

    Matthew D Budde

    2013-02-01

    Full Text Available Diffusion weighted imaging (DWI has provided unparalleled insight into the microscopic structure and organization of the central nervous system. Diffusion tensor imaging (DTI and other models of the diffusion MRI signal extract microstructural properties of tissues with relevance to the normal and injured brain. Despite the prevalence of such techniques and applications, accurate and large-scale validation has proven difficult, particularly in the human brain. In this report, human brain sections obtained from a digital public brain bank were employed to quantify anisotropy and fiber orientation using structure tensor analysis. The derived maps depict the intricate complexity of white matter fibers at a resolution not attainable with current DWI experiments. Moreover, the effects of multiple fiber bundles (i.e. crossing fibers and intravoxel fiber dispersion were demonstrated. Examination of the cortex and hippocampal regions validated specific features of previous in vivo and ex vivo DTI studies of the human brain. Despite the limitation to two dimensions, the resulting images provide a unique depiction of white matter organization at resolutions currently unattainable with DWI. The method of analysis may be used to validate tissue properties derived from DTI and alternative models of the diffusion signal.

  5. Flexible pH-Sensing Hydrogel Fibers for Epidermal Applications.

    Science.gov (United States)

    Tamayol, Ali; Akbari, Mohsen; Zilberman, Yael; Comotto, Mattia; Lesha, Emal; Serex, Ludovic; Bagherifard, Sara; Chen, Yu; Fu, Guoqing; Ameri, Shideh Kabiri; Ruan, Weitong; Miller, Eric L; Dokmeci, Mehmet R; Sonkusale, Sameer; Khademhosseini, Ali

    2016-03-01

    Epidermal pH is an indication of the skin's physiological condition. For example, pH of wound can be correlated to angiogenesis, protease activity, bacterial infection, etc. Chronic nonhealing wounds are known to have an elevated alkaline environment, while healing process occurs more readily in an acidic environment. Thus, dermal patches capable of continuous pH measurement can be used as point-of-care systems for monitoring skin disorder and the wound healing process. Here, pH-responsive hydrogel fibers are presented that can be used for long-term monitoring of epidermal wound condition. pH-responsive dyes are loaded into mesoporous microparticles and incorporated into hydrogel fibers using a microfluidic spinning system. The fabricated pH-responsive microfibers are flexible and can create conformal contact with skin. The response of pH-sensitive fibers with different compositions and thicknesses are characterized. The suggested technique is scalable and can be used to fabricate hydrogel-based wound dressings with clinically relevant dimensions. Images of the pH-sensing fibers during real-time pH measurement can be captured with a smart phone camera for convenient readout on-site. Through image processing, a quantitative pH map of the hydrogel fibers and the underlying tissue can be extracted. The developed skin dressing can act as a point-of-care device for monitoring the wound healing process. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Maps & minds : mapping through the ages

    Science.gov (United States)

    ,

    1984-01-01

    Throughout time, maps have expressed our understanding of our world. Human affairs have been influenced strongly by the quality of maps available to us at the major turning points in our history. "Maps & Minds" traces the ebb and flow of a few central ideas in the mainstream of mapping. Our expanding knowledge of our cosmic neighborhood stems largely from a small number of simple but grand ideas, vigorously pursued.

  7. Genome Regions Associated with Functional Performance of Soybean Stem Fibers in Polypropylene Thermoplastic Composites.

    Directory of Open Access Journals (Sweden)

    Yarmilla Reinprecht

    Full Text Available Plant fibers can be used to produce composite materials for automobile parts, thus reducing plastic used in their manufacture, overall vehicle weight and fuel consumption when they replace mineral fillers and glass fibers. Soybean stem residues are, potentially, significant sources of inexpensive, renewable and biodegradable natural fibers, but are not curretly used for biocomposite production due to the functional properties of their fibers in composites being unknown. The current study was initiated to investigate the effects of plant genotype on the performance characteristics of soybean stem fibers when incorporated into a polypropylene (PP matrix using a selective phenotyping approach. Fibers from 50 lines of a recombinant inbred line population (169 RILs grown in different environments were incorporated into PP at 20% (wt/wt by extrusion. Test samples were injection molded and characterized for their mechanical properties. The performance of stem fibers in the composites was significantly affected by genotype and environment. Fibers from different genotypes had significantly different chemical compositions, thus composites prepared with these fibers displayed different physical properties. This study demonstrates that thermoplastic composites with soybean stem-derived fibers have mechanical properties that are equivalent or better than wheat straw fiber composites currently being used for manufacturing interior automotive parts. The addition of soybean stem residues improved flexural, tensile and impact properties of the composites. Furthermore, by linkage and in silico mapping we identified genomic regions to which quantitative trait loci (QTL for compositional and functional properties of soybean stem fibers in thermoplastic composites, as well as genes for cell wall synthesis, were co-localized. These results may lead to the development of high value uses for soybean stem residue.

  8. Comparative genome analysis and resistance gene mapping in grain legumes

    International Nuclear Information System (INIS)

    Young, N.D.

    1998-01-01

    Using, DNA markers and genome organization, several important disease resistance genes have been analyzed in mungbean (Vigna radiata), cowpea (Vigna unguiculata), common bean (Phaseolus vulgaris), and soybean (Glycine max). In the process, medium-density linkage maps consisting of restriction fragment length polymorphism (RFLP) markers were constructed for both mungbean and cowpea. Comparisons between these maps, as well as the maps of soybean and common bean, indicate that there is significant conservation of DNA marker order, though the conserved blocks in soybean are much shorter than in the others. DNA mapping results also indicate that a gene for seed weight may be conserved between mungbean and cowpea. Using the linkage maps, genes that control bruchid (genus Callosobruchus) and powdery mildew (Erysiphe polygoni) resistance in mungbean, aphid resistance in cowpea (Aphis craccivora), and cyst nematode (Heterodera glycines) resistance in soybean have all been mapped and characterized. For some of these traits resistance was found to be oligogenic and DNA mapping uncovered multiple genes involved in the phenotype. (author)

  9. Lunar Map Catalog

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Map Catalog includes various maps of the moon's surface, including Apollo landing sites; earthside, farside, and polar charts; photography index maps; zone...

  10. Baby Brain Map

    Science.gov (United States)

    ... a Member Home Resources & Services Professional Resource Baby Brain Map Mar 17, 2016 The Brain Map was adapted in 2006 by ZERO TO ... supports Adobe Flash Player. To view the Baby Brain Map, please visit this page on a browser ...

  11. Snapshots for Semantic Maps

    National Research Council Canada - National Science Library

    Nielsen, Curtis W; Ricks, Bob; Goodrich, Michael A; Bruemmer, David; Few, Doug; Walton, Miles

    2004-01-01

    .... Semantic maps are a relatively new approach to information presentation. Semantic maps provide more detail about an environment than typical maps because they are augmented by icons or symbols that provide meaning for places or objects of interest...

  12. Fiber-Optic Sensor Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Constructs and evaluates fiber-optic sensors for a variety of measurands. These measurands include acoustic, pressure, magnetic, and electric field as well...

  13. Development of scintillating fiber tracker

    International Nuclear Information System (INIS)

    Ishikawa, Shuzo; Kawai, Toshihide; Kozaki, Tetsuo

    1995-01-01

    In order to use thin scintillating fiber (diameter 500 micron) as a particle tracking detector, we have developed a method to construct precise multi-layer scintillating fiber sheets. We have also developed dedicated machines for this purpose. This paper presents the details of the method and the machines. Using these machines, we have produced fiber sheets for CERN WA95/CHORUS, which intend to detect a neutrino oscillation in the νμ-ντ channel using Hybrid Emulsion Set-up. Fiber Trackers are used as a vertex detector which support the neutrino event location in the nuclear emulsion target. (author)

  14. mapDamage

    DEFF Research Database (Denmark)

    Ginolhac, Aurélien; Rasmussen, Morten; Gilbert, Tom

    2011-01-01

    Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequenci...... of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems....

  15. Fiber Tracking Cylinder Nesting

    International Nuclear Information System (INIS)

    Stredde, H.

    1999-01-01

    The fiber tracker consists of 8 concentric carbon fiber cylinders of varying diameters, from 399mm to 1032.2mm and two different lengths. 1.66 and 2.52 meters. Each completed cylinder is covered over the entire o.d. with scintillating fiber ribbons with a connector on each ribbon. These ribbons are axial (parallel to the beam line) at one end and stereo (at 3 deg. to the beam line) at the other. The ribbon connectors have dowel pins which are used to match with the connectors on the wave guide ribbons. These dowel pins are also used during the nesting operation, locating and positioning measurements. The nesting operation is the insertion of one cylinder into another, aligning them with one another and fastening them together into a homogeneous assembly. For ease of assembly. the nesting operation is accomplished working from largest diameter to smallest. Although the completed assembly of all 8 cylinders glued and bolted together is very stiff. individual cylinders are relatively flexible. Therefore. during this operation, No.8 must be supported in a manner which maintains its integrity and yet allows the insertion of No.7. This is accomplished by essentially building a set of dummy end plates which replicate a No.9 cylinder. These end plates are mounted on a wheeled cart that becomes the nesting cart. Provisions for a protective cover fastened to these rings has been made and will be incorporated in finished product. These covers can be easily removed for access to No.8 and/or the connection of No.8 to No.9. Another wheeled cart, transfer cart, is used to push a completed cylinder into the cylinder(s) already mounted in the nesting cart.

  16. Fiber sample presentation system for spectrophotometer cotton fiber color measurements

    Science.gov (United States)

    The Uster® High Volume Instrument (HVI) is used to class U.S. cotton for fiber color, yielding the industry accepted, cotton-specific color parameters Rd and +b. The HVI examines a 9 square inch fiber sample, and it is also used to test large AMS standard cotton “biscuits” or rectangles. Much inte...

  17. Random fiber laser based on artificially controlled backscattering fibers.

    Science.gov (United States)

    Wang, Xiaoliang; Chen, Daru; Li, Haitao; She, Lijuan; Wu, Qiong

    2018-01-10

    The random fiber laser (RFL), which is a milestone in laser physics and nonlinear optics, has attracted considerable attention recently. Most previously reported RFLs are based on distributed feedback of Rayleigh scattering amplified through the stimulated Raman-Brillouin scattering effect in single-mode fibers, which require long-distance (tens of kilometers) single-mode fibers and high threshold, up to watt level, due to the extremely small Rayleigh scattering coefficient of the fiber. We proposed and demonstrated a half-open-cavity RFL based on a segment of an artificially controlled backscattering single-mode fiber with a length of 210 m, 310 m, or 390 m. A fiber Bragg grating with a central wavelength of 1530 nm and a segment of artificially controlled backscattering single-mode fiber fabricated by using a femtosecond laser form the half-open cavity. The proposed RFL achieves thresholds of 25 mW, 30 mW, and 30 mW, respectively. Random lasing at a wavelength of 1530 nm and extinction ratio of 50 dB is achieved when a segment of 5 m erbium-doped fiber is pumped by a 980 nm laser diode in the RFL. A novel RFL with many short cavities has been achieved with low threshold.

  18. A first generation integrated physical and genetic map of the rainbow trout genome

    Science.gov (United States)

    The rainbow trout physical map was previously constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of ...

  19. Carbon Fiber Biocompatibility for Implants

    Directory of Open Access Journals (Sweden)

    Richard Petersen

    2016-01-01

    Full Text Available Carbon fibers have multiple potential advantages in developing high-strength biomaterials with a density close to bone for better stress transfer and electrical properties that enhance tissue formation. As a breakthrough example in biomaterials, a 1.5 mm diameter bisphenol-epoxy/carbon-fiber-reinforced composite rod was compared for two weeks in a rat tibia model with a similar 1.5 mm diameter titanium-6-4 alloy screw manufactured to retain bone implants. Results showed that carbon-fiber-reinforced composite stimulated osseointegration inside the tibia bone marrow measured as percent bone area (PBA to a great extent when compared to the titanium-6-4 alloy at statistically significant levels. PBA increased significantly with the carbon-fiber composite over the titanium-6-4 alloy for distances from the implant surfaces of 0.1 mm at 77.7% vs. 19.3% (p < 10−8 and 0.8 mm at 41.6% vs. 19.5% (p < 10−4, respectively. The review focuses on carbon fiber properties that increased PBA for enhanced implant osseointegration. Carbon fibers acting as polymer coated electrically conducting micro-biocircuits appear to provide a biocompatible semi-antioxidant property to remove damaging electron free radicals from the surrounding implant surface. Further, carbon fibers by removing excess electrons produced from the cellular mitochondrial electron transport chain during periods of hypoxia perhaps stimulate bone cell recruitment by free-radical chemotactic influences. In addition, well-studied bioorganic cell actin carbon fiber growth would appear to interface in close contact with the carbon-fiber-reinforced composite implant. Resulting subsequent actin carbon fiber/implant carbon fiber contacts then could help in discharging the electron biological overloads through electrochemical gradients to lower negative charges and lower concentration.

  20. Polymer optical fiber bragg grating sensors

    DEFF Research Database (Denmark)

    Stefani, Alessio; Yuan, Scott Wu; Andresen, Søren

    2010-01-01

    Fiber-optical accelerometers based on polymer optical fiber Bragg gratings are reported. We have written fiber Bragg gratings for 1550 nm and 850 nm operations, characterized their temperature and strain response, and tested their performance in a prototype accelerometer....

  1. Extraction and characterization of Retama monosperma fibers

    African Journals Online (AJOL)

    XPERT

    monosperma leaves and their mechanical, physical and chemical characteristics. The fibers .... The hook was removed gently, and the behavior of the fiber was observed ..... fibers reinforced cement mortar slabs: a comparative study. Cement.

  2. Actively doped solid core Photonic Bandgap Fiber

    DEFF Research Database (Denmark)

    Broeng, Jes; Olausson, Christina Bjarnal Thulin; Lyngsøe, Jens Kristian

    2010-01-01

    Solid photonic bandgap fibers offer distributed spectral filtering with extraordinary high suppression. This opens new possibilities of artificially tailoring the gain spectrum of fibers. We present record-performance of such fibers and outline their future applications....

  3. Fiber breakage phenomena in long fiber reinforced plastic preparation

    International Nuclear Information System (INIS)

    Huang, Chao-Tsai; Tseng, Huan-Chang; Chang, Rong-Yeu; Vlcek, Jiri

    2015-01-01

    Due to the high demand of smart green, the lightweight technologies have become the driving force for the development of automotives and other industries in recent years. Among those technologies, using short and long fiber-reinforced plastics (FRP) to replace some metal components can reduce the weight of an automotive significantly. However, the microstructures of fibers inside plastic matrix are too complicated to manage and control during the injection molding through the screw, the runner, the gate, and then into the cavity. This study focuses on the fiber breakage phenomena during the screw plastification. Results show that fiber breakage is strongly dependent on screw design and operation. When the screw geometry changes, the fiber breakage could be larger even with lower compression ratio. (paper)

  4. High-birefringent photonic crystal fiber

    DEFF Research Database (Denmark)

    Libori, Stig E. Barkou; Broeng, Jes; Knudsen, Erik

    2001-01-01

    A highly birefringent photonic crystal fiber design is analysed. Birefringence up to 10-3 is found. Random fluctuations in the cladding design are analysed, and the fiber is found to be a feasible polarization maintaining fiber.......A highly birefringent photonic crystal fiber design is analysed. Birefringence up to 10-3 is found. Random fluctuations in the cladding design are analysed, and the fiber is found to be a feasible polarization maintaining fiber....

  5. Optical fiber powered pressure sensor

    International Nuclear Information System (INIS)

    Schweizer, P.; Neveux, L.; Ostrowsky, D.B.

    1987-01-01

    In the system described, a pressure sensor and its associated electronics are optically powered by a 20 mw laser and a photovoltaic cell via an optical fiber. The sensor is periodically interrogated and sends the measures obtained back to the central unit using an LED and a second fiber. The results obtained as well as the expected evolution will be described

  6. Microstructured hollow fibers for ultrafiltration

    NARCIS (Netherlands)

    Culfaz, Pmar Zeynep; Culfaz, P.Z.; Rolevink, Hendrikus H.M.; van Rijn, C.J.M.; Lammertink, Rob G.H.; Wessling, Matthias

    2010-01-01

    Hollow fiber ultrafiltration membranes with a corrugated outer microstructure were prepared from a PES/PVP blend. The effect of spinning parameters such as air gap, take-up speed, polymer dope viscosity and coagulation value on the microstructure and membrane characteristics was investigated. Fibers

  7. Handbook of fiber optics theory and applications

    CERN Document Server

    Yeh, Chai

    2013-01-01

    Dr. Yeh supplies a firm theoretical foundation in such topics as propagation of light through fibers, fiber fabrication, loss mechanisms, and dispersion properties. He then expands from this into such practical areas as fiber splicing, measuring loss in fibers, fiber-based communications networks, remote fiber sensors, and integrated optics. Whether involved in fiber optics research, design, or practical implementation of systems, this handbook will be extremely useful.Key Features* Here is a comprehensive, ""one-stop"" reference with state-of-the-art information on fiber optics Included is da

  8. Radiation damage in optical fibers

    International Nuclear Information System (INIS)

    Lyons, P.B.; Looney, L.D.; Ogle, J.W.

    1983-01-01

    Optical fibers provide important advantages over coaxial cables for many data transmission applications. Some of these applications require that the fibers transmit data during a radiation pulse. Other applications utilize the fiber as a radiation-to-light transducer. In either case, radiation-induced luminescence and absorption must be understood. Most studies of radiation effects in fibers have emphasized time scales of interest in telecommunication systems, from the msec to hour range. Few studies have concentrated on response at times below 1 + s. At Los Alamos, both laboratory electron accelerators and nuclear tests have been used as radiation sources to probe this early time region. The use of a fiber (or any optical medium) as a Cerenkov radiation-to-light transducer is discussed. Since the radiation induces attenuation in the medium, the light output is not proportional to the radiation input. The nonlinearity introduced by this attenuation is calculated

  9. Photometric device using optical fibers

    International Nuclear Information System (INIS)

    Boisde, Gilbert; Perez, J.-J.

    1981-02-01

    Remote measurements in radioactive environment are now possible with optical fibers. Measurement instruments developed by CEA are constitued of: - an optical probe (5 mm to 1 meter optical path length), - a photometric measurement device, - optical fiber links. 'TELEPHOT' is a photometric device for industrial installations. It is uses interferentiel filters for 2 to 5 simultaneous wave lengths. 'CRUDMETER' measures the muddiness of water. It can be equipped with a high sensitivity cell of 50 cm optical path length tested up to 250 bars. Coupling a double beam spectrophotometer to a remote optical probe, up to 1 meter optical path length, is carried out by means of an optical device using optical fibers links, eventually several hundred meter long. For these equipments special step index large core fibers, 1 to 1.5 mm in diameter, have been developed as well connectors. For industrial control and research these instruments offer new prospect thanks to optical fibers use [fr

  10. Mapping the Heart

    Science.gov (United States)

    Hulse, Grace

    2012-01-01

    In this article, the author describes how her fourth graders made ceramic heart maps. The impetus for this project came from reading "My Map Book" by Sara Fanelli. This book is a collection of quirky, hand-drawn and collaged maps that diagram a child's world. There are maps of her stomach, her day, her family, and her heart, among others. The…

  11. Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection.

    Science.gov (United States)

    Yao, B C; Wu, Y; Yu, C B; He, J R; Rao, Y J; Gong, Y; Fu, F; Chen, Y F; Li, Y R

    2016-03-24

    Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel 'FRET on Fiber' concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based 'FRET on fiber' configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated 'FRET on Fiber' sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response.

  12. Perturbative modeling of Bragg-grating-based biosensors in photonic-crystal fibers

    DEFF Research Database (Denmark)

    Burani, Nicola; Lægsgaard, Jesper

    2005-01-01

    We present a modeling study carried out to support the design of a novel, to our knowledge, kind of photonic-crystal fiber (PCF)-based sensor. This device, based on a PCF Bragg grating, detects the presence of selected single-stranded DNA molecules, hybridized to a biofilm in the air holes of the...

  13. USGS Map Indices Overlay Map Service from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Map Indices service from The National Map (TNM) consists of 1x1 Degree, 30x60 Minute (100K), 15 Minute (63K), 7.5 Minute (24K), and 3.75 Minute grid...

  14. Benefits of glass fibers in solar fiber optic lighting systems.

    Science.gov (United States)

    Volotinen, Tarja T; Lingfors, David H S

    2013-09-20

    The transmission properties and coupling of solar light have been studied for glass core multimode fibers in order to verify their benefits for a solar fiber optic lighting system. The light transportation distance can be extended from 20 m with plastic fibers to over 100 m with the kind of glass fibers studied here. A high luminous flux, full visible spectrum, as well as an outstanding color rendering index (98) and correlated color temperature similar to the direct sun light outside have been obtained. Thus the outstanding quality of solar light transmitted through these fibers would improve the visibility of all kinds of objects compared to fluorescent and other artificial lighting. Annual relative lighting energy savings of 36% in Uppsala, Sweden, and 76% in Dubai were estimated in an office environment. The absolute savings can be doubled by using glass optical fibers, and are estimated to be in the order of 550 kWh/year in Sweden and 1160 kWh/year in Dubai for one system of only 0.159 m(2) total light collecting area. The savings are dependent on the fiber length, the daily usage time of the interior, the type of artificial lighting substituted, the system light output flux, and the available time of sunny weather at the geographic location.

  15. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

    Science.gov (United States)

    Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2015-12-01

    Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

  16. 7. Annex II: Maps

    OpenAIRE

    Aeberli, Annina

    2012-01-01

    Map 1: States of South Sudan UN OCHA (2012) Republic of South Sudan – States, as of 15 July 2012, Reliefweb http://reliefweb.int/map/south-sudan-republic/republic-south-sudan-states-15-july-2012-reference-map, accessed 31 July 2012. Map 2: Counties of South Sudan UN OCHA (2012) Republic of South Sudan – Counties, as of 16 July 2012, Reliefweb http://reliefweb.int/map/south-sudan-republic/republic-south-sudan-counties-16-july-2012-reference-map, accessed 31 July 2012. Map 3: Eastern Equato...

  17. Applicability of vulnerability maps

    International Nuclear Information System (INIS)

    Andersen, L.J.; Gosk, E.

    1989-01-01

    A number of aspects to vulnerability maps are discussed: the vulnerability concept, mapping purposes, possible users, and applicability of vulnerability maps. Problems associated with general-type vulnerability mapping, including large-scale maps, universal pollutant, and universal pollution scenario are also discussed. An alternative approach to vulnerability assessment - specific vulnerability mapping for limited areas, specific pollutant, and predefined pollution scenario - is suggested. A simplification of the vulnerability concept is proposed in order to make vulnerability mapping more objective and by this means more comparable. An extension of the vulnerability concept to the rest of the hydrogeological cycle (lakes, rivers, and the sea) is proposed. Some recommendations regarding future activities are given

  18. Differential maps, difference maps, interpolated maps, and long term prediction

    International Nuclear Information System (INIS)

    Talman, R.

    1988-06-01

    Mapping techniques may be thought to be attractive for the long term prediction of motion in accelerators, especially because a simple map can approximately represent an arbitrarily complicated lattice. The intention of this paper is to develop prejudices as to the validity of such methods by applying them to a simple, exactly solveable, example. It is shown that a numerical interpolation map, such as can be generated in the accelerator tracking program TEAPOT, predicts the evolution more accurately than an analytically derived differential map of the same order. Even so, in the presence of ''appreciable'' nonlinearity, it is shown to be impractical to achieve ''accurate'' prediction beyond some hundreds of cycles of oscillation. This suggests that the value of nonlinear maps is restricted to the parameterization of only the ''leading'' deviation from linearity. 41 refs., 6 figs

  19. Extracellular DNA facilitates the formation of functional amyloids in Staphylococcus aureus biofilms.

    Science.gov (United States)

    Schwartz, Kelly; Ganesan, Mahesh; Payne, David E; Solomon, Michael J; Boles, Blaise R

    2016-01-01

    Persistent staphylococcal infections often involve surface-associated communities called biofilms. Staphylococcus aureus biofilm development is mediated by the co-ordinated production of the biofilm matrix, which can be composed of polysaccharides, extracellular DNA (eDNA) and proteins including amyloid fibers. The nature of the interactions between matrix components, and how these interactions contribute to the formation of matrix, remain unclear. Here we show that the presence of eDNA in S. aureus biofilms promotes the formation of amyloid fibers. Conditions or mutants that do not generate eDNA result in lack of amyloids during biofilm growth despite the amyloidogeneic subunits, phenol soluble modulin peptides, being produced. In vitro studies revealed that the presence of DNA promotes amyloid formation by PSM peptides. Thus, this work exposes a previously unacknowledged interaction between biofilm matrix components that furthers our understanding of functional amyloid formation and S. aureus biofilm biology. © 2015 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.

  20. Pathological mechanisms underlying single large‐scale mitochondrial DNA deletions

    Science.gov (United States)

    Rocha, Mariana C.; Rosa, Hannah S.; Grady, John P.; Blakely, Emma L.; He, Langping; Romain, Nadine; Haller, Ronald G.; Newman, Jane; McFarland, Robert; Ng, Yi Shiau; Gorman, Grainne S.; Schaefer, Andrew M.; Tuppen, Helen A.; Taylor, Robert W.

    2018-01-01

    Objective Single, large‐scale deletions in mitochondrial DNA (mtDNA) are a common cause of mitochondrial disease. This study aimed to investigate the relationship between the genetic defect and molecular phenotype to improve understanding of pathogenic mechanisms associated with single, large‐scale mtDNA deletions in skeletal muscle. Methods We investigated 23 muscle biopsies taken from adult patients (6 males/17 females with a mean age of 43 years) with characterized single, large‐scale mtDNA deletions. Mitochondrial respiratory chain deficiency in skeletal muscle biopsies was quantified by immunoreactivity levels for complex I and complex IV proteins. Single muscle fibers with varying degrees of deficiency were selected from 6 patient biopsies for determination of mtDNA deletion level and copy number by quantitative polymerase chain reaction. Results We have defined 3 “classes” of single, large‐scale deletion with distinct patterns of mitochondrial deficiency, determined by the size and location of the deletion. Single fiber analyses showed that fibers with greater respiratory chain deficiency harbored higher levels of mtDNA deletion with an increase in total mtDNA copy number. For the first time, we have demonstrated that threshold levels for complex I and complex IV deficiency differ based on deletion class. Interpretation Combining genetic and immunofluorescent assays, we conclude that thresholds for complex I and complex IV deficiency are modulated by the deletion of complex‐specific protein‐encoding genes. Furthermore, removal of mt‐tRNA genes impacts specific complexes only at high deletion levels, when complex‐specific protein‐encoding genes remain. These novel findings provide valuable insight into the pathogenic mechanisms associated with these mutations. Ann Neurol 2018;83:115–130 PMID:29283441

  1. How to determine local stretching and tension in a flow-stretched DNA molecule

    DEFF Research Database (Denmark)

    Pedersen, Jonas Nyvold; Marie, Rodolphe; Kristensen, Anders

    2016-01-01

    We determine the nonuniform stretching of and tension in amega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead......, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA......-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA—e.g., native DNA extracted from human cells or bacteria—must be stretched with ease for inspection, this method applies....

  2. Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum.

    Science.gov (United States)

    Hou, Meiying; Cai, Caiping; Zhang, Shuwen; Guo, Wangzhen; Zhang, Tianzhen; Zhou, Baoliang

    2013-12-01

    Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat, SSR)-based genetic map was constructed using the interspecific cross of G. hirsutum x G. tomentosum (HT). We detected 1800 loci from 1347 pairs of polymorphic primers. Of these, 1204 loci were grouped into 35 linkage groups at LOD ≥ 4. The map covers 3320.8 cM, with a mean density of 2.76 cM per locus. We detected 420 common loci (186 in the At subgenome and 234 in Dt) between the HT map and the map of TM-1 (G. hirsutum) and Hai 7124 (G. barbadense; HB map). The linkage groups were assigned chromosome numbers based on location of common loci and the HB map as reference. A comparison of common markers revealed that no significant chromosomal rearrangement exist between G. tomentosum and G. barbadense. Interestingly, however, we detected numerous (33.7%) segregation loci deviating from 3:1 ratio (P constructed in this study will be useful for further genetic studies on cotton breeding, including mapping loci controlling quantitative traits associated with fiber quality, stress tolerance and developing chromosome segment specific introgression lines from G. tomentosum into G. hirsutum using marker-assisted selection.

  3. Enhanced post wash retention of combed DNA molecules by varying multiple combing parameters.

    Science.gov (United States)

    Yadav, Hemendra; Sharma, Pulkit

    2017-11-01

    Recent advances in genomics have created a need for efficient techniques for deciphering information hidden in various genomes. Single molecule analysis is one such technique to understand molecular processes at single molecule level. Fiber- FISH performed with the help of DNA combing can help us in understanding genetic rearrangements and changes in genome at single DNA molecule level. For performing Fiber-FISH we need high retention of combed DNA molecules post wash as Fiber-FISH requires profuse washing. We optimized combing process involving combing solution, method of DNA mounting on glass slides and coating of glass slides to enhance post-wash retention of DNA molecules. It was found that average number of DNA molecules observed post-wash per field of view was maximum with our optimized combing solution. APTES coated glass slides showed lesser retention than PEI surface but fluorescent intensity was higher in case of APTES coated surface. Capillary method used to mount DNA on glass slides also showed lesser retention but straight DNA molecules were observed as compared to force flow method. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. VEGETATION MAPPING IN WETLANDS

    Directory of Open Access Journals (Sweden)

    F. PEDROTTI

    2004-01-01

    Full Text Available The current work examines the main aspects of wetland vegetation mapping, which can be summarized as analysis of the ecological-vegetational (ecotone gradients; vegetation complexes; relationships between vegetation distribution and geomorphology; vegetation of the hydrographic basin lo which the wetland in question belongs; vegetation monitoring with help of four vegetation maps: phytosociological map of the real and potential vegetation, map of vegetation dynamical tendencies, map of vegetation series.

  5. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  6. Cloning human DNA repair genes

    International Nuclear Information System (INIS)

    Jeggo, P.A.; Carr, A.M.; Lehmann, A.R.

    1994-01-01

    Many human genes involved in the repair of UV damage have been cloned using different procedures and they have been of great value in assisting the understanding of the mechanism of nucleotide excision-repair. Genes involved in repair of ionizing radiation damage have proved more difficult to isolate. Positional cloning has localized the XRCC5 gene to a small region of chromosome 2q33-35, and a series of yeast artificial chromosomes covering this region have been isolated. Very recent work has shown that the XRCC5 gene encodes the 80 kDa subunit of the Ku DNA-binding protein. The Ku80 gene also maps to this region. Studies with fission yeast have shown that radiation sensitivity can result not only from defective DNA repair but also from abnormal cell cycle control following DNA damage. Several genes involved in this 'check-point' control in fission yeast have been isolated and characterized in detail. It is likely that a similar checkpoint control mechanism exists in human cells. (author)

  7. Green Fiber Bottle

    DEFF Research Database (Denmark)

    Didone, Mattia; Tosello, Guido

    has to have an inner coating barrier. The most reliable solution proposed is to coat the inner walls with silicon dioxide, which is not biodegradable but rather environmentally inert. To enhance the environmental footprint and sustainability of the bottle, and to be competitive with the existing...... technologies, the manufacturing technology for the production of the bottle has to offer the possibility of significant energy savings. Molded pulp products are made from wood fibers dispersed in water, and then they are formed, drained and dried. A relatively large quantity of resources (i.e. energy and time......) is consumed during the drying process. It is in this process stage that an innovative way of drying the products can be exploited by using the concept of impulse drying. Impulse drying is an advance drying technique in which water is removed from a wet paper pulp by the combination of mechanical pressure...

  8. Global mapping of transposon location.

    Directory of Open Access Journals (Sweden)

    Abram Gabriel

    2006-12-01

    Full Text Available Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

  9. Carbon Fiber from Biomass

    Energy Technology Data Exchange (ETDEWEB)

    Milbrandt, Anelia [Clean Energy Manufacturing Analysis Center, Godlen, CO (United States); Booth, Samuel [Clean Energy Manufacturing Analysis Center, Godlen, CO (United States)

    2016-09-01

    Carbon fiber (CF), known also as graphite fiber, is a lightweight, strong, and flexible material used in both structural (load-bearing) and non-structural applications (e.g., thermal insulation). The high cost of precursors (the starting material used to make CF, which comes predominately from fossil sources) and manufacturing have kept CF a niche market with applications limited mostly to high-performance structural materials (e.g., aerospace). Alternative precursors to reduce CF cost and dependence on fossil sources have been investigated over the years, including biomass-derived precursors such as rayon, lignin, glycerol, and lignocellulosic sugars. The purpose of this study is to provide a comprehensive overview of CF precursors from biomass and their market potential. We examine the potential CF production from these precursors, the state of technology and applications, and the production cost (when data are available). We discuss their advantages and limitations. We also discuss the physical properties of biomass-based CF, and we compare them to those of polyacrylonitrile (PAN)-based CF. We also discuss manufacturing and end-product considerations for bio-based CF, as well as considerations for plant siting and biomass feedstock logistics, feedstock competition, and risk mitigation strategies. The main contribution of this study is that it provides detailed technical and market information about each bio-based CF precursor in one document while other studies focus on one precursor at a time or a particular topic (e.g., processing). Thus, this publication allows for a comprehensive view of the CF potential from all biomass sources and serves as a reference for both novice and experienced professionals interested in CF production from alternative sources.

  10. Chromosome mapping by FISH to metaphase and interphase nuclei. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Trask, B.

    1997-08-01

    The overall specific aims of this project were: (1) to determine the large-scale structure of interphase and metaphase chromosomes, in order to establish new capabilities for genome mapping by fluorescence in situ hybridization (FISH); (2) to detect chromosome abnormalities associated with genetic disease and map DNA sequences relative to them in order to facilitate the identification of new genes with disease-causing mutations; (3) to establish medium resolution physical maps of selected chromosomal regions using a combined metaphase and interphase mapping strategy and to corroborate physical and genetic maps and integrate these maps with the cytogenetic map; (4) to analyze the polymorphism and sequence evolution of subtelomeric regions of human chromosomes; (5) to establish a state-of-the-art FISH and image processing facility in the Department of Molecular Biotechnology, University of Washington, in order to map DNA sequences rapidly and accurately to benefit the Human Genome Project.

  11. Antibody recognition of Z-DNA

    International Nuclear Information System (INIS)

    Lafer, E.M.; Moeller, A.; Valle, R.P.C.; Nordheim, V.A.; Rich, A.; Stollar, B.D.; Massachusetts Inst. of Tech., Cambridge)

    1983-01-01

    To measure serological reactions under physiological ionic strength, we prepared a brominated (Bl) poly(dG-dC).poly(dG-dC), which forms a stable Z helix in solutions of low salt concentration. Mice and rabbits were immunized with this polymer complexed with the basic protein methylated bovine serum albumin (MBSA), and it was discovered that the Z-DNA helix is a strong immunogen. Various antibody populations were purified from the rabbit serum by quantitative immunoprecipitation. Spleen cells from the mice were used for the preparation of hybridoma cell lines secreting monoclonal antibodies. Anti-Z-DNA antibodies were also raised by immunizing animals with poly(dG-dm 5 C).poly(dG-dm 5 C) under conditions where it was reported to be in the left-handed Z conformation as well as unmodified poly(dG-dC).poly(dG-dC) that was in the right-handed B conformation: both were complexed with MBSA. Z-DNA reactive antibodies were found in both murine and human SLE. A Z-DNA-specific as well as a dDNA and Z-DNA cross-reactive antibody population were distinguished by affinity chromatography of the SLE sera. The specificities of the various anti-Z-DNA antibody populations were measured by direct-binding and competitive radioimmunoassays, using synthetic polymers of defined structure under various ionic strengths. These studies allow us to map the possible antigenic sites for these antibodies, which serve as a model for DNA-protein recognition. The findings also established the usefulness of the antibodies as biochemical probes for Z-DNA. 29 references, 6 figures, 1 table

  12. Fabrication of elastomeric silk fibers.

    Science.gov (United States)

    Bradner, Sarah A; Partlow, Benjamin P; Cebe, Peggy; Omenetto, Fiorenzo G; Kaplan, David L

    2017-09-01

    Methods to generate fibers from hydrogels, with control over mechanical properties, fiber diameter, and crystallinity, while retaining cytocompatibility and degradability, would expand options for biomaterials. Here, we exploited features of silk fibroin protein for the formation of tunable silk hydrogel fibers. The biological, chemical, and morphological features inherent to silk were combined with elastomeric properties gained through enzymatic crosslinking of the protein. Postprocessing via methanol and autoclaving provided tunable control of fiber features. Mechanical, optical, and chemical analyses demonstrated control of fiber properties by exploiting the physical cross-links, and generating double network hydrogels consisting of chemical and physical cross-links. Structure and chemical analyses revealed crystallinity from 30 to 50%, modulus from 0.5 to 4 MPa, and ultimate strength 1-5 MPa depending on the processing method. Fabrication and postprocessing combined provided fibers with extensibility from 100 to 400% ultimate strain. Fibers strained to 100% exhibited fourth order birefringence, revealing macroscopic orientation driven by chain mobility. The physical cross-links were influenced in part by the drying rate of fabricated materials, where bound water, packing density, and microstructural homogeneity influenced cross-linking efficiency. The ability to generate robust and versatile hydrogel microfibers is desirable for bottom-up assembly of biological tissues and for broader biomaterial applications. © 2017 Wiley Periodicals, Inc.

  13. New all-fiber velocimeter

    International Nuclear Information System (INIS)

    Weng Jidong; Tan Hua; Hu Shaolou; Ma Yun; Wan Xiang

    2005-01-01

    A new all-fiber velocity interferometer system for any reflector (AFVISAR) was developed. It was conceived and realized with the purpose of using it as the basic measuring element of a complete system for multiple point velocity measurements. Its main features are that it works at 532 nm and partly adopts the multimode optical fiber. The velocimeter consists of only fibers or fiber coupled components and has no optic elements such as optic lenses or reflectors. It is therefore very compact and easy to operate. Unlike the conventional AFVISAR, which uses single-mode optic fiber components, the laser beam in this new interferometer system arrives at and reflects from the target surface through a multimode optical fiber component, and then enters and interferes in a [3x3] single-mode fiber coupler. Its working principle is elaborated on in this article. Preliminary experiments using a split Hopkins pressure bar (SHPB) device show that the new interferometer can successfully measure the velocity profiles of the metal specimen along the axial or radial direction. Further experiments on a one-stage gas gun are under consideration

  14. Dimensional stability of natural fibers

    Energy Technology Data Exchange (ETDEWEB)

    Driscoll, Mark S. [Ultraviolet Light/Electron Beam (UV/EB) Technology Center, State University of New York College of Environmental Science and Forestry (SUNY-ESF), 1 Forestry Drive, Syracuse, NY 13210 (United States); Smith, Jennifer L.; Woods, Sean; Tiss, Kenneth J. [Ultraviolet Light/Electron Beam (UV/EB) Technology Center, State University of New York College of Environmental Science and Forestry (SUNY-ESF), 1 Forestry Drive, Syracuse, NY 13210 and Sustainable Construction Management and Engineering, SUNY-ESF (United States); Larsen, L. Scott [New York State Energy Research and Development Authority (NYSERDA), 17 Columbia Circle, Albany, NY 12203 (United States)

    2013-04-19

    One of the main problems associated with the use of natural fibers as reinforcing agents in composites is their uptake of moisture. Many natural fibers are lignocellulosic, which causes them to swell and shrink as the amount of available moisture changes. Swelling and shrinking can cause composites to prematurely fail. This paper presents the results of a preliminary study that considers the use of two different low molecular weight monomers, hydroxyethyl methacrylate (HEMA) and hydroxyethyl acrylate (HEA), polymerized by electron beam ionizing radiation, to dimensionally stabilize natural fibers. Eight different treatments consisting of varying amounts of monomer, encapsulating agent, and cross-linkers, were evaluated for their ability to dimensionally stabilize sisal fiber. Results indicate that both polymerized HEA and HEMA can reduce the swelling of sisal fiber. The effectiveness of HEA and HEMA can be further enhanced with the use of a cross-linker (SR 454). The use of hydroxylated monomers to dimensionally stabilize natural fibers may play an important role in reducing delamination and improving fiber-resin adhesion in composites.

  15. Dimensional stability of natural fibers

    International Nuclear Information System (INIS)

    Driscoll, Mark S.; Smith, Jennifer L.; Woods, Sean; Tiss, Kenneth J.; Larsen, L. Scott

    2013-01-01

    One of the main problems associated with the use of natural fibers as reinforcing agents in composites is their uptake of moisture. Many natural fibers are lignocellulosic, which causes them to swell and shrink as the amount of available moisture changes. Swelling and shrinking can cause composites to prematurely fail. This paper presents the results of a preliminary study that considers the use of two different low molecular weight monomers, hydroxyethyl methacrylate (HEMA) and hydroxyethyl acrylate (HEA), polymerized by electron beam ionizing radiation, to dimensionally stabilize natural fibers. Eight different treatments consisting of varying amounts of monomer, encapsulating agent, and cross-linkers, were evaluated for their ability to dimensionally stabilize sisal fiber. Results indicate that both polymerized HEA and HEMA can reduce the swelling of sisal fiber. The effectiveness of HEA and HEMA can be further enhanced with the use of a cross-linker (SR 454). The use of hydroxylated monomers to dimensionally stabilize natural fibers may play an important role in reducing delamination and improving fiber-resin adhesion in composites.

  16. Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

    Science.gov (United States)

    Teo, Audrey S M; Verzotto, Davide; Yao, Fei; Nagarajan, Niranjan; Hillmer, Axel M

    2015-01-01

    Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35-300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and for de novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116. High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested with KpnI and 310,000 and 296,000 DNA molecules (≥ 150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software. Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.

  17. DNA preservation in silk.

    Science.gov (United States)

    Liu, Yawen; Zheng, Zhaozhu; Gong, He; Liu, Meng; Guo, Shaozhe; Li, Gang; Wang, Xiaoqin; Kaplan, David L

    2017-06-27

    The structure of DNA is susceptible to alterations at high temperature and on changing pH, irradiation and exposure to DNase. Options to protect and preserve DNA during storage are important for applications in genetic diagnosis, identity authentication, drug development and bioresearch. In the present study, the stability of total DNA purified from human dermal fibroblast cells, as well as that of plasmid DNA, was studied in silk protein materials. The DNA/silk mixtures were stabilized on filter paper (silk/DNA + filter) or filter paper pre-coated with silk and treated with methanol (silk/DNA + PT-filter) as a route to practical utility. After air-drying and water extraction, 50-70% of the DNA and silk could be retrieved and showed a single band on electrophoretic gels. 6% silk/DNA + PT-filter samples provided improved stability in comparison with 3% silk/DNA + filter samples and DNA + filter samples for DNA preservation, with ∼40% of the band intensity remaining at 37 °C after 40 days and ∼10% after exposure to UV light for 10 hours. Quantitative analysis using the PicoGreen assay confirmed the results. The use of Tris/borate/EDTA (TBE) buffer enhanced the preservation and/or extraction of the DNA. The DNA extracted after storage maintained integrity and function based on serving as a functional template for PCR amplification of the gene for zinc finger protein 750 (ZNF750) and for transgene expression of red fluorescence protein (dsRed) in HEK293 cells. The high molecular weight and high content of a crystalline beta-sheet structure formed on the coated surfaces likely accounted for the preservation effects observed for the silk/DNA + PT-filter samples. Although similar preservation effects were also obtained for lyophilized silk/DNA samples, the rapid and simple processing available with the silk-DNA-filter membrane system makes it appealing for future applications.

  18. Force induced DNA melting

    International Nuclear Information System (INIS)

    Santosh, Mogurampelly; Maiti, Prabal K

    2009-01-01

    When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates by roughly twice its initial contour length at a pulling force of about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying a force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA, this being a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double-strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA starts melting abruptly/smoothly above a critical force depending on the pulling direction. The critical force f m , at which DNA melts completely decreases as the temperature of the system is increased. The melting force in the case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the case of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to sequence of different base pairs. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.

  19. DNA damage and autophagy

    International Nuclear Information System (INIS)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Panayiotidis, Mihalis I.; Franco, Rodrigo

    2011-01-01

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  20. Effect of X-irradiation and vitamin C on DNA degradation and endogenous DNAase in embryonic chick lens cells

    International Nuclear Information System (INIS)

    Trevithick, J.R.; Chaudun, E.; Muel, A.S.; Courtois, Y.; Counis, M.F.

    1987-01-01

    The lens is an organ in which epithelial cells become elongated fibers. During this process, nuclei are transformed and the DNA is degraded. In previous studies, we described an autodigestion of the chromatin in isolated fiber nuclei but not in epithelial nuclei, but the level of DNAase activity was found to be identical in both epithelial and fiber nuclei of lenses at 11 days of development. In this study, we have investigated the possibility that x-irradiation might stimulate the nuclear endogenous activity responsible for chromatin breakdown or epithelial cells to a level comparable to that observed in fiber cells. We have observed that x-irradiation does not increase the nuclear epithelial DNAase activity. Conversely, vitamin C, suspected to prevent cataract formation by protecting DNA against free radical formation, has a damaging effect on the DNA of the lens of chick embryo in vitro. (author)