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Sample records for high resolution dna

  1. 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.

  2. 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.

  3. High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science.

    Science.gov (United States)

    Dos Santos Rocha, Alípio; de Amorim, Isis Salviano Soares; Simão, Tatiana de Almeida; da Fonseca, Adenilson de Souza; Garrido, Rodrigo Grazinoli; Mencalha, Andre Luiz

    2018-03-01

    Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics. © 2017 American Academy of Forensic Sciences.

  4. Capillary gel electrophoresis for rapid, high resolution DNA sequencing.

    OpenAIRE

    Swerdlow, H; Gesteland, R

    1990-01-01

    Capillary gel electrophoresis has been demonstrated for the separation and detection of DNA sequencing samples. Enzymatic dideoxy nucleotide chain termination was employed, using fluorescently tagged oligonucleotide primers and laser based on-column detection (limit of detection is 6,000 molecules per peak). Capillary gel separations were shown to be three times faster, with better resolution (2.4 x), and higher separation efficiency (5.4 x) than a conventional automated slab gel DNA sequenci...

  5. In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma.

    Directory of Open Access Journals (Sweden)

    Bekim Sadikovic

    Full Text Available Genetic and epigenetic changes contribute to deregulation of gene expression and development of human cancer. Changes in DNA methylation are key epigenetic factors regulating gene expression and genomic stability. Recent progress in microarray technologies resulted in developments of high resolution platforms for profiling of genetic, epigenetic and gene expression changes. OS is a pediatric bone tumor with characteristically high level of numerical and structural chromosomal changes. Furthermore, little is known about DNA methylation changes in OS. Our objective was to develop an integrative approach for analysis of high-resolution epigenomic, genomic, and gene expression profiles in order to identify functional epi/genomic differences between OS cell lines and normal human osteoblasts. A combination of Affymetrix Promoter Tilling Arrays for DNA methylation, Agilent array-CGH platform for genomic imbalance and Affymetrix Gene 1.0 platform for gene expression analysis was used. As a result, an integrative high-resolution approach for interrogation of genome-wide tumour-specific changes in DNA methylation was developed. This approach was used to provide the first genomic DNA methylation maps, and to identify and validate genes with aberrant DNA methylation in OS cell lines. This first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression has provided comprehensive evidence of the cumulative roles of epigenetic and genetic mechanisms in deregulation of gene expression networks.

  6. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

    Directory of Open Access Journals (Sweden)

    Lank Simon M

    2012-08-01

    Full Text Available Abstract Background High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. Conclusions The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.

  7. High-resolution DNA content analysis of microbiopsy samples in oral lichen planus.

    Science.gov (United States)

    Pentenero, M; Monticone, M; Marino, R; Aiello, C; Marchitto, G; Malacarne, D; Giaretti, W; Gandolfo, S; Castagnola, P

    2017-04-01

    DNA aneuploidy has been reported to be a predictor of poor prognosis in both premalignant and malignant lesions. In oral lichen planus (OLP), this hypothesis remains to be proved. This study aimed to determine the rate of occurrence of DNA aneuploidy in patients with OLP by high-resolution DNA flow cytometry. Patients with OLP were consecutively enrolled. Tissue samples were subdivided for formalin fixation and routine histological assessment and for immediate storage at -20°C for later DNA ploidy analysis, which was performed by DAPI staining of the extracted nuclei and excitation with a UV lamp. The DNA aneuploid sublines were characterized by the DNA Index. A DNA aneuploid status was observed in two of 77 patients with OLP (2.6%). When considering the clinical aspect of the OLP lesions, both DNA aneuploid cases had a reticular clinical aspect. DNA aneuploidy is an uncommon event in OLP and less frequent compared to other non-dysplastic and non-OLP oral potentially malignant disorders. The extremely low rate of DNA aneuploidy could represent an occasional finding or reflect the low rate of malignant transformation observed in patients with OLP even if the real prognostic value of DNA ploidy analysis in patients with OLP remains to be confirmed. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species.

    Directory of Open Access Journals (Sweden)

    Maslin Osathanunkul

    Full Text Available DNA barcoding coupled high resolution melting (Bar-HRM is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Croton (Euphorbiaceae, one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1 from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability.

  9. 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...

  10. High-resolution analysis of cytosine methylation in ancient DNA.

    Directory of Open Access Journals (Sweden)

    Bastien Llamas

    Full Text Available Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.

  11. High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

    International Nuclear Information System (INIS)

    Chou, Shanho; Flynn, P.; Wang, A.; Reid, B.

    1991-01-01

    Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies

  12. Rapid discrimination of Isaria javanica and Isaria poprawskii from Isaria spp. using high resolution DNA melting assays

    Science.gov (United States)

    The current study evaluates the potential of using high resolution DNA melting assays to discriminate species in the genus, Isaria. The study utilizes a previously identified 103 base pair PCR amplicon, which was reported to be selective for Isaria fumosorosea. Our study finds the amplicon selective...

  13. ‘‘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...

  14. Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA.

    Directory of Open Access Journals (Sweden)

    Ana Ramón-Laca

    Full Text Available Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat from swabs of faecal pellets. A high resolution melting (HRM assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.

  15. Methylation-Sensitive High Resolution Melting (MS-HRM).

    Science.gov (United States)

    Hussmann, Dianna; Hansen, Lise Lotte

    2018-01-01

    Methylation-Sensitive High Resolution Melting (MS-HRM) is an in-tube, PCR-based method to detect methylation levels at specific loci of interest. A unique primer design facilitates a high sensitivity of the assays enabling detection of down to 0.1-1% methylated alleles in an unmethylated background.Primers for MS-HRM assays are designed to be complementary to the methylated allele, and a specific annealing temperature enables these primers to anneal both to the methylated and the unmethylated alleles thereby increasing the sensitivity of the assays. Bisulfite treatment of the DNA prior to performing MS-HRM ensures a different base composition between methylated and unmethylated DNA, which is used to separate the resulting amplicons by high resolution melting.The high sensitivity of MS-HRM has proven useful for detecting cancer biomarkers in a noninvasive manner in urine from bladder cancer patients, in stool from colorectal cancer patients, and in buccal mucosa from breast cancer patients. MS-HRM is a fast method to diagnose imprinted diseases and to clinically validate results from whole-epigenome studies. The ability to detect few copies of methylated DNA makes MS-HRM a key player in the quest for establishing links between environmental exposure, epigenetic changes, and disease.

  16. Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers.

    Science.gov (United States)

    Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S; Garcia-Closas, Montserrat; Sherman, Mark E; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P; Khan, Javed; Chanock, Stephen

    2011-01-17

    Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  17. Detection of somatic mutations by high-resolution DNA melting (HRM analysis in multiple cancers.

    Directory of Open Access Journals (Sweden)

    Jesus Gonzalez-Bosquet

    Full Text Available Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each. HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  18. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

    Directory of Open Access Journals (Sweden)

    Zach Hensel

    Full Text Available DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R and O(L (separated by 2.3 kb, mediated by the λ repressor CI (accession number P03034, play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

  19. High-resolution AFM structure of DNA G-wires in aqueous solution.

    Science.gov (United States)

    Bose, Krishnashish; Lech, Christopher J; Heddi, Brahim; Phan, Anh Tuân

    2018-05-17

    We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G 4 T 2 G 4 ] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure.

  20. High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

    Directory of Open Access Journals (Sweden)

    Federico Comoglio

    2015-05-01

    Full Text Available At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, the genetic and chromatin features defining metazoan replication start sites remain largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and suggest that they transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence motifs, mark and predict origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship among DNA topology, chromatin, transcription, and replication initiation across metazoa.

  1. Resolution-improved in situ DNA hybridization detection based on microwave photonic interrogation.

    Science.gov (United States)

    Cao, Yuan; Guo, Tuan; Wang, Xudong; Sun, Dandan; Ran, Yang; Feng, Xinhuan; Guan, Bai-ou

    2015-10-19

    In situ bio-sensing system based on microwave photonics filter (MPF) interrogation method with improved resolution is proposed and experimentally demonstrated. A microfiber Bragg grating (mFBG) is used as sensing probe for DNA hybridization detection. Different from the traditional wavelength monitoring technique, we use the frequency interrogation scheme for resolution-improved bio-sensing detection. Experimental results show that the frequency shift of MPF notch presents a linear response to the surrounding refractive index (SRI) change over the range of 1.33 to 1.38, with a SRI resolution up to 2.6 × 10(-5) RIU, which has been increased for almost two orders of magnitude compared with the traditional fundamental mode monitoring technique (~3.6 × 10(-3) RIU). Due to the high Q value (about 27), the whole process of DNA hybridization can be in situ monitored. The proposed MPF-based bio-sensing system provides a new interrogation method over the frequency domain with improved sensing resolution and rapid interrogation rate for biochemical and environmental measurement.

  2. High resolution melting (HRM) analysis of DNA--its role and potential in food analysis.

    Science.gov (United States)

    Druml, Barbara; Cichna-Markl, Margit

    2014-09-01

    DNA based methods play an increasing role in food safety control and food adulteration detection. Recent papers show that high resolution melting (HRM) analysis is an interesting approach. It involves amplification of the target of interest in the presence of a saturation dye by the polymerase chain reaction (PCR) and subsequent melting of the amplicons by gradually increasing the temperature. Since the melting profile depends on the GC content, length, sequence and strand complementarity of the product, HRM analysis is highly suitable for the detection of single-base variants and small insertions or deletions. The review gives an introduction into HRM analysis, covers important aspects in the development of an HRM analysis method and describes how HRM data are analysed and interpreted. Then we discuss the potential of HRM analysis based methods in food analysis, i.e. for the identification of closely related species and cultivars and the identification of pathogenic microorganisms. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe

    Directory of Open Access Journals (Sweden)

    Dominika Żurek-Biesiada

    2016-06-01

    Full Text Available Single Molecule Localization Microscopy (SMLM is a recently emerged optical imaging method that was shown to achieve a resolution in the order of tens of nanometers in intact cells. Novel high resolution imaging methods might be crucial for understanding of how the chromatin, a complex of DNA and proteins, is arranged in the eukaryotic cell nucleus. Such an approach utilizing switching of a fluorescent, DNA-binding dye Vybrant® DyeCycle™ Violet has been previously demonstrated by us (Żurek-Biesiada et al., 2015 [1]. Here we provide quantitative information on the influence of the chemical environment on the behavior of the dye, discuss the variability in the DNA-associated signal density, and demonstrate direct proof of enhanced structural resolution. Furthermore, we compare different visualization approaches. Finally, we describe various opportunities of multicolor DNA/SMLM imaging in eukaryotic cell nuclei.

  4. Pyrosequencing™ : A one-step method for high resolution HLA typing

    Directory of Open Access Journals (Sweden)

    Marincola Francesco M

    2003-11-01

    Full Text Available Abstract While the use of high-resolution molecular typing in routine matching of human leukocyte antigens (HLA is expected to improve unrelated donor selection and transplant outcome, the genetic complexity of HLA still makes the current methodology limited and laborious. Pyrosequencing™ is a gel-free, sequencing-by-synthesis method. In a Pyrosequencing reaction, nucleotide incorporation proceeds sequentially along each DNA template at a given nucleotide dispensation order (NDO that is programmed into a pyrosequencer. Here we describe the design of a NDO that generates a pyrogram unique for any given allele or combination of alleles. We present examples of unique pyrograms generated from each of two heterozygous HLA templates, which would otherwise remain cis/trans ambiguous using standard sequencing based typing (SBT method. In addition, we display representative data that demonstrate long read and linear signal generation. These features are prerequisite of high-resolution typing and automated data analysis. In conclusion Pyrosequencing is a one-step method for high resolution DNA typing.

  5. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene

    DEFF Research Database (Denmark)

    Candiloro, Ida Lm; Mikeska, Thomas; Hokland, Peter

    2008-01-01

    ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (dMS-HRM) t......ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (d......MS-HRM) that involves the amplification of single templates after limiting dilution to quantify and to determine the degree of methylation. We used this approach to study methylation of the CDKN2B (p15) cell cycle progression inhibitor gene which is inactivated by DNA methylation in haematological malignancies...... the methylated alleles and assess the degree of methylation. Direct sequencing of selected dMS-HRM products was used to determine the exact DNA methylation pattern and confirmed the degree of methylation estimated by dMS-HRM. CONCLUSION: dMS-HRM is a powerful technique for the analysis of methylation in CDKN2B...

  6. Detection of plant oil DNA using high resolution melting (HRM) post PCR analysis: a tool for disclosure of olive oil adulteration.

    Science.gov (United States)

    Vietina, Michelangelo; Agrimonti, Caterina; Marmiroli, Nelson

    2013-12-15

    Extra virgin olive oil is frequently subjected to adulterations with addition of oils obtained from plants other than olive. DNA analysis is a fast and economic tool to identify plant components in oils. Extraction and amplification of DNA by PCR was tested in olives, in milled seeds and in oils, to investigate its use in olive oil traceability. DNA was extracted from different oils made of hazelnut, maize, sunflower, peanut, sesame, soybean, rice and pumpkin. Comparing the DNA melting profiles in reference plant materials and in the oils, it was possible to identify any plant components in oils and mixtures of oils. Real-Time PCR (RT-PCR) platform has been added of the new methodology of high resolution melting (HRM), both were used to analyse olive oils mixed with different percentage of other oils. Results showed HRM a cost effective method for efficient detection of adulterations in olive oils. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. eMethylsorb: electrochemical quantification of DNA methylation at CpG resolution using DNA-gold affinity interactions.

    Science.gov (United States)

    Sina, Abu Ali Ibn; Howell, Sidney; Carrascosa, Laura G; Rauf, Sakandar; Shiddiky, Muhammad J A; Trau, Matt

    2014-11-07

    We report a simple electrochemical method referred to as "eMethylsorb" for the detection of DNA methylation. The method relies on the base dependent affinity interaction of DNA with gold. The methylation status of DNA is quantified by monitoring the electrochemical current as a function of the relative adsorption level of bisulphite treated DNA samples onto a bare gold electrode. This method can successfully distinguish methylated and unmethylated epigenotypes at single CpG resolution.

  8. Localization microscopy of DNA in situ using Vybrant{sup ®} DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

    Energy Technology Data Exchange (ETDEWEB)

    Żurek-Biesiada, Dominika [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Szczurek, Aleksander T. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Prakash, Kirti [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Mohana, Giriram K. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Lee, Hyun-Keun [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Roignant, Jean-Yves [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Birk, Udo J. [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany); Dobrucki, Jurek W., E-mail: jerzy.dobrucki@uj.edu.pl [Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków (Poland); Cremer, Christoph, E-mail: c.cremer@imb-mainz.de [Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz (Germany); Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg (Germany); Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz (Germany)

    2016-05-01

    Higher order chromatin structure is not only required to compact and spatially arrange long chromatids within a nucleus, but have also important functional roles, including control of gene expression and DNA processing. However, studies of chromatin nanostructures cannot be performed using conventional widefield and confocal microscopy because of the limited optical resolution. Various methods of superresolution microscopy have been described to overcome this difficulty, like structured illumination and single molecule localization microscopy. We report here that the standard DNA dye Vybrant{sup ®} DyeCycle™ Violet can be used to provide single molecule localization microscopy (SMLM) images of DNA in nuclei of fixed mammalian cells. This SMLM method enabled optical isolation and localization of large numbers of DNA-bound molecules, usually in excess of 10{sup 6} signals in one cell nucleus. The technique yielded high-quality images of nuclear DNA density, revealing subdiffraction chromatin structures of the size in the order of 100 nm; the interchromatin compartment was visualized at unprecedented optical resolution. The approach offers several advantages over previously described high resolution DNA imaging methods, including high specificity, an ability to record images using a single wavelength excitation, and a higher density of single molecule signals than reported in previous SMLM studies. The method is compatible with DNA/multicolor SMLM imaging which employs simple staining methods suited also for conventional optical microscopy. - Highlights: • Super-resolution imaging of nuclear DNA with Vybrant Violet and blue excitation. • 90nm resolution images of DNA structures in optically thick eukaryotic nuclei. • Enhanced resolution confirms the existence of DNA-free regions inside the nucleus. • Optimized imaging conditions enable multicolor super-resolution imaging.

  9. Application of high-resolution DNA melting for genotyping in lepidopteran non-model species: Ostrinia furnacalis (Crambidae.

    Directory of Open Access Journals (Sweden)

    FengBo Li

    Full Text Available Development of an ideal marker system facilitates a better understanding of the genetic diversity in lepidopteran non-model organisms, which have abundant species, but relatively limited genomic resources. Single nucleotide polymorphisms (SNPs discovered within single-copy genes have proved to be desired markers, but SNP genotyping by current techniques remain laborious and expensive. High resolution melting (HRM curve analysis represents a simple, rapid and inexpensive genotyping method that is primarily confined to clinical and diagnostic studies. In this study, we evaluated the potential of HRM analysis for SNP genotyping in the lepidopteran non-model species Ostrinia furnacalis (Crambidae. Small amplicon and unlabeled probe assays were developed for the SNPs, which were identified in 30 females of O. furnacalis from 3 different populations by our direct sequencing. Both assays were then applied to genotype 90 unknown female DNA by prior mixing with known wild-type DNA. The genotyping results were compared with those that were obtained using bi-directional sequencing analysis. Our results demonstrated the efficiency and reliability of the HRM assays. HRM has the potential to provide simple, cost-effective genotyping assays and facilitates genotyping studies in any non-model lepidopteran species of interest.

  10. DNA oligonucleotide conformations: high resolution NMR studies

    International Nuclear Information System (INIS)

    Mellema, J.-R.

    1984-01-01

    The present work describes a DNA double-helix model, which is well comparable with the models derived from fibre-diffraction studies. The model has a mononucleotide repeat with torsion angles in accordance with average geometries as derived from 1 H NMR studies. Special attention was paid to reduce the number of short H-H nonbonding contacts, which are abundantly present in the 'classical' fibre-diffraction models. Chapter 3 describes the first complete assignment of a 1 H NMR spectrum of a DNA tetramer, d(TAAT). Preliminary conformational data derived from the spectral parameters recorded at 27 0 C are given. A more detailed analysis employing temperature-dependence studies is given in Chapter 4. (Auth.)

  11. Super-resolution structure of DNA significantly differs in buccal cells of controls and Alzheimer's patients.

    Science.gov (United States)

    Garcia, Angeles; Huang, David; Righolt, Amanda; Righolt, Christiaan; Kalaw, Maria Carmela; Mathur, Shubha; McAvoy, Elizabeth; Anderson, James; Luedke, Angela; Itorralba, Justine; Mai, Sabine

    2017-09-01

    The advent of super-resolution microscopy allowed for new insights into cellular and physiological processes of normal and diseased cells. In this study, we report for the first time on the super-resolved DNA structure of buccal cells from patients with Alzheimer's disease (AD) versus age- and gender-matched healthy, non-caregiver controls. In this super-resolution study cohort of 74 participants, buccal cells were collected and their spatial DNA organization in the nucleus examined by 3D Structured Illumination Microscopy (3D-SIM). Quantitation of the super-resolution DNA structure revealed that the nuclear super-resolution DNA structure of individuals with AD significantly differs from that of their controls (p structure of AD significantly differs in mild, moderate, and severe disease with respect to the DNA-containing and DNA-free/poor spaces. We conclude that whole genome remodeling is a feature of buccal cells in AD. © 2016 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.

  12. High-resolution melt-curve analysis of random-amplified-polymorphic-DNA markers, for the characterisation of pathogenic Leptospira

    DEFF Research Database (Denmark)

    Tulsiani, Suhella; Craig, S B; Graham, G C

    2010-01-01

    A new test for pathogenic Leptospira isolates, based on RAPD-PCR and high-resolution melt (HRM) analysis (which measures the melting temperature of amplicons in real time, using a fluorescent DNA-binding dye), has recently been developed. A characteristic profile of the amplicons can be used...... typed against 13 previously published RAPD primers, using a real-time cycler (the Corbett Life Science RotorGene 6000) and the optimised reagents from a commercial kit (Quantace SensiMix). RAPD-HRM at specific temperatures generated defining amplicon melt profiles for each of the tested serovars....... These profiles were evaluated as difference-curve graphs generated using the RotorGene software package, with a cut-off of at least 8 'U' (plus or minus). The results demonstrated that RAPD-HRM can be used to measure serovar diversity and establish identity, with a high degree of stability. The characterisation...

  13. Two high-mobility group box domains act together to underwind and kink DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez-Giraldo, R.; Acosta-Reyes, F. J. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Malarkey, C. S. [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Saperas, N. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Churchill, M. E. A., E-mail: mair.churchill@ucdenver.edu [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Campos, J. L., E-mail: mair.churchill@ucdenver.edu [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain)

    2015-06-30

    The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

  14. Two high-mobility group box domains act together to underwind and kink DNA

    International Nuclear Information System (INIS)

    Sánchez-Giraldo, R.; Acosta-Reyes, F. J.; Malarkey, C. S.; Saperas, N.; Churchill, M. E. A.; Campos, J. L.

    2015-01-01

    The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA

  15. Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy.

    Science.gov (United States)

    Zhao, Haiyan; Li, Kunpeng; Lynn, Anna Y; Aron, Keith E; Yu, Guimei; Jiang, Wen; Tang, Liang

    2017-04-04

    The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.

  16. Measuring true localization accuracy in super resolution microscopy with DNA-origami nanostructures

    International Nuclear Information System (INIS)

    Reuss, Matthias; Blom, Hans; Brismar, Hjalmar; Fördős, Ferenc; Högberg, Björn; Öktem, Ozan

    2017-01-01

    A common method to assess the performance of (super resolution) microscopes is to use the localization precision of emitters as an estimate for the achieved resolution. Naturally, this is widely used in super resolution methods based on single molecule stochastic switching. This concept suffers from the fact that it is hard to calibrate measures against a real sample (a phantom), because true absolute positions of emitters are almost always unknown. For this reason, resolution estimates are potentially biased in an image since one is blind to true position accuracy, i.e. deviation in position measurement from true positions. We have solved this issue by imaging nanorods fabricated with DNA-origami. The nanorods used are designed to have emitters attached at each end in a well-defined and highly conserved distance. These structures are widely used to gauge localization precision. Here, we additionally determined the true achievable localization accuracy and compared this figure of merit to localization precision values for two common super resolution microscope methods STED and STORM. (paper)

  17. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.

    Directory of Open Access Journals (Sweden)

    Shin-ichi Hashimoto

    Full Text Available Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5'-end transcriptome workflow for the SOLiD system and demonstrate the advantages in sensitivity and dynamic range offered by this tag-based application over traditional approaches for the study of whole genome gene expression. 5'-end transcriptome analysis was used to study whole genome gene expression within a colon cancer cell line, HT-29, treated with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5Aza. More than 20 million 25-base 5'-end tags were obtained from untreated and 5Aza-treated cells and matched to sequences within the human genome. Seventy three percent of the mapped unique tags were associated with RefSeq cDNA sequences, corresponding to approximately 14,000 different protein-coding genes in this single cell type. The level of expression of these genes ranged from 0.02 to 4,704 transcripts per cell. The sensitivity of a single sequence run of the SOLiD platform was 100-1,000 fold greater than that observed from 5'end SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5'end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology.

  18. DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

    Directory of Open Access Journals (Sweden)

    Masudur Rahman

    2016-10-01

    Full Text Available Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.

  19. DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

    Science.gov (United States)

    Rahman, Masudur; Neff, David; Green, Nathaniel; Norton, Michael L.

    2016-01-01

    Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material. PMID:28335324

  20. High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia.

    Science.gov (United States)

    Arias, Leonardo; Barbieri, Chiara; Barreto, Guillermo; Stoneking, Mark; Pakendorf, Brigitte

    2018-02-01

    Northwestern Amazonia (NWA) is a center of high linguistic and cultural diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns, with some groups being foragers and others agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners are taken from different language groups. In this study, we use high-resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural diversity on the genetic relationships and population structure of NWA groups. We collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1,030×. The mtDNA data revealed that NWA populations have high genetic diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher genetic diversity, while the foraging Nukak have lower genetic diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations. Contrary to the view of NWA as a pristine area inhabited by small human populations living in isolation, our data support a view of high diversity and contact among different ethnolinguistic groups, with movement along rivers probably facilitating this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world. © 2017 Wiley Periodicals, Inc.

  1. Localization-based super-resolution imaging meets high-content screening.

    Science.gov (United States)

    Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

    2017-12-01

    Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

  2. ITS2 barcoding DNA region combined with high resolution melting (HRM) analysis of Hyoscyami Semen, the mature seed of Hyoscyamus niger.

    Science.gov (United States)

    Xiong, Chao; Hu, Zhi-Gang; Tu, Yuan; Liu, He-Gang; Wang, Ping; Zhao, Ming-Ming; SHIi, Yu-Hua; Wu, Lan; Sun, Wei; Chen, Shi-Lin

    2016-12-01

    Hyoscyami Semen, the mature dried seed of Hyoscyamus niger L., has long been used as a traditional Chinese medicine to treat human diseases. Hyoscyami Semen is found in local markets in China. In markets, sellers and buyers commonly inadvertently mix the seeds of H. niger with the seeds of related species such as Hygrophila salicifolia (Vahl) Nees, Astragalus complanatus R. Br., Cuscuta australis R. Br., Cuscuta chinensis Lam., and Impatiens balsamina L. because of their similar morphologies or similar names. Thus, developing a reliable method for discriminating H. niger seeds from its adulterants is necessary to reduce confusion and ensure the safe use of Hyoscyami Semen. The present study was designed to evaluate the efficiency of high-resolution melting analysis combined with DNA barcoding (Bar-HRM) with internal transcribed spacer 2 to discriminate H. niger. Our results show that Bar-HRM successfully identified the adulterants and detected the proportion of H. niger DNA extract within an admixture. In particular, HRM detected H. niger DNA extract in A. complanatus DNA extract at concentrations as low as 1%. In conclusion, the Bar-HRM method developed in the present study for authenticating H. niger is rapid and cost-effective. It can be used in the future to guarantee the purity of Hyoscyami Semen for the clinical use. Copyright © 2016 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

  3. High-resolution melting of 12S rRNA and cytochrome b DNA sequences for discrimination of species within distinct European animal families.

    Directory of Open Access Journals (Sweden)

    Jana Naue

    Full Text Available The cheap and easy identification of species is necessary within multiple fields of molecular biology. The use of high-resolution melting (HRM of DNA provides a fast closed-tube method for analysis of the sequence composition of the mitochondrial genes 12S rRNA and cytochrome b. We investigated the potential use of HRM for species identification within eleven different animal groups commonly found in Europe by animal-group-specific DNA amplification followed by DNA melting. Influence factors as DNA amount, additional single base alterations, and the existence of mixed samples were taken into consideration. Visual inspection combined with mathematical evaluation of the curve shapes did resolve nearly all species within an animal group. The assay can therefore not only be used for identification of animal groups and mixture analysis but also for species identification within the respective groups. The use of a universal 12S rRNA system additionally revealed a possible approach for species discrimination, mostly by exclusion. The use of the HRM assay showed to be a reliable, fast, and cheap method for species discrimination within a broad range of different animal species and can be used in a flexible "modular" manner depending on the question to be solved.

  4. Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

    Science.gov (United States)

    Yamamoto, F; Höglund, B; Fernandez-Vina, M; Tyan, D; Rastrou, M; Williams, T; Moonsamy, P; Goodridge, D; Anderson, M; Erlich, H A; Holcomb, C L

    2015-12-01

    Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. Copyright © 2015. Published by Elsevier Inc.

  5. Molecular Dynamics Simulation of High Density DNA Arrays

    Directory of Open Access Journals (Sweden)

    Rudolf Podgornik

    2018-01-01

    Full Text Available Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and

  6. Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

    Science.gov (United States)

    Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

    2016-06-01

    We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. © 2015 Society for Laboratory Automation and Screening.

  7. Highly multiplexed targeted DNA sequencing from single nuclei.

    Science.gov (United States)

    Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

    2016-02-01

    Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

  8. Serum induced degradation of 3D DNA box origami observed by high speed atomic force microscope

    DEFF Research Database (Denmark)

    Jiang, Zaixing; Zhang, Shuai; Yang, Chuanxu

    2015-01-01

    3D DNA origami holds tremendous potential to encapsulate and selectively release therapeutic drugs. Observations of real-time performance of 3D DNA origami structures in physiological environment will contribute much to its further applications. Here, we investigate the degradation kinetics of 3D...... DNA box origami in serum using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allows characterizing the stages of serum effects on individual 3D DNA box origami with nanometer resolution. Our results indicate that the whole digest process...... is a combination of a rapid collapse phase and a slow degradation phase. The damages of box origami mainly happen in the collapse phase. Thus, the structure stability of 3D DNA box origami should be further improved, especially in the collapse phase, before clinical applications...

  9. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA.

    Science.gov (United States)

    Chandrananda, Dineika; Thorne, Natalie P; Bahlo, Melanie

    2015-06-17

    High-throughput sequencing of cell-free DNA fragments found in human plasma has been used to non-invasively detect fetal aneuploidy, monitor organ transplants and investigate tumor DNA. However, many biological properties of this extracellular genetic material remain unknown. Research that further characterizes circulating DNA could substantially increase its diagnostic value by allowing the application of more sophisticated bioinformatics tools that lead to an improved signal to noise ratio in the sequencing data. In this study, we investigate various features of cell-free DNA in plasma using deep-sequencing data from two pregnant women (>70X, >50X) and compare them with matched cellular DNA. We utilize a descriptive approach to examine how the biological cleavage of cell-free DNA affects different sequence signatures such as fragment lengths, sequence motifs at fragment ends and the distribution of cleavage sites along the genome. We show that the size distributions of these cell-free DNA molecules are dependent on their autosomal and mitochondrial origin as well as the genomic location within chromosomes. DNA mapping to particular microsatellites and alpha repeat elements display unique size signatures. We show how cell-free fragments occur in clusters along the genome, localizing to nucleosomal arrays and are preferentially cleaved at linker regions by correlating the mapping locations of these fragments with ENCODE annotation of chromatin organization. Our work further demonstrates that cell-free autosomal DNA cleavage is sequence dependent. The region spanning up to 10 positions on either side of the DNA cleavage site show a consistent pattern of preference for specific nucleotides. This sequence motif is present in cleavage sites localized to nucleosomal cores and linker regions but is absent in nucleosome-free mitochondrial DNA. These background signals in cell-free DNA sequencing data stem from the non-random biological cleavage of these fragments. This

  10. High-resolution X-ray television and high-resolution video recorders

    International Nuclear Information System (INIS)

    Haendle, J.; Horbaschek, H.; Alexandrescu, M.

    1977-01-01

    The improved transmission properties of the high-resolution X-ray television chain described here make it possible to transmit more information per television image. The resolution in the fluoroscopic image, which is visually determined, depends on the dose rate and the inertia of the television pick-up tube. This connection is discussed. In the last few years, video recorders have been increasingly used in X-ray diagnostics. The video recorder is a further quality-limiting element in X-ray television. The development of function patterns of high-resolution magnetic video recorders shows that this quality drop may be largely overcome. The influence of electrical band width and number of lines on the resolution in the X-ray television image stored is explained in more detail. (orig.) [de

  11. Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

    Directory of Open Access Journals (Sweden)

    Sudha Sharma

    2011-01-01

    Full Text Available In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.

  12. High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

    International Nuclear Information System (INIS)

    Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.; Bycroft, Mark

    2016-01-01

    In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1, which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined

  13. High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.; Bycroft, Mark, E-mail: mxb@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom)

    2016-05-23

    In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1, which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined.

  14. Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution.

    Science.gov (United States)

    Gahlon, Hailey L; Romano, Louis J; Rueda, David

    2017-11-20

    Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.

  15. Whole genome DNA methylation: beyond genes silencing

    OpenAIRE

    Tirado-Magallanes, Roberto; Rebbani, Khadija; Lim, Ricky; Pradhan, Sriharsa; Benoukraf, Touati

    2016-01-01

    The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the ...

  16. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

    Science.gov (United States)

    Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

    2014-04-01

    Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

  17. High-resolution typing of Chlamydia trachomatis: epidemiological and clinical uses.

    Science.gov (United States)

    de Vries, Henry J C; Schim van der Loeff, Maarten F; Bruisten, Sylvia M

    2015-02-01

    A state-of-the-art overview of molecular Chlamydia trachomatis typing methods that are used for routine diagnostics and scientific studies. Molecular epidemiology uses high-resolution typing techniques such as multilocus sequence typing, multilocus variable number of tandem repeats analysis, and whole-genome sequencing to identify strains based on their DNA sequence. These data can be used for cluster, network and phylogenetic analyses, and are used to unveil transmission networks, risk groups, and evolutionary pathways. High-resolution typing of C. trachomatis strains is applied to monitor treatment efficacy and re-infections, and to study the recent emergence of lymphogranuloma venereum (LGV) amongst men who have sex with men in high-income countries. Chlamydia strain typing has clinical relevance in disease management, as LGV needs longer treatment than non-LGV C. trachomatis. It has also led to the discovery of a new variant Chlamydia strain in Sweden, which was not detected by some commercial C. trachomatis diagnostic platforms. After a brief history and comparison of the various Chlamydia typing methods, the applications of the current techniques are described and future endeavors to extend scientific understanding are formulated. High-resolution typing will likely help to further unravel the pathophysiological mechanisms behind the wide clinical spectrum of chlamydial disease.

  18. High-resolution neutron diffraction studies of biological and industrial fibres

    Energy Technology Data Exchange (ETDEWEB)

    Langan, P; Mason, S A [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France); Fuller, W; Forsyth, V T; Mahendrasingam, A; Shotton, M; Simpson, L [Keele Univ. (United Kingdom); Grimm, H [FZ, Juelich (Germany); Leberman, R [EMBL, (Country Unknown)

    1997-04-01

    Neutron diffraction is becoming an important tool for studying fibres due to its complementarity to X-ray diffraction. Unlike X-rays, scattering of neutrons by polymer atoms is not a function of their atomic number. In high-resolution studies (1.5-3 A) on D19 deuteration (replacing H by D) is being used to change the relative scattering power of chosen groups making them easier to locate. Recent studies on DNA and cellulose are described. (author). 6 refs.

  19. ANL high resolution injector

    International Nuclear Information System (INIS)

    Minehara, E.; Kutschera, W.; Hartog, P.D.; Billquist, P.

    1985-01-01

    The ANL (Argonne National Laboratory) high-resolution injector has been installed to obtain higher mass resolution and higher preacceleration, and to utilize effectively the full mass range of ATLAS (Argonne Tandem Linac Accelerator System). Preliminary results of the first beam test are reported briefly. The design and performance, in particular a high-mass-resolution magnet with aberration compensation, are discussed. 7 refs., 5 figs., 2 tabs

  20. Quadruplex MAPH: improvement of throughput in high-resolution copy number screening.

    Science.gov (United States)

    Tyson, Jess; Majerus, Tamsin Mo; Walker, Susan; Armour, John Al

    2009-09-28

    Copy number variation (CNV) in the human genome is recognised as a widespread and important source of human genetic variation. Now the challenge is to screen for these CNVs at high resolution in a reliable, accurate and cost-effective way. Multiplex Amplifiable Probe Hybridisation (MAPH) is a sensitive, high-resolution technology appropriate for screening for CNVs in a defined region, for a targeted population. We have developed MAPH to a highly multiplexed format ("QuadMAPH") that allows the user a four-fold increase in the number of loci tested simultaneously. We have used this method to analyse a genomic region of 210 kb, including the MSH2 gene and 120 kb of flanking DNA. We show that the QuadMAPH probes report copy number with equivalent accuracy to simplex MAPH, reliably demonstrating diploid copy number in control samples and accurately detecting deletions in Hereditary Non-Polyposis Colorectal Cancer (HNPCC) samples. QuadMAPH is an accurate, high-resolution method that allows targeted screening of large numbers of subjects without the expense of genome-wide approaches. Whilst we have applied this technique to a region of the human genome, it is equally applicable to the genomes of other organisms.

  1. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

    Science.gov (United States)

    Ni, Yanxiang; Cao, Bo; Ma, Tszshan; Niu, Gang; Huo, Yingdong; Huang, Jiandong; Chen, Danni; Liu, Yi; Yu, Bin; Zhang, Michael Q; Niu, Hanben

    2017-01-01

    High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI: http://dx.doi.org/10.7554/eLife.21660.001 PMID:28485713

  2. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

    NARCIS (Netherlands)

    Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.

    2016-01-01

    We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell

  3. Quadruplex MAPH: improvement of throughput in high-resolution copy number screening

    Directory of Open Access Journals (Sweden)

    Walker Susan

    2009-09-01

    Full Text Available Abstract Background Copy number variation (CNV in the human genome is recognised as a widespread and important source of human genetic variation. Now the challenge is to screen for these CNVs at high resolution in a reliable, accurate and cost-effective way. Results Multiplex Amplifiable Probe Hybridisation (MAPH is a sensitive, high-resolution technology appropriate for screening for CNVs in a defined region, for a targeted population. We have developed MAPH to a highly multiplexed format ("QuadMAPH" that allows the user a four-fold increase in the number of loci tested simultaneously. We have used this method to analyse a genomic region of 210 kb, including the MSH2 gene and 120 kb of flanking DNA. We show that the QuadMAPH probes report copy number with equivalent accuracy to simplex MAPH, reliably demonstrating diploid copy number in control samples and accurately detecting deletions in Hereditary Non-Polyposis Colorectal Cancer (HNPCC samples. Conclusion QuadMAPH is an accurate, high-resolution method that allows targeted screening of large numbers of subjects without the expense of genome-wide approaches. Whilst we have applied this technique to a region of the human genome, it is equally applicable to the genomes of other organisms.

  4. High-resolution metagenomics targets major functional types in complex microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Kalyuzhnaya, Marina G.; Lapidus, Alla; Ivanova, Natalia; Copeland, Alex C.; McHardy, Alice C.; Szeto, Ernest; Salamov, Asaf; Grigoriev, Igor V.; Suciu, Dominic; Levine, Samuel R.; Markowitz, Victor M.; Rigoutsos, Isidore; Tringe, Susannah G.; Bruce, David C.; Richardson, Paul M.; Lidstrom, Mary E.; Chistoserdova, Ludmila

    2009-08-01

    Most microbes in the biosphere remain uncultured and unknown. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) allows glimpses into genetic and metabolic potentials of natural microbial communities. However, in communities of high complexity metagenomics fail to link specific microbes to specific ecological functions. To overcome this limitation, we selectively targeted populations involved in oxidizing single-carbon (C{sub 1}) compounds in Lake Washington (Seattle, USA) by labeling their DNA via stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis demonstrated specific sequence enrichments in response to different C{sub 1} substrates, highlighting ecological roles of individual phylotypes. We further demonstrated the utility of our approach by extracting a nearly complete genome of a novel methylotroph Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This approach allowing high-resolution genomic analysis of ecologically relevant species has the potential to be applied to a wide variety of ecosystems.

  5. Validation of high-resolution DNA melting analysis for mutation scanning of the CDKL5 gene: identification of novel mutations.

    Science.gov (United States)

    Raymond, Laure; Diebold, Bertrand; Leroux, Céline; Maurey, Hélène; Drouin-Garraud, Valérie; Delahaye, Andre; Dulac, Olivier; Metreau, Julia; Melikishvili, Gia; Toutain, Annick; Rivier, François; Bahi-Buisson, Nadia; Bienvenu, Thierry

    2013-01-01

    Mutations in the cyclin-dependent kinase-like 5 gene (CDKL5) have been predominantly described in epileptic encephalopathies of female, including infantile spasms with Rett-like features. Up to now, detection of mutations in this gene was made by laborious, expensive and/or time consuming methods. Here, we decided to validate high-resolution melting analysis (HRMA) for mutation scanning of the CDKL5 gene. Firstly, using a large DNA bank consisting to 34 samples carrying different mutations and polymorphisms, we validated our analytical conditions to analyse the different exons and flanking intronic sequences of the CDKL5 gene by HRMA. Secondly, we screened CDKL5 by both HRMA and denaturing high performance liquid chromatography (dHPLC) in a cohort of 135 patients with early-onset seizures. Our results showed that point mutations and small insertions and deletions can be reliably detected by HRMA. Compared to dHPLC, HRMA profiles are more discriminated, thereby decreasing unnecessary sequencing. In this study, we identified eleven novel sequence variations including four pathogenic mutations (2.96% prevalence). HRMA appears cost-effective, easy to set up, highly sensitive, non-toxic and rapid for mutation screening, ideally suited for large genes with heterogeneous mutations located along the whole coding sequence, such as the CDKL5 gene. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Validation of methylation-sensitive high-resolution melting (MS-HRM) for the detection of stool DNA methylation in colorectal neoplasms.

    Science.gov (United States)

    Xiao, Zhujun; Li, Bingsheng; Wang, Guozhen; Zhu, Weisi; Wang, Zhongqiu; Lin, Jinfeng; Xu, Angao; Wang, Xinying

    2014-04-20

    Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for assaying DNA methylation, but its feasibility for assaying stool in patients with colorectal cancer (CRC) is unknown. First, the MS-HRM and methylation-specific PCR (MSP) detection limits were tested. Second, the methylation statuses of SFRP2 and VIM were analyzed in stool samples by MS-HRM, and in matching tumor and normal colon tissues via bisulfite sequencing PCR (BSP). Third, a case-control study evaluated the diagnostic sensitivity and specificity of MS-HRM relative to results obtained with MSP and the fecal immunochemical test (FIT). Finally, the linearity and reproducibility of MS-HRM were assessed. The detection limits of MS-HRM and MSP were 1% and 5%, respectively. The diagnostic sensitivities of MS-HRM (87.3%, 55/63) in stool and BSP in matching tumor tissue (92.1%, 58/63) were highly consistent (κ=0.744). The MS-HRM assay detected 92.5% (37/40) methylation in CRCs, 94.4% (34/36) in advanced adenomas, and 8.8% (5/57) in normal controls. The results of MS-HRM analysis were stable and reliable and showed fairly good linearity for both SFRP2 (PHRM shows potential for CRC screening. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Ultra-high resolution protein crystallography

    International Nuclear Information System (INIS)

    Takeda, Kazuki; Hirano, Yu; Miki, Kunio

    2010-01-01

    Many protein structures have been determined by X-ray crystallography and deposited with the Protein Data Bank. However, these structures at usual resolution (1.5< d<3.0 A) are insufficient in their precision and quantity for elucidating the molecular mechanism of protein functions directly from structural information. Several studies at ultra-high resolution (d<0.8 A) have been performed with synchrotron radiation in the last decade. The highest resolution of the protein crystals was achieved at 0.54 A resolution for a small protein, crambin. In such high resolution crystals, almost all of hydrogen atoms of proteins and some hydrogen atoms of bound water molecules are experimentally observed. In addition, outer-shell electrons of proteins can be analyzed by the multipole refinement procedure. However, the influence of X-rays should be precisely estimated in order to derive meaningful information from the crystallographic results. In this review, we summarize refinement procedures, current status and perspectives for ultra high resolution protein crystallography. (author)

  8. Enhanced resolution of DNA restriction fragments: A procedure by two-dimensional electrophoresis and double-labeling

    International Nuclear Information System (INIS)

    Yi, M.; Au, L.C.; Ichikawa, N.; Ts'o, P.O.

    1990-01-01

    A probe-free method was developed to detect DNA rearrangement in bacteria based on the electrophoretic separation of twice-digested restriction fragments of genomic DNA into a two-dimensional (2-D) pattern. The first restriction enzyme digestion was done in solution, followed by electrophoresis of the restriction fragments in one dimension. A second restriction enzyme digestion was carried out in situ in the gel, followed by electrophoresis in a second dimension perpendicular to the first electrophoresis. The 2-D pattern provides for the resolution of 300-400 spots, which are defined and indexed by an x,y coordinate system with size markers. This approach has greatly increased the resolution power over conventional one-dimensional (1-D) electrophoresis. To study DNA rearrangement, a 2-D pattern from a test strain was compared with the 2-D pattern from a reference strain. After the first digestion, genomic DNA fragments from the test strain were labeled with 35S, while those from the reference strain were labeled with 32P. This was done to utilize the difference in the energy emission of 35S and 32P isotopes for autoradiography when two x-ray films were exposed simultaneously on top of the gel after the 2-D electrophoresis. The irradiation from the decay of 35S exposed only the lower film, whereas the irradiation from the decay of 32P exposed both the lower and upper films. Different DNA fragments existed in the test DNA compared with the reference DNA can be identified unambiguously by the differential two 2-D patterns produced on two films upon exposure to the 35S and 32P fragments in the same gel. An appropriate photographic procedure further simplified the process, allowing only the difference in DNA fragments between these two patterns to be shown in the map

  9. High resolution solar observations

    International Nuclear Information System (INIS)

    Title, A.

    1985-01-01

    Currently there is a world-wide effort to develop optical technology required for large diffraction limited telescopes that must operate with high optical fluxes. These developments can be used to significantly improve high resolution solar telescopes both on the ground and in space. When looking at the problem of high resolution observations it is essential to keep in mind that a diffraction limited telescope is an interferometer. Even a 30 cm aperture telescope, which is small for high resolution observations, is a big interferometer. Meter class and above diffraction limited telescopes can be expected to be very unforgiving of inattention to details. Unfortunately, even when an earth based telescope has perfect optics there are still problems with the quality of its optical path. The optical path includes not only the interior of the telescope, but also the immediate interface between the telescope and the atmosphere, and finally the atmosphere itself

  10. High speed, High resolution terahertz spectrometers

    International Nuclear Information System (INIS)

    Kim, Youngchan; Yee, Dae Su; Yi, Miwoo; Ahn, Jaewook

    2008-01-01

    A variety of sources and methods have been developed for terahertz spectroscopy during almost two decades. Terahertz time domain spectroscopy (THz TDS)has attracted particular attention as a basic measurement method in the fields of THz science and technology. Recently, asynchronous optical sampling (AOS)THz TDS has been demonstrated, featuring rapid data acquisition and a high spectral resolution. Also, terahertz frequency comb spectroscopy (TFCS)possesses attractive features for high precision terahertz spectroscopy. In this presentation, we report on these two types of terahertz spectrometer. Our high speed, high resolution terahertz spectrometer is demonstrated using two mode locked femtosecond lasers with slightly different repetition frequencies without a mechanical delay stage. The repetition frequencies of the two femtosecond lasers are stabilized by use of two phase locked loops sharing the same reference oscillator. The time resolution of our terahertz spectrometer is measured using the cross correlation method to be 270 fs. AOS THz TDS is presented in Fig. 1, which shows a time domain waveform rapidly acquired on a 10ns time window. The inset shows a zoom into the signal with 100ps time window. The spectrum obtained by the fast Fourier Transformation (FFT)of the time domain waveform has a frequency resolution of 100MHz. The dependence of the signal to noise ratio (SNR)on the measurement time is also investigated

  11. High Resolution Melting Analysis for fast and cheap polymorphism screening of marine populations

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Anne-Leila Meistertzheim, Isabelle Calves, Sébastien Artigaud, Carolyn S. Friedman, Christine Paillard, Jean Laroche & Claude Ferec ### Abstract This protocol permits the mutation scanning of PCR products by high-resolution DNA melting analysis requiring the inclusion of a saturating intercalating dye in the PCR mix without labelled probe. During a scanning process, fluorescent melting curves of PCR amplicons are analyzed. Mutations modifying melting curve shapes, are allowed...

  12. High-Resolution Sonars: What Resolution Do We Need for Target Recognition?

    Directory of Open Access Journals (Sweden)

    Pailhas Yan

    2010-01-01

    Full Text Available Target recognition in sonar imagery has long been an active research area in the maritime domain, especially in the mine-counter measure context. Recently it has received even more attention as new sensors with increased resolution have been developed; new threats to critical maritime assets and a new paradigm for target recognition based on autonomous platforms have emerged. With the recent introduction of Synthetic Aperture Sonar systems and high-frequency sonars, sonar resolution has dramatically increased and noise levels decreased. Sonar images are distance images but at high resolution they tend to appear visually as optical images. Traditionally algorithms have been developed specifically for imaging sonars because of their limited resolution and high noise levels. With high-resolution sonars, algorithms developed in the image processing field for natural images become applicable. However, the lack of large datasets has hampered the development of such algorithms. Here we present a fast and realistic sonar simulator enabling development and evaluation of such algorithms.We develop a classifier and then analyse its performances using our simulated synthetic sonar images. Finally, we discuss sensor resolution requirements to achieve effective classification of various targets and demonstrate that with high resolution sonars target highlight analysis is the key for target recognition.

  13. 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

  14. High Resolution Melting (HRM for High-Throughput Genotyping—Limitations and Caveats in Practical Case Studies

    Directory of Open Access Journals (Sweden)

    Marcin Słomka

    2017-11-01

    Full Text Available High resolution melting (HRM is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs. This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.

  15. High Resolution Melting (HRM) for High-Throughput Genotyping—Limitations and Caveats in Practical Case Studies

    Science.gov (United States)

    Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz

    2017-01-01

    High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup. PMID:29099791

  16. High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies.

    Science.gov (United States)

    Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz; Strapagiel, Dominik

    2017-11-03

    High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.

  17. 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.

  18. Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.

    Science.gov (United States)

    Kim, Suhng Wook; Kim, Dong-Uk; Kim, Jin Kwang; Kang, Lin-Woo; Cho, Hyun-Soo

    2008-05-01

    We have determined a 2.6A resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and beta-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.

  19. Berkeley High-Resolution Ball

    International Nuclear Information System (INIS)

    Diamond, R.M.

    1984-10-01

    Criteria for a high-resolution γ-ray system are discussed. Desirable properties are high resolution, good response function, and moderate solid angle so as to achieve not only double- but triple-coincidences with good statistics. The Berkeley High-Resolution Ball involved the first use of bismuth germanate (BGO) for anti-Compton shield for Ge detectors. The resulting compact shield permitted rather close packing of 21 detectors around a target. In addition, a small central BGO ball gives the total γ-ray energy and multiplicity, as well as the angular pattern of the γ rays. The 21-detector array is nearly complete, and the central ball has been designed, but not yet constructed. First results taken with 9 detector modules are shown for the nucleus 156 Er. The complex decay scheme indicates a transition from collective rotation (prolate shape) to single- particle states (possibly oblate) near spin 30 h, and has other interesting features

  20. A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago.

    Science.gov (United States)

    Clerc-Blain, Jessica L E; Starr, Julian R; Bull, Roger D; Saarela, Jeffery M

    2010-01-01

    Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world's some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth's landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies. © 2009 Blackwell Publishing Ltd.

  1. High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum

    DEFF Research Database (Denmark)

    Jungwirth, Britta; Sala, Claudia; Kohl, Thomas A

    2013-01-01

    of the 6C non-coding RNA gene and to non-canonical DNA binding sites within protein-coding regions. The present study underlines the dynamics within the GlxR regulon by identifying in vivo targets during growth on glucose and contributes to the expansion of knowledge of this important transcriptional......The transcriptional regulator GlxR has been characterized as a global hub within the gene-regulatory network of Corynebacterium glutamicum. Chromatin immunoprecipitation with a specific anti-GlxR antibody and subsequent high-throughput sequencing (ChIP-seq) was applied to C. glutamicum to get new...... mapping of these data on the genome sequence of C. glutamicum, 107 enriched DNA fragments were detected from cells grown with glucose as carbon source. GlxR binding sites were identified in the sequence of 79 enriched DNA fragments, of which 21 sites were not previously reported. Electrophoretic mobility...

  2. High-Resolution PET Detector. Final report

    International Nuclear Information System (INIS)

    Karp, Joel

    2014-01-01

    The objective of this project was to develop an understanding of the limits of performance for a high resolution PET detector using an approach based on continuous scintillation crystals rather than pixelated crystals. The overall goal was to design a high-resolution detector, which requires both high spatial resolution and high sensitivity for 511 keV gammas. Continuous scintillation detectors (Anger cameras) have been used extensively for both single-photon and PET scanners, however, these instruments were based on NaI(Tl) scintillators using relatively large, individual photo-multipliers. In this project we investigated the potential of this type of detector technology to achieve higher spatial resolution through the use of improved scintillator materials and photo-sensors, and modification of the detector surface to optimize the light response function.We achieved an average spatial resolution of 3-mm for a 25-mm thick, LYSO continuous detector using a maximum likelihood position algorithm and shallow slots cut into the entrance surface

  3. 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.

  4. 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...

  5. Single-base resolution and long-coverage sequencing based on single-molecule nanomanipulation

    International Nuclear Information System (INIS)

    An Hongjie; Huang Jiehuan; Lue Ming; Li Xueling; Lue Junhong; Li Haikuo; Zhang Yi; Li Minqian; Hu Jun

    2007-01-01

    We show new approaches towards a novel single-molecule sequencing strategy which consists of high-resolution positioning isolation of overlapping DNA fragments with atomic force microscopy (AFM), subsequent single-molecule PCR amplification and conventional Sanger sequencing. In this study, a DNA labelling technique was used to guarantee the accuracy in positioning the target DNA. Single-molecule multiplex PCR was carried out to test the contamination. The results showed that the two overlapping DNA fragments isolated by AFM could be successfully sequenced with high quality and perfect contiguity, indicating that single-base resolution and long-coverage sequencing have been achieved simultaneously

  6. A high throughput DNA extraction method with high yield and quality

    Directory of Open Access Journals (Sweden)

    Xin Zhanguo

    2012-07-01

    Full Text Available Abstract Background Preparation of large quantity and high quality genomic DNA from a large number of plant samples is a major bottleneck for most genetic and genomic analyses, such as, genetic mapping, TILLING (Targeting Induced Local Lesion IN Genome, and next-generation sequencing directly from sheared genomic DNA. A variety of DNA preparation methods and commercial kits are available. However, they are either low throughput, low yield, or costly. Here, we describe a method for high throughput genomic DNA isolation from sorghum [Sorghum bicolor (L. Moench] leaves and dry seeds with high yield, high quality, and affordable cost. Results We developed a high throughput DNA isolation method by combining a high yield CTAB extraction method with an improved cleanup procedure based on MagAttract kit. The method yielded large quantity and high quality DNA from both lyophilized sorghum leaves and dry seeds. The DNA yield was improved by nearly 30 fold with 4 times less consumption of MagAttract beads. The method can also be used in other plant species, including cotton leaves and pine needles. Conclusion A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.

  7. 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...

  8. High resolution sequence stratigraphy in China

    International Nuclear Information System (INIS)

    Zhang Shangfeng; Zhang Changmin; Yin Yanshi; Yin Taiju

    2008-01-01

    Since high resolution sequence stratigraphy was introduced into China by DENG Hong-wen in 1995, it has been experienced two development stages in China which are the beginning stage of theory research and development of theory research and application, and the stage of theoretical maturity and widely application that is going into. It is proved by practices that high resolution sequence stratigraphy plays more and more important roles in the exploration and development of oil and gas in Chinese continental oil-bearing basin and the research field spreads to the exploration of coal mine, uranium mine and other strata deposits. However, the theory of high resolution sequence stratigraphy still has some shortages, it should be improved in many aspects. The authors point out that high resolution sequence stratigraphy should be characterized quantitatively and modelized by computer techniques. (authors)

  9. Development of AMS high resolution injector system

    International Nuclear Information System (INIS)

    Bao Yiwen; Guan Xialing; Hu Yueming

    2008-01-01

    The Beijing HI-13 tandem accelerator AMS high resolution injector system was developed. The high resolution energy achromatic system consists of an electrostatic analyzer and a magnetic analyzer, which mass resolution can reach 600 and transmission is better than 80%. (authors)

  10. Resolution enhancement of low quality videos using a high-resolution frame

    NARCIS (Netherlands)

    Pham, T.Q.; Van Vliet, L.J.; Schutte, K.

    2006-01-01

    This paper proposes an example-based Super-Resolution (SR) algorithm of compressed videos in the Discrete Cosine Transform (DCT) domain. Input to the system is a Low-Resolution (LR) compressed video together with a High-Resolution (HR) still image of similar content. Using a training set of

  11. High resolution, high speed ultrahigh vacuum microscopy

    International Nuclear Information System (INIS)

    Poppa, Helmut

    2004-01-01

    The history and future of transmission electron microscopy (TEM) is discussed as it refers to the eventual development of instruments and techniques applicable to the real time in situ investigation of surface processes with high resolution. To reach this objective, it was necessary to transform conventional high resolution instruments so that an ultrahigh vacuum (UHV) environment at the sample site was created, that access to the sample by various in situ sample modification procedures was provided, and that in situ sample exchanges with other integrated surface analytical systems became possible. Furthermore, high resolution image acquisition systems had to be developed to take advantage of the high speed imaging capabilities of projection imaging microscopes. These changes to conventional electron microscopy and its uses were slowly realized in a few international laboratories over a period of almost 40 years by a relatively small number of researchers crucially interested in advancing the state of the art of electron microscopy and its applications to diverse areas of interest; often concentrating on the nucleation, growth, and properties of thin films on well defined material surfaces. A part of this review is dedicated to the recognition of the major contributions to surface and thin film science by these pioneers. Finally, some of the important current developments in aberration corrected electron optics and eventual adaptations to in situ UHV microscopy are discussed. As a result of all the path breaking developments that have led to today's highly sophisticated UHV-TEM systems, integrated fundamental studies are now possible that combine many traditional surface science approaches. Combined investigations to date have involved in situ and ex situ surface microscopies such as scanning tunneling microscopy/atomic force microscopy, scanning Auger microscopy, and photoemission electron microscopy, and area-integrating techniques such as x-ray photoelectron

  12. A high resolution solar atlas for fluorescence calculations

    Science.gov (United States)

    Hearn, M. F.; Ohlmacher, J. T.; Schleicher, D. G.

    1983-01-01

    The characteristics required of a solar atlas to be used for studying the fluorescence process in comets are examined. Several sources of low resolution data were combined to provide an absolutely calibrated spectrum from 2250 A to 7000A. Three different sources of high resolution data were also used to cover this same spectral range. The low resolution data were then used to put each high resolution spectrum on an absolute scale. The three high resolution spectra were then combined in their overlap regions to produce a single, absolutely calibrated high resolution spectrum over the entire spectral range.

  13. Crystal structure of the Msx-1 homeodomain/DNA complex.

    Science.gov (United States)

    Hovde, S; Abate-Shen, C; Geiger, J H

    2001-10-09

    The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

  14. High-resolution SPECT for small-animal imaging

    International Nuclear Information System (INIS)

    Qi Yujin

    2006-01-01

    This article presents a brief overview of the development of high-resolution SPECT for small-animal imaging. A pinhole collimator has been used for high-resolution animal SPECT to provide better spatial resolution and detection efficiency in comparison with a parallel-hole collimator. The theory of imaging characteristics of the pinhole collimator is presented and the designs of the pinhole aperture are discussed. The detector technologies used for the development of small-animal SPECT and the recent advances are presented. The evolving trend of small-animal SPECT is toward a multi-pinhole and a multi-detector system to obtain a high resolution and also a high detection efficiency. (authors)

  15. Cockayne syndrome group A and B proteins converge on transcription-linked resolution of non-B DNA.

    Science.gov (United States)

    Scheibye-Knudsen, Morten; Tseng, Anne; Borch Jensen, Martin; Scheibye-Alsing, Karsten; Fang, Evandro Fei; Iyama, Teruaki; Bharti, Sanjay Kumar; Marosi, Krisztina; Froetscher, Lynn; Kassahun, Henok; Eckley, David Mark; Maul, Robert W; Bastian, Paul; De, Supriyo; Ghosh, Soumita; Nilsen, Hilde; Goldberg, Ilya G; Mattson, Mark P; Wilson, David M; Brosh, Robert M; Gorospe, Myriam; Bohr, Vilhelm A

    2016-11-01

    Cockayne syndrome is a neurodegenerative accelerated aging disorder caused by mutations in the CSA or CSB genes. Although the pathogenesis of Cockayne syndrome has remained elusive, recent work implicates mitochondrial dysfunction in the disease progression. Here, we present evidence that loss of CSA or CSB in a neuroblastoma cell line converges on mitochondrial dysfunction caused by defects in ribosomal DNA transcription and activation of the DNA damage sensor poly-ADP ribose polymerase 1 (PARP1). Indeed, inhibition of ribosomal DNA transcription leads to mitochondrial dysfunction in a number of cell lines. Furthermore, machine-learning algorithms predict that diseases with defects in ribosomal DNA (rDNA) transcription have mitochondrial dysfunction, and, accordingly, this is found when factors involved in rDNA transcription are knocked down. Mechanistically, loss of CSA or CSB leads to polymerase stalling at non-B DNA in a neuroblastoma cell line, in particular at G-quadruplex structures, and recombinant CSB can melt G-quadruplex structures. Indeed, stabilization of G-quadruplex structures activates PARP1 and leads to accelerated aging in Caenorhabditis elegans In conclusion, this work supports a role for impaired ribosomal DNA transcription in Cockayne syndrome and suggests that transcription-coupled resolution of secondary structures may be a mechanism to repress spurious activation of a DNA damage response.

  16. Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

    Science.gov (United States)

    Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

    2017-09-01

    Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

  17. Application of multivariate curve resolution for the study of folding processes of DNA monitored by fluorescence resonance energy transfer

    International Nuclear Information System (INIS)

    Kumar, Praveen; Kanchan, Kajal; Gargallo, Raimundo; Chowdhury, Shantanu

    2005-01-01

    The study described in the present article used fluorescence resonance energy transfer (FRET) to monitor the folding of a 31-mer cytosine-rich DNA segment, from the promoter region of the human c-myc oncogene. Spectroscopic FRET data recorded during experiments carried out in different experimental conditions were individually and simultaneously analyzed by multivariate curve resolution. The simultaneous analysis of several data matrices allowed the resolution of the system, removing most of the ambiguities related to factor analysis. From the results obtained, we report the evidence of the formation of two ordered conformations in acidic and neutral pH values, in addition to the disordered structure found at high temperatures. These ordered conformations could be related to cytosine-tetraplex structures showing different degrees of protonation in cytosine bases

  18. High resolution time integration for SN radiation transport

    International Nuclear Information System (INIS)

    Thoreson, Greg; McClarren, Ryan G.; Chang, Jae H.

    2009-01-01

    First-order, second-order, and high resolution time discretization schemes are implemented and studied for the discrete ordinates (S N ) equations. The high resolution method employs a rate of convergence better than first-order, but also suppresses artificial oscillations introduced by second-order schemes in hyperbolic partial differential equations. The high resolution method achieves these properties by nonlinearly adapting the time stencil to use a first-order method in regions where oscillations could be created. We employ a quasi-linear solution scheme to solve the nonlinear equations that arise from the high resolution method. All three methods were compared for accuracy and convergence rates. For non-absorbing problems, both second-order and high resolution converged to the same solution as the first-order with better convergence rates. High resolution is more accurate than first-order and matches or exceeds the second-order method

  19. Regulatory Control of the Resolution of DNA Recombination Intermediates during Meiosis and Mitosis

    OpenAIRE

    Matos, Joao; Blanco, Miguel G.; Maslen, Sarah; Skehel, J. Mark; West, Stephen C.

    2011-01-01

    The efficient and timely resolution of DNA recombination intermediates is essential for bipolar chromosome segregation. Here, we show that the specialized chromosome segregation patterns of meiosis and mitosis, which require the coordination of recombination with cell-cycle progression, are achieved by regulating the timing of activation of two crossover-promoting endonucleases. In yeast meiosis, Mus81-Mms4 and Yen1 are controlled by phosphorylation events that lead to their sequential activa...

  20. High tracking resolution detectors. Final Technical Report

    International Nuclear Information System (INIS)

    Vasile, Stefan; Li, Zheng

    2010-01-01

    High-resolution tracking detectors based on Active Pixel Sensor (APS) have been valuable tools in Nuclear Physics and High-Energy Physics research, and have contributed to major discoveries. Their integration time, radiation length and readout rate is a limiting factor for the planed luminosity upgrades in nuclear and high-energy physics collider-based experiments. The goal of this program was to demonstrate and develop high-gain, high-resolution tracking detector arrays with faster readout, and shorter radiation length than APS arrays. These arrays may operate as direct charged particle detectors or as readouts of high resolution scintillating fiber arrays. During this program, we developed in CMOS large, high-resolution pixel sensor arrays with integrated readout, and reset at pixel level. Their intrinsic gain, high immunity to surface and moisture damage, will allow operating these detectors with minimal packaging/passivation requirements and will result in radiation length superior to APS. In Phase I, we designed and fabricated arrays with calorimetric output capable of sub-pixel resolution and sub-microsecond readout rate. The technical effort was dedicated to detector and readout structure development, performance verification, as well as to radiation damage and damage annealing.

  1. Ultra high resolution tomography

    Energy Technology Data Exchange (ETDEWEB)

    Haddad, W.S.

    1994-11-15

    Recent work and results on ultra high resolution three dimensional imaging with soft x-rays will be presented. This work is aimed at determining microscopic three dimensional structure of biological and material specimens. Three dimensional reconstructed images of a microscopic test object will be presented; the reconstruction has a resolution on the order of 1000 A in all three dimensions. Preliminary work with biological samples will also be shown, and the experimental and numerical methods used will be discussed.

  2. A high resolution portable spectroscopy system

    International Nuclear Information System (INIS)

    Kulkarni, C.P.; Vaidya, P.P.; Paulson, M.; Bhatnagar, P.V.; Pande, S.S.; Padmini, S.

    2003-01-01

    Full text: This paper describes the system details of a High Resolution Portable Spectroscopy System (HRPSS) developed at Electronics Division, BARC. The system can be used for laboratory class, high-resolution nuclear spectroscopy applications. The HRPSS consists of a specially designed compact NIM bin, with built-in power supplies, accommodating a low power, high resolution MCA, and on-board embedded computer for spectrum building and communication. A NIM based spectroscopy amplifier and a HV module for detector bias are integrated (plug-in) in the bin. The system communicates with a host PC via a serial link. Along-with a laptop PC, and a portable HP-Ge detector, the HRPSS offers a laboratory class performance for portable applications

  3. High-resolution melting analysis, a simple and effective method for reliable mutation scanning and frequency studies in the ACADVL gene

    DEFF Research Database (Denmark)

    Olsen, Rikke Katrine Jentoft; Dobrowolski, Steven F; Kjeldsen, Margrethe

    2010-01-01

    -long-chain acyl-CoA dehydrogenase deficiency (VLCADD), the second most common fatty acid oxidation disorder detected by expanded newborn screening, to demonstrate accurate and fast diagnostic evaluation of the ACADVL gene utilizing DNA extracted from the newborn screening dried blood spot and high resolution melt...

  4. A novel typing method for Listeria monocytogenes using high-resolution melting analysis (HRMA) of tandem repeat regions.

    Science.gov (United States)

    Ohshima, Chihiro; Takahashi, Hajime; Iwakawa, Ai; Kuda, Takashi; Kimura, Bon

    2017-07-17

    Listeria monocytogenes, which is responsible for causing food poisoning known as listeriosis, infects humans and animals. Widely distributed in the environment, this bacterium is known to contaminate food products after being transmitted to factories via raw materials. To minimize the contamination of products by food pathogens, it is critical to identify and eliminate factory entry routes and pathways for the causative bacteria. High resolution melting analysis (HRMA) is a method that takes advantage of differences in DNA sequences and PCR product lengths that are reflected by the disassociation temperature. Through our research, we have developed a multiple locus variable-number tandem repeat analysis (MLVA) using HRMA as a simple and rapid method to differentiate L. monocytogenes isolates. While evaluating our developed method, the ability of MLVA-HRMA, MLVA using capillary electrophoresis, and multilocus sequence typing (MLST) was compared for their ability to discriminate between strains. The MLVA-HRMA method displayed greater discriminatory ability than MLST and MLVA using capillary electrophoresis, suggesting that the variation in the number of repeat units, along with mutations within the DNA sequence, was accurately reflected by the melting curve of HRMA. Rather than relying on DNA sequence analysis or high-resolution electrophoresis, the MLVA-HRMA method employs the same process as PCR until the analysis step, suggesting a combination of speed and simplicity. The result of MLVA-HRMA method is able to be shared between different laboratories. There are high expectations that this method will be adopted for regular inspections at food processing facilities in the near future. Copyright © 2017. Published by Elsevier B.V.

  5. High Resolution Elevation Contours

    Data.gov (United States)

    Minnesota Department of Natural Resources — This dataset contains contours generated from high resolution data sources such as LiDAR. Generally speaking this data is 2 foot or less contour interval.

  6. Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Ying-Xu [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); Mjøs, Svein Are, E-mail: svein.mjos@kj.uib.no [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); David, Fabrice P.A. [Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne (Switzerland); Schmid, Adrien W. [Proteomics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

    2016-03-31

    Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

  7. Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

    International Nuclear Information System (INIS)

    Zeng, Ying-Xu; Mjøs, Svein Are; David, Fabrice P.A.; Schmid, Adrien W.

    2016-01-01

    Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

  8. Ultra-high resolution coded wavefront sensor

    KAUST Repository

    Wang, Congli

    2017-06-08

    Wavefront sensors and more general phase retrieval methods have recently attracted a lot of attention in a host of application domains, ranging from astronomy to scientific imaging and microscopy. In this paper, we introduce a new class of sensor, the Coded Wavefront Sensor, which provides high spatio-temporal resolution using a simple masked sensor under white light illumination. Specifically, we demonstrate megapixel spatial resolution and phase accuracy better than 0.1 wavelengths at reconstruction rates of 50 Hz or more, thus opening up many new applications from high-resolution adaptive optics to real-time phase retrieval in microscopy.

  9. High Resolution Melting (HRM) applied to wine authenticity.

    Science.gov (United States)

    Pereira, Leonor; Gomes, Sónia; Castro, Cláudia; Eiras-Dias, José Eduardo; Brazão, João; Graça, António; Fernandes, José R; Martins-Lopes, Paula

    2017-02-01

    Wine authenticity methods are in increasing demand mainly in Denomination of Origin designations. The DNA-based methodologies are a reliable means of tracking food/wine varietal composition. The main aim of this work was the study of High Resolution Melting (HRM) application as a screening method for must and wine authenticity. Three sample types (leaf, must and wine) were used to validate the three developed HRM assays (Vv1-705bp; Vv2-375bp; and Vv3-119bp). The Vv1 HRM assay was only successful when applied to leaf and must samples. The Vv2 HRM assay successfully amplified all sample types, allowing genotype discrimination based on melting temperature values. The smallest amplicon, Vv3, produced a coincident melting curve shape in all sample types (leaf and wine) with corresponding genotypes. This study presents sensitive, rapid and efficient HRM assays applied for the first time to wine samples suitable for wine authenticity purposes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing.

    Science.gov (United States)

    Schwessinger, Benjamin; Rathjen, John P

    2017-01-01

    Wheat rust fungi are complex organisms with a complete life cycle that involves two different host plants and five different spore types. During the asexual infection cycle on wheat, rusts produce massive amounts of dikaryotic urediniospores. These spores are dikaryotic (two nuclei) with each nucleus containing one haploid genome. This dikaryotic state is likely to contribute to their evolutionary success, making them some of the major wheat pathogens globally. Despite this, most published wheat rust genomes are highly fragmented and contain very little haplotype-specific sequence information. Current long-read sequencing technologies hold great promise to provide more contiguous and haplotype-phased genome assemblies. Long reads are able to span repetitive regions and phase structural differences between the haplomes. This increased genome resolution enables the identification of complex loci and the study of genome evolution beyond simple nucleotide polymorphisms. Long-read technologies require pure high molecular weight DNA as an input for sequencing. Here, we describe a DNA extraction protocol for rust spores that yields pure double-stranded DNA molecules with molecular weight of >50 kilo-base pairs (kbp). The isolated DNA is of sufficient purity for PacBio long-read sequencing, but may require additional purification for other sequencing technologies such as Nanopore and 10× Genomics.

  11. DNA nanotechnology: On-command molecular Trojans

    Science.gov (United States)

    Niemeyer, Christof M.

    2017-12-01

    Lipid-motif-decorated DNA nanocapsules filled with photoresponsive polymers are capable of delivering signalling molecules into target organisms for biological perturbations at high spatiotemporal resolution.

  12. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

    Science.gov (United States)

    van Koningsbruggen, Silvana; Gierlinski, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J; Ariyurek, Yavuz; den Dunnen, Johan T; Lamond, Angus I

    2010-11-01

    The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

  13. High resolution data acquisition

    Science.gov (United States)

    Thornton, Glenn W.; Fuller, Kenneth R.

    1993-01-01

    A high resolution event interval timing system measures short time intervals such as occur in high energy physics or laser ranging. Timing is provided from a clock (38) pulse train (37) and analog circuitry (44) for generating a triangular wave (46) synchronously with the pulse train (37). The triangular wave (46) has an amplitude and slope functionally related to the time elapsed during each clock pulse in the train. A converter (18, 32) forms a first digital value of the amplitude and slope of the triangle wave at the start of the event interval and a second digital value of the amplitude and slope of the triangle wave at the end of the event interval. A counter (26) counts the clock pulse train (37) during the interval to form a gross event interval time. A computer (52) then combines the gross event interval time and the first and second digital values to output a high resolution value for the event interval.

  14. High resolution time integration for Sn radiation transport

    International Nuclear Information System (INIS)

    Thoreson, Greg; McClarren, Ryan G.; Chang, Jae H.

    2008-01-01

    First order, second order and high resolution time discretization schemes are implemented and studied for the S n equations. The high resolution method employs a rate of convergence better than first order, but also suppresses artificial oscillations introduced by second order schemes in hyperbolic differential equations. All three methods were compared for accuracy and convergence rates. For non-absorbing problems, both second order and high resolution converged to the same solution as the first order with better convergence rates. High resolution is more accurate than first order and matches or exceeds the second order method. (authors)

  15. Structure of high-resolution NMR spectra

    CERN Document Server

    Corio, PL

    2012-01-01

    Structure of High-Resolution NMR Spectra provides the principles, theories, and mathematical and physical concepts of high-resolution nuclear magnetic resonance spectra.The book presents the elementary theory of magnetic resonance; the quantum mechanical theory of angular momentum; the general theory of steady state spectra; and multiple quantum transitions, double resonance and spin echo experiments.Physicists, chemists, and researchers will find the book a valuable reference text.

  16. High-resolution multi-slice PET

    International Nuclear Information System (INIS)

    Yasillo, N.J.; Chintu Chen; Ordonez, C.E.; Kapp, O.H.; Sosnowski, J.; Beck, R.N.

    1992-01-01

    This report evaluates the progress to test the feasibility and to initiate the design of a high resolution multi-slice PET system. The following specific areas were evaluated: detector development and testing; electronics configuration and design; mechanical design; and system simulation. The design and construction of a multiple-slice, high-resolution positron tomograph will provide substantial improvements in the accuracy and reproducibility of measurements of the distribution of activity concentrations in the brain. The range of functional brain research and our understanding of local brain function will be greatly extended when the development of this instrumentation is completed

  17. High resolution NMR spectroscopy of synthetic polymers in bulk

    International Nuclear Information System (INIS)

    Komorski, R.A.

    1986-01-01

    The contents of this book are: Overview of high-resolution NMR of solid polymers; High-resolution NMR of glassy amorphous polymers; Carbon-13 solid-state NMR of semicrystalline polymers; Conformational analysis of polymers of solid-state NMR; High-resolution NMR studies of oriented polymers; High-resolution solid-state NMR of protons in polymers; and Deuterium NMR of solid polymers. This work brings together the various approaches for high-resolution NMR studies of bulk polymers into one volume. Heavy emphasis is, of course, given to 13C NMR studies both above and below Tg. Standard high-power pulse and wide-line techniques are not covered

  18. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

    Science.gov (United States)

    Belaghzal, Houda; Dekker, Job; Gibcus, Johan H

    2017-07-01

    Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. High resolution integral holography using Fourier ptychographic approach.

    Science.gov (United States)

    Li, Zhaohui; Zhang, Jianqi; Wang, Xiaorui; Liu, Delian

    2014-12-29

    An innovative approach is proposed for calculating high resolution computer generated integral holograms by using the Fourier Ptychographic (FP) algorithm. The approach initializes a high resolution complex hologram with a random guess, and then stitches together low resolution multi-view images, synthesized from the elemental images captured by integral imaging (II), to recover the high resolution hologram through an iterative retrieval with FP constrains. This paper begins with an analysis of the principle of hologram synthesis from multi-projections, followed by an accurate determination of the constrains required in the Fourier ptychographic integral-holography (FPIH). Next, the procedure of the approach is described in detail. Finally, optical reconstructions are performed and the results are demonstrated. Theoretical analysis and experiments show that our proposed approach can reconstruct 3D scenes with high resolution.

  20. High-spatial resolution and high-spectral resolution detector for use in the measurement of solar flare hard x rays

    International Nuclear Information System (INIS)

    Desai, U.D.; Orwig, L.E.

    1988-01-01

    In the areas of high spatial resolution, the evaluation of a hard X-ray detector with 65 micron spatial resolution for operation in the energy range from 30 to 400 keV is proposed. The basic detector is a thick large-area scintillator faceplate, composed of a matrix of high-density scintillating glass fibers, attached to a proximity type image intensifier tube with a resistive-anode digital readout system. Such a detector, combined with a coded-aperture mask, would be ideal for use as a modest-sized hard X-ray imaging instrument up to X-ray energies as high as several hundred keV. As an integral part of this study it was also proposed that several techniques be critically evaluated for X-ray image coding which could be used with this detector. In the area of high spectral resolution, it is proposed to evaluate two different types of detectors for use as X-ray spectrometers for solar flares: planar silicon detectors and high-purity germanium detectors (HPGe). Instruments utilizing these high-spatial-resolution detectors for hard X-ray imaging measurements from 30 to 400 keV and high-spectral-resolution detectors for measurements over a similar energy range would be ideally suited for making crucial solar flare observations during the upcoming maximum in the solar cycle

  1. Applying high-resolution melting (HRM) technology to olive oil and wine authenticity.

    Science.gov (United States)

    Pereira, Leonor; Gomes, Sónia; Barrias, Sara; Fernandes, José Ramiro; Martins-Lopes, Paula

    2018-01-01

    Olive oil and wine production have a worldwide economic impact. Their market reliability is under great concern because of the increasing number of fraud and adulteration attempts. The need for a traceability system in all its extension is crucial particularly for the cases of olive oils and wines with certified labels, in which only a limited number of olives and grapevine varieties, respectively, are allowed in a restricted well-defined geographical area. Molecular markers have been vastly applied to the food sector, and in particular High-Resolution DNA Melting technology has been successfully applied for olive oil and wine authentication, as part of the traceability system. In this review, the applications of HRM and their usefulness for this sector considering, Safety, Security and Authenticity will be reviewed. A broad overview of the HRM technique will be presented, focusing on the aspects that are crucial for its success, in particular the new generation of fluorescent dsDNA dyes used for amplicon detection and quantification, and the data analysis. A brief outlook on the olive oil and wine authenticity procedures, based on new DNA technology advances, and in which way this may influence the future establishment of a traceability system will be discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. High resolution photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Arko, A.J.

    1988-01-01

    Photoelectron Spectroscopy (PES) covers a very broad range of measurements, disciplines, and interests. As the next generation light source, the FEL will result in improvements over the undulator that are larger than the undulater improvements over bending magnets. The combination of high flux and high inherent resolution will result in several orders of magnitude gain in signal to noise over measurements using synchrotron-based undulators. The latter still require monochromators. Their resolution is invariably strongly energy-dependent so that in the regions of interest for many experiments (h upsilon > 100 eV) they will not have a resolving power much over 1000. In order to study some of the interesting phenomena in actinides (heavy fermions e.g.) one would need resolving powers of 10 4 to 10 5 . These values are only reachable with the FEL

  3. Subnuclear localization, rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield, confocal and super-resolution microscopy.

    Science.gov (United States)

    Pierzyńska-Mach, Agnieszka; Szczurek, Aleksander; Cella Zanacchi, Francesca; Pennacchietti, Francesca; Drukała, Justyna; Diaspro, Alberto; Cremer, Christoph; Darzynkiewicz, Zbigniew; Dobrucki, Jurek W

    2016-01-01

    Unscheduled DNA synthesis (UDS) is the final stage of the process of repair of DNA lesions induced by UVC. We detected UDS using a DNA precursor, 5-ethynyl-2'-deoxyuridine (EdU). Using wide-field, confocal and super-resolution fluorescence microscopy and normal human fibroblasts, derived from healthy subjects, we demonstrate that the sub-nuclear pattern of UDS detected via incorporation of EdU is different from that when BrdU is used as DNA precursor. EdU incorporation occurs evenly throughout chromatin, as opposed to just a few small and large repair foci detected by BrdU. We attribute this difference to the fact that BrdU antibody is of much larger size than EdU, and its accessibility to the incorporated precursor requires the presence of denatured sections of DNA. It appears that under the standard conditions of immunocytochemical detection of BrdU only fragments of DNA of various length are being denatured. We argue that, compared with BrdU, the UDS pattern visualized by EdU constitutes a more faithful representation of sub-nuclear distribution of the final stage of nucleotide excision repair induced by UVC. Using the optimized integrated EdU detection procedure we also measured the relative amount of the DNA precursor incorporated by cells during UDS following exposure to various doses of UVC. Also described is the high degree of heterogeneity in terms of the UVC-induced EdU incorporation per cell, presumably reflecting various DNA repair efficiencies or differences in the level of endogenous dT competing with EdU within a population of normal human fibroblasts.

  4. 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.

  5. Rapid Detection and Differentiation of Clonorchis sinensis and Opisthorchis viverrini Using Real-Time PCR and High Resolution Melting Analysis

    OpenAIRE

    Cai, Xian-Quan; Yu, Hai-Qiong; Li, Rong; Yue, Qiao-Yun; Liu, Guo-Hua; Bai, Jian-Shan; Deng, Yan; Qiu, De-Yi; Zhu, Xing-Quan

    2014-01-01

    Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA...

  6. High-resolution regional climate model evaluation using variable-resolution CESM over California

    Science.gov (United States)

    Huang, X.; Rhoades, A.; Ullrich, P. A.; Zarzycki, C. M.

    2015-12-01

    Understanding the effect of climate change at regional scales remains a topic of intensive research. Though computational constraints remain a problem, high horizontal resolution is needed to represent topographic forcing, which is a significant driver of local climate variability. Although regional climate models (RCMs) have traditionally been used at these scales, variable-resolution global climate models (VRGCMs) have recently arisen as an alternative for studying regional weather and climate allowing two-way interaction between these domains without the need for nudging. In this study, the recently developed variable-resolution option within the Community Earth System Model (CESM) is assessed for long-term regional climate modeling over California. Our variable-resolution simulations will focus on relatively high resolutions for climate assessment, namely 28km and 14km regional resolution, which are much more typical for dynamically downscaled studies. For comparison with the more widely used RCM method, the Weather Research and Forecasting (WRF) model will be used for simulations at 27km and 9km. All simulations use the AMIP (Atmospheric Model Intercomparison Project) protocols. The time period is from 1979-01-01 to 2005-12-31 (UTC), and year 1979 was discarded as spin up time. The mean climatology across California's diverse climate zones, including temperature and precipitation, is analyzed and contrasted with the Weather Research and Forcasting (WRF) model (as a traditional RCM), regional reanalysis, gridded observational datasets and uniform high-resolution CESM at 0.25 degree with the finite volume (FV) dynamical core. The results show that variable-resolution CESM is competitive in representing regional climatology on both annual and seasonal time scales. This assessment adds value to the use of VRGCMs for projecting climate change over the coming century and improve our understanding of both past and future regional climate related to fine

  7. Section on High Resolution Optical Imaging (HROI)

    Data.gov (United States)

    Federal Laboratory Consortium — The Section on High Resolution Optical Imaging (HROI) develops novel technologies for studying biological processes at unprecedented speed and resolution. Research...

  8. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

    Directory of Open Access Journals (Sweden)

    Zdepski Anna

    2011-05-01

    Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

  9. High angular resolution at LBT

    Science.gov (United States)

    Conrad, A.; Arcidiacono, C.; Bertero, M.; Boccacci, P.; Davies, A. G.; Defrere, D.; de Kleer, K.; De Pater, I.; Hinz, P.; Hofmann, K. H.; La Camera, A.; Leisenring, J.; Kürster, M.; Rathbun, J. A.; Schertl, D.; Skemer, A.; Skrutskie, M.; Spencer, J. R.; Veillet, C.; Weigelt, G.; Woodward, C. E.

    2015-12-01

    High angular resolution from ground-based observatories stands as a key technology for advancing planetary science. In the window between the angular resolution achievable with 8-10 meter class telescopes, and the 23-to-40 meter giants of the future, LBT provides a glimpse of what the next generation of instruments providing higher angular resolution will provide. We present first ever resolved images of an Io eruption site taken from the ground, images of Io's Loki Patera taken with Fizeau imaging at the 22.8 meter LBT [Conrad, et al., AJ, 2015]. We will also present preliminary analysis of two data sets acquired during the 2015 opposition: L-band fringes at Kurdalagon and an occultation of Loki and Pele by Europa (see figure). The light curves from this occultation will yield an order of magnitude improvement in spatial resolution along the path of ingress and egress. We will conclude by providing an overview of the overall benefit of recent and future advances in angular resolution for planetary science.

  10. A method for generating high resolution satellite image time series

    Science.gov (United States)

    Guo, Tao

    2014-10-01

    There is an increasing demand for satellite remote sensing data with both high spatial and temporal resolution in many applications. But it still is a challenge to simultaneously improve spatial resolution and temporal frequency due to the technical limits of current satellite observation systems. To this end, much R&D efforts have been ongoing for years and lead to some successes roughly in two aspects, one includes super resolution, pan-sharpen etc. methods which can effectively enhance the spatial resolution and generate good visual effects, but hardly preserve spectral signatures and result in inadequate analytical value, on the other hand, time interpolation is a straight forward method to increase temporal frequency, however it increase little informative contents in fact. In this paper we presented a novel method to simulate high resolution time series data by combing low resolution time series data and a very small number of high resolution data only. Our method starts with a pair of high and low resolution data set, and then a spatial registration is done by introducing LDA model to map high and low resolution pixels correspondingly. Afterwards, temporal change information is captured through a comparison of low resolution time series data, and then projected onto the high resolution data plane and assigned to each high resolution pixel according to the predefined temporal change patterns of each type of ground objects. Finally the simulated high resolution data is generated. A preliminary experiment shows that our method can simulate a high resolution data with a reasonable accuracy. The contribution of our method is to enable timely monitoring of temporal changes through analysis of time sequence of low resolution images only, and usage of costly high resolution data can be reduces as much as possible, and it presents a highly effective way to build up an economically operational monitoring solution for agriculture, forest, land use investigation

  11. High-throughput sequencing of three Lemnoideae (duckweeds chloroplast genomes from total DNA.

    Directory of Open Access Journals (Sweden)

    Wenqin Wang

    Full Text Available BACKGROUND: Chloroplast genomes provide a wealth of information for evolutionary and population genetic studies. Chloroplasts play a particularly important role in the adaption for aquatic plants because they float on water and their major surface is exposed continuously to sunlight. The subfamily of Lemnoideae represents such a collection of aquatic species that because of photosynthesis represents one of the fastest growing plant species on earth. METHODS: We sequenced the chloroplast genomes from three different genera of Lemnoideae, Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana by high-throughput DNA sequencing of genomic DNA using the SOLiD platform. Unfractionated total DNA contains high copies of plastid DNA so that sequences from the nucleus and mitochondria can easily be filtered computationally. Remaining sequence reads were assembled into contiguous sequences (contigs using SOLiD software tools. Contigs were mapped to a reference genome of Lemna minor and gaps, selected by PCR, were sequenced on the ABI3730xl platform. CONCLUSIONS: This combinatorial approach yielded whole genomic contiguous sequences in a cost-effective manner. Over 1,000-time coverage of chloroplast from total DNA were reached by the SOLiD platform in a single spot on a quadrant slide without purification. Comparative analysis indicated that the chloroplast genome was conserved in gene number and organization with respect to the reference genome of L. minor. However, higher nucleotide substitution, abundant deletions and insertions occurred in non-coding regions of these genomes, indicating a greater genomic dynamics than expected from the comparison of other related species in the Pooideae. Noticeably, there was no transition bias over transversion in Lemnoideae. The data should have immediate applications in evolutionary biology and plant taxonomy with increased resolution and statistical power.

  12. Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs.

    Science.gov (United States)

    Mishra, Priyanka; Shukla, Ashutosh K; Sundaresan, Velusamy

    2018-01-01

    Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes ( rbcL and matK ) and intergenic spacers ( psbA-trnH and ITS ) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S . italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 ( S. alexandrina crude drug sample from Bangalore) and HSA06 ( S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S . italica subsp. micrantha . Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply

  13. Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs

    Directory of Open Access Journals (Sweden)

    Priyanka Mishra

    2018-03-01

    Full Text Available Senna alexandrina (Fabaceae is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes (rbcL and matK and intergenic spacers (psbA-trnH and ITS were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S. italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs]. HSA01 (S. alexandrina crude drug sample from Bangalore and HSA06 (S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India were found to be highly contaminated with S. italica subsp. micrantha. Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug

  14. A refined, rapid and reproducible high resolution melt (HRM-based method suitable for quantification of global LINE-1 repetitive element methylation

    Directory of Open Access Journals (Sweden)

    Tse M Yat

    2011-12-01

    Full Text Available Abstract Background The methylation of DNA is recognized as a key mechanism in the regulation of genomic stability and evidence for its role in the development of cancer is accumulating. LINE-1 methylation status represents a surrogate measure of genome-wide methylation. Findings Using high resolution melt (HRM curve analysis technology, we have established an in-tube assay that is linear (r > 0.9986 with a high amplification efficiency (90-105%, capable of discriminating between partcipant samples with small differences in methylation, and suitable for quantifying a wide range of LINE-1 methylation levels (0-100%--including the biologically relevant range of 50-90% expected in human DNA. We have optimized this procedure to perform using 2 μg of starting DNA and 2 ng of bisulfite-converted DNA for each PCR reaction. Intra- and inter-assay coefficients of variation were 1.44% and 0.49%, respectively, supporting the high reproducibility and precision of this approach. Conclusions In summary, this is a completely linear, quantitative HRM PCR method developed for the measurement of LINE-1 methylation. This cost-efficient, refined and reproducible assay can be performed using minimal amounts of starting DNA. These features make our assay suitable for high throughput analysis of multiple samples from large population-based studies.

  15. Resolution enhancement of low-quality videos using a high-resolution frame

    Science.gov (United States)

    Pham, Tuan Q.; van Vliet, Lucas J.; Schutte, Klamer

    2006-01-01

    This paper proposes an example-based Super-Resolution (SR) algorithm of compressed videos in the Discrete Cosine Transform (DCT) domain. Input to the system is a Low-Resolution (LR) compressed video together with a High-Resolution (HR) still image of similar content. Using a training set of corresponding LR-HR pairs of image patches from the HR still image, high-frequency details are transferred from the HR source to the LR video. The DCT-domain algorithm is much faster than example-based SR in spatial domain 6 because of a reduction in search dimensionality, which is a direct result of the compact and uncorrelated DCT representation. Fast searching techniques like tree-structure vector quantization 16 and coherence search1 are also key to the improved efficiency. Preliminary results on MJPEG sequence show promising result of the DCT-domain SR synthesis approach.

  16. A cloud mask methodology for high resolution remote sensing data combining information from high and medium resolution optical sensors

    Science.gov (United States)

    Sedano, Fernando; Kempeneers, Pieter; Strobl, Peter; Kucera, Jan; Vogt, Peter; Seebach, Lucia; San-Miguel-Ayanz, Jesús

    2011-09-01

    This study presents a novel cloud masking approach for high resolution remote sensing images in the context of land cover mapping. As an advantage to traditional methods, the approach does not rely on thermal bands and it is applicable to images from most high resolution earth observation remote sensing sensors. The methodology couples pixel-based seed identification and object-based region growing. The seed identification stage relies on pixel value comparison between high resolution images and cloud free composites at lower spatial resolution from almost simultaneously acquired dates. The methodology was tested taking SPOT4-HRVIR, SPOT5-HRG and IRS-LISS III as high resolution images and cloud free MODIS composites as reference images. The selected scenes included a wide range of cloud types and surface features. The resulting cloud masks were evaluated through visual comparison. They were also compared with ad-hoc independently generated cloud masks and with the automatic cloud cover assessment algorithm (ACCA). In general the results showed an agreement in detected clouds higher than 95% for clouds larger than 50 ha. The approach produced consistent results identifying and mapping clouds of different type and size over various land surfaces including natural vegetation, agriculture land, built-up areas, water bodies and snow.

  17. High-Resolution Mass Spectrometers

    Science.gov (United States)

    Marshall, Alan G.; Hendrickson, Christopher L.

    2008-07-01

    Over the past decade, mass spectrometry has been revolutionized by access to instruments of increasingly high mass-resolving power. For small molecules up to ˜400 Da (e.g., drugs, metabolites, and various natural organic mixtures ranging from foods to petroleum), it is possible to determine elemental compositions (CcHhNnOoSsPp…) of thousands of chemical components simultaneously from accurate mass measurements (the same can be done up to 1000 Da if additional information is included). At higher mass, it becomes possible to identify proteins (including posttranslational modifications) from proteolytic peptides, as well as lipids, glycoconjugates, and other biological components. At even higher mass (˜100,000 Da or higher), it is possible to characterize posttranslational modifications of intact proteins and to map the binding surfaces of large biomolecule complexes. Here we review the principles and techniques of the highest-resolution analytical mass spectrometers (time-of-flight and Fourier transform ion cyclotron resonance and orbitrap mass analyzers) and describe some representative high-resolution applications.

  18. Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

    Science.gov (United States)

    Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

    2015-10-01

    Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues

  19. USGS High Resolution Orthoimagery Collection - Historical - National Geospatial Data Asset (NGDA) High Resolution Orthoimagery

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — USGS high resolution orthorectified images from The National Map combine the image characteristics of an aerial photograph with the geometric qualities of a map. An...

  20. High-resolution characterization of a hepatocellular carcinoma genome.

    Science.gov (United States)

    Totoki, Yasushi; Tatsuno, Kenji; Yamamoto, Shogo; Arai, Yasuhito; Hosoda, Fumie; Ishikawa, Shumpei; Tsutsumi, Shuichi; Sonoda, Kohtaro; Totsuka, Hirohiko; Shirakihara, Takuya; Sakamoto, Hiromi; Wang, Linghua; Ojima, Hidenori; Shimada, Kazuaki; Kosuge, Tomoo; Okusaka, Takuji; Kato, Kazuto; Kusuda, Jun; Yoshida, Teruhiko; Aburatani, Hiroyuki; Shibata, Tatsuhiro

    2011-05-01

    Hepatocellular carcinoma, one of the most common virus-associated cancers, is the third most frequent cause of cancer-related death worldwide. By massively parallel sequencing of a primary hepatitis C virus-positive hepatocellular carcinoma (36× coverage) and matched lymphocytes (>28× coverage) from the same individual, we identified more than 11,000 somatic substitutions of the tumor genome that showed predominance of T>C/A>G transition and a decrease of the T>C substitution on the transcribed strand, suggesting preferential DNA repair. Gene annotation enrichment analysis of 63 validated non-synonymous substitutions revealed enrichment of phosphoproteins. We further validated 22 chromosomal rearrangements, generating four fusion transcripts that had altered transcriptional regulation (BCORL1-ELF4) or promoter activity. Whole-exome sequencing at a higher sequence depth (>76× coverage) revealed a TSC1 nonsense substitution in a subpopulation of the tumor cells. This first high-resolution characterization of a virus-associated cancer genome identified previously uncharacterized mutation patterns, intra-chromosomal rearrangements and fusion genes, as well as genetic heterogeneity within the tumor.

  1. High throughput screening of ligand binding to macromolecules using high resolution powder diffraction

    Science.gov (United States)

    Von Dreele, Robert B.; D'Amico, Kevin

    2006-10-31

    A process is provided for the high throughput screening of binding of ligands to macromolecules using high resolution powder diffraction data including producing a first sample slurry of a selected polycrystalline macromolecule material and a solvent, producing a second sample slurry of a selected polycrystalline macromolecule material, one or more ligands and the solvent, obtaining a high resolution powder diffraction pattern on each of said first sample slurry and the second sample slurry, and, comparing the high resolution powder diffraction pattern of the first sample slurry and the high resolution powder diffraction pattern of the second sample slurry whereby a difference in the high resolution powder diffraction patterns of the first sample slurry and the second sample slurry provides a positive indication for the formation of a complex between the selected polycrystalline macromolecule material and at least one of the one or more ligands.

  2. Texton-based super-resolution for achieving high spatiotemporal resolution in hybrid camera system

    Science.gov (United States)

    Kamimura, Kenji; Tsumura, Norimichi; Nakaguchi, Toshiya; Miyake, Yoichi

    2010-05-01

    Many super-resolution methods have been proposed to enhance the spatial resolution of images by using iteration and multiple input images. In a previous paper, we proposed the example-based super-resolution method to enhance an image through pixel-based texton substitution to reduce the computational cost. In this method, however, we only considered the enhancement of a texture image. In this study, we modified this texton substitution method for a hybrid camera to reduce the required bandwidth of a high-resolution video camera. We applied our algorithm to pairs of high- and low-spatiotemporal-resolution videos, which were synthesized to simulate a hybrid camera. The result showed that the fine detail of the low-resolution video can be reproduced compared with bicubic interpolation and the required bandwidth could be reduced to about 1/5 in a video camera. It was also shown that the peak signal-to-noise ratios (PSNRs) of the images improved by about 6 dB in a trained frame and by 1.0-1.5 dB in a test frame, as determined by comparison with the processed image using bicubic interpolation, and the average PSNRs were higher than those obtained by the well-known Freeman’s patch-based super-resolution method. Compared with that of the Freeman’s patch-based super-resolution method, the computational time of our method was reduced to almost 1/10.

  3. Immersion Gratings for Infrared High-resolution Spectroscopy

    Science.gov (United States)

    Sarugaku, Yuki; Ikeda, Yuji; Kobayashi, Naoto; Kaji, Sayumi; Sukegawa, Takashi; Sugiyama, Shigeru; Nakagawa, Takao; Arasaki, Takayuki; Kondo, Sohei; Nakanishi, Kenshi; Yasui, Chikako; Kawakita, Hideyo

    2016-10-01

    High-resolution spectroscopy in the infrared wavelength range is essential for observations of minor isotopologues, such as HDO for water, and prebiotic organic molecules like hydrocarbons/P-bearing molecules because numerous vibrational molecular bands (including non-polar molecules) are located in this wavelength range. High spectral resolution enables us to detect weak lines without spectral line confusion. This technique has been widely used in planetary sciences, e.g., cometary coma (H2O, CO, and organic molecules), the martian atmosphere (CH4, CO2, H2O and HDO), and the upper atmosphere of gas giants (H3+ and organic molecules such as C2H6). Spectrographs with higher resolution (and higher sensitivity) still have a potential to provide a plenty of findings. However, because the size of spectrographs scales with the spectral resolution, it is difficult to realize it.Immersion grating (IG), which is a diffraction grating wherein the diffraction surface is immersed in a material with a high refractive index (n > 2), provides n times higher spectral resolution compared to a reflective grating of the same size. Because IG reduces the size of spectrograph to 1/n compared to the spectrograph with the same spectral resolution using a conventional reflective grating, it is widely acknowledged as a key optical device to realize compact spectrographs with high spectral resolution.Recently, we succeeded in fabricating a CdZnTe immersion grating with the theoretically predicted diffraction efficiency by machining process using an ultrahigh-precision five-axis processing machine developed by Canon Inc. Using the same technique, we completed a practical germanium (Ge) immersion grating with both a reflection coating on the grating surface and the an AR coating on the entrance surface. It is noteworthy that the wide wavelength range from 2 to 20 um can be covered by the two immersion gratings.In this paper, we present the performances and the applications of the immersion

  4. High-Throughput Block Optical DNA Sequence Identification.

    Science.gov (United States)

    Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

    2018-01-01

    Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. High resolution tomographic instrument development

    International Nuclear Information System (INIS)

    1992-01-01

    Our recent work has concentrated on the development of high-resolution PET instrumentation reflecting in part the growing importance of PET in nuclear medicine imaging. We have developed a number of positron imaging instruments and have the distinction that every instrument has been placed in operation and has had an extensive history of application for basic research and clinical study. The present program is a logical continuation of these earlier successes. PCR-I, a single ring positron tomograph was the first demonstration of analog coding using BGO. It employed 4 mm detectors and is currently being used for a wide range of biological studies. These are of immense importance in guiding the direction for future instruments. In particular, PCR-II, a volume sensitive positron tomograph with 3 mm spatial resolution has benefited greatly from the studies using PCR-I. PCR-II is currently in the final stages of assembly and testing and will shortly be placed in operation for imaging phantoms, animals and ultimately humans. Perhaps the most important finding resulting from our previous study is that resolution and sensitivity must be carefully balanced to achieve a practical high resolution system. PCR-II has been designed to have the detection characteristics required to achieve 3 mm resolution in human brain under practical imaging situations. The development of algorithms by the group headed by Dr. Chesler is based on a long history of prior study including his joint work with Drs. Pelc and Reiderer and Stearns. This body of expertise will be applied to the processing of data from PCR-II when it becomes operational

  6. High resolution tomographic instrument development

    Energy Technology Data Exchange (ETDEWEB)

    1992-08-01

    Our recent work has concentrated on the development of high-resolution PET instrumentation reflecting in part the growing importance of PET in nuclear medicine imaging. We have developed a number of positron imaging instruments and have the distinction that every instrument has been placed in operation and has had an extensive history of application for basic research and clinical study. The present program is a logical continuation of these earlier successes. PCR-I, a single ring positron tomograph was the first demonstration of analog coding using BGO. It employed 4 mm detectors and is currently being used for a wide range of biological studies. These are of immense importance in guiding the direction for future instruments. In particular, PCR-II, a volume sensitive positron tomograph with 3 mm spatial resolution has benefited greatly from the studies using PCR-I. PCR-II is currently in the final stages of assembly and testing and will shortly be placed in operation for imaging phantoms, animals and ultimately humans. Perhaps the most important finding resulting from our previous study is that resolution and sensitivity must be carefully balanced to achieve a practical high resolution system. PCR-II has been designed to have the detection characteristics required to achieve 3 mm resolution in human brain under practical imaging situations. The development of algorithms by the group headed by Dr. Chesler is based on a long history of prior study including his joint work with Drs. Pelc and Reiderer and Stearns. This body of expertise will be applied to the processing of data from PCR-II when it becomes operational.

  7. High resolution tomographic instrument development

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    Our recent work has concentrated on the development of high-resolution PET instrumentation reflecting in part the growing importance of PET in nuclear medicine imaging. We have developed a number of positron imaging instruments and have the distinction that every instrument has been placed in operation and has had an extensive history of application for basic research and clinical study. The present program is a logical continuation of these earlier successes. PCR-I, a single ring positron tomograph was the first demonstration of analog coding using BGO. It employed 4 mm detectors and is currently being used for a wide range of biological studies. These are of immense importance in guiding the direction for future instruments. In particular, PCR-II, a volume sensitive positron tomograph with 3 mm spatial resolution has benefited greatly from the studies using PCR-I. PCR-II is currently in the final stages of assembly and testing and will shortly be placed in operation for imaging phantoms, animals and ultimately humans. Perhaps the most important finding resulting from our previous study is that resolution and sensitivity must be carefully balanced to achieve a practical high resolution system. PCR-II has been designed to have the detection characteristics required to achieve 3 mm resolution in human brain under practical imaging situations. The development of algorithms by the group headed by Dr. Chesler is based on a long history of prior study including his joint work with Drs. Pelc and Reiderer and Stearns. This body of expertise will be applied to the processing of data from PCR-II when it becomes operational.

  8. High resolution Neutron and Synchrotron Powder Diffraction

    International Nuclear Information System (INIS)

    Hewat, A.W.

    1986-01-01

    The use of high-resolution powder diffraction has grown rapidly in the past years, with the development of Rietveld (1967) methods of data analysis and new high-resolution diffractometers and multidetectors. The number of publications in this area has increased from a handful per year until 1973 to 150 per year in 1984, with a ten-year total of over 1000. These papers cover a wide area of solid state-chemistry, physics and materials science, and have been grouped under 20 subject headings, ranging from catalysts to zeolites, and from battery electrode materials to pre-stressed superconducting wires. In 1985 two new high-resolution diffractometers are being commissioned, one at the SNS laboratory near Oxford, and one at the ILL in Grenoble. In different ways these machines represent perhaps the ultimate that can be achieved with neutrons and will permit refinement of complex structures with about 250 parameters and unit cell volumes of about 2500 Angstrom/sp3/. The new European Synchotron Facility will complement the Grenoble neutron diffractometers, and extend the role of high-resolution powder diffraction to the direct solution of crystal structures, pioneered in Sweden

  9. High resolution (transformers.

    Science.gov (United States)

    Garcia-Souto, Jose A; Lamela-Rivera, Horacio

    2006-10-16

    A novel fiber-optic interferometric sensor is presented for vibrations measurements and analysis. In this approach, it is shown applied to the vibrations of electrical structures within power transformers. A main feature of the sensor is that an unambiguous optical phase measurement is performed using the direct detection of the interferometer output, without external modulation, for a more compact and stable implementation. High resolution of the interferometric measurement is obtained with this technique (transformers are also highlighted.

  10. High-resolution wavefront control of high-power laser systems

    International Nuclear Information System (INIS)

    Brase, J.; Brown, C.; Carrano, C.; Kartz, M.; Olivier, S.; Pennington, D.; Silva, D.

    1999-01-01

    Nearly every new large-scale laser system application at LLNL has requirements for beam control which exceed the current level of available technology. For applications such as inertial confinement fusion, laser isotope separation, laser machining, and laser the ability to transport significant power to a target while maintaining good beam quality is critical. There are many ways that laser wavefront quality can be degraded. Thermal effects due to the interaction of high-power laser or pump light with the internal optical components or with the ambient gas are common causes of wavefront degradation. For many years, adaptive optics based on thing deformable glass mirrors with piezoelectric or electrostrictive actuators have be used to remove the low-order wavefront errors from high-power laser systems. These adaptive optics systems have successfully improved laser beam quality, but have also generally revealed additional high-spatial-frequency errors, both because the low-order errors have been reduced and because deformable mirrors have often introduced some high-spatial-frequency components due to manufacturing errors. Many current and emerging laser applications fall into the high-resolution category where there is an increased need for the correction of high spatial frequency aberrations which requires correctors with thousands of degrees of freedom. The largest Deformable Mirrors currently available have less than one thousand degrees of freedom at a cost of approximately $1M. A deformable mirror capable of meeting these high spatial resolution requirements would be cost prohibitive. Therefore a new approach using a different wavefront control technology is needed. One new wavefront control approach is the use of liquid-crystal (LC) spatial light modulator (SLM) technology for the controlling the phase of linearly polarized light. Current LC SLM technology provides high-spatial-resolution wavefront control, with hundreds of thousands of degrees of freedom, more

  11. High-Resolution Electronics: Spontaneous Patterning of High-Resolution Electronics via Parallel Vacuum Ultraviolet (Adv. Mater. 31/2016).

    Science.gov (United States)

    Liu, Xuying; Kanehara, Masayuki; Liu, Chuan; Sakamoto, Kenji; Yasuda, Takeshi; Takeya, Jun; Minari, Takeo

    2016-08-01

    On page 6568, T. Minari and co-workers describe spontaneous patterning based on the parallel vacuum ultraviolet (PVUV) technique, enabling the homogeneous integration of complex, high-resolution electronic circuits, even on large-scale, flexible, transparent substrates. Irradiation of PVUV to the hydrophobic polymer surface precisely renders the selected surface into highly wettable regions with sharply defined boundaries, which spontaneously guides a metal nanoparticle ink into a series of circuit lines and gaps with the widths down to a resolution of 1 μm. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. High resolution UV spectroscopy and laser-focused nanofabrication

    NARCIS (Netherlands)

    Myszkiewicz, G.

    2005-01-01

    This thesis combines two at first glance different techniques: High Resolution Laser Induced Fluorescence Spectroscopy (LIF) of small aromatic molecules and Laser Focusing of atoms for Nanofabrication. The thesis starts with the introduction to the high resolution LIF technique of small aromatic

  13. High-resolution spectrometer at PEP

    International Nuclear Information System (INIS)

    Weiss, J.M.; HRS Collaboration.

    1982-01-01

    A description is presented of the High Resolution Spectrometer experiment (PEP-12) now running at PEP. The advanced capabilities of the detector are demonstrated with first physics results expected in the coming months

  14. High-resolution structure of the native histone octamer

    International Nuclear Information System (INIS)

    Wood, Christopher M.; Nicholson, James M.; Lambert, Stanley J.; Chantalat, Laurent; Reynolds, Colin D.; Baldwin, John P.

    2005-01-01

    The high-resolution (1.90 Å) model of the native histone octamer allows structural comparisons to be made with the nucleosome-core particle, along with an identification of a likely core-histone binding site. Crystals of native histone octamers (H2A–H2B)–(H4–H3)–(H3′–H4′)–(H2B′–H2A′) from chick erythrocytes in 2 M KCl, 1.35 M potassium phosphate pH 6.9 diffract X-rays to 1.90 Å resolution, yielding a structure with an R work value of 18.7% and an R free of 22.2%. The crystal space group is P6 5 , the asymmetric unit of which contains one complete octamer. This high-resolution model of the histone-core octamer allows further insight into intermolecular interactions, including water molecules, that dock the histone dimers to the tetramer in the nucleosome-core particle and have relevance to nucleosome remodelling. The three key areas analysed are the H2A′–H3–H4 molecular cluster (also H2A–H3′–H4′), the H4–H2B′ interaction (also H4′–H2B) and the H2A′–H4 β-sheet interaction (also H2A–H4′). The latter of these three regions is important to nucleosome remodelling by RNA polymerase II, as it is shown to be a likely core-histone binding site, and its disruption creates an instability in the nucleosome-core particle. A majority of the water molecules in the high-resolution octamer have positions that correlate to similar positions in the high-resolution nucleosome-core particle structure, suggesting that the high-resolution octamer model can be used for comparative studies with the high-resolution nucleosome-core particle

  15. Requirements on high resolution detectors

    Energy Technology Data Exchange (ETDEWEB)

    Koch, A. [European Synchrotron Radiation Facility, Grenoble (France)

    1997-02-01

    For a number of microtomography applications X-ray detectors with a spatial resolution of 1 {mu}m are required. This high spatial resolution will influence and degrade other parameters of secondary importance like detective quantum efficiency (DQE), dynamic range, linearity and frame rate. This note summarizes the most important arguments, for and against those detector systems which could be considered. This article discusses the mutual dependencies between the various figures which characterize a detector, and tries to give some ideas on how to proceed in order to improve present technology.

  16. High-resolution clean-sc

    NARCIS (Netherlands)

    Sijtsma, P.; Snellen, M.

    2016-01-01

    In this paper a high-resolution extension of CLEAN-SC is proposed: HR-CLEAN-SC. Where CLEAN-SC uses peak sources in “dirty maps” to define so-called source components, HR-CLEAN-SC takes advantage of the fact that source components can likewise be derived from points at some distance from the peak,

  17. Planning for shallow high resolution seismic surveys

    CSIR Research Space (South Africa)

    Fourie, CJS

    2008-11-01

    Full Text Available of the input wave. This information can be used in conjunction with this spreadsheet to aid the geophysicist in designing shallow high resolution seismic surveys to achieve maximum resolution and penetration. This Excel spreadsheet is available free from...

  18. extraction of high quality dna from polysaccharides-secreting ...

    African Journals Online (AJOL)

    cistvr

    A DNA extraction method using CTAB was used for the isolation of genomic DNA from ten. Xanthomonas campestris pathovars, ten isolates of Xanthomonas albilineans and one isolate of. Pseudomonas rubrisubalbicans. High quality DNA was obtained that was ideal for molecular analy- ses. Extracellular polysaccharides ...

  19. Whole-genome amplified DNA from stored dried blood spots is reliable in high resolution melting curve and sequencing analysis

    DEFF Research Database (Denmark)

    Winkel, Bo G; Hollegaard, Mads V; Olesen, Morten S

    2011-01-01

    BACKGROUND: The use of dried blood spots (DBS) samples in genomic workup has been limited by the relative low amounts of genomic DNA (gDNA) they contain. It remains to be proven that whole genome amplified DNA (wgaDNA) from stored DBS samples, constitutes a reliable alternative to gDNA.We wanted...

  20. Discrimination of Single-Copy IS6110 DNA Fingerprints of Mycobacterium tuberculosis Isolates by High-Resolution Minisatellite-Based Typing

    OpenAIRE

    Lee, Ann S. G.; Tang, Lynn L. H.; Lim, Irene H. K.; Bellamy, Richard; Wong, Sin-Yew

    2002-01-01

    Seven isoniazid-resistant isolates with mutations in the NADH dehydrogenase (ndh) gene were molecularly typed by IS6110-based restriction fragment length polymorphism analysis. All seven isolates with the R268H mutation had identical 1.4-kb IS6110 fingerprints. High-resolution minisatellite-based typing discriminated five of these isolates; two isolates were identical.

  1. Discrimination of single-copy IS6110 DNA fingerprints of Mycobacterium tuberculosis isolates by high-resolution minisatellite-based typing.

    Science.gov (United States)

    Lee, Ann S G; Tang, Lynn L H; Lim, Irene H K; Bellamy, Richard; Wong, Sin-Yew

    2002-02-01

    Seven isoniazid-resistant isolates with mutations in the NADH dehydrogenase (ndh) gene were molecularly typed by IS6110-based restriction fragment length polymorphism analysis. All seven isolates with the R268H mutation had identical 1.4-kb IS6110 fingerprints. High-resolution minisatellite-based typing discriminated five of these isolates; two isolates were identical.

  2. Gamma-ray spectrometer system with high efficiency and high resolution

    International Nuclear Information System (INIS)

    Moss, C.E.; Bernard, W.; Dowdy, E.J.; Garcia, C.; Lucas, M.C.; Pratt, J.C.

    1983-01-01

    Our gamma-ray spectrometer system, designed for field use, offers high efficiency and high resolution for safeguards applications. The system consists of three 40% high-purity germanium detectors and a LeCroy 3500 data acquisition system that calculates a composite spectrum for the three detectors. The LeCroy 3500 mainframe can be operated remotely from the detector array with control exercised through modems and the telephone system. System performance with a mixed source of 125 Sb, 154 Eu, and 155 Eu confirms the expected efficiency of 120% with the overall resolution showing little degradation over that of the worst detector

  3. High resolution metric imaging payload

    Science.gov (United States)

    Delclaud, Y.

    2017-11-01

    Alcatel Space Industries has become Europe's leader in the field of high and very high resolution optical payloads, in the frame work of earth observation system able to provide military government with metric images from space. This leadership allowed ALCATEL to propose for the export market, within a French collaboration frame, a complete space based system for metric observation.

  4. High-resolution X-ray diffraction studies of multilayers

    DEFF Research Database (Denmark)

    Christensen, Finn Erland; Hornstrup, Allan; Schnopper, H. W.

    1988-01-01

    High-resolution X-ray diffraction studies of the perfection of state-of-the-art multilayers are presented. Data were obtained using a triple-axis perfect-crystal X-ray diffractometer. Measurements reveal large-scale figure errors in the substrate. A high-resolution triple-axis set up is required...

  5. Isotope specific resolution recovery image reconstruction in high resolution PET imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kotasidis, Fotis A. [Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva, Switzerland and Wolfson Molecular Imaging Centre, MAHSC, University of Manchester, M20 3LJ, Manchester (United Kingdom); Angelis, Georgios I. [Faculty of Health Sciences, Brain and Mind Research Institute, University of Sydney, NSW 2006, Sydney (Australia); Anton-Rodriguez, Jose; Matthews, Julian C. [Wolfson Molecular Imaging Centre, MAHSC, University of Manchester, Manchester M20 3LJ (United Kingdom); Reader, Andrew J. [Montreal Neurological Institute, McGill University, Montreal QC H3A 2B4, Canada and Department of Biomedical Engineering, Division of Imaging Sciences and Biomedical Engineering, King' s College London, St. Thomas’ Hospital, London SE1 7EH (United Kingdom); Zaidi, Habib [Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211 Geneva (Switzerland); Geneva Neuroscience Centre, Geneva University, CH-1205 Geneva (Switzerland); Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, PO Box 30 001, Groningen 9700 RB (Netherlands)

    2014-05-15

    Purpose: Measuring and incorporating a scanner-specific point spread function (PSF) within image reconstruction has been shown to improve spatial resolution in PET. However, due to the short half-life of clinically used isotopes, other long-lived isotopes not used in clinical practice are used to perform the PSF measurements. As such, non-optimal PSF models that do not correspond to those needed for the data to be reconstructed are used within resolution modeling (RM) image reconstruction, usually underestimating the true PSF owing to the difference in positron range. In high resolution brain and preclinical imaging, this effect is of particular importance since the PSFs become more positron range limited and isotope-specific PSFs can help maximize the performance benefit from using resolution recovery image reconstruction algorithms. Methods: In this work, the authors used a printing technique to simultaneously measure multiple point sources on the High Resolution Research Tomograph (HRRT), and the authors demonstrated the feasibility of deriving isotope-dependent system matrices from fluorine-18 and carbon-11 point sources. Furthermore, the authors evaluated the impact of incorporating them within RM image reconstruction, using carbon-11 phantom and clinical datasets on the HRRT. Results: The results obtained using these two isotopes illustrate that even small differences in positron range can result in different PSF maps, leading to further improvements in contrast recovery when used in image reconstruction. The difference is more pronounced in the centre of the field-of-view where the full width at half maximum (FWHM) from the positron range has a larger contribution to the overall FWHM compared to the edge where the parallax error dominates the overall FWHM. Conclusions: Based on the proposed methodology, measured isotope-specific and spatially variant PSFs can be reliably derived and used for improved spatial resolution and variance performance in resolution

  6. Isotope specific resolution recovery image reconstruction in high resolution PET imaging

    International Nuclear Information System (INIS)

    Kotasidis, Fotis A.; Angelis, Georgios I.; Anton-Rodriguez, Jose; Matthews, Julian C.; Reader, Andrew J.; Zaidi, Habib

    2014-01-01

    Purpose: Measuring and incorporating a scanner-specific point spread function (PSF) within image reconstruction has been shown to improve spatial resolution in PET. However, due to the short half-life of clinically used isotopes, other long-lived isotopes not used in clinical practice are used to perform the PSF measurements. As such, non-optimal PSF models that do not correspond to those needed for the data to be reconstructed are used within resolution modeling (RM) image reconstruction, usually underestimating the true PSF owing to the difference in positron range. In high resolution brain and preclinical imaging, this effect is of particular importance since the PSFs become more positron range limited and isotope-specific PSFs can help maximize the performance benefit from using resolution recovery image reconstruction algorithms. Methods: In this work, the authors used a printing technique to simultaneously measure multiple point sources on the High Resolution Research Tomograph (HRRT), and the authors demonstrated the feasibility of deriving isotope-dependent system matrices from fluorine-18 and carbon-11 point sources. Furthermore, the authors evaluated the impact of incorporating them within RM image reconstruction, using carbon-11 phantom and clinical datasets on the HRRT. Results: The results obtained using these two isotopes illustrate that even small differences in positron range can result in different PSF maps, leading to further improvements in contrast recovery when used in image reconstruction. The difference is more pronounced in the centre of the field-of-view where the full width at half maximum (FWHM) from the positron range has a larger contribution to the overall FWHM compared to the edge where the parallax error dominates the overall FWHM. Conclusions: Based on the proposed methodology, measured isotope-specific and spatially variant PSFs can be reliably derived and used for improved spatial resolution and variance performance in resolution

  7. Isotope specific resolution recovery image reconstruction in high resolution PET imaging.

    Science.gov (United States)

    Kotasidis, Fotis A; Angelis, Georgios I; Anton-Rodriguez, Jose; Matthews, Julian C; Reader, Andrew J; Zaidi, Habib

    2014-05-01

    Measuring and incorporating a scanner-specific point spread function (PSF) within image reconstruction has been shown to improve spatial resolution in PET. However, due to the short half-life of clinically used isotopes, other long-lived isotopes not used in clinical practice are used to perform the PSF measurements. As such, non-optimal PSF models that do not correspond to those needed for the data to be reconstructed are used within resolution modeling (RM) image reconstruction, usually underestimating the true PSF owing to the difference in positron range. In high resolution brain and preclinical imaging, this effect is of particular importance since the PSFs become more positron range limited and isotope-specific PSFs can help maximize the performance benefit from using resolution recovery image reconstruction algorithms. In this work, the authors used a printing technique to simultaneously measure multiple point sources on the High Resolution Research Tomograph (HRRT), and the authors demonstrated the feasibility of deriving isotope-dependent system matrices from fluorine-18 and carbon-11 point sources. Furthermore, the authors evaluated the impact of incorporating them within RM image reconstruction, using carbon-11 phantom and clinical datasets on the HRRT. The results obtained using these two isotopes illustrate that even small differences in positron range can result in different PSF maps, leading to further improvements in contrast recovery when used in image reconstruction. The difference is more pronounced in the centre of the field-of-view where the full width at half maximum (FWHM) from the positron range has a larger contribution to the overall FWHM compared to the edge where the parallax error dominates the overall FWHM. Based on the proposed methodology, measured isotope-specific and spatially variant PSFs can be reliably derived and used for improved spatial resolution and variance performance in resolution recovery image reconstruction. The

  8. Difference Raman spectroscopy of DNA molecules

    International Nuclear Information System (INIS)

    Anokhin, Andrey S; Yuzyuk, Yury I; Gorelik, Vladimir S; Dovbeshko, Galina I; Pyatyshev, Alexander Yu

    2015-01-01

    In this paper the micro-Raman spectra of calf DNA for different points of DNA sample have been recorded. The Raman spectra were made with help of difference Raman spectroscopy technique. Raman spectra were recorded with high spatial resolution from different points of the wet and dry samples in different spectral range (100÷4000cm −1 ) using two lasers: argon (514.5 nm) and helium -neon (632.8 nm). The significant differences in the Raman spectra for dry and wet DNA and for different points of DNA molecules were observed. The obtained data on difference Raman scattering spectra of DNA molecules may be used for identification of DNA types and for analysis of genetic information associated with the molecular structure of this molecule

  9. Scalable Algorithms for Large High-Resolution Terrain Data

    DEFF Research Database (Denmark)

    Mølhave, Thomas; Agarwal, Pankaj K.; Arge, Lars Allan

    2010-01-01

    In this paper we demonstrate that the technology required to perform typical GIS computations on very large high-resolution terrain models has matured enough to be ready for use by practitioners. We also demonstrate the impact that high-resolution data has on common problems. To our knowledge, so...

  10. Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

    2017-10-30

    DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG)2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP21lattice of hexagonal metric. The various twinning criteria give somewhat conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.

  11. High resolution NMR imaging using a high field yokeless permanent magnet.

    Science.gov (United States)

    Kose, Katsumi; Haishi, Tomoyuki

    2011-01-01

    We measured the homogeneity and stability of the magnetic field of a high field (about 1.04 tesla) yokeless permanent magnet with 40-mm gap for high resolution nuclear magnetic resonance (NMR) imaging. Homogeneity was evaluated using a 3-dimensional (3D) lattice phantom and 3D spin-echo imaging sequences. In the central sphere (20-mm diameter), peak-to-peak magnetic field inhomogeneity was about 60 ppm, and the root-mean-square was 8 ppm. We measured room temperature, magnet temperature, and NMR frequency of the magnet simultaneously every minute for about 68 hours with and without the thermal insulator of the magnet. A simple mathematical model described the magnet's thermal property. Based on magnet performance, we performed high resolution (up to [20 µm](2)) imaging with internal NMR lock sequences of several biological samples. Our results demonstrated the usefulness of the high field small yokeless permanent magnet for high resolution NMR imaging.

  12. High resolution NMR imaging using a high field yokeless permanent magnet

    International Nuclear Information System (INIS)

    Kose, Katsumi; Haishi, Tomoyuki

    2011-01-01

    We measured the homogeneity and stability of the magnetic field of a high field (about 1.04 tesla) yokeless permanent magnet with 40-mm gap for high resolution nuclear magnetic resonance (NMR) imaging. Homogeneity was evaluated using a 3-dimensional (3D) lattice phantom and 3D spin-echo imaging sequences. In the central sphere (20-mm diameter), peak-to-peak magnetic field inhomogeneity was about 60 ppm, and the root-mean-square was 8 ppm. We measured room temperature, magnet temperature, and NMR frequency of the magnet simultaneously every minute for about 68 hours with and without the thermal insulator of the magnet. A simple mathematical model described the magnet's thermal property. Based on magnet performance, we performed high resolution (up to [20 μm] 2 ) imaging with internal NMR lock sequences of several biological samples. Our results demonstrated the usefulness of the high field small yokeless permanent magnet for high resolution NMR imaging. (author)

  13. Recent progress on DNA based walkers.

    Science.gov (United States)

    Pan, Jing; Li, Feiran; Cha, Tae-Gon; Chen, Haorong; Choi, Jong Hyun

    2015-08-01

    DNA based synthetic molecular walkers are reminiscent of biological protein motors. They are powered by hybridization with fuel strands, environment induced conformational transitions, and covalent chemistry of oligonucleotides. Recent developments in experimental techniques enable direct observation of individual walkers with high temporal and spatial resolution. The functionalities of state-of-the-art DNA walker systems can thus be analyzed for various applications. Herein we review recent progress on DNA walker principles and characterization methods, and evaluate various aspects of their functions for future applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. High resolution melting for mutation scanning of TP53 exons 5–8

    International Nuclear Information System (INIS)

    Krypuy, Michael; Dobrovic, Alexander; Ahmed, Ahmed Ashour; Etemadmoghadam, Dariush; Hyland, Sarah J; Australian Ovarian Cancer Study Group; Fazio, Anna de; Fox, Stephen B; Brenton, James D; Bowtell, David D

    2007-01-01

    p53 is commonly inactivated by mutations in the DNA-binding domain in a wide range of cancers. As mutant p53 often influences response to therapy, effective and rapid methods to scan for mutations in TP53 are likely to be of clinical value. We therefore evaluated the use of high resolution melting (HRM) as a rapid mutation scanning tool for TP53 in tumour samples. We designed PCR amplicons for HRM mutation scanning of TP53 exons 5 to 8 and tested them with DNA from cell lines hemizygous or homozygous for known mutations. We assessed the sensitivity of each PCR amplicon using dilutions of cell line DNA in normal wild-type DNA. We then performed a blinded assessment on ovarian tumour DNA samples that had been previously sequenced for mutations in TP53 to assess the sensitivity and positive predictive value of the HRM technique. We also performed HRM analysis on breast tumour DNA samples with unknown TP53 mutation status. One cell line mutation was not readily observed when exon 5 was amplified. As exon 5 contained multiple melting domains, we divided the exon into two amplicons for further screening. Sequence changes were also introduced into some of the primers to improve the melting characteristics of the amplicon. Aberrant HRM curves indicative of TP53 mutations were observed for each of the samples in the ovarian tumour DNA panel. Comparison of the HRM results with the sequencing results revealed that each mutation was detected by HRM in the correct exon. For the breast tumour panel, we detected seven aberrant melt profiles by HRM and subsequent sequencing confirmed the presence of these and no other mutations in the predicted exons. HRM is an effective technique for simple and rapid scanning of TP53 mutations that can markedly reduce the amount of sequencing required in mutational studies of TP53

  15. Progress in high-resolution x-ray holographic microscopy

    International Nuclear Information System (INIS)

    Jacobsen, C.; Kirz, J.; Howells, M.; McQuaid, K.; Rothman, S.; Feder, R.; Sayre, D.

    1987-07-01

    Among the various types of x-ray microscopes that have been demonstrated, the holographic microscope has had the largest gap between promise and performance. The difficulties of fabricating x-ray optical elements have led some to view holography as the most attractive method for obtaining the ultimate in high resolution x-ray micrographs; however, we know of no investigations prior to 1987 that clearly demonstrated submicron resolution in reconstructed images. Previous efforts suffered from problems such as limited resolution and dynamic range in the recording media, low coherent x-ray flux, and aberrations and diffraction limits in visible light reconstruction. We have addressed the recording limitations through the use of an undulator x-ray source and high-resolution photoresist recording media. For improved results in the readout and reconstruction steps, we have employed metal shadowing and transmission electron microscopy, along with numerical reconstruction techniques. We believe that this approach will allow holography to emerge as a practical method of high-resolution x-ray microscopy. 30 refs., 4 figs

  16. Progress in high-resolution x-ray holographic microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, C.; Kirz, J.; Howells, M.; McQuaid, K.; Rothman, S.; Feder, R.; Sayre, D.

    1987-07-01

    Among the various types of x-ray microscopes that have been demonstrated, the holographic microscope has had the largest gap between promise and performance. The difficulties of fabricating x-ray optical elements have led some to view holography as the most attractive method for obtaining the ultimate in high resolution x-ray micrographs; however, we know of no investigations prior to 1987 that clearly demonstrated submicron resolution in reconstructed images. Previous efforts suffered from problems such as limited resolution and dynamic range in the recording media, low coherent x-ray flux, and aberrations and diffraction limits in visible light reconstruction. We have addressed the recording limitations through the use of an undulator x-ray source and high-resolution photoresist recording media. For improved results in the readout and reconstruction steps, we have employed metal shadowing and transmission electron microscopy, along with numerical reconstruction techniques. We believe that this approach will allow holography to emerge as a practical method of high-resolution x-ray microscopy. 30 refs., 4 figs.

  17. Highly efficient DNA extraction method from skeletal remains

    Directory of Open Access Journals (Sweden)

    Irena Zupanič Pajnič

    2011-03-01

    Full Text Available Background: This paper precisely describes the method of DNA extraction developed to acquire high quality DNA from the Second World War skeletal remains. The same method is also used for molecular genetic identification of unknown decomposed bodies in routine forensic casework where only bones and teeth are suitable for DNA typing. We analysed 109 bones and two teeth from WWII mass graves in Slovenia. Methods: We cleaned the bones and teeth, removed surface contaminants and ground the bones into powder, using liquid nitrogen . Prior to isolating the DNA in parallel using the BioRobot EZ1 (Qiagen, the powder was decalcified for three days. The nuclear DNA of the samples were quantified by real-time PCR method. We acquired autosomal genetic profiles and Y-chromosome haplotypes of the bones and teeth with PCR amplification of microsatellites, and mtDNA haplotypes 99. For the purpose of traceability in the event of contamination, we prepared elimination data bases including genetic profiles of the nuclear and mtDNA of all persons who have been in touch with the skeletal remains in any way. Results: We extracted up to 55 ng DNA/g of the teeth, up to 100 ng DNA/g of the femurs, up to 30 ng DNA/g of the tibias and up to 0.5 ng DNA/g of the humerus. The typing of autosomal and YSTR loci was successful in all of the teeth, in 98 % dekalof the femurs, and in 75 % to 81 % of the tibias and humerus. The typing of mtDNA was successful in all of the teeth, and in 96 % to 98 % of the bones. Conclusions: We managed to obtain nuclear DNA for successful STR typing from skeletal remains that were over 60 years old . The method of DNA extraction described here has proved to be highly efficient. We obtained 0.8 to 100 ng DNA/g of teeth or bones and complete genetic profiles of autosomal DNA, Y-STR haplotypes, and mtDNA haplotypes from only 0.5g bone and teeth samples.

  18. High-resolution spectroscopy of gases for industrial applications

    DEFF Research Database (Denmark)

    Fateev, Alexander; Clausen, Sønnik

    High-resolution spectroscopy of gases is a powerful technique which has various fundamental and practical applications: in situ simultaneous measurements of gas temperature and gas composition, radiative transfer modeling, validation of existing and developing of new databases and etc. Existing...... databases (e.g. HITRAN, HITEMP or CDSD) can normally be used for absorption spectra calculations at limited temperature/pressure ranges. Therefore experimental measurements of absorption/transmission spectra gases (e.g. CO2, H2O or SO2) at high-resolution and elevated temperatures are essential both...... for analysis of complex experimental data and further development of the databases. High-temperature gas cell facilities available at DTU Chemical Engineering are presented and described. The gas cells and high-resolution spectrometers allow us to perform high-quality reference measurements of gases relevant...

  19. Imaging and high-sensitivity quantification of chemiluminescent labeled DNA-blots

    International Nuclear Information System (INIS)

    Dorner, G.

    1997-01-01

    The present thesis has for objective the development of both, methods of DNA labeling by chemiluminescence (via the catalytic activity of the enzyme alkaline phosphatase - AP) and an appropriate imaging system. Offering a competitive alternative to the detection of classical radio-labels in molecular-biological experiments of the blotting type, this technique should permit the realization of quantitative studies of gene expression at ultra-high sensitivity necessary in particular for differential-screening experiments. To reach our aim. we separated the project into three different parts. In a first step an imager based on a liquid-nitrogen-cooled CCD coupled to a standard optics (50 mm/fl.2) has been installed and characterized. This system offers a sensitive area of up to 625 cm 2 , a spatial resolution of 0.3-1 mm (depending on the field of view) and a sensitivity sufficient to detect 10 fg/mm 2 labeled DNA. In a second part, the chemiluminescent light-generation process in solution has been investigated to optimize the parameters temperature. pH and concentration of the substrate as well as the enzyme. The substrate offering the highest light yield (CDP-Star in addition with the enhancer EMERALD II) allows quantification of AP down to 10 -15 M within a dynamic range of 10 4 in solution. Finally. preparation, immobilization and detection of AP-labeled DNA probes (via a biotin-streptavidin-biotin-AP bridge) on nylon membranes has been optimized. A linear relation between the light intensities and the amount of DNA was observed in a range of 10 fg/mm 2 - 100 pg/mm 2 . Hybridization of the probes to bacterial cloned target-DNA has been addressed after examination of the best hybridization conditions. Our protocol includes the treatment of a proteinase, which resulted in a significantly lower background on the filter. The results of our investigations suggest that the main conditions for a reliable differential-screening experiment are fulfilled when using

  20. Towards high-resolution positron emission tomography for small volumes

    International Nuclear Information System (INIS)

    McKee, B.T.A.

    1982-01-01

    Some arguments are made regarding the medical usefulness of high spatial resolution in positron imaging, even if limited to small imaged volumes. Then the intrinsic limitations to spatial resolution in positron imaging are discussed. The project to build a small-volume, high resolution animal research prototype (SHARP) positron imaging system is described. The components of the system, particularly the detectors, are presented and brief mention is made of data acquisition and image reconstruction methods. Finally, some preliminary imaging results are presented; a pair of isolated point sources and 18 F in the bones of a rabbit. Although the detector system is not fully completed, these first results indicate that the goals of high sensitivity and high resolution (4 mm) have been realized. (Auth.)

  1. High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method

    International Nuclear Information System (INIS)

    Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

    2013-01-01

    Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal. Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005 ▶) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method

  2. High resolution drift chambers

    International Nuclear Information System (INIS)

    Va'vra, J.

    1985-07-01

    High precision drift chambers capable of achieving less than or equal to 50 μm resolutions are discussed. In particular, we compare so called cool and hot gases, various charge collection geometries, several timing techniques and we also discuss some systematic problems. We also present what we would consider an ''ultimate'' design of the vertex chamber. 50 refs., 36 figs., 6 tabs

  3. Assessment of mitochondrial functions in Daphnia pulex clones using high-resolution respirometry.

    Science.gov (United States)

    Kake-Guena, Sandrine A; Touisse, Kamal; Vergilino, Roland; Dufresne, France; Blier, Pierre U; Lemieux, Hélène

    2015-06-01

    The objectives of our study were to adapt a method to measure mitochondrial function in intact mitochondria from the small crustacean Daphnia pulex and to validate if this method was sensitive enough to characterize mitochondrial metabolism in clones of the pulex complex differing in ploidy levels, mitochondrial DNA haplotypes, and geographic origins. Daphnia clones belonging to the Daphnia pulex complex represent a powerful model to delineate the link between mitochondrial DNA evolution and mitochondrial phenotypes, as single genotypes with divergent mtDNA can be grown under various experimental conditions. Our study included two diploid clones from temperate environments and two triploid clones from subarctic environments. The whole animal permeabilization and measurement of respiration with high-resolution respirometry enabled the measurement of the functional capacity of specific mitochondrial complexes in four clones. When expressing the activity as ratios, our method detected significant interclonal variations. In the triploid subarctic clone from Kuujjurapik, a higher proportion of the maximal physiological oxidative phosphorylation (OXPHOS) capacity of mitochondria was supported by complex II, and a lower proportion by complex I. The triploid subarctic clone from Churchill (Manitoba) showed the lowest proportion of the maximal OXPHOS supported by complex II. Additional studies are required to determine if these differences in mitochondrial functions are related to differences in mitochondrial haplotypes or ploidy level and if they might be associated with fitness divergences and therefore selective value. © 2015 Wiley Periodicals, Inc.

  4. High resolution neutron spectroscopy for helium isotopes

    International Nuclear Information System (INIS)

    Abdel-Wahab, M.S.; Klages, H.O.; Schmalz, G.; Haesner, B.H.; Kecskemeti, J.; Schwarz, P.; Wilczynski, J.

    1992-01-01

    A high resolution fast neutron time-of-flight spectrometer is described, neutron time-of-flight spectra are taken using a specially designed TDC in connection to an on-line computer. The high time-of-flight resolution of 5 ps/m enabled the study of the total cross section of 4 He for neutrons near the 3/2 + resonance in the 5 He nucleus. The resonance parameters were determined by a single level Breit-Winger fit to the data. (orig.)

  5. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

    Science.gov (United States)

    Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun

    2018-06-01

    The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. A high-resolution regional reanalysis for Europe

    Science.gov (United States)

    Ohlwein, C.

    2015-12-01

    Reanalyses gain more and more importance as a source of meteorological information for many purposes and applications. Several global reanalyses projects (e.g., ERA, MERRA, CSFR, JMA9) produce and verify these data sets to provide time series as long as possible combined with a high data quality. Due to a spatial resolution down to 50-70km and 3-hourly temporal output, they are not suitable for small scale problems (e.g., regional climate assessment, meso-scale NWP verification, input for subsequent models such as river runoff simulations). The implementation of regional reanalyses based on a limited area model along with a data assimilation scheme is able to generate reanalysis data sets with high spatio-temporal resolution. Within the Hans-Ertel-Centre for Weather Research (HErZ), the climate monitoring branch concentrates efforts on the assessment and analysis of regional climate in Germany and Europe. In joint cooperation with DWD (German Meteorological Service), a high-resolution reanalysis system based on the COSMO model has been developed. The regional reanalysis for Europe matches the domain of the CORDEX EURO-11 specifications, albeit at a higher spatial resolution, i.e., 0.055° (6km) instead of 0.11° (12km) and comprises the assimilation of observational data using the existing nudging scheme of COSMO complemented by a special soil moisture analysis with boundary conditions provided by ERA-Interim data. The reanalysis data set covers the past 20 years. Extensive evaluation of the reanalysis is performed using independent observations with special emphasis on precipitation and high-impact weather situations indicating a better representation of small scale variability. Further, the evaluation shows an added value of the regional reanalysis with respect to the forcing ERA Interim reanalysis and compared to a pure high-resolution dynamical downscaling approach without data assimilation.

  7. Hybrid analysis (barcode-high resolution melting) for authentication of Thai herbal products, Andrographis paniculata (Burm.f.) Wall.ex Nees.

    Science.gov (United States)

    Osathanunkul, Maslin; Suwannapoom, Chatmongkon; Khamyong, Nuttaluck; Pintakum, Danupol; Lamphun, Santisuk Na; Triwitayakorn, Kanokporn; Osathanunkul, Kitisak; Madesis, Panagiotis

    2016-01-01

    Andrographis paniculata Nees is a medicinal plant with multiple pharmacological properties. It has been used over many centuries as a household remedy. A. paniculata products sold on the markets are in processed forms so it is difficult to authenticate. Therefore buying the herbal products poses a high-risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. High resolution melting analysis coupled with DNA barcoding (Bar-HRM) was applied to detect adulteration in commercial herbal products. The rbcL barcode was selected to use in primers design for HRM analysis to produce standard melting profile of A. paniculata species. DNA of the tested commercial products was isolated and their melting profiles were then generated and compared with the standard A. paniculata. The melting profiles of the rbcL amplicons of the three closely related herbal species (A. paniculata, Acanthus ebracteatus and Rhinacanthus nasutus) are clearly separated so that they can be distinguished by the developed method. The method was then used to authenticate commercial herbal products. HRM curves of all 10 samples tested are similar to A. paniculata which indicated that all tested products were contained the correct species as labeled. The method described in this study has been proved to be useful in aiding identification and/or authenticating A. paniculata. This Bar-HRM analysis has allowed us easily to determine the A. paniculata species in herbal products on the markets even they are in processed forms. We propose the use of DNA barcoding combined with High Resolution Melting analysis for authenticating of Andrographis paniculata products.The developed method can be used regardless of the type of the DNA template (fresh or dried tissue, leaf, and stem).rbcL region was chosen for the analysis and work well with our samplesWe can easily determine the A. paniculata species in herbal products tested

  8. Automated data processing of high-resolution mass spectra

    DEFF Research Database (Denmark)

    Hansen, Michael Adsetts Edberg; Smedsgaard, Jørn

    of the massive amounts of data. We present an automated data processing method to quantitatively compare large numbers of spectra from the analysis of complex mixtures, exploiting the full quality of high-resolution mass spectra. By projecting all detected ions - within defined intervals on both the time...... infusion of crude extracts into the source taking advantage of the high sensitivity, high mass resolution and accuracy and the limited fragmentation. Unfortunately, there has not been a comparable development in the data processing techniques to fully exploit gain in high resolution and accuracy...... infusion analyses of crude extract to find the relationship between species from several species terverticillate Penicillium, and also that the ions responsible for the segregation can be identified. Furthermore the process can automate the process of detecting unique species and unique metabolites....

  9. A Novel Low Temperature PCR Assured High-Fidelity DNA Amplification

    Directory of Open Access Journals (Sweden)

    Shaoxia Zhou

    2013-06-01

    Full Text Available As previously reported, a novel low temperature (LoTemp polymerase chain reaction (PCR catalyzed by a moderately heat-resistant (MHR DNA polymerase with a chemical-assisted denaturation temperature set at 85 °C instead of the conventional 94–96 °C can achieve high-fidelity DNA amplification of a target DNA, even after up to 120 PCR thermal cycles. Furthermore, such accurate amplification is not achievable with conventional PCR. Now, using a well-recognized L1 gene segment of the human papillomavirus (HPV type 52 (HPV-52 as the template for experiments, we demonstrate that the LoTemp high-fidelity DNA amplification is attributed to an unusually high processivity and stability of the MHR DNA polymerase whose high fidelity in template-directed DNA synthesis is independent of non-existent 3'–5' exonuclease activity. Further studies and understanding of the characteristics of the LoTemp PCR technology may facilitate implementation of DNA sequencing-based diagnostics at the point of care in community hospital laboratories.

  10. Achieving sensitive, high-resolution laser spectroscopy at CRIS

    Energy Technology Data Exchange (ETDEWEB)

    Groote, R. P. de [Instituut voor Kern- en Stralingsfysica, KU Leuven (Belgium); Lynch, K. M., E-mail: kara.marie.lynch@cern.ch [EP Department, CERN, ISOLDE (Switzerland); Wilkins, S. G. [The University of Manchester, School of Physics and Astronomy (United Kingdom); Collaboration: the CRIS collaboration

    2017-11-15

    The Collinear Resonance Ionization Spectroscopy (CRIS) experiment, located at the ISOLDE facility, has recently performed high-resolution laser spectroscopy, with linewidths down to 20 MHz. In this article, we present the modifications to the beam line and the newly-installed laser systems that have made sensitive, high-resolution measurements possible. Highlights of recent experimental campaigns are presented.

  11. Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack (Lasiantheae: Rubiaceae).

    Science.gov (United States)

    Arshed, Muhammad Jefte C; Valdez, Marcos B; Alejandro, Grecebio Jonathan D

    2017-01-01

    The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation. In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers ( mat K, rbc L, rps 16, and trn T-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species. The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, mat K and rbc L are recommended but with minimal resolution of species. While trn T-F showed moderate interspecific variations and resolution of Lasianthus species, rps 16 has the lowest interspecific divergence and resolution of species. Consequently, ITS is the potential ideal DNA barcode for Lasianthus species. ITS, mat K, and rps 16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by mat K, rbc L, trn T-F, and rps 16, respectivelyAll markers except rps 16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, mat K: maturase K, rbc L: ribulose-1,5-biphospahte-carboxylase, rps 16: ribosomal protein 16 small subunit gene.

  12. An atlas of high-resolution IRAS maps on nearby galaxies

    Science.gov (United States)

    Rice, Walter

    1993-01-01

    An atlas of far-infrared IRAS maps with near 1 arcmin angular resolution of 30 optically large galaxies is presented. The high-resolution IRAS maps were produced with the Maximum Correlation Method (MCM) image construction and enhancement technique developed at IPAC. The MCM technique, which recovers the spatial information contained in the overlapping detector data samples of the IRAS all-sky survey scans, is outlined and tests to verify the structural reliability and photometric integrity of the high-resolution maps are presented. The infrared structure revealed in individual galaxies is discussed. The atlas complements the IRAS Nearby Galaxy High-Resolution Image Atlas, the high-resolution galaxy images encoded in FITS format, which is provided to the astronomical community as an IPAC product.

  13. Development of high speed integrated circuit for very high resolution timing measurements

    International Nuclear Information System (INIS)

    Mester, Christian

    2009-10-01

    A multi-channel high-precision low-power time-to-digital converter application specific integrated circuit for high energy physics applications has been designed and implemented in a 130 nm CMOS process. To reach a target resolution of 24.4 ps, a novel delay element has been conceived. This nominal resolution has been experimentally verified with a prototype, with a minimum resolution of 19 ps. To further improve the resolution, a new interpolation scheme has been described. The ASIC has been designed to use a reference clock with the LHC bunch crossing frequency of 40 MHz and generate all required timing signals internally, to ease to use within the framework of an LHC upgrade. Special care has been taken to minimise the power consumption. (orig.)

  14. Development of high speed integrated circuit for very high resolution timing measurements

    Energy Technology Data Exchange (ETDEWEB)

    Mester, Christian

    2009-10-15

    A multi-channel high-precision low-power time-to-digital converter application specific integrated circuit for high energy physics applications has been designed and implemented in a 130 nm CMOS process. To reach a target resolution of 24.4 ps, a novel delay element has been conceived. This nominal resolution has been experimentally verified with a prototype, with a minimum resolution of 19 ps. To further improve the resolution, a new interpolation scheme has been described. The ASIC has been designed to use a reference clock with the LHC bunch crossing frequency of 40 MHz and generate all required timing signals internally, to ease to use within the framework of an LHC upgrade. Special care has been taken to minimise the power consumption. (orig.)

  15. High-resolution MRI in detecting subareolar breast abscess.

    Science.gov (United States)

    Fu, Peifen; Kurihara, Yasuyuki; Kanemaki, Yoshihide; Okamoto, Kyoko; Nakajima, Yasuo; Fukuda, Mamoru; Maeda, Ichiro

    2007-06-01

    Because subareolar breast abscess has a high recurrence rate, a more effective imaging technique is needed to comprehensively visualize the lesions and guide surgery. We performed a high-resolution MRI technique using a microscopy coil to reveal the characteristics and extent of subareolar breast abscess. High-resolution MRI has potential diagnostic value in subareolar breast abscess. This technique can be used to guide surgery with the aim of reducing the recurrence rate.

  16. Recent applications of gas chromatography with high-resolution mass spectrometry.

    Science.gov (United States)

    Špánik, Ivan; Machyňáková, Andrea

    2018-01-01

    Gas chromatography coupled to high-resolution mass spectrometry is a powerful analytical method that combines excellent separation power of gas chromatography with improved identification based on an accurate mass measurement. These features designate gas chromatography with high-resolution mass spectrometry as the first choice for identification and structure elucidation of unknown volatile and semi-volatile organic compounds. Gas chromatography with high-resolution mass spectrometry quantitative analyses was previously focused on the determination of dioxins and related compounds using magnetic sector type analyzers, a standing requirement of many international standards. The introduction of a quadrupole high-resolution time-of-flight mass analyzer broadened interest in this method and novel applications were developed, especially for multi-target screening purposes. This review is focused on the development and the most interesting applications of gas chromatography coupled to high-resolution mass spectrometry towards analysis of environmental matrices, biological fluids, and food safety since 2010. The main attention is paid to various approaches and applications of gas chromatography coupled to high-resolution mass spectrometry for non-target screening to identify contaminants and to characterize the chemical composition of environmental, food, and biological samples. The most interesting quantitative applications, where a significant contribution of gas chromatography with high-resolution mass spectrometry over the currently used methods is expected, will be discussed as well. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis.

    Science.gov (United States)

    Mohamed Zahidi, Jama'ayah; Bee Yong, Tay; Hashim, Rohaidah; Mohd Noor, Azura; Hamzah, Siti Hawa; Ahmad, Norazah

    2015-04-01

    Molecular approaches have been investigated to overcome difficulties in identification and differentiation of Brucella spp. using conventional phenotypic methods. In this study, high-resolution melt (HRM) analysis was used for rapid identification and differentiation of members of Brucella genus. A total of 41 Brucella spp. isolates from human brucellosis were subjected to HRM analysis using 4 sets of primers, which identified 40 isolates as Brucella melitensis and 1 as Brucella canis. The technique utilized low DNA concentration and was highly reproducible. The assay is shown to be a useful diagnostic tool, which can rapidly differentiate Brucella up to species level. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Ribo HRM--detection of inter- and intra-species polymorphisms within ribosomal DNA by high resolution melting analysis supported by application of artificial allelic standards.

    Science.gov (United States)

    Masny, Aleksander; Jagiełło, Agata; Płucienniczak, Grażyna; Golab, Elzbieta

    2012-09-01

    Ribo HRM, a single-tube PCR and high resolution melting (HRM) assay for detection of polymorphisms in the large subunit ribosomal DNA expansion segment V, was developed on a Trichinella model. Four Trichinella species: T. spiralis (isolates ISS3 and ISS160), T. nativa (isolates ISS10 and ISS70), T. britovi (isolates ISS2 and ISS392) and T. pseudospiralis (isolates ISS13 and ISS1348) were genotyped. Cloned allelic variants of the expansion segment V were used as standards to prepare reference HRM curves characteristic for single sequences and mixtures of several cloned sequences imitating allelic composition detected in Trichinella isolates. Using the primer pair Tsr1 and Trich1bi, it was possible to amplify a fragment of the ESV and detect PCR products obtained from the genomic DNA of pools of larvae belonging to the four investigated species: T. pseudospiralis, T. spiralis, T. britovi and T. nativa, in a single tube Real-Time PCR reaction. Differences in the shape of the HRM curves of Trichinella isolates suggested the presence of differences between examined isolates of T. nativa, T. britovi and T. pseudospiralis species. No differences were observed between T. spiralis isolates. The presence of polymorphisms within the amplified ESV sequence fragment of T. nativa T. britovi and T. pseudospiralis was confirmed by sequencing of the cloned PCR products. Novel sequences were discovered and deposited in GenBank (GenBank IDs: JN971020-JN971027, JN120902.1, JN120903.1, JN120904.1, JN120906.1, JN120905.1). Screening the ESV region of Trichinella for polymorphism is possible using the genotyping assay Ribo HRM at the current state of its development. The Ribo HRM assay could be useful in phylogenetic studies of the Trichinella genus. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Theory of high-force DNA stretching and overstretching.

    Science.gov (United States)

    Storm, C; Nelson, P C

    2003-05-01

    Single-molecule experiments on single- and double-stranded DNA have sparked a renewed interest in the force versus extension of polymers. The extensible freely jointed chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA, but this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the discrete persistent chain) that borrows features from both the FJC and the wormlike chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first value for the bend stiffness of the overstretched state. In particular, we find the effective bend stiffness for DNA in this state to be about 12 nm k(B)T, a value quite different from either the B-form or single-stranded DNA.

  20. Multi-resolution voxel phantom modeling: a high-resolution eye model for computational dosimetry.

    Science.gov (United States)

    Caracappa, Peter F; Rhodes, Ashley; Fiedler, Derek

    2014-09-21

    Voxel models of the human body are commonly used for simulating radiation dose with a Monte Carlo radiation transport code. Due to memory limitations, the voxel resolution of these computational phantoms is typically too large to accurately represent the dimensions of small features such as the eye. Recently reduced recommended dose limits to the lens of the eye, which is a radiosensitive tissue with a significant concern for cataract formation, has lent increased importance to understanding the dose to this tissue. A high-resolution eye model is constructed using physiological data for the dimensions of radiosensitive tissues, and combined with an existing set of whole-body models to form a multi-resolution voxel phantom, which is used with the MCNPX code to calculate radiation dose from various exposure types. This phantom provides an accurate representation of the radiation transport through the structures of the eye. Two alternate methods of including a high-resolution eye model within an existing whole-body model are developed. The accuracy and performance of each method is compared against existing computational phantoms.

  1. High-resolution intravital microscopy.

    Directory of Open Access Journals (Sweden)

    Volker Andresen

    Full Text Available Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy--the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and

  2. High-Resolution Intravital Microscopy

    Science.gov (United States)

    Andresen, Volker; Pollok, Karolin; Rinnenthal, Jan-Leo; Oehme, Laura; Günther, Robert; Spiecker, Heinrich; Radbruch, Helena; Gerhard, Jenny; Sporbert, Anje; Cseresnyes, Zoltan; Hauser, Anja E.; Niesner, Raluca

    2012-01-01

    Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy - the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning) while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs) of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and developmental biology

  3. Hyper-resolution urban flood modeling using high-resolution radar precipitation and LiDAR data

    Science.gov (United States)

    Noh, S. J.; Lee, S.; Lee, J.; Seo, D. J.

    2016-12-01

    Floods occur most frequently among all natural hazards, often causing widespread economic damage and loss of human lives. In particular, urban flooding is becoming increasingly costly and difficult to manage with a greater concentration of population and assets in urban centers. Despite of known benefits for accurate representation of small scale features and flow interaction among different flow domains, which have significant impact on flood propagation, high-resolution modeling has not been fully utilized due to expensive computation and various uncertainties from model structure, input and parameters. In this study, we assess the potential of hyper-resolution hydrologic-hydraulic modeling using high-resolution radar precipitation and LiDAR data for improved urban flood prediction and hazard mapping. We describe a hyper-resolution 1D-2D coupled urban flood model for pipe and surface flows and evaluate the accuracy of the street-level inundation information produced. For detailed geometric representation of urban areas and for computational efficiency, we use 1 m-resolution topographical data, processed from LiDAR measurements, in conjunction with adaptive mesh refinement. For street-level simulation in large urban areas at grid sizes of 1 to 10 m, a hybrid parallel computing scheme using MPI and openMP is also implemented in a high-performance computing system. The modeling approach developed is applied for the Johnson Creek Catchment ( 40 km2), which makes up the Arlington Urban Hydroinformatics Testbed. In addition, discussion will be given on availability of hyper-resolution simulation archive for improved real-time flood mapping.

  4. Effect of DNA sequence, ionic strength, and cationic DNA affinity binders on the methylation of DNA by N-methyl-N-nitrosourea

    International Nuclear Information System (INIS)

    Wurdeman, R.L.; Gold, B.

    1988-01-01

    DNA alkylation by N-alkyl-N-nitrosoureas is generally accepted to be responsible for their mutagenic, carcinogenic, and antineoplastic activities. The exact nature of the ultimate alkylating intermediate is still controversial, with a variety of species having been nominated. The sequence specificity for DNA alkylation by simple N-alkyl-N-nitrosoureas has not been reported, although such information is basic in understanding the specific point mutations induced by these compounds in oncogene targets. These two points are addressed by using N-methyl-N-nitrosourea methylation of a 576 base-pair 32 P-end-labeled DNA restriction fragment and high-resolution polyacrylamide sequencing gels. This method provides information on the formation of N 7 -methylguanine, by the generation of single-strand breaks upon exposure to piperidine

  5. Analysis of the impact of spatial resolution on land/water classifications using high-resolution aerial imagery

    Science.gov (United States)

    Enwright, Nicholas M.; Jones, William R.; Garber, Adrienne L.; Keller, Matthew J.

    2014-01-01

    Long-term monitoring efforts often use remote sensing to track trends in habitat or landscape conditions over time. To most appropriately compare observations over time, long-term monitoring efforts strive for consistency in methods. Thus, advances and changes in technology over time can present a challenge. For instance, modern camera technology has led to an increasing availability of very high-resolution imagery (i.e. submetre and metre) and a shift from analogue to digital photography. While numerous studies have shown that image resolution can impact the accuracy of classifications, most of these studies have focused on the impacts of comparing spatial resolution changes greater than 2 m. Thus, a knowledge gap exists on the impacts of minor changes in spatial resolution (i.e. submetre to about 1.5 m) in very high-resolution aerial imagery (i.e. 2 m resolution or less). This study compared the impact of spatial resolution on land/water classifications of an area dominated by coastal marsh vegetation in Louisiana, USA, using 1:12,000 scale colour-infrared analogue aerial photography (AAP) scanned at four different dot-per-inch resolutions simulating ground sample distances (GSDs) of 0.33, 0.54, 1, and 2 m. Analysis of the impact of spatial resolution on land/water classifications was conducted by exploring various spatial aspects of the classifications including density of waterbodies and frequency distributions in waterbody sizes. This study found that a small-magnitude change (1–1.5 m) in spatial resolution had little to no impact on the amount of water classified (i.e. percentage mapped was less than 1.5%), but had a significant impact on the mapping of very small waterbodies (i.e. waterbodies ≤ 250 m2). These findings should interest those using temporal image classifications derived from very high-resolution aerial photography as a component of long-term monitoring programs.

  6. Image Quality in High-resolution and High-cadence Solar Imaging

    Science.gov (United States)

    Denker, C.; Dineva, E.; Balthasar, H.; Verma, M.; Kuckein, C.; Diercke, A.; González Manrique, S. J.

    2018-03-01

    Broad-band imaging and even imaging with a moderate bandpass (about 1 nm) provides a photon-rich environment, where frame selection (lucky imaging) becomes a helpful tool in image restoration, allowing us to perform a cost-benefit analysis on how to design observing sequences for imaging with high spatial resolution in combination with real-time correction provided by an adaptive optics (AO) system. This study presents high-cadence (160 Hz) G-band and blue continuum image sequences obtained with the High-resolution Fast Imager (HiFI) at the 1.5-meter GREGOR solar telescope, where the speckle-masking technique is used to restore images with nearly diffraction-limited resolution. The HiFI employs two synchronized large-format and high-cadence sCMOS detectors. The median filter gradient similarity (MFGS) image-quality metric is applied, among others, to AO-corrected image sequences of a pore and a small sunspot observed on 2017 June 4 and 5. A small region of interest, which was selected for fast-imaging performance, covered these contrast-rich features and their neighborhood, which were part of Active Region NOAA 12661. Modifications of the MFGS algorithm uncover the field- and structure-dependency of this image-quality metric. However, MFGS still remains a good choice for determining image quality without a priori knowledge, which is an important characteristic when classifying the huge number of high-resolution images contained in data archives. In addition, this investigation demonstrates that a fast cadence and millisecond exposure times are still insufficient to reach the coherence time of daytime seeing. Nonetheless, the analysis shows that data acquisition rates exceeding 50 Hz are required to capture a substantial fraction of the best seeing moments, significantly boosting the performance of post-facto image restoration.

  7. Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure.

    OpenAIRE

    Felgner, P L; Gadek, T R; Holm, M; Roman, R; Chan, H W; Wenz, M; Northrop, J P; Ringold, G M; Danielsen, M

    1987-01-01

    A DNA-transfection protocol has been developed that makes use of a synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Small unilamellar liposomes containing DOTMA interact spontaneously with DNA to form lipid-DNA complexes with 100% entrapment of the DNA, DOTMA facilitates fusion of the complex with the plasma membrane of tissue culture cells, resulting in both uptake and expression of the DNA. The technique is simple, highly reproducible, and eff...

  8. Smartphone microendoscopy for high resolution fluorescence imaging

    Directory of Open Access Journals (Sweden)

    Xiangqian Hong

    2016-09-01

    Full Text Available High resolution optical endoscopes are increasingly used in diagnosis of various medical conditions of internal organs, such as the cervix and gastrointestinal (GI tracts, but they are too expensive for use in resource-poor settings. On the other hand, smartphones with high resolution cameras and Internet access have become more affordable, enabling them to diffuse into most rural areas and developing countries in the past decade. In this paper, we describe a smartphone microendoscope that can take fluorescence images with a spatial resolution of 3.1 μm. Images collected from ex vivo, in vitro and in vivo samples using the device are also presented. The compact and cost-effective smartphone microendoscope may be envisaged as a powerful tool for detecting pre-cancerous lesions of internal organs in low and middle-income countries (LMICs.

  9. High resolution mid-infrared spectroscopy based on frequency upconversion

    DEFF Research Database (Denmark)

    Dam, Jeppe Seidelin; Hu, Qi; Tidemand-Lichtenberg, Peter

    2013-01-01

    signals can be analyzed. The obtainable frequency resolution is usually in the nm range where sub nm resolution is preferred in many applications, like gas spectroscopy. In this work we demonstrate how to obtain sub nm resolution when using upconversion. In the presented realization one object point...... high resolution spectral performance by observing emission from hot water vapor in a butane gas burner....

  10. Climate change and high-resolution whole-building numerical modelling

    NARCIS (Netherlands)

    Blocken, B.J.E.; Briggen, P.M.; Schellen, H.L.; Hensen, J.L.M.

    2010-01-01

    This paper briefly discusses the need of high-resolution whole-building numerical modelling in the context of climate change. High-resolution whole-building numerical modelling can be used for detailed analysis of the potential consequences of climate change on buildings and to evaluate remedial

  11. High-speed detection of DNA translocation in nanopipettes

    Science.gov (United States)

    Fraccari, Raquel L.; Ciccarella, Pietro; Bahrami, Azadeh; Carminati, Marco; Ferrari, Giorgio; Albrecht, Tim

    2016-03-01

    We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface.We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface. Electronic supplementary information (ESI) available: Gel electrophoresis confirming lengths and purity of DNA samples, comparison between Axopatch 200B and custom-built setup, comprehensive low-noise amplifier characterization, representative I-V curves of nanopipettes used, typical scatter plots of τ vs. peak amplitude for the four LDNA's used, table of most probable τ values, a comparison between different fitting models for the DNA translocation time distribution, further details on the stochastic numerical simulation of the scaling statistics and the derivation of the extended

  12. Metallic Nanostructures Based on DNA Nanoshapes

    Directory of Open Access Journals (Sweden)

    Boxuan Shen

    2016-08-01

    Full Text Available Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds. These methods offer high resolution, versatility and throughput and could enable the fabrication of arbitrarily-shaped structures with a 10-nm feature size, thus bringing novel applications into view. In this review, we cover the evolution of DNA-based metallic nanostructures, starting from the metallized double-stranded DNA for electronics and progress to sophisticated plasmonic structures based on DNA origami objects.

  13. New approach to 3-D, high sensitivity, high mass resolution space plasma composition measurements

    International Nuclear Information System (INIS)

    McComas, D.J.; Nordholt, J.E.

    1990-01-01

    This paper describes a new type of 3-D space plasma composition analyzer. The design combines high sensitivity, high mass resolution measurements with somewhat lower mass resolution but even higher sensitivity measurements in a single compact and robust design. While the lower resolution plasma measurements are achieved using conventional straight-through time-of-flight mass spectrometry, the high mass resolution measurements are made by timing ions reflected in a linear electric field (LEF), where the restoring force that an ion experiences is proportional to the depth it travels into the LEF region. Consequently, the ion's equation of motion in that dimension is that of a simple harmonic oscillator and its travel time is simply proportional to the square root of the ion's mass/charge (m/q). While in an ideal LEF, the m/q resolution can be arbitrarily high, in a real device the resolution is limited by the field linearity which can be achieved. In this paper we describe how a nearly linear field can be produced and discuss how the design can be optimized for various different plasma regimes and spacecraft configurations

  14. High resolution CT of the chest

    Energy Technology Data Exchange (ETDEWEB)

    Barneveld Binkhuysen, F H [Eemland Hospital (Netherlands), Dept. of Radiology

    1996-12-31

    Compared to conventional CT high resolution CT (HRCT) shows several extra anatomical structures which might effect both diagnosis and therapy. The extra anatomical structures were discussed briefly in this article. (18 refs.).

  15. Methodology of high-resolution photography for mural condition database

    Science.gov (United States)

    Higuchi, R.; Suzuki, T.; Shibata, M.; Taniguchi, Y.

    2015-08-01

    Digital documentation is one of the most useful techniques to record the condition of cultural heritage. Recently, high-resolution images become increasingly useful because it is possible to show general views of mural paintings and also detailed mural conditions in a single image. As mural paintings are damaged by environmental stresses, it is necessary to record the details of painting condition on high-resolution base maps. Unfortunately, the cost of high-resolution photography and the difficulty of operating its instruments and software have commonly been an impediment for researchers and conservators. However, the recent development of graphic software makes its operation simpler and less expensive. In this paper, we suggest a new approach to make digital heritage inventories without special instruments, based on our recent our research project in Üzümlü church in Cappadocia, Turkey. This method enables us to achieve a high-resolution image database with low costs, short time, and limited human resources.

  16. High-Resolution MRI in Rectal Cancer

    International Nuclear Information System (INIS)

    Dieguez, Adriana

    2010-01-01

    High-resolution MRI is the best method of assessing the relation of the rectal tumor with the potential circumferential resection margin (CRM). Therefore it is currently considered the method of choice for local staging of rectal cancer. The primary surgery of rectal cancer is total mesorectal excision (TME), which plane of dissection is formed by the mesorectal fascia surrounding mesorectal fat and rectum. This fascia will determine the circumferential margin of resection. At the same time, high resolution MRI allows adequate pre-operative identification of important prognostic risk factors, improving the selection and indication of therapy for each patient. This information includes, besides the circumferential margin of resection, tumor and lymph node staging, extramural vascular invasion and the description of lower rectal tumors. All these should be described in detail in the report, being part of the discussion in the multidisciplinary team, the place where the decisions involving the patient with rectal cancer will take place. The aim of this study is to provide the information necessary to understand the use of high resolution MRI in the identification of prognostic risk factors in rectal cancer. The technical requirements and standardized report for this study will be describe, as well as the anatomical landmarks of importance for the total mesorectal excision (TME), as we have said is the surgery of choice for rectal cancer. (authors) [es

  17. High-resolution coherent three-dimensional spectroscopy of Br2.

    Science.gov (United States)

    Chen, Peter C; Wells, Thresa A; Strangfeld, Benjamin R

    2013-07-25

    In the past, high-resolution spectroscopy has been limited to small, simple molecules that yield relatively uncongested spectra. Larger and more complex molecules have a higher density of peaks and are susceptible to complications (e.g., effects from conical intersections) that can obscure the patterns needed to resolve and assign peaks. Recently, high-resolution coherent two-dimensional (2D) spectroscopy has been used to resolve and sort peaks into easily identifiable patterns for molecules where pattern-recognition has been difficult. For very highly congested spectra, however, the ability to resolve peaks using coherent 2D spectroscopy is limited by the bandwidth of instrumentation. In this article, we introduce and investigate high-resolution coherent three-dimensional spectroscopy (HRC3D) as a method for dealing with heavily congested systems. The resulting patterns are unlike those in high-resolution coherent 2D spectra. Analysis of HRC3D spectra could provide a means for exploring the spectroscopy of large and complex molecules that have previously been considered too difficult to study.

  18. Single-step rapid assembly of DNA origami nanostructures for addressable nanoscale bioreactors

    DEFF Research Database (Denmark)

    Fu, Yanming; Zeng, Dongdong; Chao, Jie

    2013-01-01

    nm resolution and at the single-molecule level. We attach a pair of enzymes (horseradish peroxidase and glucose oxidase) at the inner side of DNA nanotubes and observe high coupling efficiency of enzyme cascade within this confined nanospace. Hence, DNA nanostructures with such unprecedented...

  19. Use of a New High Resolution Melting Method for Genotyping Pathogenic Leptospira spp.

    Directory of Open Access Journals (Sweden)

    Florence Naze

    Full Text Available Leptospirosis is a worldwide zoonosis that is endemic in tropical areas, such as Reunion Island. The species Leptospira interrogans is the primary agent in human infections, but other pathogenic species, such as L. kirschner and L. borgpetersenii, are also associated with human leptospirosis.In this study, a melting curve analysis of the products that were amplified with the primer pairs lfb1 F/R and G1/G2 facilitated an accurate species classification of Leptospira reference strains. Next, we combined an unsupervised high resolution melting (HRM method with a new statistical approach using primers to amplify a two variable-number tandem-repeat (VNTR for typing at the subspecies level. The HRM analysis, which was performed with ScreenClust Software, enabled the identification of genotypes at the serovar level with high resolution power (Hunter-Gaston index 0.984. This method was also applied to Leptospira DNA from blood samples that were obtained from Reunion Island after 1998. We were able to identify a unique genotype that is identical to that of the L. interrogans serovars Copenhageni and Icterohaemorrhagiae, suggesting that this genotype is the major cause of leptospirosis on Reunion Island.Our simple, rapid, and robust genotyping method enables the identification of Leptospira strains at the species and subspecies levels and supports the direct genotyping of Leptospira in biological samples without requiring cultures.

  20. High resolution gamma-ray spectroscopy at high count rates with a prototype High Purity Germanium detector

    Science.gov (United States)

    Cooper, R. J.; Amman, M.; Vetter, K.

    2018-04-01

    High-resolution gamma-ray spectrometers are required for applications in nuclear safeguards, emergency response, and fundamental nuclear physics. To overcome one of the shortcomings of conventional High Purity Germanium (HPGe) detectors, we have developed a prototype device capable of achieving high event throughput and high energy resolution at very high count rates. This device, the design of which we have previously reported on, features a planar HPGe crystal with a reduced-capacitance strip electrode geometry. This design is intended to provide good energy resolution at the short shaping or digital filter times that are required for high rate operation and which are enabled by the fast charge collection afforded by the planar geometry crystal. In this work, we report on the initial performance of the system at count rates up to and including two million counts per second.

  1. Detectors for high resolution dynamic pet

    International Nuclear Information System (INIS)

    Derenzo, S.E.; Budinger, T.F.; Huesman, R.H.

    1983-05-01

    This report reviews the motivation for high spatial resolution in dynamic positron emission tomography of the head and the technical problems in realizing this objective. We present recent progress in using small silicon photodiodes to measure the energy deposited by 511 keV photons in small BGO crystals with an energy resolution of 9.4% full-width at half-maximum. In conjunction with a suitable phototube coupled to a group of crystals, the photodiode signal to noise ratio is sufficient for the identification of individual crystals both for conventional and time-of-flight positron tomography

  2. Quantitative live imaging of endogenous DNA replication in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Andrew Burgess

    Full Text Available Historically, the analysis of DNA replication in mammalian tissue culture cells has been limited to static time points, and the use of nucleoside analogues to pulse-label replicating DNA. Here we characterize for the first time a novel Chromobody cell line that specifically labels endogenous PCNA. By combining this with high-resolution confocal time-lapse microscopy, and with a simplified analysis workflow, we were able to produce highly detailed, reproducible, quantitative 4D data on endogenous DNA replication. The increased resolution allowed accurate classification and segregation of S phase into early-, mid-, and late-stages based on the unique subcellular localization of endogenous PCNA. Surprisingly, this localization was slightly but significantly different from previous studies, which utilized over-expressed GFP tagged forms of PCNA. Finally, low dose exposure to Hydroxyurea caused the loss of mid- and late-S phase localization patterns of endogenous PCNA, despite cells eventually completing S phase. Taken together, these results indicate that this simplified method can be used to accurately identify and quantify DNA replication under multiple and various experimental conditions.

  3. High Resolution Thermometry for EXACT

    Science.gov (United States)

    Panek, J. S.; Nash, A. E.; Larson, M.; Mulders, N.

    2000-01-01

    High Resolution Thermometers (HRTs) based on SQUID detection of the magnetization of a paramagnetic salt or a metal alloy has been commonly used for sub-nano Kelvin temperature resolution in low temperature physics experiments. The main applications to date have been for temperature ranges near the lambda point of He-4 (2.177 K). These thermometers made use of materials such as Cu(NH4)2Br4 *2H2O, GdCl3, or PdFe. None of these materials are suitable for EXACT, which will explore the region of the He-3/He-4 tricritical point at 0.87 K. The experiment requirements and properties of several candidate paramagnetic materials will be presented, as well as preliminary test results.

  4. High temperature and high resolution uv photoelectron spectroscopy using supersonic molecular beams

    International Nuclear Information System (INIS)

    Wang, Lai-Sheng; Reutt-Robey, J.E.; Niu, B.; Lee, Y.T.; Shirley, D.A.

    1989-07-01

    A high temperature molecular beam source with electron bombardment heating has been built for high resolution photoelectron spectroscopic studies of high temperature species and clusters. This source has the advantages of: producing an intense, continuous, seeded molecular beam, eliminating the interference of the heating mechanism from the photoelectron measurement. Coupling the source with our hemispherical electron energy analyzer, we can obtain very high resolution HeIα (584 angstrom) photoelectron spectra of high temperature species. Vibrationally-resolved photoelectron spectra of PbSe, As 2 , As 4 , and ZnCl 2 are shown to demonstrate the performance of the new source. 25 refs., 8 figs., 1 tab

  5. Ribbon scanning confocal for high-speed high-resolution volume imaging of brain.

    Directory of Open Access Journals (Sweden)

    Alan M Watson

    Full Text Available Whole-brain imaging is becoming a fundamental means of experimental insight; however, achieving subcellular resolution imagery in a reasonable time window has not been possible. We describe the first application of multicolor ribbon scanning confocal methods to collect high-resolution volume images of chemically cleared brains. We demonstrate that ribbon scanning collects images over ten times faster than conventional high speed confocal systems but with equivalent spectral and spatial resolution. Further, using this technology, we reconstruct large volumes of mouse brain infected with encephalitic alphaviruses and demonstrate that regions of the brain with abundant viral replication were inaccessible to vascular perfusion. This reveals that the destruction or collapse of large regions of brain micro vasculature may contribute to the severe disease caused by Venezuelan equine encephalitis virus. Visualization of this fundamental impact of infection would not be possible without sampling at subcellular resolution within large brain volumes.

  6. High resolution tsunami inversion for 2010 Chile earthquake

    Directory of Open Access Journals (Sweden)

    T.-R. Wu

    2011-12-01

    Full Text Available We investigate the feasibility of inverting high-resolution vertical seafloor displacement from tsunami waveforms. An inversion method named "SUTIM" (small unit tsunami inversion method is developed to meet this goal. In addition to utilizing the conventional least-square inversion, this paper also enhances the inversion resolution by Grid-Shifting method. A smooth constraint is adopted to gain stability. After a series of validation and performance tests, SUTIM is used to study the 2010 Chile earthquake. Based upon data quality and azimuthal distribution, we select tsunami waveforms from 6 GLOSS stations and 1 DART buoy record. In total, 157 sub-faults are utilized for the high-resolution inversion. The resolution reaches 10 sub-faults per wavelength. The result is compared with the distribution of the aftershocks and waveforms at each gauge location with very good agreement. The inversion result shows that the source profile features a non-uniform distribution of the seafloor displacement. The highly elevated vertical seafloor is mainly concentrated in two areas: one is located in the northern part of the epicentre, between 34° S and 36° S; the other is in the southern part, between 37° S and 38° S.

  7. High resolution tsunami inversion for 2010 Chile earthquake

    Science.gov (United States)

    Wu, T.-R.; Ho, T.-C.

    2011-12-01

    We investigate the feasibility of inverting high-resolution vertical seafloor displacement from tsunami waveforms. An inversion method named "SUTIM" (small unit tsunami inversion method) is developed to meet this goal. In addition to utilizing the conventional least-square inversion, this paper also enhances the inversion resolution by Grid-Shifting method. A smooth constraint is adopted to gain stability. After a series of validation and performance tests, SUTIM is used to study the 2010 Chile earthquake. Based upon data quality and azimuthal distribution, we select tsunami waveforms from 6 GLOSS stations and 1 DART buoy record. In total, 157 sub-faults are utilized for the high-resolution inversion. The resolution reaches 10 sub-faults per wavelength. The result is compared with the distribution of the aftershocks and waveforms at each gauge location with very good agreement. The inversion result shows that the source profile features a non-uniform distribution of the seafloor displacement. The highly elevated vertical seafloor is mainly concentrated in two areas: one is located in the northern part of the epicentre, between 34° S and 36° S; the other is in the southern part, between 37° S and 38° S.

  8. Concept for a new high resolution high intensity diffractometer

    Energy Technology Data Exchange (ETDEWEB)

    Stuhr, U [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-09-01

    A concept of a new time-of-flight powder-diffractometer for a thermal neutral beam tube at SINQ is presented. The design of the instrument optimises the contradictory conditions of high intensity and high resolution. The high intensity is achieved by using many neutron pulses simultaneously. By analysing the time-angle-pattern of the detected neutrons an assignment of the neutrons to a single pulse is possible. (author) 3 figs., tab., refs.

  9. Volumetric expiratory high-resolution CT of the lung

    International Nuclear Information System (INIS)

    Nishino, Mizuki; Hatabu, Hiroto

    2004-01-01

    We developed a volumetric expiratory high-resolution CT (HRCT) protocol that provides combined inspiratory and expiratory volumetric imaging of the lung without increasing radiation exposure, and conducted a preliminary feasibility assessment of this protocol to evaluate diffuse lung disease with small airway abnormalities. The volumetric expiratory high-resolution CT increased the detectability of the conducting airway to the areas of air trapping (P<0.0001), and added significant information about extent and distribution of air trapping (P<0.0001)

  10. Developing Visual Editors for High-Resolution Haptic Patterns

    DEFF Research Database (Denmark)

    Cuartielles, David; Göransson, Andreas; Olsson, Tony

    2012-01-01

    In this article we give an overview of our iterative work in developing visual editors for creating high resolution haptic patterns to be used in wearable, haptic feedback devices. During the past four years we have found the need to address the question of how to represent, construct and edit high...... resolution haptic patterns so that they translate naturally to the user’s haptic experience. To solve this question we have developed and tested several visual editors...

  11. High resolution SETI: Experiences and prospects

    Science.gov (United States)

    Horowitz, Paul; Clubok, Ken

    Megachannel spectroscopy with sub-Hertz resolution constitutes an attractive strategy for a microwave search for extraterrestrial intelligence (SETI), assuming the transmission of a narrowband radiofrequency beacon. Such resolution matches the properties of the interstellar medium, and the necessary Doppler corrections provide a high degree of interference rejection. We have constructed a frequency-agile receiver with an FFT-based 8 megachannel digital spectrum analyzer, on-line signal recognition, and multithreshold archiving. We are using it to conduct a meridian transit search of the northern sky at the Harvard-Smithsonian 26-m antenna, with a second identical system scheduled to begin observations in Argentina this month. Successive 400 kHz spectra, at 0.05 Hz resolution, are searched for features characteristic of an intentional narrowband beacon transmission. These spectra are centered on guessable frequencies (such as λ21 cm), referenced successively to the local standard of rest, the galactic barycenter, and the cosmic blackbody rest frame. This search has rejected interference admirably, but is greatly limited both in total frequency coverage and sensitivity to signals other than carriers. We summarize five years of high resolution SETI at Harvard, in the context of answering the questions "How useful is narrowband SETI, how serious are its limitations, what can be done to circumvent them, and in what direction should SETI evolve?" Increasingly powerful signal processing hardware, combined with ever-higher memory densities, are particularly relevant, permitting the construction of compact and affordable gigachannel spectrum analyzers covering hundreds of megahertz of instantaneous bandwidth.

  12. The high-resolution regional reanalysis COSMO-REA6

    Science.gov (United States)

    Ohlwein, C.

    2016-12-01

    Reanalyses gain more and more importance as a source of meteorological information for many purposes and applications. Several global reanalyses projects (e.g., ERA, MERRA, CSFR, JMA9) produce and verify these data sets to provide time series as long as possible combined with a high data quality. Due to a spatial resolution down to 50-70km and 3-hourly temporal output, they are not suitable for small scale problems (e.g., regional climate assessment, meso-scale NWP verification, input for subsequent models such as river runoff simulations). The implementation of regional reanalyses based on a limited area model along with a data assimilation scheme is able to generate reanalysis data sets with high spatio-temporal resolution. Within the Hans-Ertel-Centre for Weather Research (HErZ), the climate monitoring branch concentrates efforts on the assessment and analysis of regional climate in Germany and Europe. In joint cooperation with DWD (German Meteorological Service), a high-resolution reanalysis system based on the COSMO model has been developed. The regional reanalysis for Europe matches the domain of the CORDEX EURO-11 specifications, albeit at a higher spatial resolution, i.e., 0.055° (6km) instead of 0.11° (12km) and comprises the assimilation of observational data using the existing nudging scheme of COSMO complemented by a special soil moisture analysis with boundary conditions provided by ERA-Interim data. The reanalysis data set covers the past 20 years. Extensive evaluation of the reanalysis is performed using independent observations with special emphasis on precipitation and high-impact weather situations indicating a better representation of small scale variability. Further, the evaluation shows an added value of the regional reanalysis with respect to the forcing ERA Interim reanalysis and compared to a pure high-resolution dynamical downscaling approach without data assimilation.

  13. SRS station 16.3: high-resolution applications

    CERN Document Server

    Murphy, B M; Golshan, M; Moore, M; Reid, J; Kowalski, G

    2001-01-01

    Station 16.3 is a high-resolution X-ray diffraction beamline at Daresbury Laboratory Synchrotron Radiation Source. The data presented demonstrate the high-resolution available on the station utilising the recently commissioned four-reflection Si 1 1 1 monochromator and three-reflection Si 1 1 1 analyser. For comparison, a reciprocal space map of the two-bounce Si 1 1 1 monochromator and two-bounce analyser is also shown. Operation of the station is illustrated with examples for silicon, and for diamond. Lattice parameter variations were measured with accuracies in the part per million range and lattice tilts at the arc second level (DuMond, Phys. Rev. 52 (1937) 872).

  14. High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

    Science.gov (United States)

    Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

    2013-11-01

    Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

  15. Resolution-recovery-embedded image reconstruction for a high-resolution animal SPECT system.

    Science.gov (United States)

    Zeraatkar, Navid; Sajedi, Salar; Farahani, Mohammad Hossein; Arabi, Hossein; Sarkar, Saeed; Ghafarian, Pardis; Rahmim, Arman; Ay, Mohammad Reza

    2014-11-01

    The small-animal High-Resolution SPECT (HiReSPECT) is a dedicated dual-head gamma camera recently designed and developed in our laboratory for imaging of murine models. Each detector is composed of an array of 1.2 × 1.2 mm(2) (pitch) pixelated CsI(Na) crystals. Two position-sensitive photomultiplier tubes (H8500) are coupled to each head's crystal. In this paper, we report on a resolution-recovery-embedded image reconstruction code applicable to the system and present the experimental results achieved using different phantoms and mouse scans. Collimator-detector response functions (CDRFs) were measured via a pixel-driven method using capillary sources at finite distances from the head within the field of view (FOV). CDRFs were then fitted by independent Gaussian functions. Thereafter, linear interpolations were applied to the standard deviation (σ) values of the fitted Gaussians, yielding a continuous map of CDRF at varying distances from the head. A rotation-based maximum-likelihood expectation maximization (MLEM) method was used for reconstruction. A fast rotation algorithm was developed to rotate the image matrix according to the desired angle by means of pre-generated rotation maps. The experiments demonstrated improved resolution utilizing our resolution-recovery-embedded image reconstruction. While the full-width at half-maximum (FWHM) radial and tangential resolution measurements of the system were over 2 mm in nearly all positions within the FOV without resolution recovery, reaching around 2.5 mm in some locations, they fell below 1.8 mm everywhere within the FOV using the resolution-recovery algorithm. The noise performance of the system was also acceptable; the standard deviation of the average counts per voxel in the reconstructed images was 6.6% and 8.3% without and with resolution recovery, respectively. Copyright © 2014 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  16. High-resolution electron microscopy of advanced materials

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, T.E.; Kung, H.H.; Sickafus, K.E.; Gray, G.T. III; Field, R.D.; Smith, J.F. [Los Alamos National Lab., NM (United States). Materials Science and Technology Div.

    1997-11-01

    This final report chronicles a three-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The High-Resolution Electron Microscopy Facility has doubled in size and tripled in quality since the beginning of the three-year period. The facility now includes a field-emission scanning electron microscope, a 100 kV field-emission scanning transmission electron microscope (FE-STEM), a 300 kV field-emission high-resolution transmission electron microscope (FE-HRTEM), and a 300 kV analytical transmission electron microscope. A new orientation imaging microscope is being installed. X-ray energy dispersive spectrometers for chemical analysis are available on all four microscopes; parallel electron energy loss spectrometers are operational on the FE-STEM and FE-HRTEM. These systems enable evaluation of local atomic bonding, as well as chemical composition in nanometer-scale regions. The FE-HRTEM has a point-to-point resolution of 1.6 {angstrom}, but the resolution can be pushed to its information limit of 1 {angstrom} by computer reconstruction of a focal series of images. HRTEM has been used to image the atomic structure of defects such as dislocations, grain boundaries, and interfaces in a variety of materials from superconductors and ferroelectrics to structural ceramics and intermetallics.

  17. High Resolution PET with 250 micrometer LSO Detectors and Adaptive Zoom

    International Nuclear Information System (INIS)

    Cherry, Simon R.; Qi, Jinyi

    2012-01-01

    There have been impressive improvements in the performance of small-animal positron emission tomography (PET) systems since their first development in the mid 1990s, both in terms of spatial resolution and sensitivity, which have directly contributed to the increasing adoption of this technology for a wide range of biomedical applications. Nonetheless, current systems still are largely dominated by the size of the scintillator elements used in the detector. Our research predicts that developing scintillator arrays with an element size of 250 (micro)m or smaller will lead to an image resolution of 500 (micro)m when using 18F- or 64Cu-labeled radiotracers, giving a factor of 4-8 improvement in volumetric resolution over the highest resolution research systems currently in existence. This proposal had two main objectives: (i) To develop and evaluate much higher resolution and efficiency scintillator arrays that can be used in the future as the basis for detectors in a small-animal PET scanner where the spatial resolution is dominated by decay and interaction physics rather than detector size. (ii) To optimize one such high resolution, high sensitivity detector and adaptively integrate it into the existing microPET II small animal PET scanner as a 'zoom-in' detector that provides higher spatial resolution and sensitivity in a limited region close to the detector face. The knowledge gained from this project will provide valuable information for building future PET systems with a complete ring of very high-resolution detector arrays and also lay the foundations for utilizing high-resolution detectors in combination with existing PET systems for localized high-resolution imaging.

  18. Achieving High Resolution Timer Events in Virtualized Environment.

    Science.gov (United States)

    Adamczyk, Blazej; Chydzinski, Andrzej

    2015-01-01

    Virtual Machine Monitors (VMM) have become popular in different application areas. Some applications may require to generate the timer events with high resolution and precision. This however may be challenging due to the complexity of VMMs. In this paper we focus on the timer functionality provided by five different VMMs-Xen, KVM, Qemu, VirtualBox and VMWare. Firstly, we evaluate resolutions and precisions of their timer events. Apparently, provided resolutions and precisions are far too low for some applications (e.g. networking applications with the quality of service). Then, using Xen virtualization we demonstrate the improved timer design that greatly enhances both the resolution and precision of achieved timer events.

  19. Whole genome DNA copy number changes identified by high density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Huang Jing

    2004-05-01

    Full Text Available Abstract Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs. Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA, to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM and mismatch (MM probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number

  20. Compact and high-resolution optical orbital angular momentum sorter

    Directory of Open Access Journals (Sweden)

    Chenhao Wan

    2017-03-01

    Full Text Available A compact and high-resolution optical orbital angular momentum (OAM sorter is proposed and demonstrated. The sorter comprises a quadratic fan-out mapper and a dual-phase corrector positioned in the pupil plane and the Fourier plane, respectively. The optical system is greatly simplified compared to previous demonstrations of OAM sorting, and the performance in resolution and efficiency is maintained. A folded configuration is set up using a single reflective spatial light modulator (SLM to demonstrate the validity of the scheme. The two phase elements are implemented on the left and right halves of the SLM and connected by a right-angle prism. Experimental results demonstrate the high resolution of the compact OAM sorter, and the current limit in efficiency can be overcome by replacing with transmissive SLMs and removing the beam splitters. This novel scheme paves the way for the miniaturization and integration of high-resolution OAM sorters.

  1. Lipofection: A Highly Efficient, Lipid-Mediated DNA-Transfection Procedure

    Science.gov (United States)

    Felgner, Philip L.; Gadek, Thomas R.; Holm, Marilyn; Roman, Richard; Chan, Hardy W.; Wenz, Michael; Northrop, Jeffrey P.; Ringold, Gordon M.; Danielsen, Mark

    1987-11-01

    A DNA-transfection protocol has been developed that makes use of a synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Small unilamellar liposomes containing DOTMA interact spontaneously with DNA to form lipid-DNA complexes with 100% entrapment of the DNA. DOTMA facilitates fusion of the complex with the plasma membrane of tissue culture cells, resulting in both uptake and expression of the DNA. The technique is simple, highly reproducible, and effective for both transient and stable expression of transfected DNA. Depending upon the cell line, lipofection is from 5- to >100-fold more effective than either the calcium phosphate or the DEAE-dextran transfection technique.

  2. High-Throughput DNA sequencing of ancient wood.

    Science.gov (United States)

    Wagner, Stefanie; Lagane, Frédéric; Seguin-Orlando, Andaine; Schubert, Mikkel; Leroy, Thibault; Guichoux, Erwan; Chancerel, Emilie; Bech-Hebelstrup, Inger; Bernard, Vincent; Billard, Cyrille; Billaud, Yves; Bolliger, Matthias; Croutsch, Christophe; Čufar, Katarina; Eynaud, Frédérique; Heussner, Karl Uwe; Köninger, Joachim; Langenegger, Fabien; Leroy, Frédéric; Lima, Christine; Martinelli, Nicoletta; Momber, Garry; Billamboz, André; Nelle, Oliver; Palomo, Antoni; Piqué, Raquel; Ramstein, Marianne; Schweichel, Roswitha; Stäuble, Harald; Tegel, Willy; Terradas, Xavier; Verdin, Florence; Plomion, Christophe; Kremer, Antoine; Orlando, Ludovic

    2018-03-01

    Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management. © 2018 John Wiley & Sons Ltd.

  3. High resolution manometry findings in patients with esophageal epiphrenic diverticula.

    Science.gov (United States)

    Vicentine, Fernando P P; Herbella, Fernando A M; Silva, Luciana C; Patti, Marco G

    2011-12-01

    The pathophysiology of esophageal epiphrenic diverticula is still uncertain even though a concomitant motility disorder is found in the majority of patients in different series. High resolution manometry may allow detection of motor abnormalities in a higher number of patients with esophageal epiphrenic diverticula compared with conventional manometry. This study aims to evaluate the high resolution manometry findings in patients with esophageal epiphrenic diverticula. Nine individuals (mean age 63 ± 10 years, 4 females) with esophageal epiphrenic diverticula underwent high resolution manometry. A single diverticulum was observed in eight patients and multiple diverticula in one. Visual analysis of conventional tracings and color pressure plots for identification of segmental abnormalities was performed by two researchers experienced in high resolution manometry. Upper esophageal sphincter was normal in all patients. Esophageal body was abnormal in eight patients; lower esophageal sphincter was abnormal in seven patients. Named esophageal motility disorders were found in seven patients: achalasia in six, diffuse esophageal spasm in one. In one patient, a segmental hypercontractile zone was noticed with pressure of 196 mm Hg. High resolution manometry demonstrated motor abnormalities in all patients with esophageal epiphrenic diverticula.

  4. Constraining Stochastic Parametrisation Schemes Using High-Resolution Model Simulations

    Science.gov (United States)

    Christensen, H. M.; Dawson, A.; Palmer, T.

    2017-12-01

    Stochastic parametrisations are used in weather and climate models as a physically motivated way to represent model error due to unresolved processes. Designing new stochastic schemes has been the target of much innovative research over the last decade. While a focus has been on developing physically motivated approaches, many successful stochastic parametrisation schemes are very simple, such as the European Centre for Medium-Range Weather Forecasts (ECMWF) multiplicative scheme `Stochastically Perturbed Parametrisation Tendencies' (SPPT). The SPPT scheme improves the skill of probabilistic weather and seasonal forecasts, and so is widely used. However, little work has focused on assessing the physical basis of the SPPT scheme. We address this matter by using high-resolution model simulations to explicitly measure the `error' in the parametrised tendency that SPPT seeks to represent. The high resolution simulations are first coarse-grained to the desired forecast model resolution before they are used to produce initial conditions and forcing data needed to drive the ECMWF Single Column Model (SCM). By comparing SCM forecast tendencies with the evolution of the high resolution model, we can measure the `error' in the forecast tendencies. In this way, we provide justification for the multiplicative nature of SPPT, and for the temporal and spatial scales of the stochastic perturbations. However, we also identify issues with the SPPT scheme. It is therefore hoped these measurements will improve both holistic and process based approaches to stochastic parametrisation. Figure caption: Instantaneous snapshot of the optimal SPPT stochastic perturbation, derived by comparing high-resolution simulations with a low resolution forecast model.

  5. High-resolution flood modeling of urban areas using MSN_Flood

    Directory of Open Access Journals (Sweden)

    Michael Hartnett

    2017-07-01

    Full Text Available Although existing hydraulic models have been used to simulate and predict urban flooding, most of these models are inadequate due to the high spatial resolution required to simulate flows in urban floodplains. Nesting high-resolution subdomains within coarser-resolution models is an efficient solution for enabling simultaneous calculation of flooding due to tides, surges, and high river flows. MSN_Flood has been developed to incorporate moving boundaries around nested domains, permitting alternate flooding and drying along the boundary and in the interior of the domain. Ghost cells adjacent to open boundary cells convert open boundaries, in effect, into internal boundaries. The moving boundary may be multi-segmented and non-continuous, with recirculating flow across the boundary. When combined with a bespoke adaptive interpolation scheme, this approach facilitates a dynamic internal boundary. Based on an alternating-direction semi-implicit finite difference scheme, MSN_Flood was used to hindcast a major flood event in Cork City resulting from the combined pressures of fluvial, tidal, and storm surge processes. The results show that the model is computationally efficient, as the 2-m high-resolution nest is used only in the urban flooded region. Elsewhere, lower-resolution nests are used. The results also show that the model is highly accurate when compared with measured data. The model is capable of incorporating nested sub-domains when the nested boundary is multi-segmented and highly complex with lateral gradients of elevation and velocities. This is a major benefit when modelling urban floodplains at very high resolution.

  6. Reproducible high-resolution multispectral image acquisition in dermatology

    Science.gov (United States)

    Duliu, Alexandru; Gardiazabal, José; Lasser, Tobias; Navab, Nassir

    2015-07-01

    Multispectral image acquisitions are increasingly popular in dermatology, due to their improved spectral resolution which enables better tissue discrimination. Most applications however focus on restricted regions of interest, imaging only small lesions. In this work we present and discuss an imaging framework for high-resolution multispectral imaging on large regions of interest.

  7. High Resolution Energetic X-ray Imager (HREXI)

    Science.gov (United States)

    Grindlay, Jonathan

    We propose to design and build the first imaging hard X-ray detector system that incorporates 3D stacking of closely packed detector readouts in finely-spaced imaging arrays with their required data processing and control electronics. In virtually all imaging astronomical detectors, detector readout is done with flex connectors or connections that are not vertical but rather horizontal , requiring loss of focal plane area. For high resolution pixel detectors needed for high speed event-based X-ray imaging, from low energy applications (CMOS) with focusing X-ray telescopes, to hard X-ray applications with pixelated CZT for large area coded aperture telescopes, this new detector development offers great promise. We propose to extend our previous and current APRA supported ProtoEXIST program that has developed the first large area imaging CZT detectors and demonstrated their astrophysical capabilities on two successful balloon flight to a next generation High Resolution Energetic X-ray Imager (HREXI), which would incorporate microvia technology for the first time to connect the readout ASIC on each CZT crystal directly to its control and data processing system. This 3-dimensional stacking of detector and readout/control system means that large area (>2m2) imaging detector planes for a High Resolution Wide-field hard X-ray telescope can be built with initially greatly reduced detector gaps and ultimately with no gaps. This increases detector area, efficiency, and simplicity of detector integration. Thus higher sensitivity wide-field imagers will be possible at lower cost. HREXI will enable a post-Swift NASA mission such as the EREXS concept proposed to PCOS to be conducted as a future MIDEX mission. This mission would conduct a high resolution (<2 arcmin) , broad band (5 200 keV) hard X-ray survey of black holes on all scales with ~10X higher sensitivity than Swift. In the current era of Time Domain Astrophysics, such a survey capability, in conjunction with a n

  8. 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.

  9. 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.

  10. High-resolution investigations of edge effects in neutron imaging

    International Nuclear Information System (INIS)

    Strobl, M.; Kardjilov, N.; Hilger, A.; Kuehne, G.; Frei, G.; Manke, I.

    2009-01-01

    Edge enhancement is the main effect measured by the so-called inline or propagation-based neutron phase contrast imaging method. The effect has originally been explained by diffraction, and high spatial coherence has been claimed to be a necessary precondition. However, edge enhancement has also been found in conventional imaging with high resolution. In such cases the effects can produce artefacts and hinder quantification. In this letter the edge effects at cylindrical shaped samples and long straight edges have been studied in detail. The enhancement can be explained by refraction and total reflection. Using high-resolution imaging, where spatial resolutions better than 50 μm could be achieved, refraction and total reflection peaks - similar to diffraction patterns - could be separated and distinguished.

  11. High-Resolution Adaptive Optics Test-Bed for Vision Science

    International Nuclear Information System (INIS)

    Wilks, S.C.; Thomspon, C.A.; Olivier, S.S.; Bauman, B.J.; Barnes, T.; Werner, J.S.

    2001-01-01

    We discuss the design and implementation of a low-cost, high-resolution adaptive optics test-bed for vision research. It is well known that high-order aberrations in the human eye reduce optical resolution and limit visual acuity. However, the effects of aberration-free eyesight on vision are only now beginning to be studied using adaptive optics to sense and correct the aberrations in the eye. We are developing a high-resolution adaptive optics system for this purpose using a Hamamatsu Parallel Aligned Nematic Liquid Crystal Spatial Light Modulator. Phase-wrapping is used to extend the effective stroke of the device, and the wavefront sensing and wavefront correction are done at different wavelengths. Issues associated with these techniques will be discussed

  12. DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle

    OpenAIRE

    Mikheikin, Andrey; Olsen, Anita; Leslie, Kevin; Russell-Pavier, Freddie; Yacoot, Andrew; Picco, Loren; Payton, Oliver; Toor, Amir; Chesney, Alden; Gimzewski, James K.; Mishra, Bud; Reed, Jason

    2017-01-01

    Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of usin...

  13. Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling

    Science.gov (United States)

    Velez, Daniel Ortiz; Mack, Hannah; Jupe, Julietta; Hawker, Sinead; Kulkarni, Ninad; Hedayatnia, Behnam; Zhang, Yang; Lawrence, Shelley; Fraley, Stephanie I.

    2017-02-01

    In clinical diagnostics and pathogen detection, profiling of complex samples for low-level genotypes represents a significant challenge. Advances in speed, sensitivity, and extent of multiplexing of molecular pathogen detection assays are needed to improve patient care. We report the development of an integrated platform enabling the identification of bacterial pathogen DNA sequences in complex samples in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal PCR amplification, High Resolution Melting (HRM), and machine learning within 20,000 picoliter scale reactions, simultaneously. Clinically relevant concentrations of bacterial DNA molecules are separated by digitization across 20,000 reactions and amplified with universal primers targeting the bacterial 16S gene. Amplification is followed by HRM sequence fingerprinting in all reactions, simultaneously. The resulting bacteria-specific melt curves are identified by Support Vector Machine learning, and individual pathogen loads are quantified. The platform reduces reaction volumes by 99.995% and achieves a greater than 200-fold increase in dynamic range of detection compared to traditional PCR HRM approaches. Type I and II error rates are reduced by 99% and 100% respectively, compared to intercalating dye-based digital PCR (dPCR) methods. This technology could impact a number of quantitative profiling applications, especially infectious disease diagnostics.

  14. Ultra-high resolution AMOLED

    Science.gov (United States)

    Wacyk, Ihor; Prache, Olivier; Ghosh, Amal

    2011-06-01

    AMOLED microdisplays continue to show improvement in resolution and optical performance, enhancing their appeal for a broad range of near-eye applications such as night vision, simulation and training, situational awareness, augmented reality, medical imaging, and mobile video entertainment and gaming. eMagin's latest development of an HDTV+ resolution technology integrates an OLED pixel of 3.2 × 9.6 microns in size on a 0.18 micron CMOS backplane to deliver significant new functionality as well as the capability to implement a 1920×1200 microdisplay in a 0.86" diagonal area. In addition to the conventional matrix addressing circuitry, the HDTV+ display includes a very lowpower, low-voltage-differential-signaling (LVDS) serialized interface to minimize cable and connector size as well as electromagnetic emissions (EMI), an on-chip set of look-up-tables for digital gamma correction, and a novel pulsewidth- modulation (PWM) scheme that together with the standard analog control provides a total dimming range of 0.05cd/m2 to 2000cd/m2 in the monochrome version. The PWM function also enables an impulse drive mode of operation that significantly reduces motion artifacts in high speed scene changes. An internal 10-bit DAC ensures that a full 256 gamma-corrected gray levels are available across the entire dimming range, resulting in a measured dynamic range exceeding 20-bits. This device has been successfully tested for operation at frame rates ranging from 30Hz up to 85Hz. This paper describes the operational features and detailed optical and electrical test results for the new AMOLED WUXGA resolution microdisplay.

  15. Generalized Nonlinear Chirp Scaling Algorithm for High-Resolution Highly Squint SAR Imaging.

    Science.gov (United States)

    Yi, Tianzhu; He, Zhihua; He, Feng; Dong, Zhen; Wu, Manqing

    2017-11-07

    This paper presents a modified approach for high-resolution, highly squint synthetic aperture radar (SAR) data processing. Several nonlinear chirp scaling (NLCS) algorithms have been proposed to solve the azimuth variance of the frequency modulation rates that are caused by the linear range walk correction (LRWC). However, the azimuth depth of focusing (ADOF) is not handled well by these algorithms. The generalized nonlinear chirp scaling (GNLCS) algorithm that is proposed in this paper uses the method of series reverse (MSR) to improve the ADOF and focusing precision. It also introduces a high order processing kernel to avoid the range block processing. Simulation results show that the GNLCS algorithm can enlarge the ADOF and focusing precision for high-resolution highly squint SAR data.

  16. Generalized Nonlinear Chirp Scaling Algorithm for High-Resolution Highly Squint SAR Imaging

    Directory of Open Access Journals (Sweden)

    Tianzhu Yi

    2017-11-01

    Full Text Available This paper presents a modified approach for high-resolution, highly squint synthetic aperture radar (SAR data processing. Several nonlinear chirp scaling (NLCS algorithms have been proposed to solve the azimuth variance of the frequency modulation rates that are caused by the linear range walk correction (LRWC. However, the azimuth depth of focusing (ADOF is not handled well by these algorithms. The generalized nonlinear chirp scaling (GNLCS algorithm that is proposed in this paper uses the method of series reverse (MSR to improve the ADOF and focusing precision. It also introduces a high order processing kernel to avoid the range block processing. Simulation results show that the GNLCS algorithm can enlarge the ADOF and focusing precision for high-resolution highly squint SAR data.

  17. Human enamel structure studied by high resolution electron microscopy

    International Nuclear Information System (INIS)

    Wen, S.L.

    1989-01-01

    Human enamel structural features are characterized by high resolution electron microscopy. The human enamel consists of polycrystals with a structure similar to Ca10(PO4)6(OH)2. This article describes the structural features of human enamel crystal at atomic and nanometer level. Besides the structural description, a great number of high resolution images are included. Research into the carious process in human enamel is very important for human beings. This article firstly describes the initiation of caries in enamel crystal at atomic and unit-cell level and secondly describes the further steps of caries with structural and chemical demineralization. The demineralization in fact, is the origin of caries in human enamel. The remineralization of carious areas in human enamel has drawn more and more attention as its potential application is realized. This process has been revealed by high resolution electron microscopy in detail in this article. On the other hand, the radiation effects on the structure of human enamel are also characterized by high resolution electron microscopy. In order to reveal this phenomenon clearly, a great number of electron micrographs have been shown, and a physical mechanism is proposed. 26 references

  18. Refinement procedure for the image alignment in high-resolution electron tomography

    International Nuclear Information System (INIS)

    Houben, L.; Bar Sadan, M.

    2011-01-01

    High-resolution electron tomography from a tilt series of transmission electron microscopy images requires an accurate image alignment procedure in order to maximise the resolution of the tomogram. This is the case in particular for ultra-high resolution where even very small misalignments between individual images can dramatically reduce the fidelity of the resultant reconstruction. A tomographic-reconstruction based and marker-free method is proposed, which uses an iterative optimisation of the tomogram resolution. The method utilises a search algorithm that maximises the contrast in tomogram sub-volumes. Unlike conventional cross-correlation analysis it provides the required correlation over a large tilt angle separation and guarantees a consistent alignment of images for the full range of object tilt angles. An assessment based on experimental reconstructions shows that the marker-free procedure is competitive to the reference of marker-based procedures at lower resolution and yields sub-pixel accuracy even for simulated high-resolution data. -- Highlights: → Alignment procedure for electron tomography based on iterative tomogram contrast optimisation. → Marker-free, independent of object, little user interaction. → Accuracy competitive with fiducial marker methods and suited for high-resolution tomography.

  19. High resolution backscattering instruments

    International Nuclear Information System (INIS)

    Coldea, R.

    2001-01-01

    The principle of operation of indirect-geometry time-of-flight spectrometers are presented, including the IRIS at the ISIS spallation neutron source. The key features that make those types of spectrometers ideally suited for low-energy spectroscopy are: high energy resolution over a wide dynamic range, and simultaneous measurement over a large momentum transfer range provided by the wide angular detector coverage. To exemplify these features are discussed of single-crystal experiments of the spin dynamics in the two-dimensional frustrated quantum magnet Cs 2 CuCl 4 . (R.P.)

  20. Using Adobe Acrobat to create high-resolution line art images.

    Science.gov (United States)

    Woo, Hyoun Sik; Lee, Jeong Min

    2009-08-01

    The purpose of this article is to introduce a method for using Adobe Acrobat to make high-resolution and high-quality line art images. High-resolution and high-quality line art images for radiology journal submission can be generated using Adobe Acrobat as a steppingstone, and the customized PDF conversion settings can be used for converting hybrid images, including both bitmap and vector components.

  1. High-resolution axial MR imaging of tibial stress injuries

    Directory of Open Access Journals (Sweden)

    Mammoto Takeo

    2012-05-01

    Full Text Available Abstract Purpose To evaluate the relative involvement of tibial stress injuries using high-resolution axial MR imaging and the correlation with MR and radiographic images. Methods A total of 33 patients with exercise-induced tibial pain were evaluated. All patients underwent radiograph and high-resolution axial MR imaging. Radiographs were taken at initial presentation and 4 weeks later. High-resolution MR axial images were obtained using a microscopy surface coil with 60 × 60 mm field of view on a 1.5T MR unit. All images were evaluated for abnormal signals of the periosteum, cortex and bone marrow. Results Nineteen patients showed no periosteal reaction at initial and follow-up radiographs. MR imaging showed abnormal signals in the periosteal tissue and partially abnormal signals in the bone marrow. In 7 patients, periosteal reaction was not seen at initial radiograph, but was detected at follow-up radiograph. MR imaging showed abnormal signals in the periosteal tissue and entire bone marrow. Abnormal signals in the cortex were found in 6 patients. The remaining 7 showed periosteal reactions at initial radiograph. MR imaging showed abnormal signals in the periosteal tissue in 6 patients. Abnormal signals were seen in the partial and entire bone marrow in 4 and 3 patients, respectively. Conclusions Bone marrow abnormalities in high-resolution axial MR imaging were related to periosteal reactions at follow-up radiograph. Bone marrow abnormalities might predict later periosteal reactions, suggesting shin splints or stress fractures. High-resolution axial MR imaging is useful in early discrimination of tibial stress injuries.

  2. High-resolution axial MR imaging of tibial stress injuries

    Science.gov (United States)

    2012-01-01

    Purpose To evaluate the relative involvement of tibial stress injuries using high-resolution axial MR imaging and the correlation with MR and radiographic images. Methods A total of 33 patients with exercise-induced tibial pain were evaluated. All patients underwent radiograph and high-resolution axial MR imaging. Radiographs were taken at initial presentation and 4 weeks later. High-resolution MR axial images were obtained using a microscopy surface coil with 60 × 60 mm field of view on a 1.5T MR unit. All images were evaluated for abnormal signals of the periosteum, cortex and bone marrow. Results Nineteen patients showed no periosteal reaction at initial and follow-up radiographs. MR imaging showed abnormal signals in the periosteal tissue and partially abnormal signals in the bone marrow. In 7 patients, periosteal reaction was not seen at initial radiograph, but was detected at follow-up radiograph. MR imaging showed abnormal signals in the periosteal tissue and entire bone marrow. Abnormal signals in the cortex were found in 6 patients. The remaining 7 showed periosteal reactions at initial radiograph. MR imaging showed abnormal signals in the periosteal tissue in 6 patients. Abnormal signals were seen in the partial and entire bone marrow in 4 and 3 patients, respectively. Conclusions Bone marrow abnormalities in high-resolution axial MR imaging were related to periosteal reactions at follow-up radiograph. Bone marrow abnormalities might predict later periosteal reactions, suggesting shin splints or stress fractures. High-resolution axial MR imaging is useful in early discrimination of tibial stress injuries. PMID:22574840

  3. Single-cell manipulation and DNA delivery technology using atomic force microscopy and nanoneedle.

    Science.gov (United States)

    Han, Sung-Woong; Nakamura, Chikashi; Miyake, Jun; Chang, Sang-Mok; Adachi, Taiji

    2014-01-01

    The recent single-cell manipulation technology using atomic force microscopy (AFM) not only allows high-resolution visualization and probing of biomolecules and cells but also provides spatial and temporal access to the interior of living cells via the nanoneedle technology. Here we review the development and application of single-cell manipulations and the DNA delivery technology using a nanoneedle. We briefly describe various DNA delivery methods and discuss their advantages and disadvantages. Fabrication of the nanoneedle, visualization of nanoneedle insertion into living cells, DNA modification on the nanoneedle surface, and the invasiveness of nanoneedle insertion into living cells are described. Different methods of DNA delivery into a living cell, such as lipofection, microinjection, and nanoneedles, are then compared. Finally, single-cell diagnostics using the nanoneedle and the perspectives of the nanoneedle technology are outlined. The nanoneedle-based DNA delivery technology provides new opportunities for efficient and specific introduction of DNA and other biomolecules into precious living cells with a high spatial resolution within a desired time frame. This technology has the potential to be applied for many basic cellular studies and for clinical studies such as single-cell diagnostics.

  4. High-resolution esophageal pressure topography for esophageal motility disorders

    OpenAIRE

    Hashem Fakhre Yaseri; Gholamreza Hamsi; Tayeb Ramim

    2016-01-01

    Background: High-resolution manometer (HRM) of the esophagus has become the main diagnostic test in the evaluation of esophageal motility disorders. The development of high-resolution manometry catheters and software displays of manometry recordings in color-coded pressure plots have changed the diagnostic assessment of esophageal disease. The first step of the Chicago classification described abnormal esophagogastric junction deglutitive relaxation. The latest classification system, proposed...

  5. Quantitation of Acrylamide in Foods by High-Resolution Mass Spectrometry

    NARCIS (Netherlands)

    Troise, A.D.; Fogliano, Vincenzo

    2016-01-01

    The use of liquid chromatography high-resolution mass spectrometry (LC-HRMS) and direct analysis real-time high-resolution mass spectrometry (DART-HRMS) defines a new scenario in the analysis of thermal-induced toxicants, such as acrylamide. Several factors contribute to the definition of the

  6. High-spin research with HERA [High Energy-Resolution Array

    International Nuclear Information System (INIS)

    Diamond, R.M.

    1987-06-01

    The topic of this report is high spin research with the High Energy Resolution Array (HERA) at Lawrence Berkeley Laboratory. This is a 21 Ge detector system, the first with bismuth germanate (BGO) Compton suppression. The array is described briefly and some of the results obtained during the past year using this detector facility are discussed. Two types of studies are described: observation of superdeformation in the light Nd isotopes, and rotational damping at high spin and excitation energy in the continuum gamma ray spectrum

  7. Ultra high resolution soft x-ray tomography

    International Nuclear Information System (INIS)

    Haddad, W.S.; Trebes, J.E.; Goodman, D.M.

    1995-01-01

    Ultra high resolution three dimensional images of a microscopic test object were made with soft x-rays using a scanning transmission x-ray microscope. The test object consisted of two different patterns of gold bars on silicon nitride windows that were separated by ∼5μm. A series of nine 2-D images of the object were recorded at angles between -50 to +55 degrees with respect to the beam axis. The projections were then combined tomographically to form a 3-D image by means of an algebraic reconstruction technique (ART) algorithm. A transverse resolution of ∼1000 Angstrom was observed. Artifacts in the reconstruction limited the overall depth resolution to ∼6000 Angstrom, however some features were clearly reconstructed with a depth resolution of ∼1000 Angstrom. A specially modified ART algorithm and a constrained conjugate gradient (CCG) code were also developed as improvements over the standard ART algorithm. Both of these methods made significant improvements in the overall depth resolution bringing it down to ∼1200 Angstrom overall. Preliminary projection data sets were also recorded with both dry and re-hydrated human sperm cells over a similar angular range

  8. Ultra high resolution soft x-ray tomography

    International Nuclear Information System (INIS)

    Haddad, W.S.; Trebes, J.E.; Goodman, D.M.; Lee, H.R.; McNulty, I.; Zalensky, A.O.

    1995-01-01

    Ultra high resolution three dimensional images of a microscopic test object were made with soft x-rays using a scanning transmission x-ray microscope. The test object consisted of two different patterns of gold bars on silicon nitride windows that were separated by ∼5 microm. A series of nine 2-D images of the object were recorded at angles between -50 to +55 degrees with respect to the beam axis. The projections were then combined tomographically to form a 3-D image by means of an algebraic reconstruction technique (ART) algorithm. A transverse resolution of ∼ 1,000 angstrom was observed. Artifacts in the reconstruction limited the overall depth resolution to ∼ 6,000 angstrom, however some features were clearly reconstructed with a depth resolution of ∼ 1,000 angstrom. A specially modified ART algorithm and a constrained conjugate gradient (CCG) code were also developed as improvements over the standard ART algorithm. Both of these methods made significant improvements in the overall depth resolution, bringing it down to ∼ 1,200 angstrom overall. Preliminary projection data sets were also recorded with both dry and re-hydrated human sperm cells over a similar angular range

  9. High-resolution 3D imaging of polymerized photonic crystals by lab-based x-ray nanotomography with 50-nm resolution

    Science.gov (United States)

    Yin, Leilei; Chen, Ying-Chieh; Gelb, Jeff; Stevenson, Darren M.; Braun, Paul A.

    2010-09-01

    High resolution x-ray computed tomography is a powerful non-destructive 3-D imaging method. It can offer superior resolution on objects that are opaque or low contrast for optical microscopy. Synchrotron based x-ray computed tomography systems have been available for scientific research, but remain difficult to access for broader users. This work introduces a lab-based high-resolution x-ray nanotomography system with 50nm resolution in absorption and Zernike phase contrast modes. Using this system, we have demonstrated high quality 3-D images of polymerized photonic crystals which have been analyzed for band gap structures. The isotropic volumetric data shows excellent consistency with other characterization results.

  10. High-resolution nuclear magnetic resonance studies of proteins.

    Science.gov (United States)

    Jonas, Jiri

    2002-03-25

    The combination of advanced high-resolution nuclear magnetic resonance (NMR) techniques with high-pressure capability represents a powerful experimental tool in studies of protein folding. This review is organized as follows: after a general introduction of high-pressure, high-resolution NMR spectroscopy of proteins, the experimental part deals with instrumentation. The main section of the review is devoted to NMR studies of reversible pressure unfolding of proteins with special emphasis on pressure-assisted cold denaturation and the detection of folding intermediates. Recent studies investigating local perturbations in proteins and the experiments following the effects of point mutations on pressure stability of proteins are also discussed. Ribonuclease A, lysozyme, ubiquitin, apomyoglobin, alpha-lactalbumin and troponin C were the model proteins investigated.

  11. High-resolution CT of the lungs: Anatomic-pathologic correlation

    International Nuclear Information System (INIS)

    Stein, M.G.; Webb, W.R.; Finkbeiner, W.; Gamsu, G.

    1986-01-01

    The interpretation of thin-section (1.5-mm), high-resolution CT scans of the lungs has been limited by lack of direct radiologic and pathologic correlation. The author scanned fresh inflated isolated lungs from ten healthy and five diseased subjects using thin-section, high-resolution techniques. The lungs were then fixed by inflation with endobronchial Formalin. Gough sections (1 mm thick) were obtained at the same levels as the CT scans. In healthy subjects, secondary lobules were identified by the presence of visible interlobular septa and central arterioles. In some patients with disease, septal thickening was visible. In patients with honeycombing cystic areas of destroyed lung were seen, along with areas of fibrosis. Emphysema was well evaluated. Thin-section, high-resolution CT can define lung architecture and may resolve mild changes of the interstitium

  12. High-resolution x-ray imaging using a structured scintillator

    Energy Technology Data Exchange (ETDEWEB)

    Hormozan, Yashar, E-mail: hormozan@kth.se; Sychugov, Ilya; Linnros, Jan [Materials and Nano Physics, School of Information and Communication Technology, KTH Royal Institute of Technology, Electrum 229, Kista, Stockholm SE-16440 (Sweden)

    2016-02-15

    Purpose: In this study, the authors introduce a new generation of finely structured scintillators with a very high spatial resolution (a few micrometers) compared to conventional scintillators, yet maintaining a thick absorbing layer for improved detectivity. Methods: Their concept is based on a 2D array of high aspect ratio pores which are fabricated by ICP etching, with spacings (pitches) of a few micrometers, on silicon and oxidation of the pore walls. The pores were subsequently filled by melting of powdered CsI(Tl), as the scintillating agent. In order to couple the secondary emitted photons of the back of the scintillator array to a CCD device, having a larger pixel size than the pore pitch, an open optical microscope with adjustable magnification was designed and implemented. By imaging a sharp edge, the authors were able to calculate the modulation transfer function (MTF) of this finely structured scintillator. Results: The x-ray images of individually resolved pores suggest that they have been almost uniformly filled, and the MTF measurements show the feasibility of a few microns spatial resolution imaging, as set by the scintillator pore size. Compared to existing techniques utilizing CsI needles as a structured scintillator, their results imply an almost sevenfold improvement in resolution. Finally, high resolution images, taken by their detector, are presented. Conclusions: The presented work successfully shows the functionality of their detector concept for high resolution imaging and further fabrication developments are most likely to result in higher quantum efficiencies.

  13. Science with High Spatial Resolution Far-Infrared Data

    Science.gov (United States)

    Terebey, Susan (Editor); Mazzarella, Joseph M. (Editor)

    1994-01-01

    The goal of this workshop was to discuss new science and techniques relevant to high spatial resolution processing of far-infrared data, with particular focus on high resolution processing of IRAS data. Users of the maximum correlation method, maximum entropy, and other resolution enhancement algorithms applicable to far-infrared data gathered at the Infrared Processing and Analysis Center (IPAC) for two days in June 1993 to compare techniques and discuss new results. During a special session on the third day, interested astronomers were introduced to IRAS HIRES processing, which is IPAC's implementation of the maximum correlation method to the IRAS data. Topics discussed during the workshop included: (1) image reconstruction; (2) random noise; (3) imagery; (4) interacting galaxies; (5) spiral galaxies; (6) galactic dust and elliptical galaxies; (7) star formation in Seyfert galaxies; (8) wavelet analysis; and (9) supernova remnants.

  14. Textural Segmentation of High-Resolution Sidescan Sonar Images

    National Research Council Canada - National Science Library

    Kalcic, Maria; Bibee, Dale

    1995-01-01

    .... The high resolution of the 455 kHz sonar imagery also provides much information about the surficial bottom sediments, however their acoustic scattering properties are not well understood at high frequencies...

  15. High-resolution computed tomography findings in pulmonary Langerhans cell histiocytosis

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, Rosana Souza [Universidade Federal do Rio de Janeiro (HUCFF/UFRJ), RJ (Brazil). Hospital Universitario Clementino Fraga Filho. Unit of Radiology; Capone, Domenico; Ferreira Neto, Armando Leao [Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ (Brazil)

    2011-07-15

    Objective: The present study was aimed at characterizing main lung changes observed in pulmonary Langerhans cell histiocytosis by means of high-resolution computed tomography. Materials and Methods: High-resolution computed tomography findings in eight patients with proven disease diagnosed by open lung biopsy, immunohistochemistry studies and/or extrapulmonary manifestations were retrospectively evaluated. Results: Small rounded, thin-walled cystic lesions were observed in the lung of all the patients. Nodules with predominantly peripheral distribution over the lung parenchyma were observed in 75% of the patients. The lesions were diffusely distributed, predominantly in the upper and middle lung fields in all of the cases, but involvement of costophrenic angles was observed in 25% of the patients. Conclusion: Comparative analysis of high-resolution computed tomography and chest radiography findings demonstrated that thinwalled cysts and small nodules cannot be satisfactorily evaluated by conventional radiography. Because of its capacity to detect and characterize lung cysts and nodules, high-resolution computed tomography increases the probability of diagnosing pulmonary Langerhans cell histiocytosis. (author)

  16. Scanning fluorescence detector for high-throughput DNA genotyping

    Science.gov (United States)

    Rusch, Terry L.; Petsinger, Jeremy; Christensen, Carl; Vaske, David A.; Brumley, Robert L., Jr.; Luckey, John A.; Weber, James L.

    1996-04-01

    A new scanning fluorescence detector (SCAFUD) was developed for high-throughput genotyping of short tandem repeat polymorphisms (STRPs). Fluorescent dyes are incorporated into relatively short DNA fragments via polymerase chain reaction (PCR) and are separated by electrophoresis in short, wide polyacrylamide gels (144 lanes with well to read distances of 14 cm). Excitation light from an argon laser with primary lines at 488 and 514 nm is introduced into the gel through a fiber optic cable, dichroic mirror, and 40X microscope objective. Emitted fluorescent light is collected confocally through a second fiber. The confocal head is translated across the bottom of the gel at 0.5 Hz. The detection unit utilizes dichroic mirrors and band pass filters to direct light with 10 - 20 nm bandwidths to four photomultiplier tubes (PMTs). PMT signals are independently amplified with variable gain and then sampled at a rate of 2500 points per scan using a computer based A/D board. LabView software (National Instruments) is used for instrument operation. Currently, three fluorescent dyes (Fam, Hex and Rox) are simultaneously detected with peak detection wavelengths of 543, 567, and 613 nm, respectively. The detection limit for fluorescein-labeled primers is about 100 attomoles. Planned SCAFUD upgrades include rearrangement of laser head geometry, use of additional excitation lasers for simultaneous detection of more dyes, and the use of detector arrays instead of individual PMTs. Extensive software has been written for automatic analysis of SCAFUD images. The software enables background subtraction, band identification, multiple- dye signal resolution, lane finding, band sizing and allele calling. Whole genome screens are currently underway to search for loci influencing such complex diseases as diabetes, asthma, and hypertension. Seven production SCAFUDs are currently in operation. Genotyping output for the coming year is projected to be about one million total genotypes (DNA

  17. A Forward-Looking High-Resolution GPR System

    National Research Council Canada - National Science Library

    Kositsky, Joel; Milanfar, Peyman

    1999-01-01

    A high-resolution ground penetrating radar (GPR) system was designed to help define the optimal radar parameters needed for the efficient standoff detection of buried and surface-laid antitank mines...

  18. Accelerated high-resolution photoacoustic tomography via compressed sensing

    Science.gov (United States)

    Arridge, Simon; Beard, Paul; Betcke, Marta; Cox, Ben; Huynh, Nam; Lucka, Felix; Ogunlade, Olumide; Zhang, Edward

    2016-12-01

    Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant. We demonstrate that combining model-based, variational image reconstruction methods using spatial sparsity constraints with the development of novel PAT acquisition systems capable of sub-sampling the acoustic wave field can dramatically increase the acquisition speed while maintaining a good spatial resolution: first, we describe and model two general spatial sub-sampling schemes. Then, we discuss how to implement them using the FP interferometer and demonstrate the potential of these novel compressed sensing PAT devices through simulated data from a realistic numerical phantom and through measured data from a dynamic experimental phantom as well as from in vivo experiments. Our results show that images with good spatial resolution and contrast can be obtained from highly sub-sampled PAT data if variational image reconstruction techniques that describe the tissues structures with suitable sparsity-constraints are used. In particular, we examine the use of total variation (TV) regularization enhanced by Bregman iterations. These novel reconstruction strategies offer new opportunities to dramatically increase the acquisition speed of photoacoustic scanners that employ point-by-point sequential scanning as well as reducing the channel count of parallelized schemes that use detector arrays.

  19. A Very High Spatial Resolution Detector for Small Animal PET

    International Nuclear Information System (INIS)

    Kanai Shah, M.S.

    2007-01-01

    Positron Emission Tomography (PET) is an in vivo analog of autoradiography and has the potential to become a powerful new tool in imaging biological processes in small laboratory animals. PET imaging of small animals can provide unique information that can help in advancement of human disease models as well as drug development. Clinical PET scanners used for human imaging are bulky, expensive and do not have adequate spatial resolution for small animal studies. Hence, dedicated, low cost instruments are required for conducting small animal studies with higher spatial resolution than what is currently achieved with clinical as well as dedicated small animal PET scanners. The goal of the proposed project is to investigate a new all solid-state detector design for small animal PET imaging. Exceptionally high spatial resolution, good timing resolution, and excellent energy resolution are expected from the proposed detector design. The Phase I project was aimed at demonstrating the feasibility of producing high performance solid-state detectors that provide high sensitivity, spatial resolution, and timing characteristics. Energy resolution characteristics of the new detector were also investigated. The goal of the Phase II project is to advance the promising solid-state detector technology for small animal PET and determine its full potential. Detectors modules will be built and characterized and finally, a bench-top small animal PET system will be assembled and evaluated

  20. Strengthening IAEA safeguards using high-resolution commercial satellite imagery

    International Nuclear Information System (INIS)

    Zhang Hui

    2001-01-01

    Full text: In May 1997, the IAEA Board of Governors adopted the Additional Safeguards Protocol to improve its ability to detect the undeclared production of fissile material. This new strengthened safeguards system has opened the door for the IAEA to use of all types of information, including the potential use of commercial satellite imagery. We have therefore been investigating the feasibility of strengthening IAEA safeguards using commercial satellite imagery. Based on our analysis on a number of one-meter resolution IKONOS satellite images of military nuclear production facilities at nuclear states including Russia, China, India, Pakistan and Israel, we found that the new high-resolution commercial satellite imagery would play a new and valuable role in strengthening IAEA safeguards. Since 1999, images with a resolution of one meter have been available commercially from Space Imaging's IKONOS satellite. One-meter images from other companies are expected to enter the market soon. Although still an order of magnitude less capable than military imaging satellites, the capabilities of these new high-resolution commercial satellites are good enough to detect and identify the major visible characteristics of nuclear production facilities and sites. Unlike the classified spy satellite photos limited to few countries, the commercial satellite imagery is commercially available to anyone who wants to purchase it. Therefore, the new commercial satellite open a new chance that each state, international organizations, and non-governmental groups could use the commercial images to play a more proactive role in monitoring the nuclear activities in related countries and verifying the compliance of non-proliferation agreements. This could help galvanize support for intensified efforts to slow the pace of nuclear proliferation. To produce fissile materials (plutonium and highly enriched uranium) for weapons, a country would operate dedicated plutonium-production reactors and the

  1. Processing method for high resolution monochromator

    International Nuclear Information System (INIS)

    Kiriyama, Koji; Mitsui, Takaya

    2006-12-01

    A processing method for high resolution monochromator (HRM) has been developed at Japanese Atomic Energy Agency/Quantum Beam Science Directorate/Synchrotron Radiation Research unit at SPring-8. For manufacturing a HRM, a sophisticated slicing machine and X-ray diffractometer have been installed for shaping a crystal ingot and orienting precisely the surface of a crystal ingot, respectively. The specification of the slicing machine is following; Maximum size of a diamond blade is φ 350mm in diameter, φ 38.1mm in the spindle diameter, and 2mm in thickness. A large crystal such as an ingot with 100mm in diameter, 200mm in length can be cut. Thin crystal samples such as a wafer can be also cut using by another sample holder. Working distance of a main shaft with the direction perpendicular to working table in the machine is 350mm at maximum. Smallest resolution of the main shaft with directions of front-and-back and top-and-bottom are 0.001mm read by a digital encoder. 2mm/min can set for cutting samples in the forward direction. For orienting crystal faces relative to the blade direction adjustment, a one-circle goniometer and 2-circle segment are equipped on the working table in the machine. A rotation and a tilt of the stage can be done by manual operation. Digital encoder in a turn stage is furnished and has angle resolution of less than 0.01 degrees. In addition, a hand drill as a supporting device for detailed processing of crystal is prepared. Then, an ideal crystal face can be cut from crystal samples within an accuracy of about 0.01 degrees. By installation of these devices, a high energy resolution monochromator crystal for inelastic x-ray scattering and a beam collimator are got in hand and are expected to be used for nanotechnology studies. (author)

  2. High-resolution coded-aperture design for compressive X-ray tomography using low resolution detectors

    Science.gov (United States)

    Mojica, Edson; Pertuz, Said; Arguello, Henry

    2017-12-01

    One of the main challenges in Computed Tomography (CT) is obtaining accurate reconstructions of the imaged object while keeping a low radiation dose in the acquisition process. In order to solve this problem, several researchers have proposed the use of compressed sensing for reducing the amount of measurements required to perform CT. This paper tackles the problem of designing high-resolution coded apertures for compressed sensing computed tomography. In contrast to previous approaches, we aim at designing apertures to be used with low-resolution detectors in order to achieve super-resolution. The proposed method iteratively improves random coded apertures using a gradient descent algorithm subject to constraints in the coherence and homogeneity of the compressive sensing matrix induced by the coded aperture. Experiments with different test sets show consistent results for different transmittances, number of shots and super-resolution factors.

  3. Refinement procedure for the image alignment in high-resolution electron tomography.

    Science.gov (United States)

    Houben, L; Bar Sadan, M

    2011-01-01

    High-resolution electron tomography from a tilt series of transmission electron microscopy images requires an accurate image alignment procedure in order to maximise the resolution of the tomogram. This is the case in particular for ultra-high resolution where even very small misalignments between individual images can dramatically reduce the fidelity of the resultant reconstruction. A tomographic-reconstruction based and marker-free method is proposed, which uses an iterative optimisation of the tomogram resolution. The method utilises a search algorithm that maximises the contrast in tomogram sub-volumes. Unlike conventional cross-correlation analysis it provides the required correlation over a large tilt angle separation and guarantees a consistent alignment of images for the full range of object tilt angles. An assessment based on experimental reconstructions shows that the marker-free procedure is competitive to the reference of marker-based procedures at lower resolution and yields sub-pixel accuracy even for simulated high-resolution data. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Towards high resolution polarisation analysis using double polarisation and ellipsoidal analysers

    CERN Document Server

    Martin-Y-Marero, D

    2002-01-01

    Classical polarisation analysis methods lack the combination of high resolution and high count rate necessary to cope with the demand of modern condensed-matter experiments. In this work, we present a method to achieve high resolution polarisation analysis based on a double polarisation system. Coupling this method with an ellipsoidal wavelength analyser, a high count rate can be achieved whilst delivering a resolution of around 10 mu eV. This method is ideally suited to pulsed sources, although it can be adapted to continuous sources as well. (orig.)

  5. High efficiency hydrodynamic DNA fragmentation in a bubbling system

    NARCIS (Netherlands)

    Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; Van Den Berg, Albert; Eijkel, Jan C.T.; Shui, Lingling

    2017-01-01

    DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling

  6. High molecular weight DNA assembly in vivo for synthetic biology applications.

    Science.gov (United States)

    Juhas, Mario; Ajioka, James W

    2017-05-01

    DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

  7. Environmental DNA (eDNA metabarcoding assays to detect invasive invertebrate species in the Great Lakes.

    Directory of Open Access Journals (Sweden)

    Katy E Klymus

    Full Text Available Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring. We employed careful primer design and in vitro testing with mock communities to assess ability of the markers to amplify and sequence targeted species DNA, while retaining rank abundance information. In our mock communities, read abundances reflected the initial input abundance, with regressions having significant slopes (p<0.05 and high coefficients of determination (R2 for all comparisons. Tests on field environmental samples revealed similar ability of our markers to measure relative abundance. Due to the limited reference sequence data available for these invertebrate species, care must be taken when analyzing results and identifying sequence reads to species level. These markers extend eDNA metabarcoding research for molluscs and appear relevant to other invertebrate taxa, such as rotifers and bryozoans. Furthermore, the sphaeriid mussel assay is group-specific, exclusively amplifying bivalves in the Sphaeridae family and providing species-level identification. Our assays provide useful tools for managers and conservation scientists, facilitating early detection of invasive species as well as improving resolution of mollusc diversity.

  8. Transistor reset preamplifier for high-rate high-resolution spectroscopy

    International Nuclear Information System (INIS)

    Landis, D.A.; Cork, C.P.; Madden, N.W.; Goulding, F.S.

    1981-10-01

    Pulsed transistor reset of high resolution charge sensitive preamplifiers used in cooled semiconductor spectrometers can sometimes have an advantage over pulsed light reset systems. Several versions of transistor reset spectrometers using both silicon and germanium detectors have been built. This paper discusses the advantages of the transistor reset system and illustrates several configurations of the packages used for the FET and reset transistor. It also describes the preamplifer circuit and shows the performance of the spectrometer at high rates

  9. Constructing a WISE High Resolution Galaxy Atlas

    Science.gov (United States)

    Jarrett, T. H.; Masci, F.; Tsai, C. W.; Petty, S.; Cluver, M.; Assef, Roberto J.; Benford, D.; Blain, A.; Bridge, C.; Donoso, E.; hide

    2012-01-01

    After eight months of continuous observations, the Wide-field Infrared Survey Explorer (WISE) mapped the entire sky at 3.4 micron, 4.6 micron, 12 micron, and 22 micron. We have begun a dedicated WISE High Resolution Galaxy Atlas project to fully characterize large, nearby galaxies and produce a legacy image atlas and source catalog. Here we summarize the deconvolution techniques used to significantly improve the spatial resolution of WISE imaging, specifically designed to study the internal anatomy of nearby galaxies. As a case study, we present results for the galaxy NGC 1566, comparing the WISE enhanced-resolution image processing to that of Spitzer, Galaxy Evolution Explorer, and ground-based imaging. This is the first paper in a two-part series; results for a larger sample of nearby galaxies are presented in the second paper.

  10. High resolution spectroscopy in the microwave and far infrared

    Science.gov (United States)

    Pickett, Herbert M.

    1990-01-01

    High resolution rotational spectroscopy has long been central to remote sensing techniques in atmospheric sciences and astronomy. As such, laboratory measurements must supply the required data to make direct interpretation of data for instruments which sense atmospheres using rotational spectra. Spectral measurements in the microwave and far infrared regions are also very powerful tools when combined with infrared measurements for characterizing the rotational structure of vibrational spectra. In the past decade new techniques were developed which have pushed high resolution spectroscopy into the wavelength region between 25 micrometers and 2 mm. Techniques to be described include: (1) harmonic generation of microwave sources, (2) infrared laser difference frequency generation, (3) laser sideband generation, and (4) ultrahigh resolution interferometers.

  11. Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing.

    Science.gov (United States)

    Hu, Jiazhi; Meyers, Robin M; Dong, Junchao; Panchakshari, Rohit A; Alt, Frederick W; Frock, Richard L

    2016-05-01

    Unbiased, high-throughput assays for detecting and quantifying DNA double-stranded breaks (DSBs) across the genome in mammalian cells will facilitate basic studies of the mechanisms that generate and repair endogenous DSBs. They will also enable more applied studies, such as those to evaluate the on- and off-target activities of engineered nucleases. Here we describe a linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) method for the detection of genome-wide 'prey' DSBs via their translocation in cultured mammalian cells to a fixed 'bait' DSB. Bait-prey junctions are cloned directly from isolated genomic DNA using LAM-PCR and unidirectionally ligated to bridge adapters; subsequent PCR steps amplify the single-stranded DNA junction library in preparation for Illumina Miseq paired-end sequencing. A custom bioinformatics pipeline identifies prey sequences that contribute to junctions and maps them across the genome. LAM-HTGTS differs from related approaches because it detects a wide range of broken end structures with nucleotide-level resolution. Familiarity with nucleic acid methods and next-generation sequencing analysis is necessary for library generation and data interpretation. LAM-HTGTS assays are sensitive, reproducible, relatively inexpensive, scalable and straightforward to implement with a turnaround time of <1 week.

  12. High resolution and high speed positron emission tomography data acquisition

    International Nuclear Information System (INIS)

    Burgiss, S.G.; Byars, L.G.; Jones, W.F.; Casey, M.E.

    1986-01-01

    High resolution positron emission tomography (PET) requires many detectors. Thus, data collection systems for PET must have high data rates, wide data paths, and large memories to histogram the events. This design uses the VMEbus to cost effectively provide these features. It provides for several modes of operation including real time sorting, list mode data storage, and replay of stored list mode data

  13. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

    Science.gov (United States)

    Inagaki, Soichi; Henry, Isabelle M; Lieberman, Meric C; Comai, Luca

    2015-01-01

    Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

  14. Ultra high spatial and temporal resolution breast imaging at 7T.

    Science.gov (United States)

    van de Bank, B L; Voogt, I J; Italiaander, M; Stehouwer, B L; Boer, V O; Luijten, P R; Klomp, D W J

    2013-04-01

    There is a need to obtain higher specificity in the detection of breast lesions using MRI. To address this need, Dynamic Contrast-Enhanced (DCE) MRI has been combined with other structural and functional MRI techniques. Unfortunately, owing to time constraints structural images at ultra-high spatial resolution can generally not be obtained during contrast uptake, whereas the relatively low spatial resolution of functional imaging (e.g. diffusion and perfusion) limits the detection of small lesions. To be able to increase spatial as well as temporal resolution simultaneously, the sensitivity of MR detection needs to increase as well as the ability to effectively accelerate the acquisition. The required gain in signal-to-noise ratio (SNR) can be obtained at 7T, whereas acceleration can be obtained with high-density receiver coil arrays. In this case, morphological imaging can be merged with DCE-MRI, and other functional techniques can be obtained at higher spatial resolution, and with less distortion [e.g. Diffusion Weighted Imaging (DWI)]. To test the feasibility of this concept, we developed a unilateral breast coil for 7T. It comprises a volume optimized dual-channel transmit coil combined with a 30-channel receive array coil. The high density of small coil elements enabled efficient acceleration in any direction to acquire ultra high spatial resolution MRI of close to 0.6 mm isotropic detail within a temporal resolution of 69 s, high spatial resolution MRI of 1.5 mm isotropic within an ultra high temporal resolution of 6.7 s and low distortion DWI at 7T, all validated in phantoms, healthy volunteers and a patient with a lesion in the right breast classified as Breast Imaging Reporting and Data System (BI-RADS) IV. Copyright © 2012 John Wiley & Sons, Ltd.

  15. High-Resolution X-ray Emission and X-ray Absorption Spectroscopy

    NARCIS (Netherlands)

    Groot, F.M.F. de

    2000-01-01

    In this review, high-resolution X-ray emission and X-ray absorption spectroscopy will be discussed. The focus is on the 3d transition-metal systems. To understand high-resolution X-ray emission and reso-nant X-ray emission, it is first necessary to spend some time discussing the X-ray absorption

  16. High-resolution flurescence spectroscopy in immunoanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Grubor, Nenad M. [Iowa State Univ., Ames, IA (United States)

    2005-01-01

    The work presented in this dissertation combines highly sensitive and selective fluorescence line-narrowing spectroscopy (FLNS) detection with various modes of immunoanalytical techniques. It has been shown that FLNS is capable of directly probing molecules immunocomplexed with antibodies, eliminating analytical ambiguities that may arise from interferences that accompany traditional immunochemical techniques. Moreover, the utilization of highly cross-reactive antibodies for highly specific analyte determination has been demonstrated. Finally, they demonstrate the first example of the spectral resolution of diastereomeric analytes based on their interaction with a cross-reactive antibody.

  17. High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) for the characterisation of pathogenic leptospires: intra-serovar divergence, inter-serovar convergence, and evidence of attenuation in Leptospira reference collections.

    Science.gov (United States)

    Tulsiani, S M; Craig, S B; Graham, G C; Cobbold, R C; Dohnt, M F; Burns, M-A; Jansen, C C; Leung, L K-P; Field, H E; Smythe, L D

    2010-07-01

    High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) is a novel technology that has emerged as a possible method to characterise leptospires to serovar level. RAPD-HRM has recently been used to measure intra-serovar convergence between strains of the same serovar as well as inter-serovar divergence between strains of different serovars. The results indicate that intra-serovar heterogeneity and inter-serovar homogeneity may limit the application of RAPD-HRM in routine diagnostics. They also indicate that genetic attenuation of aged, high-passage-number isolates could undermine the use of RAPD-HRM or any other molecular technology. Such genetic attenuation may account for a general decrease seen in titres of rabbit hyperimmune antibodies over time. Before RAPD-HRM can be further advanced as a routine diagnostic tool, strains more representative of the wild-type serovars of a given region need to be identified. Further, RAPD-HRM analysis of reference strains indicates that the routine renewal of reference collections, with new isolates, may be needed to maintain the genetic integrity of the collections.

  18. Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini using real-time PCR and high resolution melting analysis.

    Science.gov (United States)

    Cai, Xian-Quan; Yu, Hai-Qiong; Li, Rong; Yue, Qiao-Yun; Liu, Guo-Hua; Bai, Jian-Shan; Deng, Yan; Qiu, De-Yi; Zhu, Xing-Quan

    2014-01-01

    Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini.

  19. Rapid Detection and Differentiation of Clonorchis sinensis and Opisthorchis viverrini Using Real-Time PCR and High Resolution Melting Analysis

    Directory of Open Access Journals (Sweden)

    Xian-Quan Cai

    2014-01-01

    Full Text Available Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini.

  20. Optimization of PCR Condition: The First Study of High Resolution Melting Technique for Screening of APOA1 Variance.

    Science.gov (United States)

    Wahyuningsih, Hesty; K Cayami, Ferdy; Bahrudin, Udin; A Sobirin, Mochamad; Ep Mundhofir, Farmaditya; Mh Faradz, Sultana; Hisatome, Ichiro

    2017-03-01

    High resolution melting (HRM) is a post-PCR technique for variant screening and genotyping based on the different melting points of DNA fragments. The advantages of this technique are that it is fast, simple, and efficient and has a high output, particularly for screening of a large number of samples. APOA1 encodes apolipoprotein A1 (apoA1) which is a major component of high density lipoprotein cholesterol (HDL-C). This study aimed to obtain an optimal quantitative polymerase chain reaction (qPCR)-HRM condition for screening of APOA1 variance. Genomic DNA was isolated from a peripheral blood sample using the salting out method. APOA1 was amplified using the RotorGeneQ 5Plex HRM. The PCR product was visualized with the HRM amplification curve and confirmed using gel electrophoresis. The melting profile was confirmed by looking at the melting curve. Five sets of primers covering the translated region of APOA1 exons were designed with expected PCR product size of 100-400 bps. The amplified segments of DNA were amplicons 2, 3, 4A, 4B, and 4C. Amplicons 2, 3 and 4B were optimized at an annealing temperature of 60 °C at 40 PCR cycles. Amplicon 4A was optimized at an annealing temperature of 62 °C at 45 PCR cycles. Amplicon 4C was optimized at an annealing temperature of 63 °C at 50 PCR cycles. In addition to the suitable procedures of DNA isolation and quantification, primer design and an estimated PCR product size, the data of this study showed that appropriate annealing temperature and PCR cycles were important factors in optimization of HRM technique for variant screening in APOA1 .

  1. Developing DNA nanotechnology using single-molecule fluorescence.

    Science.gov (United States)

    Tsukanov, Roman; Tomov, Toma E; Liber, Miran; Berger, Yaron; Nir, Eyal

    2014-06-17

    CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and

  2. Stem cell identity and template DNA strand segregation.

    Science.gov (United States)

    Tajbakhsh, Shahragim

    2008-12-01

    The quest for stem cell properties to distinguish their identity from that of committed daughters has led to a re-investigation of the notion that DNA strands are not equivalent, and 'immortal' DNA strands are retained in stem cells whereas newly replicated DNA strands segregate to the differentiating daughter cell during mitosis. Whether this process occurs only in stem cells, and also in all tissues, remains unclear. That individual chromosomes can be also partitioned non-randomly raises the question if this phenomenon is related to the immortal DNA hypothesis, and it underscores the need for high-resolution techniques to observe these events empirically. Although initially postulated as a mechanism to avoid DNA replication errors, alternative views including epigenetic regulation and sister chromatid silencing may provide insights into this process.

  3. Development of a high-resolution cavity-beam position monitor

    Directory of Open Access Journals (Sweden)

    Yoichi Inoue

    2008-06-01

    Full Text Available We have developed a high-resolution cavity-beam position monitor (BPM to be used at the focal point of the ATF2, which is a test beam line that is now being built to demonstrate stable orbit control at ∼nanometer resolution. The design of the cavity structure was optimized for the Accelerator Test Facility (ATF beam in various ways. For example, the cavity has a rectangular shape in order to isolate two dipole modes in orthogonal directions, and a relatively thin gap that is less sensitive to trajectory inclination. A two stage homodyne mixer with highly sensitive electronics and phase-sensitive detection was also developed. Two BPM blocks, each containing two cavity BPMs, were installed in the existing ATF beam line using a rigid support frame. After testing the basic characteristics, we measured the resolution using three BPMs. The system demonstrated 8.7 nm position resolution over a dynamic range of 5  μm.

  4. Development of a high-resolution cavity-beam position monitor

    Science.gov (United States)

    Inoue, Yoichi; Hayano, Hitoshi; Honda, Yosuke; Takatomi, Toshikazu; Tauchi, Toshiaki; Urakawa, Junji; Komamiya, Sachio; Nakamura, Tomoya; Sanuki, Tomoyuki; Kim, Eun-San; Shin, Seung-Hwan; Vogel, Vladimir

    2008-06-01

    We have developed a high-resolution cavity-beam position monitor (BPM) to be used at the focal point of the ATF2, which is a test beam line that is now being built to demonstrate stable orbit control at ˜nanometer resolution. The design of the cavity structure was optimized for the Accelerator Test Facility (ATF) beam in various ways. For example, the cavity has a rectangular shape in order to isolate two dipole modes in orthogonal directions, and a relatively thin gap that is less sensitive to trajectory inclination. A two stage homodyne mixer with highly sensitive electronics and phase-sensitive detection was also developed. Two BPM blocks, each containing two cavity BPMs, were installed in the existing ATF beam line using a rigid support frame. After testing the basic characteristics, we measured the resolution using three BPMs. The system demonstrated 8.7 nm position resolution over a dynamic range of 5μm.

  5. Classification of high resolution satellite images

    OpenAIRE

    Karlsson, Anders

    2003-01-01

    In this thesis the Support Vector Machine (SVM)is applied on classification of high resolution satellite images. Sveral different measures for classification, including texture mesasures, 1st order statistics, and simple contextual information were evaluated. Additionnally, the image was segmented, using an enhanced watershed method, in order to improve the classification accuracy.

  6. High-resolution and high-throughput multichannel Fourier transform spectrometer with two-dimensional interferogram warping compensation

    Science.gov (United States)

    Watanabe, A.; Furukawa, H.

    2018-04-01

    The resolution of multichannel Fourier transform (McFT) spectroscopy is insufficient for many applications despite its extreme advantage of high throughput. We propose an improved configuration to realise both performance using a two-dimensional area sensor. For the spectral resolution, we obtained the interferogram of a larger optical path difference by shifting the area sensor without altering any optical components. The non-linear phase error of the interferometer was successfully corrected using a phase-compensation calculation. Warping compensation was also applied to realise a higher throughput to accumulate the signal between vertical pixels. Our approach significantly improved the resolution and signal-to-noise ratio by factors of 1.7 and 34, respectively. This high-resolution and high-sensitivity McFT spectrometer will be useful for detecting weak light signals such as those in non-invasive diagnosis.

  7. A new method for high-resolution characterization of hydraulic conductivity

    Science.gov (United States)

    Liu, Gaisheng; Butler, J.J.; Bohling, Geoffrey C.; Reboulet, Ed; Knobbe, Steve; Hyndman, D.W.

    2009-01-01

    A new probe has been developed for high-resolution characterization of hydraulic conductivity (K) in shallow unconsolidated formations. The probe was recently applied at the Macrodispersion Experiment (MADE) site in Mississippi where K was rapidly characterized at a resolution as fine as 0.015 m, which has not previously been possible. Eleven profiles were obtained with K varying up to 7 orders of magnitude in individual profiles. Currently, high-resolution (0.015-m) profiling has an upper K limit of 10 m/d; lower-resolution (???0.4-m) mode is used in more permeable zones pending modifications. The probe presents a new means to help address unresolved issues of solute transport in heterogeneous systems. Copyright 2009 by the American Geophysical Union.

  8. Evaluation of a High-Resolution Regional Reanalysis for Europe

    Science.gov (United States)

    Ohlwein, C.; Wahl, S.; Keller, J. D.; Bollmeyer, C.

    2014-12-01

    Reanalyses gain more and more importance as a source of meteorological information for many purposes and applications. Several global reanalyses projects (e.g., ERA, MERRA, CSFR, JMA9) produce and verify these data sets to provide time series as long as possible combined with a high data quality. Due to a spatial resolution down to 50-70km and 3-hourly temporal output, they are not suitable for small scale problems (e.g., regional climate assessment, meso-scale NWP verification, input for subsequent models such as river runoff simulations). The implementation of regional reanalyses based on a limited area model along with a data assimilation scheme is able to generate reanalysis data sets with high spatio-temporal resolution. Within the Hans-Ertel-Centre for Weather Research (HErZ), the climate monitoring branch concentrates efforts on the assessment and analysis of regional climate in Germany and Europe. In joint cooperation with DWD (German Meteorological Service), a high-resolution reanalysis system based on the COSMO model has been developed. The regional reanalysis for Europe matches the domain of the CORDEX EURO-11 specifications, albeit at a higher spatial resolution, i.e., 0.055° (6km) instead of 0.11° (12km) and comprises the assimilation of observational data using the existing nudging scheme of COSMO complemented by a special soil moisture analysis with boundary conditions provided by ERA-Interim data. The reanalysis data set covers 6 years (2007-2012) and is currently extended to 16 years. Extensive evaluation of the reanalysis is performed using independent observations with special emphasis on precipitation and high-impact weather situations indicating a better representation of small scale variability. Further, the evaluation shows an added value of the regional reanalysis with respect to the forcing ERA Interim reanalysis and compared to a pure high-resolution dynamical downscaling approach without data assimilation.

  9. A Novel Low Energy Electron Microscope for DNA Sequencing and Surface Analysis

    Science.gov (United States)

    Mankos, M.; Shadman, K.; Persson, H.H.J.; N’Diaye, A.T.; Schmid, A.K.; Davis, R.W.

    2014-01-01

    Monochromatic, aberration-corrected, dual-beam low energy electron microscopy (MAD-LEEM) is a novel technique that is directed towards imaging nanostructures and surfaces with sub-nanometer resolution. The technique combines a monochromator, a mirror aberration corrector, an energy filter, and dual beam illumination in a single instrument. The monochromator reduces the energy spread of the illuminating electron beam, which significantly improves spectroscopic and spatial resolution. Simulation results predict that the novel aberration corrector design will eliminate the second rank chromatic and third and fifth order spherical aberrations, thereby improving the resolution into the sub-nanometer regime at landing energies as low as one hundred electron-Volts. The energy filter produces a beam that can extract detailed information about the chemical composition and local electronic states of non-periodic objects such as nanoparticles, interfaces, defects, and macromolecules. The dual flood illumination eliminates charging effects that are generated when a conventional LEEM is used to image insulating specimens. A potential application for MAD-LEEM is in DNA sequencing, which requires high resolution to distinguish the individual bases and high speed to reduce the cost. The MAD-LEEM approach images the DNA with low electron impact energies, which provides nucleobase contrast mechanisms without organometallic labels. Furthermore, the micron-size field of view when combined with imaging on the fly provides long read lengths, thereby reducing the demand on assembling the sequence. Experimental results from bulk specimens with immobilized single-base oligonucleotides demonstrate that base specific contrast is available with reflected, photo-emitted, and Auger electrons. Image contrast simulations of model rectangular features mimicking the individual nucleotides in a DNA strand have been developed to translate measurements of contrast on bulk DNA to the detectability of

  10. A novel low energy electron microscope for DNA sequencing and surface analysis.

    Science.gov (United States)

    Mankos, M; Shadman, K; Persson, H H J; N'Diaye, A T; Schmid, A K; Davis, R W

    2014-10-01

    Monochromatic, aberration-corrected, dual-beam low energy electron microscopy (MAD-LEEM) is a novel technique that is directed towards imaging nanostructures and surfaces with sub-nanometer resolution. The technique combines a monochromator, a mirror aberration corrector, an energy filter, and dual beam illumination in a single instrument. The monochromator reduces the energy spread of the illuminating electron beam, which significantly improves spectroscopic and spatial resolution. Simulation results predict that the novel aberration corrector design will eliminate the second rank chromatic and third and fifth order spherical aberrations, thereby improving the resolution into the sub-nanometer regime at landing energies as low as one hundred electron-Volts. The energy filter produces a beam that can extract detailed information about the chemical composition and local electronic states of non-periodic objects such as nanoparticles, interfaces, defects, and macromolecules. The dual flood illumination eliminates charging effects that are generated when a conventional LEEM is used to image insulating specimens. A potential application for MAD-LEEM is in DNA sequencing, which requires high resolution to distinguish the individual bases and high speed to reduce the cost. The MAD-LEEM approach images the DNA with low electron impact energies, which provides nucleobase contrast mechanisms without organometallic labels. Furthermore, the micron-size field of view when combined with imaging on the fly provides long read lengths, thereby reducing the demand on assembling the sequence. Experimental results from bulk specimens with immobilized single-base oligonucleotides demonstrate that base specific contrast is available with reflected, photo-emitted, and Auger electrons. Image contrast simulations of model rectangular features mimicking the individual nucleotides in a DNA strand have been developed to translate measurements of contrast on bulk DNA to the detectability of

  11. High resolution satellite imagery : from spies to pipeline management

    Energy Technology Data Exchange (ETDEWEB)

    Adam, S. [Canadian Geomatic Solutions Ltd., Calgary, AB (Canada); Farrell, M. [TransCanada Transmission, Calgary, AB (Canada)

    2000-07-01

    The launch of Space Imaging's IKONOS satellite in September 1999 has opened the door for corridor applications. The technology has been successfully implemented by TransCanada PipeLines in mapping over 1500 km of their mainline. IKONOS is the world's first commercial high resolution satellite which collects data at 1-meter black/white and 4-meter multi-spectral. Its use is regulated by the U.S. government. It is the best source of high resolution satellite image data. Other sources include the Indian Space Agency's IRS-1 C/D satellite and the Russian SPIN-2 which provides less reliable coverage. In addition, two more high resolution satellites may be launched this year to provide imagery every day of the year. IKONOS scenes as narrow as 5 km can be purchased. TransCanada conducted a pilot study to determine if high resolution satellite imagery is as effective as ortho-photos for identifying population structures within a buffer of TransCanada's east line right-of-way. The study examined three unique segments where residential, commercial, industrial and public features were compared. It was determined that IKONOS imagery is as good as digital ortho-photos for updating structures from low to very high density areas. The satellite imagery was also logistically easier than ortho-photos to acquire. This will be even more evident when the IKONOS image archives begins to grow. 4 tabs., 3 figs.

  12. High resolution radar satellite imagery analysis for safeguards applications

    Energy Technology Data Exchange (ETDEWEB)

    Minet, Christian; Eineder, Michael [German Aerospace Center, Remote Sensing Technology Institute, Department of SAR Signal Processing, Wessling, (Germany); Rezniczek, Arnold [UBA GmbH, Herzogenrath, (Germany); Niemeyer, Irmgard [Forschungszentrum Juelich, Institue of Energy and Climate Research, IEK-6: Nuclear Waste Management and Reactor Safety, Juelich, (Germany)

    2011-12-15

    For monitoring nuclear sites, the use of Synthetic Aperture Radar (SAR) imagery shows essential promises. Unlike optical remote sensing instruments, radar sensors operate under almost all weather conditions and independently of the sunlight, i.e. time of the day. Such technical specifications are required both for continuous and for ad-hoc, timed surveillance tasks. With Cosmo-Skymed, TerraSARX and Radarsat-2, high-resolution SAR imagery with a spatial resolution up to 1m has recently become available. Our work therefore aims to investigate the potential of high-resolution TerraSAR data for nuclear monitoring. This paper focuses on exploiting amplitude of a single acquisition, assessing amplitude changes and phase differences between two acquisitions, and PS-InSAR processing of an image stack.

  13. Effects of display resolution and size on primary diagnosis of chest images using a high-resolution electronic work station

    International Nuclear Information System (INIS)

    Fuhrman, C.R.; Cooperstein, L.A.; Herron, J.; Good, W.F.; Good, B.; Gur, D.; Maitz, G.; Tabor, E.; Hoy, R.J.

    1987-01-01

    To evaluate the acceptability of electronically displayed planar images, the authors have a high-resolution work station. This system utilizes a high-resolution film digitizer (100-micro resolution) interfaced to a mainframe computer and two high-resolution (2,048 X 2,048) display devices (Azuray). In a clinically simulated multiobserver blind study (19 cases and five observers) a prodetermined series of reading sessions is stored on magnetic disk and is transferred to the displays while the preceding set of images is being reviewed. Images can be linearly processed on the fly into 2,000 X 2,000 full resolution, 1,000 X 1,000 minified display, or 1,000 X 1,000 interpolated for full-size display. Results of the study indicate that radiologists accept but do not like significant minification (more than X2), and they rate 2,000 X 2,000 images as having better diagnostic quality than 1,000 X 1,000 images

  14. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

    Directory of Open Access Journals (Sweden)

    Soichi Inagaki

    Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

  15. Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

    Directory of Open Access Journals (Sweden)

    Eveson J Paige

    2006-08-01

    Full Text Available Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide. This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will

  16. High-resolution phylogenetic microbial community profiling

    Energy Technology Data Exchange (ETDEWEB)

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  17. High-resolution melting (HRM) re-analysis of a polyposis patients cohort reveals previously undetected heterozygous and mosaic APC gene mutations.

    Science.gov (United States)

    Out, Astrid A; van Minderhout, Ivonne J H M; van der Stoep, Nienke; van Bommel, Lysette S R; Kluijt, Irma; Aalfs, Cora; Voorendt, Marsha; Vossen, Rolf H A M; Nielsen, Maartje; Vasen, Hans F A; Morreau, Hans; Devilee, Peter; Tops, Carli M J; Hes, Frederik J

    2015-06-01

    Familial adenomatous polyposis is most frequently caused by pathogenic variants in either the APC gene or the MUTYH gene. The detection rate of pathogenic variants depends on the severity of the phenotype and sensitivity of the screening method, including sensitivity for mosaic variants. For 171 patients with multiple colorectal polyps without previously detectable pathogenic variant, APC was reanalyzed in leukocyte DNA by one uniform technique: high-resolution melting (HRM) analysis. Serial dilution of heterozygous DNA resulted in a lowest detectable allelic fraction of 6% for the majority of variants. HRM analysis and subsequent sequencing detected pathogenic fully heterozygous APC variants in 10 (6%) of the patients and pathogenic mosaic variants in 2 (1%). All these variants were previously missed by various conventional scanning methods. In parallel, HRM APC scanning was applied to DNA isolated from polyp tissue of two additional patients with apparently sporadic polyposis and without detectable pathogenic APC variant in leukocyte DNA. In both patients a pathogenic mosaic APC variant was present in multiple polyps. The detection of pathogenic APC variants in 7% of the patients, including mosaics, illustrates the usefulness of a complete APC gene reanalysis of previously tested patients, by a supplementary scanning method. HRM is a sensitive and fast pre-screening method for reliable detection of heterozygous and mosaic variants, which can be applied to leukocyte and polyp derived DNA.

  18. Analysis strategies for high-resolution UHF-fMRI data.

    Science.gov (United States)

    Polimeni, Jonathan R; Renvall, Ville; Zaretskaya, Natalia; Fischl, Bruce

    2018-03-01

    Functional MRI (fMRI) benefits from both increased sensitivity and specificity with increasing magnetic field strength, making it a key application for Ultra-High Field (UHF) MRI scanners. Most UHF-fMRI studies utilize the dramatic increases in sensitivity and specificity to acquire high-resolution data reaching sub-millimeter scales, which enable new classes of experiments to probe the functional organization of the human brain. This review article surveys advanced data analysis strategies developed for high-resolution fMRI at UHF. These include strategies designed to mitigate distortion and artifacts associated with higher fields in ways that attempt to preserve spatial resolution of the fMRI data, as well as recently introduced analysis techniques that are enabled by these extremely high-resolution data. Particular focus is placed on anatomically-informed analyses, including cortical surface-based analysis, which are powerful techniques that can guide each step of the analysis from preprocessing to statistical analysis to interpretation and visualization. New intracortical analysis techniques for laminar and columnar fMRI are also reviewed and discussed. Prospects for single-subject individualized analyses are also presented and discussed. Altogether, there are both specific challenges and opportunities presented by UHF-fMRI, and the use of proper analysis strategies can help these valuable data reach their full potential. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. A High-Resolution Stopwatch for Cents

    Science.gov (United States)

    Gingl, Z.; Kopasz, K.

    2011-01-01

    A very low-cost, easy-to-make stopwatch is presented to support various experiments in mechanics. The high-resolution stopwatch is based on two photodetectors connected directly to the microphone input of a sound card. Dedicated free open-source software has been developed and made available to download. The efficiency is demonstrated by a free…

  20. Genome-wide DNA methylation patterns and transcription analysis in sheep muscle.

    Directory of Open Access Journals (Sweden)

    Christine Couldrey

    Full Text Available DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using methodology known as reduced representation bisulfite sequencing (RRBS. While RRBS has proven to be effective in understanding DNA methylation landscapes in humans, mice, and rats, to date, few studies have utilised this powerful method for investigating DNA methylation in agricultural animals. Here we describe the utilisation of RRBS to investigate DNA methylation in sheep Longissimus dorsi muscles. RRBS analysis of ∼1% of the genome from Longissimus dorsi muscles provided data of suitably high precision and accuracy for DNA methylation analysis, at all levels of resolution from genome-wide to individual nucleotides. Combining RRBS data with mRNAseq data allowed the sheep Longissimus dorsi muscle methylome to be compared with methylomes from other species. While some species differences were identified, many similarities were observed between DNA methylation patterns in sheep and other more commonly studied species. The RRBS data presented here highlights the complexity of epigenetic regulation of genes. However, the similarities observed across species are promising, in that knowledge gained from epigenetic studies in human and mice may be applied, with caution, to agricultural species. The ability to accurately measure DNA methylation in agricultural animals will contribute an additional layer of information to the genetic analyses currently being used to maximise production gains in these species.

  1. Ring artifact correction for high-resolution micro CT

    International Nuclear Information System (INIS)

    Kyriakou, Yiannis; Prell, Daniel; Kalender, Willi A

    2009-01-01

    In high-resolution micro CT using flat detectors (FD), imperfect or defect detector elements may cause concentric-ring artifacts due to their continuous over- or underestimation of attenuation values, which often disturb image quality. We here present a dedicated image-based ring artifact correction method for high-resolution micro CT, based on median filtering of the reconstructed image and working on a transformed version of the reconstructed images in polar coordinates. This post-processing method reduced ring artifacts in the reconstructed images and improved image quality for phantom and in in vivo scans. Noise and artifacts were reduced both in transversal and in multi-planar reformations along the longitudinal axis. (note)

  2. Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization.

    Science.gov (United States)

    Liao, Can; Fu, Fang; Yang, Xin; Sun, Yi-Min; Li, Dong-Zhi

    2011-06-01

    Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis. Following the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction. All the 30 samples were negative by conventional karyotyping analysis. Microdeletions on chromosome 17q21.31-q21.32 with approximately 1.3 Mb were identified in four patients by high resolution array-CGH analysis. This included the female reproductive secretory pathway related factor N-ethylmaleimide-sensitive factor (NSF) gene. The results of the present study suggest that there may be critical regions regulating primary ovarian insufficiency in women with a 17q21.31-q21.32 microdeletion. This effect might be due to the loss of function of the NSF gene/genes within the deleted region or to effects on contiguous genes.

  3. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+".

    Directory of Open Access Journals (Sweden)

    Markus H Antwerpen

    Full Text Available The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

  4. Solvated protein–DNA docking using HADDOCK

    International Nuclear Information System (INIS)

    Dijk, Marc van; Visscher, Koen M.; Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J.

    2013-01-01

    Interfacial water molecules play an important role in many aspects of protein–DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein–DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein–DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein–DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein–DNA complexes.

  5. Solvated protein-DNA docking using HADDOCK

    Energy Technology Data Exchange (ETDEWEB)

    Dijk, Marc van; Visscher, Koen M.; Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands)

    2013-05-15

    Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.

  6. High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species.

    Directory of Open Access Journals (Sweden)

    Ricardo Andrade Zampieri

    2016-02-01

    Full Text Available Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases. These diseases are increasingly important public health problems in many countries both within and outside endemic regions. Thus, an accurate differential diagnosis is extremely relevant for understanding epidemiological profiles and for the administration of the best therapeutic protocol.Exploring the High Resolution Melting (HRM dissociation profiles of two amplicons using real time polymerase chain reaction (real-time PCR targeting heat-shock protein 70 coding gene (hsp70 revealed differences that allowed the discrimination of genomic DNA samples of eight Leishmania species found in the Americas, including Leishmania (Leishmania infantum chagasi, L. (L. amazonensis, L. (L. mexicana, L. (Viannia lainsoni, L. (V. braziliensis, L. (V. guyanensis, L. (V. naiffi and L. (V. shawi, and three species found in Eurasia and Africa, including L. (L. tropica, L. (L. donovani and L. (L. major. In addition, we tested DNA samples obtained from standard promastigote culture, naturally infected phlebotomines, experimentally infected mice and clinical human samples to validate the proposed protocol.HRM analysis of hsp70 amplicons is a fast and robust strategy that allowed for the detection and discrimination of all Leishmania species responsible for the Leishmaniases in Brazil and Eurasia/Africa with high sensitivity and accuracy. This method could detect less than one parasite per reaction, even in the presence of host DNA.

  7. High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species.

    Science.gov (United States)

    Zampieri, Ricardo Andrade; Laranjeira-Silva, Maria Fernanda; Muxel, Sandra Marcia; Stocco de Lima, Ana Carolina; Shaw, Jeffrey Jon; Floeter-Winter, Lucile Maria

    2016-02-01

    Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases. These diseases are increasingly important public health problems in many countries both within and outside endemic regions. Thus, an accurate differential diagnosis is extremely relevant for understanding epidemiological profiles and for the administration of the best therapeutic protocol. Exploring the High Resolution Melting (HRM) dissociation profiles of two amplicons using real time polymerase chain reaction (real-time PCR) targeting heat-shock protein 70 coding gene (hsp70) revealed differences that allowed the discrimination of genomic DNA samples of eight Leishmania species found in the Americas, including Leishmania (Leishmania) infantum chagasi, L. (L.) amazonensis, L. (L.) mexicana, L. (Viannia) lainsoni, L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) naiffi and L. (V.) shawi, and three species found in Eurasia and Africa, including L. (L.) tropica, L. (L.) donovani and L. (L.) major. In addition, we tested DNA samples obtained from standard promastigote culture, naturally infected phlebotomines, experimentally infected mice and clinical human samples to validate the proposed protocol. HRM analysis of hsp70 amplicons is a fast and robust strategy that allowed for the detection and discrimination of all Leishmania species responsible for the Leishmaniases in Brazil and Eurasia/Africa with high sensitivity and accuracy. This method could detect less than one parasite per reaction, even in the presence of host DNA.

  8. Digital approach to high-resolution pulse processing for semiconductor detectors

    International Nuclear Information System (INIS)

    Georgiev, A.; Buchner, A.; Gast, W.; Lieder, R.M.

    1992-01-01

    A new design philosophy for processing signals produced by high resolution, large volume semiconductor detectors is described. These detectors, to be used in the next generation of spectrometer arrays for nuclear research (i.e. EUROBALL, etc.), present a set of problems like resolution degradation due to charge trapping and ballistic defect effects, low resolution at a high count rate, poor long term stability, etc. To solve these problems, a new design approach has been developed, including reconstruction of the event charge, providing a pure triangular residual function, and suppressing low frequency noise. 5 refs., 4 figs

  9. Digital approach to high-resolution pulse processing for semiconductor detectors

    Energy Technology Data Exchange (ETDEWEB)

    Georgiev, A [Sofia Univ. (Bulgaria); Buchner, A [Forschungszentrum Rossendorf (Germany); Gast, W; Lieder, R M [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Kernphysik; Stein, J [Target System Electronic GmbH, Solingen, (Germany)

    1992-08-01

    A new design philosophy for processing signals produced by high resolution, large volume semiconductor detectors is described. These detectors, to be used in the next generation of spectrometer arrays for nuclear research (i.e. EUROBALL, etc.), present a set of problems like resolution degradation due to charge trapping and ballistic defect effects, low resolution at a high count rate, poor long term stability, etc. To solve these problems, a new design approach has been developed, including reconstruction of the event charge, providing a pure triangular residual function, and suppressing low frequency noise. 5 refs., 4 figs.

  10. Enhancing GIS Capabilities for High Resolution Earth Science Grids

    Science.gov (United States)

    Koziol, B. W.; Oehmke, R.; Li, P.; O'Kuinghttons, R.; Theurich, G.; DeLuca, C.

    2017-12-01

    Applications for high performance GIS will continue to increase as Earth system models pursue more realistic representations of Earth system processes. Finer spatial resolution model input and output, unstructured or irregular modeling grids, data assimilation, and regional coordinate systems present novel challenges for GIS frameworks operating in the Earth system modeling domain. This presentation provides an overview of two GIS-driven applications that combine high performance software with big geospatial datasets to produce value-added tools for the modeling and geoscientific community. First, a large-scale interpolation experiment using National Hydrography Dataset (NHD) catchments, a high resolution rectilinear CONUS grid, and the Earth System Modeling Framework's (ESMF) conservative interpolation capability will be described. ESMF is a parallel, high-performance software toolkit that provides capabilities (e.g. interpolation) for building and coupling Earth science applications. ESMF is developed primarily by the NOAA Environmental Software Infrastructure and Interoperability (NESII) group. The purpose of this experiment was to test and demonstrate the utility of high performance scientific software in traditional GIS domains. Special attention will be paid to the nuanced requirements for dealing with high resolution, unstructured grids in scientific data formats. Second, a chunked interpolation application using ESMF and OpenClimateGIS (OCGIS) will demonstrate how spatial subsetting can virtually remove computing resource ceilings for very high spatial resolution interpolation operations. OCGIS is a NESII-developed Python software package designed for the geospatial manipulation of high-dimensional scientific datasets. An overview of the data processing workflow, why a chunked approach is required, and how the application could be adapted to meet operational requirements will be discussed here. In addition, we'll provide a general overview of OCGIS

  11. Real-time Tracking of DNA Fragment Separation by Smartphone.

    Science.gov (United States)

    Tao, Chunxian; Yang, Bo; Li, Zhenqing; Zhang, Dawei; Yamaguchi, Yoshinori

    2017-06-01

    Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.

  12. Extraction of high quality DNA from seized Moroccan cannabis resin (Hashish.

    Directory of Open Access Journals (Sweden)

    Moulay Abdelaziz El Alaoui

    Full Text Available The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004 adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR amplification of tetrahydrocannabinolic acid (THCA synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances.

  13. Molecular design of sequence specific DNA alkylating agents.

    Science.gov (United States)

    Minoshima, Masafumi; Bando, Toshikazu; Shinohara, Ken-ichi; Sugiyama, Hiroshi

    2009-01-01

    Sequence-specific DNA alkylating agents have great interest for novel approach to cancer chemotherapy. We designed the conjugates between pyrrole (Py)-imidazole (Im) polyamides and DNA alkylating chlorambucil moiety possessing at different positions. The sequence-specific DNA alkylation by conjugates was investigated by using high-resolution denaturing polyacrylamide gel electrophoresis (PAGE). The results showed that polyamide chlorambucil conjugates alkylate DNA at flanking adenines in recognition sequences of Py-Im polyamides, however, the reactivities and alkylation sites were influenced by the positions of conjugation. In addition, we synthesized conjugate between Py-Im polyamide and another alkylating agent, 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI). DNA alkylation reactivies by both alkylating polyamides were almost comparable. In contrast, cytotoxicities against cell lines differed greatly. These comparative studies would promote development of appropriate sequence-specific DNA alkylating polyamides against specific cancer cells.

  14. Computer simulation of high resolution transmission electron micrographs: theory and analysis

    International Nuclear Information System (INIS)

    Kilaas, R.

    1985-03-01

    Computer simulation of electron micrographs is an invaluable aid in their proper interpretation and in defining optimum conditions for obtaining images experimentally. Since modern instruments are capable of atomic resolution, simulation techniques employing high precision are required. This thesis makes contributions to four specific areas of this field. First, the validity of a new method for simulating high resolution electron microscope images has been critically examined. Second, three different methods for computing scattering amplitudes in High Resolution Transmission Electron Microscopy (HRTEM) have been investigated as to their ability to include upper Laue layer (ULL) interaction. Third, a new method for computing scattering amplitudes in high resolution transmission electron microscopy has been examined. Fourth, the effect of a surface layer of amorphous silicon dioxide on images of crystalline silicon has been investigated for a range of crystal thicknesses varying from zero to 2 1/2 times that of the surface layer

  15. Sequence-specific DNA alkylation by tandem Py-Im polyamide conjugates.

    Science.gov (United States)

    Taylor, Rhys Dylan; Kawamoto, Yusuke; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

    2014-09-01

    Tandem N-methylpyrrole-N-methylimidazole (Py-Im) polyamides with good sequence-specific DNA-alkylating activities have been designed and synthesized. Three alkylating tandem Py-Im polyamides with different linkers, which each contained the same moiety for the recognition of a 10 bp DNA sequence, were evaluated for their reactivity and selectivity by DNA alkylation, using high-resolution denaturing gel electrophoresis. All three conjugates displayed high reactivities for the target sequence. In particular, polyamide 1, which contained a β-alanine linker, displayed the most-selective sequence-specific alkylation towards the target 10 bp DNA sequence. The tandem Py-Im polyamide conjugates displayed greater sequence-specific DNA alkylation than conventional hairpin Py-Im polyamide conjugates (4 and 5). For further research, the design of tandem Py-Im polyamide conjugates could play an important role in targeting specific gene sequences. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. The development of high resolution silicon x-ray microcalorimeters

    Science.gov (United States)

    Porter, F. S.; Kelley, R. L.; Kilbourne, C. A.

    2005-12-01

    Recently we have produced x-ray microcalorimeters with resolving powers approaching 2000 at 5.9 keV using a spare XRS microcalorimeter array. We attached 400 um square, 8 um thick HgTe absorbers using a variety of attachment methods to an XRS array and ran the detector array at temperatures between 40 and 60 mK. The best results were for absorbers attached using the standard XRS absorber-pixel thermal isolation scheme utilizing SU8 polymer tubes. In this scenario we achieved a resolution of 3.2 eV FWHM at 5.9 keV. Substituting a silicon spacer for the SU8 tubes also yielded sub-4eV results. In contrast, absorbers attached directly to the thermistor produced significant position dependence and thus degraded resolution. Finally, we tested standard 640um-square XRS detectors at reduced bias power at 50mK and achieved a resolution of 3.7eV, a 50% improvement over the XRS flight instrument. Implanted silicon microcalorimeters are a mature flight-qualified technology that still has a substantial phase space for future development. We will discuss these new high resolution results, the various absorber attachment schemes, planned future improvements, and, finally, their relevance to future high resolution x-ray spectrometers including Constellation-X.

  17. High resolution muon computed tomography at neutrino beam facilities

    International Nuclear Information System (INIS)

    Suerfu, B.; Tully, C.G.

    2016-01-01

    X-ray computed tomography (CT) has an indispensable role in constructing 3D images of objects made from light materials. However, limited by absorption coefficients, X-rays cannot deeply penetrate materials such as copper and lead. Here we show via simulation that muon beams can provide high resolution tomographic images of dense objects and of structures within the interior of dense objects. The effects of resolution broadening from multiple scattering diminish with increasing muon momentum. As the momentum of the muon increases, the contrast of the image goes down and therefore requires higher resolution in the muon spectrometer to resolve the image. The variance of the measured muon momentum reaches a minimum and then increases with increasing muon momentum. The impact of the increase in variance is to require a higher integrated muon flux to reduce fluctuations. The flux requirements and level of contrast needed for high resolution muon computed tomography are well matched to the muons produced in the pion decay pipe at a neutrino beam facility and what can be achieved for momentum resolution in a muon spectrometer. Such an imaging system can be applied in archaeology, art history, engineering, material identification and whenever there is a need to image inside a transportable object constructed of dense materials

  18. Depth of interaction resolution measurements for a high resolution PET detector using position sensitive avalanche photodiodes

    International Nuclear Information System (INIS)

    Yang Yongfeng; Dokhale, Purushottam A; Silverman, Robert W; Shah, Kanai S; McClish, Mickel A; Farrell, Richard; Entine, Gerald; Cherry, Simon R

    2006-01-01

    We explore dual-ended read out of LSO arrays with two position sensitive avalanche photodiodes (PSAPDs) as a high resolution, high efficiency depth-encoding detector for PET applications. Flood histograms, energy resolution and depth of interaction (DOI) resolution were measured for unpolished LSO arrays with individual crystal sizes of 1.0, 1.3 and 1.5 mm, and for a polished LSO array with 1.3 mm pixels. The thickness of the crystal arrays was 20 mm. Good flood histograms were obtained for all four arrays, and crystals in all four arrays can be clearly resolved. Although the amplitude of each PSAPD signal decreases as the interaction depth moves further from the PSAPD, the sum of the two PSAPD signals is essentially constant with irradiation depth for all four arrays. The energy resolutions were similar for all four arrays, ranging from 14.7% to 15.4%. A DOI resolution of 3-4 mm (including the width of the irradiation band which is ∼2 mm) was obtained for all the unpolished arrays. The best DOI resolution was achieved with the unpolished 1 mm array (average 3.5 mm). The DOI resolution for the 1.3 mm and 1.5 mm unpolished arrays was 3.7 and 4.0 mm respectively. For the polished array, the DOI resolution was only 16.5 mm. Summing the DOI profiles across all crystals for the 1 mm array only degraded the DOI resolution from 3.5 mm to 3.9 mm, indicating that it may not be necessary to calibrate the DOI response separately for each crystal within an array. The DOI response of individual crystals in the array confirms this finding. These results provide a detailed characterization of the DOI response of these PSAPD-based PET detectors which will be important in the design and calibration of a PET scanner making use of this detector approach

  19. A high resolution x-ray fluorescence spectrometer for near edge absorption studies

    International Nuclear Information System (INIS)

    Stojanoff, V.; Hamalainen, K.; Siddons, D.P.; Hastings, J.B.; Berman, L.E.; Cramer, S.; Smith, G.

    1991-01-01

    A high resolution fluorescence spectrometer using a Johann geometry in a back scattering arrangement was developed. The spectrometer, with a resolution of 0.3 eV at 6.5 keV, combined with an incident beam, with a resolution of 0.7 eV, form the basis of a high resolution instrument for measuring x-ray absorption spectra. The advantages of the instrument are illustrated with the near edge absorption spectrum of dysprosium nitrate. 10 refs., 4 figs

  20. High Frequency High Spectral Resolution Focal Plane Arrays for AtLAST

    Science.gov (United States)

    Baryshev, Andrey

    2018-01-01

    Large collecting area single dish telescope such as ATLAST will be especially effective for medium (R 1000) and high (R 50000) spectral resolution observations. Large focal plane array is a natural solution to increase mapping speed. For medium resolution direct detectors with filter banks (KIDs) and or heterodyne technology can be employed. We will analyze performance limits of comparable KID and SIS focal plane array taking into account quantum limit and high background condition of terrestrial observing site. For large heterodyne focal plane arrays, a high current density AlN junctions open possibility of large instantaneous bandwidth >40%. This and possible multi frequency band FPSs presents a practical challenge for spatial sampling and scanning strategies. We will discuss phase array feeds as a possible solution, including a modular back-end system, which can be shared between KID and SIS based FPA. Finally we will discuss achievable sensitivities and pixel co unts for a high frequency (>500 GHz) FPAs and address main technical challenges: LO distribution, wire counts, bias line multiplexing, and monolithic vs. discrete mixer component integration.

  1. A new omni-directional multi-camera system for high resolution surveillance

    Science.gov (United States)

    Cogal, Omer; Akin, Abdulkadir; Seyid, Kerem; Popovic, Vladan; Schmid, Alexandre; Ott, Beat; Wellig, Peter; Leblebici, Yusuf

    2014-05-01

    Omni-directional high resolution surveillance has a wide application range in defense and security fields. Early systems used for this purpose are based on parabolic mirror or fisheye lens where distortion due to the nature of the optical elements cannot be avoided. Moreover, in such systems, the image resolution is limited to a single image sensor's image resolution. Recently, the Panoptic camera approach that mimics the eyes of flying insects using multiple imagers has been presented. This approach features a novel solution for constructing a spherically arranged wide FOV plenoptic imaging system where the omni-directional image quality is limited by low-end sensors. In this paper, an overview of current Panoptic camera designs is provided. New results for a very-high resolution visible spectrum imaging and recording system inspired from the Panoptic approach are presented. The GigaEye-1 system, with 44 single cameras and 22 FPGAs, is capable of recording omni-directional video in a 360°×100° FOV at 9.5 fps with a resolution over (17,700×4,650) pixels (82.3MP). Real-time video capturing capability is also verified at 30 fps for a resolution over (9,000×2,400) pixels (21.6MP). The next generation system with significantly higher resolution and real-time processing capacity, called GigaEye-2, is currently under development. The important capacity of GigaEye-1 opens the door to various post-processing techniques in surveillance domain such as large perimeter object tracking, very-high resolution depth map estimation and high dynamicrange imaging which are beyond standard stitching and panorama generation methods.

  2. EMODnet High Resolution Seabed Mapping - further developing a high resolution digital bathymetry for European seas

    Science.gov (United States)

    Schaap, D.; Schmitt, T.

    2017-12-01

    Access to marine data is a key issue for the EU Marine Strategy Framework Directive and the EU Marine Knowledge 2020 agenda and includes the European Marine Observation and Data Network (EMODnet) initiative. EMODnet aims at assembling European marine data, data products and metadata from diverse sources in a uniform way. The EMODnet Bathymetry project has developed Digital Terrain Models (DTM) for the European seas. These have been produced from survey and aggregated data sets that are indexed with metadata by adopting the SeaDataNet Catalogue services. SeaDataNet is a network of major oceanographic data centres around the European seas that manage, operate and further develop a pan-European infrastructure for marine and ocean data management. The latest EMODnet Bathymetry DTM release has a grid resolution of 1/8 arcminute and covers all European sea regions. Use has been made of circa 7800 gathered survey datasets and composite DTMs. Catalogues and the EMODnet DTM are published at the dedicated EMODnet Bathymetry portal including a versatile DTM viewing and downloading service. End December 2016 the Bathymetry project has been succeeded by EMODnet High Resolution Seabed Mapping (HRSM). This continues gathering of bathymetric in-situ data sets with extra efforts for near coastal waters and coastal zones. In addition Satellite Derived Bathymetry data are included to fill gaps in coverage of the coastal zones. The extra data and composite DTMs will increase the coverage of the European seas and its coastlines, and provide input for producing an EMODnet DTM with a common resolution of 1/16 arc minutes. The Bathymetry Viewing and Download service will be upgraded to provide a multi-resolution map and including 3D viewing. The higher resolution DTMs will also be used to determine best-estimates of the European coastline for a range of tidal levels (HAT, MHW, MSL, Chart Datum, LAT), thereby making use of a tidal model for Europe. Extra challenges will be `moving to the

  3. High resolution microphotonic needle for endoscopic imaging (Conference Presentation)

    Science.gov (United States)

    Tadayon, Mohammad Amin; Mohanty, Aseema; Roberts, Samantha P.; Barbosa, Felippe; Lipson, Michal

    2017-02-01

    GRIN (Graded index) lens have revolutionized micro endoscopy enabling deep tissue imaging with high resolution. The challenges of traditional GRIN lenses are their large size (when compared with the field of view) and their limited resolution. This is because of the relatively weak NA in standard graded index lenses. Here we introduce a novel micro-needle platform for endoscopy with much higher resolution than traditional GRIN lenses and a FOV that corresponds to the whole cross section of the needle. The platform is based on polymeric (SU-8) waveguide integrated with a microlens micro fabricated on a silicon substrate using a unique molding process. Due to the high index of refraction of the material the NA of the needle is much higher than traditional GRIN lenses. We tested the probe in a fluorescent dye solution (19.6 µM Alexa Flour 647 solution) and measured a numerical aperture of 0.25, focal length of about 175 µm and minimal spot size of about 1.6 µm. We show that the platform can image a sample with the field of view corresponding to the cross sectional area of the waveguide (80x100 µm2). The waveguide size can in principle be modified to vary size of the imaging field of view. This demonstration, combined with our previous work demonstrating our ability to implant the high NA needle in a live animal, shows that the proposed system can be used for deep tissue imaging with very high resolution and high field of view.

  4. Imaging collagen type I fibrillogenesis with high spatiotemporal resolution

    International Nuclear Information System (INIS)

    Stamov, Dimitar R; Stock, Erik; Franz, Clemens M; Jähnke, Torsten; Haschke, Heiko

    2015-01-01

    Fibrillar collagens, such as collagen type I, belong to the most abundant extracellular matrix proteins and they have received much attention over the last five decades due to their large interactome, complex hierarchical structure and high mechanical stability. Nevertheless, the collagen self-assembly process is still incompletely understood. Determining the real-time kinetics of collagen type I formation is therefore pivotal for better understanding of collagen type I structure and function, but visualising the dynamic self-assembly process of collagen I on the molecular scale requires imaging techniques offering high spatiotemporal resolution. Fast and high-speed scanning atomic force microscopes (AFM) provide the means to study such processes on the timescale of seconds under near-physiological conditions. In this study we have applied fast AFM tip scanning to study the assembly kinetics of fibrillar collagen type I nanomatrices with a temporal resolution reaching eight seconds for a frame size of 500 nm. By modifying the buffer composition and pH value, the kinetics of collagen fibrillogenesis can be adjusted for optimal analysis by fast AFM scanning. We furthermore show that amplitude-modulation imaging can be successfully applied to extract additional structural information from collagen samples even at high scan rates. Fast AFM scanning with controlled amplitude modulation therefore provides a versatile platform for studying dynamic collagen self-assembly processes at high resolution. - Highlights: • Continuous non-invasive time-lapse investigation of collagen I fibrillogenesis in situ. • Imaging of collagen I self-assembly with high spatiotemporal resolution. • Application of setpoint modulation to study the hierarchical structure of collagen I. • Observing real-time formation of the D-banding pattern in collagen I

  5. Imaging collagen type I fibrillogenesis with high spatiotemporal resolution

    Energy Technology Data Exchange (ETDEWEB)

    Stamov, Dimitar R, E-mail: stamov@jpk.com [JPK Instruments AG, Bouchéstrasse 12, 12435 Berlin (Germany); Stock, Erik [JPK Instruments AG, Bouchéstrasse 12, 12435 Berlin (Germany); Franz, Clemens M [DFG-Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1a, 76131 Karlsruhe (Germany); Jähnke, Torsten; Haschke, Heiko [JPK Instruments AG, Bouchéstrasse 12, 12435 Berlin (Germany)

    2015-02-15

    Fibrillar collagens, such as collagen type I, belong to the most abundant extracellular matrix proteins and they have received much attention over the last five decades due to their large interactome, complex hierarchical structure and high mechanical stability. Nevertheless, the collagen self-assembly process is still incompletely understood. Determining the real-time kinetics of collagen type I formation is therefore pivotal for better understanding of collagen type I structure and function, but visualising the dynamic self-assembly process of collagen I on the molecular scale requires imaging techniques offering high spatiotemporal resolution. Fast and high-speed scanning atomic force microscopes (AFM) provide the means to study such processes on the timescale of seconds under near-physiological conditions. In this study we have applied fast AFM tip scanning to study the assembly kinetics of fibrillar collagen type I nanomatrices with a temporal resolution reaching eight seconds for a frame size of 500 nm. By modifying the buffer composition and pH value, the kinetics of collagen fibrillogenesis can be adjusted for optimal analysis by fast AFM scanning. We furthermore show that amplitude-modulation imaging can be successfully applied to extract additional structural information from collagen samples even at high scan rates. Fast AFM scanning with controlled amplitude modulation therefore provides a versatile platform for studying dynamic collagen self-assembly processes at high resolution. - Highlights: • Continuous non-invasive time-lapse investigation of collagen I fibrillogenesis in situ. • Imaging of collagen I self-assembly with high spatiotemporal resolution. • Application of setpoint modulation to study the hierarchical structure of collagen I. • Observing real-time formation of the D-banding pattern in collagen I.

  6. High-resolution fiber-optic microendoscopy for in situ cellular imaging.

    Science.gov (United States)

    Pierce, Mark; Yu, Dihua; Richards-Kortum, Rebecca

    2011-01-11

    Many biological and clinical studies require the longitudinal study and analysis of morphology and function with cellular level resolution. Traditionally, multiple experiments are run in parallel, with individual samples removed from the study at sequential time points for evaluation by light microscopy. Several intravital techniques have been developed, with confocal, multiphoton, and second harmonic microscopy all demonstrating their ability to be used for imaging in situ. With these systems, however, the required infrastructure is complex and expensive, involving scanning laser systems and complex light sources. Here we present a protocol for the design and assembly of a high-resolution microendoscope which can be built in a day using off-the-shelf components for under US$5,000. The platform offers flexibility in terms of image resolution, field-of-view, and operating wavelength, and we describe how these parameters can be easily modified to meet the specific needs of the end user. We and others have explored the use of the high-resolution microendoscope (HRME) in in vitro cell culture, in excised and living animal tissues, and in human tissues in vivo. Users have reported the use of several different fluorescent contrast agents, including proflavine, benzoporphyrin-derivative monoacid ring A (BPD-MA), and fluoroscein, all of which have received full, or investigational approval from the FDA for use in human subjects. High-resolution microendoscopy, in the form described here, may appeal to a wide range of researchers working in the basic and clinical sciences. The technique offers an effective and economical approach which complements traditional benchtop microscopy, by enabling the user to perform high-resolution, longitudinal imaging in situ.

  7. Compressed sensing cine imaging with high spatial or high temporal resolution for analysis of left ventricular function.

    Science.gov (United States)

    Goebel, Juliane; Nensa, Felix; Schemuth, Haemi P; Maderwald, Stefan; Gratz, Marcel; Quick, Harald H; Schlosser, Thomas; Nassenstein, Kai

    2016-08-01

    To assess two compressed sensing cine magnetic resonance imaging (MRI) sequences with high spatial or high temporal resolution in comparison to a reference steady-state free precession cine (SSFP) sequence for reliable quantification of left ventricular (LV) volumes. LV short axis stacks of two compressed sensing breath-hold cine sequences with high spatial resolution (SPARSE-SENSE HS: temporal resolution: 40 msec, in-plane resolution: 1.0 × 1.0 mm(2) ) and high temporal resolution (SPARSE-SENSE HT: temporal resolution: 11 msec, in-plane resolution: 1.7 × 1.7 mm(2) ) and of a reference cine SSFP sequence (standard SSFP: temporal resolution: 40 msec, in-plane resolution: 1.7 × 1.7 mm(2) ) were acquired in 16 healthy volunteers on a 1.5T MR system. LV parameters were analyzed semiautomatically twice by one reader and once by a second reader. The volumetric agreement between sequences was analyzed using paired t-test, Bland-Altman plots, and Passing-Bablock regression. Small differences were observed between standard SSFP and SPARSE-SENSE HS for stroke volume (SV; -7 ± 11 ml; P = 0.024), ejection fraction (EF; -2 ± 3%; P = 0.019), and myocardial mass (9 ± 9 g; P = 0.001), but not for end-diastolic volume (EDV; P = 0.079) and end-systolic volume (ESV; P = 0.266). No significant differences were observed between standard SSFP and SPARSE-SENSE HT regarding EDV (P = 0.956), SV (P = 0.088), and EF (P = 0.103), but for ESV (3 ± 5 ml; P = 0.039) and myocardial mass (8 ± 10 ml; P = 0.007). Bland-Altman analysis showed good agreement between the sequences (maximum bias ≤ -8%). Two compressed sensing cine sequences, one with high spatial resolution and one with high temporal resolution, showed good agreement with standard SSFP for LV volume assessment. J. Magn. Reson. Imaging 2016;44:366-374. © 2016 Wiley Periodicals, Inc.

  8. 1024 matrix image reconstruction: usefulness in high resolution chest CT

    International Nuclear Information System (INIS)

    Jeong, Sun Young; Chung, Myung Jin; Chong, Se Min; Sung, Yon Mi; Lee, Kyung Soo

    2006-01-01

    We tried to evaluate whether high resolution chest CT with a 1,024 matrix has a significant advantage in image quality compared to a 512 matrix. Each set of 512 and 1024 matrix high resolution chest CT scans with both 0.625 mm and 1.25 mm slice thickness were obtained from 26 patients. Seventy locations that contained twenty-four low density lesions without sharp boundary such as emphysema, and forty-six sharp linear densities such as linear fibrosis were selected; these were randomly displayed on a five mega pixel LCD monitor. All the images were masked for information concerning the matrix size and slice thickness. Two chest radiologists scored the image quality of each ar rowed lesion as follows: (1) undistinguishable, (2) poorly distinguishable, (3) fairly distinguishable, (4) well visible and (5) excellently visible. The scores were compared from the aspects of matrix size, slice thickness and the different observers by using ANOVA tests. The average and standard deviation of image quality were 3.09 (± .92) for the 0.625 mm x 512 matrix, 3.16 (± .84) for the 0.625 mm x 1024 matrix, 2.49 (± 1.02) for the 1.25 mm x 512 matrix, and 2.35 (± 1.02) for the 1.25 mm x 1024 matrix, respectively. The image quality on both matrices of the high resolution chest CT scans with a 0.625 mm slice thickness was significantly better than that on the 1.25 mm slice thickness (ρ < 0.001). However, the image quality on the 1024 matrix high resolution chest CT scans was not significantly different from that on the 512 matrix high resolution chest CT scans (ρ = 0.678). The interobserver variation between the two observers was not significant (ρ = 0.691). We think that 1024 matrix image reconstruction for high resolution chest CT may not be clinical useful

  9. DNA: Polymer and molecular code

    Science.gov (United States)

    Shivashankar, G. V.

    1999-10-01

    The thesis work focusses upon two aspects of DNA, the polymer and the molecular code. Our approach was to bring single molecule micromanipulation methods to the study of DNA. It included a home built optical microscope combined with an atomic force microscope and an optical tweezer. This combined approach led to a novel method to graft a single DNA molecule onto a force cantilever using the optical tweezer and local heating. With this method, a force versus extension assay of double stranded DNA was realized. The resolution was about 10 picoN. To improve on this force measurement resolution, a simple light backscattering technique was developed and used to probe the DNA polymer flexibility and its fluctuations. It combined the optical tweezer to trap a DNA tethered bead and the laser backscattering to detect the beads Brownian fluctuations. With this technique the resolution was about 0.1 picoN with a millisecond access time, and the whole entropic part of the DNA force-extension was measured. With this experimental strategy, we measured the polymerization of the protein RecA on an isolated double stranded DNA. We observed the progressive decoration of RecA on the l DNA molecule, which results in the extension of l , due to unwinding of the double helix. The dynamics of polymerization, the resulting change in the DNA entropic elasticity and the role of ATP hydrolysis were the main parts of the study. A simple model for RecA assembly on DNA was proposed. This work presents a first step in the study of genetic recombination. Recently we have started a study of equilibrium binding which utilizes fluorescence polarization methods to probe the polymerization of RecA on single stranded DNA. In addition to the study of material properties of DNA and DNA-RecA, we have developed experiments for which the code of the DNA is central. We studied one aspect of DNA as a molecular code, using different techniques. In particular the programmatic use of template specificity makes

  10. Study on a high resolution positron emission tomography scanner for brain study

    International Nuclear Information System (INIS)

    Nohara, N.; Tomitani, T.; Yamamoto, M.; Murayama, H.; Tanaka, E.

    1990-01-01

    The spatial resolution of positron emission tomography (PET) scanners is usually limited by the finite size of crystals such as bismuth germanate (BGO). To attain high resolution as well as high sensitivity, it is essential to use a large number of small BGO crystals arranged in close-packing on circular rings. In developing high resolution PET scanners, however, there are two physical factors limiting the spatial resolution. One is the finite range of positrons before annihilation and the other the deviation from 180 degrees of annihilation photons. The effect of the factors on the spatial resolution has been evaluated for positron-emitting sources as a function of detector ring radius. A high resolution PET scanner has been developed for brain study, aiming to have spatial resolutions as high as less than 4-mm FWHM in tomographic plane and less than 6-mm FWHM in axial direction at the detector ring center. For the goal of the high resolutions a multi-segment type of photomultiplier tubes has been specially designed and developed, which allows one tube to be directly coupled by four BGO crystals. The scanner consists of five detector rings of 47-cm in diameter, using all 1200 BGO crystals each measuring 5 mm x 12 mm x 30 mm. The scanner provides simultaneous 9 images by combination of in-plane and cross-plane, offering a 24-cm dia. x7.4-cm field-of-view. Physical performance of the scanner was investigated. At the ring center, the spatial resolution in the tomographic plane was measured to be 3.5-mm FWHM. The axial resolution was measured to be 5.7-mm FWHM for in-plane and 5.3-mm FWHM for cross-plane. Sensitivity for a 20-cm dia. uniform source was measured to be 9.5 kcps/μCi/ml for in-plane and 15.3 kcps/μCi/ml for cross-plane. (J.P.N.)

  11. Beam-transport system for high-resolution heavy-ion spectroscopy

    International Nuclear Information System (INIS)

    Roussel, P.; Kashy, E.

    1980-01-01

    A method is given to adjust a beam-transport system to the requirements of high-energy resolution heavy-ion spectroscopy. The results of a test experiment performed on a MP tandem with a 12 C beam are shown. A drastic improvement in energy resolution is obtained for a kinematical factor K=1/p dp/dtheta=0.12 [fr

  12. Workshop on high-resolution, large-acceptance spectrometers

    Energy Technology Data Exchange (ETDEWEB)

    Zeidman, B. (ed.)

    1981-01-01

    The purpose of the Workshop on High-Resolution, Large-Acceptance Spectrometers was to provide a means for exchange of information among those actively engaged in the design and construction of these new spectrometers. Thirty-seven papers were prepared for the data base.

  13. Very high-resolution regional climate simulations over Scandinavia-present climate

    DEFF Research Database (Denmark)

    Christensen, Ole B.; Christensen, Jens H.; Machenhauer, Bennert

    1998-01-01

    realistically simulated. It is found in particular that in mountainous regions the high-resolution simulation shows improvements in the simulation of hydrologically relevant fields such as runoff and snow cover. Also, the distribution of precipitation on different intensity classes is most realistically...... on a high-density station network for the Scandinavian countries compiled for the present study. The simulated runoff is compared with observed data from Sweden extracted from a Swedish climatological atlas. These runoff data indicate that the precipitation analyses are underestimating the true...... simulated in the high-resolution simulation. It does, however, inherit certain large-scale systematic errors from the driving GCM. In many cases these errors increase with increasing resolution. Model verification of near-surface temperature and precipitation is made using a new gridded climatology based...

  14. Directed PCR-free engineering of highly repetitive DNA sequences

    Directory of Open Access Journals (Sweden)

    Preissler Steffen

    2011-09-01

    Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

  15. Digital signal processors for cryogenic high-resolution x-ray detector readout

    International Nuclear Information System (INIS)

    Friedrich, Stephan; Drury, Owen B.; Bechstein, Sylke; Hennig, Wolfgang; Momayezi, Michael

    2003-01-01

    We are developing fast digital signal processors (DSPs) to read out superconducting high-resolution X-ray detectors with on-line pulse processing. For superconducting tunnel junction (STJ) detector read-out, the DSPs offer online filtering, rise time discrimination and pile-up rejection. Compared to analog pulse processing, DSP readout somewhat degrades the detector resolution, but improves the spectral purity of the detector response. We discuss DSP performance with our 9-channel STJ array for synchrotron-based high-resolution X-ray spectroscopy. (author)

  16. High spatial resolution CT image reconstruction using parallel computing

    International Nuclear Information System (INIS)

    Yin Yin; Liu Li; Sun Gongxing

    2003-01-01

    Using the PC cluster system with 16 dual CPU nodes, we accelerate the FBP and OR-OSEM reconstruction of high spatial resolution image (2048 x 2048). Based on the number of projections, we rewrite the reconstruction algorithms into parallel format and dispatch the tasks to each CPU. By parallel computing, the speedup factor is roughly equal to the number of CPUs, which can be up to about 25 times when 25 CPUs used. This technique is very suitable for real-time high spatial resolution CT image reconstruction. (authors)

  17. High resolution and simultaneous monitoring of airborne radionuclides

    International Nuclear Information System (INIS)

    Abe, T.; Yamaguchi, Y.; Muguntha Manikandan, N.; Komura, K.

    2005-01-01

    By using 11 extremely low background Ge detectors at Ogoya Underground Laboratory, it became possible to investigate temporal variations of airborne 212 Pb (T 1/2 =10.6 h) along with 210 Pb and 7 Be with order of magnitude higher time resolution. Then, we have measured airborne nuclides at three monitoring points, (1) roof of our laboratory (LLRL; 40 m ASL), (2) Shinshiku Plateau (640 m ASL) located about 8 km from LLRL as a comparison of vertical distribution, and (3) Hegura Island (10 m ASL) at about 50 km from Wajima located north of Noto Peninsula facing on the Sea of Japan (about 180 km to the north-northeast of LLRL), to investigate influence of Asian continent. Airborne nuclides were collected by high volume air samplers at intervals of a few hours at either two or three points simultaneously. In the same manner, high resolution monitoring was carried out also at the time of passage of typhoon and cold front. In this study, we observed drastic temporal variations of airborne radionuclides and correlations of multiple monitoring points. The results indicate that high resolution and simultaneous monitoring is very useful to understand dynamic state of variations of airborne nuclides due to short and long-term air-mass movement. (author)

  18. High-resolution multimodal clinical multiphoton tomography of skin

    Science.gov (United States)

    König, Karsten

    2011-03-01

    This review focuses on multimodal multiphoton tomography based on near infrared femtosecond lasers. Clinical multiphoton tomographs for 3D high-resolution in vivo imaging have been placed into the market several years ago. The second generation of this Prism-Award winning High-Tech skin imaging tool (MPTflex) was introduced in 2010. The same year, the world's first clinical CARS studies have been performed with a hybrid multimodal multiphoton tomograph. In particular, non-fluorescent lipids and water as well as mitochondrial fluorescent NAD(P)H, fluorescent elastin, keratin, and melanin as well as SHG-active collagen has been imaged with submicron resolution in patients suffering from psoriasis. Further multimodal approaches include the combination of multiphoton tomographs with low-resolution wide-field systems such as ultrasound, optoacoustical, OCT, and dermoscopy systems. Multiphoton tomographs are currently employed in Australia, Japan, the US, and in several European countries for early diagnosis of skin cancer, optimization of treatment strategies, and cosmetic research including long-term testing of sunscreen nanoparticles as well as anti-aging products.

  19. Integrated High Resolution Monitoring of Mediterranean vegetation

    Science.gov (United States)

    Cesaraccio, Carla; Piga, Alessandra; Ventura, Andrea; Arca, Angelo; Duce, Pierpaolo; Mereu, Simone

    2017-04-01

    The study of the vegetation features in a complex and highly vulnerable ecosystems, such as Mediterranean maquis, leads to the need of using continuous monitoring systems at high spatial and temporal resolution, for a better interpretation of the mechanisms of phenological and eco-physiological processes. Near-surface remote sensing techniques are used to quantify, at high temporal resolution, and with a certain degree of spatial integration, the seasonal variations of the surface optical and radiometric properties. In recent decades, the design and implementation of global monitoring networks involved the use of non-destructive and/or cheaper approaches such as (i) continuous surface fluxes measurement stations, (ii) phenological observation networks, and (iii) measurement of temporal and spatial variations of the vegetation spectral properties. In this work preliminary results from the ECO-SCALE (Integrated High Resolution Monitoring of Mediterranean vegetation) project are reported. The project was manly aimed to develop an integrated system for environmental monitoring based on digital photography, hyperspectral radiometry , and micrometeorological techniques during three years of experimentation (2013-2016) in a Mediterranean site of Italy (Capo Caccia, Alghero). The main results concerned the analysis of chromatic coordinates indices from digital images, to characterized the phenological patterns for typical shrubland species, determining start and duration of the growing season, and the physiological status in relation to different environmental drought conditions; then the seasonal patterns of canopy phenology, was compared to NEE (Net Ecosystem Exchange) patterns, showing similarities. However, maximum values of NEE and ER (Ecosystem respiration), and short term variation, seemed mainly tuned by inter annual pattern of meteorological variables, in particular of temperature recorded in the months preceding the vegetation green-up. Finally, green signals

  20. A multi-channel high-resolution time recorder system

    International Nuclear Information System (INIS)

    Zhang Lingyun; Yang Xiaojun; Song Kezhu; Wang Yanfang

    2004-01-01

    This paper introduces a multi-channel and high-speed time recorder system, which was originally designed to work in the experiments of quantum cryptography research. The novelty of the system is that all the hardware logic is performed by only one FPGA. The system can achieve several desirable features, such as simplicity, high resolution and high processing speed. (authors)

  1. Application of high resolution synchrotron micro-CT radiation in dental implant osseointegration

    DEFF Research Database (Denmark)

    Neldam, Camilla Albeck; Lauridsen, Torsten; Rack, Alexander

    2015-01-01

    The purpose of this study was to describe a refined method using high-resolution synchrotron radiation microtomography (SRmicro-CT) to evaluate osseointegration and peri-implant bone volume fraction after titanium dental implant insertion. SRmicro-CT is considered gold standard evaluating bone...... microarchitecture. Its high resolution, high contrast, and excellent high signal-to-noise-ratio all contribute to the highest spatial resolutions achievable today. Using SRmicro-CT at a voxel size of 5 μm in an experimental goat mandible model, the peri-implant bone volume fraction was found to quickly increase...

  2. DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle.

    Science.gov (United States)

    Mikheikin, Andrey; Olsen, Anita; Leslie, Kevin; Russell-Pavier, Freddie; Yacoot, Andrew; Picco, Loren; Payton, Oliver; Toor, Amir; Chesney, Alden; Gimzewski, James K; Mishra, Bud; Reed, Jason

    2017-11-21

    Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new "nanomapping" method to detect and map precisely BCL2-IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM "nanomapping" technique can be complementary to both sequencing and other physical mapping approaches.

  3. An angle encoder for super-high resolution and super-high accuracy using SelfA

    Science.gov (United States)

    Watanabe, Tsukasa; Kon, Masahito; Nabeshima, Nobuo; Taniguchi, Kayoko

    2014-06-01

    Angular measurement technology at high resolution for applications such as in hard disk drive manufacturing machines, precision measurement equipment and aspherical process machines requires a rotary encoder with high accuracy, high resolution and high response speed. However, a rotary encoder has angular deviation factors during operation due to scale error or installation error. It has been assumed to be impossible to achieve accuracy below 0.1″ in angular measurement or control after the installation onto the rotating axis. Self-calibration (Lu and Trumper 2007 CIRP Ann. 56 499; Kim et al 2011 Proc. MacroScale; Probst 2008 Meas. Sci. Technol. 19 015101; Probst et al Meas. Sci. Technol. 9 1059; Tadashi and Makoto 1993 J. Robot. Mechatronics 5 448; Ralf et al 2006 Meas. Sci. Technol. 17 2811) and cross-calibration (Probst et al 1998 Meas. Sci. Technol. 9 1059; Just et al 2009 Precis. Eng. 33 530; Burnashev 2013 Quantum Electron. 43 130) technologies for a rotary encoder have been actively discussed on the basis of the principle of circular closure. This discussion prompted the development of rotary tables which achieve reliable and high accuracy angular verification. We apply these technologies for the development of a rotary encoder not only to meet the requirement of super-high accuracy but also to meet that of super-high resolution. This paper presents the development of an encoder with 221 = 2097 152 resolutions per rotation (360°), that is, corresponding to a 0.62″ signal period, achieved by the combination of a laser rotary encoder supplied by Magnescale Co., Ltd and a self-calibratable encoder (SelfA) supplied by The National Institute of Advanced Industrial Science & Technology (AIST). In addition, this paper introduces the development of a rotary encoder to guarantee ±0.03″ accuracy at any point of the interpolated signal, with respect to the encoder at the minimum resolution of 233, that is, corresponding to a 0.0015″ signal period after

  4. Quantifying and containing the curse of high resolution coronal imaging

    Directory of Open Access Journals (Sweden)

    V. Delouille

    2008-10-01

    Full Text Available Future missions such as Solar Orbiter (SO, InterHelioprobe, or Solar Probe aim at approaching the Sun closer than ever before, with on board some high resolution imagers (HRI having a subsecond cadence and a pixel area of about (80 km2 at the Sun during perihelion. In order to guarantee their scientific success, it is necessary to evaluate if the photon counts available at these resolution and cadence will provide a sufficient signal-to-noise ratio (SNR. For example, if the inhomogeneities in the Quiet Sun emission prevail at higher resolution, one may hope to locally have more photon counts than in the case of a uniform source. It is relevant to quantify how inhomogeneous the quiet corona will be for a pixel pitch that is about 20 times smaller than in the case of SoHO/EIT, and 5 times smaller than TRACE. We perform a first step in this direction by analyzing and characterizing the spatial intermittency of Quiet Sun images thanks to a multifractal analysis. We identify the parameters that specify the scale-invariance behavior. This identification allows next to select a family of multifractal processes, namely the Compound Poisson Cascades, that can synthesize artificial images having some of the scale-invariance properties observed on the recorded images. The prevalence of self-similarity in Quiet Sun coronal images makes it relevant to study the ratio between the SNR present at SoHO/EIT images and in coarsened images. SoHO/EIT images thus play the role of "high resolution" images, whereas the "low-resolution" coarsened images are rebinned so as to simulate a smaller angular resolution and/or a larger distance to the Sun. For a fixed difference in angular resolution and in Spacecraft-Sun distance, we determine the proportion of pixels having a SNR preserved at high resolution given a particular increase in effective area. If scale-invariance continues to prevail at smaller scales, the conclusion reached with SoHO/EIT images can be transposed

  5. A High-resolution Reanalysis for the European CORDEX Region

    Science.gov (United States)

    Bentzien, Sabrina; Bollmeyer, Christoph; Crewell, Susanne; Friederichs, Petra; Hense, Andreas; Keller, Jan; Keune, Jessica; Kneifel, Stefan; Ohlwein, Christian; Pscheidt, Ieda; Redl, Stephanie; Steinke, Sandra

    2014-05-01

    A High-resolution Reanalysis for the European CORDEX Region Within the Hans-Ertel-Centre for Weather Research (HErZ), the climate monitoring branch concentrates efforts on the assessment and analysis of regional climate in Germany and Europe. In joint cooperation with DWD (German Meteorological Service), a high-resolution reanalysis system based on the COSMO model has been developed. Reanalyses gain more and more importance as a source of meteorological information for many purposes and applications. Several global reanalyses projects (e.g., ERA, MERRA, CSFR, JMA9) produce and verify these data sets to provide time series as long as possible combined with a high data quality. Due to a spatial resolution down to 50-70km and 3-hourly temporal output, they are not suitable for small scale problems (e.g., regional climate assessment, meso-scale NWP verification, input for subsequent models such as river runoff simulations). The implementation of regional reanalyses based on a limited area model along with a data assimilation scheme is able to generate reanalysis data sets with high spatio-temporal resolution. The work presented here focuses on the regional reanalysis for Europe with a domain matching the CORDEX-EURO-11 specifications, albeit at a higher spatial resolution, i.e., 0.055° (6km) instead of 0.11° (12km). The COSMO reanalysis system comprises the assimilation of observational data using the existing nudging scheme of COSMO and is complemented by a special soil moisture analysis and boundary conditions given by ERA-interim data. The reanalysis data set currently covers 6 years (2007-2012). The evaluation of the reanalyses is done using independent observations with special emphasis on precipitation and high-impact weather situations. The development and evaluation of the COSMO-based reanalysis for the CORDEX-Euro domain can be seen as a preparation for joint European activities on the development of an ensemble system of regional reanalyses for Europe.

  6. High Time Resolution Astrophysics

    CERN Document Server

    Phelan, Don; Shearer, Andrew

    2008-01-01

    High Time Resolution Astrophysics (HTRA) is an important new window to the universe and a vital tool in understanding a range of phenomena from diverse objects and radiative processes. This importance is demonstrated in this volume with the description of a number of topics in astrophysics, including quantum optics, cataclysmic variables, pulsars, X-ray binaries and stellar pulsations to name a few. Underlining this science foundation, technological developments in both instrumentation and detectors are described. These instruments and detectors combined cover a wide range of timescales and can measure fluxes, spectra and polarisation. These advances make it possible for HTRA to make a big contribution to our understanding of the Universe in the next decade.

  7. High resolution ultrasonic densitometer

    International Nuclear Information System (INIS)

    Dress, W.B.

    1983-01-01

    The velocity of torsional stress pulses in an ultrasonic waveguide of non-circular cross section is affected by the temperature and density of the surrounding medium. Measurement of the transit times of acoustic echoes from the ends of a sensor section are interpreted as level, density, and temperature of the fluid environment surrounding that section. This paper examines methods of making these measurements to obtain high resolution, temperature-corrected absolute and relative density and level determinations of the fluid. Possible applications include on-line process monitoring, a hand-held density probe for battery charge state indication, and precise inventory control for such diverse fluids as uranium salt solutions in accountability storage and gasoline in service station storage tanks

  8. Simulation study for high resolution alpha particle spectrometry with mesh type collimator

    International Nuclear Information System (INIS)

    Park, Seunghoon; Kwak, Sungwoo; Kang, Hanbyeol; Shin, Jungki; Park, Iljin

    2014-01-01

    An alpha particle spectrometry with a mesh type collimator plays a crucial role in identifying specific radionuclide in a radioactive source collected from the atmosphere or environment. The energy resolution is degraded without collimation because particles with a high angle have a longer path to travel in the air. Therefore, collision with the background increases. The collimator can cut out particles which traveling at a high angle. As a result, an energy distribution with high resolution can be obtained. Therefore, the mesh type collimator is simulated for high resolution alpha particle spectrometry. In conclusion, the collimator can improve resolution. With collimator, the collimator is a role of cutting out particles with a high angle, so, low energy tail and broadened energy distribution can be reduced. The mesh diameter is found out as an important factor to control resolution and counting efficiency. Therefore, a target particle, for example, 235 U, can be distinguished by a detector with a collimator under a mixture of various nuclides, for example: 232 U, 238 U, and 232 Th

  9. Highlighting the DNA damage response with ultrashort laser pulses in the near infrared and kinetic modeling

    Directory of Open Access Journals (Sweden)

    Elisa eFerrando-May

    2013-07-01

    Full Text Available Our understanding of the mechanisms governing the response to DNA damage in higher eucaryotes crucially depends on our ability to dissect the temporal and spatial organization of the cellular machinery responsible for maintaining genomic integrity. To achieve this goal, we need experimental tools to inflict DNA lesions with high spatial precision at pre-defined locations, and to visualize the ensuing reactions with adequate temporal resolution. Near-infrared femtosecond laser pulses focused through high-aperture objective lenses of advanced scanning microscopes offer the advantage of inducing DNA damage in a 3D-confined volume of subnuclear dimensions. This high spatial resolution results from the highly nonlinear nature of the excitation process. Here we review recent progress based on the increasing availability of widely tunable and user-friendly technology of ultrafast lasers in the near infrared. We present a critical evaluation of this approach for DNA microdamage as compared to the currently prevalent use of UV or VIS laser irradiation, the latter in combination with photosensitizers. Current and future applications in the field of DNA repair and DNA-damage dependent chromatin dynamics are outlined. Finally, we discuss the requirement for proper simulation and quantitative modeling. We focus in particular on approaches to measure the effect of DNA damage on the mobility of nuclear proteins and consider the pros and cons of frequently used analysis models for FRAP and photoactivation and their applicability to nonlinear photoperturbation experiments.

  10. Low-resolution ship detection from high-altitude aerial images

    Science.gov (United States)

    Qi, Shengxiang; Wu, Jianmin; Zhou, Qing; Kang, Minyang

    2018-02-01

    Ship detection from optical images taken by high-altitude aircrafts such as unmanned long-endurance airships and unmanned aerial vehicles has broad applications in marine fishery management, ship monitoring and vessel salvage. However, the major challenge is the limited capability of information processing on unmanned high-altitude platforms. Furthermore, in order to guarantee the wide detection range, unmanned aircrafts generally cruise at high altitudes, resulting in imagery with low-resolution targets and strong clutters suffered by heavy clouds. In this paper, we propose a low-resolution ship detection method to extract ships from these high-altitude optical images. Inspired by a recent research on visual saliency detection indicating that small salient signals could be well detected by a gradient enhancement operation combined with Gaussian smoothing, we propose the facet kernel filtering to rapidly suppress cluttered backgrounds and delineate candidate target regions from the sea surface. Then, the principal component analysis (PCA) is used to compute the orientation of the target axis, followed by a simplified histogram of oriented gradient (HOG) descriptor to characterize the ship shape property. Finally, support vector machine (SVM) is applied to discriminate real targets and false alarms. Experimental results show that the proposed method actually has high efficiency in low-resolution ship detection.

  11. Gas scintillation glass GEM detector for high-resolution X-ray imaging and CT

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, T., E-mail: fujiwara-t@aist.go.jp [Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan); Mitsuya, Y. [Nuclear Professional School, The University of Tokyo, Tokai, Naka, Ibaraki 319-1188 (Japan); Fushie, T. [Radiment Lab. Inc., Setagaya, Tokyo 156-0044 (Japan); Murata, K.; Kawamura, A.; Koishikawa, A. [XIT Co., Naruse, Machida, Tokyo 194-0045 (Japan); Toyokawa, H. [Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan); Takahashi, H. [Institute of Engineering Innovation, School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8654 (Japan)

    2017-04-01

    A high-spatial-resolution X-ray-imaging gaseous detector has been developed with a single high-gas-gain glass gas electron multiplier (G-GEM), scintillation gas, and optical camera. High-resolution X-ray imaging of soft elements is performed with a spatial resolution of 281 µm rms and an effective area of 100×100 mm. In addition, high-resolution X-ray 3D computed tomography (CT) is successfully demonstrated with the gaseous detector. It shows high sensitivity to low-energy X-rays, which results in high-contrast radiographs of objects containing elements with low atomic numbers. In addition, the high yield of scintillation light enables fast X-ray imaging, which is an advantage for constructing CT images with low-energy X-rays.

  12. Novel techniques in VUV high-resolution spectroscopy

    NARCIS (Netherlands)

    Ubachs, W.M.G.; Salumbides, E.J.; Eikema, K.S.E.; de Oliveira, N.; Nahon, L.

    2014-01-01

    Novel VUV sources and techniques for VUV spectroscopy are reviewed. Laser-based VUV sources have been developed via non-linear upconversion of laser pulses in the nanosecond (ns), the picosecond (ps), and femtosecond (fs) domain, and are applied in high-resolution gas phase spectroscopic studies.

  13. Duchenne muscular dystrophy: High-resolution melting curve ...

    African Journals Online (AJOL)

    Duchenne muscular dystrophy: High-resolution melting curve analysis as an affordable diagnostic mutation scanning tool in a South African cohort. ... Genetic screening for D/BMD in South Africa currently includes multiple ligase-dependent probe amplification (MLPA) for exonic deletions and duplications and linkage ...

  14. Production of highly knotted DNA by means of cosmid circularization inside phage capsids

    Directory of Open Access Journals (Sweden)

    Trigueros Sonia

    2007-12-01

    Full Text Available Abstract Background The formation of DNA knots is common during biological transactions. Yet, functional implications of knotted DNA are not fully understood. Moreover, potential applications of DNA molecules condensed by means of knotting remain to be explored. A convenient method to produce abundant highly knotted DNA would be highly valuable for these studies. Results We had previously shown that circularization of the 11.2 kb linear DNA of phage P4 inside its viral capsid generates complex knots by the effect of confinement. We demonstrate here that this mechanism is not restricted to the viral genome. We constructed DNA cosmids as small as 5 kb and introduced them inside P4 capsids. Such cosmids were then recovered as a complex mixture of highly knotted DNA circles. Over 250 μg of knotted cosmid were typically obtained from 1 liter of bacterial culture. Conclusion With this biological system, DNA molecules of varying length and sequence can be shaped into very complex and heterogeneous knotted forms. These molecules can be produced in preparative amounts suitable for systematic studies and applications.

  15. High-Resolution 3 T MR Microscopy Imaging of Arterial Walls

    International Nuclear Information System (INIS)

    Sailer, Johannes; Rand, Thomas; Berg, Andreas; Sulzbacher, Irene; Peloschek, P.; Hoelzenbein, Thomas; Lammer, Johannes

    2006-01-01

    Purpose. To achieve a high spatial resolution in MR imaging that allows for clear visualization of anatomy and even histology and documentation of plaque morphology in in vitro samples from patients with advanced atherosclerosis. A further objective of our study was to evaluate whether T2-weighted high-resolution MR imaging can provide accurate classification of atherosclerotic plaque according to a modified American Heart Association classification. Methods. T2-weighted images of arteries were obtained in 13 in vitro specimens using a 3 T MR unit (Medspec 300 Avance/Bruker, Ettlingen, Germany) combined with a dedicated MR microscopy system. Measurement parameters were: T2-weighted sequences with TR 3.5 sec, TE 15-120 msec; field of view (FOV) 1.4 x 1.4; NEX 8; matrix 192; and slice thickness 600 μm. MR measurements were compared with corresponding histologic sections. Results. We achieved excellent spatial and contrast resolution in all specimens. We found high agreement between MR images and histology with regard to the morphology and extent of intimal proliferations in all but 2 specimens. We could differentiate fibrous caps and calcifications from lipid plaque components based on differences in signal intensity in order to differentiate hard and soft atheromatous plaques. Hard plaques with predominantly intimal calcifications were found in 7 specimens, and soft plaques with a cholesterol/lipid content in 5 cases. In all specimens, hemorrhage or thrombus formation, and fibrotic and hyalinized tissue could be detected on both MR imaging and histopathology. Conclusion. High-resolution, high-field MR imaging of arterial walls demonstrates the morphologic features, volume, and extent of intimal proliferations with high spatial and contrast resolution in in vitro specimens and can differentiate hard and soft plaques

  16. Motivation for an SSC detector with ultra-high resolution photon detection

    International Nuclear Information System (INIS)

    Gunion, J.F.; Kane, G.

    1992-01-01

    It is well known that incorporating ultra-high resolution photon detection into a general purpose detector for the SSC will be extremely difficult. The authors will argue that the physics signals that could be missed without such resolution are of such importance that a special purpose detector designed specifically for photon final state modes should be constructed, if sufficient resolution cannot be achieved with general purpose detectors. The potentially great value of these signals as a probe of extremely high mass scales is stressed

  17. Comparison of Two Grid Refinement Approaches for High Resolution Regional Climate Modeling: MPAS vs WRF

    Science.gov (United States)

    Leung, L.; Hagos, S. M.; Rauscher, S.; Ringler, T.

    2012-12-01

    This study compares two grid refinement approaches using global variable resolution model and nesting for high-resolution regional climate modeling. The global variable resolution model, Model for Prediction Across Scales (MPAS), and the limited area model, Weather Research and Forecasting (WRF) model, are compared in an idealized aqua-planet context with a focus on the spatial and temporal characteristics of tropical precipitation simulated by the models using the same physics package from the Community Atmosphere Model (CAM4). For MPAS, simulations have been performed with a quasi-uniform resolution global domain at coarse (1 degree) and high (0.25 degree) resolution, and a variable resolution domain with a high-resolution region at 0.25 degree configured inside a coarse resolution global domain at 1 degree resolution. Similarly, WRF has been configured to run on a coarse (1 degree) and high (0.25 degree) resolution tropical channel domain as well as a nested domain with a high-resolution region at 0.25 degree nested two-way inside the coarse resolution (1 degree) tropical channel. The variable resolution or nested simulations are compared against the high-resolution simulations that serve as virtual reality. Both MPAS and WRF simulate 20-day Kelvin waves propagating through the high-resolution domains fairly unaffected by the change in resolution. In addition, both models respond to increased resolution with enhanced precipitation. Grid refinement induces zonal asymmetry in precipitation (heating), accompanied by zonal anomalous Walker like circulations and standing Rossby wave signals. However, there are important differences between the anomalous patterns in MPAS and WRF due to differences in the grid refinement approaches and sensitivity of model physics to grid resolution. This study highlights the need for "scale aware" parameterizations in variable resolution and nested regional models.

  18. Toward high-resolution NMR spectroscopy of microscopic liquid samples

    Energy Technology Data Exchange (ETDEWEB)

    Butler, Mark C.; Mehta, Hardeep S.; Chen, Ying; Reardon, Patrick N.; Renslow, Ryan S.; Khbeis, Michael; Irish, Duane; Mueller, Karl T.

    2017-01-01

    A longstanding limitation of high-resolution NMR spectroscopy is the requirement for samples to have macroscopic dimensions. Commercial probes, for example, are designed for volumes of at least 5 mL, in spite of decades of work directed toward the goal of miniaturization. Progress in miniaturizing inductive detectors has been limited by a perceived need to meet two technical requirements: (1) minimal separation between the sample and the detector, which is essential for sensitivity, and (2) near-perfect magnetic-field homogeneity at the sample, which is typically needed for spectral resolution. The first of these requirements is real, but the second can be relaxed, as we demonstrate here. By using pulse sequences that yield high-resolution spectra in an inhomogeneous field, we eliminate the need for near-perfect field homogeneity and the accompanying requirement for susceptibility matching of microfabricated detector components. With this requirement removed, typical imperfections in microfabricated components can be tolerated, and detector dimensions can be matched to those of the sample, even for samples of volume << 5 uL. Pulse sequences that are robust to field inhomogeneity thus enable small-volume detection with optimal sensitivity. We illustrate the potential of this approach to miniaturization by presenting spectra acquired with a flat-wire detector that can easily be scaled to subnanoliter volumes. In particular, we report high-resolution NMR spectroscopy of an alanine sample of volume 500 pL.

  19. Gamma-Ray Imager With High Spatial And Spectral Resolution

    Science.gov (United States)

    Callas, John L.; Varnell, Larry S.; Wheaton, William A.; Mahoney, William A.

    1996-01-01

    Gamma-ray instrument developed to enable both two-dimensional imaging at relatively high spatial resolution and spectroscopy at fractional-photon-energy resolution of about 10 to the negative 3rd power in photon-energy range from 10 keV to greater than 10 MeV. In its spectroscopic aspect, instrument enables identification of both narrow and weak gamma-ray spectral peaks.

  20. Fuzzy Classification of High Resolution Remote Sensing Scenes Using Visual Attention Features

    Directory of Open Access Journals (Sweden)

    Linyi Li

    2017-01-01

    Full Text Available In recent years the spatial resolutions of remote sensing images have been improved greatly. However, a higher spatial resolution image does not always lead to a better result of automatic scene classification. Visual attention is an important characteristic of the human visual system, which can effectively help to classify remote sensing scenes. In this study, a novel visual attention feature extraction algorithm was proposed, which extracted visual attention features through a multiscale process. And a fuzzy classification method using visual attention features (FC-VAF was developed to perform high resolution remote sensing scene classification. FC-VAF was evaluated by using remote sensing scenes from widely used high resolution remote sensing images, including IKONOS, QuickBird, and ZY-3 images. FC-VAF achieved more accurate classification results than the others according to the quantitative accuracy evaluation indices. We also discussed the role and impacts of different decomposition levels and different wavelets on the classification accuracy. FC-VAF improves the accuracy of high resolution scene classification and therefore advances the research of digital image analysis and the applications of high resolution remote sensing images.

  1. Variational data assimilation system with nesting model for high resolution ocean circulation

    Energy Technology Data Exchange (ETDEWEB)

    Ishikawa, Yoichi; Igarashi, Hiromichi; Hiyoshi, Yoshimasa; Sasaki, Yuji; Wakamatsu, Tsuyoshi; Awaji, Toshiyuki [Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology, 3173-25 Showa-machi, Kanazawa-Ku, Yokohama 236-0001 (Japan); In, Teiji [Japan Marine Science Foundation, 4-24, Minato-cho, Mutsu, Aomori, 035-0064 (Japan); Nakada, Satoshi [Graduate School of Maritime Science, Kobe University, 5-1-1, Fukae-minamimachi, Higashinada-Ku, Kobe, 658-0022 (Japan); Nishina, Kei, E-mail: ishikaway@jamstec.go.jp [Graduate School of Science, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-Ku, Kyoto, 606-8502 (Japan)

    2015-10-15

    To obtain the high-resolution analysis fields for ocean circulation, a new incremental approach is developed using a four-dimensional variational data assimilation system with nesting models. The results show that there are substantial biases when using a classical method combined with data assimilation and downscaling, caused by different dynamics resulting from the different resolutions of the models used within the nesting models. However, a remarkable reduction in biases of the low-resolution model relative to the high-resolution model was observed using our new approach in narrow strait regions, such as the Tsushima and Tsugaru straits, where the difference in the dynamics represented by the high- and low-resolution models is substantial. In addition, error reductions are demonstrated in the downstream region of these narrow channels associated with the propagation of information through the model dynamics. (paper)

  2. Real-time database for high resolution neutron monitor measurements

    Energy Technology Data Exchange (ETDEWEB)

    Steigies, Christian T.; Rother, Oliver M.; Wimmer-Schweingruber, Robert F.; Heber, Bernd [IEAP, Christian-Albrechts-Universitaet zu Kiel (Germany)

    2008-07-01

    The worldwide network of standardised neutron monitors is, after 50 years, still the state-of-the-art instrumentation to measure spectral variations of the primary cosmic ray component. These measurements are an ideal complement to space based cosmic ray measurements. Data from the approximately 50 IGY and NM64 neutron monitors is stored locally but also available through data collections sites like the World Data Center (WDC) or the IZMIRAN ftp server. The data from the WDC is in a standard format, but only hourly values are available. IZMIRAN collects the data in the best available time resolution, but the data arrives on the ftp server only hours, sometimes days, after the measurements. Also, the high time-resolution measurements of the different stations do not have a common format, a conversion routine for each station is needed before they can be used for scientific analysis. Supported by the 7th framework program of the European Commission, we are setting up a real-time database where high resolution cosmic ray measurements will be stored and accessible immediately after the measurement. Stations that do not have 1-minute resolution measurements will be upgraded to 1-minute or better resolution with an affordable standard registration system, that will submit the measurements to the database via the internet in real-time.

  3. Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy.

    Science.gov (United States)

    Meroni, Alice; Lazzaro, Federico; Muzi-Falconi, Marco; Podestà, Alessandro

    2018-01-01

    We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.

  4. High resolution imaging of boron carbide microstructures

    International Nuclear Information System (INIS)

    MacKinnon, I.D.R.; Aselage, T.; Van Deusen, S.B.

    1986-01-01

    Two samples of boron carbide have been examined using high resolution transmission electron microscopy (HRTEM). A hot-pressed B 13 C 2 sample shows a high density of variable width twins normal to (10*1). Subtle shifts or offsets of lattice fringes along the twin plane and normal to approx.(10*5) were also observed. A B 4 C powder showed little evidence of stacking disorder in crystalline regions

  5. A subspace approach to high-resolution spectroscopic imaging.

    Science.gov (United States)

    Lam, Fan; Liang, Zhi-Pei

    2014-04-01

    To accelerate spectroscopic imaging using sparse sampling of (k,t)-space and subspace (or low-rank) modeling to enable high-resolution metabolic imaging with good signal-to-noise ratio. The proposed method, called SPectroscopic Imaging by exploiting spatiospectral CorrElation, exploits a unique property known as partial separability of spectroscopic signals. This property indicates that high-dimensional spectroscopic signals reside in a very low-dimensional subspace and enables special data acquisition and image reconstruction strategies to be used to obtain high-resolution spatiospectral distributions with good signal-to-noise ratio. More specifically, a hybrid chemical shift imaging/echo-planar spectroscopic imaging pulse sequence is proposed for sparse sampling of (k,t)-space, and a low-rank model-based algorithm is proposed for subspace estimation and image reconstruction from sparse data with the capability to incorporate prior information and field inhomogeneity correction. The performance of the proposed method has been evaluated using both computer simulations and phantom studies, which produced very encouraging results. For two-dimensional spectroscopic imaging experiments on a metabolite phantom, a factor of 10 acceleration was achieved with a minimal loss in signal-to-noise ratio compared to the long chemical shift imaging experiments and with a significant gain in signal-to-noise ratio compared to the accelerated echo-planar spectroscopic imaging experiments. The proposed method, SPectroscopic Imaging by exploiting spatiospectral CorrElation, is able to significantly accelerate spectroscopic imaging experiments, making high-resolution metabolic imaging possible. Copyright © 2014 Wiley Periodicals, Inc.

  6. DNA-based techniques for authentication of processed food and food supplements.

    Science.gov (United States)

    Lo, Yat-Tung; Shaw, Pang-Chui

    2018-02-01

    Authentication of food or food supplements with medicinal values is important to avoid adverse toxic effects, provide consumer rights, as well as for certification purpose. Compared to morphological and spectrometric techniques, molecular authentication is found to be accurate, sensitive and reliable. However, DNA degradation and inclusion of inhibitors may lead to failure in PCR amplification. This paper reviews on the existing DNA extraction and PCR protocols, and the use of small size DNA markers with sufficient discriminative power for molecular authentication. Various emerging new molecular techniques such as isothermal amplification for on-site diagnosis, next-generation sequencing for high-throughput species identification, high resolution melting analysis for quick species differentiation, DNA array techniques for rapid detection and quantitative determination in food products are also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

    Directory of Open Access Journals (Sweden)

    Zhao Patrick X

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L., a species with high economic value but limited genomic resources. Results The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1 chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. Conclusions We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

  8. Rapid detection of Echinococcus species by a high-resolution melting (HRM) approach.

    Science.gov (United States)

    Santos, Guilherme Brzoskowski; Espínola, Sergio Martín; Ferreira, Henrique Bunselmeyer; Margis, Rogerio; Zaha, Arnaldo

    2013-11-14

    High-resolution melting (HRM) provides a low-cost, fast and sensitive scanning method that allows the detection of DNA sequence variations in a single step, which makes it appropriate for application in parasite identification and genotyping. The aim of this work was to implement an HRM-PCR assay targeting part of the mitochondrial cox1 gene to achieve an accurate and fast method for Echinococcus spp. differentiation. For melting analysis, a total of 107 samples from seven species were used in this study. The species analyzed included Echinococcus granulosus (n = 41) and Echinococcus ortleppi (n = 50) from bovine, Echinococcus vogeli (n = 2) from paca, Echinococcus oligarthra (n = 3) from agouti, Echinococcus multilocularis (n = 6) from monkey and Echinococcus canadensis (n = 2) and Taenia hydatigena (n = 3) from pig. DNA extraction was performed, and a 444-bp fragment of the cox1 gene was amplified. Two approaches were used, one based on HRM analysis, and a second using SYBR Green Tm-based. In the HRM analysis, a specific profile for each species was observed. Although some species exhibited almost the same melting temperature (Tm) value, the HRM profiles could be clearly discriminated. The SYBR Green Tm-based analysis showed differences between E. granulosus and E. ortleppi and between E. vogeli and E. oligarthra. In this work, we report the implementation of HRM analysis to differentiate species of the genus Echinococcus using part of the mitochondrial gene cox1. This method may be also potentially applied to identify other species belonging to the Taeniidae family.

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

    Science.gov (United States)

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

    2016-05-01

    DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community. © 2015 John Wiley & Sons Ltd.

  10. DNA origami-based shape IDs for single-molecule nanomechanical genotyping

    Science.gov (United States)

    Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

    2017-04-01

    Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

  11. High-resolution spectroscopic probes of collisions and half-collisions

    Energy Technology Data Exchange (ETDEWEB)

    Hall, G.E. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    Research in this program explores the dynamics of gas phase collisions and photodissociation by high-resolution laser spectroscopy. Simultaneous state and velocity detection frequently permits a determination of scalar or vector correlations among products. The correlated product distributions are always more informative, and often easier to interpret than the uncorrelated product state distributions. The authors have recently built an apparatus to record transient absorption spectra with 50 nS time resolution and 20 MHz frequency resolution using a single frequency Ti:sapphire laser. The photodissociation of NCCN and C{sub 2}H{sub 5}SCN at 193 nm is discussed.

  12. The demonstration of the auditory ossicles by high resolution CT

    International Nuclear Information System (INIS)

    Lloyd, G.A.S.; Boulay, G.H. du; Phelps, P.D.; Pullicino, P.

    1979-01-01

    The high resolution CT scanning system introduced by EMI in 1978 has added a new dimension to computerised tomography in otology. The apparatus used for this study was an EMI CT 5005 body scanner adapted for head and neck scanning and incorporating a high resolution facility. The latter has proved most advantageous in areas of relatively high differential absorption, so that its application to the demonstration of abnormalities in the petrous temporal bone, and in particular middle ear disease, has been very rewarding. Traumatic ossicular disruptions may now be demonstrated and the high contrast of CT often shows them better than conventional hypocycloidal tomography. The stapes is also better visualised and congenital abnormalities of its superstructure have been recorded. These studies have been achieved with a very acceptable level of radiation to the eye, lens and cornea and the technique is clearly a rival to conventional pluridirectional tomography in the assessment of the petrous temporal bone. With further design improvements high resolution CT could completely replace existing techniques. (orig.) [de

  13. Use of electroporation for high-molecular-weight DNA-mediated gene transfer.

    Science.gov (United States)

    Jastreboff, M M; Ito, E; Bertino, J R; Narayanan, R

    1987-08-01

    Electroporation was used to introduce high-molecular-weight DNA into murine hematopoietic cells and NIH3T3 cells. CCRF-CEM cells were stably transfected with SV2NEO plasmid and the genomic DNA from G-418-resistant clones (greater than 65 kb) was introduced into mouse bone marrow and NIH3T3 cells by electroporation. NEO sequences and expression were detected in the hematopoietic tissues of lethally irradiated mice, with 24% of individual spleen colonies expressing NEO. The frequency of genomic DNA transfer into NIH3T3 cells was 0.25 X 10(-3). Electroporation thus offers a powerful mode of gene transfer not only of cloned genes but also of high-molecular-weight DNA into cells.

  14. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    2012-01-01

    High Resolution NMR: Theory and Chemical Applications discusses the principles and theory of nuclear magnetic resonance and how this concept is used in the chemical sciences. This book is written at an intermediate level, with mathematics used to augment verbal descriptions of the phenomena. This text pays attention to developing and interrelating four approaches - the steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The style of this book is based on the assumption that the reader has an acquaintance with the general principles of quantum mechanics, but no extensive background in quantum theory or proficiency in mathematics is required. This book begins with a description of the basic physics, together with a brief account of the historical development of the field. It looks at the study of NMR in liquids, including high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. This book is intended to assis...

  15. Principles of high resolution NMR in solids

    CERN Document Server

    Mehring, Michael

    1983-01-01

    The field of Nuclear Magnetic Resonance (NMR) has developed at a fascinating pace during the last decade. It always has been an extremely valuable tool to the organic chemist by supplying molecular "finger print" spectra at the atomic level. Unfortunately the high resolution achievable in liquid solutions could not be obtained in solids and physicists and physical chemists had to live with unresolved lines open to a wealth of curve fitting procedures and a vast amount of speculations. High resolution NMR in solids seemed to be a paradoxon. Broad structure­ less lines are usually encountered when dealing with NMR in solids. Only with the recent advent of mUltiple pulse, magic angle, cross-polarization, two-dimen­ sional and multiple-quantum spectroscopy and other techniques during the last decade it became possible to resolve finer details of nuclear spin interactions in solids. I have felt that graduate students, researchers and others beginning to get involved with these techniques needed a book which trea...

  16. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1999-01-01

    High Resolution NMR provides a broad treatment of the principles and theory of nuclear magnetic resonance (NMR) as it is used in the chemical sciences. It is written at an "intermediate" level, with mathematics used to augment, rather than replace, clear verbal descriptions of the phenomena. The book is intended to allow a graduate student, advanced undergraduate, or researcher to understand NMR at a fundamental level, and to see illustrations of the applications of NMR to the determination of the structure of small organic molecules and macromolecules, including proteins. Emphasis is on the study of NMR in liquids, but the treatment also includes high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. Careful attention is given to developing and interrelating four approaches - steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The presentation is based on the assumption that the reader has an acquaintan...

  17. High resolution study of high mass pairs and high transverse momentum particles

    International Nuclear Information System (INIS)

    Smith, S.R.

    1983-01-01

    Preliminary experiments involving the high resolution spectrometer (experiment 605) at Fermilab are described. The spectrometer is designed for the study of pairs of particles at large invariant masses and single particles at large transverse momenta. A number of applications of the apparatus in the study of Drell-Yan processes, e.g. transverse momentum measurement, are discussed

  18. High-resolution RCMs as pioneers for future GCMs

    Science.gov (United States)

    Schar, C.; Ban, N.; Arteaga, A.; Charpilloz, C.; Di Girolamo, S.; Fuhrer, O.; Hoefler, T.; Leutwyler, D.; Lüthi, D.; Piaget, N.; Ruedisuehli, S.; Schlemmer, L.; Schulthess, T. C.; Wernli, H.

    2017-12-01

    Currently large efforts are underway to refine the horizontal resolution of global and regional climate models to O(1 km), with the intent to represent convective clouds explicitly rather than using semi-empirical parameterizations. This refinement will move the governing equations closer to first principles and is expected to reduce the uncertainties of climate models. High resolution is particularly attractive in order to better represent critical cloud feedback processes (e.g. related to global climate sensitivity and extratropical summer convection) and extreme events (such as heavy precipitation events, floods, and hurricanes). The presentation will be illustrated using decade-long simulations at 2 km horizontal grid spacing, some of these covering the European continent on a computational mesh with 1536x1536x60 grid points. To accomplish such simulations, use is made of emerging heterogeneous supercomputing architectures, using a version of the COSMO limited-area weather and climate model that is able to run entirely on GPUs. Results show that kilometer-scale resolution dramatically improves the simulation of precipitation in terms of the diurnal cycle and short-term extremes. The modeling framework is used to address changes of precipitation scaling with climate change. It is argued that already today, modern supercomputers would in principle enable global atmospheric convection-resolving climate simulations, provided appropriately refactored codes were available, and provided solutions were found to cope with the rapidly growing output volume. A discussion will be provided of key challenges affecting the design of future high-resolution climate models. It is suggested that km-scale RCMs should be exploited to pioneer this terrain, at a time when GCMs are not yet available at such resolutions. Areas of interest include the development of new parameterization schemes adequate for km-scale resolution, the exploration of new validation methodologies and data

  19. High density FTA plates serve as efficient long-term sample storage for HLA genotyping.

    Science.gov (United States)

    Lange, V; Arndt, K; Schwarzelt, C; Boehme, I; Giani, A S; Schmidt, A H; Ehninger, G; Wassmuth, R

    2014-02-01

    Storage of dried blood spots (DBS) on high-density FTA(®) plates could constitute an appealing alternative to frozen storage. However, it remains controversial whether DBS are suitable for high-resolution sequencing of human leukocyte antigen (HLA) alleles. Therefore, we extracted DNA from DBS that had been stored for up to 4 years, using six different methods. We identified those extraction methods that recovered sufficient high-quality DNA for reliable high-resolution HLA sequencing. Further, we confirmed that frozen whole blood samples that had been stored for several years can be transferred to filter paper without compromising HLA genotyping upon extraction. Concluding, DNA derived from high-density FTA(®) plates is suitable for high-resolution HLA sequencing, provided that appropriate extraction protocols are employed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. High-resolution MR imaging of talar osteochondral lesions with new classification

    Energy Technology Data Exchange (ETDEWEB)

    Griffith, James Francis; Lau, Domily Ting Yi; Yeung, David Ka Wai [Prince of Wales Hospital, Chinese University of Hong Kong, Department of Imaging and Interventional Radiology, Shatin, NT (China); Wong, Margaret Wan Nar [Prince of Wales Hospital, Chinese University of Hong Kong, Department of Orthopaedics and Traumatology, Shatin (China)

    2012-04-15

    Retrospective review of high-resolution MR imaging features of talar dome osteochondral lesions and development of new classification system based on these features. Over the past 7 years, 70 osteochondral lesions of the talar dome from 70 patients (49 males, 21 females, mean age 42 years, range 15-62 years) underwent high-resolution MR imaging with a microscopy coil at 1.5 T. Sixty-one (87%) of 70 lesions were located on the medial central aspect and ten (13%) lesions were located on the lateral central aspect of the talar dome. Features evaluated included cartilage fracture, osteochondral junction separation, subchondral bone collapse, bone:bone separation, and marrow change. Based on these findings, a new five-part grading system was developed. Signal-to-noise characteristics of microscopy coil imaging at 1.5 T were compared to dedicated ankle coil imaging at 3 T. Microscopy coil imaging at 1.5 T yielded 20% better signal-to-noise characteristics than ankle coil imaging at 3 T. High-resolution MR revealed that osteochondral junction separation, due to focal collapse of the subchondral bone, was a common feature, being present in 28 (45%) of 61 medial central osteochondral lesions. Reparative cartilage hypertrophy and bone:bone separation in the absence of cartilage fracture were also common findings. Complete osteochondral separation was uncommon. A new five-part grading system incorporating features revealed by high-resolution MR imaging was developed. High-resolution MRI reveals clinically pertinent features of talar osteochondral lesions, which should help comprehension of symptomatology and enhance clinical decision-making. These features were incorporated in a new MR-based grading system. Whenever possible, symptomatic talar osteochondral lesions should be assessed by high-resolution MR imaging. (orig.)

  1. High-resolution MR imaging of talar osteochondral lesions with new classification

    International Nuclear Information System (INIS)

    Griffith, James Francis; Lau, Domily Ting Yi; Yeung, David Ka Wai; Wong, Margaret Wan Nar

    2012-01-01

    Retrospective review of high-resolution MR imaging features of talar dome osteochondral lesions and development of new classification system based on these features. Over the past 7 years, 70 osteochondral lesions of the talar dome from 70 patients (49 males, 21 females, mean age 42 years, range 15-62 years) underwent high-resolution MR imaging with a microscopy coil at 1.5 T. Sixty-one (87%) of 70 lesions were located on the medial central aspect and ten (13%) lesions were located on the lateral central aspect of the talar dome. Features evaluated included cartilage fracture, osteochondral junction separation, subchondral bone collapse, bone:bone separation, and marrow change. Based on these findings, a new five-part grading system was developed. Signal-to-noise characteristics of microscopy coil imaging at 1.5 T were compared to dedicated ankle coil imaging at 3 T. Microscopy coil imaging at 1.5 T yielded 20% better signal-to-noise characteristics than ankle coil imaging at 3 T. High-resolution MR revealed that osteochondral junction separation, due to focal collapse of the subchondral bone, was a common feature, being present in 28 (45%) of 61 medial central osteochondral lesions. Reparative cartilage hypertrophy and bone:bone separation in the absence of cartilage fracture were also common findings. Complete osteochondral separation was uncommon. A new five-part grading system incorporating features revealed by high-resolution MR imaging was developed. High-resolution MRI reveals clinically pertinent features of talar osteochondral lesions, which should help comprehension of symptomatology and enhance clinical decision-making. These features were incorporated in a new MR-based grading system. Whenever possible, symptomatic talar osteochondral lesions should be assessed by high-resolution MR imaging. (orig.)

  2. Excised radicle tips as a source of genomic DNA for PCR-based ...

    Indian Academy of Sciences (India)

    2012-12-13

    Dec 13, 2012 ... Cotton; cry1Ac; genomic DNA isolation; high-resolution melting curve analysis; radicle tip; seed purity testing .... cooled to 40°C. Fluorescence data for melting curves were ... greatly increased by introducing automation.

  3. Identification of Uvaria sp by barcoding coupled with high-resolution melting analysis (Bar-HRM).

    Science.gov (United States)

    Osathanunkul, M; Madesis, P; Ounjai, S; Pumiputavon, K; Somboonchai, R; Lithanatudom, P; Chaowasku, T; Wipasa, J; Suwannapoom, C

    2016-01-13

    DNA barcoding, which was developed about a decade ago, relies on short, standardized regions of the genome to identify plant and animal species. This method can be used to not only identify known species but also to discover novel ones. Numerous sequences are stored in online databases worldwide. One of the ways to save cost and time (by omitting the sequencing step) in species identification is to use available barcode data to design optimized primers for further analysis, such as high-resolution melting analysis (HRM). This study aimed to determine the effectiveness of the hybrid method Bar-HRM (DNA barcoding combined with HRM) to identify species that share similar external morphological features, rather than conduct traditional taxonomic identification that require major parts (leaf, flower, fruit) of the specimens. The specimens used for testing were those, which could not be identified at the species level and could either be Uvaria longipes or Uvaria wrayias, indicated by morphological identification. Primer pairs derived from chloroplast regions (matK, psbA-trnH, rbcL, and trnL) were used in the Bar-HRM. The results obtained from psbA-trnH primers were good enough to help in identifying the specimen while the rest were not. Bar-HRM analysis was proven to be a fast and cost-effective method for plant species identification.

  4. High resolution positron tomography

    International Nuclear Information System (INIS)

    Brownell, G.L.; Burnham, C.A.

    1982-01-01

    The limits of spatial resolution in practical positron tomography are examined. The four factors that limit spatial resolution are: positron range; small angle deviation; detector dimensions and properties; statistics. Of these factors, positron range may be considered the fundamental physical limitation since it is independent of instrument properties. The other factors are to a greater or lesser extent dependent on the design of the tomograph

  5. High-intensity xenon plasma discharge lamp for bulk-sensitive high-resolution photoemission spectroscopy.

    Science.gov (United States)

    Souma, S; Sato, T; Takahashi, T; Baltzer, P

    2007-12-01

    We have developed a highly brilliant xenon (Xe) discharge lamp operated by microwave-induced electron cyclotron resonance (ECR) for ultrahigh-resolution bulk-sensitive photoemission spectroscopy (PES). We observed at least eight strong radiation lines from neutral or singly ionized Xe atoms in the energy region of 8.4-10.7 eV. The photon flux of the strongest Xe I resonance line at 8.437 eV is comparable to that of the He Ialpha line (21.218 eV) from the He-ECR discharge lamp. Stable operation for more than 300 h is achieved by efficient air-cooling of a ceramic tube in the resonance cavity. The high bulk sensitivity and high-energy resolution of PES using the Xe lines are demonstrated for some typical materials.

  6. High resolution, position sensitive detector for energetic particle beams

    International Nuclear Information System (INIS)

    Marsh, E.P.; Strathman, M.D.; Reed, D.A.; Odom, R.W.; Morse, D.H.; Pontau, A.E.

    1993-01-01

    The performance and design of an imaging position sensitive, particle beam detector will be presented. The detector is minimally invasive, operates a wide dynamic range (>10 10 ), and exhibits high spatial resolution. The secondary electrons produced when a particle beam passes through a thin foil are imaged using stigmatic ion optics onto a two-dimensional imaging detector. Due to the low scattering cross section of the 6 nm carbon foil the detector is a minimal perturbation on the primary beam. A prototype detector with an image resolution of approximately 5 μm for a field of view of 1 mm has been reported. A higher resolution detector for imaging small beams (<50 μm) with an image resolution of better than 0.5 μm has since been developed and its design is presented. (orig.)

  7. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparisons with Other Methods

    International Nuclear Information System (INIS)

    Wu, Liyou; Yi, T.Y.; Van Nostrand, Joy; Zhou, Jizhong

    2010-01-01

    Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site (Hanford Reach of the Columbia River (HRCR), 11 strains), Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

  8. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy; Zhou, Jizhong

    2010-05-17

    Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.

  9. Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.

    Science.gov (United States)

    Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

    2007-10-30

    We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 x 10(8) bound targets per cm(2) sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

  10. High-resolution mapping of forest carbon stocks in the Colombian Amazon

    Directory of Open Access Journals (Sweden)

    G. P. Asner

    2012-07-01

    Full Text Available High-resolution mapping of tropical forest carbon stocks can assist forest management and improve implementation of large-scale carbon retention and enhancement programs. Previous high-resolution approaches have relied on field plot and/or light detection and ranging (LiDAR samples of aboveground carbon density, which are typically upscaled to larger geographic areas using stratification maps. Such efforts often rely on detailed vegetation maps to stratify the region for sampling, but existing tropical forest maps are often too coarse and field plots too sparse for high-resolution carbon assessments. We developed a top-down approach for high-resolution carbon mapping in a 16.5 million ha region (> 40% of the Colombian Amazon – a remote landscape seldom documented. We report on three advances for large-scale carbon mapping: (i employing a universal approach to airborne LiDAR-calibration with limited field data; (ii quantifying environmental controls over carbon densities; and (iii developing stratification- and regression-based approaches for scaling up to regions outside of LiDAR coverage. We found that carbon stocks are predicted by a combination of satellite-derived elevation, fractional canopy cover and terrain ruggedness, allowing upscaling of the LiDAR samples to the full 16.5 million ha region. LiDAR-derived carbon maps have 14% uncertainty at 1 ha resolution, and the regional map based on stratification has 28% uncertainty in any given hectare. High-resolution approaches with quantifiable pixel-scale uncertainties will provide the most confidence for monitoring changes in tropical forest carbon stocks. Improved confidence will allow resource managers and decision makers to more rapidly and effectively implement actions that better conserve and utilize forests in tropical regions.

  11. The implementation of sea ice model on a regional high-resolution scale

    Science.gov (United States)

    Prasad, Siva; Zakharov, Igor; Bobby, Pradeep; McGuire, Peter

    2015-09-01

    The availability of high-resolution atmospheric/ocean forecast models, satellite data and access to high-performance computing clusters have provided capability to build high-resolution models for regional ice condition simulation. The paper describes the implementation of the Los Alamos sea ice model (CICE) on a regional scale at high resolution. The advantage of the model is its ability to include oceanographic parameters (e.g., currents) to provide accurate results. The sea ice simulation was performed over Baffin Bay and the Labrador Sea to retrieve important parameters such as ice concentration, thickness, ridging, and drift. Two different forcing models, one with low resolution and another with a high resolution, were used for the estimation of sensitivity of model results. Sea ice behavior over 7 years was simulated to analyze ice formation, melting, and conditions in the region. Validation was based on comparing model results with remote sensing data. The simulated ice concentration correlated well with Advanced Microwave Scanning Radiometer for EOS (AMSR-E) and Ocean and Sea Ice Satellite Application Facility (OSI-SAF) data. Visual comparison of ice thickness trends estimated from the Soil Moisture and Ocean Salinity satellite (SMOS) agreed with the simulation for year 2010-2011.

  12. Performance of a high resolution cavity beam position monitor system

    Science.gov (United States)

    Walston, Sean; Boogert, Stewart; Chung, Carl; Fitsos, Pete; Frisch, Joe; Gronberg, Jeff; Hayano, Hitoshi; Honda, Yosuke; Kolomensky, Yury; Lyapin, Alexey; Malton, Stephen; May, Justin; McCormick, Douglas; Meller, Robert; Miller, David; Orimoto, Toyoko; Ross, Marc; Slater, Mark; Smith, Steve; Smith, Tonee; Terunuma, Nobuhiro; Thomson, Mark; Urakawa, Junji; Vogel, Vladimir; Ward, David; White, Glen

    2007-07-01

    It has been estimated that an RF cavity Beam Position Monitor (BPM) could provide a position measurement resolution of less than 1 nm. We have developed a high resolution cavity BPM and associated electronics. A triplet comprised of these BPMs was installed in the extraction line of the Accelerator Test Facility (ATF) at the High Energy Accelerator Research Organization (KEK) for testing with its ultra-low emittance beam. The three BPMs were each rigidly mounted inside an alignment frame on six variable-length struts which could be used to move the BPMs in position and angle. We have developed novel methods for extracting the position and tilt information from the BPM signals including a robust calibration algorithm which is immune to beam jitter. To date, we have demonstrated a position resolution of 15.6 nm and a tilt resolution of 2.1 μrad over a dynamic range of approximately ±20 μm.

  13. The high resolution shear wave seismic reflection technique

    International Nuclear Information System (INIS)

    Johnson, W.J.; Clark, J.C.

    1991-04-01

    This report presents the state-of-the-art of the high resolution S-wave reflection technique. Published and unpublished literature has been reviewed and discussions have been held with experts. Result is to confirm that the proposed theoretical and practical basis for identifying aquifer systems using both P- and S-wave reflections is sound. Knowledge of S-wave velocity and P-wave velocity is a powerful tool for assessing the fluid characteristics of subsurface layers. Material properties and lateral changes in material properties such as change from clay to sand, can be inferred from careful dual evaluation of P and S-wave records. The high resolution S-wave reflection technique has seen its greatest application to date as part of geotechnical studies for building foundations in the Far East. Information from this type of study has been evaluated and will be incorporated in field studies. In particular, useful information regarding S-wave sources, noise suppression and recording procedures will be incorporated within the field studies. Case histories indicate that the best type of site for demonstrating the power of the high resolution S-wave technique will be in unconsolidated soil without excessive structural complexities. More complex sites can form the basis for subsequent research after the basic principles of the technique can be established under relatively uncomplicated conditions

  14. Rapid screening for targeted genetic variants via high-resolution melting curve analysis.

    Science.gov (United States)

    Chambliss, Allison B; Resnick, Molly; Petrides, Athena K; Clarke, William A; Marzinke, Mark A

    2017-03-01

    Current methods for the detection of single nucleotide polymorphisms (SNPs) associated with aberrant drug-metabolizing enzyme function are hindered by long turnaround times and specialized techniques and instrumentation. In this study, we describe the development and validation of a high-resolution melting (HRM) curve assay for the rapid screening of variant genotypes for targeted genetic polymorphisms in the cytochrome P450 enzymes CYP2C9, CYP2C19, and CYP3A5. Sequence-specific primers were custom-designed to flank nine SNPs within the genetic regions of aforementioned drug metabolizing enzymes. PCR amplification was performed followed by amplicon denaturation by precise temperature ramping in order to distinguish genotypes by melting temperature (Tm). A standardized software algorithm was used to assign amplicons as 'reference' or 'variant' as compared to duplicate reference sequence DNA controls for each SNP. Intra-assay (n=5) precision of Tms for all SNPs was ≤0.19%, while inter-assay (n=20) precision ranged from 0.04% to 0.21%. When compared to a reference method of Sanger sequencing, the HRM assay produced no false negative results, and overcall frequency ranged from 0% to 26%, depending on the SNP. Furthermore, HRM genotyping displayed accuracy over input DNA concentrations ranging from 10 to 200 ng/μL. The presented assay provides a rapid method for the screening for genetic variants in targeted CYP450 regions with a result of 'reference' or 'variant' available within 2 h from receipt of extracted DNA. The method can serve as a screening approach to rapidly identify individuals with variant sequences who should be further investigated by reflexed confirmatory testing for aberrant cytochrome P450 enzymatic activity. Rapid knowledge of variant status may aid in the avoidance of adverse clinical events by allowing for dosing of normal metabolizer patients immediately while identifying the need to wait for confirmatory testing in those patients who are

  15. Charge-coupled devices for particle detection with high spatial resolution

    International Nuclear Information System (INIS)

    Farley, F.J.; Damerell, C.J.S.; Gillman, A.R.; Wickens, F.J.

    1980-10-01

    The results of a study of the possible application of a thin microelectronic device (the charge-coupled device) to high energy physics as particle detectors with good spatial resolution which can distinguish between tracks emerging from the primary vertex and those from secondary vertices due to the decay of short lived particles with higher flavours, are reported. Performance characteristics indicating the spatial resolution, particle discrimination, time resolution, readout time and lifetime of such detectors have been obtained. (U.K.)

  16. Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.

    Science.gov (United States)

    Lyons, Eli; Sheridan, Paul; Tremmel, Georg; Miyano, Satoru; Sugano, Sumio

    2017-10-24

    High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.

  17. Rapid calibrated high-resolution hyperspectral imaging using tunable laser source

    Science.gov (United States)

    Nguyen, Lam K.; Margalith, Eli

    2009-05-01

    We present a novel hyperspectral imaging technique based on tunable laser technology. By replacing the broadband source and tunable filters of a typical NIR imaging instrument, several advantages are realized, including: high spectral resolution, highly variable field-of-views, fast scan-rates, high signal-to-noise ratio, and the ability to use optical fiber for efficient and flexible sample illumination. With this technique, high-resolution, calibrated hyperspectral images over the NIR range can be acquired in seconds. The performance of system features will be demonstrated on two example applications: detecting melamine contamination in wheat gluten and separating bovine protein from wheat protein in cattle feed.

  18. High Resolution Higher Energy X-ray Microscope for Mesoscopic Materials

    International Nuclear Information System (INIS)

    Snigireva, I; Snigirev, A

    2013-01-01

    We developed a novel X-ray microscopy technique to study mesoscopically structured materials, employing compound refractive lenses. The easily seen advantage of lens-based methodology is the possibility to retrieve high resolution diffraction pattern and real-space images in the same experimental setup. Methodologically the proposed approach is similar to the studies of crystals by high resolution transmission electron microscopy. The proposed microscope was applied for studying of mesoscopic materials such as natural and synthetic opals, inverted photonic crystals

  19. In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA.

    Directory of Open Access Journals (Sweden)

    Janet L Smith

    2015-05-01

    Full Text Available DnaA, the replication initiation protein in bacteria, is an AAA+ ATPase that binds and hydrolyzes ATP and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA in vitro at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing (IDAP-Seq. We used these data to identify 269 binding regions, refine the consensus sequence of the DnaA binding site, and compare the relative affinity of binding regions for ATP-DnaA and ADP-DnaA. Most sites had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but a few had a strong preference for binding ATP-DnaA. Of the 269 sites, only the eight strongest binding ones have been observed to bind DnaA in vivo, suggesting that other cellular factors or the amount of available DnaA in vivo restricts DnaA binding to these additional sites. Conversely, we found several chromosomal regions that were bound by DnaA in vivo but not in vitro, and that the nucleoid-associated protein Rok was required for binding in vivo. Our in vitro characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on in vivo binding and regulation of DnaA, and is an approach that should be adaptable to many other DNA binding proteins.

  20. Visualization of complex DNA damage along accelerated ions tracks

    Science.gov (United States)

    Kulikova, Elena; Boreyko, Alla; Bulanova, Tatiana; Ježková, Lucie; Zadneprianetc, Mariia; Smirnova, Elena

    2018-04-01

    The most deleterious DNA lesions induced by ionizing radiation are clustered DNA double-strand breaks (DSB). Clustered or complex DNA damage is a combination of a few simple lesions (single-strand breaks, base damage etc.) within one or two DNA helix turns. It is known that yield of complex DNA lesions increases with increasing linear energy transfer (LET) of radiation. For investigation of the induction and repair of complex DNA lesions, human fibroblasts were irradiated with high-LET 15N ions (LET = 183.3 keV/μm, E = 13MeV/n) and low-LET 60Co γ-rays (LET ≈ 0.3 keV/μm) radiation. DNA DSBs (γH2AX and 53BP1) and base damage (OGG1) markers were visualized by immunofluorecence staining and high-resolution microscopy. The obtained results showed slower repair kinetics of induced DSBs in cells irradiated with accelerated ions compared to 60Co γ-rays, indicating induction of more complex DNA damage. Confirming previous assumptions, detailed 3D analysis of γH2AX/53BP1 foci in 15N ions tracks revealed more complicated structure of the foci in contrast to γ-rays. It was shown that proteins 53BP1 and OGG1 involved in repair of DNA DSBs and modified bases, respectively, were colocalized in tracks of 15N ions and thus represented clustered DNA DSBs.

  1. Solutions on high-resolution multiple configuration system sensors

    Science.gov (United States)

    Liu, Hua; Ding, Quanxin; Guo, Chunjie; Zhou, Liwei

    2014-11-01

    For aim to achieve an improved resolution in modern image domain, a method of continuous zoom multiple configuration, with a core optics is attempt to establish model by novel principle on energy transfer and high accuracy localization, by which the system resolution can be improved with a level in nano meters. A comparative study on traditional vs modern methods can demonstrate that the dialectical relationship and their balance is important, among Merit function, Optimization algorithms and Model parameterization. The effect of system evaluated criterion that MTF, REA, RMS etc. can support our arguments qualitatively.

  2. Development of high-energy resolution inverse photoemission technique

    International Nuclear Information System (INIS)

    Asakura, D.; Fujii, Y.; Mizokawa, T.

    2005-01-01

    We developed a new inverse photoemission (IPES) machine based on a new idea to improve the energy resolution: off-plane Eagle mounting of the optical system in combination with dispersion matching between incoming electron and outgoing photon. In order to achieve dispersion matching, we have employed a parallel plate electron source and have investigated whether the electron beam is obtained as expected. In this paper, we present the principle and design of the new IPES method and report the current status of the high-energy resolution IPES machine

  3. [Rapid detection of hot spot mutations of FGFR3 gene with PCR-high resolution melting assay].

    Science.gov (United States)

    Li, Shan; Wang, Han; Su, Hua; Gao, Jinsong; Zhao, Xiuli

    2017-08-10

    To identify the causative mutations in five individuals affected with dyschondroplasia and develop an efficient procedure for detecting hot spot mutations of the FGFR3 gene. Genomic DNA was extracted from peripheral blood samples with a standard phenol/chloroform method. PCR-Sanger sequencing was used to analyze the causative mutations in the five probands. PCR-high resolution melting (HRM) was developed to detect the identified mutations. A c.1138G>A mutation in exon 8 was found in 4 probands, while a c.1620C>G mutation was found in exon 11 of proband 5 whom had a mild phenotype. All patients were successfully distinguished from healthy controls with the PCR-HRM method. The results of HRM analysis were highly consistent with that of Sanger sequencing. The Gly380Arg and Asn540Lys are hot spot mutations of the FGFR3 gene among patients with ACH/HCH. PCR-HRM analysis is more efficient for detecting hot spot mutations of the FGFR3 gene.

  4. Colloidal silica films for high-capacity DNA arrays

    Science.gov (United States)

    Glazer, Marc Irving

    The human genome project has greatly expanded the amount of genetic information available to researchers, but before this vast new source of data can be fully utilized, techniques for rapid, large-scale analysis of DNA and RNA must continue to develop. DNA arrays have emerged as a powerful new technology for analyzing genomic samples in a highly parallel format. The detection sensitivity of these arrays is dependent on the quantity and density of immobilized probe molecules. We have investigated substrates with a porous, "three-dimensional" surface layer as a means of increasing the surface area available for the synthesis of oligonucleotide probes, thereby increasing the number of available probes and the amount of detectable bound target. Porous colloidal silica films were created by two techniques. In the first approach, films were deposited by spin-coating silica colloid suspensions onto flat glass substrates, with the pores being formed by the natural voids between the solid particles (typically 23nm pores, 35% porosity). In the second approach, latex particles were co-deposited with the silica and then pyrolyzed, creating films with larger pores (36 nm), higher porosity (65%), and higher surface area. For 0.3 mum films, enhancements of eight to ten-fold and 12- to 14-fold were achieved with the pure silica films and the films "templated" with polymer latex, respectively. In gene expression assays for up to 7,000 genes using complex biological samples, the high-capacity films provided enhanced signals and performed equivalently or better than planar glass on all other functional measures, confirming that colloidal silica films are a promising platform for high-capacity DNA arrays. We have also investigated the kinetics of hybridization on planar glass and high-capacity substrates. Adsorption on planar arrays is similar to ideal Langmuir-type adsorption, although with an "overshoot" at high solution concentration. Hybridization on high-capacity films is

  5. High-Resolution Reciprocal Space Mapping for Characterizing Deformation Structures

    DEFF Research Database (Denmark)

    Pantleon, Wolfgang; Wejdemann, Christian; Jakobsen, Bo

    2014-01-01

    With high-angular resolution three-dimensional X-ray diffraction (3DXRD), quantitative information is gained about dislocation structures in individual grains in the bulk of a macroscopic specimen by acquiring reciprocal space maps. In high-resolution 3D reciprocal space maps of tensile......-deformed copper, individual, almost dislocation-free subgrains are identified from high-intensity peaks and distinguished by their unique combination of orientation and elastic strain; dislocation walls manifest themselves as a smooth cloud of lower intensity. The elastic strain shows only minor variations within...... dynamics is followed in situ during varying loading conditions by reciprocal space mapping: during uninterrupted tensile deformation, formation of subgrains is observed concurrently with broadening of Bragg reflections shortly after the onset of plastic deformation. When the traction is terminated, stress...

  6. Self-triggered image intensifier tube for high-resolution UHECR imaging detector

    CERN Document Server

    Sasaki, M; Jobashi, M

    2003-01-01

    The authors have developed a self-triggered image intensifier tube with high-resolution imaging capability. An image detected by a first image intensifier tube as an electrostatic lens with a photocathode diameter of 100 mm is separated by a half-mirror into a path for CCD readout (768x494 pixels) and a fast control to recognize and trigger the image. The proposed system provides both a high signal-to-noise ratio to improve single photoelectron detection and excellent spatial resolution between 207 and 240 mu m rendering this device a potentially essential tool for high-energy physics and astrophysics experiments, as well as high-speed photography. When combined with a 1-arcmin resolution optical system with 50 deg. field-of-view proposed by the present authors, the observation of ultra high-energy cosmic rays and high-energy neutrinos using this device is expected, leading to revolutionary progress in particle astrophysics as a complementary technique to traditional astronomical observations at multiple wave...

  7. High spectral resolution X-ray observations of AGN

    NARCIS (Netherlands)

    Kaastra, J.S.

    2008-01-01

    brief overview of some highlights of high spectral resolution X-ray observations of AGN is given, mainly obtained with the RGS of XMM-Newton. Future prospects for such observations with XMM-Newton are given.

  8. Fast DNA analysis by laser mass spectrometry for human genome analysis

    International Nuclear Information System (INIS)

    Tang, K.; Taranenko, N. I.; Allman, S. L.; Chang, L. Y.; Chen, C. H.

    1995-01-01

    Fast DNA sequencing by laser mass spectrometry is possible if the following 3 criteria are met: (1) Size of DNA fragment should be greater than 300 nucleotides. (2) Enough sensitivity to detect DNA produce from polymerases chain reactins (PCR). (3) Higher resolution of mass spectr. So far, the firt 2 criteria are met: If the resolution can be significantly improve, fast DNA sequencing by laser mass spectrometry weil be a reality in the near feature

  9. A high resolution 16 k multi-channel analyzer PC add-on card

    International Nuclear Information System (INIS)

    Kulkarni, C.P.; Paulson, Molly; Vaidya, P.P.

    2001-01-01

    This paper describes the system details of a 16 K channel resolution Multi-Channel Analyzer (MCA) developed at Electronics Division, BARC, which is used in high resolution nuclear spectroscopy systems for pulse height analysis. The high resolution data acquisition PC add-on card is architectured using a state of the art digital circuit design technology which makes use of a Field Programmable Gate Array (FPGA), and some of the most modern and advanced analog counterparts like low power, high speed and high precision comparators, Op-amps, ADCs and DACs etc. The 16 K MCA card gives an economic, compact, and low power alternative for nuclear pulse spectroscopy use. (author)

  10. An angle encoder for super-high resolution and super-high accuracy using SelfA

    International Nuclear Information System (INIS)

    Watanabe, Tsukasa; Kon, Masahito; Nabeshima, Nobuo; Taniguchi, Kayoko

    2014-01-01

    Angular measurement technology at high resolution for applications such as in hard disk drive manufacturing machines, precision measurement equipment and aspherical process machines requires a rotary encoder with high accuracy, high resolution and high response speed. However, a rotary encoder has angular deviation factors during operation due to scale error or installation error. It has been assumed to be impossible to achieve accuracy below 0.1″ in angular measurement or control after the installation onto the rotating axis. Self-calibration (Lu and Trumper 2007 CIRP Ann. 56 499; Kim et al 2011 Proc. MacroScale; Probst 2008 Meas. Sci. Technol. 19 015101; Probst et al Meas. Sci. Technol. 9 1059; Tadashi and Makoto 1993 J. Robot. Mechatronics 5 448; Ralf et al 2006 Meas. Sci. Technol. 17 2811) and cross-calibration (Probst et al 1998 Meas. Sci. Technol. 9 1059; Just et al 2009 Precis. Eng. 33 530; Burnashev 2013 Quantum Electron. 43 130) technologies for a rotary encoder have been actively discussed on the basis of the principle of circular closure. This discussion prompted the development of rotary tables which achieve reliable and high accuracy angular verification. We apply these technologies for the development of a rotary encoder not only to meet the requirement of super-high accuracy but also to meet that of super-high resolution. This paper presents the development of an encoder with 2 21 = 2097 152 resolutions per rotation (360°), that is, corresponding to a 0.62″ signal period, achieved by the combination of a laser rotary encoder supplied by Magnescale Co., Ltd and a self-calibratable encoder (SelfA) supplied by The National Institute of Advanced Industrial Science and Technology (AIST). In addition, this paper introduces the development of a rotary encoder to guarantee ±0.03″ accuracy at any point of the interpolated signal, with respect to the encoder at the minimum resolution of 2 33 , that is, corresponding to a 0.0015″ signal period

  11. Assessment of prediction skill in equatorial Pacific Ocean in high resolution model of CFS

    Science.gov (United States)

    Arora, Anika; Rao, Suryachandra A.; Pillai, Prasanth; Dhakate, Ashish; Salunke, Kiran; Srivastava, Ankur

    2018-01-01

    The effect of increasing atmospheric resolution on prediction skill of El Niño southern oscillation phenomenon in climate forecast system model is explored in this paper. Improvement in prediction skill for sea surface temperature (SST) and winds at all leads compared to low resolution model in the tropical Indo-Pacific basin is observed. High resolution model is able to capture extreme events reasonably well. As a result, the signal to noise ratio is improved in the high resolution model. However, spring predictability barrier (SPB) for summer months in Nino 3 and Nino 3.4 region is stronger in high resolution model, in spite of improvement in overall prediction skill and dynamics everywhere else. Anomaly correlation coefficient of SST in high resolution model with observations in Nino 3.4 region targeting boreal summer months when predicted at lead times of 3-8 months in advance decreased compared its lower resolution counterpart. It is noted that higher variance of winds predicted in spring season over central equatorial Pacific compared to observed variance of winds results in stronger than normal response on subsurface ocean, hence increases SPB for boreal summer months in high resolution model.

  12. High-Resolution Near Real-Time Drought Monitoring in South Asia

    Science.gov (United States)

    Aadhar, S.; Mishra, V.

    2017-12-01

    Drought in South Asia affect food and water security and pose challenges for millions of people. For policy-making, planning and management of water resources at the sub-basin or administrative levels, high-resolution datasets of precipitation and air temperature are required in near-real time. Here we develop a high resolution (0.05 degree) bias-corrected precipitation and temperature data that can be used to monitor near real-time drought conditions over South Asia. Moreover, the dataset can be used to monitor climatic extremes (heat waves, cold waves, dry and wet anomalies) in South Asia. A distribution mapping method was applied to correct bias in precipitation and air temperature (maximum and minimum), which performed well compared to the other bias correction method based on linear scaling. Bias-corrected precipitation and temperature data were used to estimate Standardized precipitation index (SPI) and Standardized Precipitation Evapotranspiration Index (SPEI) to assess the historical and current drought conditions in South Asia. We evaluated drought severity and extent against the satellite-based Normalized Difference Vegetation Index (NDVI) anomalies and satellite-driven Drought Severity Index (DSI) at 0.05˚. We find that the bias-corrected high-resolution data can effectively capture observed drought conditions as shown by the satellite-based drought estimates. High resolution near real-time dataset can provide valuable information for decision-making at district and sub- basin levels.

  13. New detector developments for high resolution positron emission tomography

    International Nuclear Information System (INIS)

    Ziegler, S.I.; Pichler, B.; Lorenz, E.

    1998-01-01

    The strength of quantitative, functional imaging using positron emission tomography, specially in small animals, is limited due to the spatial resolution. Therefore, various tomograph designs employing new scintillators, light sensors, or coincidence electronic are investigated to improve resolution without losses in sensitivity. Luminous scintillators with short light decay time in combination with novel readout schemes using photomultipliers or semiconductor detectors are currently tested by several groups and are implemented in tomographs for small animals. This review summarises the state of development in high resolution positron emission tomography with a detailed description of a system incorporating avalanche photodiode arrays and small scintillation crystals. (orig.) [de

  14. High Resolution Thz and FIR Spectroscopy of SOCl_2

    Science.gov (United States)

    Martin-Drumel, M. A.; Cuisset, A.; Sadovskii, D. A.; Mouret, G.; Hindle, F.; Pirali, O.

    2013-06-01

    Thionyl chloride (SOCl_2) is an extremely powerful oxidant widely used in industrial processes and playing a role in the chemistry of the atmosphere. In addition, it has a molecular configuration similar to that of phosgene (COCl_2), and is therefore of particular interest for security and defense applications. Low resolution vibrational spectra of gas phase SOCl_2 as well as high resolution pure rotational transitions up to 25 GHz have previously been investigated. To date no high resolution data are reported at frequencies higher than 25 GHz. We have investigated the THz absorption spectrum of SOCl_2 in the spectral region 70-650 GHz using a frequency multiplier chain coupled to a 1 m long single path cell containing a pressure of about 15 μbar. At the time of the writing, about 8000 pure rotational transitions of SO^{35}Cl_2 with highest J and K_a values of 110 and 50 respectively have been assigned on the spectrum. We have also recorded the high resolution FIR spectra of SOCl_2 in the spectral range 50-700 wn using synchrotron radiation at the AILES beamline of SOLEIL facility. A White-type cell aligned with an absorption path length of 150 m has been used to record, at a resolution of 0.001 wn, two spectra at pressures of 5 and 56 μbar of SOCl_2. On these spectra all FIR modes of SOCl_2 are observed (ν_2 to ν_6) and present a resolved rotational structure. Their analysis is in progress. T. J. Johnson et al., J. Phys. Chem. A 107, 6183 (2003) D. E. Martz and R. T. Lagemann, J. Chem. Phys. 22,1193 (1954) H. S. P. Müller and M. C. L. Gerry, J. Chem. Soc. Faraday Trans. 90, 3473 (1994)

  15. A high resolution large dynamic range TDC circuit implementation

    International Nuclear Information System (INIS)

    Lei Wuhu; Liu Songqiu; Ye Weiguo; Han Hui; Li Pengyu

    2003-01-01

    Time measurement technology is usually used in nuclear experimentation. There are many methods of time measurement. The implementation method of Time to Digital Conversion (TDC) by means of electronic is a classical technology. The range and resolution of TDC is different according with different usage. A wide range and high resolution TDC circuit, including its theory and implementation way, is introduced in this paper. The test result is also given. (authors)

  16. A high resolution large dynamic range TDC circuit implementation

    International Nuclear Information System (INIS)

    Lei Wuhu; Liu Songqiu; Li Pengyu; Han Hui; Ye Yanlin

    2005-01-01

    Time measurement technology is usually used in nuclear experimentation. There are many methods of time measurement. The implementation method of Time to Digital Conversion (TDC) by means of electronics is a classical technology. The range and resolution of TDC is different according with different usage. A wide range and high resolution TDC circuit, including its theory and implementation way, is introduced in this paper. The test result is also given. (authors)

  17. High-resolution retinal imaging using adaptive optics and Fourier-domain optical coherence tomography

    Science.gov (United States)

    Olivier, Scot S.; Werner, John S.; Zawadzki, Robert J.; Laut, Sophie P.; Jones, Steven M.

    2010-09-07

    This invention permits retinal images to be acquired at high speed and with unprecedented resolution in three dimensions (4.times.4.times.6 .mu.m). The instrument achieves high lateral resolution by using adaptive optics to correct optical aberrations of the human eye in real time. High axial resolution and high speed are made possible by the use of Fourier-domain optical coherence tomography. Using this system, we have demonstrated the ability to image microscopic blood vessels and the cone photoreceptor mosaic.

  18. An optimized rapid bisulfite conversion method with high recovery of cell-free DNA.

    Science.gov (United States)

    Yi, Shaohua; Long, Fei; Cheng, Juanbo; Huang, Daixin

    2017-12-19

    Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However, the recovery of bisulfite-converted DNA based on current methods is very poor for the methylation analysis of cell-free DNA. We optimized a rapid method for the crucial steps of bisulfite conversion with high recovery of cell-free DNA. A rapid deamination step and alkaline desulfonation was combined with the purification of DNA on a silica column. The conversion efficiency and recovery of bisulfite-treated DNA was investigated by the droplet digital PCR. The optimization of the reaction results in complete cytosine conversion in 30 min at 70 °C and about 65% of recovery of bisulfite-treated cell-free DNA, which is higher than current methods. The method allows high recovery from low levels of bisulfite-treated cell-free DNA, enhancing the analysis sensitivity of methylation detection from cell-free DNA.

  19. High-heat tank safety issue resolution program plan

    International Nuclear Information System (INIS)

    Wang, O.S.

    1993-12-01

    The purpose of this program plan is to provide a guide for selecting corrective actions that will mitigate and/or remediate the high-heat waste tank safety issue for single-shell tank (SST) 241-C-106. This program plan also outlines the logic for selecting approaches and tasks to mitigate and resolve the high-heat safety issue. The identified safety issue for high-heat tank 241-C-106 involves the potential release of nuclear waste to the environment as the result of heat-induced structural damage to the tank's concrete, if forced cooling is interrupted for extended periods. Currently, forced ventilation with added water to promote thermal conductivity and evaporation cooling is used to cool the waste. At this time, the only viable solution identified to resolve this safety issue is the removal of heat generating waste in the tank. This solution is being aggressively pursued as the permanent solution to this safety issue and also to support the present waste retrieval plan. Tank 241-C-106 has been selected as the first SST for retrieval. The program plan has three parts. The first part establishes program objectives and defines safety issues, drivers, and resolution criteria and strategy. The second part evaluates the high-heat safety issue and its mitigation and remediation methods and alternatives according to resolution logic. The third part identifies major tasks and alternatives for mitigation and resolution of the safety issue. Selected tasks and best-estimate schedules are also summarized in the program plan

  20. Mastering high resolution tip-enhanced Raman spectroscopy: towards a shift of perception.

    Science.gov (United States)

    Richard-Lacroix, Marie; Zhang, Yao; Dong, Zhenchao; Deckert, Volker

    2017-07-03

    Recent years have seen tremendous improvement of our understanding of high resolution reachable in TERS experiments, forcing us to re-evaluate our understanding of the intrinsic limits of this field, but also exposing several inconsistencies. On the one hand, more and more recent experimental results have provided us with clear indications of spatial resolutions down to a few nanometres or even on the subnanometre scale. Moreover, lessons learned from recent theoretical investigations clearly support such high resolutions, and vice versa the obvious theoretical impossibility to evade high resolution from a purely plasmonic point of view. On the other hand, most of the published TERS results still, to date, claim a resolution on the order of tens of nanometres that would be somehow limited by the tip apex, a statement well accepted for the past 2 decades. Overall, this now leads the field to a fundamental question: how can this divergence be justified? The answer to this question brings up an equally critical one: how can this gap be bridged? This review aims at raising a fundamental discussion related to the resolution limits of tip-enhanced Raman spectroscopy, at revisiting our comprehension of the factors limiting it both from a theoretical and an experimental point of view and at providing indications on how to move the field ahead. It is our belief that a much deeper understanding of the real accessible lateral resolution in TERS and the practical factors that limit them will simultaneously help us to fully explore the potential of this technique for studying nanoscale features in organic, inorganic and biological systems, and also to improve both the reproducibility and the accuracy of routine TERS studies. A significant improvement of our comprehension of the accessible resolution in TERS is thus critical for a broad audience, even in certain contexts where high resolution TERS is not the desired outcome.

  1. High resolution, position sensitive detector for energetic particle beams

    Energy Technology Data Exchange (ETDEWEB)

    Marsh, E P [Charles Evans and Associates, Redwood City, CA (United States); Strathman, M D [Charles Evans and Associates, Redwood City, CA (United States); Reed, D A [Charles Evans and Associates, Redwood City, CA (United States); Odom, R W [Charles Evans and Associates, Redwood City, CA (United States); Morse, D H [Sandia National Labs., Livermore, CA (United States); Pontau, A E [Sandia National Labs., Livermore, CA (United States)

    1993-05-01

    The performance and design of an imaging position sensitive, particle beam detector will be presented. The detector is minimally invasive, operates a wide dynamic range (>10[sup 10]), and exhibits high spatial resolution. The secondary electrons produced when a particle beam passes through a thin foil are imaged using stigmatic ion optics onto a two-dimensional imaging detector. Due to the low scattering cross section of the 6 nm carbon foil the detector is a minimal perturbation on the primary beam. A prototype detector with an image resolution of approximately 5 [mu]m for a field of view of 1 mm has been reported. A higher resolution detector for imaging small beams (<50 [mu]m) with an image resolution of better than 0.5 [mu]m has since been developed and its design is presented. (orig.)

  2. The performance of TOF near backscattering spectrometer DNA in MLF, J-PARC

    International Nuclear Information System (INIS)

    Shibata, Kaoru; Kawakita, Yukinobu; Kambara, Wataru; Inamura, Yasuhiro; Nakatani, Takeshi; Nakajima, Kenji; Arai, Masatoshi; Takahashi, Nobuaki; Matsuura, Masato; Yamada, Takeshi; Tominaga, Taiki; Kobayashi, Makoto

    2015-01-01

    The time-of-flight (TOF) type near-backscattering spectrometer (n-BSS), DNA, with Si crystal analyzers was built and started operation in 2012 at the Materials and Life Science Experimental Facility (MLF) of the Japan Proton Accelerator Research Complex (J-PARC). DNA is the first n-BSS with pulse shaping chopper installed at a spallation pulsed neutron source. It offers currently the highest energy-resolution of about 2.4 micro eV by operating a pulse shaping double-disk chopper at 225 Hz whose phase is optimized to the narrowest slit of 10 mm width. Energy resolution can be flexibly compromised with intensity during experiment by using two type slits with different widths and changing the copper frequency. An example of measurement with high energy-resolution under the condition that the pulse shaping chopper was operated is shown, where the limited measurable energy range was widely expanded by multi incident energy band technique. The experimental data demonstrate extremely high signal-to-noise ratio (∼10"5) of this spectrometer. (author)

  3. WRF high resolution dynamical downscaling of ERA-Interim for Portugal

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Pedro M.M. [University of Lisbon, Instituto Dom Luiz, Lisbon (Portugal); Faculdade de Ciencias da Universidade de Lisboa, Lisbon (Portugal); Cardoso, Rita M.; Miranda, Pedro M.A.; Medeiros, Joana de [University of Lisbon, Instituto Dom Luiz, Lisbon (Portugal); Belo-Pereira, Margarida; Espirito-Santo, Fatima [Instituto de Meteorologia, Lisbon (Portugal)

    2012-11-15

    This study proposes a dynamically downscaled climatology of Portugal, produced by a high resolution (9 km) WRF simulation, forced by 20 years of ERA-Interim reanalysis (1989-2008), nested in an intermediate domain with 27 km of resolution. The Portuguese mainland is characterized by large precipitation gradients, with observed mean annual precipitation ranging from about 400 to over 2,200 mm, with a very wet northwest and rather dry southeast, largely explained by orographic processes. Model results are compared with all available stations with continuous records, comprising daily information in 32 stations for temperature and 308 for precipitation, through the computation of mean climatologies, standard statistical errors on daily to seasonally timescales, and distributions of extreme events. Results show that WRF at 9 km outperforms ERA-Interim in all analyzed variables, with good results in the representation of the annual cycles in each region. The biases of minimum and maximum temperature are reduced, with improvement of the description of temperature variability at the extreme range of its distribution. The largest gain of the high resolution simulations is visible in the rainiest regions of Portugal, where orographic enhancement is crucial. These improvements are striking in the high ranking percentiles in all seasons, describing extreme precipitation events. WRF results at 9 km compare favorably with published results supporting its use as a high-resolution regional climate model. This higher resolution allows a better representation of extreme events that are of major importance to develop mitigation/adaptation strategies by policy makers and downstream users of regional climate models in applications such as flash floods or heat waves. (orig.)

  4. Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability.

    Science.gov (United States)

    Schalbetter, Stephanie A; Mansoubi, Sahar; Chambers, Anna L; Downs, Jessica A; Baxter, Jonathan

    2015-08-18

    Faithful genome duplication and inheritance require the complete resolution of all intertwines within the parental DNA duplex. This is achieved by topoisomerase action ahead of the replication fork or by fork rotation and subsequent resolution of the DNA precatenation formed. Although fork rotation predominates at replication termination, in vitro studies have suggested that it also occurs frequently during elongation. However, the factors that influence fork rotation and how rotation and precatenation may influence other replication-associated processes are unknown. Here we analyze the causes and consequences of fork rotation in budding yeast. We find that fork rotation and precatenation preferentially occur in contexts that inhibit topoisomerase action ahead of the fork, including stable protein-DNA fragile sites and termination. However, generally, fork rotation and precatenation are actively inhibited by Timeless/Tof1 and Tipin/Csm3. In the absence of Tof1/Timeless, excessive fork rotation and precatenation cause extensive DNA damage following DNA replication. With Tof1, damage related to precatenation is focused on the fragile protein-DNA sites where fork rotation is induced. We conclude that although fork rotation and precatenation facilitate unwinding in hard-to-replicate contexts, they intrinsically disrupt normal chromosome duplication and are therefore restricted by Timeless/Tipin.

  5. High-resolution near real-time drought monitoring in South Asia

    OpenAIRE

    Aadhar, Saran; Mishra, Vimal

    2017-01-01

    Drought in South Asia affect food and water security and pose challenges for millions of people. For policy-making, planning, and management of water resources at sub-basin or administrative levels, high-resolution datasets of precipitation and air temperature are required in near-real time. We develop a high-resolution (0.05°) bias-corrected precipitation and temperature data that can be used to monitor near real-time drought conditions over South Asia. Moreover, the dataset can be used to m...

  6. High resolution estimates of the corrosion risk for cultural heritage in Italy

    International Nuclear Information System (INIS)

    De Marco, Alessandra; Screpanti, Augusto; Mircea, Mihaela; Piersanti, Antonio; Proietti, Chiara; Fornasier, M. Francesca

    2017-01-01

    Air pollution plays a pivotal role in the deterioration of many materials used in buildings and cultural monuments causing an inestimable damage. This study aims to estimate the impacts of air pollution (SO 2 , HNO 3 , O 3 , PM 10 ) and meteorological conditions (temperature, precipitation, relative humidity) on limestone, copper and bronze based on high resolution air quality data-base produced with AMS-MINNI modelling system over the Italian territory over the time period 2003–2010. A comparison between high resolution data (AMS-MINNI grid, 4 × 4 km) and low resolution data (EMEP grid, 50 × 50 km) has been performed. Our results pointed out that the corrosion levels for limestone, copper and bronze are decreased in Italy from 2003 to 2010 in relation to decrease of pollutant concentrations. However, some problem related to air pollution persists especially in Northern and Southern Italy. In particular, PM 10 and HNO 3 are considered the main responsible for limestone corrosion. Moreover, the high resolution data (AMS-MINNI) allowed the identification of risk areas that are not visible with the low resolution data (EMEP modelling system) in all considered years and, especially, in the limestone case. Consequently, high resolution air quality simulations are suitable to provide concrete benefits in providing information for national effective policy against corrosion risk for cultural heritage, also in the context of climate changes that are affecting strongly Mediterranean basin. - Highlights: • Air pollution plays a pivotal role in the deterioration of cultural materials. • Limestone, copper and bronze corrosion levels decreased in Italy from 2003 to 2010. • PM 10 is considered the main responsible for limestone corrosion in Northern Italy. • HNO3 is considered the main responsible for limestone corrosion in all analyzed years. • High-resolution data are particularly useful to define area at risk for corrosion. - Importance of the high-resolution

  7. High-resolution computer-aided moire

    Science.gov (United States)

    Sciammarella, Cesar A.; Bhat, Gopalakrishna K.

    1991-12-01

    This paper presents a high resolution computer assisted moire technique for the measurement of displacements and strains at the microscopic level. The detection of micro-displacements using a moire grid and the problem associated with the recovery of displacement field from the sampled values of the grid intensity are discussed. A two dimensional Fourier transform method for the extraction of displacements from the image of the moire grid is outlined. An example of application of the technique to the measurement of strains and stresses in the vicinity of the crack tip in a compact tension specimen is given.

  8. High flux and high resolution VUV beam line for synchrotron radiation

    International Nuclear Information System (INIS)

    Wilcke, H.; Boehmer, W.; Schwentner, N.

    1982-04-01

    A beam line has been optimized for high flux and high resolution in the wavelength range from 30 nm to 300 nm. Sample chambers for luminescence spectroscopy on gaseous, liquid and solid samples and for photoelectron spectroscopy have been integrated. The synchrotron radiation from the storage ring DORIS (at DESY, Hamburg) emitted into 50 mrad in horizontal and into 2.2 mrad in vertical direction is focused by a cylindrical and a plane elliptical mirror into the entrance slit of a 2m normal incidence monochromator. The light flux from the exit slit is focused by a rotational elliptic mirror onto the sample yielding a size of the light spot of 4 x 0.15 mm 2 . The light flux at the sample reaches 7 x 10 12 photons nm -1 s -1 at 8 eV photon energy for a current of 100 mA in DORIS. A resolution of 0.007 nm has been obtained. (orig.)

  9. Rapid detection of SMARCB1 sequence variation using high resolution melting

    Directory of Open Access Journals (Sweden)

    Ashley David M

    2009-12-01

    Full Text Available Abstract Background Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM, for detecting sequence variations in SMARCB1. Methods Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4% showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA. A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to

  10. Rapid detection of SMARCB1 sequence variation using high resolution melting

    International Nuclear Information System (INIS)

    Dagar, Vinod; Chow, Chung-Wo; Ashley, David M; Algar, Elizabeth M

    2009-01-01

    Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening

  11. Development of high resolution Michelson interferometer for stable phase-locked ultrashort pulse pair generation.

    Science.gov (United States)

    Okada, Takumi; Komori, Kazuhiro; Goshima, Keishiro; Yamauchi, Shohgo; Morohashi, Isao; Sugaya, Takeyoshi; Ogura, Mutsuo; Tsurumachi, Noriaki

    2008-10-01

    We developed a high resolution Michelson interferometer with a two-frequency He-Ne laser positioning system in order to stabilize the relative phase of a pulse pair. The control resolution corresponded to a 12 as time resolution or a phase of 1.5 degrees at 900 nm. This high resolution Michelson interferometer can generate a phase-locked pulse pair either with a specific relative phase such as 0 or pi radians or with an arbitrary phase. Coherent control of an InAs self-assembled quantum dot was demonstrated using the high resolution Michelson interferometer with a microspectroscopy system.

  12. Study on the performance of large area MRPC with high position resolution

    Energy Technology Data Exchange (ETDEWEB)

    Yue Qian, E-mail: yueq@mail.tsinghua.edu.cn [Department of Engineering Physics, Tsinghua University, Beijing 100084 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education (China); Wu Yucheng; Li Yuanjing; Ye Jin; Cheng Jianping; Wang Yi; Li Jin [Department of Engineering Physics, Tsinghua University, Beijing 100084 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education (China)

    2012-01-01

    Multi-gap resistive plate chamber (MRPC), which is mostly developed in high energy physics domain with excellent time resolution, is also highlighted in imaging applications. A set of 50 cm Multiplication-Sign 50 cm large area MRPC with high position resolution was successfully developed by our group and different experiments have been done to test its performances. Cosmic ray muons were used to do the test and proper high voltage and working gas were chosen. Data analysis indicates its good detection efficiency and good position resolution, which encourages further study of its application in RPC-PET and muon tomography.

  13. High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System.

    Science.gov (United States)

    Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C T; Shui, Lingling

    2017-01-18

    DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1-10 Kbp fragment lengths with a yield of 75.30-91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

  14. High-resolution satellite imagery is an important yet underutilized resource in conservation biology.

    Science.gov (United States)

    Boyle, Sarah A; Kennedy, Christina M; Torres, Julio; Colman, Karen; Pérez-Estigarribia, Pastor E; de la Sancha, Noé U

    2014-01-01

    Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making.

  15. Utilization of Short-Simulations for Tuning High-Resolution Climate Model

    Science.gov (United States)

    Lin, W.; Xie, S.; Ma, P. L.; Rasch, P. J.; Qian, Y.; Wan, H.; Ma, H. Y.; Klein, S. A.

    2016-12-01

    Many physical parameterizations in atmospheric models are sensitive to resolution. Tuning the models that involve a multitude of parameters at high resolution is computationally expensive, particularly when relying primarily on multi-year simulations. This work describes a complementary set of strategies for tuning high-resolution atmospheric models, using ensembles of short simulations to reduce the computational cost and elapsed time. Specifically, we utilize the hindcast approach developed through the DOE Cloud Associated Parameterization Testbed (CAPT) project for high-resolution model tuning, which is guided by a combination of short (tests have been found to be effective in numerous previous studies in identifying model biases due to parameterized fast physics, and we demonstrate that it is also useful for tuning. After the most egregious errors are addressed through an initial "rough" tuning phase, longer simulations are performed to "hone in" on model features that evolve over longer timescales. We explore these strategies to tune the DOE ACME (Accelerated Climate Modeling for Energy) model. For the ACME model at 0.25° resolution, it is confirmed that, given the same parameters, major biases in global mean statistics and many spatial features are consistent between Atmospheric Model Intercomparison Project (AMIP)-type simulations and CAPT-type hindcasts, with just a small number of short-term simulations for the latter over the corresponding season. The use of CAPT hindcasts to find parameter choice for the reduction of large model biases dramatically improves the turnaround time for the tuning at high resolution. Improvement seen in CAPT hindcasts generally translates to improved AMIP-type simulations. An iterative CAPT-AMIP tuning approach is therefore adopted during each major tuning cycle, with the former to survey the likely responses and narrow the parameter space, and the latter to verify the results in climate context along with assessment in

  16. Validation of High-resolution Climate Simulations over Northern Europe.

    Science.gov (United States)

    Muna, R. A.

    2005-12-01

    Two AMIP2-type (Gates 1992) experiments have been performed with climate versions of ARPEGE/IFS model examine for North Atlantic North Europe, and Norwegian region and analyzed the effect of increasing resolution on the simulated biases. The ECMWF reanalysis or ERA-15 has been used to validate the simulations. Each of the simulations is an integration of the period 1979 to 1996. The global simulations used observed monthly mean sea surface temperatures (SST) as lower boundary condition. All aspects but the horizontal resolutions are similar in the two simulations. The first simulation has a uniform horizontal resolution of T63L. The second one has a variable resolution (T106Lc3) with the highest resolution in the Norwegian Sea. Both simulations have 31 vertical layers in the same locations. For each simulation the results were divided into two seasons: winter (DJF) and summer (JJA). The parameters investigated were mean sea level pressure, geopotential and temperature at 850 hPa and 500 hPa. To find out the causes of temperature bias during summer, latent and sensible heat flux, total cloud cover and total precipitation were analyzed. The high-resolution simulation exhibits more or less realistic climate over Nordic, Artic and European region. The overall performance of the simulations shows improvements of generally all fields investigated with increasing resolution over the target area both in winter (DJF) and summer (JJA).

  17. Optimal conditions to use Pfu exo(-) DNA polymerase for highly efficient ligation-mediated polymerase chain reaction protocols.

    Science.gov (United States)

    Angers, M; Cloutier, J F; Castonguay, A; Drouin, R

    2001-08-15

    Ligation-Mediated Polymerase Chain Reaction (LMPCR) is the most sensitive sequencing technique available to map single-stranded DNA breaks at the nucleotide level of resolution using genomic DNA. LMPCR has been adapted to map DNA damage and reveal DNA-protein interactions inside living cells. However, the sequence context (GC content), the global break frequency and the current combination of DNA polymerases used in LMPCR affect the quality of the results. In this study, we developed and optimized an LMPCR protocol adapted for Pyrococcus furiosus exo(-) DNA polymerase (Pfu exo(-)). The relative efficiency of Pfu exo(-) was compared to T7-modified DNA polymerase (Sequenase 2.0) at the primer extension step and to Thermus aquaticus DNA polymerase (Taq) at the PCR amplification step of LMPCR. At all break frequencies tested, Pfu exo(-) proved to be more efficient than Sequenase 2.0. During both primer extension and PCR amplification steps, the ratio of DNA molecules per unit of DNA polymerase was the main determinant of the efficiency of Pfu exo(-), while the efficiency of Taq was less affected by this ratio. Substitution of NaCl for KCl in the PCR reaction buffer of Taq strikingly improved the efficiency of the DNA polymerase. Pfu exo(-) was clearly more efficient than Taq to specifically amplify extremely GC-rich genomic DNA sequences. Our results show that a combination of Pfu exo(-) at the primer extension step and Taq at the PCR amplification step is ideal for in vivo DNA analysis and DNA damage mapping using LMPCR.

  18. Development and features of an X-ray detector with high spatial resolution

    International Nuclear Information System (INIS)

    Hartmann, H.

    1979-09-01

    A laboratory model of an X-ray detector with high spatial resolution was developed and constructed. It has no spectral resolution, but a local resolution of 20 μm which is about ten times as high as that of position-sensitive proportional counters and satisfies the requirements of the very best Wolter telescopes with regard to spatial resolution. The detector will be used for laboratory tests of the 80 cm Wolter telescope which is being developed for Spacelab flights. The theory of the wire grid detector and the physics of the photoelectric effect has been developed, and model calculations and numerical calculations have been carried out. (orig./WB) [de

  19. High Resolution Tracking Devices Based on Capillaries Filled with Liquid Scintillator

    CERN Multimedia

    Bonekamper, D; Vassiltchenko, V; Wolff, T

    2002-01-01

    %RD46 %title\\\\ \\\\The aim of the project is to develop high resolution tracking devices based on thin glass capillary arrays filled with liquid scintillator. This technique provides high hit densities and a position resolution better than 20 $\\mu$m. Further, their radiation hardness makes them superior to other types of tracking devices with comparable performance. Therefore, the technique is attractive for inner tracking in collider experiments, microvertex devices, or active targets for short-lived particle detection. High integration levels in the read-out based on the use of multi-pixel photon detectors and the possibility of optical multiplexing allow to reduce considerably the number of output channels, and, thus, the cost for the detector.\\\\ \\\\New optoelectronic devices have been developed and tested: the megapixel Electron Bombarded CCD (EBCCD), a high resolution image-detector having an outstanding capability of single photo-electron detection; the Vacuum Image Pipeline (VIP), a high-speed gateable pi...

  20. Capturing Snapshots of APE1 Processing DNA Damage

    Science.gov (United States)

    Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J.; Dyrkheeva, Nadezhda S.; Wilson, Samuel H.

    2015-01-01

    DNA apurinic-apyrimidinic (AP) sites are prevalent non-coding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive due in part to limited structural information. We report multiple high-resolution human APE1:DNA structures that divulge novel features of the APE1 reaction, including the metal binding site, nucleophile, and arginine clamps that mediate product release. We also report APE1:DNA structures with a T:G mismatch 5′ to the AP-site, representing a clustered lesion occurring in methylated CpG dinucleotides. These reveal that APE1 molds the T:G mismatch into a unique Watson-Crick like geometry that distorts the active site reducing incision. These snapshots provide mechanistic clarity for APE1, while affording a rational framework to manipulate biological responses to DNA damage. PMID:26458045

  1. Structure and mechanism of human DNA polymerase [eta

    Energy Technology Data Exchange (ETDEWEB)

    Biertümpfel, Christian; Zhao, Ye; Kondo, Yuji; Ramón-Maiques, Santiago; Gregory, Mark; Lee, Jae Young; Masutani, Chikahide; Lehmann, Alan R.; Hanaoka, Fumio; Yang, Wei (Sussex); (NIH); (Gakushuin); (Osaka)

    2010-11-03

    The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase {eta} (Pol{eta}), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Pol{eta} at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Pol{eta} acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Pol{eta} orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Pol{eta} missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Pol{eta} in replicating through D loop and DNA fragile sites.

  2. Modelling high-resolution electron microscopy based on core-loss spectroscopy

    International Nuclear Information System (INIS)

    Allen, L.J.; Findlay, S.D.; Oxley, M.P.; Witte, C.; Zaluzec, N.J.

    2006-01-01

    There are a number of factors affecting the formation of images based on core-loss spectroscopy in high-resolution electron microscopy. We demonstrate unambiguously the need to use a full nonlocal description of the effective core-loss interaction for experimental results obtained from high angular resolution electron channelling electron spectroscopy. The implications of this model are investigated for atomic resolution scanning transmission electron microscopy. Simulations are used to demonstrate that core-loss spectroscopy images formed using fine probes proposed for future microscopes can result in images that do not correspond visually with the structure that has led to their formation. In this context, we also examine the effect of varying detector geometries. The importance of the contribution to core-loss spectroscopy images by dechannelled or diffusely scattered electrons is reiterated here

  3. High resolution color imagery for orthomaps and remote sensing

    Energy Technology Data Exchange (ETDEWEB)

    Fricker, Peter [Leica Geosystems GIS and Mapping, LLC (Switzerland); Gallo, M. Guillermo [Leica Geosystems GIS and Mapping, LLC (United States)

    2005-07-01

    The ADS40 Airborne Digital Pushbroom Sensor is currently the only commercial sensor capable of acquiring color and false color strip images in the low decimeter range at the same high resolution as the black and white stereo images. This high resolution of 12,000 pixels across the entire swath and 100% forward overlap in the image strips result in high quality DSM's, True Ortho's and at the same time allow unbiased remote sensing applications due to color strip images unchanged by pan-sharpening. The paper gives details on how the pushbroom sensor achieves these seemingly difficult technical challenges. It describes how a variety of mapping applications benefit from this sensor, a sensor which acts as a satellite pushbroom sensor within the airborne environment. (author)

  4. High resolution solar observations from first principles to applications

    Science.gov (United States)

    Verdoni, Angelo P.

    2009-10-01

    The expression "high-resolution observations" in Solar Physics refers to the spatial, temporal and spectral domains in their entirety. High-resolution observations of solar fine structure are a necessity to answer many of the intriguing questions related to solar activity. However, a researcher building instruments for high-resolution observations has to cope with the fact that these three domains often have diametrically opposed boundary conditions. Many factors have to be considered in the design of a successful instrument. Modern post-focus instruments are more closely linked with the solar telescopes that they serve than in past. In principle, the quest for high-resolution observations already starts with the selection of the observatory site. The site survey of the Advanced Technology Solar Telescope (ATST) under the stewardship of the National Solar Observatory (NSO) has identified Big Bear Solar Observatory (BBSO) as one of the best sites for solar observations. In a first step, the seeing characteristics at BBSO based on the data collected for the ATST site survey are described. The analysis will aid in the scheduling of high-resolution observations at BBSO as well as provide useful information concerning the design and implementation of a thermal control system for the New Solar Telescope (NST). NST is an off-axis open-structure Gregorian-style telescope with a 1.6 m aperture. NST will be housed in a newly constructed 5/8-sphere ventilated dome. With optics exposed to the surrounding air, NST's open-structure design makes it particularly vulnerable to the effects of enclosure-related seeing. In an effort to mitigate these effects, the initial design of a thermal control system for the NST dome is presented. The goal is to remediate thermal related seeing effects present within the dome interior. The THermal Control System (THCS) is an essential component for the open-telescope design of NST to work. Following these tasks, a calibration routine for the

  5. Pneumonia: high-resolution CT findings in 114 patients

    Energy Technology Data Exchange (ETDEWEB)

    Reittner, Pia [Department of Radiology, Vancouver Hospital and Health Sciences Center, 855 W. 12th Ave., Vancouver, BC (Canada); Department of Radiology, Karl Franzens University and University Hospital Graz, Auenbruggerplatz 9, 8036 Graz (Austria); Ward, Suzanne; Heyneman, Laura; Mueller, Nestor L. [Department of Radiology, Vancouver Hospital and Health Sciences Center, 855 W. 12th Ave., Vancouver, BC (Canada); Johkoh, Takeshi [Department of Radiology, Osaka University Medical School, 2-2 Yamadaoka, Suita, Osaka 565-0825 (Japan)

    2003-03-01

    The objective of the present study was to assess the high-resolution CT appearances of different types of pneumonia. The high-resolution CT scans obtained in 114 patients (58 immunocompetent, 59 immunocompromised) with bacterial, Mycoplasma pneumoniae, viral, fungal, and Pneumocystis carinii pneumonias were analyzed retrospectively by two independent observers for presence, pattern, and distribution of abnormalities. Areas of air-space consolidation were not detected in patients with viral pneumonia and were less frequently seen in patients with Pneumocystis carinii pneumonia (2 of 22 patients, 9%) than in bacterial (30 of 35, 85%), Mycoplasma pneumoniae (22 of 28, 79%), and fungal pneumonias (15 of 20, 75%; p<0.01). There was no significant difference in the prevalence or distribution of consolidation between bacterial, Mycoplasma pneumoniae, and fungal pneumonias. Extensive symmetric bilateral areas of ground-glass attenuation were present in 21 of 22 (95%) patients with Pneumocystis carinii pneumonia and were not seen in other pneumonias except in association with areas of consolidation and nodules. Centrilobular nodules were present less commonly in bacterial pneumonia (6 of 35 patients, 17%) than in Mycoplasma pneumoniae (24 of 28, 96%), viral (7 of 9, 78%), or fungal (12 of 20, 92%) pneumonia (p<0.01). Except for Pneumocystis carinii pneumonia and Mycoplasma pneumoniae pneumonia, which often have a characteristic appearance, high-resolution CT is of limited value in the differential diagnosis of the various types of infective pneumonia. (orig.)

  6. Pneumonia: high-resolution CT findings in 114 patients

    International Nuclear Information System (INIS)

    Reittner, Pia; Ward, Suzanne; Heyneman, Laura; Mueller, Nestor L.; Johkoh, Takeshi

    2003-01-01

    The objective of the present study was to assess the high-resolution CT appearances of different types of pneumonia. The high-resolution CT scans obtained in 114 patients (58 immunocompetent, 59 immunocompromised) with bacterial, Mycoplasma pneumoniae, viral, fungal, and Pneumocystis carinii pneumonias were analyzed retrospectively by two independent observers for presence, pattern, and distribution of abnormalities. Areas of air-space consolidation were not detected in patients with viral pneumonia and were less frequently seen in patients with Pneumocystis carinii pneumonia (2 of 22 patients, 9%) than in bacterial (30 of 35, 85%), Mycoplasma pneumoniae (22 of 28, 79%), and fungal pneumonias (15 of 20, 75%; p<0.01). There was no significant difference in the prevalence or distribution of consolidation between bacterial, Mycoplasma pneumoniae, and fungal pneumonias. Extensive symmetric bilateral areas of ground-glass attenuation were present in 21 of 22 (95%) patients with Pneumocystis carinii pneumonia and were not seen in other pneumonias except in association with areas of consolidation and nodules. Centrilobular nodules were present less commonly in bacterial pneumonia (6 of 35 patients, 17%) than in Mycoplasma pneumoniae (24 of 28, 96%), viral (7 of 9, 78%), or fungal (12 of 20, 92%) pneumonia (p<0.01). Except for Pneumocystis carinii pneumonia and Mycoplasma pneumoniae pneumonia, which often have a characteristic appearance, high-resolution CT is of limited value in the differential diagnosis of the various types of infective pneumonia. (orig.)

  7. Toward quantitative fluorescence microscopy with DNA origami nanorulers.

    Science.gov (United States)

    Beater, Susanne; Raab, Mario; Tinnefeld, Philip

    2014-01-01

    The dynamic development of fluorescence microscopy has created a large number of new techniques, many of which are able to overcome the diffraction limit. This chapter describes the use of DNA origami nanostructures as scaffold for quantifying microscope properties such as sensitivity and resolution. The DNA origami technique enables placing of a defined number of fluorescent dyes in programmed geometries. We present a variety of DNA origami nanorulers that include nanorulers with defined labeling density and defined distances between marks. The chapter summarizes the advantages such as practically free choice of dyes and labeling density and presents examples of nanorulers in use. New triangular DNA origami nanorulers that do not require photoinduced switching by imaging transient binding to DNA nanostructures are also reported. Finally, we simulate fluorescence images of DNA origami nanorulers and reveal that the optimal DNA nanoruler for a specific application has an intermark distance that is roughly 1.3-fold the expected optical resolution. © 2014 Elsevier Inc. All rights reserved.

  8. Topography improvements in MEMS DMs for high-contrast, high-resolution imaging, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This project will develop and demonstrate an innovative microfabrication process to substantially improve the surface quality achievable in high-resolution...

  9. Scene Classification Using High Spatial Resolution Multispectral Data

    National Research Council Canada - National Science Library

    Garner, Jamada

    2002-01-01

    ...), High-spatial resolution (8-meter), 4-color MSI data from IKONOS provide a new tool for scene classification, The utility of these data are studied for the purpose of classifying the Elkhorn Slough and surrounding wetlands in central...

  10. Rapid Detection and Identification of Human Hookworm Infections through High Resolution Melting (HRM) Analysis

    Science.gov (United States)

    Ngui, Romano; Lim, Yvonne A. L.; Chua, Kek Heng

    2012-01-01

    Background Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR) coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species. Methods Real-time PCR coupled with HRM analysis targeting the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA as the genetic marker was used to identify and distinguish hookworm species in human samples. Unique and distinct characteristics of HRM patterns were produced for each of the five hookworm species. The melting curves were characterized by peaks of 79.24±0.05°C and 83.00±0.04°C for Necator americanus, 79.12±0.10°C for Ancylostoma duodenale, 79.40±0.10°C for Ancylostoma ceylanicum, 79.63±0.05°C for Ancylostoma caninum and 79.70±0.14°C for Ancylostoma braziliense. An evaluation of the method's sensitivity and specificity revealed that this assay was able to detect as low as 0.01 ng/µl hookworm DNA and amplification was only recorded for hookworm positive samples. Conclusion The HRM assay developed in this study is a rapid and straightforward method for the diagnosis, identification and discrimination of five human hookworms. This assay is simple compared to other probe-based genotyping methods as it does not require multiplexing, DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of human hookworm species. PMID:22844538

  11. Rapid detection and identification of human hookworm infections through high resolution melting (HRM analysis.

    Directory of Open Access Journals (Sweden)

    Romano Ngui

    Full Text Available BACKGROUND: Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR coupled with high resolution melting-curve (HRM analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species. METHODS: Real-time PCR coupled with HRM analysis targeting the second internal transcribed spacer (ITS-2 of nuclear ribosomal DNA as the genetic marker was used to identify and distinguish hookworm species in human samples. Unique and distinct characteristics of HRM patterns were produced for each of the five hookworm species. The melting curves were characterized by peaks of 79.24±0.05°C and 83.00±0.04°C for Necator americanus, 79.12±0.10°C for Ancylostoma duodenale, 79.40±0.10°C for Ancylostoma ceylanicum, 79.63±0.05°C for Ancylostoma caninum and 79.70±0.14°C for Ancylostoma braziliense. An evaluation of the method's sensitivity and specificity revealed that this assay was able to detect as low as 0.01 ng/µl hookworm DNA and amplification was only recorded for hookworm positive samples. CONCLUSION: The HRM assay developed in this study is a rapid and straightforward method for the diagnosis, identification and discrimination of five human hookworms. This assay is simple compared to other probe-based genotyping methods as it does not require multiplexing, DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of human hookworm species.

  12. Preliminary report on the development of a high resolution PET camera using semiconductor detectors

    International Nuclear Information System (INIS)

    Kikuchi, Yohei; Ishii, Keizo; Yamazaki, Hiromichi; Matsuyama, Shigeo; Yamaguchi, Takashi; Yamamoto, Yusuke; Sato, Takemi; Aoki, Yasushi; Aoki, Kenichi

    2005-01-01

    We are developing a PET camera using small semiconductor detectors, whose resolution is equivalent to the physical limit of spatial resolution. First, a coincidence system of 16 Schottky CdTe detectors of 0.5 mm width obtained a resolution of <1 mm and it was confirmed that the Schottky CdTe detector is suitable for high resolution PET. Next, the performance of a pair of 32 channel CdTe arrays (1.2 mm width per channel) was investigated for the development of the prototype of high resolution PET. The time resolution between opposing detector pair was 13 ns (FWHM) when high voltage (700 V) was applied. The image of a 0.6 mm diameter point source was obtained in an experiment with opposing detector arrays using four channels, indicating that, a higher resolution can be achieved with the 32 channel CdTe array

  13. High resolution reservoir geological modelling using outcrop information

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Changmin; Lin Kexiang; Liu Huaibo [Jianghan Petroleum Institute, Hubei (China)] [and others

    1997-08-01

    This is China`s first case study of high resolution reservoir geological modelling using outcrop information. The key of the modelling process is to build a prototype model and using the model as a geological knowledge bank. Outcrop information used in geological modelling including seven aspects: (1) Determining the reservoir framework pattern by sedimentary depositional system and facies analysis; (2) Horizontal correlation based on the lower and higher stand duration of the paleo-lake level; (3) Determining the model`s direction based on the paleocurrent statistics; (4) Estimating the sandbody communication by photomosaic and profiles; (6) Estimating reservoir properties distribution within sandbody by lithofacies analysis; and (7) Building the reservoir model in sandbody scale by architectural element analysis and 3-D sampling. A high resolution reservoir geological model of Youshashan oil field has been built by using this method.

  14. Turbine component casting core with high resolution region

    Science.gov (United States)

    Kamel, Ahmed; Merrill, Gary B.

    2014-08-26

    A hollow turbine engine component with complex internal features can include a first region and a second, high resolution region. The first region can be defined by a first ceramic core piece formed by any conventional process, such as by injection molding or transfer molding. The second region can be defined by a second ceramic core piece formed separately by a method effective to produce high resolution features, such as tomo lithographic molding. The first core piece and the second core piece can be joined by interlocking engagement that once subjected to an intermediate thermal heat treatment process thermally deform to form a three dimensional interlocking joint between the first and second core pieces by allowing thermal creep to irreversibly interlock the first and second core pieces together such that the joint becomes physically locked together providing joint stability through thermal processing.

  15. High-resolution neutron-diffraction measurements to 8 kbar

    Science.gov (United States)

    Bull, C. L.; Fortes, A. D.; Ridley, C. J.; Wood, I. G.; Dobson, D. P.; Funnell, N. P.; Gibbs, A. S.; Goodway, C. M.; Sadykov, R.; Knight, K. S.

    2017-10-01

    We describe the capability to measure high-resolution neutron powder diffraction data to a pressure of at least 8 kbar. We have used the HRPD instrument at the ISIS neutron source and a piston-cylinder design of pressure cell machined from a null-scattering titanium zirconium alloy. Data were collected under hydrostatic conditions from an elpasolite perovskite La?NiMnO?; by virtue of a thinner cell wall on the incident-beam side of the cell, it was possible to obtain data in the instrument's highest resolution back-scattering detector banks up to a maximum pressure of 8.5 kbar.

  16. Kinetic Energy from Supernova Feedback in High-resolution Galaxy Simulations

    Science.gov (United States)

    Simpson, Christine M.; Bryan, Greg L.; Hummels, Cameron; Ostriker, Jeremiah P.

    2015-08-01

    We describe a new method for adding a prescribed amount of kinetic energy to simulated gas modeled on a cartesian grid by directly altering grid cells’ mass and velocity in a distributed fashion. The method is explored in the context of supernova (SN) feedback in high-resolution (˜10 pc) hydrodynamic simulations of galaxy formation. Resolution dependence is a primary consideration in our application of the method, and simulations of isolated explosions (performed at different resolutions) motivate a resolution-dependent scaling for the injected fraction of kinetic energy that we apply in cosmological simulations of a 109 M⊙ dwarf halo. We find that in high-density media (≳50 cm-3) with coarse resolution (≳4 pc per cell), results are sensitive to the initial kinetic energy fraction due to early and rapid cooling. In our galaxy simulations, the deposition of small amounts of SN energy in kinetic form (as little as 1%) has a dramatic impact on the evolution of the system, resulting in an order-of-magnitude suppression of stellar mass. The overall behavior of the galaxy in the two highest resolution simulations we perform appears to converge. We discuss the resulting distribution of stellar metallicities, an observable sensitive to galactic wind properties, and find that while the new method demonstrates increased agreement with observed systems, significant discrepancies remain, likely due to simplistic assumptions that neglect contributions from SNe Ia and stellar winds.

  17. The spectrometer of the High-Resolution Multi position Thomson Scattering Diagnostic for TJ-II

    International Nuclear Information System (INIS)

    Herranz, J.; Barth, C. J.; Castejon, F.; Lopez-Sanchez, A.; Mirones, E.; Pastor, I.; Perez, D.; Rodriguez, C.

    2001-01-01

    Since 1998, a high-resolution multiposition thompson scattering system is in operation at the stellarator TJ-II, combining high accuracy and excellent spatial resolution. A description of the diagnostic spectrometer is presented. The main characteristics of the spectrometer that allow YJ-II Thomson scattering diagnostic to have high spatial and spectral resolution are described in this paper. (Author)

  18. Construction of a high resolution electron beam profile monitor

    International Nuclear Information System (INIS)

    Norem, J.; Dawson, J.; Haberichter, W.; Novak, W.; Reed, L.; Yang, X.F.

    1993-01-01

    Bremsstrahlung from an electron beam on a heavy target can be used to image the beam profile using collimators and slits. The limiting resolution using this system is determined by Fresnel diffraction, and is ∼ √(λd/2), where λ is the photon wavelength and d is determined by the linear dimensions of the system. For linear colliders this resolution could be a few nm. The highest resolution requires detectors which see only high energy, (small λ), photons, and this is accomplished by converting photons to pairs, and detecting Cherenkov light in a nearly forward angle with a CCD detector or streak camera. Tests are planned at the Argonne APS and SLAC FFTB

  19. DNA-dispersed graphene/NiO hybrid materials for highly sensitive non-enzymatic glucose sensor

    International Nuclear Information System (INIS)

    Lv Wei; Jin Fengmin; Guo Quangui; Yang Quanhong; Kang Feiyu

    2012-01-01

    Highlights: ► We investigated the potential of GNS/NiO/DNA hybrid used as a nonenzymatic sensor. ► DNA is a highly efficient disperse agent for GNS/NiO hybrid than ionic surfactants. ► GNS/NiO/DNA hybrid shows fast electron transfer in the electrochemical reaction. ► GNS/NiO/DNA hybrid shows good detection performance towards glucose. - Abstract: We demonstrate graphene nanosheet/NiO hybrids (GNS/NiO) as the active material for high-performance non-enzymatic glucose sensors. Such sensors are fabricated by DNA-dispersed GNS/NiO suspension deposited on glassy carbon electrodes. ss-DNA shows strong dispersing ability for the GNS/NiO hybrid materials resulting in stable water-dispersible GNS/NiO/DNA hybrids with fully separated layers. The GNS/NiO/DNA hybrids show enhanced electron transfer in the electrocatalytic reaction process, and accordingly, such hybrids modified electrodes show good sensing performance towards glucose and are characterized by large detection ranges, short response periods, low detection limit and high sensitivity and stability.

  20. Resolution of RNA using high-performance liquid chromatography

    NARCIS (Netherlands)

    Mclaughlin, L.W.; Bischoff, Rainer

    1987-01-01

    High-performance liquid chromatographic techniques can be very effective for the resolution and isolation of nucleic acids. The characteristic ionic (phosphodiesters) and hydrophobic (nucleobases) properties of RNAs can be exploited for their separation. In this respect anion-exchange and

  1. High-Resolution Remote Sensing Image Building Extraction Based on Markov Model

    Science.gov (United States)

    Zhao, W.; Yan, L.; Chang, Y.; Gong, L.

    2018-04-01

    With the increase of resolution, remote sensing images have the characteristics of increased information load, increased noise, more complex feature geometry and texture information, which makes the extraction of building information more difficult. To solve this problem, this paper designs a high resolution remote sensing image building extraction method based on Markov model. This method introduces Contourlet domain map clustering and Markov model, captures and enhances the contour and texture information of high-resolution remote sensing image features in multiple directions, and further designs the spectral feature index that can characterize "pseudo-buildings" in the building area. Through the multi-scale segmentation and extraction of image features, the fine extraction from the building area to the building is realized. Experiments show that this method can restrain the noise of high-resolution remote sensing images, reduce the interference of non-target ground texture information, and remove the shadow, vegetation and other pseudo-building information, compared with the traditional pixel-level image information extraction, better performance in building extraction precision, accuracy and completeness.

  2. MR-Venography Using High Resolution True-FISP

    Energy Technology Data Exchange (ETDEWEB)

    Spuentrup, E. [Technische Hochschule Aachen (Germany). Klinik fuer Radiologische Diagnostik; Beth Israel Deaconess Medical Center, Boston, MA (United States). Dept. of Medicine; Harvard Medical School, Boston, MA (United States); Buecker, A.; Guenther, R.W. [Technische Hochschule Aachen (Germany). Klinik fuer Radiologische Diagnostik; Stuber, M. [Beth Israel Deaconess Medical Center, Boston, MA (United States). Dept. of Medicine; Harvard Medical School, Boston, MA (United States); Philips Med. Syst., Best (Netherlands)

    2001-08-01

    A new fast MR-venography approach using a high resolution True-FISP imaging sequence was investigated in 20 patients suffering from 23 deep vein thromboses. Diagnosis was proven by X-ray venography, CT or ultrasound examination. The presented technique allowed for clear thrombus visualization with a high contrast to the surrounding blood pool even in calf veins. Acquisition time was less than 10 minutes for imaging the pelvis and the legs. No contrast media was needed. The presented high resolution True-FISP MR-veography is a promising non-invasive, fast MR-venography approach for detection of deep venous thrombosis. (orig.) [German] Eine neue schnelle, oertlich hochaufgeloeste MR-Phlebographietechnik mit einer axialen True-FISP Bildgebungssequenz wurde an 20 Patienten mit 23 nach-gewiesenen tiefen Beinvenenthrombosen untersucht. Die Befunde wurden mit einer konventionellen Roentgenphlebographie, einer CT oder einer Sonographie gesichert. Die vorgestellte Technik erlaubte in allen Faellen eine Thrombusdarstellung mit hohem Kontrast zum umgebenden venoesen Blut, wobei aufgrund der hohen Ortsaufloesung auch die Unterschenkelvenen beurteilt werden konnten. Die Datenaufnahmezeit zur Untersuchung des Beckens und der Beine betrug weniger als 10 Minuten. Kontrastmittel wurde nicht benoetigt. Die vorgestellte MR-Phlebographietechnik unter Verwendung einer oertlich hochauf-geloesten True-FISP Sequenz ist eine neue, vielversprechende, nicht-invasive Technik zur Diagnostik der tiefen Bein- und Beckenvenenthrombose. (orig.)

  3. 3D high spectral and spatial resolution imaging of ex vivo mouse brain

    International Nuclear Information System (INIS)

    Foxley, Sean; Karczmar, Gregory S.; Domowicz, Miriam; Schwartz, Nancy

    2015-01-01

    Purpose: Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T 2 * -weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T 2 * and resonance frequency. Methods: The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm 3 and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16–24 h). Results: High contrast T 2 * -weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at −7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in the water resonance that is not

  4. Study of fish response using particle image velocimetry and high-speed, high-resolution imaging

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Z. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Richmond, M. C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mueller, R. P. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gruensch, G. R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2004-10-01

    Fish swimming has fascinated both engineers and fish biologists for decades. Digital particle image velocimetry (DPIV) and high-speed, high-resolution digital imaging are recently developed analysis tools that can help engineers and biologists better understand how fish respond to turbulent environments. This report details studies to evaluate DPIV. The studies included a review of existing literature on DPIV, preliminary studies to test the feasibility of using DPIV conducted at our Flow Biology Laboratory in Richland, Washington September through December 2003, and applications of high-speed, high-resolution digital imaging with advanced motion analysis to investigations of fish injury mechanisms in turbulent shear flows and bead trajectories in laboratory physical models. Several conclusions were drawn based on these studies, which are summarized as recommendations for proposed research at the end of this report.

  5. Dye laser light for high-resolution classical photography

    International Nuclear Information System (INIS)

    Geissler, K.K.

    1982-01-01

    The test run with the bubble chamber HOLEBC in October 1981 offered the opportunity of checking the usefulness of de-speckled dye laser light for illumination purposes in high-resolution classical dark field photography of small bubble chambers. (orig./HSI)

  6. High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field

    International Nuclear Information System (INIS)

    Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Lipton, Andrew S.; Berthold, Deborah A.; Rienstra, Chad M.

    2010-01-01

    Magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy of uniformly- 13 C, 15 N labeled protein samples provides insight into atomic-resolution chemistry and structure. Data collection efficiency has advanced remarkably in the last decade; however, the study of larger proteins is still challenged by relatively low resolution in comparison to solution NMR. In this study, we present a systematic analysis of SSNMR protein spectra acquired at 11.7, 17.6 and 21.1 Tesla ( 1 H frequencies of 500, 750, and 900 MHz). For two protein systems-GB1, a 6 kDa nanocrystalline protein and DsbA, a 21 kDa nanocrystalline protein-line narrowing is demonstrated in all spectral regions with increasing field. Resolution enhancement is greatest in the aliphatic region, including methine, methylene and methyl sites. The resolution for GB1 increases markedly as a function of field, and for DsbA, resolution in the C-C region increases by 42%, according to the number of peaks that can be uniquely picked and integrated in the 900 MHz spectra when compared to the 500 MHz spectra. Additionally, chemical exchange is uniquely observed in the highest field spectra for at least two isoleucine Cδ1 sites in DsbA. These results further illustrate the benefits of high-field MAS SSNMR spectroscopy for protein structural studies.

  7. Design of a high-resolution high-stability positioning mechanism for crystal optics

    International Nuclear Information System (INIS)

    Shu, D.; Toellner, T. S.; Alp, E. E.

    1999-01-01

    The authors present a novel miniature multi-axis driving structure that will allow positioning of two crystals with better than 50-nrad angular resolution and nanometer linear driving sensitivity.The precision and stability of this structure allow the user to align or adjust an assembly of crystals to achieve the same performance as does a single channel-cut crystal, so they call it an artificial channel-cut crystal. In this paper, the particular designs and specifications, as well as the test results,for a two-axis driving structure for a high-energy-resolution artificial channel-cut crystal monochromator are presented

  8. An interferometer for high-resolution optical surveillance from geostationary orbit

    Science.gov (United States)

    Bonino, L.; Bresciani, F.; Piasini, G.; Flebus, C.; Lecat, J.-H.; Roose, S.; Pisani, M.; Cabral, A.; Rebordão, J.; Proença, C.; Costal, J.; Lima, P. U.; Loix, N.; Musso, F.

    2017-11-01

    The activities described in this paper have been developed in the frame of the EUCLID CEPA 9 RTP 9.9 "High Resolution Optical Satellite Sensor" project of the WEAO Research Cell. They have been focused on the definition of an interferometric instrument optimised for the high-resolution optical surveillance from geostationary orbit (GEO) by means of the synthetic aperture technique, and on the definition and development of the related enabling technologies. In this paper we describe the industrial team, the selected mission specifications and overview of the whole design and manufacturing activities performed.

  9. High resolution spectroscopy in solids by nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Bonagamba, T.J.

    1991-07-01

    The nuclear magnetic resonance (NMR) techniques for High Resolution Spectroscopy in Solids are described. Also the construction project of a partially home made spectrometer and its applications in the characterization of solid samples are shown in detail. The high resolution spectrometer used is implemented with the double resonance multiple pulses sequences and magic angle spinning (MAS) and can be used with solid and liquid samples. The maximum spinning frequency for the MAS experiment is in excess of 5 Khz, the double resonance sequences can be performed with any type of nucleus, in the variable temperature operating range with nitrogen gas: -120 0 C to +160 0 C, and is fully controlled by a Macintosh IIci microcomputer. (author)

  10. DSM GENERATION FROM HIGH RESOLUTION COSMO-SKYMED IMAGERY WITH RADARGRAMMETRIC MODEL

    OpenAIRE

    P. Capaldo; M. Crespi; F. Fratarcangeli; A. Nascetti; F. Pieralice

    2012-01-01

    The availability of new high resolution radar spaceborne sensors offers new interesting potentialities for the geomatics application: spatial and temporal change detection, features extraction, generation of Digital Surface (DSMs). As regards the DSMs generation from new high resolution data (as SpotLight imagery), the development and the accuracy assessment of method based on radargrammetric approach are topics of great interest and relevance. The aim of this investigation is the DSM generat...

  11. High-throughput STR analysis for DNA database using direct PCR.

    Science.gov (United States)

    Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

    2013-07-01

    Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. © 2013 American Academy of Forensic Sciences Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

  12. High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.

    Science.gov (United States)

    Baños-Mateos, Soledad; van Roon, Anne-Marie M; Lang, Ulla F; Maslen, Sarah L; Skehel, J Mark; Lamers, Meindert H

    2017-10-11

    High-fidelity DNA replication depends on a proofreading 3'-5' exonuclease that is associated with the replicative DNA polymerase. The replicative DNA polymerase DnaE1 from the major pathogen Mycobacterium tuberculosis (Mtb) uses its intrinsic PHP-exonuclease that is distinct from the canonical DEDD exonucleases found in the Escherichia coli and eukaryotic replisomes. The mechanism of the PHP-exonuclease is not known. Here, we present the crystal structure of the Mtb DnaE1 polymerase. The PHP-exonuclease has a trinuclear zinc center, coordinated by nine conserved residues. Cryo-EM analysis reveals the entry path of the primer strand in the PHP-exonuclease active site. Furthermore, the PHP-exonuclease shows a striking similarity to E. coli endonuclease IV, which provides clues regarding the mechanism of action. Altogether, this work provides important insights into the PHP-exonuclease and reveals unique properties that make it an attractive target for novel anti-mycobacterial drugs.The polymerase and histidinol phosphatase (PHP) domain in the DNA polymerase DnaE1 is essential for mycobacterial high-fidelity DNA replication. Here, the authors determine the DnaE1 crystal structure, which reveals the PHP-exonuclease mechanism that can be exploited for antibiotic development.

  13. High-resolution CT findings in Streptococcus milleri pulmonary infection

    International Nuclear Information System (INIS)

    Okada, F.; Ono, A.; Ando, Y.; Nakayama, T.; Ishii, H.; Hiramatsu, K.; Sato, H.; Kira, A.; Otabe, M.; Mori, H.

    2013-01-01

    Aim: To assess pulmonary high-resolution computed tomography (CT) findings in patients with acute Streptococcus milleri pulmonary infection. Materials and methods: Sixty consecutive patients with acute S. milleri pneumonia who had undergone high-resolution CT chest examinations between January 2004 and March 2010 were retrospectively identified. Twenty-seven patients with concurrent infections were excluded. The final study group comprised 33 patients (25 men, 8 women; aged 20–88 years, mean 63.1 years) with S. milleri infection. The patients' clinical findings were assessed. Parenchymal abnormalities, enlarged lymph nodes, and pleural effusion were evaluated on high-resolution CT. Results: Underlying conditions included malignancy (n = 15), a smoking habit (n = 11), and diabetes mellitus (n = 8). CT images of all patients showed abnormal findings, including ground-glass opacity (n = 24), bronchial wall thickening (n = 23), consolidation (n = 17), and cavities (n = 7). Pleural effusion was found in 18 patients, and complex pleural effusions were found in seven patients. Conclusion: Pulmonary infection caused by S. milleri was observed mostly in male patients with underlying conditions such as malignancy or a smoking habit. The CT findings in patients with S. milleri consisted mainly of ground-glass opacity, bronchial wall thickening, pleural effusions, and cavities

  14. Low-Power Amplifier-Discriminators for High Time Resolution Detection

    CERN Document Server

    Despeisse, M; Anghinolfi, F; Tiuraniemi, S; Osmic, F; Riedler, P; Kluge, A; Ceccucci, A

    2009-01-01

    Low-power amplifier-discriminators based on a so-called NINO architecture have been developed with high time resolution for the readout of radiation detectors. Two different circuits were integrated in the NINO13 chip, processed in IBM 130 nm CMOS technology. The LCO version (Low Capacitance and consumption Optimization) was designed for potential use as front-end electronics in the Gigatracker of the NA62 experiment at CERN. It was developed as pixel readout for solid-state pixel detectors to permit minimum ionizing particle detection with less than 180 ps rms resolution per pixel on the output pulse, for power consumption below 300 mu W per pixel. The HCO version (High Capacitance Optimization) was designed with 4 mW power consumption per channel to provide timing resolution below 20 ps rms on the output pulse, for charges above 10 fC. Results presented show the potential of the LCO and HCO circuits for the precise timing readout of solid-state detectors, vacuum tubes or gas detectors, for applications in h...

  15. High resolution melt curve analysis based on methylation status for human semen identification.

    Science.gov (United States)

    Fachet, Caitlyn; Quarino, Lawrence; Karnas, K Joy

    2017-03-01

    A high resolution melt curve assay to differentiate semen from blood, saliva, urine, and vaginal fluid based on methylation status at the Dapper Isoform 1 (DACT1) gene was developed. Stains made from blood, saliva, urine, semen, and vaginal fluid were obtained from volunteers and DNA was isolated using either organic extraction (saliva, urine, and vaginal fluid) or Chelex ® 100 extraction (blood and semen). Extracts were then subjected to bisulfite modification in order to convert unmethylated cytosines to uracil, consequently creating sequences whose amplicons have melt curves that vary depending on their initial methylation status. When primers designed to amplify the promoter region of the DACT1 gene were used, DNA from semen samples was distinguishable from other fluids by a having a statistically significant lower melting temperature. The assay was found to be sperm-significant since semen from a vasectomized man produced a melting temperature similar to the non-semen body fluids. Blood and semen stains stored up to 5 months and tested at various intervals showed little variation in melt temperature indicating the methylation status was stable during the course of the study. The assay is a more viable method for forensic science practice than most molecular-based methods for body fluid stain identification since it is time efficient and utilizes instrumentation common to forensic biology laboratories. In addition, the assay is advantageous over traditional presumptive chemical methods for body fluid identification since results are confirmatory and the assay offers the possibility of multiplexing which may test for multiple body fluids simultaneously.

  16. High-Resolution Scintimammography: A Pilot Study

    Energy Technology Data Exchange (ETDEWEB)

    Rachel F. Brem; Joelle M. Schoonjans; Douglas A. Kieper; Stan Majewski; Steven Goodman; Cahid Civelek

    2002-07-01

    This study evaluated a novel high-resolution breast-specific gamma camera (HRBGC) for the detection of suggestive breast lesions. Methods: Fifty patients (with 58 breast lesions) for whom a scintimammogram was clinically indicated were prospectively evaluated with a general-purpose gamma camera and a novel HRBGC prototype. The results of conventional and high-resolution nuclear studies were prospectively classified as negative (normal or benign) or positive (suggestive or malignant) by 2 radiologists who were unaware of the mammographic and histologic results. All of the included lesions were confirmed by pathology. Results: There were 30 benign and 28 malignant lesions. The sensitivity for detection of breast cancer was 64.3% (18/28) with the conventional camera and 78.6% (22/28) with the HRBGC. The specificity with both systems was 93.3% (28/30). For the 18 nonpalpable lesions, sensitivity was 55.5% (10/18) and 72.2% (13/18) with the general-purpose camera and the HRBGC, respectively. For lesions 1 cm, 7 of 15 were detected with the general-purpose camera and 10 of 15 with the HRBGC. Four lesions (median size, 8.5 mm) were detected only with the HRBGC and were missed by the conventional camera. Conclusion: Evaluation of indeterminate breast lesions with an HRBGC results in improved sensitivity for the detection of cancer, with greater improvement shown for nonpalpable and 1-cm lesions.

  17. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    International Nuclear Information System (INIS)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

    2014-01-01

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication

  18. Analysis of JC virus DNA replication using a quantitative and high-throughput assay

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States); Gagnon, David [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Gjoerup, Ole [Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111 (United States); Archambault, Jacques [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Bullock, Peter A., E-mail: Peter.Bullock@tufts.edu [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States)

    2014-11-15

    Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.

  19. High-Resolution Powder Diffractometer HRPT for Thermal Neutrons at SINQ

    International Nuclear Information System (INIS)

    Fischer, P.; Koch, M.; Koennecke, M.; Pomjakushin, V.; Schefer, J.; Schlumpf, N.

    1999-01-01

    The new neutron powder diffractometer at the Swiss continuous spallation neutron source SINQ is designed as a flexible instrument for high resolution [best values δd/d: ( -3 with d = lattice spacing in the high resolution or high intensity modes, respectively]. It uses large scattering angles 2Θ M = 120 deg or 90 deg of the monochromator, a 28 cm high, vertically focusing wafer type Ge(hkk) monochromator and a position-sensitive 3 He detector(3.6 bar) produced by Cerca at Romans, France. It has 1600 (25x64) detectors with an angular separation of 0.1 deg and includes modern electronics developed by E. Berruyer, Cerca and PSI. The SICS software of PSI controls the instrument with a server running on an unix workstation and clients written in Java through the TCP/IP network. The design principles and first experiences are presented. The interdisciplinary applications of HRPT will permit high-resolution refinement of chemical and magnetic structures as well as phase analysis including the detection of defects and internal microstrain. In particular real-time investigations of chemical or structural changes and of magnetic phase transitions in crystalline, quasicrystalline, amorphous and liquid samples including technically interesting new materials are possible. (author)

  20. Characterization of a high resolution and high sensitivity pre-clinical PET scanner with 3D event reconstruction

    CERN Document Server

    Rissi, M; Bolle, E; Dorholt, O; Hines, K E; Rohne, O; Skretting, A; Stapnes, S; Volgyes, D

    2012-01-01

    COMPET is a preclinical PET scanner aiming towards a high sensitivity, a high resolution and MRI compatibility by implementing a novel detector geometry. In this approach, long scintillating LYSO crystals are used to absorb the gamma-rays. To determine the point of interaction (P01) between gamma-ray and crystal, the light exiting the crystals on one of the long sides is collected with wavelength shifters (WLS) perpendicularly arranged to the crystals. This concept has two main advantages: (1) The parallax error is reduced to a minimum and is equal for the whole field of view (FOV). (2) The P01 and its energy deposit is known in all three dimension with a high resolution, allowing for the reconstruction of Compton scattered gamma-rays. Point (1) leads to a uniform point source resolution (PSR) distribution over the whole FOV, and also allows to place the detector close to the object being imaged. Both points (1) and (2) lead to an increased sensitivity and allow for both high resolution and sensitivity at the...