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Sample records for fiberoptic dna probe

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2018-01-24

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

  2. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

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

  3. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

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

  4. Comparative study of the endoscope-based bevelled and volume fiber-optic Raman probes for optical diagnosis of gastric dysplasia in vivo at endoscopy.

    Science.gov (United States)

    Wang, Jianfeng; Lin, Kan; Zheng, Wei; Ho, Khek Yu; Teh, Ming; Yeoh, Khay Guan; Huang, Zhiwei

    2015-11-01

    This study aims to compare the diagnostic performance of the two different endoscope-based fiber-optic Raman probe designs (i.e., bevelled and volume Raman probes) for real-time, in vivo detection of gastric dysplasia at endoscopy. To conduct the clinical comparison, a total of 1,050 in vivo tissue Raman spectra (normal: n = 864; dysplasia: n = 186) were acquired from 66 gastric patients (normal: n = 48; dysplasia: n = 18) by using bevelled Raman probe, while a total of 1,913 in vivo tissue Raman spectra (normal: n = 1,786; dysplasia: n = 127) were acquired from 98 gastric patients (normal: n = 87; dysplasia: n = 11) by using volume Raman probe. The bevelled Raman probe provides approximately twofold improvements in tissue Raman-to-autofluorescence intensity ratios as compared to the use of volume Raman probe. Partial least squares discriminant analysis together with leave-one patient-out cross-validation on in vivo tissue Raman spectra acquired yields a diagnostic accuracy of 93.0 % (sensitivity of 92.5 %; specificity of 93.1 %) for differentiating gastric dysplasia from normal gastric tissue by using the bevelled fiber-optic Raman probe, which is superior to the diagnostic performance (accuracy of 88.4 %; sensitivity of 85.8 %; specificity of 88.6 %) by using the volume Raman probe. This work demonstrates that the Raman spectroscopic technique coupled with bevelled fiber-optic Raman probe has great potential to enhance in vivo diagnosis of gastric precancer and early cancer at endoscopy. Graphical Abstract Comparison of in vivo gastric tissue Raman spectra acquired by using bevelled and volume fiber-optic Raman probes.

  5. Beveled fiber-optic probe couples a ball lens for improving depth-resolved fluorescence measurements of layered tissue: Monte Carlo simulations

    International Nuclear Information System (INIS)

    Jaillon, Franck; Zheng Wei; Huang Zhiwei

    2008-01-01

    In this study, we evaluate the feasibility of designing a beveled fiber-optic probe coupled with a ball lens for improving depth-resolved fluorescence measurements of epithelial tissue using Monte Carlo (MC) simulations. The results show that by using the probe configuration with a beveled tip collection fiber and a flat tip excitation fiber associated with a ball lens, discrimination of fluorescence signals generated in different tissue depths is achievable. In comparison with a flat-tip collection fiber, the use of a large bevel angled collection fiber enables a better differentiation between the shallow and deep tissue layers by changing the excitation-collection fiber separations. This work suggests that the beveled fiber-optic probe coupled with a ball lens has the potential to facilitate depth-resolved fluorescence measurements of epithelial tissues

  6. Fiber-optic system for dual-modality imaging of glucose probes 18F-FDG and 6-NBDG in atherosclerotic plaques.

    Directory of Open Access Journals (Sweden)

    Raiyan T Zaman

    Full Text Available Atherosclerosis is a progressive inflammatory condition that underlies coronary artery disease (CAD-the leading cause of death in the United States. Thus, the ultimate goal of this research is to advance our understanding of human CAD by improving the characterization of metabolically active vulnerable plaques within the coronary arteries using a novel catheter-based imaging system. The aims of this study include (1 developing a novel fiber-optic imaging system with a scintillator to detect both 18F and fluorescent glucose probes, and (2 validating the system on ex vivo murine plaques.A novel design implements a flexible fiber-optic catheter consisting of both a radio-luminescence and a fluorescence imaging system to detect radionuclide 18F-fluorodeoxyglucose (18F-FDG and the fluorescent analog 6-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-ylamino-6-Deoxyglucose (6-NBDG, respectively. Murine macrophage-rich atherosclerotic carotid plaques were imaged ex vivo after intravenous delivery of 18F-FDG or 6-NBDG. Confirmatory optical imaging by IVIS-200 and autoradiography were also performed.Our fiber-optic imaging system successfully visualized both 18F-FDG and 6-NBDG probes in atherosclerotic plaques. For 18F-FDG, the ligated left carotid arteries (LCs exhibited 4.9-fold higher radioluminescence signal intensity compared to the non-ligated right carotid arteries (RCs (2.6 × 10(4 ± 1.4 × 10(3 vs. 5.4 × 10(3 ± 1.3 × 10(3 A.U., P = 0.008. Similarly, for 6-NBDG, the ligated LCs emitted 4.3-fold brighter fluorescent signals than the control RCs (1.6 × 10(2 ± 2.7 × 10(1 vs. 3.8 × 10(1 ± 5.9 A.U., P = 0.002. The higher uptake of both 18F-FDG and 6-NBDG in ligated LCs were confirmed with the IVIS-200 system. Autoradiography further verified the higher uptake of 18F-FDG by the LCs.This novel fiber-optic imaging system was sensitive to both radionuclide and fluorescent glucose probes taken up by murine atherosclerotic plaques. In addition, 6-NBDG is a

  7. In-vivo fluorescence detection of breast cancer growth factor receptors by fiber-optic probe

    Science.gov (United States)

    Bustamante, Gilbert; Wang, Bingzhi; DeLuna, Frank; Sun, LuZhe; Ye, Jing Yong

    2018-02-01

    Breast cancer treatment options often include medications that target the overexpression of growth factor receptors, such as the proto-oncogene human epidermal growth factor receptor 2 (HER2/neu) and epidermal growth factor receptor (EGFR) to suppress the abnormal growth of cancerous cells and induce cancer regression. Although effective, certain treatments are toxic to vital organs, and demand assurance that the pursued receptor is present at the tumor before administration of the drug. This requires diagnostic tools to provide tumor molecular signatures, as well as locational information. In this study, we utilized a fiber-optic probe to characterize in vivo HER2 and EGFR overexpressed tumors through the fluorescence of targeted dyes. HER2 and EGFR antibodies were conjugated with ICG-Sulfo-OSu and Alexa Fluor 680, respectively, to tag BT474 (HER2+) and MDA-MB-468 (EGFR+) tumors. The fiber was inserted into the samples via a 30-gauge needle. Different wavelengths of a supercontinuum laser were selected to couple into the fiber and excite the corresponding fluorophores in the samples. The fluorescence from the dyes was collected through the same fiber and quantified by a time-correlated single photon counter. Fluorescence at different antibody-dye concentrations was measured for calibration. Mice with subcutaneous HER2+ and/or EGFR+ tumors received intravenous injections of the conjugates and were later probed at the tumor sites. The measured fluorescence was used to distinguish between tumor types and to calculate the concentration of the antibody-dye conjugates, which were detectable at levels as low as 40 nM. The fiber-optic probe presents a minimally invasive instrument to characterize the molecular signatures of breast cancer in vivo.

  8. Chromosome-specific DNA Repeat Probes

    Energy Technology Data Exchange (ETDEWEB)

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  9. Feasibility Study on Fiber-optic Radiation Sensor for Remote Gamma-ray Spectroscopy

    International Nuclear Information System (INIS)

    Jeon, Hyesu; Jang, Kyoung Won; Shin, Sang Hun and others

    2014-01-01

    In this study, we fabricated a fiber-optic radiation sensor using an optical fiber and various scintillators. To select an adequate inorganic scintillator for the sensing probe of fiber-optic radiation sensor, 5 types of scintillators were evaluated. The spectra of gamma-rays emitted from a Na-22 radiation source were measured by using the manufactured sensors. As a result, the BGO was suitable for the sensing probe of fiber-optic radiation sensor due to its high scintillation output and exact photoelectric peak for the gamma-ray energy. The basic principle of radiation detection is to detect the signals caused by interactions between radiations and materials. There are various types of radiation detectors depending on types of radiation to be detected and physical quantities to be measured. As one of the radiation detectors, a fiber-optic radiation sensor using a scintillator and an optical fiber has two advantages such as no space restraint and remote sensing. Moreover, in nuclear environments, this kind of sensor has immunities for electromagnetic field, temperature, and pressure. Thus, the fiber-optic radiation sensor can be used in various fields including nondestructive inspection, radioactive waste management, nuclear safety, radiodiagnosis and radiation therapy. As a fundamental study of the fiber-optic radiation sensor for remote gamma-ray spectroscopy, in this study, we fabricated a fiber-optic radiation sensor using an optical fiber and various scintillators. To select an adequate inorganic scintillator for the sensing probe of fiber-optic radiation sensor, 5 types of scintillators were evaluated. The spectra of gamma-rays emitted from a Na-22 radiation source were measured by using the manufactured sensors

  10. DNA Probe for Lactobacillus delbrueckii

    Science.gov (United States)

    Delley, Michèle; Mollet, Beat; Hottinger, Herbert

    1990-01-01

    From a genomic DNA library of Lactobacillus delbrueckii subsp. bulgaricus, a clone was isolated which complements a leucine auxotrophy of an Escherichia coli strain (GE891). Subsequent analysis of the clone indicated that it could serve as a specific DNA probe. Dot-blot hybridizations with over 40 different Lactobacillus strains showed that this clone specifically recognizes L. delbrueckii subsp. delbrueckii, bulgaricus, and lactis. The sensitivity of the method was tested by using an α-32P-labeled DNA probe. Images PMID:16348233

  11. Feasibility of Ultra-Thin Fiber-Optic Dosimeters for Radiotherapy Dosimetry.

    Science.gov (United States)

    Lee, Bongsoo; Kwon, Guwon; Shin, Sang Hun; Kim, Jaeseok; Yoo, Wook Jae; Ji, Young Hoon; Jang, Kyoung Won

    2015-11-17

    In this study, prototype ultra-thin fiber-optic dosimeters were fabricated using organic scintillators, wavelength shifting fibers, and plastic optical fibers. The sensor probes of the ultra-thin fiber-optic dosimeters consisted of very thin organic scintillators with thicknesses of 100, 150 and 200 μm. These types of sensors cannot only be used to measure skin or surface doses but also provide depth dose measurements with high spatial resolution. With the ultra-thin fiber-optic dosimeters, surface doses for gamma rays generated from a Co-60 therapy machine were measured. Additionally, percentage depth doses in the build-up regions were obtained by using the ultra-thin fiber-optic dosimeters, and the results were compared with those of external beam therapy films and a conventional fiber-optic dosimeter.

  12. Miniature fiber-optic multiphoton microscopy system using frequency-doubled femtosecond Er-doped fiber laser.

    Science.gov (United States)

    Huang, Lin; Mills, Arthur K; Zhao, Yuan; Jones, David J; Tang, Shuo

    2016-05-01

    We report on a miniature fiber-optic multiphoton microscopy (MPM) system based on a frequency-doubled femtosecond Er-doped fiber laser. The femtosecond pulses from the laser source are delivered to the miniature fiber-optic probe at 1.58 µm wavelength, where a standard single mode fiber is used for delivery without the need of free-space dispersion compensation components. The beam is frequency-doubled inside the probe by a periodically poled MgO:LiNbO3 crystal. Frequency-doubled pulses at 786 nm with a maximum power of 80 mW and a pulsewidth of 150 fs are obtained and applied to excite intrinsic signals from tissues. A MEMS scanner, a miniature objective, and a multimode collection fiber are further used to make the probe compact. The miniature fiber-optic MPM system is highly portable and robust. Ex vivo multiphoton imaging of mammalian skins demonstrates the capability of the system in imaging biological tissues. The results show that the miniature fiber-optic MPM system using frequency-doubled femtosecond fiber laser can potentially bring the MPM imaging for clinical applications.

  13. DNA probe for lactobacillus delbrueckii

    Energy Technology Data Exchange (ETDEWEB)

    Delley, M.; Mollet, B.; Hottinger, H. (Nestle Research Centre, Lausanne (Switzerland))

    1990-06-01

    From a genomic DNA library of Lactobacillus delbrueckii subsp. bulgaricus, a clone was isolated which complements a leucine auxotrophy of an Escherichia coli strain (GE891). Subsequent analysis of the clone indicated that it could serve as a specific DNA probe. Dot-blot hybridizations with over 40 different Lactobacillus strains showed that this clone specifically recognized L. delbrueckii subsp. delbrueckii, bulgaricus, and lactis. The sensitivity of the method was tested by using an {alpha}-{sup 32}P-labeled probe.

  14. DNA probe for lactobacillus delbrueckii

    International Nuclear Information System (INIS)

    Delley, M.; Mollet, B.; Hottinger, H.

    1990-01-01

    From a genomic DNA library of Lactobacillus delbrueckii subsp. bulgaricus, a clone was isolated which complements a leucine auxotrophy of an Escherichia coli strain (GE891). Subsequent analysis of the clone indicated that it could serve as a specific DNA probe. Dot-blot hybridizations with over 40 different Lactobacillus strains showed that this clone specifically recognized L. delbrueckii subsp. delbrueckii, bulgaricus, and lactis. The sensitivity of the method was tested by using an α- 32 P-labeled probe

  15. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    黄承志; 李原芳; 黄新华; 范美坤

    2000-01-01

    The microarray of DNA probes with 5’ -NH2 and 5’ -Tex/3’ -NH2 modified terminus on 10 um carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) is characterized in the preseni paper. it was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentra-tion of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  16. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The microarray of DNA probes with 5′-NH2 and 5′-Tex/3′-NH2 modified terminus on 10 m m carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)- carbodiimide (EDC) is characterized in the present paper. It was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentration of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  17. Probe Selection for DNA Microarrays using OligoWiz

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Juncker, Agnieszka; Nielsen, Henrik Bjørn

    2007-01-01

    Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client-server appl......Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client......-server application that offers a detailed graphical interface and real-time user interaction on the client side, and massive computer power and a large collection of species databases (400, summer 2007) on the server side. Probes are selected according to five weighted scores: cross-hybridization, deltaT(m), folding...... computer skills and can be executed from any Internet-connected computer. The probe selection procedure for a standard microarray design targeting all yeast transcripts can be completed in 1 h....

  18. DNA stable-isotope probing (DNA-SIP).

    Science.gov (United States)

    Dunford, Eric A; Neufeld, Josh D

    2010-08-02

    DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and nutrients into cellular biomass. As such, this cultivation-independent technique has been an important methodology for assigning metabolic function to the diverse communities inhabiting a wide range of terrestrial and aquatic environments. Following the incubation of an environmental sample with stable-isotope labelled compounds, extracted nucleic acid is subjected to density gradient ultracentrifugation and subsequent gradient fractionation to separate nucleic acids of differing densities. Purification of DNA from cesium chloride retrieves labelled and unlabelled DNA for subsequent molecular characterization (e.g. fingerprinting, microarrays, clone libraries, metagenomics). This JoVE video protocol provides visual step-by-step explanations of the protocol for density gradient ultracentrifugation, gradient fractionation and recovery of labelled DNA. The protocol also includes sample SIP data and highlights important tips and cautions that must be considered to ensure a successful DNA-SIP analysis.

  19. Surface-enhanced Raman scattering based nonfluorescent probe for multiplex DNA detection.

    Science.gov (United States)

    Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

    2007-06-01

    To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive, and multiplex format, an alternative surface-enhanced Raman scattering based probe was designed and fabricated to covalently attach both DNA probing sequence and nonfluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the nonfluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA to its complementary targets was successfully accomplished with a long-term goal to use nonfluorescent RTags in a Raman-based DNA microarray platform.

  20. Whole genomic DNA probe for detection of Porphyromonas endodontalis.

    Science.gov (United States)

    Nissan, R; Makkar, S R; Sela, M N; Stevens, R

    2000-04-01

    The purpose of the present study was to develop a DNA probe for Porphyromonas endodontalis. Pure cultures of P. endodontalis were grown in TYP medium, in an anaerobic chamber. DNA was extracted from the P. endodontalis and labeled using the Genius System by Boehringer Mannheim. The labeled P. endodontalis DNA was used in dot-blot hybridization reactions with homologous (P. endodontalis) and unrelated bacterial samples. To determine specificity, strains of 40 other oral bacterial species (e.g. Porphyromonas gingivalis, Porphyromonas asaccharolytica, and Prevotella intermedia) were spotted and reacted with the P. endodontalis DNA probe. None of the panel of 40 oral bacteria hybridized with the P. endodontalis probe, whereas the blot of the homologous organism showed a strong positive reaction. To determine the sensitivity of the probe, dilutions of a P. endodontalis suspension of known concentration were blotted onto a nylon membrane and reacted with the probe. The results of our investigation indicate that the DNA probe that we have prepared specifically detects only P. endodontalis and can detect at least 3 x 10(4) cells.

  1. Labelling of HBV-DNA probe using reagent made in China

    International Nuclear Information System (INIS)

    Wang Quanshi

    1991-01-01

    The labelling hepatitis Bvirus DNA (HBV-DNA) probe was studied by using reagent made in China. The results showed that: (1) The dNTPs with high specific activity was necessary for the labelling of nigh specific activity HBV-DNA probe; (2) reaction of labelling HBV-DNA probe was completed in a few minutes; (3) 0.37 MBq 3 H dTTP (specific activity 1.554TBq/mmol) was enough to label 1 μg HBV-DNA and the specific activity of probe reached 3.4 x 10 cpm/μg; (4) 7 MBqα- 32 P dATP (specific activity > 111 TBq/mmol) can label HBV-DNA probe to specific activity 1.35 x 10 cpm/μg. It was concluded that the reagent made in China can be used for the study in molecular biology

  2. Genotypic characterization of Rickettsiae by DNA probes generated from Rickettsia Prowazekii DNA

    International Nuclear Information System (INIS)

    Demkin, V.V.; Rydkina, E.B.; Likhoded, L.Ya.; Ignatovich, V.F.; Genig, V.A.; Balayeva, N.M.

    1994-01-01

    Southern blot analysis of HindIII-cleaved rickettsial DNA was used for genotypic characterization of the typhus group (TG) species (R. prowazekii, R. typhi, R. canada) and a few species were of the spotted fever group (SFG)rickettsiae (R. sibirica, R. conorii, R. akari). Four different DNA probes were employed. PBH11 and PBH13 probes were morphospecific HindIII fragment of R prowazekii DNA. MW218 probe contained the gene for 51 K antigen and MW264 probe contained the citrate synthase gene of R. prowazekii. All the probes hybridized with the tested TG and SFG rickettsial DNAs, forming from 1 to 5 bands, but they did not with R. tsutsudamushi or C. burnetii DNAs. All the probes demonstrated specific hybridization pattern with TG species and R. akari. PBH11. PBH13 and MW264 probes clearly distinguished R. sibirica and R. conorii from the other tested rickettsiae, but not from each other. However, these two species differed slightly with MW218 probe. Several strains of each species were analyzed in this way and except for strains of R. conorii identical intra-species pattern were obtained. These data lead us to consider the obtained hybridization patterns as criteria for genotypic identification. (author)

  3. Colorimetric DNA detection of transgenic plants using gold nanoparticles functionalized with L-shaped DNA probes

    Science.gov (United States)

    Nourisaeid, Elham; Mousavi, Amir; Arpanaei, Ayyoob

    2016-01-01

    In this study, a DNA colorimetric detection system based on gold nanoparticles functionalized with L-shaped DNA probes was prepared and evaluated. We investigated the hybridization efficiency of the L-shaped probes and studied the effect of nanoparticle size and the L-shaped DNA probe length on the performance of the as-prepared system. Probes were attached to the surface of gold nanoparticles using an adenine sequence. An optimal sequence of 35S rRNA gene promoter from the cauliflower mosaic virus, which is frequently used in the development of transgenic plants, and the two complementary ends of this gene were employed as model target strands and probe molecules, respectively. The spectrophotometric properties of the as-prepared systems indicated that the large NPs show better changes in the absorption spectrum and consequently present a better performance. The results of this study revealed that the probe/Au-NPs prepared using a vertical spacer containing 5 thymine oligonucleotides exhibited a stronger spectrophotometric response in comparison to that of larger probes. These results in general indicate the suitable performance of the L-shaped DNA probe-functionalized Au-NPs, and in particular emphasize the important role of the gold nanoparticle size and length of the DNA probes in enhancing the performance of such a system.

  4. Bio-analytical applications of mid-infrared spectroscopy using silver halide fiber-optic probes

    International Nuclear Information System (INIS)

    Heise, H.M.; Kuepper, L.; Butvina, L.N.

    2002-01-01

    Infrared-spectroscopy has proved to be a powerful method for the study of various biomedical samples, in particular for in-vitro analysis in the clinical laboratory and for non-invasive diagnostics. In general, the analysis of biofluids such as whole blood, urine, microdialysates and bioreactor broth media takes advantage of the fact that a multitude of analytes can be quantified simultaneously and rapidly without the need for reagents. Progress in the quality of infrared silver halide fibers enabled us to construct several flexible fiber-optic probes of different geometries, which are particularly suitable for the measurement of small biosamples. Recent trends show that dry film measurements by mid-infrared spectroscopy could revolutionize analytical tools in the clinical chemistry laboratory, and an example is given. Infrared diagnostic tools show a promising potential for patients, and minimal-invasive blood glucose assays or skin tissue pathology in particular cannot be left out using mid-infrared fiber-based probes. Other applications include the measurement of skin samples including penetration studies of vitamins and constituents of cosmetic cream formulations. A further field is the micro-domain analysis of biopsy samples from bog mummified corpses, and recent results on the chemistry of dermis and hair samples are reported. Another field of application, for which results are reported, is food analysis and bio-reactor monitoring

  5. Development of DNA probes for Candida albicans

    International Nuclear Information System (INIS)

    Cheung, L.L.; Hudson, J.B.

    1988-01-01

    An attempt was made to produce DNA probes that could be used as a rapid and efficient means of detecting candidiasis (invasive Candida infection) in immunocompromised patients. Whole DNA from Candida albicans was digested with restriction endonuclease, and the resulting fragments were randomly cloned into a plasmid vector. Several recombinant plasmids were evaluated for cross-hybridization to various other Candida species, other fungal DNAs, and to nonfungal DNAs. Cross reactions were observed between the probes and different yeasts, but none with unrelated DNAs. Some recombinants were genus-specific, and two of these were applied to the analysis of C. albicans growth curves. It became evident that, although both 32 P- and biotin-labelled probes could be made quite sensitive, a possible limitation in their diagnostic potential was the poor liberation of Candida DNA from cells. Thus, better methods of treatment of clinical specimens will be required before such probes will be useful in routine diagnosis

  6. Development of DNA probes for Candida albicans

    Energy Technology Data Exchange (ETDEWEB)

    Cheung, L.L.; Hudson, J.B.

    1988-07-01

    An attempt was made to produce DNA probes that could be used as a rapid and efficient means of detecting candidiasis (invasive Candida infection) in immunocompromised patients. Whole DNA from Candida albicans was digested with restriction endonuclease, and the resulting fragments were randomly cloned into a plasmid vector. Several recombinant plasmids were evaluated for cross-hybridization to various other Candida species, other fungal DNAs, and to nonfungal DNAs. Cross reactions were observed between the probes and different yeasts, but none with unrelated DNAs. Some recombinants were genus-specific, and two of these were applied to the analysis of C. albicans growth curves. It became evident that, although both /sup 32/P- and biotin-labelled probes could be made quite sensitive, a possible limitation in their diagnostic potential was the poor liberation of Candida DNA from cells. Thus, better methods of treatment of clinical specimens will be required before such probes will be useful in routine diagnosis.

  7. Synthesis and detection of 3'-OH terminal biotin-labeled DNA probes

    International Nuclear Information System (INIS)

    Brakel, C.L.; Engelhardt, D.L.

    1985-01-01

    Nick translation has been used to prepare biotin-dUTP-containing DNA probes. These stable DNA probes have been identified, following hybridization to target DNA, by fluorescence using antibiotin antibodies or by enzyme reactions in which the enzyme has been linked to avidin or streptavidin. It is probable that this technology will be applicable to certain diagnostic determinations and that, with sufficient sensitivity, this technology might provide a system for obtaining rapid and specific diagnoses in situations presently requiring time-consuming growth assays. The sensitivity of this assay can be increased in two ways: (1) by increasing the amount of biotin contained in the DNA probes, and (2) by increasing the response to individual biotin molecules in the DNA probes. This report demonstrates that terminal deoxynucleotide transferase can be employed to increase the biotin content of DNA probes. We also introduce a new streptavidin-linked enzyme system that produces a greater response to biotinylated DNA probes than does streptavidin-linked horseradish peroxidase

  8. Time-resolved laser-excited Shpol'skii spectrometry with a fiber-optic probe and ICCD camera

    International Nuclear Information System (INIS)

    Bystol, Adam J.; Campiglia, Andres D.; Gillispie, Gregory D.

    2000-01-01

    Improved methodology for chemical analysis via laser-excited Shpol'skii spectrometry is reported. The complications of traditional methodology for measurements at liquid nitrogen temperature are avoided by freezing the distal end of a bifurcated fiber-optic probe directly into the sample matrix. Emission wavelength-time matrices were rapidly collected by automatically incrementing the gate delay of an intensified charge-coupled device (ICCD) camera relative to the laser excitation pulse. The excitation source is a compact frequency-doubled tunable dye laser whose bandwidth (<0.03 nm) is well matched for Shpol'skii spectroscopy. Data reproducibility for quantitative analysis purposes and analytical figures of merit are demonstrated for several polycyclic aromatic hydrocarbons at 77 K. Although not attempted in this study, time-resolved excitation-emission matrices could easily be collected with this instrumental system. (c) 2000 Society for Applied Spectroscopy

  9. Quantitative in situ monitoring of an elevated temperature reaction using a water-cooled mid-infrared fiber-optic probe.

    Science.gov (United States)

    Maclaurin, P; Crabb, N C; Wells, I; Worsfold, P J; Coombs, D

    1996-04-01

    A novel water-cooled mid-infrared fiber-optic probe is described which is heatable to 230 °C. The probe has chalcogenide fibers and a ZnSe internal reflection element and is compact and fully flexible, allowing access to a wide range of standard laboratory reaction vessels and fume cupboard arrangements. Performance is demonstrated via the in situ analysis of an acid-catalyzed esterification reaction in toluene at 110 °C, and the results are compared with those from a conventional extractive sampling loop flow cell arrangement. Particular emphasis is given to the quantitative interpretation of the spectroscopic data, using gas chromatographic reference data. Calibration data are presented for univariate and partial least squares models, with an emphasis on procedures for improving the quality of interpreparation calibration and prediction through the use of focused reference analysis regimes. Subset univariate procedures are presented that yield relative errors of spectroscopy combined with bias correction partial least squares procedures for the efficient in situ quantitative analysis of laboratory scale reactions.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-12-16

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-12-04

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

  12. Detection of polyaromatic compounds using antibody-based fiberoptics fluoroimmunosensors

    International Nuclear Information System (INIS)

    Vo-Dinh, T.; Tromberg, B.J.; Griffin, G.D.; Ambrose, K.R.; Sepaniak, M.J.; Alarie, J.P.

    1987-01-01

    In this work we have investigated the performance of an antibody-based fiberoptics sensor for the detection of the carcinogen benzo(a)pyrene and its DNA-adduct product BP-tetrol. The excellent sensitivity of this device - femtomole limits of detection for BP - illustrates that it has considerable potential to perform analyses of chemical and biological samples at trace levels in complex matrices. The results indicate that fiberoptics-based fluoroimmunosensors can be useful in a wide spectrum of biochemical and clinical analyses. 17 refs., 4 figs., 1 tab

  13. Detection of polyaromatic compounds using antibody-based fiberoptics fluoroimmunosensors

    Energy Technology Data Exchange (ETDEWEB)

    Vo-Dinh, T.; Tromberg, B.J.; Griffin, G.D.; Ambrose, K.R.; Sepaniak, M.J.; Alarie, J.P.

    1987-01-01

    In this work we have investigated the performance of an antibody-based fiberoptics sensor for the detection of the carcinogen benzo(a)pyrene and its DNA-adduct product BP-tetrol. The excellent sensitivity of this device - femtomole limits of detection for BP - illustrates that it has considerable potential to perform analyses of chemical and biological samples at trace levels in complex matrices. The results indicate that fiberoptics-based fluoroimmunosensors can be useful in a wide spectrum of biochemical and clinical analyses. 17 refs., 4 figs., 1 tab.

  14. Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

    Science.gov (United States)

    Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

    2013-01-01

    Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052

  15. Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

    Directory of Open Access Journals (Sweden)

    Yuji Miyahara

    2013-02-01

    Full Text Available Peptide nucleic acid (PNA has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

  16. Evaluation of the Detection Efficiency of LYSO Scintillator in the Fiber-Optic Radiation Sensor

    Directory of Open Access Journals (Sweden)

    Chan Hee Park

    2014-01-01

    Full Text Available The aim of this study was to develop and evaluate fiber-optic sensors for the remote detection of gamma rays in areas that are difficult to access, such as a spent fuel pool. The fiber-optic sensor consists of a light-generating probe, such as scintillators for radiation detection, plastic optical fibers, and light-measuring devices, such as PMT. The (Lu,Y2SiO5:Ce(LYSO:Ce scintillator was chosen as the light-generating probe. The (Lu,Y2SiO5:Ce(LYSO:Ce scintillator has higher scintillation efficiency than the others and transmits light well through an optical fiber because its refraction index is similar to the refractive index of the optical fiber. The fiber-optic radiation sensor using the (Lu,Y2SiO5:Ce(LYSO:Ce scintillator was evaluated in terms of the detection efficiency and reproducibility for examining its applicability as a radiation sensor.

  17. Protocols for 16S rDNA Array Analyses of Microbial Communities by Sequence-Specific Labeling of DNA Probes

    Directory of Open Access Journals (Sweden)

    Knut Rudi

    2003-01-01

    Full Text Available Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and regions with relatively high variability. The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes. Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.

  18. Mobile fiber-optic sensor for detection of oral and cervical cancer in the developing world.

    Science.gov (United States)

    Yu, Bing; Nagarajan, Vivek Krishna; Ferris, Daron G

    2015-01-01

    Oral and cervical cancers are a growing global health problem that disproportionately impacts women and men living in the developing world. The high death rate in developing countries is largely due to the fact that these countries do not have the appropriate medical infrastructure and resources to support the organized screening and diagnostic programs that are available in the developed world. Diffuse reflectance spectroscopy (DRS) with a fiber-optic probe can noninvasively quantify the optical properties of epithelial tissues and has shown the potential as a cost-effective, easy-to-use, and sensitive tool for diagnosis of early precancerous changes in the cervix and oral cavity. However, current fiber-optic DRS systems have not been designed to be robust and reliable for use in developing countries. They are subject to various sources of systematic or random errors, arising from the uncontrolled probe-tissue interface and lack of real-time calibration, use bulky and expensive optical components, and require extensive training. This chapter describes a portable DRS device that is specifically designed for detection of oral and cervical cancers in resource-poor settings. The device uses an innovative smart fiber-optic probe to eliminate operator bias, state-of-the-art photonics components to reduce size and power consumption, and automated software to reduce the need of operator training. The size and cost of the smart fiber-optic DRS system may be further reduced by incorporating a smartphone based spectrometer.

  19. DNA Probe for Lactobacillus delbrueckii

    OpenAIRE

    Delley, Michèle; Mollet, Beat; Hottinger, Herbert

    1990-01-01

    From a genomic DNA library of Lactobacillus delbrueckii subsp. bulgaricus, a clone was isolated which complements a leucine auxotrophy of an Escherichia coli strain (GE891). Subsequent analysis of the clone indicated that it could serve as a specific DNA probe. Dot-blot hybridizations with over 40 different Lactobacillus strains showed that this clone specifically recognizes L. delbrueckii subsp. delbrueckii, bulgaricus, and lactis. The sensitivity of the method was tested by using an α-32P-l...

  20. Local pH Monitoring of Small Cluster of Cells using a Fiber-Optic Dual-Core Micro-Probe.

    Science.gov (United States)

    Chen, Sisi; Yang, Qingbo; Xiao, Hai; Shi, Honglan; Ma, Yinfa

    2017-03-31

    Biological studies of tissues and cells have enabled numerous discoveries, but these studies still bear potential risks of invalidation because of cell heterogeneity. Through high-accuracy techniques, recent studies have demonstrated that discrepancies do exist between the results from low-number-cell studies and cell-population-based results. Thus the urgent need to re-evaluate key principles on limited number of cells has been provoked. In this study, a novel designed dual-core fiber-optic pH micro-probe was fabricated and demonstrated for niche environment pH sensing with high spatial resolution. An organic-modified silicate (OrMoSils) sol-gel thin layer was functionalized by entrapping a pH indicator, 2', 7'-Bis (2-carbonylethyl)-5(6)-carboxyfluorescein (BCECF), on a ~70 μm sized probe tip. Good linear correlation between fluorescence ratio of I 560 nm /I 640 nm and intercellular pH values was obtained within a biological-relevant pH range from 6.20 to 7.92 (R 2 = 0.9834), and with a pH resolution of 0.035 ± 0.005 pH units. The probe's horizontal spatial resolution was demonstrated to be less than 2mm. Moreover, the probe was evaluated by measuring the localized extracellular pH changes of cultured human lung cancer cells (A549) when exposed to titanium dioxide nanoparticles (TiO 2 NPs). Results showed that the probe has superior capability for fast, local, and continual monitoring of a small cluster of cells, which provides researchers a fast and accurate technique to conduct local pH measurements for cell heterogeneity-related studies.

  1. Detecting the effects of toxic agents on spermatogenesis using DNA probes

    International Nuclear Information System (INIS)

    Hecht, N.B.

    1987-01-01

    Advances in the molecular biology of spermatogenesis suggest that DNA probes can be used to monitor the effects of toxic agents in male germ cells of mammals. Molecular hybridization analyses with DNA probes can provide a reproducible methodology capable of detecting changes ranging from massive deletions to single base pair substitutions in the genome of exposed individuals. A constantly increasing number of DNA probes that can be used to detect such alterations in human sperm DNA exist for both ubiquitously expressed proteins and for genes solely expressed in the testis. In this chapter, the currently available testicular stage-specific and/or cell type-specific DNA probes and the techniques by which they can be utilized in reproductive toxicology studies are discussed. The advantages, limitations, and future technological advances of this novel biological marker system for the human male reproductive system are also considered

  2. Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes.

    Science.gov (United States)

    Jahandeh, Nadia; Ranjbar, Reza; Behzadi, Payam; Behzadi, Elham

    2015-01-01

    The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.

  3. Detection of TTV-DNA in PBMC using digoxigenin labelled probe by in situ hybridization

    International Nuclear Information System (INIS)

    Liu Yang; Qi Qige

    2002-01-01

    To determine TTV-DNA in PBMC in patients with viral hepatitis, a study of in situ hybridization using digoxigenin labelled probe by PCR method to the TTV ORF1 region was performed on PBMC. Results showed that the detection rate of TTV-DNA using double-stranded probe in TTV-DNA positive group in sera was 58.06 (18/31), and the detection rate of TTV-DNA using double-stranded probe in TTV-DNA negative group in sera was 27.59 (8/29). For TTV-DNA positive group detected by double- stranded probe, then we use negative- stranded probe to detect their replication. The detection rate was 22.2%(4/18). Conclusions: TTV can infect PBMC and replicate in PBMC

  4. Leishmania diagnostic and identification py using 32P labelled DNA probes

    International Nuclear Information System (INIS)

    Andrade, Antero Silva Ribeiro de; Melo, Maria Norma de

    1999-10-01

    P 32 labelled DNA probes are valious instruments for the parasitic diseases by using hybridization reaction. In this paper we describe the methodology and present the foundations for the radioactive probes production, based on the kinetoplast DNA (kDNA), for the Leishmania diagnostic an identification. We also describe the kDNA purification protocol from Leishmania reference cepa, the process of P 32 labelling of the kDNA by using the nick translation method, gathering, sample preparation and treatment, the optimum conditions for the hybridization reaction and the procedures for the autoradiography

  5. Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

    Science.gov (United States)

    Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

    2013-12-03

    We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

  6. Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

    Science.gov (United States)

    Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

    2016-04-01

    An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay. © The Author(s) 2016.

  7. Design of 240,000 orthogonal 25mer DNA barcode probes.

    Science.gov (United States)

    Xu, Qikai; Schlabach, Michael R; Hannon, Gregory J; Elledge, Stephen J

    2009-02-17

    DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.

  8. Applications of DNA-Stable Isotope Probing in Bioremediation Studies

    Science.gov (United States)

    Chen, Yin; Vohra, Jyotsna; Murrell, J. Colin

    DNA-stable isotope probing, a method to identify active microorganisms without the prerequisite of cultivation, has been widely applied in the study of microorganisms involved in the degradation of environmental pollutants. Recent advances and technique considerations in applying DNA-SIP in bioremediation are highlighted. A detailed protocol of a DNA-SIP experiment is provided.

  9. Highly Sensitive Temperature Sensors Based on Fiber-Optic PWM and Capacitance Variation Using Thermochromic Sensing Membrane

    Directory of Open Access Journals (Sweden)

    Md. Rajibur Rahaman Khan

    2016-07-01

    Full Text Available In this paper, we propose a temperature/thermal sensor that contains a Rhodamine-B sensing membrane. We applied two different sensing methods, namely, fiber-optic pulse width modulation (PWM and an interdigitated capacitor (IDC-based temperature sensor to measure the temperature from 5 °C to 100 °C. To the best of our knowledge, the fiber-optic PWM-based temperature sensor is reported for the first time in this study. The proposed fiber-optic PWM temperature sensor has good sensing ability; its sensitivity is ~3.733 mV/°C. The designed temperature-sensing system offers stable sensing responses over a wide dynamic range, good reproducibility properties with a relative standard deviation (RSD of ~0.021, and the capacity for a linear sensing response with a correlation coefficient of R2 ≈ 0.992 over a wide sensing range. In our study, we also developed an IDC temperature sensor that is based on the capacitance variation principle as the IDC sensing element is heated. We compared the performance of the proposed temperature-sensing systems with different fiber-optic temperature sensors (which are based on the fiber-optic wavelength shift method, the long grating fiber-optic Sagnac loop, and probe type fiber-optics in terms of sensitivity, dynamic range, and linearity. We observed that the proposed sensing systems have better sensing performance than the above-mentioned sensing system.

  10. Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes.

    Science.gov (United States)

    García-Cañas, Virginia; Mondello, Monica; Cifuentes, Alejandro

    2011-05-01

    New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive

  11. Characterizing shock waves in hydrogel using high speed imaging and a fiber-optic probe hydrophone

    Science.gov (United States)

    Anderson, Phillip A.; Betney, M. R.; Doyle, H. W.; Tully, B.; Ventikos, Y.; Hawker, N. A.; Roy, Ronald A.

    2017-05-01

    The impact of a stainless steel disk-shaped projectile launched by a single-stage light gas gun is used to generate planar shock waves with amplitudes on the order of 102MPa in a hydrogel target material. These shock waves are characterized using ultra-high-speed imaging as well as a fiber-optic probe hydrophone. Although the hydrogel equation of state (EOS) is unknown, the combination of these measurements with conservation of mass and momentum allows us to calculate pressure. It is also shown that although the hydrogel behaves similarly to water, the use of a water EOS underpredicts pressure amplitudes in the hydrogel by ˜10 % at the shock front. Further, the water EOS predicts pressures approximately 2% higher than those determined by conservation laws for a given value of the shock velocity. Shot to shot repeatability is controlled to within 10%, with the shock speed and pressure increasing as a function of the velocity of the projectile at impact. Thus the projectile velocity may be used as an adequate predictor of shock conditions in future work with a restricted suite of diagnostics.

  12. Absolute and direct microRNA quantification using DNA-gold nanoparticle probes.

    Science.gov (United States)

    Degliangeli, Federica; Kshirsagar, Prakash; Brunetti, Virgilio; Pompa, Pier Paolo; Fiammengo, Roberto

    2014-02-12

    DNA-gold nanoparticle probes are implemented in a simple strategy for direct microRNA (miRNA) quantification. Fluorescently labeled DNA-probe strands are immobilized on PEGylated gold nanoparticles (AuNPs). In the presence of target miRNA, DNA-RNA heteroduplexes are formed and become substrate for the endonuclease DSN (duplex-specific nuclease). Enzymatic hydrolysis of the DNA strands yields a fluorescence signal due to diffusion of the fluorophores away from the gold surface. We show that the molecular design of our DNA-AuNP probes, with the DNA strands immobilized on top of the PEG-based passivation layer, results in nearly unaltered enzymatic activity toward immobilized heteroduplexes compared to substrates free in solution. The assay, developed in a real-time format, allows absolute quantification of as little as 0.2 fmol of miR-203. We also show the application of the assay for direct quantification of cancer-related miR-203 and miR-21 in samples of extracted total RNA from cell cultures. The possibility of direct and absolute quantification may significantly advance the use of microRNAs as biomarkers in the clinical praxis.

  13. Use of Ti plasmid DNA probes for determining tumorigenicity of agrobacterium strains

    International Nuclear Information System (INIS)

    Burr, T.J.; Norelli, J.L.; Katz, B.H.; Bishop, A.L.

    1990-01-01

    Probes consisting of T-DNA genes from the Ti plasmid of Agrobacterium tumefaciens were used for determining tumorigenicity of strains. Two 32 P-labeled probes hybridized with 28 of 28 tumorigenic strains of the pathogen but not with 20 of 22 nontumorigenic strains. One probe, pTHE17, consists of all but the far left portion of the T-DNA of strain C58. Probe SmaI7 consists of SmaI fragment 7 of pTiC58, including onc genes 1, 4, and 6a and most of 2. Another probe, pAL4044, consisting of the vir region of strain Ach-5, hybridized with several nontumorigenic as well as tumorigenic strains. Colony hybridizations were done with 28 tumorigenic and 22 nontumorigenic Agrobacterium strains. About 10 6 CFU of the different tumorigenic strains were detectable with this method. Southern analyses confirmed the presence or absence of Ti plasmids in strains for which tumorigenicity was questioned. Colony hybridization with the T-DNA probes provides a rapid and sensitive means for determining the tumorigenic nature of Agrobacterium strains

  14. Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers

    DEFF Research Database (Denmark)

    Yao, Danfeng; Kim, Junyoung; Yu, Fang

    2005-01-01

    at an intermediate sodium concentration (approximately 100 mM). These effects were mainly ascribed to the electrostatic cross talk among the hybridized DNA molecules and the secondary structure of PCR amplicons. For the negatively charged DNA probes, the hybridization reaction was subjected additionally to the DNA....../DNA electrostatic barrier, particularly in lower ionic strength range (e.g., 10 approximately 150 mM Na(+)). The electrostatic cross talk was shown to be largely reduced if the PNA probe layer was sufficiently diluted by following a strategic templated immobilization method. As a consequence, a pseudo...

  15. 2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage

    International Nuclear Information System (INIS)

    El-Yazbi, Amira F.; Loppnow, Glen R.

    2012-01-01

    Highlights: ► Molecular beacon with 2AP bases detects DNA damage in a simple mix-and-read assay. ► Molecular beacons with 2AP bases detect damage at a 17.2 nM limit of detection. ► The 2AP molecular beacon is linear over a 0–3.5 μM concentration range for damage. - Abstract: Nucleic acid exposure to radiation and chemical insults leads to damage and disease. Thus, detection and understanding DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we develop a fluorescence sensor of 2-aminopurine (2AP), a fluorescent analogue of adenine, incorporated in the loop of a hairpin probe for the quantification of ultraviolet (UV) C-induced nucleic acid damage. Our results show that the selectivity of the 2AP hairpin probe to UV-induced nucleic acid damage is comparable to molecular beacon (MB) probes of DNA damage. The calibration curve for the 2AP hairpin probe shows good linearity (R 2 = 0.98) with a limit of detection of 17.2 nM. This probe is a simple, fast and economic fluorescence sensor for the quantification of UV-induced damage in DNA.

  16. Reflection-mode micro-spherical fiber-optic probes for in vitro real-time and single-cell level pH sensing.

    Science.gov (United States)

    Yang, Qingbo; Wang, Hanzheng; Lan, Xinwei; Cheng, Baokai; Chen, Sisi; Shi, Honglan; Xiao, Hai; Ma, Yinfa

    2015-02-01

    pH sensing at the single-cell level without negatively affecting living cells is very important but still a remaining issue in the biomedical studies. A 70 μm reflection-mode fiber-optic micro-pH sensor was designed and fabricated by dip-coating thin layer of organically modified aerogel onto a tapered spherical probe head. A pH sensitive fluorescent dye 2', 7'-Bis (2-carbonylethyl)-5(6)-carboxyfluorescein (BCECF) was employed and covalently bonded within the aerogel networks. By tuning the alkoxide mixing ratio and adjusting hexamethyldisilazane (HMDS) priming procedure, the sensor can be optimized to have high stability and pH sensing ability. The in vitro real-time sensing capability was then demonstrated in a simple spectroscopic way, and showed linear measurement responses with a pH resolution up to an average of 0.049 pH unit within a narrow, but biological meaningful pH range of 6.12-7.81. Its novel characterizations of high spatial resolution, reflection mode operation, fast response and high stability, great linear response within biological meaningful pH range and high pH resolutions, make this novel pH probe a very cost-effective tool for chemical/biological sensing, especially within the single cell level research field.

  17. In-situ investigation of protein and DNA structure using UVRRS

    Science.gov (United States)

    Greek, L. Shane; Schulze, H. Georg; Blades, Michael W.; Haynes, Charles A.; Turner, Robin F. B.

    1997-05-01

    Ultraviolet resonance Raman spectroscopy (UVRRS) has the potential to become a sensitive, specific, versatile bioanalytical and biophysical technique for routine investigations of proteins, DNA, and their monomeric components, as well as a variety smaller, physiologically important aromatic molecules. The transition of UVRRS from a complex, specialized spectroscopic method to a common laboratory assay depends upon several developments, including a robust sample introduction method permitting routine, in situ analysis in standard laboratory environments. To this end, we recently reported the first fiber-optic probes suitable for deep-UV pulsed laser UVRRS. In this paper, we extend this work by demonstrating the applicability of such probes to studies of biochemical relevance, including investigations of the resonance enhancement of phosphotyrosine, thermal denaturation of RNase T1, and specific and non-specific protein binding. The advantages and disadvantages of the probes are discussed with reference to sample conditions and probe design considerations.

  18. Rapid detection of Listeria monocytogenes in foods, by a combination of PCR and DNA probe.

    Science.gov (United States)

    Ingianni, A; Floris, M; Palomba, P; Madeddu, M A; Quartuccio, M; Pompei, R

    2001-10-01

    Listeria monocytogenes is a frequent contaminant of water and foods. Its rapid detection is needed before some foods can be prepared for marketing. In this work L. monocytogenes has been searched for in foods, by a combination of polymerase chain reaction (PCR) and a DNA probe. Both PCR and the probe were prepared for recognizing a specific region of the internalin gene, which is responsible for the production of one of the most important pathogenic factors of Listeria. The combined use of PCR and the DNA probe was used for the detection of L. monocytogenes in over 180 environmental and food samples. Several detection methods were compared in this study, namely conventional culture methods; direct PCR; PCR after an enrichment step; a DNA probe alone; a DNA probe after enrichment and another commercially available gene-probe. Finally PCR and the DNA probe were used in series on all the samples collected. When the DNA probe was associated with the PCR, specific and accurate detection of listeria in the samples could be obtained in about a working-day. The present molecular method showed some advantages in terms of rapidity and specificity in comparison to the other aforementioned tests. In addition, it resulted as being easy to handle, even for non-specialized personnel in small diagnostic microbiology laboratories. Copyright 2001 Academic Press.

  19. Hawking spectrum for a fiber-optical analog of the event horizon

    Science.gov (United States)

    Bermudez, David; Leonhardt, Ulf

    2016-05-01

    Hawking radiation has been regarded as a more general phenomenon than in gravitational physics, in particular in laboratory analogs of the event horizon. Here we consider the fiber-optical analog of the event horizon, where intense light pulses in fibers establish horizons for probe light. Then, we calculate the Hawking spectrum in an experimentally realizable system. We found that the Hawking radiation is peaked around group-velocity horizons in which the speed of the pulse matches the group velocity of the probe light. The radiation nearly vanishes at the phase horizon where the speed of the pulse matches the phase velocity of light.

  20. Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection.

    Science.gov (United States)

    Yao, B C; Wu, Y; Yu, C B; He, J R; Rao, Y J; Gong, Y; Fu, F; Chen, Y F; Li, Y R

    2016-03-24

    Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel 'FRET on Fiber' concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based 'FRET on fiber' configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated 'FRET on Fiber' sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response.

  1. DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Kwan, Johnson; Baumgartner, Adolf; Weier, Jingly F.; Wang, Mei; Escudero, Tomas; Munne' , Santiago; Zitzelsberger, Horst F.; Weier, Heinz-Ulrich

    2009-01-30

    Structural chromosome aberrations are hallmarks of many human genetic diseases. The precise mapping of translocation breakpoints in tumors is important for identification of genes with altered levels of expression, prediction of tumor progression, therapy response, or length of disease-free survival as well as the preparation of probes for detection of tumor cells in peripheral blood. Similarly, in vitro fertilization (IVF) and preimplantation genetic diagnosis (PGD) for carriers of balanced, reciprocal translocations benefit from accurate breakpoint maps in the preparation of patient-specific DNA probes followed by a selection of normal or balanced oocytes or embryos. We expedited the process of breakpoint mapping and preparation of case-specific probes by utilizing physically mapped bacterial artificial chromosome (BAC) clones. Historically, breakpoint mapping is based on the definition of the smallest interval between proximal and distal probes. Thus, many of the DNA probes prepared for multi-clone and multi-color mapping experiments do not generate additional information. Our pooling protocol described here with examples from thyroid cancer research and PGD accelerates the delineation of translocation breakpoints without sacrificing resolution. The turnaround time from clone selection to mapping results using tumor or IVF patient samples can be as short as three to four days.

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

    Science.gov (United States)

    Ferguson, Jane A.

    2001-06-01

    and O2. This sensor is useful for monitoring bioprocesses such as (beer) fermentation and for clinical situations such as blood gas analysis. DNA sensors were created by attaching short single strands of DNA (probes) to the fiber tip. A matching single strand (target) forms a strong interacting pair with the probe upon contact. The target strands in a sample are labeled with a fluorescent dye. When a probe-target pair is formed and excitation light is sent down the fiber, the fiber bearing the pair emits light that is captured and detected. A high density DNA array was created by isolating thousands of discrete DNA sensors on the tip of an imaging optical fiber. This array was made possible by the formation of microwells on the imaging fiber tip. Microspheres functionalized with DNA were placed in the wells of the fiber and each microsphere was independently and simultaneously monitored. (Abstract shortened by UMI.)

  3. The fiber-optic imaging and manipulation of neural activity during animal behavior.

    Science.gov (United States)

    Miyamoto, Daisuke; Murayama, Masanori

    2016-02-01

    Recent progress with optogenetic probes for imaging and manipulating neural activity has further increased the relevance of fiber-optic systems for neural circuitry research. Optical fibers, which bi-directionally transmit light between separate sites (even at a distance of several meters), can be used for either optical imaging or manipulating neural activity relevant to behavioral circuitry mechanisms. The method's flexibility and the specifications of the light structure are well suited for following the behavior of freely moving animals. Furthermore, thin optical fibers allow researchers to monitor neural activity from not only the cortical surface but also deep brain regions, including the hippocampus and amygdala. Such regions are difficult to target with two-photon microscopes. Optogenetic manipulation of neural activity with an optical fiber has the advantage of being selective for both cell-types and projections as compared to conventional electrophysiological brain tissue stimulation. It is difficult to extract any data regarding changes in neural activity solely from a fiber-optic manipulation device; however, the readout of data is made possible by combining manipulation with electrophysiological recording, or the simultaneous application of optical imaging and manipulation using a bundle-fiber. The present review introduces recent progress in fiber-optic imaging and manipulation methods, while also discussing fiber-optic system designs that are suitable for a given experimental protocol. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  4. Construction and applications of DNA probes for detection of polychlorinated biphenyl-degrading genotypes in toxic organic-contaminated soil environments

    International Nuclear Information System (INIS)

    Walia, S.; Khan, A.; Rosenthal, N.

    1990-01-01

    Several DNA probes for polychlorinated biphenyl (PCB)-degrading genotypes were constructed from PCB-degrading bacteria. These laboratory-engineered DNA probes were used for the detection, enumeration, and isolation of specific bacteria degrading PCBs. Dot blot analysis of purified DNA from toxic organic chemical-contaminated soil bacterial communities showed positive DNA-DNA hybridization with a 32P-labeled DNA probe (pAW6194, cbpABCD). Less than 1% of bacterial colonies isolated from garden topsoil and greater than 80% of bacteria isolated from PCB-contaminated soils showed DNA homologies with 32P-labeled DNA probes. Some of the PCB-degrading bacterial isolates detected by the DNA probe method did not show biphenyl clearance. The DNA probe method was found to detect additional organisms with greater genetic potential to degrade PCBs than the biphenyl clearance method did. Results from this study demonstrate the usefulness of DNA probes in detecting specific PCB-degrading bacteria, abundance of PCB-degrading genotypes, and genotypic diversity among PCB-degrading bacteria in toxic chemical-polluted soil environments. We suggest that the DNA probe should be used with caution for accurate assessment of PCB-degradative capacity within soils and further recommend that a combination of DNA probe and biodegradation assay be used to determine the abundance of PCB-degrading bacteria in the soil bacterial community

  5. Application of synthetic DNA probes to the analysis of DNA sequence variants in man

    International Nuclear Information System (INIS)

    Wallace, R.B.; Petz, L.D.; Yam, P.Y.

    1986-01-01

    Oligonucleotide probes provide a tool to discriminate between any two alleles on the basis of hybridization. Random sampling of the genome with different oligonucleotide probes should reveal polymorphism in a certain percentage of the cases. In the hope of identifying polymorphic regions more efficiently, we chose to take advantage of the proposed hypermutability of repeated DNA sequences and the specificity of oligonucleotide hybridization. Since, under appropriate conditions, oligonucleotide probes require complete base pairing for hybridization to occur, they will only hybridize to a subset of the members of a repeat family when all members of the family are not identical. The results presented here suggest that oligonucleotide hybridization can be used to extend the genomic sequences that can be tested for the presence of RFLPs. This expands the tools available to human genetics. In addition, the results suggest that repeated DNA sequences are indeed more polymorphic than single-copy sequences. 28 references, 2 figures

  6. Data Mining Empowers the Generation of a Novel Class of Chromosome-specific DNA Probes

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Hui; Weier, Heinz-Ulrich G.; Kwan, Johnson; Wang, Mei; O' Brien, Benjamin

    2011-03-08

    Probes that allow accurate delineation of chromosome-specific DNA sequences in interphase or metaphase cell nuclei have become important clinical tools that deliver life-saving information about the gender or chromosomal make-up of a product of conception or the probability of an embryo to implant, as well as the definition of tumor-specific genetic signatures. Often such highly specific DNA probes are proprietary in nature and have been the result of extensive probe selection and optimization procedures. We describe a novel approach that eliminates costly and time consuming probe selection and testing by applying data mining and common bioinformatics tools. Similar to a rational drug design process in which drug-protein interactions are modeled in the computer, the rational probe design described here uses a set of criteria and publicly available bioinformatics software to select the desired probe molecules from libraries comprised of hundreds of thousands of probe molecules. Examples describe the selection of DNA probes for the human X and Y chromosomes, both with unprecedented performance, but in a similar fashion, this approach can be applied to other chromosomes or species.

  7. Coaxial atomic force microscope probes for dielectrophoresis of DNA under different buffer conditions

    Science.gov (United States)

    Tao, Yinglei; Kumar Wickramasinghe, H.

    2017-02-01

    We demonstrate a coaxial AFM nanoprobe device for dielectrophoretic (DEP) trapping of DNA molecules in Tris-EDTA (TE) and phosphate-buffered saline (PBS) buffers. The DEP properties of 20 nm polystyrene beads were studied with coaxial probes in media with different conductivities. Due to the special geometry of our DEP probe device, sufficiently high electric fields were generated at the probe end to focus DNA molecules with positive DEP. DEP trapping for both polystyrene beads and DNA molecules was quantitatively analyzed over the frequency range from 100 kHz to 50 MHz and compared with the Clausius-Mossotti theory. Finally, we discussed the negative effect of medium salinity during DEP trapping.

  8. In vivo detection of plutonium in the tracheobronchial lymph nodes with a fiber-optic coupled scintillator

    International Nuclear Information System (INIS)

    Swinth, K.L.; Park, J.F.; Voelz, G.L.; Ewins, J.H.

    1976-01-01

    An intraesophageal probe was developed for measuring plutonium in the tracheobronchial lymph nodes. The probe uses a fiber-optic coupled NaI(Tl) scintillator as a detector and has a detection limit one-tenth that of a solid-state probe previously used for this measurement. The probe, with a projected sensitivity of 1 cpm/nCi, was used to detect plutonium in the lymph nodes of 11 experimentally exposed dogs. Tests on an accidentally exposed human volunteer yielded positive counts from the lymph nodes from an amount estimated at 7 nCi in the tracheobronchial lymph nodes

  9. Comparison of two fiber-optical temperature measurement systems in magnetic fields up to 9.4 Tesla.

    Science.gov (United States)

    Buchenberg, Waltraud B; Dadakova, Tetiana; Groebner, Jens; Bock, Michael; Jung, Bernd

    2015-05-01

    Precise temperature measurements in the magnetic field are indispensable for MR safety studies and for temperature calibration during MR-guided thermotherapy. In this work, the interference of two commonly used fiber-optical temperature measurement systems with the static magnetic field B0 was determined. Two fiber-optical temperature measurement systems, a GaAs-semiconductor and a phosphorescent phosphor ceramic, were compared for temperature measurements in B0 . The probes and a glass thermometer for reference were placed in an MR-compatible tube phantom within a water bath. Temperature measurements were carried out at three different MR systems covering static magnetic fields up to B0  = 9.4T, and water temperatures were changed between 25°C and 65°C. The GaAs-probe significantly underestimated absolute temperatures by an amount related to the square of B0 . A maximum difference of ΔT = -4.6°C was seen at 9.4T. No systematic temperature difference was found with the phosphor ceramic probe. For both systems, the measurements were not dependent on the orientation of the sensor to B0 . Temperature measurements with the phosphor ceramic probe are immune to magnetic fields up to 9.4T, whereas the GaAs-probes either require a recalibration inside the MR system or a correction based on the square of B0. © 2014 Wiley Periodicals, Inc.

  10. [The recent development of fiber-optic chemical sensor].

    Science.gov (United States)

    Wang, Jian; Wei, Jian-ping; Yang, Bo; Gao, Zhi-yang; Zhang, Li-wei; Yang, Xue-feng

    2014-08-01

    The present article provides a brief review of recent research on fiber-optic chemical sensor technology and the future development trends. Especially, fiber-optic pH chemical sensor, fiber-optic ion chemicl sensor, and fiber-optic gas chemical sensor are introduced respectively. Sensing film preparation methods such as chemical bonding method and sol-gel method were briefly reviewed. The emergence of new type fiber-microstructured optical fiber opened up a new development direction for fiber-optic chemical sensor. Because of its large inner surface area, flexible design of structure, having internal sensing places in fibers, it has rapidly become an important development direction and research focus of the fiber-optic chemical sensors. The fiber-optic chemical sensor derived from microstructured optical fiber is also discussed in detail. Finally, we look to the future of the fiber-optic chemical sensor.

  11. Determination for Enterobacter cloacae based on a europium ternary complex labeled DNA probe

    Science.gov (United States)

    He, Hui; Niu, Cheng-Gang; Zeng, Guang-Ming; Ruan, Min; Qin, Pin-Zhu; Liu, Jing

    2011-11-01

    The fast detection and accurate diagnosis of the prevalent pathogenic bacteria is very important for the treatment of disease. Nowadays, fluorescence techniques are important tools for diagnosis. A two-probe tandem DNA hybridization assay was designed for the detection of Enterobacter cloacae based on time-resolved fluorescence. In this work, the authors synthesized a novel europium ternary complex Eu(TTA) 3(5-NH 2-phen) with intense luminescence, high fluorescence quantum yield and long lifetime before. We developed a method based on this europium complex for the specific detection of original extracted DNA from E. cloacae. In the hybridization assay format, the reporter probe was labeled with Eu(TTA) 3(5-NH 2-phen) on the 5'-terminus, and the capture probe capture probe was covalent immobilized on the surface of the glutaraldehyde treated glass slides. The original extracted DNA of samples was directly used without any DNA purification and amplification. The detection was conducted by monitoring the fluorescence intensity from the glass surface after DNA hybridization. The detection limit of the DNA was 5 × 10 -10 mol L -1. The results of the present work proved that this new approach was easy to operate with high sensitivity and specificity. It could be conducted as a powerful tool for the detection of pathogen microorganisms in the environment.

  12. Novel Fiber-Optic Ring Acoustic Emission Sensor.

    Science.gov (United States)

    Wei, Peng; Han, Xiaole; Xia, Dong; Liu, Taolin; Lang, Hao

    2018-01-13

    Acoustic emission technology has been applied to many fields for many years. However, the conventional piezoelectric acoustic emission sensors cannot be used in extreme environments, such as those with heavy electromagnetic interference, high pressure, or strong corrosion. In this paper, a novel fiber-optic ring acoustic emission sensor is proposed. The sensor exhibits high sensitivity, anti-electromagnetic interference, and corrosion resistance. First, the principle of a novel fiber-optic ring sensor is introduced. Different from piezoelectric and other fiber acoustic emission sensors, this novel sensor includes both a sensing skeleton and a sensing fiber. Second, a heterodyne interferometric demodulating method is presented. In addition, a fiber-optic ring sensor acoustic emission system is built based on this method. Finally, fiber-optic ring acoustic emission experiments are performed. The novel fiber-optic ring sensor is glued onto the surface of an aluminum plate. The 150 kHz standard continuous sinusoidal signals and broken lead signals are successfully detected by the novel fiber-optic ring acoustic emission sensor. In addition, comparison to the piezoelectric acoustic emission sensor is performed, which shows the availability and reliability of the novel fiber-optic ring acoustic emission sensor. In the future, this novel fiber-optic ring acoustic emission sensor will provide a new route to acoustic emission detection in harsh environments.

  13. Probe Microscopic Studies of DNA Molecules on Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    Kazuo Umemura

    2016-10-01

    Full Text Available Hybrids of DNA and carbon nanotubes (CNTs are promising nanobioconjugates for nanobiosensors, carriers for drug delivery, and other biological applications. In this review, nanoscopic characterization of DNA-CNT hybrids, in particular, characterization by scanning probe microscopy (SPM, is summarized. In many studies, topographical imaging by atomic force microscopy has been performed. However, some researchers have demonstrated advanced SPM operations in order to maximize its unique and valuable functions. Such sophisticated approaches are attractive and will have a significant impact on future studies of DNA-CNT hybrids.

  14. DNA imaging and quantification using chemi-luminescent probes

    International Nuclear Information System (INIS)

    Dorner, G.; Redjdal, N.; Laniece, P.; Siebert, R.; Tricoire, H.; Valentin, L.

    1999-01-01

    During this interdisciplinary study we have developed an ultra sensitive and reliable imaging system of DNA labelled by chemiluminescence. Based on a liquid nitrogen cooled CCD, the system achieves sensitivities down to 10 fg/mm 2 labelled DNA over a surface area of 25 x 25 cm 2 with a sub-millimeter resolution. Commercially available chemi-luminescent - and enhancer molecules are compared and their reaction conditions optimized for best signal-to-noise ratios. Double labelling was performed to verify quantification with radioactive probes. (authors)

  15. Novel Fiber-Optic Ring Acoustic Emission Sensor

    Directory of Open Access Journals (Sweden)

    Peng Wei

    2018-01-01

    Full Text Available Acoustic emission technology has been applied to many fields for many years. However, the conventional piezoelectric acoustic emission sensors cannot be used in extreme environments, such as those with heavy electromagnetic interference, high pressure, or strong corrosion. In this paper, a novel fiber-optic ring acoustic emission sensor is proposed. The sensor exhibits high sensitivity, anti-electromagnetic interference, and corrosion resistance. First, the principle of a novel fiber-optic ring sensor is introduced. Different from piezoelectric and other fiber acoustic emission sensors, this novel sensor includes both a sensing skeleton and a sensing fiber. Second, a heterodyne interferometric demodulating method is presented. In addition, a fiber-optic ring sensor acoustic emission system is built based on this method. Finally, fiber-optic ring acoustic emission experiments are performed. The novel fiber-optic ring sensor is glued onto the surface of an aluminum plate. The 150 kHz standard continuous sinusoidal signals and broken lead signals are successfully detected by the novel fiber-optic ring acoustic emission sensor. In addition, comparison to the piezoelectric acoustic emission sensor is performed, which shows the availability and reliability of the novel fiber-optic ring acoustic emission sensor. In the future, this novel fiber-optic ring acoustic emission sensor will provide a new route to acoustic emission detection in harsh environments.

  16. The generation of radiolabeled DNA and RNA probes with polymerase chain reaction

    International Nuclear Information System (INIS)

    Schowalter, D.B.; Sommer, S.S.

    1989-01-01

    By including a radioactive triphosphate during polymerase chain reaction (PCR), probes of very high specific activity can be generated. The advantages of PCR labeling include (1) uniform labeling with a specific activity of 5 X 10(9) cpm/micrograms or higher (sensitivity of detection: 0.028 pg of target DNA per 24 h); (2) ease of regulation of both the specific activity and the amount of labeled probe produced; (3) efficient labeling of fragments less than 500 bp; (4) efficient incorporation over a wide range of input DNA template; (5) labeling with subnanogram amounts of input DNA; and (6) direct labeling of genomic DNA. The minimal amount of input DNA allows a virtually unlimited number of PCR labeling reactions to be performed on DNA generated by one amplification under the previously described nonlabeling conditions. This obviates the need for CsCl gradients or other large scale methods of DNA preparation. The above advantages except for the very high specific activity can also be achieved by transcript labeling after an amplification where one or both of PCR primers contain a phage promoter sequence

  17. Cloning and Characterization of a Complex DNA Fingerprinting Probe for Candida parapsilosis

    Science.gov (United States)

    Enger, Lee; Joly, Sophie; Pujol, Claude; Simonson, Patricia; Pfaller, Michael; Soll, David R.

    2001-01-01

    Candida parapsilosis accounts for a significant number of nosocomial fungemias, but in fact, no effective and verified genetic fingerprinting method has emerged for assessing the relatedness of independent isolates for epidemiological studies. A complex 15-kb DNA fingerprinting probe, Cp3-13, was therefore isolated from a library of C. parapsilosis genomic DNA fragments. The efficacy of Cp3-13 for DNA fingerprinting was verified by a comparison of its clustering capacity with those of randomly amplified polymorphic DNA analysis and internally transcribed spacer region sequencing, by testing species specificity, and by assessing its capacity to identify microevolutionary changes both in vitro and in vivo. Southern blot hybridization of EcoRI/SalI-digested DNA with Cp3-13 provides a fingerprinting system that (i) identifies the same strain in independent isolates, (ii) discriminates between unrelated isolates, (iii) separates independent isolates into valid groups in a dendrogram, (iv) identifies microevolution in infecting populations, and (v) is amenable to automatic computer-assisted DNA fingerprint analysis. This probe is now available for epidemiological studies. PMID:11158125

  18. 21 CFR 876.4530 - Gastroenterology-urology fiberoptic retractor.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Gastroenterology-urology fiberoptic retractor. 876... SERVICES (CONTINUED) MEDICAL DEVICES GASTROENTEROLOGY-UROLOGY DEVICES Surgical Devices § 876.4530 Gastroenterology-urology fiberoptic retractor. (a) Identification. A gastroenterology-urology fiberoptic retractor...

  19. In-plane ultrasonic needle tracking using a fiber-optic hydrophone

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Wenfeng, E-mail: wenfeng.xia@ucl.ac.uk; Desjardins, Adrien E. [Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London WC1E 6BT (United Kingdom); Mari, Jean Martial [Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom and GePaSud, University of French Polynesia, Faa’a 98702, French Polynesia (France); West, Simeon J. [Department of Anaesthesia, University College Hospital, Main Theatres, Maple Bridge Link Corridor, Podium 3, 235 Euston Road, London NW1 2BU (United Kingdom); Ginsberg, Yuval; David, Anna L. [Institute for Women’s Health, University College London, 86-96 Chenies Mews, London WC1E 6HX (United Kingdom); Ourselin, Sebastien [Center for Medical Imaging Computing, University College London, Gower Street, London WC1E 6BT (United Kingdom)

    2015-10-15

    Purpose: Accurate and efficient guidance of needles to procedural targets is critically important during percutaneous interventional procedures. Ultrasound imaging is widely used for real-time image guidance in a variety of clinical contexts, but with this modality, uncertainties about the location of the needle tip within the image plane lead to significant complications. Whilst several methods have been proposed to improve the visibility of the needle, achieving accuracy and compatibility with current clinical practice is an ongoing challenge. In this paper, the authors present a method for directly visualizing the needle tip using an integrated fiber-optic ultrasound receiver in conjunction with the imaging probe used to acquire B-mode ultrasound images. Methods: Needle visualization and ultrasound imaging were performed with a clinical ultrasound imaging system. A miniature fiber-optic ultrasound hydrophone was integrated into a 20 gauge injection needle tip to receive transmissions from individual transducer elements of the ultrasound imaging probe. The received signals were reconstructed to create an image of the needle tip. Ultrasound B-mode imaging was interleaved with needle tip imaging. A first set of measurements was acquired in water and tissue ex vivo with a wide range of insertion angles (15°–68°) to study the accuracy and sensitivity of the tracking method. A second set was acquired in an in vivo swine model, with needle insertions to the brachial plexus. A third set was acquired in an in vivo ovine model for fetal interventions, with insertions to different locations within the uterine cavity. Two linear ultrasound imaging probes were used: a 14–5 MHz probe for the first and second sets, and a 9–4 MHz probe for the third. Results: During insertions in tissue ex vivo and in vivo, the imaged needle tip had submillimeter axial and lateral dimensions. The signal-to-noise (SNR) of the needle tip was found to depend on the insertion angle. With

  20. Use of a D17Z1 oligonucleotide probe for human DNA quantitation prior to PCR analysis of polymorphic DNA markers

    Energy Technology Data Exchange (ETDEWEB)

    Walsh, S.; Alavaren, M.; Varlaro, J. [Roche Molecular Systems, Alameda, CA (United States)] [and others

    1994-09-01

    The alpha-satellite DNA locus D17Z1 contains primate-specific sequences which are repeated several hundred times per chromosome 17. A probe that was designed to hybridize to a subset of the D17Z1 sequence can be used for very sensitive and specific quantitation of human DNA. Sample human genomic DNA is immobilized on nylon membrane using a slot blot apparatus, and then hybridized with a biotinylated D17Z1 oligonucleotide probe. The subsequent binding of streptavidin-horseradish peroxidase to the bound probe allows for either calorimetric (TMB) or chemiluminescent (ECL) detection. Signals obtained for sample DNAs are then compared to the signals obtained for a series of human DNA standards. For either detection method, forty samples can be quantitated in less than two hours, with a sensitivity of 150 pg. As little as 20 pg of DNA can be quantitated when using chemiluminescent detection with longer film exposures. PCR analysis of several VNTR and STR markers has indicated that optimal typing results are generally obtained within a relatively narrow range of input DNA quantities. Too much input DNA can lead to PCR artifacts such as preferential amplification of smaller alleles, non-specific amplification products, and exaggeration of the DNA synthesis slippage products that are seen with STR markers. Careful quantitation of human genomic DNA prior to PCR can avoid or minimize these problems and ultimately give cleaner, more unambiguous PCR results.

  1. Mismatch discrimination of lipidated DNA and LNA-probes (LiNAs) in hybridization-controlled liposome assembly

    DEFF Research Database (Denmark)

    Jakobsen, Ulla; Vogel, Stefan

    2016-01-01

    Assays for mismatch discrimination and detection of single nucleotide variations by hybridization-controlled assembly of liposomes, which do not require tedious surface chemistry, are versatile for both DNA and RNA targets. We report herein a comprehensive study on different DNA and LNA (locked...... assay in the context of mismatch discrimination and SNP detection are presented. The advantages of membrane-anchored LiNA-probes compared to chemically attached probes on solid nanoparticles (e.g. gold nanoparticles) are described. Key functionalities such as non-covalent attachment of LiNA probes...... without the need for long spacers and the inherent mobility of membrane-anchored probes in lipid-bilayer membranes will be described for several different probe designs....

  2. Gold nanoparticle-based probes for the colorimetric detection of Mycobacterium avium subspecies paratuberculosis DNA.

    Science.gov (United States)

    Ganareal, Thenor Aristotile Charles S; Balbin, Michelle M; Monserate, Juvy J; Salazar, Joel R; Mingala, Claro N

    2018-02-12

    Gold nanoparticle (AuNP) is considered to be the most stable metal nanoparticle having the ability to be functionalized with biomolecules. Recently, AuNP-based DNA detection methods captured the interest of researchers worldwide. Paratuberculosis or Johne's disease, a chronic gastroenteritis in ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), was found to have negative effect in the livestock industry. In this study, AuNP-based probes were evaluated for the specific and sensitive detection of MAP DNA. AuNP-based probe was produced by functionalization of AuNPs with thiol-modified oligonucleotide and was confirmed by Fourier-Transform Infrared (FTIR) spectroscopy. UV-Vis spectroscopy and Scanning Electron Microscopy (SEM) were used to characterize AuNPs. DNA detection was done by hybridization of 10 μL of DNA with 5 μL of probe at 63 °C for 10 min and addition of 3 μL salt solution. The method was specific to MAP with detection limit of 103 ng. UV-Vis and SEM showed dispersion and aggregation of the AuNPs for the positive and negative results, respectively, with no observed particle growth. This study therefore reports an AuNP-based probes which can be used for the specific and sensitive detection of MAP DNA. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Probe DNA-Cisplatin Interaction with Solid-State Nanopores

    Science.gov (United States)

    Zhou, Zhi; Hu, Ying; Li, Wei; Xu, Zhi; Wang, Pengye; Bai, Xuedong; Shan, Xinyan; Lu, Xinghua; Nanopore Collaboration

    2014-03-01

    Understanding the mechanism of DNA-cisplatin interaction is essential for clinical application and novel drug design. As an emerging single-molecule technology, solid-state nanopore has been employed in biomolecule detection and probing DNA-molecule interactions. Herein, we reported a real-time monitoring of DNA-cisplatin interaction by employing solid-state SiN nanopores. The DNA-cisplatin interacting process is clearly classified into three stages by measuring the capture rate of DNA-cisplatin adducts. In the first stage, the negative charged DNA molecules were partially discharged due to the bonding of positive charged cisplatin and forming of mono-adducts. In the second stage, forming of DNA-cisplatin di-adducts with the adjacent bases results in DNA bending and softening. The capture rate increases since the softened bi-adducts experience a lower barrier to thread into the nanopores. In the third stage, complex structures, such as micro-loop, are formed and the DNA-cisplatin adducts are aggregated. The capture rate decreases to zero as the aggregated adduct grows to the size of the pore. The characteristic time of this stage was found to be linear with the diameter of the nanopore and this dynamic process can be described with a second-order reaction model. We are grateful to Laboratory of Microfabrication, Dr. Y. Yao, and Prof. R.C. Yu (Institute of Physics, Chinese Academy of Sciences) for technical assistance.

  4. Flexible fiberoptic bronchoscopy in respiratory care: Diagnostic yield ...

    African Journals Online (AJOL)

    Introduction: Flexible fiberoptic bronchoscopy (FOB) is a key diagnostic and therapeutic procedure in pulmonology. Experience with fiberoptic bronchoscopy is scanty in most developing countries. Objectives: The goal of this study was to report our experience and clinical utility of fiberoptic bronchoscopy. Methods: A review ...

  5. Exciton-controlled fluorescence: application to hybridization-sensitive fluorescent DNA probe.

    Science.gov (United States)

    Okamoto, Akimitsu; Ikeda, Shuji; Kubota, Takeshi; Yuki, Mizue; Yanagisawa, Hiroyuki

    2009-01-01

    A hybridization-sensitive fluorescent probe has been designed for nucleic acid detection, using the concept of fluorescence quenching caused by the intramolecular excitonic interaction of fluorescence dyes. We synthesized a doubly thiazole orange-labeled nucleotide showing high fluorescence intensity for a hybrid with the target nucleic acid and effective quenching for the single-stranded state. This exciton-controlled fluorescent probe was applied to living HeLa cells using microinjection to visualize intracellular mRNA localization. Immediately after injection of the probe into the cell, fluorescence was observed from the probe hybridizing with the target RNA. This fluorescence rapidly decreased upon addition of a competitor DNA. Multicoloring of this probe resulted in the simple simultaneous detection of plural target nucleic acid sequences. This probe realized a large, rapid, reversible change in fluorescence intensity in sensitive response to the amount of target nucleic acid, and facilitated spatiotemporal monitoring of the behavior of intracellular RNA.

  6. UW Imaging of Seismic-Physical-Models in Air Using Fiber-Optic Fabry-Perot Interferometer.

    Science.gov (United States)

    Rong, Qiangzhou; Hao, Yongxin; Zhou, Ruixiang; Yin, Xunli; Shao, Zhihua; Liang, Lei; Qiao, Xueguang

    2017-02-17

    A fiber-optic Fabry-Perot interferometer (FPI) has been proposed and demonstrated for the ultrasound wave (UW) imaging of seismic-physical models. The sensor probe comprises a single mode fiber (SMF) that is inserted into a ceramic tube terminated by an ultra-thin gold film. The probe performs with an excellent UW sensitivity thanks to the nanolayer gold film, and thus is capable of detecting a weak UW in air medium. Furthermore, the compact sensor is a symmetrical structure so that it presents a good directionality in the UW detection. The spectral band-side filter technique is used for UW interrogation. After scanning the models using the sensing probe in air, the two-dimensional (2D) images of four physical models are reconstructed.

  7. Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture

    International Nuclear Information System (INIS)

    Edelstein, P.H.

    1986-01-01

    A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with 125 I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture

  8. Development of a biotinylated DNA probe for detection of infectious hematopoietic necrosis virus

    Science.gov (United States)

    Deering, R.E.; Arakawa, C.K.; Oshima, K.H.; O'Hara, P.J.; Landolt, M.L.; Winton, J.R.

    1991-01-01

    A nonrad~oact~ve DNA probe assay was developed to detect and ~dent~fy infect~ous hernatopoiet~c necrosls virus (IHNV) uslng a dot blot format The probe a synthet~c DNA oligonucleot~de labeled enzymatlcally w~th biotln hybnd~zed spec~f~cally w~th nucleocaps~d mRNA extracted from Infected cells early In the vlrus repl~cation cycle A rap~d guan~dln~um th~ocyanate based RNA extraction method uslng RNAzol B and rn~crocentrifuge tubes eff~c~ently pioduced h~gh qual~ty RNA from 3 commonly used f~sh cell llnes, CHSE-214, CHH-1, and EPC The probe reacted with 6 d~verse ~solates of IHNV, but d~d not react \

  9. Development of Prevotella intermedia-specific PCR primers based on the nucleotide sequences of a DNA probe Pig27.

    Science.gov (United States)

    Kim, Min Jung; Hwang, Kyung Hwan; Lee, Young-Seok; Park, Jae-Yoon; Kook, Joong-Ki

    2011-03-01

    The aim of this study was to develop Prevotella intermedia-specific PCR primers based on the P. intermedia-specific DNA probe. The P. intermedia-specific DNA probe was screened by inverted dot blot hybridization and confirmed by Southern blot hybridization. The nucleotide sequences of the species-specific DNA probes were determined using a chain termination method. Southern blot analysis showed that the DNA probe, Pig27, detected only the genomic DNA of P. intermedia strains. PCR showed that the PCR primers, Pin-F1/Pin-R1, had species-specificity for P. intermedia. The detection limits of the PCR primer sets were 0.4pg of the purified genomic DNA of P. intermedia ATCC 49046. These results suggest that the PCR primers, Pin-F1/Pin-R1, could be useful in the detection of P. intermedia as well as in the development of a PCR kit in epidemiological studies related to periodontal diseases. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

  10. DNA probes for distinguishing Psychodopygus wellcomei from Psychodopygus complexus (Diptera: Psychodidae

    Directory of Open Access Journals (Sweden)

    P. D. Ready

    1991-03-01

    Full Text Available Genomic DNA fragments from males of Psychodopygus wellcomei were isolated and shown to be useful as sensitive diagnostic probles for positively separting individuals of this species from those of Ps. complexus. These two members of the Ps. squamiventris series are found sympatrically in foci of cutaneous leishmaniasis in the hill forests of southern Pará State. Of the two species, only Ps. welcomei is thought to be an important vector of Leishmania braziliensis sensu stricto, buth this is based on circumstantial evidence because of the difficulties of identifying female sandflies wothin the series. The diagnostic probes were isolated from a library of Ps. wellcomei built by ligationg short fragments of Sau 3A-resistricted, genomic DNA into the plasmid vector PUC 18. Differential screening of 1316 library clones with total genomic DNA of Ps. Wellcomei and Ps. complexus identified 5 recombinants, with cross-hybridizing inserts of repetitive DNA, that showed strong specificity for Ps. wellcomei. As little as 0.4% of the DNA extracted from an individual sandfly (=ca. 0.5 namograms was specifically detected. The diagnostic probes were used to identify as Ps. wellcomei a wild-caught female sandfly found infected with L. braziliensis s.s., providing only the second positive association between these two species.

  11. The detection of HBV DNA with gold-coated iron oxide nanoparticle gene probes

    International Nuclear Information System (INIS)

    Xi Dong; Luo Xiaoping; Lu Qianghua; Yao Kailun; Liu Zuli; Ning Qin

    2008-01-01

    Gold-coated iron oxide nanoparticle Hepatitis B virus (HBV) DNA probes were prepared, and their application for HBV DNA measurement was studied. Gold-coated iron oxide nanoparticles were prepared by the citrate reduction of tetra-chloroauric acid in the presence of iron oxide nanoparticles which were added as seeds. With a fluorescence-based method, the maximal surface coverage of hexaethiol 30-mer oligonucleotides and the maximal percentage of hybridization strands on gold-coated iron oxide nanoparticles were (120 ± 8) oligonucleotides per nanoparticle, and (14 ± 2%), respectively, which were comparable with those of (132 ± 10) and (22 ± 3%) in Au nanoparticle groups. Large network aggregates were formed when gold-coated iron oxide nanoparticle HBV DNA gene probe was applied to detect HBV DNA molecules as evidenced by transmission electron microscopy and the high specificity was verified by blot hybridization. Our results further suggested that detecting DNA with iron oxide nanoparticles and magnetic separator was feasible and might be an alternative effective method

  12. Fiber-Optic Chemical Sensors and Fiber-Optic Bio-Sensors

    Science.gov (United States)

    Pospíšilová, Marie; Kuncová, Gabriela; Trögl, Josef

    2015-01-01

    This review summarizes principles and current stage of development of fiber-optic chemical sensors (FOCS) and biosensors (FOBS). Fiber optic sensor (FOS) systems use the ability of optical fibers (OF) to guide the light in the spectral range from ultraviolet (UV) (180 nm) up to middle infrared (IR) (10 µm) and modulation of guided light by the parameters of the surrounding environment of the OF core. The introduction of OF in the sensor systems has brought advantages such as measurement in flammable and explosive environments, immunity to electrical noises, miniaturization, geometrical flexibility, measurement of small sample volumes, remote sensing in inaccessible sites or harsh environments and multi-sensing. The review comprises briefly the theory of OF elaborated for sensors, techniques of fabrications and analytical results reached with fiber-optic chemical and biological sensors. PMID:26437407

  13. Fiber-Optic Chemical Sensors and Fiber-Optic Bio-Sensors.

    Science.gov (United States)

    Pospíšilová, Marie; Kuncová, Gabriela; Trögl, Josef

    2015-09-30

    This review summarizes principles and current stage of development of fiber-optic chemical sensors (FOCS) and biosensors (FOBS). Fiber optic sensor (FOS) systems use the ability of optical fibers (OF) to guide the light in the spectral range from ultraviolet (UV) (180 nm) up to middle infrared (IR) (10 μm) and modulation of guided light by the parameters of the surrounding environment of the OF core. The introduction of OF in the sensor systems has brought advantages such as measurement in flammable and explosive environments, immunity to electrical noises, miniaturization, geometrical flexibility, measurement of small sample volumes, remote sensing in inaccessible sites or harsh environments and multi-sensing. The review comprises briefly the theory of OF elaborated for sensors, techniques of fabrications and analytical results reached with fiber-optic chemical and biological sensors.

  14. Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide

    Science.gov (United States)

    Wang, Feng; Liu, Juewen

    2014-05-01

    Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg2+-T15 and Ag+-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate is further tested for surface hybridization. This is the first demonstration of using metallated DNA as a polymeric material for interfacing with nanoscale materials.Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg2+-T15 and Ag+-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate

  15. Fiber-Optic Chemical Sensors and Fiber-Optic Bio-Sensors

    Czech Academy of Sciences Publication Activity Database

    Pospíšilová, M.; Kuncová, Gabriela; Trögl, J.

    2015-01-01

    Roč. 15, č. 10 (2015), s. 25208-25259 ISSN 1424-8220 Institutional support: RVO:67985858 Keywords : fiber-optic sensor * chemical sensors * enzymatic sensor Subject RIV: JB - Sensors, Measurment, Regulation Impact factor: 2.033, year: 2015

  16. Rapid Identification of Seven Waterborne Exophiala Species by RCA DNA Padlock Probes.

    Science.gov (United States)

    Najafzadeh, M J; Vicente, V A; Feng, Peiying; Naseri, A; Sun, Jiufeng; Rezaei-Matehkolaei, A; de Hoog, G S

    2018-03-05

    The black yeast genus Exophiala includes numerous potential opportunistic species that potentially cause systematic and disseminated infections in immunocompetent individuals. Species causing systemic disease have ability to grow at 37-40 °C, while others consistently lack thermotolerance and are involved in diseases of cold-blooded, waterborne vertebrates and occasionally invertebrates. We explain a fast and sensitive assay for recognition and identification of waterborne Exophiala species without sequencing. The ITS rDNA region of seven Exophiala species (E. equina, E. salmonis, E. opportunistica, E. pisciphila, E. aquamarina, E. angulospora and E. castellanii) along with the close relative Veronaea botryosa was sequenced and aligned for the design of specific padlock probes for the detection of characteristic single-nucleotide polymorphisms. The assay demonstrated to successfully amplify DNA of target fungi, allowing detection at the species level. Amplification products were visualized on 1% agarose gels to confirm specificity of probe-template binding. Amounts of reagents were reduced to prevent the generation of false positive results. The simplicity, tenderness, robustness and low expenses provide padlock probe assay (RCA) a definite place as a very practical method among isothermal approaches for DNA diagnostics.

  17. Probing the DNA Structural Requirements for Facilitated Diffusion

    Science.gov (United States)

    2015-01-01

    DNA glycosylases perform a genome-wide search to locate damaged nucleotides among a great excess of undamaged nucleotides. Many glycosylases are capable of facilitated diffusion, whereby multiple sites along the DNA are sampled during a single binding encounter. Electrostatic interactions between positively charged amino acids and the negatively charged phosphate backbone are crucial for facilitated diffusion, but the extent to which diffusing proteins rely on the double-helical structure DNA is not known. Kinetic assays were used to probe the DNA searching mechanism of human alkyladenine DNA glycosylase (AAG) and to test the extent to which diffusion requires B-form duplex DNA. Although AAG excises εA lesions from single-stranded DNA, it is not processive on single-stranded DNA because dissociation is faster than N-glycosidic bond cleavage. However, the AAG complex with single-stranded DNA is sufficiently stable to allow for DNA annealing when a complementary strand is added. This observation provides evidence of nonspecific association of AAG with single-stranded DNA. Single-strand gaps, bubbles, and bent structures do not impede the search by AAG. Instead, these flexible or bent structures lead to the capture of a nearby site of damage that is more efficient than that of a continuous B-form duplex. The ability of AAG to negotiate these helix discontinuities is inconsistent with a sliding mode of diffusion but can be readily explained by a hopping mode that involves microscopic dissociation and reassociation. These experiments provide evidence of relatively long-range hops that allow a searching protein to navigate around DNA binding proteins that would serve as obstacles to a sliding protein. PMID:25495964

  18. Investigation of paternity establishing without the putative father using hypervariable DNA probes.

    Science.gov (United States)

    Yokoi, T; Odaira, T; Nata, M; Sagisaka, K

    1990-09-01

    Seven kinds of DNA probes which recognize hypervariable loci were applied for paternity test. The putative father was decreased and unavailable for the test. The two legitimate children and their mother (the deceased's wife) and the four illegitimate children and their mother (the deceased's kept mistress) were available for analysis. Paternity index of four illegitimate child was investigated. Allelic frequencies and their confidence intervals among unrelated Japanese individuals were previously reported from our laboratory, and co-dominant segregation of the polymorphism was confirmed in family studies. Cumulative paternity indices of four illegitimate children from 16 kinds of standard blood group markers were 165, 42, 0.09, and 36, respectively. On the other hand, cumulative paternity indices from 7 kinds of DNA probes are 2,363, 4,685, 57,678, and 54,994, respectively, which are 14, 113, 640, 864, and 1,509 times higher than that from standard blood group markers. The DNA analyses gave nearly conclusive evidence that the putative father was the biological father of the children. Especially, the paternity relation of the third illegitimate child could not be established without the DNA analyses. Accordingly, DNA polymorphism is considered to be informative enough for paternity test.

  19. Iodination as a probe for small regions of disrupted secondary structure in double-stranded DNA

    DEFF Research Database (Denmark)

    Jensen, Kaj Frank; Nes, Ingolf F.; Wells, Robert D.

    1976-01-01

    Conditions were established where the thallium-catalyzed iodination of random coil DNA proceeded 100–200 times faster than for native DNA. This reaction was explored as a probe for localized regions of disrupted base pairs in duplex DNA. A heteroduplex was constructed between DNA fragments produced...

  20. Fiber-Optic Chemical Sensors and Fiber-Optic Bio-Sensors

    Directory of Open Access Journals (Sweden)

    Marie Pospíšilová

    2015-09-01

    Full Text Available This review summarizes principles and current stage of development of fiber-optic chemical sensors (FOCS and biosensors (FOBS. Fiber optic sensor (FOS systems use the ability of optical fibers (OF to guide the light in the spectral range from ultraviolet (UV (180 nm up to middle infrared (IR (10 μm and modulation of guided light by the parameters of the surrounding environment of the OF core. The introduction of OF in the sensor systems has brought advantages such as measurement in flammable and explosive environments, immunity to electrical noises, miniaturization, geometrical flexibility, measurement of small sample volumes, remote sensing in inaccessible sites or harsh environments and multi-sensing. The review comprises briefly the theory of OF elaborated for sensors, techniques of fabrications and analytical results reached with fiber-optic chemical and biological sensors.

  1. A fiber-optic polarimetric demonstration kit

    International Nuclear Information System (INIS)

    Eftimov, T; Dimitrova, T L; Ivanov, G

    2012-01-01

    A simple and multifunctional fiber-optic polarimetric kit on the basis of highly birefringent single-mode fibers is presented. The fiber-optic polarimetric kit allows us to perform the following laboratory exercises: (i) fiber excitation and the measurement of numerical aperture, (ii) polarization preservation and (iii) obtain polarization-sensitive fiberized interferometers.

  2. Multi-Probe Based Artificial DNA Encoding and Matching Classifier for Hyperspectral Remote Sensing Imagery

    Directory of Open Access Journals (Sweden)

    Ke Wu

    2016-08-01

    Full Text Available In recent years, a novel matching classification strategy inspired by the artificial deoxyribonucleic acid (DNA technology has been proposed for hyperspectral remote sensing imagery. Such a method can describe brightness and shape information of a spectrum by encoding the spectral curve into a DNA strand, providing a more comprehensive way for spectral similarity comparison. However, it suffers from two problems: data volume is amplified when all of the bands participate in the encoding procedure and full-band comparison degrades the importance of bands carrying key information. In this paper, a new multi-probe based artificial DNA encoding and matching (MADEM method is proposed. In this method, spectral signatures are first transformed into DNA code words with a spectral feature encoding operation. After that, multiple probes for interesting classes are extracted to represent the specific fragments of DNA strands. During the course of spectral matching, the different probes are compared to obtain the similarity of different types of land covers. By computing the absolute vector distance (AVD between different probes of an unclassified spectrum and the typical DNA code words from the database, the class property of each pixel is set as the minimum distance class. The main benefit of this strategy is that the risk of redundant bands can be deeply reduced and critical spectral discrepancies can be enlarged. Two hyperspectral image datasets were tested. Comparing with the other classification methods, the overall accuracy can be improved from 1.22% to 10.09% and 1.19% to 15.87%, respectively. Furthermore, the kappa coefficient can be improved from 2.05% to 15.29% and 1.35% to 19.59%, respectively. This demonstrated that the proposed algorithm outperformed other traditional classification methods.

  3. Multiplex Ligation-Dependent Probe Amplification Technique for Copy Number Analysis on Small Amounts of DNA Material

    DEFF Research Database (Denmark)

    Sørensen, Karina; Andersen, Paal; Larsen, Lars

    2008-01-01

    The multiplex ligation-dependent probe amplification (MLPA) technique is a sensitive technique for relative quantification of up to 50 different nucleic acid sequences in a single reaction, and the technique is routinely used for copy number analysis in various syndromes and diseases. The aim...... of the study was to exploit the potential of MLPA when the DNA material is limited. The DNA concentration required in standard MLPA analysis is not attainable from dried blood spot samples (DBSS) often used in neonatal screening programs. A novel design of MLPA probes has been developed to permit for MLPA...... analysis on small amounts of DNA. Six patients with congenital adrenal hyperplasia (CAH) were used in this study. DNA was extracted from both whole blood and DBSS and subjected to MLPA analysis using normal and modified probes. Results were analyzed using GeneMarker and manual Excel analysis. A total...

  4. Rapid colorimetric assay for detection of Listeria monocytogenes in food samples using LAMP formation of DNA concatemers and gold nanoparticle-DNA probe complex

    Science.gov (United States)

    Wachiralurpan, Sirirat; Sriyapai, Thayat; Areekit, Supatra; Sriyapai, Pichapak; Augkarawaritsawong, Suphitcha; Santiwatanakul, Somchai; Chansiri, Kosum

    2018-04-01

    ABSTRACT Listeria monocytogenes is a major foodborne pathogen of global health concern. Herein, the rapid diagnosis of L. monocytogenes has been achieved using loop-mediated isothermal amplification (LAMP) based on the phosphatidylcholine-phospholipase C gene (plcB). Colorimetric detection was then performed through the formation of DNA concatemers and a gold nanoparticle/DNA probe complex (GNP/DNA probe). The overall detection process was accomplished within approximately 1 h with no need for complicated equipment. The limits of detection for L. monocytogenes in the forms of purified genomic DNA and pure culture were 800 fg and 2.82 CFU mL-1, respectively. No cross reactions were observed from closely related bacteria species. The LAMP-GNP/DNA probe assay was applied to the detection of 200 raw chicken meat samples and compared to routine standard methods. The data revealed that the specificity, sensitivity and accuracy were 100%, 90.20% and 97.50%, respectively. The present assay was 100% in conformity with LAMP-agarose gel electrophoresis assay. Five samples that were negative by both assays appeared to have the pathogen at below the level of detection. The assay can be applied as a rapid direct screening method for L. monocytogenes.

  5. Effect of structure variation of the aptamer-DNA duplex probe on the performance of displacement-based electrochemical aptamer sensors.

    Science.gov (United States)

    Pang, Jie; Zhang, Ziping; Jin, Haizhu

    2016-03-15

    Electrochemical aptamer-based (E-AB) sensors employing electrode-immobilized, redox-tagged aptamer probes have emerged as a promising platform for the sensitive and quick detection of target analytes ranging from small molecules to proteins. Signal generation in this class of sensor is linked to change in electron transfer efficiency upon binding-induced change in flexibility/conformation of the aptamer probe. Because of this signaling mechanism, signal gains of these sensors can be improved by employing a displacement-based recognition system, which links target binding with a large-scale flexibility/conformation shift from the aptamer-DNA duplex to the single-stranded DNA or the native aptamer. Despite the relatively large number of displacement-based E-AB sensor samples, little attention has been paid to the structure variation of the aptamer-DNA duplex probe. Here we detail the effects of complementary length and position of the aptamer-DNA duplex probe on the performance of a model displacement-based E-AB sensor for ATP. We find that, greater background suppression and signal gain are observed with longer complementary length of the aptamer-DNA duplex probe. However, sensor equilibration time slows monotonically with increasing complementary length; and with too many target binding sites in aptamer sequence being occupied by the complementary DNA, the aptamer-target binding does not occur and no signal gain observed. We also demonstrate that signal gain of the displacement-based E-AB sensor is strongly dependent on the complementary position of the aptamer-DNA duplex probe, with complementary position located at the electrode-attached or redox-tagged end of the duplex probe, larger background suppression and signal increase than that of the middle position are observed. These results highlight the importance of rational structure design of the aptamer-DNA duplex probe and provide new insights into the optimization of displacement-based E-AB sensors. Copyright

  6. DNA polymorphisms in the Sahiwal breed of Zebu cattle revealed by synthetic oligonucleotide probes

    International Nuclear Information System (INIS)

    Shashikanth; Yadav, B.R.

    2005-01-01

    Genomic DNA of 15 randomly selected unrelated animals and from two sire families (11 animals) of the Sahiwal breed of Zebu cattle were investigated. Four oligonucleotide probes - (GTG) 5 , (TCC) 5 , (GT) 8 and (GT) 12 - were used on genomic DNA digested with restriction enzymes AluI, HinfI, MboI, EcoRI and HaeIII in different combinations. All four probes produced multiloci fingerprints with differing levels of polymorphisms. Total bands and shared bands in the fingerprints of each individual were in the range of 2.5 to 23.0 KB. Band number ranged from 9 to 17, with 0.48 average band sharing. Probes (GT) 8 , (GT) 12 and (TCC) 5 produced fingerprinting patterns of medium to low polymorphism, whereas probe (GTG) 5 produced highly polymorphic patterns. Probe (GTG) 5 in combination with the HaeIII enzyme was highly polymorphic with a heterozygosity level of 0.85, followed by (GT) 8 , (TCC) 5 and (GT) 12 with heterozygosity levels of 0.70, 0.65 and 0.30, respectively. Probe GTG 5 or its complementary sequence CAC 5 produced highly polymorphic fingerprints, indicating that the probe can be used for analysing population structure, parentage verification and identifying loci controlling quantitative traits and fertility status. (author)

  7. A sensitive DNA biosensor based on a facile sulfamide coupling reaction for capture probe immobilization

    International Nuclear Information System (INIS)

    Wang, Qingxiang; Ding, Yingtao; Gao, Feng; Jiang, Shulian; Zhang, Bin; Ni, Jiancong; Gao, Fei

    2013-01-01

    Graphical abstract: A novel DNA biosensor was fabricated through a facile sulfamide coupling reaction between probe DNA and the sulfonic dye of 1-amino-2-naphthol-4-sulfonic acid that electrodeposited on a glassy carbon electrode. -- Highlights: •A versatile sulfonic dye of ANS was electrodeposited on a GCE. •A DNA biosensor was fabricated based on a facile sulfamide coupling reaction. •High probe DNA density of 3.18 × 10 13 strands cm −2 was determined. •A wide linear range and a low detection limit were obtained. -- Abstract: A novel DNA biosensor was fabricated through a facile sulfamide coupling reaction. First, the versatile sulfonic dye molecule of 1-amino-2-naphthol-4-sulfonate (AN-SO 3 − ) was electrodeposited on the surface of a glassy carbon electrode (GCE) to form a steady and ordered AN-SO 3 − layer. Then the amino-terminated capture probe was covalently grafted to the surface of SO 3 − -AN deposited GCE through the sulfamide coupling reaction between the amino groups in the probe DNA and the sulfonic groups in the AN-SO 3 − . The step-by-step modification process was characterized by electrochemistry and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Using Ru(NH 3 ) 6 3+ as probe, the probe density and the hybridization efficiency of the biosensor were determined to be 3.18 × 10 13 strands cm −2 and 86.5%, respectively. The hybridization performance of the biosensor was examined by differential pulse voltammetry using Co(phen) 3 3+/2+ (phen = 1,10-phenanthroline) as the indicator. The selectivity experiments showed that the biosensor presented distinguishable response after hybridization with the three-base mismatched, non-complementary and complementary sequences. Under the optimal conditions, the oxidation peak currents of Co(phen) 3 3+/2+ increased linearly with the logarithm values of the concentration of the complementary sequences in the range from 1.0 × 10 −13 M to 1.0 × 10 −8 M with

  8. A family of fiber-optic based pressure sensors for intracochlear measurements

    Science.gov (United States)

    Olson, Elizabeth S.; Nakajima, Hideko H.

    2015-02-01

    Fiber-optic pressure sensors have been developed for measurements of intracochlear pressure. The present family of transducers includes an 81 μm diameter sensor employing a SLED light source and single-mode optic fiber, and LED/multi-mode sensors with 126 and 202 μm diameter. The 126 μm diameter pressure sensor also has been constructed with an electrode adhered to its side, for coincident pressure and voltage measurements. These sensors have been used for quantifying cochlear mechanical impedances, informing our understanding of conductive hearing loss and its remediation, and probing the operation of the cochlear amplifier.

  9. Common-path low-coherence interferometry fiber-optic sensor guided microincision

    Science.gov (United States)

    Zhang, Kang; Kang, Jin U.

    2011-09-01

    We propose and demonstrate a common-path low-coherence interferometry (CP-LCI) fiber-optic sensor guided precise microincision. The method tracks the target surface and compensates the tool-to-surface relative motion with better than +/-5 μm resolution using a precision micromotor connected to the tool tip. A single-fiber distance probe integrated microdissector was used to perform an accurate 100 μm incision into the surface of an Intralipid phantom. The CP-LCI guided incision quality in terms of depth was evaluated afterwards using three-dimensional Fourier-domain optical coherence tomography imaging, which showed significant improvement of incision accuracy compared to free-hand-only operations.

  10. Detection of supercoiled hepatitis B virus DNA and related forms by means of molecular hybridization to an oligonucleotide probe

    International Nuclear Information System (INIS)

    Lin, H.J.; Chung, H.T.; Lai, C.L.; Leong, S.; Tam, O.S.

    1989-01-01

    A novel assay for supercoiled and other fully double-stranded forms of hepatitis B virus (HBV) DNA in blood is presented that utilizes molecular hybridisation to a radiophosphorous-labeled oligonucleotide probe. The probe [5'-d(ACGTGCAGAGGTGAAGCGA)] is complementary to the S(+)-strand sequence furthest downstream, at the end of the gap. We examined blood specimens from 137 healthy HBsAg-positive individuals, applying the probe to dots representing 2-3.5 ml serum or plasma. We found that supercoiled HBV is present in many HBV DNA-positive blood specimens albeit in small quantities. Of the 104 specimens that were positive for HBV DNA of any form, 53 annealed to the probe. Serial specimens from the same subject taken over a period of months showed that the proportion of supercoil to other HBV DNA forms was variable. The presence of supercoil HBV DNA was not closely correlated with the level of serum HBV DNA polymerase. The supercoil is an HBV DNA form that can persist in the liver in the presence or absence of other replicative intermediates. This assay may enable further characterization of the status of HBV infection

  11. Detection of DNA fingerprints of cultivated rice by hybridization with a human minisatellite DNA probe

    International Nuclear Information System (INIS)

    Dallas, J.F.

    1988-01-01

    A human minisatellite DNA probe detects several restriction fragment length polymorphisms in cultivars of Asian and African rice. Certain fragments appear to be inherited in a Mendelian fashion and may represent unlinked loci. The hybridization patterns appear to be cultivar-specific and largely unchanged after the regeneration of plants from tissue culture. The results suggest that these regions of the rice genome may be used to generate cultivar-specific DNA fingerprints. The demonstration of similarity between a human minisatellite sequence and polymorphic regions in the rice genome suggests that such regions also occur in the genomes of many other plant species

  12. Distributed Fiber-Optic Sensors for Vibration Detection.

    Science.gov (United States)

    Liu, Xin; Jin, Baoquan; Bai, Qing; Wang, Yu; Wang, Dong; Wang, Yuncai

    2016-07-26

    Distributed fiber-optic vibration sensors receive extensive investigation and play a significant role in the sensor panorama. Optical parameters such as light intensity, phase, polarization state, or light frequency will change when external vibration is applied on the sensing fiber. In this paper, various technologies of distributed fiber-optic vibration sensing are reviewed, from interferometric sensing technology, such as Sagnac, Mach-Zehnder, and Michelson, to backscattering-based sensing technology, such as phase-sensitive optical time domain reflectometer, polarization-optical time domain reflectometer, optical frequency domain reflectometer, as well as some combinations of interferometric and backscattering-based techniques. Their operation principles are presented and recent research efforts are also included. Finally, the applications of distributed fiber-optic vibration sensors are summarized, which mainly include structural health monitoring and perimeter security, etc. Overall, distributed fiber-optic vibration sensors possess the advantages of large-scale monitoring, good concealment, excellent flexibility, and immunity to electromagnetic interference, and thus show considerable potential for a variety of practical applications.

  13. Photoenzyme probes of photodamage to cells and cellular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, B. M.

    1979-01-01

    Development of photoenzyme probes for detection of ultraviolet damage to cells and DNA is reviewed with special emphasis on a process using polyethylene glycol to induce cell fusion. Polyethylene glycol is easy to obtain and handle, is gentle to the cells and does not induce latent or productive virus infection; therefore, it may be a general method for insertion of exogenous enzymes into mammalian cells. (PCS)

  14. Fiber-Optic Surface Temperature Sensor Based on Modal Interference

    Directory of Open Access Journals (Sweden)

    Frédéric Musin

    2016-07-01

    Full Text Available Spatially-integrated surface temperature sensing is highly useful when it comes to controlling processes, detecting hazardous conditions or monitoring the health and safety of equipment and people. Fiber-optic sensing based on modal interference has shown great sensitivity to temperature variation, by means of cost-effective image-processing of few-mode interference patterns. New developments in the field of sensor configuration, as described in this paper, include an innovative cooling and heating phase discrimination functionality and more precise measurements, based entirely on the image processing of interference patterns. The proposed technique was applied to the measurement of the integrated surface temperature of a hollow cylinder and compared with a conventional measurement system, consisting of an infrared camera and precision temperature probe. As a result, the optical technique is in line with the reference system. Compared with conventional surface temperature probes, the optical technique has the following advantages: low heat capacity temperature measurement errors, easier spatial deployment, and replacement of multiple angle infrared camera shooting and the continuous monitoring of surfaces that are not visually accessible.

  15. Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

    Science.gov (United States)

    Munir, Ahsan; Waseem, Hassan; Williams, Maggie R.; Stedtfeld, Robert D.; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A.

    2017-01-01

    Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131). PMID:28555058

  16. Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

    Directory of Open Access Journals (Sweden)

    Ahsan Munir

    2017-05-01

    Full Text Available Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs. Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131.

  17. Fiber-Optic Sensor Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Constructs and evaluates fiber-optic sensors for a variety of measurands. These measurands include acoustic, pressure, magnetic, and electric field as well...

  18. A specific DNA probe which identifies Babesia bovis in whole blood.

    Science.gov (United States)

    Petchpoo, W; Tan-ariya, P; Boonsaeng, V; Brockelman, C R; Wilairat, P; Panyim, S

    1992-05-01

    A genomic library of Babesia bovis DNA from the Mexican strain M was constructed in plasmid pUN121 and cloned in Escherichia coli. Several recombinants which hybridized strongly to radioactively labeled B. bovis genomic DNA in an in situ screening were selected and further analyzed for those which specifically hybridized to B. bovis DNA. It was found that pMU-B1 had the highest sensitivity, detecting 25 pg of purified B. bovis DNA, and 300 parasites in 10 microliters of whole infected blood, or 0.00025% parasitemia. pMU-B1 contained a 6.0 kb B. bovis DNA insert which did not cross-hybridize to Babesia bigemina, Trypanosoma evansi, Plasmodium falciparum, Anaplasma marginale, Boophilus microplus and cow DNA. In the Southern blot analysis of genomic DNA, pMU-B1 could differentiate between two B. bovis geographic isolates, Mexican strain M and Thai isolate TS4. Thus, the pMU-B1 probe will be useful in the diagnosis of Babesia infection in cattle and ticks, and in the differentiation of B. bovis strains.

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

    Science.gov (United States)

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

    1994-01-01

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

  20. [A new class of exciplex-formed probe detect of specific sequence DNA].

    Science.gov (United States)

    Li, Qing-Yong; Zu, Yuan-Gang; Lü, Hong-Yan; Wang, Li-Min

    2009-07-01

    The present research was to develop the exciplex-based fluorescence detection of DNA. A SNP-containing region of cytochrome P450 2C9 DNA systems was evaluated to define some of the structural and associated requirement of this new class of exciplex-formed probe, and a 24-base target was selected which contains single-nucleotide polymorphisms (SNP) in genes coding for cytochrome P450. The two probes were all 12-base to give coverage of a 24-base target region to ensure specificity within the human genome. Exciplex partners used in this study were prepared using analogous phosphoramide attachment to the 3'- or 5'-phosphate group of the appropriate oligonucleotide probes. The target effectively assembled its own detector by hybridization from components which were non-fluorescent at the detection wavelength, leading to the huge improvement in terms of decreased background. This research provides details of the effects of different partner, position of partners and different excitation wavelengths for the split-oligonucleotide probe system for exciplex-based fluorescence detection of DNA. This study demonstrates that the emission intensity of the excimer formed by new pyrene derivative is the highest in these excimer and exciplex, and the excimer is easy to be formed and not sensitive to the position of partners. However the exciplex formed by the new pyrene derivative and naphthalene emitted strongly at -505 nm with large Stokes shifts (120-130 nm), and the monomer emission at 390 and 410 nm is nearly zero. Excitation wavelength of 400 nm is the best for I(e505)/I(m410) (exciplex emission at 505 nm/monomer emission at 410 nm) of the exciplex. This method features lower background and high sensitivity. Moreover the exciplex is sensitive to the steric factor, different position of partners and microenvironment, so this exciplex system is promising and could be tried to identify the SNP genes.

  1. Multiplexed fluorescent microarray for human salivary protein analysis using polymer microspheres and fiber-optic bundles.

    Science.gov (United States)

    Nie, Shuai; Benito-Peña, Elena; Zhang, Huaibin; Wu, Yue; Walt, David R

    2013-10-10

    Herein, we describe a protocol for simultaneously measuring six proteins in saliva using a fiber-optic microsphere-based antibody array. The immuno-array technology employed combines the advantages of microsphere-based suspension array fabrication with the use of fluorescence microscopy. As described in the video protocol, commercially available 4.5 μm polymer microspheres were encoded into seven different types, differentiated by the concentration of two fluorescent dyes physically trapped inside the microspheres. The encoded microspheres containing surface carboxyl groups were modified with monoclonal capture antibodies through EDC/NHS coupling chemistry. To assemble the protein microarray, the different types of encoded and functionalized microspheres were mixed and randomly deposited in 4.5 μm microwells, which were chemically etched at the proximal end of a fiber-optic bundle. The fiber-optic bundle was used as both a carrier and for imaging the microspheres. Once assembled, the microarray was used to capture proteins in the saliva supernatant collected from the clinic. The detection was based on a sandwich immunoassay using a mixture of biotinylated detection antibodies for different analytes with a streptavidin-conjugated fluorescent probe, R-phycoerythrin. The microarray was imaged by fluorescence microscopy in three different channels, two for microsphere registration and one for the assay signal. The fluorescence micrographs were then decoded and analyzed using a homemade algorithm in MATLAB.

  2. Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY® FL-labeled probe or primer

    Science.gov (United States)

    Kurata, Shinya; Kanagawa, Takahiro; Yamada, Kazutaka; Torimura, Masaki; Yokomaku, Toyokazu; Kamagata, Yoichi; Kurane, Ryuichiro

    2001-01-01

    We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY® FL fluorescence was quenched by its interaction with a uniquely positioned guanine. This approach makes use of an oligonucleotide probe or primer containing a BODIPY® FL-modified cytosine at its 5′-end. When such a probe was hybridized with a target DNA, its fluorescence was quenched by the guanine in the target, complementary to the modified cytosine, and the quench rate was proportional to the amount of target DNA. This widely applicable technique will be used directly with larger samples or in conjunction with the polymerase chain reaction to quantify small DNA samples. PMID:11239011

  3. Fiber-optic dosimeters for radiation therapy

    Science.gov (United States)

    Li, Enbang; Archer, James

    2017-10-01

    According to the figures provided by the World Health Organization, cancer is a leading cause of death worldwide, accounting for 8.8 million deaths in 2015. Radiation therapy, which uses x-rays to destroy or injure cancer cells, has become one of the most important modalities to treat the primary cancer or advanced cancer. The newly developed microbeam radiation therapy (MRT), which uses highly collimated, quasi-parallel arrays of x-ray microbeams (typically 50 μm wide and separated by 400 μm) produced by synchrotron sources, represents a new paradigm in radiotherapy and has shown great promise in pre-clinical studies on different animal models. Measurements of the absorbed dose distribution of microbeams are vitally important for clinical acceptance of MRT and for developing quality assurance systems for MRT, hence are a challenging and important task for radiation dosimetry. On the other hand, during the traditional LINAC based radiotherapy and breast cancer brachytherapy, skin dose measurements and treatment planning also require a high spatial resolution, tissue equivalent, on-line dosimeter that is both economical and highly reliable. Such a dosimeter currently does not exist and remains a challenge in the development of radiation dosimetry. High resolution, water equivalent, optical and passive x-ray dosimeters have been developed and constructed by using plastic scintillators and optical fibers. The dosimeters have peak edge-on spatial resolutions ranging from 50 to 500 microns in one dimension, with a 10 micron resolution dosimeter under development. The developed fiber-optic dosimeters have been test with both LINAC and synchrotron x-ray beams. This work demonstrates that water-equivalent and high spatial resolution radiation detection can be achieved with scintillators and optical fiber systems. Among other advantages, the developed fiber-optic probes are also passive, energy independent, and radiation hard.

  4. Distributed fiber?optic temperature sensing for hydrologic systems

    NARCIS (Netherlands)

    Selker, J.S.; Thévenaz, L.; Huwald, H.; Mallet, A.; Luxemburg, W.M.J.; Van de Giesen, N.; Stejskal, M.; Zeman, J.; Westhoff, M.; Parlange, M.B.

    2006-01-01

    Instruments for distributed fiber-optic measurement of temperature are now available with temperature resolution of 0.01°C and spatial resolution of 1 m with temporal resolution of fractions of a minute along standard fiber-optic cables used for communication with lengths of up to 30,000 m. We

  5. Distributed fiber-optic temperature sensing for hydrologic systems

    NARCIS (Netherlands)

    Selker, John S.; Thévenaz, Luc; Huwald, Hendrik; Mallet, Alfred; Luxemburg, Wim; van de Giesen, Nick C.; Stejskal, Martin; Zeman, Josef; Westhoff, Martijn; Parlange, Marc B.

    2006-01-01

    Instruments for distributed fiber-optic measurement of temperature are now available with temperature resolution of 0.01°C and spatial resolution of 1 m with temporal resolution of fractions of a minute along standard fiber-optic cables used for communication with lengths of up to 30,000 m. We

  6. Direct fluorescence in situ hybridization on human metaphase chromosomes using quantum dot-platinum labeled DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Gyoyeon [Chemical Kinomics Research Center, Future Convergence Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Biological Chemistry, Korea University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Deajeon (Korea, Republic of); Lee, Hansol [Chemical Kinomics Research Center, Future Convergence Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Lee, Jiyeon, E-mail: jylee@kist.re.kr [Chemical Kinomics Research Center, Future Convergence Research Division, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Biological Chemistry, Korea University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Deajeon (Korea, Republic of)

    2015-11-13

    The telomere shortening in chromosomes implies the senescence, apoptosis, or oncogenic transformation of cells. Since detecting telomeres in aging and diseases like cancer, is important, the direct detection of telomeres has been a very useful biomarker. We propose a telomere detection method using a newly synthesized quantum dot (QD) based probe with oligonucleotide conjugation and direct fluorescence in situ hybridization (FISH). QD-oligonucleotides were prepared with metal coordination bonding based on platinum-guanine binding reported in our previous work. The QD-oligonucleotide conjugation method has an advantage where any sequence containing guanine at the end can be easily bound to the starting QD-Pt conjugate. A synthesized telomeric oligonucleotide was bound to the QD-Pt conjugate successfully and this probe hybridized specifically on the telomere of fabricated MV-4-11 and MOLT-4 chromosomes. Additionally, the QD-telomeric oligonucleotide probe successfully detected the telomeres on the CGH metaphase slide. Due to the excellent photostability and high quantum yield of QDs, the QD-oligonucleotide probe has high fluorescence intensity when compared to the organic dye-oligonucleotide probe. Our QD-oligonucleotide probe, conjugation method of this QD probe, and hybridization protocol with the chromosomes can be a useful tool for chromosome painting and FISH. - Highlights: • We prepared a probe linked between QD and telomeric oligonucleotide with platinum-guanine bonding. • Telomeres were detected by our new telomere probes successfully in three different human metaphase chromosomes. • QDPt-DNA probe has high fluorescence intensity in comparison with organic dye-DNA probe.

  7. A Noninvasive Miniaturized-Wireless Laser-Doppler Fiber-Optic Sensor for Understanding Distal Fingertip Injuries in Astronauts

    Science.gov (United States)

    Ansari, Rafat R.; Jones, Jeffrey A.; Pollonini, Luca; Rodriquez, Mikael; Opperman, Roedolph; Hochstein, Jason

    2009-01-01

    During extra-vehicular activities (EVAs) or spacewalks astronauts over use their fingertips under pressure inside the confined spaces of gloves/space suits. The repetitive hand motion is a probable cause for discomfort and injuries to the fingertips. We describe a new wireless fiber-optic probe that can be integrated inside the astronaut glove for noninvasive blood perfusion measurements in distal fingertips. In this preliminary study, we present blood perfusion measurements while performing hand-grip exercises simulating the use of space tools.

  8. Frequency-Shifted Interferometry — A Versatile Fiber-Optic Sensing Technique

    Directory of Open Access Journals (Sweden)

    Fei Ye

    2014-06-01

    Full Text Available Fiber-optic sensing is a field that is developing at a fast pace. Novel fiber-optic sensor designs and sensing principles constantly open doors for new opportunities. In this paper, we review a fiber-optic sensing technique developed in our research group called frequency-shifted interferometry (FSI. This technique uses a continuous-wave light source, an optical frequency shifter, and a slow detector. We discuss the operation principles of several FSI implementations and show their applications in fiber length and dispersion measurement, locating weak reflections along a fiber link, fiber-optic sensor multiplexing, and high-sensitivity cavity ring-down measurement. Detailed analysis of FSI system parameters is also presented.

  9. Fetal sex determination in the first trimester of pregnancy using a Y chromosome-specific DNA probe

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Y.; Huang, S.; Chen, M.; Huang, Y.; Zhang, M.; Dong, J.; Ku, A.; Xu, S.

    1987-05-01

    Prenatal determination of fetal sex is important for the prevention of X-linked disorders such as hemophilia, Lesch-Nyhan syndrome and Duchenne muscular dystrophy. The complex procedures of prenatal diagnosis for X-linked disorders are unnecessary if the fetus is female, because usually no clinical symptoms ever appear in female. pY 3.4 probe used in this work for sex determination is a 3.4 kilobase human repeat sequence. The probe is specific for the Y chromosome of males and can be used for sex determination. The other prove pBLUR used in this paper as control is a widely dispersed, highly repeated human Alu family DNA sequence, represented equally in male and female DNA. On the basis of the relative densities of the autoradiographic spots produced by hybridization of fetal DNA with pY3.4 and pBLUR, the sex of fetus can be clearly identified. Further the authors can determine the radioactive intensity (cpm) of the hybridized DNA spots and the ratio of hybridization with Y3.4 to pBLUR (Y3.4/pBLUR x 10). Results show that the hybridization ratio of DNA from chorionic villi of male (1.03 +/- 0.24) is significantly higher than that of female (0.16 +/- 0.09). Therefore, sex determination of the fetus can be made, based on the ratio of pY3.4/pBLUR x 10. If necessary they can also use Southern hybridization with pY 3.4 probe of DNA isolated from chorionic villi to confirm the result of dot hybridization.

  10. Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

    Directory of Open Access Journals (Sweden)

    Townsend Henrik J

    2005-11-01

    Full Text Available Abstract High-density oligonucleotide (oligo arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L. Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ and may be used to facilitate transcriptomic analyses of a wide range of plant and animal

  11. Scanning Probe Optical Tweezers: a new tool to study DNA-protein interactions

    NARCIS (Netherlands)

    Huisstede, J.H.G.

    2006-01-01

    The main goal of the work described in this thesis is to construct a microscope in which OT and scanning probe microscopy (SPM) are combined, to be able to localize proteins while simultaneously controlling the tension within the DNA molecule. This apparatus enables the study of the effect of

  12. Water-equivalent one-dimensional scintillating fiber-optic dosimeter for measuring therapeutic photon beam

    International Nuclear Information System (INIS)

    Moon, Jinsoo; Won Jang, Kyoung; Jae Yoo, Wook; Han, Ki-Tek; Park, Jang-Yeon; Lee, Bongsoo

    2012-01-01

    In this study, we fabricated a one-dimensional scintillating fiber-optic dosimeter, which consists of 9 scintillating fiber-optic dosimeters, septa, and PMMA blocks for measuring surface and percentage depth doses of a therapeutic photon beam. Each dosimeter embedded in the 1-D scintillating fiber-optic dosimeter is composed of square type organic scintillators and plastic optical fibers. Also black PVC films are used as septa to minimize cross-talk between the scintillating fiber-optic dosimeters. To construct a dosimeter system, a 1-D scintillating fiber-optic dosimeter and a CMOS image sensor were combined with 20 m-length plastic optical fibers. Using the dosimeter system, we measured surface and percentage depth doses of 6 and 15 MV photon beams and compared the results with those of EBT films and an ionization chamber. - Highlights: ► Fabrication of a one-dimensional scintillating fiber-optic dosimeter. ► The one-dimensional scintillating fiber-optic dosimeter has 9 scintillating fiber-optic dosimeters. ► Measurements of surface and percentage depth doses of a therapeutic photon beam. ► The results were compared with those of EBT films and an ionization chamber.

  13. Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA using boric acid-functionalized nano-microsphere fluorescent probes.

    Science.gov (United States)

    Chen, Hua-Yan; Wei, Jing-Ru; Pan, Jiong-Xiu; Zhang, Wei; Dang, Fu-Quan; Zhang, Zhi-Qi; Zhang, Jing

    2017-05-15

    5-hydroxymethylcytosine (5hmC) is the sixth base of DNA. It is involved in active DNA demethylation and can be a marker of diseases such as cancer. In this study, we developed a simple and sensitive 2-(4-boronophenyl)quinoline-4-carboxylic acid modified poly (glycidyl methacrylate (PBAQA-PGMA) fluorescent probe to detect the 5hmC content of genomic DNA based on T4 β-glucosyltransferase-catalyzed glucosylation of 5hmC. The fluorescence-enhanced intensity recorded from the DNA sample was proportional to its 5-hydroxymethylcytosine content and could be quantified by fluorescence spectrophotometry. The developed probe showed good detection sensitivity and selectivity and a good linear relationship between the fluorescence intensity and the concentration of 5 hmC within a 0-100nM range. Compared with other fluorescence detection methods, this method not only could determine trace amounts of 5 hmC from genomic DNA but also could eliminate the interference of fluorescent dyes and the need for purification. It also could avoid multiple labeling. Because the PBAQA-PGMA probe could enrich the content of glycosyl-5-hydroxymethyl-2-deoxycytidine from a complex ground substance, it will broaden the linear detection range and improve sensitivity. The limit of detection was calculated to be 0.167nM after enrichment. Furthermore, the method was successfully used to detect 5-hydroxymethylcytosine from mouse tissues. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Fiber-optic combined FPI/FBG sensors for monitoring of radiofrequency thermal ablation of liver tumors: ex vivo experiments.

    Science.gov (United States)

    Tosi, Daniele; Macchi, Edoardo Gino; Braschi, Giovanni; Cigada, Alfredo; Gallati, Mario; Rossi, Sandro; Poeggel, Sven; Leen, Gabriel; Lewis, Elfed

    2014-04-01

    We present a biocompatible, all-glass, 0.2 mm diameter, fiber-optic probe that combines an extrinsic Fabry-Perot interferometry and a proximal fiber Bragg grating sensor; the probe enables dual pressure and temperature measurement on an active 4 mm length, with 40 Pa and 0.2°C nominal accuracy. The sensing system has been applied to monitor online the radiofrequency thermal ablation of tumors in liver tissue. Preliminary experiments have been performed in a reference chamber with uniform heating; further experiments have been carried out on ex vivo porcine liver, which allowed the measurement of a steep temperature gradient and monitoring of the local pressure increase during the ablation procedure.

  15. Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis

    Directory of Open Access Journals (Sweden)

    Stougaard Magnus

    2007-11-01

    Full Text Available Abstract Background In situ detection of short sequence elements in genomic DNA requires short probes with high molecular resolution and powerful specific signal amplification. Padlock probes can differentiate single base variations. Ligated padlock probes can be amplified in situ by rolling circle DNA synthesis and detected by fluorescence microscopy, thus enhancing PRINS type reactions, where localized DNA synthesis reports on the position of hybridization targets, to potentially reveal the binding of single oligonucleotide-size probe molecules. Such a system has been presented for the detection of mitochondrial DNA in fixed cells, whereas attempts to apply rolling circle detection to metaphase chromosomes have previously failed, according to the literature. Methods Synchronized cultured cells were fixed with methanol/acetic acid to prepare chromosome spreads in teflon-coated diagnostic well-slides. Apart from the slide format and the chromosome spreading everything was done essentially according to standard protocols. Hybridization targets were detected in situ with padlock probes, which were ligated and amplified using target primed rolling circle DNA synthesis, and detected by fluorescence labeling. Results An optimized protocol for the spreading of condensed metaphase chromosomes in teflon-coated diagnostic well-slides was developed. Applying this protocol we generated specimens for target primed rolling circle DNA synthesis of padlock probes recognizing a 40 nucleotide sequence in the male specific repetitive satellite I sequence (DYZ1 on the Y-chromosome and a 32 nucleotide sequence in the repetitive kringle IV domain in the apolipoprotein(a gene positioned on the long arm of chromosome 6. These targets were detected with good efficiency, but the efficiency on other target sites was unsatisfactory. Conclusion Our aim was to test the applicability of the method used on mitochondrial DNA to the analysis of nuclear genomes, in particular as

  16. Identification of salivary Lactobacillus rhamnosus species by DNA profiling and a specific probe.

    Science.gov (United States)

    Richard, B; Groisillier, A; Badet, C; Dorignac, G; Lonvaud-Funel, A

    2001-03-01

    The Lactobacillus genus has been shown to be associated with the dental carious process, but little is known about the species related to the decay, although Lactobacillus rhamnosus is suspected to be the most implicated species. Conventional identification methods based on biochemical criteria lead to ambiguous results, since the Lactobacillus species found in saliva are phenotypically close. To clarify the role of this genus in the evolution of carious disease, this work aimed to find a rapid and reliable method for identifying the L. rhamnosus species. Methods based on hybridization with DNA probes and DNA amplification by PCR were used. The dominant salivary Lactobacillus species (reference strains from the ATCC) were selected for this purpose as well as some wild strains isolated from children's saliva. DNA profiling using semirandom polymorphic DNA amplification (semi-RAPD) generated specific patterns for L. rhamnosus ATCC 7469. The profiles of all L. rhamnosus strains tested were similar and could be grouped; these strains shared four common fragments. Wild strains first identified with classic methods shared common patterns with the L. rhamnosus species and could be reclassified. One fragment of the profile was purified, cloned, used as a probe and found to be specific to the L. rhamnosus species. These results may help to localize this species within its ecological niche and to elucidate the progression of the carious process.

  17. DNA-based stable isotope probing: a link between community structure and function

    Czech Academy of Sciences Publication Activity Database

    Uhlík, Ondřej; Ječná, K.; Leigh, M. B.; Macková, Martina; Macek, Tomáš

    2009-01-01

    Roč. 407, č. 12 (2009), s. 3611-3619 ISSN 0048-9697 Grant - others:GA MŠk(CZ) 2B08031 Program:2B Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA-based stable isotope probing * microbial diversity * bioremediation Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.905, year: 2009

  18. Luminescent platinum(II) complexes with functionalized N-heterocyclic carbene or diphosphine selectively probe mismatched and abasic DNA

    OpenAIRE

    Che, CM; Chen, T; To, WP; Zou, T; FUNG, SK; Lok, CN; YANG, C; Cao, B

    2016-01-01

    The selective targeting of mismatched DNA overexpressed in cancer cells is an appealing strategy in designing cancer diagnosis and therapy protocols. Few luminescent probes that specifically detect intracellular mismatched DNA have been reported. Here we used Pt(II) complexes with luminescence sensitive to subtle changes in the local environment and report several Pt(II) complexes that selectively bind to and identify DNA mismatches. We evaluated the complexes' DNA-binding characteristics by ...

  19. Fiber-optic dipping liquid analyzer: theoretical and experimental study of light transmission

    International Nuclear Information System (INIS)

    Zhou Ai; Liu Zhihai; Yuan Libo

    2009-01-01

    A fiber-optic dipping liquid analyzer (FDLA) is developed for measuring liquid properties such as concentration, refractive index, surface tension, and viscosity. An important feature of the FDLA is that a liquid drop is introduced on the end face of a fiber probe, and the drop can be regarded as a planar-convex lens. The light transmitting path and receiving power are affected by the refractive index of the liquid drop. We present a theoretical and experimental analysis of the light transmission. A mathematical model of receiving power is established based on paraxial refraction imaging and fiber reflective intensity modulation methods. Sucrose-water solutions were tested with the FDLA. The experimental results agree well with the theoretical analysis.

  20. Ultrasensitive FRET-based DNA sensor using PNA/DNA hybridization.

    Science.gov (United States)

    Yang, Lan-Hee; Ahn, Dong June; Koo, Eunhae

    2016-12-01

    In the diagnosis of genetic diseases, rapid and highly sensitive DNA detection is crucial. Therefore, many strategies for detecting target DNA have been developed, including electrical, optical, and mechanical methods. Herein, a highly sensitive FRET based sensor was developed by using PNA (Peptide Nucleic Acid) probe and QD, in which red color QDs are hybridized with capture probes, reporter probes and target DNAs by EDC-NHS coupling. The hybridized probe with target DNA gives off fluorescent signal due to the energy transfer from QD to Cy5 dye in the reporter probe. Compared to the conventional DNA sensor using DNA probes, the DNA sensor using PNA probes shows higher FRET factor and efficiency due to the higher reactivity between PNA and target DNA. In addition, to elicit the effect of the distance between the donor and the acceptor, we have investigated two types of the reporter probes having Cy5 dyes attached at the different positions of the reporter probes. Results show that the shorter the distance between QDs and Cy5s, the stronger the signal intensity. Furthermore, based on the fluorescence microscopy images using microcapillary chips, the FRET signal is enhanced to be up to 276% times stronger than the signal obtained using the cuvette by the fluorescence spectrometer. These results suggest that the PNA probe system conjugated with QDs can be used as ultrasensitive DNA nanosensors. Copyright © 2016. Published by Elsevier B.V.

  1. Development and Validation of A Spectrofluorimetric Determination of Calf Thymus DNA Using a Terbium-Danofloxacin Probe

    Directory of Open Access Journals (Sweden)

    Naser Soltani

    2016-03-01

    Full Text Available Background: Analysis of biomolecules is required in many biomedical research areas. A spectrofluorimetric method is proposed for determination of calf thymus DNA (ctDNA based on the fluorescence enhancement of terbium-danofloxacin (Tb3+-Dano in the presence of ctDNA. Methods: A probe with maximum excitation and emission wavelengths of 347 nm and 545 nm, respectively, was developed. The enhanced fluorescence intensity of Tb3+-Dano system was proportional to the concentration of ctDNA. The effective factors and the optimum conditions for the determination of ctDNA were studied. Under the optimum conditions of [Tris buffer]= 0.01 mol L-1 (pH 7.8, [ Tb3+]= 1×10-5 mol L-1 and [Dano]= 5×10-5 mol L-1, the maximum response was achieved. The developed method was evaluated in terms of accuracy, precision and limit of detection. Results: The linear concentration range for quantification of ctDNA was 36-3289 ng mL-1 and the detection limit (S/N=3 was 8 ng mL-1. The concentration of DNA extracted from Escherichia coli as an extracted sample was also determined using the developed probe. The concentration of DNA in extracted sample was determined using UV assay and developed method, the results were satisfactory. Conclusion: The proposed method is a simple, practical and relatively interference free method to follow up the concentrations of ctDNA.

  2. Spectrophotometric, colorimetric and visually detection of Pseudomonas aeruginosa ETA gene based gold nanoparticles DNA probe and endonuclease enzyme

    Science.gov (United States)

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

    2018-06-01

    Colorimetric DNA detection is preferred over other methods for clinical molecular diagnosis because it does not require expensive equipment. In the present study, the colorimetric method based on gold nanoparticles (GNPs) and endonuclease enzyme was used for the detection of P. aeruginosa ETA gene. Firstly, the primers and probe for P. aeruginosa exotoxin A (ETA) gene were designed and checked for specificity by the PCR method. Then, GNPs were synthesized using the citrate reduction method and conjugated with the prepared probe to develop the new nano-biosensor. Next, the extracted target DNA of the bacteria was added to GNP-probe complex to check its efficacy for P. aeruginosa ETA gene diagnosis. A decrease in absorbance was seen when GNP-probe-target DNA cleaved into the small fragments of BamHI endonuclease due to the weakened electrostatic interaction between GNPs and the shortened DNA. The right shift of the absorbance peak from 530 to 562 nm occurred after adding the endonuclease. It was measured using a UV-VIS absorption spectroscopy that indicates the existence of the P. aeruginosa ETA gene. Sensitivity was determined in the presence of different concentrations of target DNA of P. aeruginosa. The results obtained from the optimized conditions showed that the absorbance value has linear correlation with concentration of target DNA (R: 0.9850) in the range of 10-50 ng mL-1 with the limit detection of 9.899 ng mL-1. Thus, the specificity of the new method for detection of P. aeruginosa was established in comparison with other bacteria. Additionally, the designed assay was quantitatively applied to detect the P. aeruginosa ETA gene from 103 to 108 CFU mL-1 in real samples with a detection limit of 320 CFU mL-1.

  3. High-performance analysis of single interphase cells with custom DNA probes spanning translocation break points

    Science.gov (United States)

    Weier, Heinz-Ulli G.; Munne, S.; Lersch, Robert A.; Marquez, C.; Wu, J.; Pedersen, Roger A.; Fung, Jingly

    1999-06-01

    The chromatin organization of interphase cell nuclei, albeit an object of intense investigation, is only poorly understood. In the past, this has hampered the cytogenetic analysis of tissues derived from specimens where only few cells were actively proliferating or a significant number of metaphase cells could be obtained by induction of growth. Typical examples of such hard to analyze cell systems are solid tumors, germ cells and, to a certain extent, fetal cells such as amniocytes, blastomeres or cytotrophoblasts. Balanced reciprocal translocations that do not disrupt essential genes and thus do not led to disease symptoms exit in less than one percent of the general population. Since the presence of translocations interferes with homologue pairing in meiosis, many of these individuals experience problems in their reproduction, such as reduced fertility, infertility or a history of spontaneous abortions. The majority of translocation carriers enrolled in our in vitro fertilization (IVF) programs carry simple translocations involving only two autosomes. While most translocations are relatively easy to spot in metaphase cells, the majority of cells biopsied from embryos produced by IVF are in interphase and thus unsuitable for analysis by chromosome banding or FISH-painting. We therefore set out to analyze single interphase cells for presence or absence of specific translocations. Our assay, based on fluorescence in situ hybridization (FISH) of breakpoint-spanning DNA probes, detects translocations in interphase by visual microscopic inspection of hybridization domains. Probes are prepared so that they span a breakpoint and cover several hundred kb of DNA adjacent to the breakpoint. On normal chromosomes, such probes label a contiguous stretch of DNA and produce a single hybridization domain per chromosome in interphase cells. The translocation disrupts the hybridization domain and the resulting two fragments appear as physically separated hybridization domains in

  4. Usefulness of the secondary probe pTBN12 in DNA fingerprinting of Mycobacterium tuberculosis.

    OpenAIRE

    Chaves, F; Yang, Z; el Hajj, H; Alonso, M; Burman, W J; Eisenach, K D; Dronda, F; Bates, J H; Cave, M D

    1996-01-01

    A comparison was made between DNA fingerprints of Mycobacterium tuberculosis produced with the insertion sequence IS6110 and those produced with the polymorphic GC-rich repetitive sequence contained in the plasmid pTBN12. A total of 302 M. tuberculosis isolates from the prison system in Madrid, Spain, and the Denver Public Health Department (Denver, Colo.) were analyzed with the two probes. Both probes identified the same isolates in the same clusters when the fingerprints had six or more cop...

  5. Isolation and characterization of DNA probes from a flow-sorted human chromosome 8 library that detect restriction fragment length polymorphism (RFLP).

    Science.gov (United States)

    Wood, S; Starr, T V; Shukin, R J

    1986-01-01

    We have used a recombinant DNA library constructed from flow-sorted human chromosome 8 as a source of single-copy human probes. These probes have been screened for restriction fragment length polymorphism (RFLP) by hybridization to Southern transfers of genomic DNA from five unrelated individuals. We have detected six RFLPs distributed among four probes after screening 741 base pairs for restriction site variation. These RFLPs all behave as codominant Mendelian alleles. Two of the probes detect rare variants, while the other two detect RFLPs with PIC values of .36 and .16. Informative probes will be useful for the construction of a linkage map for chromosome 8 and for the localization of mutant alleles to this chromosome. Images Fig. 1 PMID:2879441

  6. DNA probe labeling with digoxigenin-dUTP and its application in gene diagnosis

    International Nuclear Information System (INIS)

    Liu Guoyang

    1992-01-01

    DNA probe labeling by the randomly primed incorporation of digoxigenin-dUTP is reported. The sensitivity of color reaction and hybridization were 32 fg and 200 fg, respectively, and both were specific for the target. Single-copy and multi-copy gene fragments among 2 μg human genomic DNA were detected by β IVS II, Fr 3-42 and 3'HVR labeled with digoxigenin-dUTP. The results were consistent with a radioactive control assay. This method has been successfully used in the gene diagnosis of adult polycystic kidney disease

  7. DNA-based stable isotope probing: a link between community structure and function

    International Nuclear Information System (INIS)

    Uhlik, Ondrej; Jecna, Katerina; Leigh, Mary Beth; Mackova, Martina; Macek, Tomas

    2009-01-01

    DNA-based molecular techniques permit the comprehensive determination of microbial diversity but generally do not reveal the relationship between the identity and the function of microorganisms. The first direct molecular technique to enable the linkage of phylogeny with function is DNA-based stable isotope probing (DNA-SIP). Applying this method first helped describe the utilization of simple compounds, such as methane, methanol or glucose and has since been used to detect microbial communities active in the utilization of a wide variety of compounds, including various xenobiotics. The principle of the method lies in providing 13C-labeled substrate to a microbial community and subsequent analyses of the 13C-DNA isolated from the community. Isopycnic centrifugation permits separating 13C-labeled DNA of organisms that utilized the substrate from 12C-DNA of the inactive majority. As the whole metagenome of active populations is isolated, its follow-up analysis provides successful taxonomic identification as well as the potential for functional gene analyses. Because of its power, DNA-SIP has become one of the leading techniques of microbial ecology research. But from other point of view, it is a labor-intensive method that requires careful attention to detail during each experimental step in order to avoid misinterpretation of results.

  8. Label-free fluorescence strategy for sensitive detection of adenosine triphosphate using a loop DNA probe with low background noise.

    Science.gov (United States)

    Lin, Chunshui; Cai, Zhixiong; Wang, Yiru; Zhu, Zhi; Yang, Chaoyong James; Chen, Xi

    2014-07-15

    A simple, rapid, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection was developed using a loop DNA probe with low background noise. In this strategy, a loop DNA probe, which is the substrate for both ligation and digestion enzyme reaction, was designed. SYBR green I (SG I), a double-stranded specific dye, was applied for the readout fluorescence signal. Exonuclease I (Exo I) and exonuclease III (Exo III), sequence-independent nucleases, were selected to digest the loop DNA probe in order to minimize the background fluorescence signal. As a result, in the absence of ATP, the loop DNA was completely digested by Exo I and Exo III, leading to low background fluorescence owing to the weak electrostatic interaction between SG I and mononucleotides. On the other hand, ATP induced the ligation of the nicking site, and the sealed loop DNA resisted the digestion of Exo I and ExoIII, resulting in a remarkable increase of fluorescence response. Upon background noise reduction, the sensitivity of the ATP determination was improved significantly, and the detection limitation was found to be 1.2 pM, which is much lower than that in almost all the previously reported methods. This strategy has promise for wide application in the determination of ATP.

  9. Non-destructive evaluation of fiber-reinforced composites with a fast 2D fiber-optic laser-ultrasound scanner

    Science.gov (United States)

    Pelivanov, Ivan; Buma, Takashi; Xia, Jinjun; Wei, Chen-Wei; Shtokolov, Alex; O'Donnell, Matthew

    2015-03-01

    Laser ultrasonic (LU) inspection represents an attractive, non-contact method to evaluate composite materials. Current non-contact systems, however, have relatively low sensitivity compared to contact piezoelectric detection. They are also difficult to adjust, very expensive, and strongly influenced by environmental noise. Here, we demonstrate that most of these drawbacks can be eliminated by combining a new generation of compact, inexpensive fiber lasers with new developments in fiber telecommunication optics and an optimally designed balanced probe scheme. In particular, a new type of a balanced fiber-optic Sagnac interferometer is presented as part of an all-optical LU pump-probe system for high speed non-destructive testing and evaluation (NDT&E) of aircraft composites. The performance of the LU system is demonstrated on a composite sample typically used in the aircraft industry. Wide-band ultrasound probe signals are generated directly at the sample surface with a pulsed diode-pumped laser delivering nanosecond laser pulses at a 1 kHz repetition rate with a pulse energy of 2 mJ. A balanced fiber-optic Sagnac interferometer is employed to detect pressure signals in a 1-10 MHz frequency range at the same point (an 8 μm focal spot) on the composite surface. A fast (up to 100 mm/s) 2D translation system is employed to move the sample during scanning and produce a complete B-scan consisting of one thousand A-scans in less than a second. The sensitivity of this system, in terms of the noise equivalent pressure, is found to be only 10 dB above the Nyquist thermal noise limit. To our knowledge, this is the best reported sensitivity for a non-contact ultrasonic detector of this dimension.

  10. Fiber optic probe enabled by surface-enhanced Raman scattering for early diagnosis of potential acute rejection of kidney transplant

    Science.gov (United States)

    Chi, Jingmao; Chen, Hui; Tolias, Peter; Du, Henry

    2014-06-01

    We have explored the use of a fiber-optic probe with surface-enhanced Raman scattering (SERS) sensing modality for early, noninvasive and, rapid diagnosis of potential renal acute rejection (AR) and other renal graft dysfunction of kidney transplant patients. Multimode silica optical fiber immobilized with colloidal Ag nanoparticles at the distal end was used for SERS measurements of as-collected urine samples at 632.8 nm excitation wavelength. All patients with abnormal renal graft function (3 AR episodes and 2 graft failure episodes) who were clinically diagnosed independently show common unique SERS spectral features in the urines collected just one day after transplant. SERS-based fiber-optic probe has excellent potential to be a bedside tool for early diagnosis of kidney transplant patients for timely medical intervention of patients at high risk of transplant dysfunction.

  11. Fiber-Optic Magnetometry and Thermometry Using Optically Detected Magnetic Resonance With Nitrogen-Vacancy Centers in Diamond

    Science.gov (United States)

    Blakley, Sean Michael

    Nitrogen--vacancy diamond (NVD) quantum sensors are an emerging technology that has shown great promise in areas like high-resolution thermometry and magnetometry. Optical fibers provide attractive new application paradigms for NVD technology. A detailed description of the fabrication processes associated with the development of novel fiber-optic NVD probes are presented in this work. The demonstrated probes are tested on paradigmatic model systems designed to ascertain their suitability for use in challenging biological environments. Methods employing optically detected magnetic resonance (ODMR) are used to accurately measure and map temperature distributions of small objects and to demonstrate emergent temperature-dependent phenomena in genetically modified living organisms. These methods are also used to create detailed high resolution spatial maps of both magnetic scalar and magnetic vector field distributions of spatially localized weak field features in the presence of a noisy, high-field background.

  12. Detection of adenovirus in nasopharyngeal specimens by radioactive and nonradioactive DNA probes

    International Nuclear Information System (INIS)

    Hyypiae, T.

    1985-01-01

    The presence of adenovirus DNA in clinical specimens was analyzed by nucleic acid hybridization assays by both radioactive and enzymatic detection systems. The sensitivity of the hybridization tests was in the range of 10 to 100 pg of homologous adenovirus DNA. Minimal background was noticed with unrelated viral and nonviral DNA. Twenty-four nasopharyngeal mucus aspirate specimens, collected from children with acute respiratory infection, were assayed in the hybridization tests and also by an enzyme immunoassay for adenovirus hexon antigen which was used as a reference test. Sixteen specimens positive by the enzyme immunoassay also were positive in the two nucleic acid hybridization tests, and the remaining eight specimens were negative in all of the tests. The results indicate that nucleid acid hybridization tests with both radioactive and nonradioactive probes can be used for diagnosis of microbial infections

  13. Synthesis of novel fluorescent probe Tb(III)-7-carboxymethoxy-4-methylcoumarin complex for sensing of DNA

    International Nuclear Information System (INIS)

    Hussein, Belal H.M.; Azab, Hassan A.; Fathalla, Walid; Ali, Sherin A.M.

    2013-01-01

    New fluorescent probe Tb(III) (7-carboxymethoxy-4-methylcoumarin)2(SCN) (C2H5OH)(H2O) was synthesized and characterized by spectroscopy and thermal analysis. The absorption and fluorescence spectra of 7-carboxymethoxy-4-methylcoumarin (CMMC) and Tb(III)–CMMC complex have been measured in different solvents. The interactions of Tb(III)–CMMC complex with calf thymus nucleic acid (CT-DNA) have been investigated using steady state fluorescence measurements. The changes in the fluorescence intensity have been used for the quantitative determination of DNA with LOD of 3.45 ng in methanol–water (9:1, v/v). The association constants of DNA with Tb(III)–CMMC complex was found to be 2.62×1010 M −1 . - Highlights: ► New fluorescent probe Terbium (III)-7-carboxy methoxy-4-methylcoumarin complex has been synthesized and characterized. ► FTIR spectrum of Tb(III)-complex shows a characteristic band for thiocyanate group. ► DNA interaction with Terbium (III)-7-carboxy methoxy-4-methylcoumarin has been studied by fluorescence techniques. ► The change in the fluorescence intensity has been used for the quantitative determination of DNA. ► The result was better than most of the well-known methods including the ethidium bromide method.

  14. Detection of mutations using microarrays of poly(C)10-poly(T)10 modified DNA probes immobilized on agarose films

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Petersen, Jesper; Stoltenborg, M.

    2006-01-01

    Allele-specific hybridization to a DNA microarray call be a useful method for genotyping patient DNA. In this article, we demonstrate that 13- to 17-base oligonucleotides tagged with a poly(T)10-poly(C)10 tail (TC tag), but otherwise unmodified, can be crosslinked by UV light irradiation to an ag......Allele-specific hybridization to a DNA microarray call be a useful method for genotyping patient DNA. In this article, we demonstrate that 13- to 17-base oligonucleotides tagged with a poly(T)10-poly(C)10 tail (TC tag), but otherwise unmodified, can be crosslinked by UV light irradiation...... to an agarose film grafted onto unmodified glass. Microarrays of TC-tagged probes immobilized on the agarose film can be used to diagnose Mutations in the human P-globin gene, which encodes the beta-chains in hemoglobin. Although the probes differed widely regarding inciting point temperature (similar to 20...... degrees C), a single stringency wash still gave sufficiently high discrimination signals between perfect match and mismatch probes to allow robust mutation detection. In all, 270 genotypings were performed on patient materials, and no genotype was incorrectly classified. Quality control experiments...

  15. Measurements of spectral responses for developing fiber-optic pH sensor

    Science.gov (United States)

    Yoo, Wook Jae; Heo, Ji Yeon; Jang, Kyoung Won; Seo, Jeong Ki; Moon, Jin Soo; Park, Jang-Yeon; Park, Byung Gi; Cho, Seunghyun; Lee, Bongsoo

    2011-01-01

    In this study, we have fabricated a fiber-optic pH sensor, which is composed of a light source, a pH-sensing probe, plastic optical fibers and a spectrometer, for determining the degree of infection by Helicobacter pylori in the stomach. As pH indicators, phenol red and m-cresol purple are used, and pH liquid solutions are prepared by mixing phenol red or m-cresol purple solutions and various kinds of pH buffer solutions. The light emitted by a light source is guided by plastic optical fibers to the pH liquid solution, and the optical characteristic of a reflected light is changed according to the color variations of the pH indicator in the pH-sensing probe. Therefore, we have measured the intensities and wavelength shifts of the reflected lights, which change according to the color variations of indicators at different pH values, by using a spectrometer for spectral analysis. Also, the relationships between the pH values of liquid solutions and the optical properties of the modulated lights are obtained on the basis of the changes of the colors of indicators.

  16. Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing.

    Science.gov (United States)

    Guo, Bingyuan; Sheng, Yingying; Zhou, Ke; Liu, Quansheng; Liu, Lei; Wu, Hai-Chen

    2018-03-26

    A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination by DNA Hybridization Probes.

    Science.gov (United States)

    Chen, Sherry Xi; Seelig, Georg

    2016-04-20

    Even a single-nucleotide difference between the sequences of two otherwise identical biological nucleic acids can have dramatic functional consequences. Here, we use model-guided reaction pathway engineering to quantitatively improve the performance of selective hybridization probes in recognizing single nucleotide variants (SNVs). Specifically, we build a detection system that combines discrimination by competition with DNA strand displacement-based catalytic amplification. We show, both mathematically and experimentally, that the single nucleotide selectivity of such a system in binding to single-stranded DNA and RNA is quadratically better than discrimination due to competitive hybridization alone. As an additional benefit the integrated circuit inherits the property of amplification and provides at least 10-fold better sensitivity than standard hybridization probes. Moreover, we demonstrate how the detection mechanism can be tuned such that the detection reaction is agnostic to the position of the SNV within the target sequence. in contrast, prior strand displacement-based probes designed for kinetic discrimination are highly sensitive to position effects. We apply our system to reliably discriminate between different members of the let-7 microRNA family that differ in only a single base position. Our results demonstrate the power of systematic reaction network design to quantitatively improve biotechnology.

  18. Influence of Divalent Counterions on the Dynamics in DNA as Probed by Using a Minor-Groove Binder.

    Science.gov (United States)

    Paul, Sneha; Ahmed, Tasnim; Samanta, Anunay

    2017-08-05

    DNA dynamics, to which water, counterions, and DNA motions contribute, is a topic of considerable interest because it is closely related to the efficiency of biological functions performed by it. Simulation studies and experiments suggest that the counterion dynamics in DNA probed by a minor-groove binder are similar for various monovalent counterions. To date, the influence on DNA dynamics of higher-valence counterions, which are also present around DNA and are known to bind more strongly to it than monovalent ions, has not been studied. Herein we investigated DNA dynamics in the presence of Mg 2+ and Ca 2+ , chosen for their relative abundance in cells, by using minor-groove binder 4',6-diamidino-2-phenylindole (DAPI) as a fluorescence probe. The dynamics, as measured from the time-resolved fluorescence Stokes shifts of DAPI bound to calf thymus DNA on a subpicosecond-to-nanosecond timescale, were found to be very similar in the presence of both the divalent ions and Na + ions. The observation is explained by considering the screening of the electric field of the divalent ion by its hydration shell, preferential binding of the ions to the phosphate groups, and displacement of ions from the minor groove by DAPI due to the stronger binding interaction of the latter. Furthermore, the similarity of our results in the presence of Na + to those reported for smaller oligonucleotides suggests that the chain length of DNA does not influence the DNA dynamics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Neocarzinostatin as a probe for DNA protection activity--molecular interaction with caffeine.

    Science.gov (United States)

    Chin, Der-Hang; Li, Huang-Hsien; Kuo, Hsiu-Maan; Chao, Pei-Dawn Lee; Liu, Chia-Wen

    2012-04-01

    Neocarzinostatin (NCS), a potent mutagen and carcinogen, consists of an enediyne prodrug and a protein carrier. It has a unique double role in that it intercalates into DNA and imposes radical-mediated damage after thiol activation. Here we employed NCS as a probe to examine the DNA-protection capability of caffeine, one of common dietary phytochemicals with potential cancer-chemopreventive activity. NCS at the nanomolar concentration range could induce significant single- and double-strand lesions in DNA, but up to 75 ± 5% of such lesions were found to be efficiently inhibited by caffeine. The percentage of inhibition was caffeine-concentration dependent, but was not sensitive to the DNA-lesion types. The well-characterized activation reactions of NCS allowed us to explore the effect of caffeine on the enediyne-generated radicals. Postactivation analyses by chromatographic and mass spectroscopic methods identified a caffeine-quenched enediyne-radical adduct, but the yield was too small to fully account for the large inhibition effect on DNA lesions. The affinity between NCS chromophore and DNA was characterized by a fluorescence-based kinetic method. The drug-DNA intercalation was hampered by caffeine, and the caffeine-induced increases in DNA-drug dissociation constant was caffeine-concentration dependent, suggesting importance of binding affinity in the protection mechanism. Caffeine has been shown to be both an effective free radical scavenger and an intercalation inhibitor. Our results demonstrated that caffeine ingeniously protected DNA against the enediyne-induced damages mainly by inhibiting DNA intercalation beforehand. The direct scavenging of the DNA-bound NCS free radicals by caffeine played only a minor role. Copyright © 2011 Wiley Periodicals, Inc.

  20. Probing the Structure of DNA Aptamers with a Classic Heterocycle.

    Directory of Open Access Journals (Sweden)

    G. Reid Bishop

    2004-02-01

    Full Text Available DNA aptamers are synthetic, single-stranded DNA oligonucleotides selectedby SELEX methods for their binding with specific ligands. Here we present ethidiumbinding results for three related DNA aptamers (PDB code: 1OLD, 1DB6, and 2ARGthat bind L-argininamide (L-Arm. The ligand bound form of each aptamer's structurehas been reported and each are found to be composed primarily of two domainsconsisting of a stem helical region and a loop domain that forms a binding pocket for thecognate ligand. Previous thermodynamic experiments demonstrated that the DNAaptamer 1OLD undergoes a large conformational ordering upon binding to L-Arm. Herewe extend those linkage binding studies by examining the binding of the heterocyclicintercalator ethidium to each of the three aptamers by fluorescence and absorptionspectrophotometric titrations. Our results reveal that ethidium binds to each aptamer with∆Go's in the range of -8.7 to -9.4 kcal/mol. The stoichiometry of binding is 2:1 for eachaptamer and is quantitatively diminished in the presence of L-Arm as is the overallfluorescence intensity of ethidium. Together, these results demonstrate that a portion ofthe bound ethidium is excluded from the aptamer in the presence of a saturating amountof L-Arm. These results demonstrate the utility of ethidium and related compounds forthe probing of non-conventional DNA structures and reveal an interesting fundamentalthermodynamic linkage in DNA aptamers. Results are discussed in the context of thethermodynamic stability and structure of each of the aptamers examined.

  1. A New FRET-Based Sensitive DNA Sensor for Medical Diagnostics using PNA Probe and Water-Soluble Blue Light Emitting Polymer

    Directory of Open Access Journals (Sweden)

    Nidhi Mathur

    2008-01-01

    Full Text Available A reliable, fast, and low-cost biosensor for medical diagnostics using DNA sequence detection has been developed and tested for the detection of the bacterium “Bacillus anthracis.” In this sensor, Poly [9,9-di (6,6′- N, N′ trimethylammonium hexylfluorenyl-2, 7-diyl-alt-co- (1,4-phenylene] dibromide salt (PFP has been taken as cationic conjugated polymer (CCP and PNA attached with fluorescein dye (PNAC∗ as a probe. The basic principle of this sensor is that when a PNAC∗ probe is hybridized with a single strand DNA (ssDNA having complementary sequence, Forster resonance energy transfer (FRET may take place from PFP to the PNAC∗/DNA complex. If the FRET is efficient, the photoluminescence from the PFP will be highly quenched and that from PNAC∗ will be enhanced. On the other hand, if the DNA sequence is noncomplementary to PNA, FRET will not occur.

  2. Fiber-optic coupled pressure transducer

    International Nuclear Information System (INIS)

    Tallman, C.R.; Wingate, F.P.; Ballard, E.O.

    1979-01-01

    A fiber-optic coupled pressure transducer was developed for measurement of pressure transients produced by fast electrical discharges in laser cavities. A detailed description of the design and performance will be given. Shock tube performance and measurements in direct electrical discharge regions will be presented

  3. Characterization of Actinomyces with genomic DNA fingerprints and rRNA gene probes.

    Science.gov (United States)

    Bowden, G; Johnson, J; Schachtele, C

    1993-08-01

    Cellular DNA from 25 Actinomyces naeslundii and Actinomyces viscosus strains belonging to the 7 taxonomic clusters of Fillery et al. (1978) and several unclustered strains was obtained by enzymatic and N-lauroylsarcosine/guanidine isothiocyanate treatment of whole cells, followed by extraction of the nucleic acid. The DNA samples were digested with restriction endonucleases BamHI or PvuII, and agarose gel electrophoresis was used to obtain DNA fingerprints. The DNA fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for comparison between the taxonomic cluster strains and strains within clusters. Representative strains from each taxonomic cluster provided different BamHI DNA fingerprints and ribotype patterns with 3 to 9 distinct bands. Some strains within a cluster showed identical ribotype patterns with both endonucleases (A. naeslundii B120 and A. naeslundii B102 from cluster 3), while others showed the same pattern with BamHI but a different pattern with PvuII (A. naeslundii ATCC 12104 and 398A from cluster 5). A viscosus ATCC 15987 (cluster 7) and its parent strain T6 yielded identical fingerprint and ribotype patterns. The genomic diversity revealed by DNA fingerprinting and ribotyping demonstrates that these techniques, which do not require phenotypic expression, are suited for study of the oral ecology of the Actinomyces, and for epidemiological tracking of specific Actinomyces strains associated with caries lesions and sites of periodontal destruction.

  4. Synthesis of novel fluorescent probe Tb(III)-7-carboxymethoxy-4-methylcoumarin complex for sensing of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Hussein, Belal H.M., E-mail: belalhussein102@yahoo.com [Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia (Egypt); Azab, Hassan A. [Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia (Egypt); Fathalla, Walid [Department of Mathematical and Physical Sciences, Faculty of Engineering, Port-Said University, Port-Said (Egypt); Ali, Sherin A.M. [Department of Mathematical and Physical Sciences, Faculty of Engineering, Suez Canal University, Ismailia (Egypt)

    2013-02-15

    New fluorescent probe Tb(III) (7-carboxymethoxy-4-methylcoumarin)2(SCN) (C2H5OH)(H2O) was synthesized and characterized by spectroscopy and thermal analysis. The absorption and fluorescence spectra of 7-carboxymethoxy-4-methylcoumarin (CMMC) and Tb(III)-CMMC complex have been measured in different solvents. The interactions of Tb(III)-CMMC complex with calf thymus nucleic acid (CT-DNA) have been investigated using steady state fluorescence measurements. The changes in the fluorescence intensity have been used for the quantitative determination of DNA with LOD of 3.45 ng in methanol-water (9:1, v/v). The association constants of DNA with Tb(III)-CMMC complex was found to be 2.62 Multiplication-Sign 1010 M{sup -1}. - Highlights: Black-Right-Pointing-Pointer New fluorescent probe Terbium (III)-7-carboxy methoxy-4-methylcoumarin complex has been synthesized and characterized. Black-Right-Pointing-Pointer FTIR spectrum of Tb(III)-complex shows a characteristic band for thiocyanate group. Black-Right-Pointing-Pointer DNA interaction with Terbium (III)-7-carboxy methoxy-4-methylcoumarin has been studied by fluorescence techniques. Black-Right-Pointing-Pointer The change in the fluorescence intensity has been used for the quantitative determination of DNA. Black-Right-Pointing-Pointer The result was better than most of the well-known methods including the ethidium bromide method.

  5. Regional localization of DNA probes on the short arm of chromosome 11 using aniridia-Wilms' tumor-associated deletions

    NARCIS (Netherlands)

    Mannens, M.; Slater, R. M.; Heyting, C.; Geurts van Kessel, A.; Goedde-Salz, E.; Frants, R. R.; van Ommen, G. J.; Pearson, P. L.

    1987-01-01

    We are interested in the precise localization of various DNA probes on the short arm of chromosome 11 for our research on the aniridia-Wilms' tumor association (AWTA), assigned to region 11p13 (Knudson and Strong 1972; Riccardi et al. 1978). For this purpose we have screened lymphocyte DNA and

  6. Online analysis by a fiber-optic diode array spectrophotometer

    International Nuclear Information System (INIS)

    Van Hare, D.R.; Prather, W.S.; O'Rourke, P.E.

    1987-01-01

    An online photometric analyzer has been developed which can make remote measurements over the 350 to 900 nm region at distances of up to 100 feet. The analyzer consists of a commercially available diode array spectrophotometer interfaced to a fiber-optic multiplexer to allow online monitoring of up to ten locations sequentially. The development of the fiber-optic interface is discussed and data from several online applications are presented to demonstrate the capabilities of the measurement system

  7. Fiber-Optic Micrometeoroid/Orbital Debris Impact Detector System

    Science.gov (United States)

    Christiansen, Eric L.; Tennyson, R. C.; Morison, W. D.

    2012-01-01

    A document describes a reliable, lightweight micrometeoroid/orbital debris (MMOD) detection system that can be located at strategic positions of "high consequence" to provide real-time warning of a penetration, its location, and the extent of the damage to a spacecraft. The concept is to employ fiber-optic sensors to detect impact damage and penetration of spacecraft structures. The fibers are non-electrical, employ light waves, and are immune to electromagnetic interference. The fiber-optic sensor array can be made as a stand-alone product, being bonded to a flexible membrane material or a structure that is employed as a MMOD shield material. The optical sensors can also be woven into hybrid MMOD shielding fabrics. The glass fibers of the fiber-optic sensor provide a dual purpose in contributing to the breakup of MMOD projectiles. The grid arrays can be made in a modular configuration to provide coverage over any area desired. Each module can be connected to a central scanner instrument and be interrogated in a continuous or periodic mode.

  8. DNA Probes Show Genetic Variation in Cyanobacterial Symbionts of the Azolla Fern and a Closer Relationship to Free-Living Nostoc Strains than to Free-Living Anabaena Strains

    Science.gov (United States)

    Plazinski, Jacek; Zheng, Qi; Taylor, Rona; Croft, Lynn; Rolfe, Barry G.; Gunning, Brian E. S.

    1990-01-01

    Twenty-two isolates of Anabaena azollae derived from seven Azolla species from various geographic and ecological sources were characterized by DNA-DNA hybridization. Cloned DNA fragments derived from the genomic sequences of three different A. azollae isolates were used to detect restriction fragment length polymorphism among all symbiotic anabaenas. DNA clones were radiolabeled and hybridized against southern blot transfers of genomic DNAs of different isolates of A. azollae digested with restriction endonucleases. Eight DNA probes were selected to identify the Anabaena strains tested. Two were strain specific and hybridized only to A. azollae strains isolated from Azolla microphylla or Azolla caroliniana. One DNA probe was section specific (hybridized only to anabaenas isolated from Azolla ferns representing the section Euazolla), and five other probes gave finer discrimination among anabaenas representing various ecotypes of Azolla species. These cloned genomic DNA probes identified 11 different genotypes of A. azollae isolates. These included three endosymbiotic genotypes within Azolla filiculoides species and two genotypes within both A. caroliniana and Azolla pinnata endosymbionts. Although we were not able to discriminate among anabaenas extracted from different ecotypes of Azolla nilotica, Azolla mexicina, Azolla rubra and Azolla microphylla species, each of the endosymbionts was easily identified as a unique genotype. When total DNA isolated from free-living Anabaena sp. strain PCC7120 was screened, none of the genomic DNA probes gave detectable positive hybridization. Total DNA of Nostoc cycas PCC7422 hybridized with six of eight genomic DNA fragments. These data imply that the dominant symbiotic organism in association with Azolla spp. is more closely related to Nostoc spp. than to free-living Anabaena spp. Images PMID:16348182

  9. PCR associated with hybridization with DNA radioactive probes for diagnosis of asymptomatic infection caused by Leishmania Chagasi

    International Nuclear Information System (INIS)

    Andrade, Antero Silva Ribeiro de; Moreno, Elizabeth Castro; Gomes, Rosangela Fatima; Melo, Maria Norma de; Carneiro, Mariangela; Fernandes, Octavio

    2002-01-01

    Detection systems for diagnosis of leishmaniasis based on PCR are very promising due to their sensitivity and specificity. Secondary detection by specific radioactive DNA probes, able to type the PCR amplified products, increase the specificity and raise about tem-fold the sensitivity of the assay. The aim of this work was evaluate PCR and hybridization as a tool to identify Leishmania (Leishmania) chagasi (the specie that cause the visceral leishmaniasis in Brazil) infection in asymptomatic persons living in a endemic area. Material and Methods: A group of 226 asymptomatic individuals, living in General Carneiro (MG), was selected. Blood samples were harvested and the DNA extracted from the mononucleate cells. PCR was performed using primers addressed to the kinetoplast DNA minicircles. This protocol gives a positive reaction for all Leishmania species. The amplified products were further hybridized with cloned L.chagasi minicircles labeled with 32 P. Results: were identified 111 samples PCR positive, 2 of them hybridization negative and 133 samples hybridization positive, 24 of them PCR negative. The occurrence of samples with hybridization positive and PCR negative was expected since hybridization, with DNA probes labeled with 32 P, increase the sensitivity of the assay. The samples that presented positive PCR and negative hybridization were probably due the presence of other Leishmania species, likely L. (V.) braziliensis (that produce tegumentary leishmaniasis in the region), since L. (L.) chagasi cloned minicircles were used as hybridization probe. We conclude that this procedure is a valuable tool to access subclinical L. (L.) chagasi infections in epidemiological studies. (author)

  10. Portable evanescent wave fiber biosensor for highly sensitive detection of Shigella

    Science.gov (United States)

    Xiao, Rui; Rong, Zhen; Long, Feng; Liu, Qiqi

    2014-11-01

    A portable evanescent wave fiber biosensor was developed to achieve the rapid and highly sensitive detection of Shigella. In this study, a DNA probe was covalently immobilized onto fiber-optic biosensors that can hybridize with a fluorescently labeled complementary DNA. The sensitivity of detection for synthesized oligonucleotides can reach 10-10 M. The surface of the sensor can be regenerated with 0.5% sodium dodecyl sulfate solution (pH 1.9) for over 30 times without significant deterioration of performance. The total analysis time for a single sample, including the time for measurement and surface regeneration, was less than 6 min. We employed real-time polymerase chain reaction (PCR) and compared the results of both methods to investigate the actual Shigella DNA detection capability of the fiber-optic biosensor. The fiber-optic biosensor could detect as low as 102 colony-forming unit/mL Shigella. This finding was comparable with that by real-time PCR, which suggests that this method is a potential alternative to existing detection methods.

  11. A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

    Science.gov (United States)

    Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

    2017-01-01

    A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

  12. New concepts of fluorescent probes for specific detection of DNA sequences: bis-modified oligonucleotides in excimer and exciplex detection.

    Science.gov (United States)

    Gbaj, A; Bichenkova, Ev; Walsh, L; Savage, He; Sardarian, Ar; Etchells, Ll; Gulati, A; Hawisa, S; Douglas, Kt

    2009-12-01

    The detection of single base mismatches in DNA is important for diagnostics, treatment of genetic diseases, and identification of single nucleotide polymorphisms. Highly sensitive, specific assays are needed to investigate genetic samples from patients. The use of a simple fluorescent nucleoside analogue in detection of DNA sequence and point mutations by hybridisation in solution is described in this study. The 5'-bispyrene and 3'-naphthalene oligonucleotide probes form an exciplex on hybridisation to target in water and the 5'-bispyrene oligonucleotide alone is an adequate probe to determine concentration of target present. It was also indicated that this system has a potential to identify mismatches and insertions. The aim of this work was to investigate experimental structures and conditions that permit strong exciplex emission for nucleic acid detectors, and show how such exciplexes can register the presence of mismatches as required in SNP analysis. This study revealed that the hybridisation of 5'-bispyrenyl fluorophore to a DNA target results in formation of a fluorescent probe with high signal intensity change and specificity for detecting a complementary target in a homogeneous system. Detection of SNP mutations using this split-probe system is a highly specific, simple, and accessible method to meet the rigorous requirements of pharmacogenomic studies. Thus, it is possible for the system to act as SNP detectors and it shows promise for future applications in genetic testing.

  13. A fiber-optic tiltmeter system based on the moiré-fringe effect

    International Nuclear Information System (INIS)

    Kim, Dae-Hyun

    2009-01-01

    This paper presents a novel fiber-optic tiltmeter system for the health monitoring of large-size structures. The system is composed of a sensor head, a light control unit and a signal processing unit. The sensing mechanism of the sensor head is based on an integration of the moiré-fringe phenomenon with fiber optics to achieve a robust performance in addition to its immunity to EM interference, easy cabling and low cost. In this paper, a prototype of the fiber-optic tiltmeter system has been developed successfully. From an experimental test, the fiber-optic tiltmeter was proven to be a prospective sensor for the monitoring of the tilt angle of a civil structure with good stability and linearity. Finally, the test also successfully demonstrates the performance and the potential of the novel fiber-optic tiltmeter system to monitor the health of civil structures

  14. Improving Probe Immobilization for Label-Free Capacitive Detection of DNA Hybridization on Microfabricated Gold Electrodes

    Directory of Open Access Journals (Sweden)

    Sandro Carrara

    2008-02-01

    Full Text Available Alternative approaches to labeled optical detection for DNA arrays are actively investigated for low-cost point-of-care applications. In this domain, label-free capacitive detection is one of the most intensely studied techniques. It is based on the idea to detect the Helmholtz ion layer displacements when molecular recognition occurs at the electrodes/solution interface. The sensing layer is usually prepared by using thiols terminated DNA single-strength oligonucleotide probes on top of the sensor electrodes. However, published data shows evident time drift, which greatly complicates signal conditioning and processing and ultimately increases the uncertainty in DNA recognition sensing. The aim of this work is to show that newly developed ethylene-glycol functionalized alkanethiols greatly reduce time drift, thereby significantly improving capacitance based label-free detection of DNA.

  15. Development of a PCR/LDR/flow-through hybridization assay using a capillary tube, probe DNA-immobilized magnetic beads and chemiluminescence detection.

    Science.gov (United States)

    Hommatsu, Manami; Okahashi, Hisamitsu; Ohta, Keisuke; Tamai, Yusuke; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

    2013-01-01

    A polymerase chain reaction (PCR)/ligase detection reaction (LDR)/flow-through hybridization assay using chemiluminescence (CL) detection was developed for analyzing point mutations in gene fragments with high diagnostic value for colorectal cancers. A flow-through hybridization format using a capillary tube, in which probe DNA-immobilized magnetic beads were packed, provided accelerated hybridization kinetics of target DNA (i.e. LDR product) to the probe DNA. Simple fluid manipulations enabled both allele-specific hybridization and the removal of non-specifically bound DNA in the wash step. Furthermore, the use of CL detection greatly simplified the detection scheme, since CL does not require a light source for excitation of the fluorescent dye tags on the LDR products. Preliminary results demonstrated that this analytical system could detect both homozygous and heterozygous mutations, without the expensive instrumentation and cumbersome procedures required by conventional DNA microarray-based methods.

  16. Genetic effect of A-bomb radiation- Analysis of minisatellite regions detected by DNA fingerprint probe

    International Nuclear Information System (INIS)

    Kodaira, Mieko

    1999-01-01

    In author's laboratory, screening of mutation in germ cells of A-bomb survivors is under investigation with use of 8 single-locus minisatellite probes and no increase in mutation rate has been detected hitherto. This paper reported results of screening on the minisatellite region, which consisting of short repeated base sequence, using a DNA fingerprint probe for 33.15 core sequence. Subjects were 50 A-bomb survivor families exposed to mean dose of 1.9 Sv (exposed group) or 0 Gy (control), having 64 or 60 children, respectively. DNA was extracted from their B cells established by EB virus and subjected to agarose-gel electrophoresis followed by southern blotting with some improvements for fingerprinting. On the fingerprints, numbers of the band detected in regions of >3.5 kb were 1080 in children of the exposed group (16.9/child) and 1024 (17.1) in the control group, indicating no detectable effect of exposure on the germ cell mutation rate in the region.(K.H.)

  17. Fluorescent Quantification of DNA Based on Core-Shell Fe3O4@SiO2@Au Nanocomposites and Multiplex Ligation-Dependent Probe Amplification.

    Science.gov (United States)

    Fan, Jing; Yang, Haowen; Liu, Ming; Wu, Dan; Jiang, Hongrong; Zeng, Xin; Elingarami, Sauli; Ll, Zhiyang; Li, Song; Liu, Hongna; He, Nongyue

    2015-02-01

    In this research, a novel method for relative fluorescent quantification of DNA based on Fe3O4@SiO2@Au gold-coated magnetic nanocomposites (GMNPs) and multiplex ligation- dependent probe amplification (MLPA) has been developed. With the help of self-assembly, seed-mediated growth and chemical reduction method, core-shell Fe3O4@SiO2@Au GMNPs were synthesized. Through modified streptavidin on the GMNPs surface, we obtained a bead chip which can capture the biotinylated probes. Then we designed MLPA probes which were tagged with biotin or Cy3 and target DNA on the basis of human APP gene sequence. The products from the thermostable DNA ligase induced ligation reactions and PCR amplifications were incubated with SA-GMNPs. After washing, magnetic separation, spotting, the fluorescent scanning results showed our method can be used for the relative quantitative analysis of the target DNA in the concentration range of 03004~0.5 µM.

  18. Application of GelGreen™ in Cesium Chloride Density Gradients for DNA-Stable Isotope Probing Experiments.

    Directory of Open Access Journals (Sweden)

    Jingfeng Gao

    Full Text Available In this study, GelGreen™ was investigated as a replacement for SYBR® Safe to stain DNA in cesium chloride (CsCl density gradients for DNA-stable isotope probing (SIP experiments. Using environmental DNA, the usage of GelGreen™ was optimized for sensitivity compared to SYBR® Safe, its optimal concentration, detection limit for environmental DNA and its application in environmental DNA-SIP assay. Results showed that GelGreen™ was more sensitive than SYBR® Safe, while the optimal dosage (15X concentration needed was approximately one-third of SYBR® Safe, suggesting that its sensitivity was three times more superior than SYBR® Safe. At these optimal parameters, the detection limit of GelGreen™-stained environmental DNA was as low as 0.2 μg, but the usage of 0.5 μg environmental DNA was recommended to produce a more consistent DNA band. In addition, a modified needle extraction procedure was developed to withdraw DNA effectively by fractionating CsCl density gradients into four or five fractions. The successful application of GelGreen™ staining with 13C-labeled DNA from enriched activated sludge suggests that this stain was an excellent alternative of SYBR® Safe in CsCl density gradients for DNA-SIP assays.

  19. Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization

    International Nuclear Information System (INIS)

    Collomb, J.; Finance, C.; Alabouch, S.; Laporte, J.

    1992-01-01

    Genomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned in E. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes , were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabelling with 32 P and enzymatic labelling through covalent linkage to peroxidase and chemiluminescence detection. The radioactive probe 174 detected as little as 1 to 3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the family Coronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in faecal samples using enzymatic probe was compared with conventional diagnostic methods. (authors)

  20. Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Collomb, J; Finance, C; Alabouch, S [Lab. de Microbiologie Moleculaire, Faculte des Sciences Pharmaceutiques et Biologiques, Univ. de Nancy I, Nancy (France); Laporte, J [Station de Virologie et d' Immunologie Moleculaires, INRA, Jouy-en-Josas (France)

    1992-01-01

    Genomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned in E. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes , were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabeled with [sup 32]P and enzymatic labeled through covalent linkage to peroxidase for chemiluminescence detection. The radioactive probe 174 detected as little as 1-3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the family Coronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in fecal samples using enzymatic probe was compared with conventional diagnostic methods. (authors).

  1. Design of a fiber-optic interrogator module for telecommunication satellites

    Science.gov (United States)

    Putzer, Philipp; Koch, Alexander W.; Plattner, Markus; Hurni, Andreas; Manhart, Markus

    2017-11-01

    In this paper we present the results of the radiation tests performed on the optical components of the fiber-optic interrogator module as a part of the Hybrid Sensor Bus (HSB) system. The HSB-system is developed in the frame of an ESAARTES program and will be verified as flight demonstrator onboard the German Heinrich Hertz satellite in 2016. The HSB system is based on a modular concept which includes sensor interrogation modules based on I2C electrical and fiber Bragg grating (FBG) fiber-optical sensor elements. Onboard fiber-optic sensing allows the implementation of novel control and monitoring methods. For read-out of multiple FBG sensors, a design based on a tunable laser diode as well as a design based on a spectrometer is considered. The expected and tested total ionizing dose (TID) applicable to the HSB system is in the range between 100 krad and 300 krad inside the satellite in the geostationary orbit over a life time of 15 years. We present radiation test results carried out on critical optical components to be used in the fiber-optic interrogation module. These components are a modulated grating Y-branch (MGY) tunable laser diode acting as light source for the tuning laser approach, the line detector of a spectrometer, photodetectors and the FBG sensors acting as sensor elements. A detailed literature inquiry of radiation effects on optical fibers and FBG sensors, is also included in the paper. The fiber-optic interrogator module implemented in the HSB system is based on the most suitable technology, which sustains the harsh environment in the geostationary orbit.

  2. Quantitative cognitive-test characterization of reconnectable implantable fiber-optic neurointerfaces for optogenetic neurostimulation.

    Science.gov (United States)

    Fedotov, I V; Ivashkina, O I; Pochechuev, M S; Roshchina, M A; Toropova, K A; Fedotov, A B; Anokhin, K V; Zheltikov, A M

    2017-11-01

    Cognitive tests on representative groups of freely behaving transgenic mice are shown to enable a quantitative characterization of reconnectable implantable fiber-optic neurointerfaces for optogenetic neurostimulation. A systematic analysis of such tests provides a robust quantitative measure for the cognitive effects induced by fiber-optic neurostimulation, validating the performance of fiber-optic neurointerfaces for long-term optogenetic brain stimulations and showing no statistically significant artifacts in the behavior of transgenic mice due to interface implantation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. DNA imaging and quantification using chemi-luminescent probes; Imagerie et quantification d`ADN par chimiluminescence

    Energy Technology Data Exchange (ETDEWEB)

    Dorner, G; Redjdal, N; Laniece, P; Siebert, R; Tricoire, H; Valentin, L [Groupe I.P.B., Experimental Research Division, Inst. de Physique Nucleaire, Paris-11 Univ., 91 - Orsay (France)

    1999-11-01

    During this interdisciplinary study we have developed an ultra sensitive and reliable imaging system of DNA labelled by chemiluminescence. Based on a liquid nitrogen cooled CCD, the system achieves sensitivities down to 10 fg/mm{sup 2} labelled DNA over a surface area of 25 x 25 cm{sup 2} with a sub-millimeter resolution. Commercially available chemi-luminescent - and enhancer molecules are compared and their reaction conditions optimized for best signal-to-noise ratios. Double labelling was performed to verify quantification with radioactive probes. (authors) 1 fig.

  4. Electrochemical detection of human papillomavirus DNA type 16 using a pyrrolidinyl peptide nucleic acid probe immobilized on screen-printed carbon electrodes.

    Science.gov (United States)

    Jampasa, Sakda; Wonsawat, Wanida; Rodthongkum, Nadnudda; Siangproh, Weena; Yanatatsaneejit, Pattamawadee; Vilaivan, Tirayut; Chailapakul, Orawon

    2014-04-15

    An electrochemical biosensor based on an immobilized anthraquinone-labeled pyrrolidinyl peptide nucleic acid (acpcPNA) probe was successfully developed for the selective detection of human papillomavirus (HPV) type 16 DNA. A 14-mer acpcPNA capture probe was designed to recognize a specific 14 nucleotide region of HPV type 16 L1 gene. The redox-active label anthraquinone (AQ) was covalently attached to the N-terminus of the acpcPNA probe through an amide bond. The probe was immobilized onto a chitosan-modified disposable screen-printed carbon electrode via a C-terminal lysine residue using glutaraldehyde as a cross-linking agent. Hybridization with the target DNA was studied by measuring the electrochemical signal response of the AQ label using square-wave voltammetric analysis. The calibration curve exhibited a linear range between 0.02 and 12.0 µM with a limit of detection and limit of quantitation of 4 and 14 nM, respectively. This DNA sensing platform was successfully applied to detect the HPV type 16 DNA from a PCR amplified (240 bp fragment of the L1 gene) sample derived from the HPV type 16 positive human cancer cell line (SiHa), and failed to detect the HPV-negative c33a cell line. The sensor probe exhibited very high selectivity for the complementary 14 base oligonucleotide over the non-complementary oligonucleotides with sequences derived from HPV types 18, 31 and 33. The proposed sensor provides an inexpensive tool for the early stage detection of HPV type 16, which is an important biomarker for cervical cancer. © 2013 Elsevier B.V. All rights reserved.

  5. Overview of Fiber-Optical Sensors

    Science.gov (United States)

    Depaula, Ramon P.; Moore, Emery L.

    1987-01-01

    Design, development, and sensitivity of sensors using fiber optics reviewed. State-of-the-art and probable future developments of sensors using fiber optics described in report including references to work in field. Serves to update previously published surveys. Systems incorporating fiber-optic sensors used in medical diagnosis, navigation, robotics, sonar, power industry, and industrial controls.

  6. DETECTION OF DNA DAMAGE USING A FIBEROPTIC BIOSENSOR

    Science.gov (United States)

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

  7. Norrie disease: linkage analysis using a 4.2-kb RFLP detected by a human ornithine aminotransferase cDNA probe.

    Science.gov (United States)

    Ngo, J T; Bateman, J B; Cortessis, V; Sparkes, R S; Mohandas, T; Inana, G; Spence, M A

    1989-05-01

    Previous study has shown that the usual DNA marker for Norrie disease, the L1.28 probe which identifies the DXS7 locus, can recombine with the disease locus. In this study, we used a human ornithine aminotransferase (OAT) cDNA which detects OAT-related DNA sequences mapped to the same region on the X chromosome as that of the L1.28 probe to investigate the family with Norrie disease who exhibited the recombinational event. When genomic DNA from this family was digested with the PvuII restriction endonuclease, we found a restriction fragment length polymorphism (RFLP) of 4.2 kb in size. This fragment was absent in the affected males and cosegregated with the disease locus; we calculated a lod score of 0.602, at theta = 0.00. No deletion could be detected by chromosomal analysis or on Southern blots with other enzymes. These results suggest that one of the OAT-related sequences on the X chromosome may be in close proximity to the Norrie disease locus and represent the first report which indicates that the OAT cDNA may be useful for the identification of carrier status and/or prenatal diagnosis.

  8. Automated design of genomic Southern blot probes

    Directory of Open Access Journals (Sweden)

    Komiyama Noboru H

    2010-01-01

    Full Text Available Abstract Background Sothern blotting is a DNA analysis technique that has found widespread application in molecular biology. It has been used for gene discovery and mapping and has diagnostic and forensic applications, including mutation detection in patient samples and DNA fingerprinting in criminal investigations. Southern blotting has been employed as the definitive method for detecting transgene integration, and successful homologous recombination in gene targeting experiments. The technique employs a labeled DNA probe to detect a specific DNA sequence in a complex DNA sample that has been separated by restriction-digest and gel electrophoresis. Critically for the technique to succeed the probe must be unique to the target locus so as not to cross-hybridize to other endogenous DNA within the sample. Investigators routinely employ a manual approach to probe design. A genome browser is used to extract DNA sequence from the locus of interest, which is searched against the target genome using a BLAST-like tool. Ideally a single perfect match is obtained to the target, with little cross-reactivity caused by homologous DNA sequence present in the genome and/or repetitive and low-complexity elements in the candidate probe. This is a labor intensive process often requiring several attempts to find a suitable probe for laboratory testing. Results We have written an informatic pipeline to automatically design genomic Sothern blot probes that specifically attempts to optimize the resultant probe, employing a brute-force strategy of generating many candidate probes of acceptable length in the user-specified design window, searching all against the target genome, then scoring and ranking the candidates by uniqueness and repetitive DNA element content. Using these in silico measures we can automatically design probes that we predict to perform as well, or better, than our previous manual designs, while considerably reducing design time. We went on to

  9. Development and Characterization of Complex DNA Fingerprinting Probes for the Infectious Yeast Candida dubliniensis

    Science.gov (United States)

    Joly, Sophie; Pujol, Claude; Rysz, Michal; Vargas, Kaaren; Soll, David R.

    1999-01-01

    Using a strategy to clone large genomic sequences containing repetitive elements from the infectious yeast Candida dubliniensis, the three unrelated sequences Cd1, Cd24, and Cd25, with respective molecular sizes of 15,500, 10,000, and 16,000 bp, were cloned and analyzed for their efficacy as DNA fingerprinting probes. Each generated a complex Southern blot hybridization pattern with endonuclease-digested genomic DNA. Cd1 generated an extremely variable pattern that contained all of the bands of the pattern generated by the repeat element RPS of Candida albicans. We demonstrated that Cd1 does not contain RPS but does contain a repeat element associated with RPS throughout the C. dubliniensis genome. The Cd1 pattern was the least stable over time both in vitro and in vivo and for that reason proved most effective in assessing microevolution. Cd24, which did not exhibit microevolution in vitro, was highly variable in vivo, suggesting in vivo-dependent microevolution. Cd25 was deemed the best probe for broad epidemiological studies, since it was the most stable over time, was the only truly C. dubliniensis-specific probe of the three, generated the most complex pattern, was distributed throughout all C. dubliniensis chromosomes, and separated a worldwide collection of 57 C. dubliniensis isolates into two distinct groups. The presence of a species-specific repetitive element in Cd25 adds weight to the already substantial evidence that C. dubliniensis represents a bona fide species. PMID:10074523

  10. Hg(2+) detection using a phosphorothioate RNA probe adsorbed on graphene oxide and a comparison with thymine-rich DNA.

    Science.gov (United States)

    Huang, Po-Jung Jimmy; van Ballegooie, Courtney; Liu, Juewen

    2016-06-07

    Mercury is a highly toxic heavy metal and many DNA-based biosensors have been recently developed for Hg(2+) detection in water. Among them, thymine-rich DNA is the most commonly used for designing Hg(2+) sensors. However, the thymine-Hg(2+) interaction is strongly affected by the buffer conditions. We recently reported a molecular beacon containing phosphorothioate (PS)-modified RNA linkages that can be cleaved by Hg(2+). In this work, the fluorescence quenching and DNA adsorption properties of nano-sized graphene oxide (NGO) were used to develop a new sensor using the PS-RNA chemistry. Three DNA probes, containing one, three and five PS-RNA linkages, respectively, were tested. Finally, a fluorophore-labeled poly-A DNA with five PS-RNA linkages was selected and adsorbed by NGO. In the presence of Hg(2+), the fluorophore was released from NGO due to the cleavage reaction, resulting in a fluorescence enhancement. This sensor is highly selective for Hg(2+) with a detection limit of 8.5 nM Hg(2+). For comparison, a fluorophore-labeled poly-T DNA was also tested, which responded to Hg(2+) more slowly and was inhibited by high NaCl concentrations, while the PS-RNA probe was more tolerant to different buffer conditions. This work indicates a new method for interfacing DNA with NGO for Hg(2+) detection.

  11. Architecture for fiber-optic sensors and actuators in aircraft propulsion systems

    Science.gov (United States)

    Glomb, W. L., Jr.

    1990-01-01

    This paper describes a design for fiber-optic sensing and control in advanced aircraft Electronic Engine Control (EEC). The recommended architecture is an on-engine EEC which contains electro-optic interface circuits for fiber-optic sensors. Size and weight are reduced by multiplexing arrays of functionally similar sensors on a pairs of optical fibers to common electro-optical interfaces. The architecture contains interfaces to seven sensor groups. Nine distinct fiber-optic sensor types were found to provide the sensing functions. Analysis revealed no strong discriminator (except reliability of laser diodes and remote electronics) on which to base a selection of preferred common interface type. A hardware test program is recommended to assess the relative maturity of the technologies and to determine real performance in the engine environment.

  12. Feasibility Study on the Development of 2-channel Embedded Infrared Fiber-optic Sensor for Thermometry of Secondary Water System in Nuclear Power Plant

    International Nuclear Information System (INIS)

    Yoo, W. J.; Jang, K. W.; Seo, J. K.; Moon, J.; Han, K. T.; Lee, B.; Park, B. G.

    2011-01-01

    Any warm object by measuring the emitted infrared (IR) radiation. The radiometers using infrared optical fibers are based on the relationship between the temperature of a heat source and the quality and the quantity of an IR radiation. To measure physical properties including a temperature, optical fiber-based sensor has many advantages, such as small size, low cost, high resolution, remote sensing and immunity to electromagnetic radiation over conventional electrical sensors. In this study, we carried out the feasibility study on the development of an embedded IR fiber-optic sensor for thermometry of the secondary water system in a nuclear power plant. The 2-channel embedded fiberoptic temperature sensor was fabricated using two identical IR optical fibers for accurate thermometry without complicated calibration processes. To decide accurate temperature of the water, we measured the difference between the IR radiations emitted from the two temperature sensing probes according to the temperature variation of the water

  13. Lingual traction to facilitate fiber-optic intubation of difficult airways: a single-anesthesiologist randomized trial.

    Science.gov (United States)

    Ching, Yiu-Hei; Karlnoski, Rachel A; Chen, Henian; Camporesi, Enrico M; Shah, Vimal V; Padhya, Tapan A; Mangar, Devanand

    2015-04-01

    Flexible fiber-optic bronchoscope-guided orotracheal intubation is a valuable technique with demonstrated benefits in the management of difficult airways. Despite its popularity with anesthesia providers, the technique is not fail-safe and airway-related complications secondary to failed intubation attempts remain an important problem. We sought to determine the effect of incorporating lingual traction on the success rate of fiber-optic bronchoscope-guided intubation in patients with anticipated difficult airways. In this prospective, randomized, cohort study, we enrolled 91 adult patients with anticipated difficult airways scheduled for elective surgery to undergo fiber-optic bronchoscope-guided orotracheal intubation alone or with lingual traction by an individual anesthesiologist after induction of general anesthesia and neuromuscular blockade. A total of 78 patients were randomized: 39 patients to the fiber-optic bronchoscope-guided intubation with lingual traction group and 39 patients to the fiber-optic bronchoscope-guided intubation alone group. The primary endpoint was the rate of successful first attempt intubations. The secondary outcome was sore throat grade on post-operative day 1. Fiber-optic intubation with lingual traction compared to fiber-optic intubation alone resulted in a higher success rate (92.3 vs. 74.4 %, χ (2) = 4.523, p = 0.033) and greater odds for successful first attempt intubation (OR 4.138, 95 % CI 1.041-16.444, p = 0.044). Sore throat severity on post-operative day 1 was not significantly different but trended towards worsening grades with lingual traction. In this study, lingual traction was shown to be a valuable maneuver for facilitating fiber-optic bronchoscope-guided intubation in the management of patients with anticipated difficult airways.

  14. Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

    Science.gov (United States)

    Kékedy-Nagy, László; Shipovskov, Stepan; Ferapontova, Elena E

    2016-08-16

    Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the "on-off" signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami , E. ; Clima , L. ; Gothelf , K. ; Ferapontova , E. E. Anal. Chem. 2011 , 83 , 1594 ) providing the robust "off-on" nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.

  15. The interaction of taurine-salicylaldehyde Schiff base copper(II) complex with DNA and the determination of DNA using the complex as a fluorescence probe

    Science.gov (United States)

    Zhang, Xiaoyan; Wang, Yong; Zhang, Qianru; Yang, Zhousheng

    2010-09-01

    The interaction of taurine-salicylaldehyde Schiff base copper(II) (Cu(TSSB) 22+) complex with DNA was explored by using UV-vis, fluorescence spectrophotometry, and voltammetry. In pH 7.4 Tris-HCl buffer solution, the binding constant of the Cu(TSSB) 22+ complex interaction with DNA was 3.49 × 10 4 L mol -1. Moreover, due to the fluorescence enhancing of Cu(TSSB) 22+ complex in the presence of DNA, a method for determination of DNA with Cu(TSSB) 22+ complex as a fluorescence probe was developed. The fluorescence spectra indicated that the maximum excitation and emission wavelength were 389 nm and 512 nm, respectively. Under optimal conditions, the calibration graphs are linear over the range of 0.03-9.03 μg mL -1 for calf thymus DNA (CT-DNA), 0.10-36 μg mL -1 for yeast DNA and 0.01-10.01 μg mL -1 for salmon DNA (SM-DNA), respectively. The corresponding detection limits are 7 ng mL -1 for CT-DNA, 3 ng mL -1 for yeast DNA and 3 ng mL -1 for SM-DNA. Using this method, DNA in synthetic samples was determined with satisfactory results.

  16. New Concepts of Fluorescent Probes for Specific Detection of DNA Sequences: Bis-Modified Oligonucleotides in Excimer and Exciplex Detection

    Directory of Open Access Journals (Sweden)

    Gbaj A

    2009-01-01

    Full Text Available The detection of single base mismatches in DNA is important for diagnostics, treatment of genetic diseases, and identification of single nucleotide polymorphisms. Highly sensitive, specific assays are needed to investigate genetic samples from patients. The use of a simple fluorescent nucleoside analogue in detection of DNA sequence and point mutations by hybridisation in solution is described in this study. The 5’-bispyrene and 3’-naphthalene oligonucleotide probes form an exciplex on hybridisation to target in water and the 5’-bispyrene oligonucleotide alone is an adequate probe to determine concentration of target present. It was also indicated that this system has a potential to identify mismatches and insertions. The aim of this work was to investigate experimental structures and conditions that permit strong exciplex emission for nucleic acid detectors, and show how such exciplexes can register the presence of mismatches as required in SNP analysis. This study revealed that the hybridisation of 5'-bispyrenyl fluorophore to a DNA target results in formation of a fluorescent probe with high signal intensity change and specificity for detecting a complementary target in a homogeneous system. Detection of SNP mutations using this split-probe system is a highly specific, simple, and accessible method to meet the rigorous requirements of pharmacogenomic studies. Thus, it is possible for the system to act as SNP detectors and it shows promise for future applications in genetic testing.

  17. Dexmedetomidine premedication for fiberoptic intubation in patients of temporomandibular joint ankylosis: A randomized clinical trial

    Directory of Open Access Journals (Sweden)

    Kumkum Gupta

    2012-01-01

    Full Text Available Background : Fiberoptic intubation is the gold standard technique for difficult airway management in patients of temporomandibular joint. This study was aimed to evaluate the clinical efficacy and safety of dexmedetomidine as premedication with propofol infusion for fiberoptic intubation. Methods: Consent was obtained from 46 adult patients of temporomandibular joint ankylosis, scheduled for gap arthroplasty. They were enrolled for thisdouble-blind, randomized, prospective clinical trial with two treatment groups - Group D and Group P, of 23 patients each. Group D patients had received premedication of dexmedetomidine 1 μg/kg infused over 10 min followed by sedative propofol infusion and the control Group P patients were given only propofol infusion to achieve sedation. Condition achieved at endoscopy, intubating conditions, hemodynamic changes and postoperative events were evaluated as primary outcome. Results : The fiberoptic intubation was successful with satisfactory endoscopic and intubating condition in all patients. Dexmedetomidine premedication has provided satisfactory conditions for fiberoptic intubation and attenuated the hemodynamic response of fiberoptic intubation than the propofol group. Conclusion : Fiberoptic intubation was found to be easier with dexmedetomidine premedication along with sedative infusion of propofol with complete amnesia of the procedure, hemodynamic stability and preservation of patent airway.

  18. Fiber-optic seismic sensor

    International Nuclear Information System (INIS)

    Finch, G. W.; Udd, E.

    1985-01-01

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

  19. Detection of Hepatitis B Virus M204I Mutation by Quantum Dot-Labeled DNA Probe

    Directory of Open Access Journals (Sweden)

    Cheng Zhang

    2017-04-01

    Full Text Available Quantum dots (QDs are semiconductor nanoparticles with a diameter of less than 10 nm, which have been widely used as fluorescent probes in biochemical analysis and vivo imaging because of their excellent optical properties. Sensitive and convenient detection of hepatitis B virus (HBV gene mutations is important in clinical diagnosis. Therefore, we developed a sensitive, low-cost and convenient QDs-mediated fluorescent method for the detection of HBV gene mutations in real serum samples from chronic hepatitis B (CHB patients who had received lamivudine or telbivudine antiviral therapy. We also evaluated the efficiency of this method for the detection of drug-resistant mutations compared with direct sequencing. In CHB, HBV DNA from the serum samples of patients with poor response or virological breakthrough can be hybridized to probes containing the M204I mutation to visualize fluorescence under fluorescence microscopy, where fluorescence intensity is related to the virus load, in our method. At present, the limits of the method used to detect HBV genetic variations by fluorescence quantum dots is 103 IU/mL. These results show that QDs can be used as fluorescent probes to detect viral HBV DNA polymerase gene variation, and is a simple readout system without complex and expensive instruments, which provides an attractive platform for the detection of HBV M204I mutation.

  20. Radioactively labelled DNA probes for crop improvement. Proceedings of a final research co-ordination meeting

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-11-01

    With the advent of DNA molecular marker technology in the 1980s plant breeding had a new and powerful tool with which to increase its efficacy. Such markers are abundant and directly reveal information about the genotype and therefore are more useful than simple phenotypic markers. In plant breeding applications, molecular markers reveal information about variability and genetic relationships, and enable genetic mapping, which greatly assists the breeder in selection of parents and progeny, as well as in management of breeding strategies. Furthermore, molecular markers linked to phenotypic traits permit very early selection of superior progenies from breeding populations, therefore significantly reducing the need for field testing and greatly increasing efficiency of plant breeding programmes. For this to occur the oligonucleotide probes for labelling genetic markers and/or the primers for polymerase chain reactions to amplify genetic markers needed to be also accessible to scientists in developing Member States. In addition, technical information, training and troubleshooting were needed to support the utilization of DNA markers. In the early 1990s there was a dramatic increase in requests for access to this technology. This co-ordinated research project (CRP) facilitated the transfer of molecular marker technology, in terms of both material and information, from advanced laboratories to assist breeding programmes in developing countries. Two other CRPs were conducted concurrently in order to assist developing Member States to utilise molecular markers - Application of DNA Based Marker Mutations for Improvement of Cereals and other Sexually Reproduced Crop Plants, and Use of Novel DNA Fingerprinting Techniques for the Detection and Characterisation of Genetic Variation in Vegetatively Propagated Crops (IAEA-TECDOC-1010 and IAEA-TECDOC-1047, respectively). The present CRP built upon the success of the former projects by ensuring the availability of probes

  1. Radioactively labelled DNA probes for crop improvement. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    2001-11-01

    With the advent of DNA molecular marker technology in the 1980s plant breeding had a new and powerful tool with which to increase its efficacy. Such markers are abundant and directly reveal information about the genotype and therefore are more useful than simple phenotypic markers. In plant breeding applications, molecular markers reveal information about variability and genetic relationships, and enable genetic mapping, which greatly assists the breeder in selection of parents and progeny, as well as in management of breeding strategies. Furthermore, molecular markers linked to phenotypic traits permit very early selection of superior progenies from breeding populations, therefore significantly reducing the need for field testing and greatly increasing efficiency of plant breeding programmes. For this to occur the oligonucleotide probes for labelling genetic markers and/or the primers for polymerase chain reactions to amplify genetic markers needed to be also accessible to scientists in developing Member States. In addition, technical information, training and troubleshooting were needed to support the utilization of DNA markers. In the early 1990s there was a dramatic increase in requests for access to this technology. This co-ordinated research project (CRP) facilitated the transfer of molecular marker technology, in terms of both material and information, from advanced laboratories to assist breeding programmes in developing countries. Two other CRPs were conducted concurrently in order to assist developing Member States to utilise molecular markers - Application of DNA Based Marker Mutations for Improvement of Cereals and other Sexually Reproduced Crop Plants, and Use of Novel DNA Fingerprinting Techniques for the Detection and Characterisation of Genetic Variation in Vegetatively Propagated Crops (IAEA-TECDOC-1010 and IAEA-TECDOC-1047, respectively). The present CRP built upon the success of the former projects by ensuring the availability of probes

  2. Temperature-independent refractometer based on fiber-optic Fabry-Perot interferometer

    Science.gov (United States)

    Li, Jiacheng; Qiao, Xueguang; Wang, Ruohui; Rong, Qiangzhou; Bao, Weijia; Shao, Zhihua; Yang, Tingting

    2016-04-01

    A miniature fiber-optic refractometer based on Fabry-Perot interferometer (FPI) has been proposed and experimentally demonstrated. The sensing head consists of a short section of photonics crystal fiber (PCF) spliced to a single mode fiber (SMF), in which the end-face of the PCF is etched to remove holey structure with hydrofluoric (HF) acid. A Fabry-Perot interference spectrum is achieved based on the reflections from the fusion splicing interface and the end-face of the core of PCF. The interference fringe is sensitive to the external refractive index (RI) with an intensity-referenced sensitivity of 358.27 dB/RIU ranging from 1.33 to 1.38. The sensor has also been implemented for the concentration measurement of λ-phage DNA solution. In addition, the dip intensity is insensitive to the ambient temperature variation, making it a good candidate for temperature-independent bio-sensing area.

  3. Fiber-Optic Pressure Sensor With Dynamic Demodulation Developed

    Science.gov (United States)

    Lekki, John D.

    2002-01-01

    Researchers at the NASA Glenn Research Center developed in-house a method to detect pressure fluctuations using a fiber-optic sensor and dynamic signal processing. This work was in support of the Intelligent Systems Controls and Operations project under NASA's Information Technology Base Research Program. We constructed an optical pressure sensor by attaching a fiber-optic Bragg grating to a flexible membrane and then adhering the membrane to one end of a small cylinder. The other end of the cylinder was left open and exposed to pressure variations from a pulsed air jet. These pressure variations flexed the membrane, inducing a strain in the fiber-optic grating. This strain was read out optically with a dynamic spectrometer to record changes in the wavelength of light reflected from the grating. The dynamic spectrometer was built in-house to detect very small wavelength shifts induced by the pressure fluctuations. The spectrometer is an unbalanced interferometer specifically designed for maximum sensitivity to wavelength shifts. An optimum pathlength difference, which was determined empirically, resulted in a 14-percent sensitivity improvement over theoretically predicted path-length differences. This difference is suspected to be from uncertainty about the spectral power difference of the signal reflected from the Bragg grating. The figure shows the output of the dynamic spectrometer as the sensor was exposed to a nominally 2-kPa peak-to-peak square-wave pressure fluctuation. Good tracking, sensitivity, and signal-to-noise ratios are evident even though the sensor was constructed as a proof-of-concept and was not optimized in any way. Therefore the fiber-optic Bragg grating, which is normally considered a good candidate as a strain or temperature sensor, also has been shown to be a good candidate for a dynamic pressure sensor.

  4. Monitoring of itaconic acid hydrogenation in a trickle bed reactor using fiber-optic coupled near-infrared spectroscopy.

    Science.gov (United States)

    Wood, Joseph; Turner, Paul H

    2003-03-01

    Near-infrared (NIR) spectroscopy has been applied to determine the conversion of itaconic acid in the effluent stream of a trickle bed reactor. Hydrogenation of itaconic to methyl succinic acid was carried out, with the trickle bed operating in recycle mode. For the first time, NIR spectra of itaconic and methyl succinic acids in aqueous solution, and aqueous mixtures withdrawn from the reactor over a range of reaction times, have been recorded using a fiberoptic sampling probe. The infrared spectra displayed a clear isolated absorption band at a wavenumber of 6186 cm(-1) (wavelength 1.617 microm) resulting from the =C-H bonds of itaconic acid, which was found to decrease in intensity with increasing reaction time. The feature could be more clearly observed from plots of the first derivatives of the spectra. A partial least-squares (PLS) model was developed from the spectra of 13 reference samples and was used successfully to calculate the concentration of the two acids in the reactor effluent solution. Itaconic acid conversions of 23-29% were calculated after 360 min of reaction time. The potential of FT-NIR with fiber-optic sampling for remote monitoring of three-phase catalytic reactors and validation of catalytic reactor models is highlighted in the paper.

  5. GENETIC DIVERSITY OF TYPHA LATIFOLIA (TYPHACEAE) AND THE IMPACT OF POLLUTANTS EXAMINED WITH TANDEM-REPETITIVE DNA PROBES

    Science.gov (United States)

    Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated "core" sequences (GACA, GATA, and GCAC). The principal objectives of this investigation w...

  6. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples

    International Nuclear Information System (INIS)

    Voordouw, G.; Voordouw, J.K.; Karkhoff-Schweizer, R.R.; Fedorak, P.M.; Westlake, D.W.S.

    1991-01-01

    A novel method for identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a standard) to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples

  7. Standing waves in fiber-optic interferometers

    NARCIS (Netherlands)

    De Haan, V.; Santbergen, R.; Tijssen, M.; Zeman, M.

    2011-01-01

    A study is presented giving the response of three types of fiber-optic interferometers by which a standing wave through an object is investigated. The three types are a Sagnac, Mach–Zehnder and Michelson–Morley interferometer. The response of the Mach–Zehnder interferometer is similar to the Sagnac

  8. A “four-ferrocene” modified stem-loop structure as a probe for sensitive detection and single-base mismatch discrimination of DNA

    International Nuclear Information System (INIS)

    Chatelain, Grégory; Ripert, Micaël; Farre, Carole; Ansanay-Alex, Salomé; Chaix, Carole

    2012-01-01

    We report the use of a four-ferrocene modified oligonucleotide as a probe for DNA detection with a gold electrode microsystem. This oligonucleotide is synthesized by automated solid-phase synthesis with four successive ferrocene moieties at the 5′-end and a C6-thiol modifier group at the 3′-end. The grafting of this 4Fc-DNA probe on a gold electrode microsystem results in the appearance of the ferrocene redox couple in cyclic voltammetry. The probe sequence is a stem-loop structure that folds efficiently on the electrode, thus optimizing electron transfer. Such architecture serves as sensor for DNA detection which is based on hybridization. The resulting disposable voltammetric sensor allowed direct, reagentless DNA detection in a small volume (20 μL). Electrochemical response upon hybridization with complementary short sequence (30-base length) and long sequence (50-base length) strands was observed by differential pulse voltammetry. Current variations were compared. The longer the sequence, the greater the decrease in current. The system's detection limit was estimated at 3.5 pM (0.07 fmol in 20 μL) with the 50-base length target and provided a dynamic detection range between 3.5 pM and 5 nM. Single mismatch detection showed a good level of sensitivity. The system was regenerated twice with no significant loss of Fc signal. Finally, 1 pM sensitivity was reached with a long chain analog of DNA PCR products of Influenza virus.

  9. Immunoglobulin heavy-chain fluorescence in situ hybridization-chromogenic in situ hybridization DNA probe split signal in the clonality assessment of lymphoproliferative processes on cytological samples.

    Science.gov (United States)

    Zeppa, Pio; Sosa Fernandez, Laura Virginia; Cozzolino, Immacolata; Ronga, Valentina; Genesio, Rita; Salatiello, Maria; Picardi, Marco; Malapelle, Umberto; Troncone, Giancarlo; Vigliar, Elena

    2012-12-25

    The human immunoglobulin heavy-chain (IGH) locus at chromosome 14q32 is frequently involved in different translocations of non-Hodgkin lymphoma (NHL), and the detection of any breakage involving the IGH locus should identify a B-cell NHL. The split-signal IGH fluorescence in situ hybridization-chromogenic in situ hybridization (FISH-CISH) DNA probe is a mixture of 2 fluorochrome-labeled DNAs: a green one that binds the telomeric segment and a red one that binds the centromeric segment, both on the IGH breakpoint. In the current study, the authors tested the capability of the IGH FISH-CISH DNA probe to detect IGH translocations and diagnose B-cell lymphoproliferative processes on cytological samples. Fifty cytological specimens from cases of lymphoproliferative processes were tested using the split-signal IGH FISH-CISH DNA probe and the results were compared with light-chain assessment by flow cytometry (FC), IGH status was tested by polymerase chain reaction (PCR), and clinicohistological data. The signal score produced comparable results on FISH and CISH analysis and detected 29 positive, 15 negative, and 6 inadequate cases; there were 29 true-positive cases (66%), 9 true-negative cases (20%), 6 false-negative cases (14%), and no false-positive cases (0%). Comparing the sensitivity of the IGH FISH-CISH DNA split probe with FC and PCR, the highest sensitivity was obtained by FC, followed by FISH-CISH and PCR. The split-signal IGH FISH-CISH DNA probe is effective in detecting any translocation involving the IGH locus. This probe can be used on different samples from different B-cell lymphoproliferative processes, although it is not useful for classifying specific entities. Cancer (Cancer Cytopathol) 2012;. © 2012 American Cancer Society. Copyright © 2012 American Cancer Society.

  10. ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly

    Directory of Open Access Journals (Sweden)

    Spang Rainer

    2009-12-01

    Full Text Available Abstract Background The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis. Results We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/. Conclusions ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.

  11. Multi-dimensional fiber-optic radiation sensor for ocular proton therapy dosimetry

    International Nuclear Information System (INIS)

    Jang, K.W.; Yoo, W.J.; Moon, J.; Han, K.T.; Park, B.G.; Shin, D.; Park, S-Y.; Lee, B.

    2012-01-01

    In this study, we fabricated a multi-dimensional fiber-optic radiation sensor, which consists of organic scintillators, plastic optical fibers and a water phantom with a polymethyl methacrylate structure for the ocular proton therapy dosimetry. For the purpose of sensor characterization, we measured the spread out Bragg-peak of 120 MeV proton beam using a one-dimensional sensor array, which has 30 fiber-optic radiation sensors with a 1.5 mm interval. A uniform region of spread out Bragg-peak using the one-dimensional fiber-optic radiation sensor was obtained from 20 to 25 mm depth of a phantom. In addition, the Bragg-peak of 109 MeV proton beam was measured at the depth of 11.5 mm of a phantom using a two-dimensional sensor array, which has 10×3 sensor array with a 0.5 mm interval.

  12. Electronic Detection of DNA Hybridization by Coupling Organic Field-Effect Transistor-Based Sensors and Hairpin-Shaped Probes

    Directory of Open Access Journals (Sweden)

    Corrado Napoli

    2018-03-01

    Full Text Available In this paper, the electronic transduction of DNA hybridization is presented by coupling organic charge-modulated field-effect transistors (OCMFETs and hairpin-shaped probes. These probes have shown interesting properties in terms of sensitivity and selectivity in other kinds of assays, in the form of molecular beacons (MBs. Their integration with organic-transistor based sensors, never explored before, paves the way to a new class of low-cost, easy-to-use, and portable genetic sensors with enhanced performances. Thanks to the peculiar characteristics of the employed sensor, measurements can be performed at relatively high ionic strengths, thus optimizing the probes’ functionality without affecting the detection ability of the device. A complete electrical characterization of the sensor is reported, including calibration with different target concentrations in the measurement environment and selectivity evaluation. In particular, DNA hybridization detection for target concentration as low as 100 pM is demonstrated.

  13. Fiberoptic laryngoscopy under general anesthesia in neonates

    NARCIS (Netherlands)

    L.J. Hoeve (Hans); R.H.M. van Poppelen

    1990-01-01

    textabstractAbstract In the Sophia Children's Hospital we perform fiberoptic laryngoscopy in neonates under general anesthesia without the use of muscle relaxants in the diagnostics of functional laryngeal disorders. The necessary diagnostic and anesthetic equipment is described. Special attention

  14. CATV Fiberoptic Cable Markets In The U.S.

    Science.gov (United States)

    Kessler, John N.

    1984-03-01

    "Bandwidth on a metropolitan CATV cable plant is a resource that may be compared today with the crude oil beneath the Arabian desert at the turn of the century. It will provide a radically new two-way communications medium for homes and businesses, and it will change not only the way we communicate but possibly even the way we live." This prediction was made last year by William Zachman, vice president of research for International Data Corp. If Zachman is right, and our research tends to indicate he is, then fiberoptics will become the transmission medium that will facilitate two-way broadband communication. However, many of the multiple system CATV operators in the U.S. as well as many of the manufacturers of fiberoptic waveguide and cable believe that interactive video systems are not really very important. They are wrong. Broadband fiberoptic systems have just begun to impact the U.S. communications market. And within 5 years, tremendous changes will occur not only with regard to growth, but with regard to the supplier industry structure. Interactive, switched, video systems in the U.S. go back to the early 1960s, and the experiments at Bell Laboratories with what was then called Picturephone. This was com-pressed video transmission via telephone lines from one subscriber to another. Field trials were conducted in several U.S. cities for a period of years. But the commercial response to Picturephone at that time was so lacking that AT&T discontinued the trials and the work. But that is changing. Part of the reason for the change is due to the changing communication needs of the U.S. and of the world: the increase in the amount of information used by large numbers of people, the concurrent rise in the use of computers, the digitization of communications media, the rise in the level of experience with electronic communications, and perhaps most importantly the convergence of audio, data, image and video communications. There are technological reasons for the slow

  15. Using Monoclonal Antibody to Determine Lead Ions with a Localized Surface Plasmon Resonance Fiber-optic Biosensor

    Directory of Open Access Journals (Sweden)

    Mon-Fu Chung

    2008-01-01

    Full Text Available A novel reflection-based localized surface plasmon resonance (LSPR fiber-optic probe has been developed to determine the heavy metal lead ion concentration. Monoclonal antibody as the detecting probe containing massive amino groups to capture Pb(II-chelate complexes was immobilized onto gold nanoparticle-modified optical fiber (NMAuOF. The optimal immobilizing conditions of monoclonal antibody on to the NMAuOF are 189 μg/mL in pH7.4 PBS for 2 h at 25°C. The absorbability of the functionalized NMAuOF sensor increases to 12.2 % upon changing the Pb(II-EDTA level from 10 to 100 ppb with a detection limit of 0.27 ppb. The sensor retains 92.7 % of its original activity and gives reproducible results after storage in 5% D-( -Trehalose dehydrate solution at 4°C for 35 days. In conclusion, the monoclonal antibody-functionalized NMAuOF sensor shows a promising result for determining the concentration of Pb(II with high sensitivity.

  16. Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays

    DEFF Research Database (Denmark)

    Petersen, J.; Poulsen, Lena; Petronis, S.

    2008-01-01

    is called a multi-thermal array washer (MTAW), and it has eight individually controlled heating zones, each of which corresponds to the location of a subarray on a slide. Allele-specific oligonucleotide probes for nine mutations in the beta-globin gene were spotted in eight identical subarrays at positions......DNA microarrays are generally operated at a single condition, which severely limits the freedom of designing probes for allele-specific hybridization assays. Here, we demonstrate a fluidic device for multi-stringency posthybridization washing of microarrays on microscope slides. This device...

  17. Dumbbell DNA-templated CuNPs as a nano-fluorescent probe for detection of enzymes involved in ligase-mediated DNA repair.

    Science.gov (United States)

    Qing, Taiping; He, Xiaoxiao; He, Dinggeng; Ye, Xiaosheng; Shangguan, Jingfang; Liu, Jinquan; Yuan, Baoyin; Wang, Kemin

    2017-08-15

    DNA repair processes are responsible for maintaining genome stability. Ligase and polynucleotide kinase (PNK) have important roles in ligase-mediated DNA repair. The development of analytical methods to monitor these enzymes involved in DNA repair pathways is of great interest in biochemistry and biotechnology. In this work, we reported a new strategy for label-free monitoring PNK and ligase activity by using dumbbell-shaped DNA templated copper nanoparticles (CuNPs). In the presence of PNK and ligase, the dumbbell-shaped DNA probe (DP) was locked and could resist the digestion of exonucleases and then served as an efficient template for synthesizing fluorescent CuNPs. However, in the absence of ligase or PNK, the nicked DP could be digested by exonucleases and failed to template fluorescent CuNPs. Therefore, the fluorescence changes of CuNPs could be used to evaluate these enzymes activity. Under the optimal conditions, highly sensitive detection of ligase activity of about 1U/mL and PNK activity down to 0.05U/mL is achieved. To challenge the practical application capability of this strategy, the detection of analyte in dilute cells extracts was also investigated and showed similar linear relationships. In addition to ligase and PNK, this sensing strategy was also extended to the detection of phosphatase, which illustrates the versatility of this strategy. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. 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

  19. The use of AMPPD as an alternative substrate for AP-mediated detection of nonradiolabeled DNA probes in Eucalyptus saligna

    OpenAIRE

    De Moura Campos Pardini, M. I. [UNESP; Wolff, J. L C [UNESP; Lopes, C. R. [UNESP

    1993-01-01

    We present a non-radioactive alternative to Southern's (J. Mol. Biol. 98: 503-517, 1975) DNA-DNA hybridization technique. The use of AMPPD - Disodium 3-(4-Methoxyspiro {1,2-dioxetane-3,2'tricyclo[3.3.1.1(3,7)]decan}-4-yl)phyenyl phosphate as an alternative substrate for AP-mediated detection of digoxigenin-11 dUTP-labeled probes made possible the simple and nonhazardous reuse of blots. We used 0.8 % agarose gels containing 30 mug per lane of Eucalyptus saligna DNA, digested with Eco RI, elect...

  20. Transbronchial Catheter Drainage via Fiberoptic Bronchoscope in Intractable Lung Abscess

    Science.gov (United States)

    Jeong, Man Pyo; Kim, Woo Sung; Han, Sung Koo; Shim, Young Soo; Kim, Keun Youl; Han, Yong Chol

    1989-01-01

    The use of the fiberoptic bronchoscope as a drainage procedure for lung abscess has become more and more widespread. We have recently adopted the technique of inserting a simple polyethylene catheter through the flexible fiberoptic bronchoscope into the abscess cavity of 11 patients with lung absess. All cases had not responded to aggressive postural drainage and adequate antibiotic therapy for at least a week. The results were as follows: Among 11 patients, the therapeutic response was dramatic in 6 patients.In the successful group, the abscess sizes were greater than 8cm in diameter and the air-fluid levels were higher than two-thirds of the cavity.Additional diagnoses, other than bacterial lung abscess, could be made in 2 cases when otherwise the diagnosis would have remained in doubt. The authors suggest that catheter drainage via fiberoptic bronchoscpope is an effective treatment modality in the large lung abscess with a high air-fluid level which is intractable to other medical approaches, and it is also a safe procedure. PMID:2487405

  1. Detection of human papillomavirus type 6/11 DNA in conjunctival papillomas by in situ hybridization with radioactive probes

    International Nuclear Information System (INIS)

    McDonnell, P.J.; McDonnell, J.M.; Kessis, T.; Green, W.R.; Shah, K.V.

    1987-01-01

    Twenty-three conjunctival papillomas and 28 conjunctival dysplasias were examined for human papillomavirus (HPV)-DNA sequences by in situ hybridization with nick-translated 35 S-labeled HPV probes. Adjacent paraffin sections were hybridized with HPV type 2, 6, 16, and 18 probes at Tm - 17 degrees C. Fifteen tissues, all papillomas, displayed positive hybridization with the HPV-6 probe. Infection with HPV-6 (or the closely related HPV-11) appeared to be responsible for most of the conjunctival papillomas of children and young adults. The presence of genital tract HPV-6 in these lesions suggests that some of the infections were acquired during passage through an infected birth canal. The lack of hybridization in adult conjunctival dysplasias indicates either that HPVs are not associated with this condition or that the probes and the technique utilized were not adequate for demonstration of this association

  2. The use of radionuclide DNA probe technology for epidemiological studies of tegumentary leishmaniasis in Mato Grosso state, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Antero Silva Ribeiro de [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN), Belo Horizonte, MG (Brazil); Fernandes, Octavio [Fundacao Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ (Brazil). Dept. de Medicina Tropical; Heub, Marcia; Fontes, Cor Jesus [Universidade Federal do Mato Grosso, Cuiaba, MT (Brazil). Hospital Universitario Julio Muller; Carvalho, Maria de Lourdes Ribeiro; Melo, Maria Norma de [Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil). Dept. de Parasitologia

    2005-10-15

    DNA hybridisation, using probes labelled with 32 P, was used to type Leishmania samples isolated from patients living in endemic areas of Mato Grosso State (Brazil), and clinically diagnosed as having tegumentary leishmaniasis. k DNA cloned mini-circle probes specific for the Leishmania mexicana and Leishmania braziliensis complexes were used. The results showed that L. braziliensis is the predominant group infecting human patients in the state. Sixty-eight samples were typed, 64 samples (94.1%) belonging to the L. braziliensis complex and only four (5.9%) belonging to the L. mexicana complex. Accurate identification of the Leishmania permits better orientation of the medical follow-up, since clinical manifestations may vary depending on the complex to which the parasite belongs. The epidemiological information furnished by the identification of the Leishmania in given endemic area is also essential for the design of appropriate control measures. (author)

  3. The use of radionuclide DNA probe technology for epidemiological studies of tegumentary leishmaniasis in Mato Grosso state, Brazil

    International Nuclear Information System (INIS)

    Andrade, Antero Silva Ribeiro de; Fernandes, Octavio; Heub, Marcia; Fontes, Cor Jesus; Carvalho, Maria de Lourdes Ribeiro; Melo, Maria Norma de

    2005-01-01

    DNA hybridisation, using probes labelled with 32 P, was used to type Leishmania samples isolated from patients living in endemic areas of Mato Grosso State (Brazil), and clinically diagnosed as having tegumentary leishmaniasis. k DNA cloned mini-circle probes specific for the Leishmania mexicana and Leishmania braziliensis complexes were used. The results showed that L. braziliensis is the predominant group infecting human patients in the state. Sixty-eight samples were typed, 64 samples (94.1%) belonging to the L. braziliensis complex and only four (5.9%) belonging to the L. mexicana complex. Accurate identification of the Leishmania permits better orientation of the medical follow-up, since clinical manifestations may vary depending on the complex to which the parasite belongs. The epidemiological information furnished by the identification of the Leishmania in given endemic area is also essential for the design of appropriate control measures. (author)

  4. Typing for HLA-DPB1*03 and HLA-DPB1*06 using allele-specific DNA in vitro amplification and allele-specific oligonucleotide probes. Detection of "new" DPB1*06 variants

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P

    1989-01-01

    DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes has recently been reported. The resulting DNA amplification was specific for the HLA-DPB locus. Typing for the individual DPB alleles was exclusively dependent on the hybridizations of the probe...

  5. Characterization of rat brain NCAM mRNA using DNA oligonucleotide probes

    DEFF Research Database (Denmark)

    Andersson, A M; Gaardsvoll, H; Giladi, E

    1990-01-01

    A number of different isoforms of the neural cell adhesion molecule (NCAM) have been identified. The difference between these is due to alternative splicing of a single NCAM gene. In rat brain NCAM mRNAs with sizes of 7.4, 6.7, 5.2, 4.3 and 2.9 kb have been reported. We have synthesized six DNA...... oligonucleotides, that hybridize to different exons in the NCAM gene. Furthermore we have constructed three oligonucleotides, that exclusively hybridize to mRNAs lacking certain exons, by letting them consist of sequences adjacent to both sides of the splice sites. By means of these probes we have characterized...... the five NCAM mRNAs in rat brain....

  6. Method and apparatus for synthesis of arrays of DNA probes

    Science.gov (United States)

    Cerrina, Francesco; Sussman, Michael R.; Blattner, Frederick R.; Singh-Gasson, Sangeet; Green, Roland

    2002-04-23

    The synthesis of arrays of DNA probes sequences, polypeptides, and the like is carried out using a patterning process on an active surface of a substrate. An image is projected onto the active surface of the substrate utilizing an image former that includes a light source that provides light to a micromirror device comprising an array of electronically addressable micromirrors, each of which can be selectively tilted between one of at least two positions. Projection optics receives the light reflected from the micromirrors along an optical axis and precisely images the micromirrors onto the active surface of the substrate, which may be used to activate the surface of the substrate. The first level of bases may then be applied to the substrate, followed by development steps, and subsequent exposure of the substrate utilizing a different pattern of micromirrors, with further repeats until the elements of a two dimensional array on the substrate surface have an appropriate base bound thereto. The micromirror array can be controlled in conjunction with a DNA synthesizer supplying appropriate reagents to a flow cell containing the active substrate to control the sequencing of images presented by the micromirror array in coordination of the reagents provided to the substrate.

  7. Preparing to perform an awake fiberoptic intubation.

    LENUS (Irish Health Repository)

    Walsh, M E

    2012-02-03

    Fiberoptically guided tracheal intubation represents one of the most important advances in airway management to occur in the past thirty years. Perhaps its most important role is in management of the anticipated difficult airway. This is a situation in which the dangers of encountering the life-threatening "can\\'t intubate, can\\'t ventilate" situation can be avoided by placement of an endotracheal tube while the patient is awake. Although skill at the procedure of endoscopy is obviously necessary in this setting, these authors hold that success or failure of the technique frequently depends on the adequacy of preparation. These measures include 1) pre-operative assessment of the patient; 2) careful explanation of what lies in store; 3) "setting the stage"; 4) preparing the equipment to be used; and 5) preparing the patient (antisialogue, sedation, application of topical anesthesia to the upper airway). If these preparatory measures are carried out meticulously, the likelihood of performing a successful and comfortable awake fiberoptic tracheal intubation is greatly increased.

  8. Study of polarization properties of fiber-optics probes with use of a binary phase plate.

    Science.gov (United States)

    Alferov, S V; Khonina, S N; Karpeev, S V

    2014-04-01

    We conduct a theoretical and experimental study of the distribution of the electric field components in the sharp focal domain when rotating a zone plate with a π-phase jump placed in the focused beam. Comparing the theoretical and experimental results for several kinds of near-field probes, an analysis of the polarization sensitivity of different types of metal-coated aperture probes is conducted. It is demonstrated that with increasing diameter of the non-metal-coated tip part there occurs an essential redistribution of sensitivity in favor of the transverse electric field components and an increase of the probe's energy throughput.

  9. Probing DNA in nanopores via tunneling: from sequencing to ``quantum'' analogies

    Science.gov (United States)

    di Ventra, Massimiliano

    2012-02-01

    Fast and low-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced so that drugs could be tailored to his/her specific illnesses; doctors could know in advance patients' likelihood to develop a given ailment; cures to major diseases could be found faster [1]. However, this goal of ``personalized medicine'' is hampered today by the high cost and slow speed of DNA sequencing methods. In this talk, I will discuss the sequencing protocol we suggest which requires the measurement of the distributions of transverse currents during the translocation of single-stranded DNA into nanopores [2-5]. I will support our conclusions with a combination of molecular dynamics simulations coupled to quantum mechanical calculations of electrical current in experimentally realizable systems [2-5]. I will also discuss recent experiments that support these theoretical predictions. In addition, I will show how this relatively unexplored area of research at the interface between solids, liquids, and biomolecules at the nanometer length scale is a fertile ground to study quantum phenomena that have a classical counterpart, such as ionic quasi-particles, ionic ``quantized'' conductance [6,7] and Coulomb blockade [8]. Work supported in part by NIH. [4pt] [1] M. Zwolak, M. Di Ventra, Physical Approaches to DNA Sequencing and Detection, Rev. Mod. Phys. 80, 141 (2008).[0pt] [2] M. Zwolak and M. Di Ventra, Electronic signature of DNA nucleotides via transverse transport, Nano Lett. 5, 421 (2005).[0pt] [3] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Fast DNA sequencing via transverse electronic transport, Nano Lett. 6, 779 (2006).[0pt] [4] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport, Biophys. J. 93, 2384 (2007).[0pt] [5] M. Krems, M. Zwolak, Y.V. Pershin, and M. Di Ventra, Effect of noise on DNA sequencing via transverse electronic transport

  10. Development of techniques using DNA analysis method for detection/analysis of radiation-induced mutation. Development of an useful probe/primer and improvement of detection efficacy

    International Nuclear Information System (INIS)

    Maekawa, Hideaki; Tsuchida, Kozo; Hashido, Kazuo; Takada, Naoko; Kameoka, Yosuke; Hirata, Makoto

    1999-01-01

    Previously, it was demonstrated that detection of centromere became easy and reliable through fluorescent staining by FISH method using a probe of the sequence preserved in α-satelite DNA. Since it was, however, found inappropriate to detect dicentrics based on the relative amount of DNA probe on each chromosome. A prove which allows homogeneous detection of α-satelite DNA for each chromosome was constructed. A presumed sequence specific to kinetochore, CENP-B box was amplified by PCR method and the product DNA was used as a probe. However, the variation in amounts of probe DNA among chromosomes was decreased by only about 20%. Then, a program for image processing of the results obtained from FISH using α-satelite DNA was constructed to use as a marker for centromere. When compared with detection of abnormal chromosomes stained by the conventional method, calculation efficacy for only detection of centromere was improved by the use of this program. Calculation to discriminate the normal or not was still complicated and the detection efficacy was little improved. Chromosomal abnormalities in lymphocytes were used to detect the effects of radiation. In this method, it is needed to shift the phase of cells into metaphase. The mutation induced by radiation might be often repaired during shifting. To exclude this possibility, DNA extraction was conducted at a low temperature and immediately after exposure to 137 Cs, and a rapid genome detection method was established using the genome DNA. As the model genomes, the following three were used: 1) long chain repeated sequences widely dispersed over chromosome, 2) cluster genes, 3) single copy genes. The effects of radiation were detectable at 1-2 Gy for the long repeated sequences and at 7 Gy for the cluster genes, respectively, whereas no significant effects were observed at any Gy tested for the single copy genes. Amplification was marked in the cells exposed at 1-10 Gy (peak at 4 Gy), suggesting that these regions had

  11. Distributed fiber-optic temperature sensing: recent improvements and Nagra's applications in the Mont Terri URL

    International Nuclear Information System (INIS)

    Vogt, Tobias; Mueller, Herwig R.; Vietor, Tim; Frieg, Bernd

    2012-01-01

    Document available in extended abstract form only. Full text of publication follows: The application of fiber-optic sensors in large experiments in underground rock laboratories (URL) and for monitoring of pilot repositories offers several advantages in contrast to conventional sensors. By means of optical fibers distributed temperature and deformation measurements can be performed without electric or mechanical components at the measurement location reducing the risk of corrosion and sensor failure. As fiber-optic strain sensors are to some extend still in a prototype stage, we focus here on Raman spectra distributed fiber-optic temperature sensing (DTS). In DTS a fiber-optic cable, which is the temperature sensor, is connected to a light reading unit that sends laser-pulses into the fiber. The backscattered light is detected with high temporal resolution. From the two-way-light-travel-time the location of backscattering is determined. For the temperature information the amplitude ratio of the Stokes and anti-Stokes signals is analyzed. The Stokes and anti- Stokes signals are the result of the Raman effect. The ratio of these signals provides a quantity that depends only on the temperature of the fiber at the location of backscatter. With commercial DTS setups it is possible to measure the temperature distribution along several kilometer long cables with a temperature resolution of 0.01 C and a spatial resolution of 1 m. Recent developments in DTS focus on better temperature precision and resolution. This advancement can be achieved by experiment-specific calibration techniques and sensor-layout as well as improved instruments. To realize high spatial resolution (cm range) wrapped fiber-optic cables can be applied. Another promising approach to monitor moisture along a fiber-optic cable installed in unconsolidated material are heatable cables. We will present a selection of the most recent advancements which may improve temperature monitoring in natural and

  12. Sensitive detection of mercury and copper ions by fluorescent DNA/Ag nanoclusters in guanine-rich DNA hybridization.

    Science.gov (United States)

    Peng, Jun; Ling, Jian; Zhang, Xiu-Qing; Bai, Hui-Ping; Zheng, Liyan; Cao, Qiu-E; Ding, Zhong-Tao

    2015-02-25

    In this work, we designed a new fluorescent oligonucleotides-stabilized silver nanoclusters (DNA/AgNCs) probe for sensitive detection of mercury and copper ions. This probe contains two tailored DNA sequence. One is a signal probe contains a cytosine-rich sequence template for AgNCs synthesis and link sequence at both ends. The other is a guanine-rich sequence for signal enhancement and link sequence complementary to the link sequence of the signal probe. After hybridization, the fluorescence of hybridized double-strand DNA/AgNCs is 200-fold enhanced based on the fluorescence enhancement effect of DNA/AgNCs in proximity of guanine-rich DNA sequence. The double-strand DNA/AgNCs probe is brighter and stable than that of single-strand DNA/AgNCs, and more importantly, can be used as novel fluorescent probes for detecting mercury and copper ions. Mercury and copper ions in the range of 6.0-160.0 and 6-240 nM, can be linearly detected with the detection limits of 2.1 and 3.4 nM, respectively. Our results indicated that the analytical parameters of the method for mercury and copper ions detection are much better than which using a single-strand DNA/AgNCs. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  14. Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

    Science.gov (United States)

    Steger, Doris; Berry, David; Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

    2011-01-01

    The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.

  15. Fiber-optic couplers as displacement sensors

    Science.gov (United States)

    Baruch, Martin C.; Gerdt, David W.; Adkins, Charles M.

    2003-04-01

    We introduce the novel concept of using a fiber-optic coupler as a versatile displacement sensor. Comparatively long fiber-optic couplers, with a coupling region of approximately 10 mm, are manufactured using standard communication SM fiber and placed in a looped-back configuration. The result is a displacement sensor, which is robust and highly sensitive over a wide dynamic range. This displacement sensor resolves 1-2 μm over distances of 1-1.5 mm and is characterized by the essential absence of a 'spring constant' plaguing other strain gauge-type sensors. Consequently, it is possible to couple to extremely weak vibrations, such as the skin displacement affected by arterial heart beat pulsations. Used as a wrist-worn heartbeat monitor, the fidelity of the arterial pulse signal has been shown to be so high that it is possible to not only determine heartbeat and breathing rates, but to implement a new single-point blood pressure measurement scheme which does not squeeze the arm. In an application as a floor vibration sensor for the non-intrusive monitoring of independently living elderly, the sensor has been shown to resolve the distinct vibration spectra of different persons and different events.

  16. Comparison of Distributed Acoustic Sensing (DAS) from Fiber-Optic Cable to Three Component Geophones in an Underground Mine

    Science.gov (United States)

    Speece, M. A.; Nesladek, N. J.; Kammerer, C.; Maclaughlin, M.; Wang, H. F.; Lord, N. E.

    2017-12-01

    We conducted experiments in the Underground Education Mining Center on the Montana Tech campus, Butte, Montana, to make a direct comparison between Digital Acoustic Sensing (DAS) and three-component geophones in a mining setting. The sources used for this project where a vertical sledgehammer, oriented shear sledgehammer, and blasting caps set off in both unstemmed and stemmed drillholes. Three-component Geospace 20DM geophones were compared with three different types of fiber-optic cable: (1) Brugg strain, (2) Brugg temperature, and (3) Optical Cable Corporation strain. We attached geophones to the underground mine walls and on the ground surface above the mine. We attached fiber-optic cables to the mine walls and placed fiber-optic cable in boreholes drilled through an underground pillar. In addition, we placed fiber-optic cables in a shallow trench at the surface of the mine. We converted the DAS recordings from strain rate to strain prior to comparison with the geophone data. The setup of the DAS system for this project led to a previously unknown triggering problem that compromised the early samples of the DAS traces often including the first-break times on the DAS records. Geophones clearly recorded the explosives; however, the large amount of energy and its close distance from the fiber-optic cables seemed to compromise the entire fiber loop. The underground hammer sources produced a rough match between the DAS records and the geophone records. However, the sources on the surface of the mine, specifically the sources oriented inline with the fiber-optic cables, produced a close match between the fiber-optic traces and the geophone traces. All three types of fiber-optic cable that were in the mine produced similar results, and one type did not clearly outperform the others. Instead, the coupling of the cable to rock appears to be the most important factor determining DAS data quality. Moreover, we observed the importance of coupling in the boreholes, where

  17. DNA Binding Hydroxyl Radical Probes.

    Science.gov (United States)

    Tang, Vicky J; Konigsfeld, Katie M; Aguilera, Joe A; Milligan, Jamie R

    2012-01-01

    The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA.

  18. Fiber-optic communication systems

    CERN Document Server

    Agrawal, Govind P

    2010-01-01

    This book provides a comprehensive account of fiber-optic communication systems. The 3rd edition of this book is used worldwide as a textbook in many universities. This 4th edition incorporates recent advances that have occurred, in particular two new chapters. One deals with the advanced modulation formats (such as DPSK, QPSK, and QAM) that are increasingly being used for improving spectral efficiency of WDM lightwave systems. The second chapter focuses on new techniques such as all-optical regeneration that are under development and likely to be used in future communication systems. All othe

  19. Fiber-optic displacement sensors on the Hunters Trophy UGT impulse gauge experiments

    Energy Technology Data Exchange (ETDEWEB)

    Green, R.E.L.; Poutiatine, A.I.

    1995-03-01

    As part of a program to develop gauges for measurement of various mechanical properties in hostile environments, the authors fielded purely optical displacement sensors at the ends of long fiber-optic cables as supplements to the regular displacement sensors of four impulse gauges fielded as part of a materials study on the Hunters Trophy underground effects test at the Nevada Test Site. These fiber-optic sensor systems and their performance on the Hunters Trophy test are described in this report.

  20. Fiber-based hybrid probe for non-invasive cerebral monitoring in neonatology

    Science.gov (United States)

    Rehberger, Matthias; Giovannella, Martina; Pagliazzi, Marco; Weigel, Udo; Durduran, Turgut; Contini, Davide; Spinelli, Lorenzo; Pifferi, Antonio; Torricelli, Alessandro; Schmitt, Robert

    2015-07-01

    Improved cerebral monitoring systems are needed to prevent preterm infants from long-term cognitive and motor restrictions. Combining advanced near-infrared diffuse spectroscopy measurement technologies, time-resolved spectroscopy (TRS) and diffuse correlation spectroscopy (DCS) will introduce novel indicators of cerebral oxygen metabolism and blood flow for neonatology. For non-invasive sensing a fiber-optical probe is used to send and receive light from the infant head. In this study we introduce a new fiber-based hybrid probe that is designed for volume production. The probe supports TRS and DCS measurements in a cross geometry, thus both technologies gain information on the same region inside the tissue. The probe is highly miniaturized to perform cerebral measurements on heads of extreme preterm infants down to head diameters of 6cm. Considerations concerning probe production focus on a reproducible accuracy in shape and precise optical alignment. In this way deviations in measurement data within a series of probes should be minimized. In addition to that, requirements for clinical use like robustness and hygiene are considered. An additional soft-touching sleeve made of FDA compatible silicone allows for a flexible attachment with respect to the individual anatomy of each patient. We present the technical concept of the hybrid probe and corresponding manufacturing methods. A prototype of the probe is shown and tested on tissue phantoms as well as in vivo to verify its operational reliability.

  1. Nonisotopic DNA probe techniques

    National Research Council Canada - National Science Library

    Kricka, Larry J

    1992-01-01

    The objective of this book is to bring together descriptions of the principal nonisotopic methods for DNA hybridization assays, together with experimental details of the methods, including labelling...

  2. A Study on the Response Characteristics of a Fiber-Optic Radiation Sensor Model Based on Cerenkov Principle

    Energy Technology Data Exchange (ETDEWEB)

    Han, Hwa Jeong; Kim, Beom Kyu; Park, Byung Gi [Soonchunhyang Univ., Asan (Korea, Republic of)

    2016-10-15

    In recent year, various fiber-optic radiation sensors using Cerenkov principle have been developed without employing any scintillators for measuring high-energy photon, electron, etc. The main advantages of the optical fibers are the remote transmission of the light signal and immunity to pressure and electromagnetic waves. Therefore, the sensors utilizing the optical fibers can be used in hazardous radiation environments, such as the high-level radiation areas of a nuclear facility. The study to be simulated a fiber-optic radiation sensor based on Cerenkov principle and to be analyzed the response characteristics of the sensor. For the aforementioned study, the GEANT simulation toolkit was used. It is able to take into all the optical properties of fibers and is found to be appropriate to realistically describe the response of fiber-optic radiation sensor. In the recently, the fiber-optic radiation sensor have been developed in nuclear industry. Because sensor can detect gamma ray in harsh nuclear environments. In this study, we analyzed response characteristics of the fiber-optic radiation sensor. We have simulated the Monte Carlo model, for detecting the Cerenkov radiation using the fiber-optic radiation sensor. And the y-axis distribution of Cerenkov photons was obtained using output file. Simulation is performed with reference to the method of the previous research, and then the simulation results exhibited a good agreement with the previous research.

  3. A Study on the Response Characteristics of a Fiber-Optic Radiation Sensor Model Based on Cerenkov Principle

    International Nuclear Information System (INIS)

    Han, Hwa Jeong; Kim, Beom Kyu; Park, Byung Gi

    2016-01-01

    In recent year, various fiber-optic radiation sensors using Cerenkov principle have been developed without employing any scintillators for measuring high-energy photon, electron, etc. The main advantages of the optical fibers are the remote transmission of the light signal and immunity to pressure and electromagnetic waves. Therefore, the sensors utilizing the optical fibers can be used in hazardous radiation environments, such as the high-level radiation areas of a nuclear facility. The study to be simulated a fiber-optic radiation sensor based on Cerenkov principle and to be analyzed the response characteristics of the sensor. For the aforementioned study, the GEANT simulation toolkit was used. It is able to take into all the optical properties of fibers and is found to be appropriate to realistically describe the response of fiber-optic radiation sensor. In the recently, the fiber-optic radiation sensor have been developed in nuclear industry. Because sensor can detect gamma ray in harsh nuclear environments. In this study, we analyzed response characteristics of the fiber-optic radiation sensor. We have simulated the Monte Carlo model, for detecting the Cerenkov radiation using the fiber-optic radiation sensor. And the y-axis distribution of Cerenkov photons was obtained using output file. Simulation is performed with reference to the method of the previous research, and then the simulation results exhibited a good agreement with the previous research

  4. Development of plasma bolometers using fiber-optic temperature sensors

    Energy Technology Data Exchange (ETDEWEB)

    Reinke, M. L., E-mail: reinkeml@ornl.gov [Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Han, M.; Liu, G. [University of Nebraska-Lincoln, Lincoln, Nebraska 68588 (United States); Eden, G. G. van [Dutch Institute for Fundamental Energy Research, De Zaale 20, 5612 AJ Eindhoven (Netherlands); Evenblij, R.; Haverdings, M. [Technobis, Pyrietstraat 2, 1812 SC Alkmaar (Netherlands); Stratton, B. C. [Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543 (United States)

    2016-11-15

    Measurements of radiated power in magnetically confined plasmas are important for exhaust studies in present experiments and expected to be a critical diagnostic for future fusion reactors. Resistive bolometer sensors have long been utilized in tokamaks and helical devices but suffer from electromagnetic interference (EMI). Results are shown from initial testing of a new bolometer concept based on fiber-optic temperature sensor technology. A small, 80 μm diameter, 200 μm long silicon pillar attached to the end of a single mode fiber-optic cable acts as a Fabry–Pérot cavity when broadband light, λ{sub o} ∼ 1550 nm, is transmitted along the fiber. Changes in temperature alter the optical path length of the cavity primarily through the thermo-optic effect, resulting in a shift of fringes reflected from the pillar detected using an I-MON 512 OEM spectrometer. While initially designed for use in liquids, this sensor has ideal properties for use as a plasma bolometer: a time constant, in air, of ∼150 ms, strong absorption in the spectral range of plasma emission, immunity to local EMI, and the ability to measure changes in temperature remotely. Its compact design offers unique opportunities for integration into the vacuum environment in places unsuitable for a resistive bolometer. Using a variable focus 5 mW, 405 nm, modulating laser, the signal to noise ratio versus power density of various bolometer technologies are directly compared, estimating the noise equivalent power density (NEPD). Present tests show the fiber-optic bolometer to have NEPD of 5-10 W/m{sup 2} when compared to those of the resistive bolometer which can achieve <0.5 W/m{sup 2} in the laboratory, but this can degrade to 1-2 W/m{sup 2} or worse when installed on a tokamak. Concepts are discussed to improve the signal to noise ratio of this new fiber-optic bolometer by reducing the pillar height and adding thin metallic coatings, along with improving the spectral resolution of the interrogator.

  5. Fiber-Optic Monitoring System of Particle Counters

    Directory of Open Access Journals (Sweden)

    A. A. Titov

    2016-01-01

    Full Text Available The article considers development of a fiber-optic system to monitor the counters of particles. Presently, optical counters of particles, which are often arranged at considerable distance from each other, are used to study the saltation phenomenon. For monitoring the counters, can be used electric communication lines.However, it complicates and raises the price of system Therefore, we offered a fiber-optic system and the counter of particles, free from these shortcomings. The difference between the offered counter of particles and the known one is that the input of radiation to the counter and the output of radiation scattering on particles are made by the optical fibers, and direct radiation is entered the optical fiber rather than is delayed by a light trap and can be used for lighting the other counters thereby allowing to use their connection in series.The work involved a choice of the quartz multimode optical fiber for communication, defining the optical fiber and lenses parameters of the counter of particles, and a selection of the radiation source and the photo-detector.Using the theory of light diffraction on a particle, a measuring range of the particle sizes has been determined. The system speed has been estimated, and it has been shown that a range of communication can reach 200km.It should be noted that modulation noise of counters of particles connected in series have the impact on the useful signal. To assess the extent of this influence we have developed a calculation procedure to illustrate that with ten counters connected in series this influence on the signal-to-noise ratio will be insignificant.Thus, it has been shown that the offered fiber-optic system can be used for monitoring the counters of particles across the desertified territories. 

  6. Multi-Stress Monitoring System with Fiber-Optic Mandrels and Fiber Bragg Grating Sensors in a Sagnac Loop.

    Science.gov (United States)

    Kim, Hyunjin; Sampath, Umesh; Song, Minho

    2015-07-29

    Fiber Bragg grating sensors are placed in a fiber-optic Sagnac loop to combine the grating temperature sensors and the fiber-optic mandrel acoustic emission sensors in single optical circuit. A wavelength-scanning fiber-optic laser is used as a common light source for both sensors. A fiber-optic attenuator is placed at a specific position in the Sagnac loop in order to separate buried Bragg wavelengths from the Sagnac interferometer output. The Bragg wavelength shifts are measured with scanning band-pass filter demodulation and the mandrel output is analyzed by applying a fast Fourier transform to the interference signal. This hybrid-scheme could greatly reduce the size and the complexity of optical circuitry and signal processing unit, making it suitable for low cost multi-stress monitoring of large scale power systems.

  7. Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction

    Science.gov (United States)

    Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

    2014-01-01

    DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag+-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.

  8. Preclinical detection of porcine circovirus type 2 infection using an ultrasensitive nanoparticle DNA probe-based PCR assay.

    Directory of Open Access Journals (Sweden)

    Yong Huang

    Full Text Available Porcine circovirus type 2 (PCV2 has emerged as one of the most important pathogens affecting swine production globally. Preclinical identification of PCV2 is very important for effective prophylaxis of PCV2-associated diseases. In this study, we developed an ultrasensitive nanoparticle DNA probe-based PCR assay (UNDP-PCR for PCV2 detection. Magnetic microparticles coated with PCV2 specific DNA probes were used to enrich PCV2 DNA from samples, then gold nanoparticles coated with PCV2 specific oligonucleotides were added to form a sandwich nucleic acid-complex. After the complex was formed, the oligonucleotides were released and characterized by PCR. This assay exhibited about 500-fold more sensitive than conventional PCR, with a detection limit of 2 copies of purified PCV2 genomic DNA and 10 viral copies of PCV2 in serum. The assay has a wide detection range for all of PCV2 genotypes with reliable reproducibility. No cross-reactivity was observed from the samples of other related viruses including porcine circovirus type 1, porcine parvovirus, porcine pseudorabies virus, porcine reproductive and respiratory syndrome virus and classical swine fever virus. The positive detection rate of PCV2 specific UNDP-PCR in 40 preclinical field samples was 27.5%, which appeared greater than that by conventional and real-time PCR and appeared application potency in evaluation of the viral loads levels of preclinical infection samples. The UNDP-PCR assay reported here can reliably rule out false negative results from antibody-based assays, provide a nucleic acid extraction free, specific, ultrasensitive, economic and rapid diagnosis method for preclinical PCV2 infection in field, which may help prevent large-scale outbreaks.

  9. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Neufeld, Josh D; Bodrossy, Levente; Stralis-Pavese, Nancy; McNamara, Niall P; Ostle, Nick; Briones, Maria J I; Murrell, J Colin

    2008-10-01

    Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

  10. Fiber-optic control of the ZT-P experiment

    International Nuclear Information System (INIS)

    Caudill, L.D.; Chandler, G.I.; Hall, C.R.; Trujillo, J.F.

    1986-01-01

    The computer control system for the ZT-P experiment has been implemented using a fiber-optic link in all 161 control signal paths. Four classes of control signals are used in this design. These are (a) digital-out, an on--off signal from computer to machine actuator, (b) digital-in, an on--off signal from machine sensor to computer, (c) analog-out, a 0--10-V analog signal from computer to machine actuator, (d) analog-in, a 0--1-mA analog signal from machine sensor to computer. The digital-in and the digital-out class of signals require no control power at the machine. The analog-out and the analog-in class of signals use available machine power for control. This unique power arrangement and the use of fiber-optic links totally isolate the electrically noisy machine areas from the sensitive electronics in the computer control. Advantages of this system including low cost, small size, personnel safety, and ease of maintenance and modification are discussed

  11. Fiber-optic control of the ZT-P experiment

    International Nuclear Information System (INIS)

    Caudill, L.D.; Chandler, G.I.; Hall, C.R.; Trujillo, J.F.

    1986-01-01

    The computer control system for the ZT-P experiment has been implemented using a fiber-optic link in all 161 control signal paths. Four classes of control signals are used in this design. These are: (a) digital-out, an on-off signal from computer to machine actuator, (b) digital-in, an on-off signal from machine sensor to computer, (c) analog-out, a 0 to 10 volt analog signal from computer to machine actuator, (d) analog-in, a 0 to +1 milliampere analog signal from machine sensor to computer. The digital-in and the digital-out class of signals require no control power at the machine. The analog-out and the analog-in class of signals use available machine power for control. This unique power arrangement and the use of fiber-optic links totally isolate the electrically noisy machine areas from the sensitive electronics in the computer control. Advantages of this system including low cost, small size, personnel safety, and ease of maintenance and modification are discussed

  12. Fiber-optic control of the ZT-P experiment

    International Nuclear Information System (INIS)

    Caudill, L.D.; Chandler, G.I.; Hall, C.R.; Trujillo, J.F.

    1986-01-01

    The computer control system for the ZT-P experiment has been implemented using a fiber-optic link in all 161 control signal paths. Four classes of control signals are used in this design. These are: digital-out; an on-off signal from computer to machine actuator, digital-in, and on-off signal from machine sensor to computer, analog-out, a 0 - 10 volt analog signal from computer to machine actuator, analog-in, 0 to +1 milliampere analog signal from machine sensor to computer. The digital-in and the digital-out class of signals require no control power at the machine end. The analog-out and the analog-in class of signals use available machine power for control. This unique power arrangement and the use of fiber-optic links serve to totally isolate electrically noisy machine areas from the sensitive electronics in the computer control. Advantages, including low cost, small size, personnel safety, and ease of maintenance and modification are discussed

  13. Fiber-optic evanescent-field sensor for attitude measurement

    Science.gov (United States)

    Liu, Yun; Chen, Shimeng; Liu, Zigeng; Guang, Jianye; Peng, Wei

    2017-11-01

    We proposed a new approach to attitude measurement by an evanescent field-based optical fiber sensing device and demonstrated a liquid pendulum. The device consisted of three fiber-optic evanescent-filed sensors which were fabricated by tapered single mode fibers and immersed in liquid. Three fiber Bragg gratings were used to measure the changes in evanescent field. And their reflection peaks were monitored in real time as measurement signals. Because every set of reflection responses corresponded to a unique attitude, the attitude of the device could be measured by the three fiber-optic evanescent-filed sensors. After theoretical analysis, computerized simulation and experimental verification, regular responses were obtained using this device for attitude measurement. The measurement ranges of dihedral angle and direction angle were 0°-50° and 0°-360°. The device is based on cost-effective power-referenced scheme. It can be used in electromagnetic or nuclear radiation environment.

  14. Combined pulsed dye laser and fiberoptic Nd-YAG laser for the treatment of hypertrophic port wine stain.

    Science.gov (United States)

    Radmanesh, Mohammed; Radmanesh, Ramin

    2017-10-01

    The hypertrophic Port Wine Stain (PWS) is only partially and superficially treated with the Pulsed dye laser (PDL) because of its limited depth of penetration. We used combined PDL and fiberoptic 1444-nm Nd-YAG laser to treat a case with hypertrophic PWS. After tumescent anesthesia, few holes were made by a 16-gauge needle on different sides of the lesion. The fiberoptic tip of 1444-nm Nd-YAG laser was inserted within the holes and was pushed forward while triggering. In a fan pattern and by a back and forth movement, the subcutaneous and deep dermal areas were coagulated. The skin and outer mucosal surfaces were then treated by PDL. The fiberoptic system used was Accusculpt 1444-nm Nd-YAG laser (Lutronic lasers, South Korea), and the PDL used was 585 nm Nlite system (Chromogenex UK). The parameters used for PDL were fluence = 9 Joules/cm 2 and the spot size was 5 mm. The parameters used for fiberoptic 1444-nm Nd-YAG laser were: Pulse rate = 30 Hz, pulse energy = 300 mJ, power = 6 W, and the total energy = 4000 J for the whole face and mucosa. Little sign of regression and moderate purpura were detected immediately after combined fiberoptic Nd-YAG and PDL therapy. The lesion gradually regressed within 4 months with satisfactory color and volume change. Combined fiberoptic Nd-YAG laser and PDL can be used for the treatment of deeper and superficial layers of hypertrophic PWS.

  15. Indication for fiberoptic bronchoscopy in HIV-infected patients suspected for Pneumocystis carinii pneumonia

    DEFF Research Database (Denmark)

    Orholm, M; Lundgren, Jens Dilling; Nielsen, T L

    1990-01-01

    During a six-month period, 40 consecutive fiberoptic bronchoscopic procedures including bronchoalveolar lavage, bronchial brushing and forceps biopsy were performed in local anaesthesia on 34 HIV-infected males presenting symptoms compatible with Pneumocystis carinii pneumonia. In 23 examinations...... did not differ with regard to history, clinical examination, immunology, serology or chest radiograph. We conclude that fiberoptic bronchoscopy should be performed on wide indications in HIV-infected patients with symptoms compatible with P. carinii pneumonia. The procedure is easily performed...

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

    Science.gov (United States)

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

    2017-12-01

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

  17. Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids

    International Nuclear Information System (INIS)

    El-Yazbi, Amira F.; Loppnow, Glen R.

    2013-01-01

    Graphical abstract: -- Highlights: •Simple, inexpensive, mix-and-read assay for positive detection of DNA damage. •Recognition of undamaged DNA via hybridization to a hairpin probe. •Terbium(III) fluorescence reports the amount of damage by binding to ssDNA. •Tb/hairpin is a highly selective and sensitive fluorescent probe for DNA damage. -- Abstract: Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb 3+ ). Single-stranded oligonucleotides greatly enhance the Tb 3+ emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb 3+ /hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb 3+ , producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb 3+ /hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb 3+ /hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36 ± 1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage

  18. DNA Binding Hydroxyl Radical Probes

    OpenAIRE

    Tang, Vicky J; Konigsfeld, Katie M; Aguilera, Joe A; Milligan, Jamie R

    2012-01-01

    The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different c...

  19. End-tidal carbon dioxide monitoring during flexible fiberoptic ...

    African Journals Online (AJOL)

    In recent years, flexible fiberoptic bronchoscopy (FFB) has been applied for diagnostic and some therapeutic purposes. During FFB and even in the presence of supplemental oxygen, hypoventilation leading to hypoxia and desaturation may occur; this is aggravated by the use of suction. Arterial oxygen saturation is usually ...

  20. Identification of the autotrophic denitrifying community in nitrate removal reactors by DNA-stable isotope probing.

    Science.gov (United States)

    Xing, Wei; Li, Jinlong; Cong, Yuan; Gao, Wei; Jia, Zhongjun; Li, Desheng

    2017-04-01

    Autotrophic denitrification has attracted increasing attention for wastewater with insufficient organic carbon sources. Nevertheless, in situ identification of autotrophic denitrifying communities in reactors remains challenging. Here, a process combining micro-electrolysis and autotrophic denitrification with high nitrate removal efficiency was presented. Two batch reactors were fed organic-free nitrate influent, with H 13 CO 3 - and H 12 CO 3 - as inorganic carbon sources. DNA-based stable-isotope probing (DNA-SIP) was used to obtain molecular evidence for autotrophic denitrifying communities. The results showed that the nirS gene was strongly labeled by H 13 CO 3 - , demonstrating that the inorganic carbon source was assimilated by autotrophic denitrifiers. High-throughput sequencing and clone library analysis identified Thiobacillus-like bacteria as the most dominant autotrophic denitrifiers. However, 88% of nirS genes cloned from the 13 C-labeled "heavy" DNA fraction showed low similarity with all culturable denitrifiers. These findings provided functional and taxonomical identification of autotrophic denitrifying communities, facilitating application of autotrophic denitrification process for wastewater treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Dendrimer-based biosensor for chemiluminescent detection of DNA hybridization

    International Nuclear Information System (INIS)

    Liu, P.; Hun, X.; Qing, H.

    2011-01-01

    We report on a highly sensitive chemiluminescent (CL) biosensor for the sequence-specific detection of DNA using a novel bio barcode DNA probe modified with gold nanoparticles that were covered with a dendrimer. The modified probe is composed of gold nanoparticles, a dendrimer, the CL reagent, and the DNA. The capture probe DNA was immobilized on magnetic beads covered with gold. It first hybridizes with the target DNA and then with one terminal end of the signal DNA on the barcoded DNA probe. CL was generated by adding H 2 O 2 and Co(II) ions as the catalyst. The immobilization of dendrimer onto the gold nanoparticles can significantly enhance sensitivity and gives a detection limit of 6 fmol L -1 of target DNA. (author)

  2. Constellation Shaping for Fiber-optic Channels with QAM and High Spectral Efficiency

    DEFF Research Database (Denmark)

    Yankov, Metodi Plamenov; Zibar, Darko; Larsen, Knud J.

    2014-01-01

    In this letter the fiber-optic communication channel with Quadrature Amplitude Modulation (QAM) input constella- tion is treated. Using probabilistic shaping, we show that high order QAM constellations can achieve and slightly exceed the lower bound on the channel capacity, set by ring constellat......In this letter the fiber-optic communication channel with Quadrature Amplitude Modulation (QAM) input constella- tion is treated. Using probabilistic shaping, we show that high order QAM constellations can achieve and slightly exceed the lower bound on the channel capacity, set by ring...... constellations in [1]. We then propose a mapping function for turbo coded bit interleaved coded modulation based on optimization of the mu- tual information between the channel input and output. Using this mapping, spectral efficiency as high as 6.5 bits/s/Hz/polarization is achieved on a simulated single...... channel long-haul fiber-optical link excluding the pilot overhead, used for synchronization, and taking into account frequency and phase mismatch impairments, as well as laser phase noise and analog-to-digital conversion quantization impairments. The simulations suggest that major improvements can...

  3. Fiberoptic bronchoscopy in the diagnosis and therapeutic decision for respiratory infections in hematological febrile neutropenic patients

    Directory of Open Access Journals (Sweden)

    Luiza Bento

    2014-06-01

    Full Text Available Background: Febrile neutropenia is a common complication in patients undergoing chemotherapy or hematopoietic Stem Cell Transplantation (HSCT. Flexible fiberoptic bronchoscopy has been used to aid in the diagnosis of pulmonary diseases. However, there is no consensus regarding the benefit of the exam in establishing diagnosis and in changing the treatment of lung disease in this context. Previous retrospective studies, quite heterogeneous and with non-HIV immunocompromised patients, showed that the yield of fiberoptic bronchoscopy in establishing etiology ranges from 13% to 81%, and in changing therapy, from 5% to 51%. Aim: To evaluate the efficiency of Fiberoptic bronchoscopy and the procedure-related risk for neutropenic patients with hematologic malignancy. Methods: This retrospective cross-sectional study analyzed the medical records of patients with hematologic malignancy with febrile neutropenia who had undergone diagnostic fiberoptic bronchoscopy between January 2011 and December 2012 at the Hospital de Clínicas de Porto Alegre. Results: A total of 45 patients were included: 18 (36% tested positive for bronchoalveolar lavage, with change in therapeutic management occurring for 95% of them. The procedure-related risk was 2.2%, with one patient showing desaturation immediately after the procedure. Conclusion:  Despite the limited number of patients, our findings indicate that fiberoptic bronchoscopy in neutropenic patients is safe, and the results are similar to those previously reported.

  4. Fiber-optical sensor with intensity compensation model in college teaching of physics experiment

    Science.gov (United States)

    Su, Liping; Zhang, Yang; Li, Kun; Zhang, Yu

    2017-08-01

    Optical fiber sensor technology is one of the main contents of modern information technology, which has a very important position in modern science and technology. Fiber optic sensor experiment can improve students' enthusiasm and broaden their horizons in college physics experiment. In this paper the main structure and working principle of fiberoptical sensor with intensity compensation model are introduced. And thus fiber-optical sensor with intensity compensation model is applied to measure micro displacement of Young's modulus measurement experiment and metal linear expansion coefficient measurement experiment in the college physics experiment. Results indicate that the measurement accuracy of micro displacement is higher than that of the traditional methods using fiber-optical sensor with intensity compensation model. Meanwhile this measurement method makes the students understand on the optical fiber, sensor and nature of micro displacement measurement method and makes each experiment strengthen relationship and compatibility, which provides a new idea for the reform of experimental teaching.

  5. Influence of probe pressure on diffuse reflectance spectra of human skin measured in vivo

    Science.gov (United States)

    Popov, Alexey P.; Bykov, Alexander V.; Meglinski, Igor V.

    2017-11-01

    Mechanical pressure superficially applied on the human skin surface by a fiber-optic probe influences the spatial distribution of blood within the cutaneous tissues. Upon gradual load of weight on the probe, a stepwise increase in the skin reflectance spectra is observed. The decrease in the load follows the similar inverse staircase-like tendency. The observed stepwise reflectance spectra changes are due to, respectively, sequential extrusion of blood from the topical cutaneous vascular beds and their filling afterward. The obtained results are confirmed by Monte Carlo modeling. This implies that pressure-induced influence during the human skin diffuse reflectance spectra measurements in vivo should be taken into consideration, in particular, in the rapidly developing area of wearable gadgets for real-time monitoring of various human body parameters.

  6. Fiberoptic microneedles: novel optical diffusers for interstitial delivery of therapeutic light.

    Science.gov (United States)

    Kosoglu, Mehmet A; Hood, Robert L; Rossmeisl, John H; Grant, David C; Xu, Yong; Robertson, John L; Rylander, Marissa Nichole; Rylander, Christopher G

    2011-11-01

    Photothermal therapies have limited efficacy and application due to the poor penetration depth of light inside tissue. In earlier work, we described the development of novel fiberoptic microneedles to provide a means to mechanically penetrate dermal tissue and deliver light directly into a localized target area.This paper presents an alternate fiberoptic microneedle design with the capability of delivering more diffuse, but therapeutically useful photothermal energy. Laser lipolysis is envisioned as a future clinical application for this design. A novel fiberoptic microneedle was developed using hydrofluoric acid etching of optical fiber to permit diffuse optical delivery. Microneedles etched for 10, 30, and 50 minutes, and an optical fiber control were compared with three techniques. First, red light delivery from the microneedles was evaluated by imaging the reflectance of the light from a white paper.Second, spatial temperature distribution of the paper in response to near-IR light (1,064 nm, 1 W CW) was recorded using infrared thermography. Third, ex vivo adipose tissue response during 1,064 nm, (5 W CW)irradiation was recorded with bright field microscopy. Acid etching exposed a 3 mm length of the fiber core, allowing circumferential delivery of light along this length. Increasing etching time decreased microneedle diameter, resulting in increased uniformity of red and 1,064 nm light delivery along the microneedle axis. For equivalent total energy delivery, thinner microneedles reduced carbonization in the adipose tissue experiments. We developed novel microscale optical diffusers that provided a more homogeneous light distribution from their surfaces, and compared performance to a flat-cleaved fiber, a device currently utilized in clinical practice. These fiberoptic microneedles can potentially enhance clinical laser procedures by providing direct delivery of diffuse light to target chromophores, while minimizing undesirable photothermal damage in adjacent

  7. Fiber-optic polarization diversity detection for rotary probe optical coherence tomography.

    Science.gov (United States)

    Lee, Anthony M D; Pahlevaninezhad, Hamid; Yang, Victor X D; Lam, Stephen; MacAulay, Calum; Lane, Pierre

    2014-06-15

    We report a polarization diversity detection scheme for optical coherence tomography with a new, custom, miniaturized fiber coupler with single mode (SM) fiber inputs and polarization maintaining (PM) fiber outputs. The SM fiber inputs obviate matching the optical lengths of the X and Y OCT polarization channels prior to interference and the PM fiber outputs ensure defined X and Y axes after interference. Advantages for this scheme include easier alignment, lower cost, and easier miniaturization compared to designs with free-space bulk optical components. We demonstrate the utility of the detection system to mitigate the effects of rapidly changing polarization states when imaging with rotating fiber optic probes in Intralipid suspension and during in vivo imaging of human airways.

  8. An evanescent wave biosensor--Part I: Fluorescent signal acquisition from step-etched fiber optic probes.

    Science.gov (United States)

    Anderson, G P; Golden, J P; Ligler, F S

    1994-06-01

    A fiber-optic biosensor capable of remote continuous monitoring has recently been designed. To permit sensing at locations separate from the optoelectronic instrumentation, long optical fibers are utilized. An evanescent wave immuno-probe is prepared by removing the cladding near the distal end of the fiber and covalently attaching antibodies to the core. Probes with a radius unaltered from that of the original core inefficiently returned the signal produced upon binding the fluorescent-labelled antigen. To elucidate the limiting factors in signal acquisition, a series of fibers with increasingly reduced probe core radius was examined. The results were consistent with the V-number mismatch, the difference in mode carrying capacity between the clad and unclad fiber, being a critical factor in limiting signal coupling from the fiber probe. However, it was also delineated that conditions which conserve excitation power, such that power in the evanescent wave is optimized, must also be met to obtain a maximal signal. The threshold sensitivity for the optimal step-etched fiber probe was improved by over 20-fold in an immunoassay, although, it was demonstrated that signal acquisition decreased along the probe length, suggesting that a sensor region of uniform radius is not ideal.

  9. Fiber-optic intra-aortic balloon therapy and its role within cardiac surgery.

    Science.gov (United States)

    Yarham, G; Clements, A; Morris, C; Cumberland, T; Bryan, M; Oliver, M; Burrows, H; Mulholland, J

    2013-03-01

    The patient population has changed and the cardiothoracic team are now operating on patients with more co-morbidity. One of the significant aspects of this increased co-morbidity, which affects both short- and long-term outcomes, is compromised left ventricular function. Intra-aortic balloon pump (IABP) technology offers these patients and the cardiac team an easily accessible, cost-effective, mechanical assist device. Arterial pressure monitoring for IABP therapy: Fluid-filled transducers used to measure the aortic waveform can be unreliable and inconsistent. Fiber-optic manometers located in the very tip of the IAB catheters provide accurate and fast, high quality measurements. This, in turn, presents the opportunity for the hardware and algorithm to measure key markers on the arterial waveform and optimise left ventricular support. It also provides the potential for automatic in vivo calibration, further increasing the accuracy and quality of the IAB support. The effect of fiber-optic IABP therapy on clinical management: A dual centre prospective audit comparing fluid-filled versus fiber-optic arterial pressure monitoring showed a 96% reduction in IAB-related perfusion on-site call-outs (17 vs. 1, respectively) and a 94% reduction in sub-optimal timing (55/98 vs. 2/94, respectively). The improved timing algorithms utilise the pressure information received 50 msecs faster than with fluid-filled transducers, measuring key markers on the pressure waveform and adjusting inflation and deflation accurately on a beat per beat basis. Fiber-optic IAB technology and, specifically, these improved algorithms provide better beat per beat mechanical support. Given our evolving patient population, this technology will not only play an increased role, but will have a significant impact on cardiac surgery.

  10. Electrical potential-assisted DNA hybridization. How to mitigate electrostatics for surface DNA hybridization.

    Science.gov (United States)

    Tymoczko, Jakub; Schuhmann, Wolfgang; Gebala, Magdalena

    2014-12-24

    Surface-confined DNA hybridization reactions are sensitive to the number and identity of DNA capture probes and experimental conditions such as the nature and the ionic strength of the electrolyte solution. When the surface probe density is high or the concentration of bulk ions is much lower than the concentration of ions within the DNA layer, hybridization is significantly slowed down or does not proceed at all. However, high-density DNA monolayers are attractive for designing high-sensitivity DNA sensors. Thus, circumventing sluggish DNA hybridization on such interfaces allows a high surface concentration of target DNA and improved signal/noise ratio. We present potential-assisted hybridization as a strategy in which an external voltage is applied to the ssDNA-modified interface during the hybridization process. Results show that a significant enhancement of hybridization can be achieved using this approach.

  11. Highly sensitive DNA sensors based on cerium oxide nanorods

    Science.gov (United States)

    Nguyet, Nguyen Thi; Hai Yen, Le Thi; Van Thu, Vu; lan, Hoang; Trung, Tran; Vuong, Pham Hung; Tam, Phuong Dinh

    2018-04-01

    In this work, a CeO2 nanorod (NR)-based electrochemical DNA sensor was developed to identify Salmonella that causes food-borne infections. CeO2 NRs were synthesized without templates via a simple and unexpensive hydrothermal approach at 170 °C for 12 h by using CeO(NO3)3·6H2O as a Ce source. The DNA probe was immobilized onto the CeO2 NR-modified electrode through covalent attachment. The characteristics of the hybridized DNA were analyzed through electrochemical impedance spectroscopy (EIS) with [Fe(CN)6]3-/4- as a redox probe. Experimental results showed that electron transfer resistance (Ret) increased after the DNA probe was attached to the electrode surface and increased further after the DNA probe hybridized with its complementary sequence. A linear response of Ret to the target DNA concentration was found from 0.01 μM to 2 μM. The detection limit and sensitivity of the DNA sensor were 0.01 μM and 3362.1 Ω μM-1 cm-2, respectively. Various parameters, such as pH value, ionic strength, DNA probe concentration, and hybridization time, influencing DNA sensor responses were also investigated.

  12. Development of a Meso-Scale Fiberoptic Rotation Sensor for a Torsion Actuator.

    Science.gov (United States)

    Sheng, Jun; Desai, Jaydev P

    2018-01-01

    This paper presents the development of a meso-scale fiberoptic rotation sensor for a shape memory alloy (SMA) torsion actuator for neurosurgical applications. Within the sensor, a rotary head with a reflecting surface is capable of modulating the light intensity collected by optical fibers when the rotary head is coupled to the torsion actuator. The mechanism of light intensity modulation is modeled, followed by experimental model verification. Meanwhile, working performances for different rotary head designs, optical fibers, and fabrication materials are compared. After the calibration of the fiberoptic rotation sensor, the sensor is capable of precisely measuring rotary motion and controlling the SMA torsion actuator with feedback control.

  13. Fiber-Optic Shape Sensing for Intelligent Solar Sail Deployment, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna Innovations proposes to develop a distributed fiber-optic shape sensor to provide a control system for the deployment of ultra-lightweight inflatable support...

  14. Mechano-genetic DNA hydrogels as a simple, reconstituted model to probe the effect of active fluctuations on gene transcription

    Science.gov (United States)

    Nguyen, Dan; Saleh, Omar

    Active fluctuations - non-directed fluctuations attributable, not to thermal energy, but to non-equilibrium processes - are thought to influence biology by increasing the diffusive motion of biomolecules. Dense DNA regions within cells (i.e. chromatin) are expected to exhibit such phenomena, as they are cross-linked networks that continually experience propagating forces arising from dynamic cellular activity. Additional agitation within these gene-encoding DNA networks could have potential genetic consequences. By changing the local mobility of transcriptional machinery and regulatory proteins towards/from their binding sites, and thereby influencing transcription rates, active fluctuations could prove to be a physical means of modulating gene expression. To begin probing this effect, we construct genetic DNA hydrogels, as a simple, reconstituted model of chromatin, and quantify transcriptional output from these hydrogels in the presence/absence of active fluctuations.

  15. 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.

  16. Branched-DNA signal amplification combined with paper chromatography hybridization assay and used in hepatitis B virus DNA detection

    International Nuclear Information System (INIS)

    Fu, F.Z.; Liu, L.X.; Wang, W.Q.; Sun, S. H.; Liu, L.B.

    2002-01-01

    Nucleic acids detection method is vital to the clinical pathogen diagnosis. The established method can be classified into target direct amplification and signal amplification format according to the target DNA or RNA being directly amplified or not. Those methods have advantages and disadvantages respectively in the clinical application. In the United States of American, branched-DNA as a strong signal amplifier is broadly used in the quantification of the nucleic acids. To gain satisfied sensitivity, some expensive label molecular and instruments should be adopted. Personnel should be special trained to perform. Hence, those can't be widely carried out in the Third World. To avoid those disadvantages, we used the branched-DNA amplifier in the paper chromatography hybridization assay. Methods: Branched DNA signal amplifier and series of probes complementary to the nucleic acid sequence of hepatitis B virus (HBV) have been synthesized. HBV-DNA or it's capture probe were immobilized on the high flow nitrocellulose strip. Having loaded at one end of the strip in turn, probes or HBV-DNA in the hybridization solution migrate to the opposite end of the strip by capillary forces and hybridizes to the immobilized DNA. The branched-DNA signal amplifier and probe labeled with biotin or 32P were then loaded. Through streptavidin-alkaline phosphatase (SA-AP) conjugate and NBT/BCIP ( the specific chromogenic substrate of AP) or autoradiography, the result can be visualized by color reaction or image production on the X-ray film. Results: The sensitivity of this HBV-DNA detection method used probe labeled with biotin and 32P are 1ng and 10pg. The method using the probe labeled with biotin is simple and rapid (2h) without depending on special instruments, it also avoids the pollution of EtBr which can lead to tumor. And the method using the probe labeled with 32P is simple and sensitive, with the exception of long time autoradiography and the inconvenient isotopic disposal

  17. GENETIC VARIATION IN RED RASPBERRIES (RUBUS IDAEUS L.; ROSACEAE) FROM SITES DIFFERING IN ORGANIC POLLUTANTS COMPARED WITH SYNTHETIC TANDEM REPEAT DNA PROBES

    Science.gov (United States)

    Two synthetic tandem repetitive DNA probes were used to compare genetic variation at variable-number-tandem-repeat (VNTR) loci among Rubus idaeus L. var. strigosus (Michx.) Maxim. (Rosaceae) individuals sampled at eight sites contaminated by pollutants (N = 39) and eight adjacent...

  18. Fluorescent carbon nanoparticle-based lateral flow biosensor for ultrasensitive detection of DNA.

    Science.gov (United States)

    Takalkar, Sunitha; Baryeh, Kwaku; Liu, Guodong

    2017-12-15

    We report a fluorescent carbon nanoparticle (FCN)-based lateral flow biosensor for ultrasensitive detection of DNA. Fluorescent carbon nanoparticle with a diameter of around 15nm was used as a tag to label a detection DNA probe, which was complementary with the part of target DNA. A capture DNA probe was immobilized on the test zone of the lateral flow biosensor. Sandwich-type hybridization reactions among the FCN-labeled DNA probe, target DNA and capture DNA probe were performed on the lateral flow biosensor. In the presence of target DNA, FCNs were captured on the test zone of the biosensor and the fluorescent intensity of the captured FCNs was measured with a portable fluorescent reader. After systematic optimizations of experimental parameters (the components of running buffers, the concentration of detection DNA probe used in the preparation of FCN-DNA conjugates, the amount of FCN-DNA dispensed on the conjugate pad and the dispensing cycles of the capture DNA probes on the test-zone), the biosensor could detect a minimum concentration of 0.4 fM DNA. This study provides a rapid and low-cost approach for DNA detection with high sensitivity, showing great promise for clinical application and biomedical diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Spectroscopic investigation on interaction and sonodynamic damage of Riboflavin to DNA under ultrasonic irradiation by using Methylene Blue as fluorescent probe

    Science.gov (United States)

    Wang, Qi; Wu, Qiong; Wang, Jun; Chen, Dandan; Fan, Ping; Wang, Baoxin

    2014-01-01

    In this paper, the Riboflavin (RF) as a sonosensitizer and Methylene Blue (MB) as a fluorescent probe were used to study the interaction and sonodynamic damage to Deoxyribonucleic Acid (DNA) by fluorescence and UV-vis spectroscopy. The results showed that the RF could efficiently bind to DNA in aqueous solution and exchange with the MB through competing reaction. And then, under ultrasonic irradiation, the RF could obviously damage the DNA. In addition, the influencing factors such as ultrasonic irradiation time and RF concentration on the sonodynamic damage to DNA were also considered. The experimental results showed that the sonodynamic damage degree increase with the increase of ultrasonic irradiation time and RF concentration. Perhaps, this paper may offer some important subjects for broadening the application of RF in sonodynamic therapy (SDT) technologies for tumor treatment.

  20. An in vivo investigation of photoplethysmographic signals and preliminary pulse oximetry estimation from the bowel using a new fiberoptic sensor.

    Science.gov (United States)

    Hickey, Michelle; Samuels, Neal; Randive, Nilesh; Langford, Richard M; Kyriacou, Panayiotis A

    2011-05-01

    The continuous monitoring of splanchnic organ oxygen saturation could make the early detection of inadequate tissue oxygenation feasible, reducing the risk of hypoperfusion, severe ischemia, multiple organ failure, and, ultimately, death. Current methods for assessing splanchnic perfusion have not been widely accepted for use in the clinical care environment. In an attempt to overcome the limitations of the current techniques, a new fiberoptic photoplethysmographic (PPG)/pulse oximetry sensor was developed as a means of assessing splanchnic organ perfusion during surgery in humans. A new fiberoptic splanchnic pulse oximeter and an optically identical fiberoptic finger pulse oximeter have been developed. Simultaneous PPG signals and preliminary estimates of arterial oxygen saturation from the bowel (small and large) and finger were obtained in 17 patients (3 men and 14 women) undergoing open laparotomy. Good quality PPG signals were obtained from the small and large bowel and from the finger in all patients (lower 95% confidence limit for the proportion was 0.64). Comparisons of blood oxygen saturation values acquired when using the splanchnic and the finger fiberoptic sensors and a commercial finger pulse oximeter indicated that there was no statistically significant difference between them (all P>0.454). A Bland and Altman plot of the difference between blood oxygen saturation values from the bowel fiberoptic pulse oximeter and the fiberoptic finger pulse oximeter against their mean showed that the limits of agreement between the 2 pulse oximeters were -3.8% and 4.2% for small bowel measurements, and -3.4% and 4.3% for large bowel measurements. The 95% prediction interval for the difference between the 2 devices was between -4.2% and 4.7%. This study demonstrated that good quality PPG signals can be obtained from the bowel using a new fiberoptic sensor. Further evaluation is required to determine whether fiberoptic pulse oximetry of the bowel may provide a

  1. Dramatically improved RNA in situ hybridization signals using LNA-modified probes

    DEFF Research Database (Denmark)

    Thomsen, Rune; Nielsen, Peter Stein; Jensen, Torben Heick

    2005-01-01

    . This increases the thermal stability of hybrids formed with RNA. The LNA-based probes detect specific RNAs in fixed yeast cells with an efficiency far better than conventional DNA oligonucleotide probes of the same sequence. Using this probe design, we were also able to detect poly(A)+ RNA accumulation within......In situ detection of RNA by hybridization with complementary probes is a powerful technique. Probe design is a critical parameter in successful target detection. We have evaluated the efficiency of fluorescent DNA oligonucleotides modified to contain locked nucleic acid (LNA) residues...

  2. Fiber-optic triggered release of liposome in vivo: implication of personalized chemotherapy

    Directory of Open Access Journals (Sweden)

    Huang HL

    2015-08-01

    Full Text Available Huei-Ling Huang,1 Pei-Hsuan Lu,1 Hung-Chih Yang,1 Gi-Da Lee,1,2 Han-Ru Li,1 Kuo-Chih Liao1 1Graduate Institute of Biomedical Engineering, National Chung Hsing University, 2Department of Radiology, Taichung Veterans General Hospital, Taichung, Taiwan Abstract: The aim of this research is to provide proof of principle by applying the fiber-optic triggered release of photo-thermally responsive liposomes embedded with gold nanoparticles (AuNPs using a 200 µm fiber with 65 mW and 532 nm excitation for topical release in vivo. The tunable delivery function can be paired with an apoptosis biosensor based on the same fiber-optic configuration for providing real-time evaluation of chemotherapy efficacy in vivo to perform as a personalized chemotherapy system. The pattern of topical release triggered by laser excitation conveyed through optical fibers was monitored by the increase in fluorescence resulting from the dilution of self-quenching (75 mM fluorescein encapsulated in liposomes. In in vitro studies (in 37°C phosphate buffer saline, the AuNP-embedded liposomes showed a more efficient triggered release (74.53%±1.63% in 40 minutes than traditional temperature-responsive liposomes without AuNPs (14.53%±3.17% or AuNP-liposomes without excitation (21.92%±2.08% by spectroscopic measurements. Using the mouse xenograft studies, we first demonstrated that the encapsulation of fluorescein in liposomes resulted in a more substantial content retention (81% in the tumor than for free fluorophores (14% at 120 minutes after administration from in vivo fluorescence imaging. Furthermore, the preliminary results also suggested the tunable release capability of the system by demonstrating consecutive triggered releases with fiber-optic guided laser excitation. Keywords: fiber-optic guided excitation, light excitation triggered release, photo-thermal responsive liposome, gold nanoparticles, tunable release in vivo

  3. Robotic arm design for a remotely-deployed, in situ waste characterization probe

    International Nuclear Information System (INIS)

    Kress, R.L.; Jansen, J.F.; Haas, J.W.

    1991-01-01

    This paper describes some design considerations for a system which will combine robotics and laser spectroscopy to produce an in situ monitoring system for heterogeneous waste materials. The new system will provide faster, cheaper, safer, and more complete characterization of mixed solids and liquids stored in tanks and drums or buried in pits. A small, fiberoptic multiprobe that performs Raman and fluorescence measurements of wastes composed of a variety of organic and inorganic compounds will be described. Design considerations for a novel sensor platform that positions and stabilizes the multiprobe relative to the sampling point in order to make accurate spectroscopic measurements and deploys the sensor in hazardous environments with minimal risk to workers will be presented. The core of the platform will be a 3-Degrees-Of-Freedom (3-DOF), spherical coordinate end effector equipped with a proximity sensor that compensates for errors introduced by the flexible nature of the support arm. The platform can be adapted to operate the most robotic deployment systems used in hazardous environments. The multisensor probe will be coupled to remote, portable laser spectrometer systems by a fiber-optic bundle. 5 refs

  4. Robotic arm design for a remotely-deployed, in situ waste characterization probe

    International Nuclear Information System (INIS)

    Kress, Reid; Haas, John; Jansen, John

    1992-01-01

    This paper describes some design considerations for a system which will combine robotics and laser spectroscopy to produce an in situ monitoring system for heterogeneous waste materials. The new system will provide faster, cheaper) safer, and more complete characterization of mixed solids and liquids stored in tanks and drums or buried in pits. A small, fiberoptic multiprobe that performs Raman and fluorescence measurements of wastes composed of a variety of organic and inorganic compounds will be described. Design considerations for a novel sensor platform that positions and stabilizes the multiprobe relative to the sampling point in order to male accurate spectroscopic measurements and deploys the sensor in hazardous environments with minimal risk to workers will be presented. The core of (he platform will be a 3-Degrees-Of-Freedom (3-DOF), spherical coordinate end effector equipped with a proximity sensor that compensates for errors introduced by the flexible nature of the support arm. The platform can be adapted to operate with most robotic deployment systems used in hazardous environments. The multisensor probe will be coupled to remote, portable laser spectrometer systems by a fiber-optic bundle. (author)

  5. A Rotational BODIPY Nucleotide: An Environment-Sensitive Fluorescence-Lifetime Probe for DNA Interactions and Applications in Live-Cell Microscopy

    Czech Academy of Sciences Publication Activity Database

    Dziuba, Dmytro; Jurkiewicz, Piotr; Cebecauer, Marek; Hof, Martin; Hocek, Michal

    2016-01-01

    Roč. 55, č. 1 (2016), s. 174-178 ISSN 1433-7851 R&D Projects: GA ČR GBP206/12/G151; GA ČR(CZ) GC14-03141J Institutional support: RVO:61388963 ; RVO:61388955 Keywords : DNA * fluorescence spectroscopy * fluorescent probes * nucleosides * time-resolved spectroscopy Subject RIV: CC - Organic Chemistry ; BO - Biophysics (UFCH-W) Impact factor: 11.994, year: 2016

  6. PCR associated with hybridization with DNA radioactive probes for diagnosis of asymptomatic infection caused by Leishmania Chagasi; PCR associado a hibridizacao com sondas radioativas de DNA para a identificacao de infeccao subclinica causada por Leishmania Chagasi

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Antero Silva Ribeiro de [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Belo Horizonte, MG (Brazil); Moreno, Elizabeth Castro [Fundacao Nacional de Saude, Belo Horizonte, MG (Brazil). Coordenacao Regional de Minas Gerais; Gomes, Rosangela Fatima; Melo, Maria Norma de; Carneiro, Mariangela [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Parasitologia; Fernandes, Octavio [Fundacao Inst. Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ (Brazil). Dept. de Medicina Tropical

    2002-07-01

    Detection systems for diagnosis of leishmaniasis based on PCR are very promising due to their sensitivity and specificity. Secondary detection by specific radioactive DNA probes, able to type the PCR amplified products, increase the specificity and raise about tem-fold the sensitivity of the assay. The aim of this work was evaluate PCR and hybridization as a tool to identify Leishmania (Leishmania) chagasi (the specie that cause the visceral leishmaniasis in Brazil) infection in asymptomatic persons living in a endemic area. Material and Methods: A group of 226 asymptomatic individuals, living in General Carneiro (MG), was selected. Blood samples were harvested and the DNA extracted from the mononucleate cells. PCR was performed using primers addressed to the kinetoplast DNA minicircles. This protocol gives a positive reaction for all Leishmania species. The amplified products were further hybridized with cloned L.chagasi minicircles labeled with {sup 32} P. Results: were identified 111 samples PCR positive, 2 of them hybridization negative and 133 samples hybridization positive, 24 of them PCR negative. The occurrence of samples with hybridization positive and PCR negative was expected since hybridization, with DNA probes labeled with {sup 32} P, increase the sensitivity of the assay. The samples that presented positive PCR and negative hybridization were probably due the presence of other Leishmania species, likely L. (V.) braziliensis (that produce tegumentary leishmaniasis in the region), since L. (L.) chagasi cloned minicircles were used as hybridization probe. We conclude that this procedure is a valuable tool to access subclinical L. (L.) chagasi infections in epidemiological studies. (author)

  7. Fiber-optic Raman spectroscopy for in vivo diagnosis of gastric dysplasia.

    Science.gov (United States)

    Wang, Jianfeng; Lin, Kan; Zheng, Wei; Ho, Khek Yu; Teh, Ming; Yeoh, Khay Guan; Huang, Zhiwei

    2016-06-23

    This study aims to assess the clinical utility of a rapid fiber-optic Raman spectroscopy technique developed for enhancing in vivo diagnosis of gastric precancer during endoscopic examination. We have developed a real-time fiber-optic Raman spectroscopy system capable of simultaneously acquiring both fingerprint (FP) (i.e., 800-1800 cm(-1)) and high-wavenumber (HW) (i.e., 2800-3600 cm(-1)) Raman spectra from gastric tissue in vivo at endoscopy. A total of 5792 high-quality in vivo FP/HW Raman spectra (normal (n = 5160); dysplasia (n = 155), and adenocarcinoma (n = 477)) were acquired in real-time from 441 tissue sites (normal (n = 396); dysplasia (n = 11), and adenocarcinoma (n = 34)) of 191 gastric patients (normal (n = 172); dysplasia (n = 6), and adenocarcinoma (n = 13)) undergoing routine endoscopic examinations. Partial least squares discriminant analysis (PLS-DA) together with leave-one-patient-out cross validation (LOPCV) were implemented to develop robust spectral diagnostic models. The FP/HW Raman spectra differ significantly between normal, dysplasia and adenocarcinoma of the stomach, which can be attributed to changes in proteins, lipids, nucleic acids, and the bound water content. PLS-DA and LOPCV show that the fiber-optic FP/HW Raman spectroscopy provides diagnostic sensitivities of 96.0%, 81.8% and 88.2%, and specificities of 86.7%, 95.3% and 95.6%, respectively, for the classification of normal, dysplastic and cancerous gastric tissue, superior to either the FP or HW Raman techniques alone. Further dichotomous PLS-DA analysis yields a sensitivity of 90.9% (10/11) and specificity of 95.9% (380/396) for the detection of gastric dysplasia using FP/HW Raman spectroscopy, substantiating its clinical advantages over white light reflectance endoscopy (sensitivity: 90.9% (10/11), and specificity: 51.0% (202/396)). This work demonstrates that the fiber-optic FP/HW Raman spectroscopy technique has great promise for enhancing in vivo diagnosis of gastric

  8. The use of radionuclide DNA probe technology for epidemiological studies of tegumentary leishmaniasis in Mato Grosso state

    Directory of Open Access Journals (Sweden)

    Antero Silva Ribeiro de Andrade

    2005-10-01

    Full Text Available DNA hybridisation, using probes labelled with 32P, was used to type Leishmania samples isolated from patients living in endemic areas of Mato Grosso State (Brazil, and clinically diagnosed as having tegumentary leishmaniasis. kDNA cloned mini-circle probes specific for the Leishmania mexicana and Leishmania braziliensis complexes were used. The results showed that L. braziliensis is the predominant group infecting human patients in the state. Sixty-eight samples were typed, 64 samples (94.1% belonging to the L. braziliensis complex and only four (5.9% belonging to the L. mexicana complex. Accurate identification of the Leishmania permits better orientation of the medical follow-up, since clinical manifestations may vary depending on the complex to which the parasite belongs. The epidemiological information furnished by the identification of the Leishmania in given endemic area is also essential for the design of appropriate control measuresHibridização, utilizando sondas de DNA marcadas com 32P, foi utilizada para a tipagem de amostras de Leishmania isoladas de pacientes do estado do Mato Grosso (Brasil, diagnosticados clinicamente como portadores de leishmaniose tegumentar. Sondas de minicírculos clonados de kDNA, específicas para os complexos Leishmania mexicana e Leishmania braziliensis, foram utilizadas. Os resultados demonstraram que o complexo L. brasiliensis é o grupo predominante infectando pacientes humanos no estado do Mato Grosso. Foram tipadas 68 amostras: 64 (94,1% foram identificadas como pertencentes ao complexo L. brasiliensis e somente 4 (5,9% como pertencentes ao complexo L. mexicana. A tipagem de Leishmania é importante para um melhor acompanhamento médico, uma vez que as manifestações clínicas podem variar em função do complexo ao qual o parasita pertence. A informação fornecida pela identificação também é essencial para a definição das medidas de controle mais adequadas e compreensão da epidemiologia da

  9. Gene probes: principles and protocols

    National Research Council Canada - National Science Library

    Aquino de Muro, Marilena; Rapley, Ralph

    2002-01-01

    ... of labeled DNA has allowed genes to be mapped to single chromosomes and in many cases to a single chromosome band, promoting significant advance in human genome mapping. Gene Probes: Principles and Protocols presents the principles for gene probe design, labeling, detection, target format, and hybridization conditions together with detailed protocols, accom...

  10. Modeling of Thermal Phase Noise in a Solid Core Photonic Crystal Fiber-Optic Gyroscope.

    Science.gov (United States)

    Song, Ningfang; Ma, Kun; Jin, Jing; Teng, Fei; Cai, Wei

    2017-10-26

    A theoretical model of the thermal phase noise in a square-wave modulated solid core photonic crystal fiber-optic gyroscope has been established, and then verified by measurements. The results demonstrate a good agreement between theory and experiment. The contribution of the thermal phase noise to the random walk coefficient of the gyroscope is derived. A fiber coil with 2.8 km length is used in the experimental solid core photonic crystal fiber-optic gyroscope, showing a random walk coefficient of 9.25 × 10 -5 deg/√h.

  11. Fiber-optic Fourier transform infrared spectroscopy for remote label-free sensing of medical device surface contamination

    Science.gov (United States)

    Hassan, Moinuddin; Tan, Xin; Welle, Elissa; Ilev, Ilko

    2013-05-01

    As a potential major source of biochemical contamination, medical device surfaces are of critical safety concerns in the clinical practice and public health. The development of innovative sensing methods for accurate and real-time detection of medical device surface contamination is essential to protect patients from high risk infection. In this paper, we demonstrate an alternative fiber-optic Fourier Transform Infrared (FTIR) spectroscopy based sensing approach for remote, non-contact, and label-free detection of biochemical contaminants in the mid-infrared (mid-IR) region. The sensing probe is designed using mid-IR hollow fibers and FTIR measurements are carried out in reflection mode. Bovine Serum Albumin (BSA) and bacterial endotoxin of different concentrations under thoroughly dry condition are used to evaluate the detection sensitivity. The devised system can identify ≤0.0025% (≤4 × 1011 molecules) BSA and 0.5% (0.5 EU/ml) endotoxin concentration. The developed sensing approach may be applied to detect various pathogens that pose public health threats.

  12. Measurement of entrance surface dose on an anthropomorphic thorax phantom using a miniature fiber-optic dosimeter.

    Science.gov (United States)

    Yoo, Wook Jae; Shin, Sang Hun; Jeon, Dayeong; Hong, Seunghan; Sim, Hyeok In; Kim, Seon Geun; Jang, Kyoung Won; Cho, Seunghyun; Youn, Won Sik; Lee, Bongsoo

    2014-04-01

    A miniature fiber-optic dosimeter (FOD) system was fabricated using a plastic scintillating fiber, a plastic optical fiber, and a multi-pixel photon counter to measure real-time entrance surface dose (ESD) during radiation diagnosis. Under varying exposure parameters of a digital radiography (DR) system, we measured the scintillating light related to the ESD using the sensing probe of the FOD, which was placed at the center of the beam field on an anthropomorphic thorax phantom. Also, we obtained DR images using a flat panel detector of the DR system to evaluate the effects of the dosimeter on image artifacts during posteroanterior (PA) chest radiography. From the experimental results, the scintillation output signals of the FOD were similar to the ESDs including backscatter simultaneously obtained using a semiconductor dosimeter. We demonstrated that the proposed miniature FOD can be used to measure real-time ESDs with minimization of DR image artifacts in the X-ray energy range of diagnostic radiology.

  13. Measurement of Entrance Surface Dose on an Anthropomorphic Thorax Phantom Using a Miniature Fiber-Optic Dosimeter

    Directory of Open Access Journals (Sweden)

    Wook Jae Yoo

    2014-04-01

    Full Text Available A miniature fiber-optic dosimeter (FOD system was fabricated using a plastic scintillating fiber, a plastic optical fiber, and a multi-pixel photon counter to measure real-time entrance surface dose (ESD during radiation diagnosis. Under varying exposure parameters of a digital radiography (DR system, we measured the scintillating light related to the ESD using the sensing probe of the FOD, which was placed at the center of the beam field on an anthropomorphic thorax phantom. Also, we obtained DR images using a flat panel detector of the DR system to evaluate the effects of the dosimeter on image artifacts during posteroanterior (PA chest radiography. From the experimental results, the scintillation output signals of the FOD were similar to the ESDs including backscatter simultaneously obtained using a semiconductor dosimeter. We demonstrated that the proposed miniature FOD can be used to measure real-time ESDs with minimization of DR image artifacts in the X-ray energy range of diagnostic radiology.

  14. Induced Förster resonance energy transfer by encapsulation of DNA-scaffold based probes inside a plant virus based protein cage

    Science.gov (United States)

    de Ruiter, Mark V.; Overeem, Nico J.; Singhai, Gaurav; Cornelissen, Jeroen J. L. M.

    2018-05-01

    Insight into the assembly and disassembly of viruses can play a crucial role in developing cures for viral diseases. Specialized fluorescent probes can benefit the study of interactions within viruses, especially during cell studies. In this work, we developed a strategy based on Förster resonance energy transfer (FRET) to study the assembly of viruses without labeling the exterior of viruses. Instead, we exploit their encapsulation of nucleic cargo, using three different fluorescent ATTO dyes linked to single-stranded DNA oligomers, which are hybridised to a longer DNA strand. FRET is induced upon assembly of the cowpea chlorotic mottle virus, which forms monodisperse icosahedral particles of about 22 nm, thereby increasing the FRET efficiency by a factor of 8. Additionally, encapsulation of the dyes in virus-like particles induces a two-step FRET. When the formed constructs are disassembled, this FRET signal is fully reduced to the value before encapsulation. This reversible behavior makes the system a good probe for studying viral assembly and disassembly. It, furthermore, shows that multi-component supramolecular materials are stabilized in the confinement of a protein cage.

  15. Study of distributed fiber-optic laser-ultrasound generation based on ghost-mode of tilted fiber Bragg gratings

    Science.gov (United States)

    Tian, Jiajun; Zhang, Qi; Han, Ming

    2013-05-01

    Fiber-optic ultrasonic transducers are an important component of an active ultrasonic testing system for structural health monitoring. Fiber-optic transducers have several advantages such as small size, light weight, and immunity to electromagnetic interference that make them much more attractive than the current available piezoelectric transducers, especially as embedded and permanent transducers in active ultrasonic testing for structural health monitoring. In this paper, a distributed fiber-optic laser-ultrasound generation based on the ghost-mode of tilted fiber Bragg gratings is studied. The influences of the laser power and laser pulse duration on the laser-ultrasound generation are investigated. The results of this paper are helpful to understand the working principle of this laser-ultrasound method and improve the ultrasonic generation efficiency.

  16. A fiber-optic setup for quantification of root surface demineralization

    NARCIS (Netherlands)

    vanderVeen, MH; tenBosch, JJ

    A fiber-optic fluorescence observation (FOFO) technique has been developed for the quantification of demineralized root dentin, The method was tested on 40 specimens of in vitro demineralized parts of human root dentin, Fluorescein sodium salt was used as a penetrating dye, The fluorescein sodium

  17. Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing.

    Science.gov (United States)

    Cébron, Aurélie; Bodrossy, Levente; Chen, Yin; Singer, Andrew C; Thompson, Ian P; Prosser, James I; Murrell, J Colin

    2007-10-01

    A considerable amount of methane produced during decomposition of landfill waste can be oxidized in landfill cover soil by methane-oxidizing bacteria (methanotrophs) thus reducing greenhouse gas emissions to the atmosphere. The identity of active methanotrophs in Roscommon landfill cover soil, a slightly acidic peat soil, was assessed by DNA-stable isotope probing (SIP). Landfill cover soil slurries were incubated with (13)C-labelled methane and under either nutrient-rich nitrate mineral salt medium or water. The identity of active methanotrophs was revealed by analysis of (13)C-labelled DNA fractions. The diversity of functional genes (pmoA and mmoX) and 16S rRNA genes was analyzed using clone libraries, microarrays and denaturing gradient gel electrophoresis. 16S rRNA gene analysis revealed that the cover soil was mainly dominated by Type II methanotrophs closely related to the genera Methylocella and Methylocapsa and to Methylocystis species. These results were supported by analysis of mmoX genes in (13)C-DNA. Analysis of pmoA gene diversity indicated that a significant proportion of active bacteria were also closely related to the Type I methanotrophs, Methylobacter and Methylomonas species. Environmental conditions in the slightly acidic peat soil from Roscommon landfill cover allow establishment of both Type I and Type II methanotrophs.

  18. Kansas Communication and Instruction System through Fiber-Optic Transmission.

    Science.gov (United States)

    Kansas State Dept. of Education, Topeka.

    Schools and communities will restructure as they move into the next decade. The success of this restructuring will be dependent upon access to and sharing of quality teaching and information through an expanded communication system. One of the major two-way interactive technologies is the fiber-optic cable: a delivery system that will provide…

  19. Prevalence of Visible and Occult Blood on the Surfaces of Fiberoptic Bronchoscopes

    National Research Council Canada - National Science Library

    McKamey, Jeffrey

    2000-01-01

    .... This study was conducted to determine if current cleaning, disinfection and sterilization procedures used at one medical center was adequate to remove visible and occult blood from fiberoptic bronchoscopes...

  20. Development of DNA biosensor based on TiO2 nanoparticles

    Science.gov (United States)

    Nadzirah, Sh.; Hashim, U.; Rusop, M.

    2018-05-01

    A novel technique of DNA hybridization on the TiO2 nanoparticles film was developed by dropping a single droplet of target DNA onto the surface of TiO2 for the study of various concentrations of target DNA. The surface of TiO2 nanoparticle film was functionalized with APTES and covalently immobilized with 1 µM probe DNA on the silanized TiO2 nanoparticles surface. The effect of silanization, immobilization and hybridization were quantitatively measured by the output current signal obtained using a picoammeter. The 1 µM target DNA was found to be the most effective target towards the 1 µM probe DNA as the output current signal was within range; while the output current signal of the 10 µM target DNA was observed to beyond the range of the probe DNA control due to the excessive concentration as compared to the probe DNA. This approach has several advantages such as rapid, simple, low cost, and sensitive current signal during detection of different target DNA concentrations.

  1. High-Frequency Flush Mounted Miniature LOX Fiber-Optic Pressure Sensor, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna Innovations is teaming with the University of Alabama, Huntsville, to develop a miniature flush-mounted fiber-optic pressure sensor that will allow accurate,...

  2. Linearization of Positional Response Curve of a Fiber-optic Displacement Sensor

    Science.gov (United States)

    Babaev, O. G.; Matyunin, S. A.; Paranin, V. D.

    2018-01-01

    Currently, the creation of optical measuring instruments and sensors for measuring linear displacement is one of the most relevant problems in the area of instrumentation. Fiber-optic contactless sensors based on the magneto-optical effect are of special interest. They are essentially contactless, non-electrical and have a closed optical channel not subject to contamination. The main problem of this type of sensors is the non-linearity of their positional response curve due to the hyperbolic nature of the magnetic field intensity variation induced by moving the magnetic source mounted on the controlled object relative to the sensing element. This paper discusses an algorithmic method of linearizing the positional response curve of fiber-optic displacement sensors in any selected range of the displacements to be measured. The method is divided into two stages: 1 - definition of the calibration function, 2 - measurement and linearization of the positional response curve (including its temperature stabilization). The algorithm under consideration significantly reduces the number of points of the calibration function, which is essential for the calibration of temperature dependence, due to the use of the points that randomly deviate from the grid points with uniform spacing. Subsequent interpolation of the deviating points and piecewise linear-plane approximation of the calibration function reduces the microcontroller storage capacity for storing the calibration function and the time required to process the measurement results. The paper also presents experimental results of testing real samples of fiber-optic displacement sensors.

  3. Detection of a new submicroscopic Norrie disease deletion interval with a novel DNA probe isolated by differential Alu PCR fingerprint cloning

    NARCIS (Netherlands)

    Bergen, A. A.; Wapenaar, M. C.; Schuurman, E. J.; Diergaarde, P. J.; Lerach, H.; Monaco, A. P.; Bakker, E.; Bleeker-Wagemakers, E. M.; van Ommen, G. J.

    1993-01-01

    Differential Alu PCR fingerprint cloning was used to isolate a DNA probe from the Xp11.4-->p11.21 region of the human X chromosome. This novel sequence, cpXr318 (DXS742), detects a new submicroscopic deletion interval at the Norrie disease locus (NDP). Combining our data with the consensus genetic

  4. Improving comparability between microarray probe signals by thermodynamic intensity correction

    DEFF Research Database (Denmark)

    Bruun, G. M.; Wernersson, Rasmus; Juncker, Agnieszka

    2007-01-01

    different probes. It is therefore of great interest to correct for the variation between probes. Much of this variation is sequence dependent. We demonstrate that a thermodynamic model for hybridization of either DNA or RNA to a DNA microarray, which takes the sequence-dependent probe affinities...... determination of transcription start sites for a subset of yeast genes. In another application, we identify present/absent calls for probes hybridized to the sequenced Escherichia coli strain O157:H7 EDL933. The model improves the correct calls from 85 to 95% relative to raw intensity measures. The model thus...... makes applications which depend on comparisons between probes aimed at different sections of the same target more reliable....

  5. Polymerase chain reaction and conventional DNA tests in detection of HPV DNA in cytologically normal and abnormal cervical scrapes

    DEFF Research Database (Denmark)

    Kalia, A.; Jalava, T.; Nieminen, P.

    1992-01-01

    Med.mikrobiologi, polymerase chain reaction, DNA tests, human papillomavirus (HPV), cervical smear, hybridisation, cytologi, affiProbe HPV test, ViraType test......Med.mikrobiologi, polymerase chain reaction, DNA tests, human papillomavirus (HPV), cervical smear, hybridisation, cytologi, affiProbe HPV test, ViraType test...

  6. Characterization and immunological identification of cDNA clones encoding two human DNA topoisomerase II isozymes

    International Nuclear Information System (INIS)

    Chung, T.D.Y.; Drake, F.H.; Tan, K.B.; Per, S.R.; Crooke, S.T.; Mirabelli, C.K.

    1989-01-01

    Several DNA topoisomerase II partial cDNA clones obtained from a human Raji-HN2 cDNA library were sequenced and two classes of nucleotide sequences were found. One member of the first class, SP1, was identical to an internal fragment of human HeLa cell Topo II cDNA described earlier. A member of the second class, SP11, shared extensive nucleotide (75%) and predicted peptide (92%) sequence similarities with the first two-thirds of HeLa Topo II. Each class of cDNAs hybridized to unique, nonoverlapping restriction enzyme fragments of genomic DNA from several human cell lines. Synthetic 24-mer oligonucleotide probes specific for each cDNA class hybridized to 6.5-kilobase mRNAs; furthermore, hybridization of probe specific for one class was not blocked by probe specific for the other. Antibodies raised against a synthetic SP1-encoded dodecapeptide specifically recognized the 170-kDa form of Topo II, while antibodies raised against the corresponding SP11-encoded dodecapeptide, or a second unique SP11-encoded tridecapeptide, selectively recognized the 180-kDa form of Topo II. These data provide genetic and immunochemical evidence for two Topo II isozymes

  7. [Development of a novel real-time PCR method for detection of HSV types 1 and 2 DNA using HybProbe chemistry].

    Science.gov (United States)

    Chudzik, Emilia; Karabin, Karolina; Dzieciątkowski, Tomasz; Majewska, Anna; Przybylski, Maciej; Midak-Siewirska, Anna; Łuczak, Mirosław; Młynarczyk, Grazyna

    2010-01-01

    Herpes simplex viruses types 1 and 2 are members of the Alphaherpesviridae subfamily, as they can infect both skin and nerves and develop latent infection within the dorsal root and trigeminal ganglia. Infections with these viruses are common worldwide and cause wide range of clinical syndromes. Although HSV-1/2 infect healthy children and adults, disease is more severe and extensive in the immunocompromised individuals and/or during neuroinfections. The aim of the study was development of real-time PCR assay for detection and differentiation of herpes simplex viruses type 1 and 2. DNA in clinical samples, using specific dual-channel HybProbe chemistry. The nalytical sensitivity of assay was tested using serial dilutions of HSV-1 and HSV-2 DNA in range between 10 degrees and 10(-5). (4.35 x 10(5)-4.00 x 10(2) copies/ml and 4.18 x 10(5)-3.82 x 10(2) copies/ml, respectively). Thirty four cell line isolates and sixteen clinical samples taken from a group of adult patients with neurological signs were tested for the presence of HSV-1/2 DNA in the LightCycler instrument. Described in-house real-time PCR assay detected herpesviral DNA in all cell line isolates (31 of them were HSV-1 positive; 3 were HSV-2 positive) and in 10 clinical samples (positive only for HSV-1). The conclusion is that developed HybProbe-based real-time PCR test is very reliable and valuable tool for detection and differentiation of HSV-1/2 viremia in different kind of samples. The high level of sensitivity and accuracy provided by this assay is favorable for the quantification of herpes simplex virus 1 and 2 DNA in clinical specimens, especially during low-copy infections.

  8. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    2010-09-01

    Full Text Available International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  9. Unlabeled probes for the detection and typing of herpes simplex virus.

    Science.gov (United States)

    Dames, Shale; Pattison, David C; Bromley, L Kathryn; Wittwer, Carl T; Voelkerding, Karl V

    2007-10-01

    Unlabeled probe detection with a double-stranded DNA (dsDNA) binding dye is one method to detect and confirm target amplification after PCR. Unlabeled probes and amplicon melting have been used to detect small deletions and single-nucleotide polymorphisms in assays where template is in abundance. Unlabeled probes have not been applied to low-level target detection, however. Herpes simplex virus (HSV) was chosen as a model to compare the unlabeled probe method to an in-house reference assay using dual-labeled, minor groove binding probes. A saturating dsDNA dye (LCGreen Plus) was used for real-time PCR. HSV-1, HSV-2, and an internal control were differentiated by PCR amplicon and unlabeled probe melting analysis after PCR. The unlabeled probe technique displayed 98% concordance with the reference assay for the detection of HSV from a variety of archived clinical samples (n = 182). HSV typing using unlabeled probes was 99% concordant (n = 104) to sequenced clinical samples and allowed for the detection of sequence polymorphisms in the amplicon and under the probe. Unlabeled probes and amplicon melting can be used to detect and genotype as few as 10 copies of target per reaction, restricted only by stochastic limitations. The use of unlabeled probes provides an attractive alternative to conventional fluorescence-labeled, probe-based assays for genotyping and detection of HSV and might be useful for other low-copy targets where typing is informative.

  10. Two-photon fluorescence and fluorescence imaging of two styryl heterocyclic dyes combined with DNA.

    Science.gov (United States)

    Gao, Chao; Liu, Shu-yao; Zhang, Xian; Liu, Ying-kai; Qiao, Cong-de; Liu, Zhao-e

    2016-03-05

    Two new styryl heterocyclic two-photon (TP) materials, 4-[4-(N-methyl)styrene]-imidazo [4,5-f][1,10] phenanthroline-benzene iodated salt (probe-1) and 4,4-[4-(N-methyl)styrene]-benzene iodated salt (probe-2) were successfully synthesized and studied as potential fluorescent probes of DNA detection. The linear and nonlinear photophysical properties of two compounds in different solvents were investigated. The absorption, one- and two-photon fluorescent spectra of the free dye and dye-DNA complex were also examined to evaluate their photophysical properties. The binding constants of dye-DNA were obtained according to Scatchard equation with good values. The results showed that two probes could be used as fluorescent DNA probes by two-photon excitation, and TP fluorescent properties of probe-1 are superior to that of probe-2. The fluorescent method date indicated that the mechanisms of dye-DNA complex interaction may be groove binding for probe-1 and electrostatic interaction for probe-2, respectively. The MTT assay experiments showed two probes are low toxicity. Moreover, the TP fluorescence imaging of DNA detection in living cells at 800 nm indicated that the ability to locate in cell nuclei of probe-1 is better than that of probe-2. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  12. Fiber-Optic Magnetic-Field-Strength Measurement System for Lightning Detection

    Science.gov (United States)

    Gurecki, Jay; Scully, Robert; Davis, Allen; Kirkendall, Clay; Bucholtz, Frank

    2011-01-01

    A fiber-optic sensor system is designed to measure magnetic fields associated with a lightning stroke. Field vector magnitudes are detected and processed for multiple locations. Since physical limitations prevent the sensor elements from being located in close proximity to highly conductive materials such as aluminum, the copper wire sensor elements (3) are located inside a 4-cubic-in. (.66-cubic-cm) plastic housing sensor head and connected to a fiber-optic conversion module by shielded cabling, which is limited to the shortest length feasible. The signal path between the conversion module and the avionics unit which processes the signals are fiber optic, providing enhanced immunity from electromagnetic radiation incident in the vicinity of the measurements. The sensors are passive, lightweight, and much smaller than commercial B-dot sensors in the configuration which measures a three-dimensional magnetic field. The system is expandable, and provides a standard-format output signal for downstream processing. Inside of the sensor head, three small search coils, each having a few turns on a circular form, are mounted orthogonally inside the non-metallic housing. The fiber-optic conversion module comprises three interferometers, one for each search coil. Each interferometer has a high bandwidth optical phase modulator that impresses the signal received from its search coil onto its output. The output of each interferometer travels by fiber optic cable to the avionics unit, and the search coil signal is recovered by an optical phase demodulator. The output of each demodulator is fed to an analog-to-digital converter, whose sampling rate is determined by the maximum expected rate of rise and peak signal magnitude. The output of the digital processor is a faithful reproduction of the coil response to the incident magnetic field. This information is provided in a standard output format on a 50-ohm port that can be connected to any number of data collection and processing

  13. Videolaryngoscopy versus Fiber-optic Intubation through a Supraglottic Airway in Children with a Difficult Airway: An Analysis from the Multicenter Pediatric Difficult Intubation Registry.

    Science.gov (United States)

    Burjek, Nicholas E; Nishisaki, Akira; Fiadjoe, John E; Adams, H Daniel; Peeples, Kenneth N; Raman, Vidya T; Olomu, Patrick N; Kovatsis, Pete G; Jagannathan, Narasimhan; Hunyady, Agnes; Bosenberg, Adrian; Tham, See; Low, Daniel; Hopkins, Paul; Glover, Chris; Olutoye, Olutoyin; Szmuk, Peter; McCloskey, John; Dalesio, Nicholas; Koka, Rahul; Greenberg, Robert; Watkins, Scott; Patel, Vikram; Reynolds, Paul; Matuszczak, Maria; Jain, Ranu; Khalil, Samia; Polaner, David; Zieg, Jennifer; Szolnoki, Judit; Sathyamoorthy, Kumar; Taicher, Brad; Riveros Perez, N Ricardo; Bhattacharya, Solmaletha; Bhalla, Tarun; Stricker, Paul; Lockman, Justin; Galvez, Jorge; Rehman, Mohamed; Von Ungern-Sternberg, Britta; Sommerfield, David; Soneru, Codruta; Chiao, Franklin; Richtsfeld, Martina; Belani, Kumar; Sarmiento, Lina; Mireles, Sam; Bilen Rosas, Guelay; Park, Raymond; Peyton, James

    2017-09-01

    The success rates and related complications of various techniques for intubation in children with difficult airways remain unknown. The primary aim of this study is to compare the success rates of fiber-optic intubation via supraglottic airway to videolaryngoscopy in children with difficult airways. Our secondary aim is to compare the complication rates of these techniques. Observational data were collected from 14 sites after management of difficult pediatric airways. Patient age, intubation technique, success per attempt, use of continuous ventilation, and complications were recorded for each case. First-attempt success and complications were compared in subjects managed with fiber-optic intubation via supraglottic airway and videolaryngoscopy. Fiber-optic intubation via supraglottic airway and videolaryngoscopy had similar first-attempt success rates (67 of 114, 59% vs. 404 of 786, 51%; odds ratio 1.35; 95% CI, 0.91 to 2.00; P = 0.16). In subjects less than 1 yr old, fiber-optic intubation via supraglottic airway was more successful on the first attempt than videolaryngoscopy (19 of 35, 54% vs. 79 of 220, 36%; odds ratio, 2.12; 95% CI, 1.04 to 4.31; P = 0.042). Complication rates were similar in the two groups (20 vs. 13%; P = 0.096). The incidence of hypoxemia was lower when continuous ventilation through the supraglottic airway was used throughout the fiber-optic intubation attempt. In this nonrandomized study, first-attempt success rates were similar for fiber-optic intubation via supraglottic airway and videolaryngoscopy. Fiber-optic intubation via supraglottic airway is associated with higher first-attempt success than videolaryngoscopy in infants with difficult airways. Continuous ventilation through the supraglottic airway during fiber-optic intubation attempts may lower the incidence of hypoxemia.

  14. A repetitive probe for FISH analysis of bovine interphase nuclei

    Directory of Open Access Journals (Sweden)

    Cribiu Edmond

    2000-03-01

    Full Text Available Abstract The purpose of this study was to generate repetitive DNA sequence probes for the analysis of interphase nuclei by fluorescent in situ hybridisation (FISH. Such probes are useful for the diagnosis of chromosomal abnormalities in bovine preimplanted embryos. Of the seven probes (E1A, E4A, Ba, H1A, W18, W22, W5 that were generated and partially sequenced, five corresponded to previously described Bos taurus repetitive DNA (E1A, E4A, Ba, W18, W5, one probe (W22 shared no homology with other DNA sequences and one (H1A displayed a significant homology with Rattus norvegicus mRNA for secretin receptor transmembrane domain 3. Fluorescent in situ hybridisation was performed on metaphase bovine fibroblast cells and showed that five of the seven probes hybridised most centromeres (E1A, E4A, Ba, W18, W22, one labelled the arms of all chromosomes (W5 and the H1A probe was specific to three chromosomes (ch14, ch20, and ch25. Moreover, FISH with H1A resulted in interpretable signals on interphase nuclei in 88% of the cases, while the other probes yielded only dispersed overlapping signals.

  15. A cell-surface-anchored ratiometric fluorescent probe for extracellular pH sensing.

    Science.gov (United States)

    Ke, Guoliang; Zhu, Zhi; Wang, Wei; Zou, Yuan; Guan, Zhichao; Jia, Shasha; Zhang, Huimin; Wu, Xuemeng; Yang, Chaoyong James

    2014-09-10

    Accurate sensing of the extracellular pH is a very important yet challenging task in biological and clinical applications. This paper describes the development of an amphiphilic lipid-DNA molecule as a simple yet useful cell-surface-anchored ratiometric fluorescent probe for extracellular pH sensing. The lipid-DNA probe, which consists of a hydrophobic diacyllipid tail and a hydrophilic DNA strand, is modified with two fluorescent dyes; one is pH-sensitive as pH indicator and the other is pH-insensitive as an internal reference. The lipid-DNA probe showed sensitive and reversible response to pH change in the range of 6.0-8.0, which is suitable for most extracellular studies. In addition, based on simple hydrophobic interactions with the cell membrane, the lipid-DNA probe can be easily anchored on the cell surface with negligible cytotoxicity, excellent stability, and unique ratiometric readout, thus ensuring its accurate sensing of extracellular pH. Finally, this lipid-DNA-based ratiometric pH indicator was successfully used for extracellular pH sensing of cells in 3D culture environment, demonstrating the potential applications of the sensor in biological and medical studies.

  16. Surface plasmon resonance-based fiber-optic hydrogen gas sensor utilizing palladium supported zinc oxide multilayers and their nanocomposite.

    Science.gov (United States)

    Tabassum, Rana; Gupta, Banshi D

    2015-02-10

    We analyze surface plasmon resonance-based fiber-optic sensor for sensing of small concentrations of hydrogen gas in the visible region of the electromagnetic spectrum. One of the two probes considered has multilayers of zinc oxide (ZnO) and palladium (Pd) while the other has layer of their composite over a silver coated unclad core of the fiber. The analysis is carried out for different volume fractions of palladium nanoparticles dispersed in zinc oxide host material in the nanocomposite layer. For the analysis, a Maxwell-Garnett model is adopted for calculating the dielectric function of a ZnO:Pd nanocomposite having nanoparticles of dimensions smaller than the wavelength of radiation used. The effects of the volume fraction of the nanoparticles in the nanocomposite and the thickness of the nanocomposite layer on the figure of merit of the sensor have been studied. The film thickness of the layer and the volume fraction of nanoparticles in the ZnO:Pd nanocomposite layer have been optimized to achieve the maximum value of the figure of merit of the sensor. It has been found that the figure of merit of the sensing probe coated with ZnO:Pd nanocomposite is more than twofold of the sensing probe coated with multilayers of Pd and ZnO over a silver coated unclad core of the fiber; hence, the sensor with a nanocomposite layer works better than that with multilayers of zinc oxide and palladium. The sensor can be used for online monitoring and remote sensing of hydrogen gas.

  17. Development and Testing of a Post-Installable Deepwater Monitoring System Using Fiber-Optic Sensors

    Science.gov (United States)

    Seaman, Calvin H.; Brower, David V.; Le, Suy Q.; Tang, Henry H.

    2015-01-01

    This paper addresses the design and development of a fiber-optic monitoring system that can be deployed on existing deepwater risers and flowlines; and provides a summary of test article fabrication and the subsequent laboratory testing performed at the National Aeronautics and Space Administration-Johnson Space Center (NASA-JSC). A major challenge of a post-installed instrumentation system is to ensure adequate coupling between the instruments and the riser or flowline of interest. This work investigates the sensor coupling for pipelines that are suspended in a water column (from topside platform to seabed) using a fiber-optic sensor clamp and subsea bonding adhesive. The study involved the design, fabrication, and test of several prototype clamps that contained fiber-optic sensors. A mold was produced by NASA using 3-D printing methods that allowed the casting of polyurethane clamp test articles to accommodate 4-inch and 8-inch diameter pipes. The prototype clamps were installed with a subsea adhesive in a "wet" environment and then tested in the NASA Structures Test Laboratory (STL). The tension, compression, and bending test data showed that the prototype sensor clamps achieved good structural coupling, and could provide high quality strain measurement for active monitoring.

  18. Computational imaging through a fiber-optic bundle

    Science.gov (United States)

    Lodhi, Muhammad A.; Dumas, John Paul; Pierce, Mark C.; Bajwa, Waheed U.

    2017-05-01

    Compressive sensing (CS) has proven to be a viable method for reconstructing high-resolution signals using low-resolution measurements. Integrating CS principles into an optical system allows for higher-resolution imaging using lower-resolution sensor arrays. In contrast to prior works on CS-based imaging, our focus in this paper is on imaging through fiber-optic bundles, in which manufacturing constraints limit individual fiber spacing to around 2 μm. This limitation essentially renders fiber-optic bundles as low-resolution sensors with relatively few resolvable points per unit area. These fiber bundles are often used in minimally invasive medical instruments for viewing tissue at macro and microscopic levels. While the compact nature and flexibility of fiber bundles allow for excellent tissue access in-vivo, imaging through fiber bundles does not provide the fine details of tissue features that is demanded in some medical situations. Our hypothesis is that adapting existing CS principles to fiber bundle-based optical systems will overcome the resolution limitation inherent in fiber-bundle imaging. In a previous paper we examined the practical challenges involved in implementing a highly parallel version of the single-pixel camera while focusing on synthetic objects. This paper extends the same architecture for fiber-bundle imaging under incoherent illumination and addresses some practical issues associated with imaging physical objects. Additionally, we model the optical non-idealities in the system to get lower modelling errors.

  19. Theoretical Analysis of the Optical Propagation Characteristics in a Fiber-Optic Surface Plasmon Resonance Sensor

    Directory of Open Access Journals (Sweden)

    Xiaolin Zheng

    2013-06-01

    Full Text Available Surface plasmon resonance (SPR sensor is widely used for its high precision and real-time analysis. Fiber-optic SPR sensor is easy for miniaturization, so it is commonly used in the development of portable detection equipment. It can also be used for remote, real-time, and online detection. In this study, a wavelength modulation fiber-optic SPR sensor is designed, and theoretical analysis of optical propagation in the optical fiber is also done. Compared with existing methods, both the transmission of a skew ray and the influence of the chromatic dispersion are discussed. The resonance wavelength is calculated at two different cases, in which the chromatic dispersion in the fiber core is considered. According to the simulation results, a novel multi-channel fiber-optic SPR sensor is likewise designed to avoid defaults aroused by the complicated computation of the skew ray as well as the chromatic dispersion. Avoiding the impact of skew ray can do much to improve the precision of this kind of sensor.

  20. Deoxyribonucleic Acid Probes Analyses for the Detection of Periodontal Pathogens.

    Science.gov (United States)

    Al Yahfoufi, Zoubeida; Hadchiti, Wahib; Berberi, Antoine

    2015-09-01

    In clinical microbiology several techniques have been used to identify bacteria. Recently, Deoxyribonucleic acid (DNA)-based techniques have been introduced to detect human microbial pathogens in periodontal diseases. Deoxyribonucleic acid probes can detect bacteria at a very low level if we compared with the culture methods. These probes have shown rapid and cost-effective microbial diagnosis, good sensitivity and specificity for some periodontal pathogens in cases of severe periodontitis. Eighty-five patients were recruited for the study. Twenty-one subjects ranging between 22 and 48 years of age fulfilled the inclusion and exclusion criteria. Seventy-eight samples became available for DNA probe analysis from the deepest pockets in each quadrant. All 21 patients showed positive results for Prevotella intermedia; also, Prevotella gingivalis was identified in 19 subjects, Aggregatibacter actinomycetemcomitans in 6 subjects. P. intermedia was diagnosed positive in 82% of the subgingival samples taken, 79% for P. gingivalis, and 23% for A. actinomycetemcomitans. This study shows a high frequency of putative periodontal pathogens by using DNA probe technology, which is semi-quantitative in this study. Deoxyribonucleic acid probes can detect bacteria at very low level about 10(3) which is below the detection level of culture methods. The detection threshold of cultural methods. The three types of bacteria can be detected rapidly with high sensitivity by using the DNA probe by general practitioners, and thus can help in the diagnosis process and the treatment.

  1. Expression of proto-oncogenes in non-Hodgkin's lymphomas by in situ hybridization with biotinylated DNA probes

    International Nuclear Information System (INIS)

    Hamatani, Kiyohiro; Yoshida, Kuniko; Abe, Masumi; Shimaoka, Katsutaro; Shiku, Hiroshi; Akiyama, Mitoshi; Kondo, Hisayoshi.

    1989-11-01

    Expression of six proto-oncogenes (fos, myc, myb, Ki-ras, Ha-ras, and N-ras) in 43 cases of non-Hodgkin's lymphoma was analyzed by means of in situ hybridization. Biotinylated DNA probes of the six oncogenes and those of the immunoglobulin H-chain (IgH) gene and the T cell receptor β-chain (TCRβ) gene were used. The results of in situ hybridization performed under blind conditions by IgH and TCRβ gene probes were compatible with those of typing by cell surface markers. The nuclear protein-related proto-oncogenes, fos myc, and myb, were expressed in about 70 % - 80 % of all cases regardless of phenotypes, histology or histologic grade. On the contrary, genes of the ras family were expressed in fewer cases except for the Ki-ras gene which was more frequently expressed by cases of the T cell immunophenotype with a high malignancy grade. The results of dot hybridization with RNA extracted from some cases were compatible with those of in situ hybridization, further demonstrating the specificity of in situ hybridization. (author)

  2. Passive (self-powered) fiber-optic sensors

    International Nuclear Information System (INIS)

    McElhaney, S.A.; Falter, D.D.; Todd, R.A.; Simpson, M.L.; Mihalczo, J.T.

    1992-01-01

    ORNL is developing new group of fiber-optic sensors for characterizing physical aspects such as ambient temperature. These sensors exploit the inherent property of thermographic materials that the lifetime and/or intensity of the emitted fluorescence decreases with increasing temperature. Unlike current fluorescent temperature sensors that use a light source for excitation, these sensors are totally passive (self-powered) and use either an embedded or external radiation source. A proof-of-principle temperature sensor was developed, based on this concept, using a well-known thermographic material, magnesium fluorogermanate. Experimental results showed that the radiation-induced fluorescence resulted in an intensity change but no significant decay rate change with increasing temperature

  3. High-Frequency Flush Mounted Miniature LOX Fiber-Optic Pressure Sensor II, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna Innovations has teamed with the University of Alabama, Huntsville, to develop a miniature flush-mounted fiber-optic pressure sensor that will allow accurate,...

  4. Fiber-optic triggered release of liposome in vivo: implication of personalized chemotherapy.

    Science.gov (United States)

    Huang, Huei-Ling; Lu, Pei-Hsuan; Yang, Hung-Chih; Lee, Gi-Da; Li, Han-Ru; Liao, Kuo-Chih

    2015-01-01

    The aim of this research is to provide proof of principle by applying the fiber-optic triggered release of photo-thermally responsive liposomes embedded with gold nanoparticles (AuNPs) using a 200 μm fiber with 65 mW and 532 nm excitation for topical release in vivo. The tunable delivery function can be paired with an apoptosis biosensor based on the same fiber-optic configuration for providing real-time evaluation of chemotherapy efficacy in vivo to perform as a personalized chemotherapy system. The pattern of topical release triggered by laser excitation conveyed through optical fibers was monitored by the increase in fluorescence resulting from the dilution of self-quenching (75 mM) fluorescein encapsulated in liposomes. In in vitro studies (in 37°C phosphate buffer saline), the AuNP-embedded liposomes showed a more efficient triggered release (74.53%±1.63% in 40 minutes) than traditional temperature-responsive liposomes without AuNPs (14.53%±3.17%) or AuNP-liposomes without excitation (21.92%±2.08%) by spectroscopic measurements. Using the mouse xenograft studies, we first demonstrated that the encapsulation of fluorescein in liposomes resulted in a more substantial content retention (81%) in the tumor than for free fluorophores (14%) at 120 minutes after administration from in vivo fluorescence imaging. Furthermore, the preliminary results also suggested the tunable release capability of the system by demonstrating consecutive triggered releases with fiber-optic guided laser excitation.

  5. FIBER-OPTIC BIOSENSOR FOR DIRECT DETERMINATION OF ORGANOPHOSPHATE NERVE AGENTS. (R823663)

    Science.gov (United States)

    A fiber-optic enzyme biosensor for the direct measurement of organophosphate nerveagents was developed. The basic element of this biosensor is organophosphorus hydrolaseimmobilized on a nylon membrane and attached to the common end of a bifurcated optical fiberbundle....

  6. DNA-PK dependent targeting of DNA-ends to a protein complex assembled on matrix attachment region DNA sequences

    International Nuclear Information System (INIS)

    Mauldin, S.K.; Getts, R.C.; Perez, M.L.; DiRienzo, S.; Stamato, T.D.

    2003-01-01

    Full text: We find that nuclear protein extracts from mammalian cells contain an activity that allows DNA ends to associate with circular pUC18 plasmid DNA. This activity requires the catalytic subunit of DNA-PK (DNA-PKcs) and Ku since it was not observed in mutants lacking Ku or DNA-PKcs but was observed when purified Ku/DNA-PKcs was added to these mutant extracts. Competition experiments between pUC18 and pUC18 plasmids containing various nuclear matrix attachment region (MAR) sequences suggest that DNA ends preferentially associate with plasmids containing MAR DNA sequences. At a 1:5 mass ratio of MAR to pUC18, approximately equal amounts of DNA end binding to the two plasmids were observed, while at a 1:1 ratio no pUC18 end-binding was observed. Calculation of relative binding activities indicates that DNA-end binding activities to MAR sequences was 7 to 21 fold higher than pUC18. Western analysis of proteins bound to pUC18 and MAR plasmids indicates that XRCC4, DNA ligase IV, scaffold attachment factor A, topoisomerase II, and poly(ADP-ribose) polymerase preferentially associate with the MAR plasmid in the absence or presence of DNA ends. In contrast, Ku and DNA-PKcs were found on the MAR plasmid only in the presence of DNA ends. After electroporation of a 32P-labeled DNA probe into human cells and cell fractionation, 87% of the total intercellular radioactivity remained in nuclei after a 0.5M NaCl extraction suggesting the probe was strongly bound in the nucleus. The above observations raise the possibility that DNA-PK targets DNA-ends to a repair and/or DNA damage signaling complex which is assembled on MAR sites in the nucleus

  7. Highly sensitive fiber-optic oxygen sensor based on palladium tetrakis (4-carboxyphenyl)porphyrin doped in ormosil

    International Nuclear Information System (INIS)

    Chu, Cheng-Shane; Chuang, Chih-Yung

    2014-01-01

    A simple, low-cost technique for fabrication of highly sensitive fiber-optic oxygen sensor is described. An organically modified silicate (ORMOSIL) as a matrix for the fabrication of oxygen sensing film was produced. The technique is based on coating the end of a plastic optical fiber with ormosil composite xerogel film sequestered with luminophore palladium (II) meso-tetra(4-carboxyphenyl)porphyrin (PdTCPP) prepared by a sol–gel process. The composite xerogel studied is tetraethylorthosilane (TEOS)/n-octyltriethoxysilane (Octyl-triEOS). Result shows that, expect for PdTCPP-doped TEOS/Octyl-triEOS composite xerogel show the high sensitivity and linear Stern–Volmer relationship which indicate the homogenous environment of the luminophore. The sensitivity of the optical oxygen sensor is quantified in terms of the ratio I N2 /I O2 , where I N2 and I O2 represent the detected fluorescence intensities in pure nitrogen and pure oxygen environments, respectively. The experimental result reveals that the PdTCPP-doped TEOS/Octyl-triEOS oxygen sensor has sensitivity of 153. - Highlights: • A simple, low-cost technique for fabrication of highly sensitive fiber-optic oxygen sensor is described. • ORMOSIL was produced to serve as a matrix for the fabrication of oxygen sensing film. • The fiber-optic oxygen sensor has sensitivity of I N2 /I 100O2 =153. • The stable and reproducible signals were obtained with the fiber-optic oxygen sensor

  8. Radioactive probes for human gene localisation by in situ hybridisation

    International Nuclear Information System (INIS)

    Fennell, S.J.

    1980-07-01

    Radioactive probes of high specific activity have been used for human gene localisation on metaphase chromosome preparations. Human 5S ribosomal RNA was used as a model system, as a probe for the localisation of human 5S ribosomal genes. 125 I-labelled mouse 5S ribosomal RNA was used to study the 5S ribosomal gene content and arrangement in families with translocations on the long arm of chromosome 1 close to or containing the 5S ribosomal RNA locus, by in situ hybridisation to human metaphase chromosomes from peripheral blood cultures. This confirmed the chromosomal assignment of 5S ribosomal genes to 1q 42-43. In situ hybridisation probes were also prepared from recombinant plasmids containing Xenopus laevis oocyte 5S or 28S/18S gene sequences to give [ 3 H]-labelled cRNA and [ 3 H]-labelled nick-translated plasmid DNA. Studies on the kinetics of hybridisation of plasmid probes with and without ribosomal gene sequences questioned the role of plasmid DNA for amplification of signal during gene localisation. Gene localisation was obtained with nick-translated plasmid DNA containing the 28S/18S ribosomal DNA insert after short exposure times, but poor results were obtained using a [ 3 H]-labelled cRNA probe transcribed from the plasmid with the 5S gene insert. (author)

  9. Evaluation of fiberoptic dermofluorometry as a means of clinically assessing tissue perfusion.

    Science.gov (United States)

    Leopold, P W; Chang, B B; Shah, D M; Corson, J D; Shandall, A A; Young, H L; Leather, R P; Karmody, A M

    1987-01-01

    Fiberoptic dermofluorometry (FDF) transcutaneously measures fluorescence, following an intravenous injection of sodium fluorescein (NaFl), which is transmitted along a fiberoptic bundle to a photomultiplier tube and converted into dermofluorescence units (DFU). In five normal subjects studied, the plasma concentration of NaFl peaked at 5-15 minutes before decaying with first order kinetics and corresponding dermofluorescence (DF) rose to a peak between 10-20 minutes before decaying. Peak DF in the head and neck was significantly higher (P less than .001) compared to other skin sites which were similar. Application to patients (n = 16) undergoing successful lower limb revascularization showed a significant (P less than 0.01) improvement in perfusion at the foot level only. The reproducibility of FDF was poor when studied on the control limbs. We conclude that FDF does not, at present, constitute a valid measure of skin perfusion.

  10. Electrogenerated chemiluminescence detection for deoxyribonucleic acid hybridization based on gold nanoparticles carrying multiple probes

    International Nuclear Information System (INIS)

    Wang Hui; Zhang Chengxiao; Li Yan; Qi Honglan

    2006-01-01

    A novel sensitive electrogenerated chemiluminescence (ECL) method for the detection deoxyribonucleic acid (DNA) hybridization based on gold nanoparticles carrying multiple probes was developed. Ruthenium bis(2,2'-bipyridine)(2,2'-bipyridine-4,4'-dicarboxylic acid)-N-hydroxysuccinimide ester (Ru(bpy) 2 (dcbpy)NHS) was used as a ECL label and gold nanoparticle as a carrier. Probe single strand DNA (ss-DNA) was self-assembled at the 3'-terminal with a thiol group to the surface of gold nanoparticle and covalently labeled at the 5'-terminal of a phosphate group with Ru(bpy) 2 (dcbpy)NHS and the resulting conjugate (Ru(bpy) 2 (dcbpy)NHS)-ss-DNA-Au, was taken as a ECL probe. When target analyte ss-DNA was immobilized on a gold electrode by self-assembled monolayer technique and then hybridized with the ECL probe to form a double-stranded DNA (ds-DNA), a strong ECL response was electrochemically generated. The ECL intensity was linearly related to the concentration of the complementary sequence (target ss-DNA) in the range from 1.0 x 10 -11 to 1.0 x 10 -8 mol L -1 , and the linear regression equation was S = 57301 + 4579.6 lg C (unit of C is mol L -1 ). A detection limit of 5.0 x 10 -12 mol L -1 for target ss-DNA was achieved. The ECL signal generated from many reporters of ECL probe prepared is greatly amplified, compared to the convention scheme which is based on one reporter per hybridization event

  11. Microcantilver-based DNA hybridization sensors for Salmonella identification

    Directory of Open Access Journals (Sweden)

    Carlo Ricciardi

    2012-02-01

    Full Text Available The detection of pathogenic microorganisms in foods remains a challenging since the safety of foodstuffs has to be ensured by the food producing companies. Conventional methods for the detection and identification of bacteria mainly rely on specific microbiological and biochemical identification. Biomolecular methods, are commonly used as a support for traditional techniques, thanks to their high sensitivity, specificity and not excessive costs. However, new methods like biosensors for example, can be an exciting alternative to the more traditional tecniques for the detection of pathogens in food. In this study we report Salmonella enterica serotype Enteritidis DNA detection through a novel class of label-free biosensors: microcantilevers (MCs. In general, MCs can operate as a microbalance and is used to detect the mass of the entities anchored to the cantilever surface using the decrease in the resonant frequency. We use DNA hybridization as model reaction system and for this reason, specific single stranded probe DNA of the pathogen and three different DNA targets (single-stranded complementary DNA, PCR product and serial dilutions of DNA extracted from S. Enteritidis strains were applied. Two protocols were reported in order to allow the probe immobilization on cantilever surface: i MC surface was functionalized with 3-aminopropyltriethoxysilane and glutaraldehyde and an amino-modified DNA probe was used; ii gold-coated sensors and thiolated DNA probes were used in order to generate a covalent bonding (Th-Au. For the first one, measures after hybridization with the PCR product showed related frequency shift 10 times higher than hybridization with complementary probe and detectable signals were obtained at the concentrations of 103 and 106 cfu/mL after hybridization with bacterial DNA. There are currently optimizations of the second protocol, where preliminary results have shown to be more uniform and therefore more precise within each of the

  12. Fiber-Optic Temperature and Pressure Sensors Applied to Radiofrequency Thermal Ablation in Liver Phantom: Methodology and Experimental Measurements

    Directory of Open Access Journals (Sweden)

    Daniele Tosi

    2015-01-01

    Full Text Available Radiofrequency thermal ablation (RFA is a procedure aimed at interventional cancer care and is applied to the treatment of small- and midsize tumors in lung, kidney, liver, and other tissues. RFA generates a selective high-temperature field in the tissue; temperature values and their persistency are directly related to the mortality rate of tumor cells. Temperature measurement in up to 3–5 points, using electrical thermocouples, belongs to the present clinical practice of RFA and is the foundation of a physical model of the ablation process. Fiber-optic sensors allow extending the detection of biophysical parameters to a vast plurality of sensing points, using miniature and noninvasive technologies that do not alter the RFA pattern. This work addresses the methodology for optical measurement of temperature distribution and pressure using four different fiber-optic technologies: fiber Bragg gratings (FBGs, linearly chirped FBGs (LCFBGs, Rayleigh scattering-based distributed temperature system (DTS, and extrinsic Fabry-Perot interferometry (EFPI. For each instrument, methodology for ex vivo sensing, as well as experimental results, is reported, leading to the application of fiber-optic technologies in vivo. The possibility of using a fiber-optic sensor network, in conjunction with a suitable ablation device, can enable smart ablation procedure whereas ablation parameters are dynamically changed.

  13. Enhanced peptide nucleic acid binding to supercoiled DNA: possible implications for DNA "breathing" dynamics

    DEFF Research Database (Denmark)

    Bentin, T; Nielsen, Peter E.

    1996-01-01

    The influence of DNA topology on peptide nucleic acid (PNA) binding was studied. Formation of sequence-specific PNA2/dsDNA (double-stranded DNA) complexes was monitored by a potassium permanganate probing/primer extension assay. At low ionic strengths, the binding of PNA was 2-3 times more...

  14. Numerical Investigations on a Distributed Fiber-Optic Lighting System with an End Reflector

    International Nuclear Information System (INIS)

    Li Shuhua; Gong Huaping; Tu Yumeng; Meng Ying

    2011-01-01

    A novel distributed fiber-optic decorative lighting system with the reflection coating on the extremity of fiber-optic is designed, which used the multi-mold optical fiber made up of large core diameter(Diameter of core and cladding is 105μm and 125μm, respectly). After introducing the distributional optical fiber decorative lighting system briefly, the ralationship between corrosion depth of the optical fiber core and the leakage of fiber-optic has been analyzed with the Rsoft, and then the relationship of the lighting power and the uniformity of lighting power with the leakage rate of optical fiber lamp, the reflective of reflection coating has been discussed.The simulation analysis shows that, when the core diameter is corroded to 80∼85 μm, the leakage rate of optical fiber may achieve 5.0%, which suits the optical fiber decorative lighting. Considering all kinds of factors, when optical fiber lamp's quantity is 20, the coating index of reflection is 95%, optical fiber lamp's leakage of light rate is 5.0%, and the optical fiber lamp's distance is 1 meter, the quite high illuminating power may be achieved, as well as the good lighting uniformity.Finally the experimental study of decorative lighting system is given. And the experimental result is in keeping well with the theory simulation conclusion.

  15. Using Distributed Fiber-Optic Sensing Systems to Estimate Inflow and Reservoir Properties

    NARCIS (Netherlands)

    Farshbaf Zinati, F.

    2014-01-01

    Recent developments in the deployment of distributed fiber-optic sensing systems in horizontal wells carry the promise to lead to a new, cheap and reliable way of monitoring production and reservoir performance. Practical applicability of distributed pressure sensing for quantitative inflow

  16. Optical Coupling Structures of Fiber-Optic Mach-Zehnder Interferometers Using CO2 Laser Irradiation

    Directory of Open Access Journals (Sweden)

    Chien-Hsing Chen

    2014-01-01

    Full Text Available The Mach-Zehnder interferometer (MZI can be used to test changes in the refractive index of sucrose solutions at different concentrations. However, the popularity of this measurement tool is limited by its substantial size and portability. Therefore, the MZI was integrated with a small fiber-optic waveguide component to develop an interferometer with fiber-optic characteristics, specifically a fiber-optic Mach-Zehnder interferometer (FO-MZI. Optical fiber must be processed to fabricate two optical coupling structures. The two optical coupling structures are a duplicate of the beam splitter, an optical component of the interferometer. Therefore, when the sensor length and the two optical coupling structures vary, the time or path for optical transmission in the sensor changes, thereby influencing the back-end interference signals. The researchers successfully developed an asymmetrical FO-MZI with sensing abilities. The spacing value between the troughs of the sensor length and interference signal exhibited an inverse relationship. In addition, image analysis was employed to examine the size-matching relationship between various sensor lengths and the coupling and decoupling structure. Furthermore, the spectral wavelength shift results measured using a refractive index sensor indicate that FO-MZIs with a sensor length of 38 mm exhibited excellent sensitivity, measuring 59.7 nm/RIU.

  17. Implantable fiber-optic interface for parallel multisite long-term optical dynamic brain interrogation in freely moving mice

    Science.gov (United States)

    Doronina-Amitonova, L. V.; Fedotov, I. V.; Ivashkina, O. I.; Zots, M. A.; Fedotov, A. B.; Anokhin, K. V.; Zheltikov, A. M.

    2013-01-01

    Seeing the big picture of functional responses within large neural networks in a freely functioning brain is crucial for understanding the cellular mechanisms behind the higher nervous activity, including the most complex brain functions, such as cognition and memory. As a breakthrough toward meeting this challenge, implantable fiber-optic interfaces integrating advanced optogenetic technologies and cutting-edge fiber-optic solutions have been demonstrated, enabling a long-term optogenetic manipulation of neural circuits in freely moving mice. Here, we show that a specifically designed implantable fiber-optic interface provides a powerful tool for parallel long-term optical interrogation of distinctly separate, functionally different sites in the brain of freely moving mice. This interface allows the same groups of neurons lying deeply in the brain of a freely behaving mouse to be reproducibly accessed and optically interrogated over many weeks, providing a long-term dynamic detection of genome activity in response to a broad variety of pharmacological and physiological stimuli. PMID:24253232

  18. Multipoint fiber-optic laser-ultrasonic actuator based on fiber core-opened tapers.

    Science.gov (United States)

    Tian, Jiajun; Dong, Xiaolong; Gao, Shimin; Yao, Yong

    2017-11-27

    In this study, a novel fiber-optic, multipoint, laser-ultrasonic actuator based on fiber core-opened tapers (COTs) is proposed and demonstrated. The COTs were fabricated by splicing single-mode fibers using a standard fiber splicer. A COT can effectively couple part of a core mode into cladding modes, and the coupling ratio can be controlled by adjusting the taper length. Such characteristics are used to obtain a multipoint, laser-ultrasonic actuator with balanced signal strength by reasonably controlling the taper lengths of the COTs. As a prototype, we constructed an actuator that generated ultrasound at four points with a balanced ultrasonic strength by connecting four COTs with coupling ratios of 24.5%, 33.01%, 49.51%, and 87.8% in a fiber link. This simple-to-fabricate, multipoint, laser-ultrasonic actuator with balanced ultrasound signal strength has potential applications in fiber-optic ultrasound testing technology.

  19. HindIII RFLP on chromosome 8 detected with a calbindin 27 kDa cDNA probe, HBSC21

    Energy Technology Data Exchange (ETDEWEB)

    Parmentier, M; Vassart, G

    1988-10-11

    A 1.8 kb for EcoRI fragment of the human calbindin cDNA clone HBSC21 was subcloned into M13mp18 and used as a probe. HindIII identifies a 2 allele polymorphism with a band at 4.7 kb (A1) and a band at 4.3 kb (A2). A constant band is located at 5.3 kb. The calbindin 27 kDa gene was assigned to chromosome 8 using chinese hamster-human and mouse-human cell hybrids. Co-dominant segregation was demonstrated in 3 families (total of 20 individuals).

  20. Development, distribution and application of DNA markers for cereal research

    International Nuclear Information System (INIS)

    Qi, X.; Stephenson, P.; Devos, K.M.; Gale, M.D.

    2001-01-01

    DNA probes and primers are important resources for molecular genetic research and molecular breeding. Presently, more than 2500 wheat probes, 400 barley probes, 800 foxtail, pearl millet and finger millet probes, and approximately 150 wheat microsatellite (SSR) primer pairs have been developed and maintained in our DNA Resource Centre at the John Innes Centre (JIC). To accelerate probe and primer distribution, an 'anchor set' and a 'supplementary anchor set', containing 73 and 31 wheat RFLP probes, respectively, and a standard set of 42 primer pairs for wheat SSR markers were selected. Similarly, a set of 52 pearl millet probes has been selected for distribution. More than 8000 wheat RFLP probes, 2000 wheat SSR primer pairs, 700 millet probes and 200 barley probes have been distributed to more than 250 research groups in 40 countries. Our wheat and millet probes and other grass cDNA probes have been used for comparative genetic studies. The revealed conservation of gene content and gene order has been used to construct maps of many grass species and to predict the locations of key genes from one crop species to another. Developed SSR and AFLP markers in wheat, barley and millet are particularly suited for genetic diversity analyses and map construction. (author)

  1. Detection of Helicobacter Pylori Genome with an Optical Biosensor Based on Hybridization of Urease Gene with a Gold Nanoparticles-Labeled Probe

    Science.gov (United States)

    Shahrashoob, M.; Mohsenifar, A.; Tabatabaei, M.; Rahmani-Cherati, T.; Mobaraki, M.; Mota, A.; Shojaei, T. R.

    2016-05-01

    A novel optics-based nanobiosensor for sensitive determination of the Helicobacter pylori genome using a gold nanoparticles (AuNPs)-labeled probe is reported. Two specific thiol-modified capture and signal probes were designed based on a single-stranded complementary DNA (cDNA) region of the urease gene. The capture probe was immobilized on AuNPs, which were previously immobilized on an APTES-activated glass, and the signal probe was conjugated to different AuNPs as well. The presence of the cDNA in the reaction mixture led to the hybridization of the AuNPs-labeled capture probe and the signal probe with the cDNA, and consequently the optical density of the reaction mixture (AuNPs) was reduced proportionally to the cDNA concentration. The limit of detection was measured at 0.5 nM.

  2. Generation of species-specific DNA probes for Leishmania aethiopica

    NARCIS (Netherlands)

    Laskay, T.; Kiessling, R.; Rinke deWit, T. F.; Wirth, D. F.

    1991-01-01

    We report here the cloning of kinetoplast DNA (kDNA) sequences from Leishmania aethiopica in order to develop a specific and sensitive method for the identification of the parasite. Analysis of the cloned kDNA sequences showed different taxonomic specificities demonstrating sequence diversity within

  3. Using DNA-Stable Isotope Probing to Identify MTBE- and TBA-Degrading Microorganisms in Contaminated Groundwater.

    Science.gov (United States)

    Key, Katherine C; Sublette, Kerry L; Duncan, Kathleen; Mackay, Douglas M; Scow, Kate M; Ogles, Dora

    2013-01-01

    Although the anaerobic biodegradation of methyl tert -butyl ether (MTBE) and tert -butyl alcohol (TBA) has been documented in the laboratory and the field, knowledge of the microorganisms and mechanisms involved is still lacking. In this study, DNA-stable isotope probing (SIP) was used to identify microorganisms involved in anaerobic fuel oxygenate biodegradation in a sulfate-reducing MTBE and TBA plume. Microorganisms were collected in the field using Bio-Sep® beads amended with 13 C 5 -MTBE, 13 C 1 -MTBE (only methoxy carbon labeled), or 13 C 4 -TBA. 13 C-DNA and 12 C-DNA extracted from the Bio-Sep beads were cloned and 16S rRNA gene sequences were used to identify the indigenous microorganisms involved in degrading the methoxy group of MTBE and the tert -butyl group of MTBE and TBA. Results indicated that microorganisms were actively degrading 13 C-labeled MTBE and TBA in situ and the 13 C was incorporated into their DNA. Several sequences related to known MTBE- and TBA-degraders in the Burkholderiales and the Sphingomonadales orders were detected in all three 13 C clone libraries and were likely to be primary degraders at the site. Sequences related to sulfate-reducing bacteria and iron-reducers, such as Geobacter and Geothrix , were only detected in the clone libraries where MTBE and TBA were fully labeled with 13 C, suggesting that they were involved in processing carbon from the tert -butyl group. Sequences similar to the Pseudomonas genus predominated in the clone library where only the methoxy carbon of MTBE was labeled with 13 C. It is likely that members of this genus were secondary degraders cross-feeding on 13 C-labeled metabolites such as acetate.

  4. Spatial Frequency Multiplexing of Fiber-Optic Interferometric Refractive Index Sensors Based on Graded-Index Multimode Fibers

    Science.gov (United States)

    Liu, Li; Gong, Yuan; Wu, Yu; Zhao, Tian; Wu, Hui-Juan; Rao, Yun-Jiang

    2012-01-01

    Fiber-optic interferometric sensors based on graded-index multimode fibers have very high refractive-index sensitivity, as we previously demonstrated. In this paper, spatial-frequency multiplexing of this type of fiber-optic refractive index sensors is investigated. It is estimated that multiplexing of more than 10 such sensors is possible. In the multiplexing scheme, one of the sensors is used to investigate the refractive index and temperature responses. The fast Fourier transform (FFT) of the combined reflective spectra is analyzed. The intensity of the FFT spectra is linearly related with the refractive index and is not sensitive to the temperature.

  5. Templated Chemistry for Sequence-Specific Fluorogenic Detection of Duplex DNA

    Science.gov (United States)

    Li, Hao; Franzini, Raphael M.; Bruner, Christopher; Kool, Eric T.

    2015-01-01

    We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine, designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of ca. 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably, demonstrating high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and may allow detection of double stranded DNA, at least for homopurine-homopyrimidine target sites, under native, non-disturbing conditions. PMID:20859985

  6. Dynamics analysis of microsphere in a dual-beam fiber-optic trap with transverse offset.

    Science.gov (United States)

    Chen, Xinlin; Xiao, Guangzong; Luo, Hui; Xiong, Wei; Yang, Kaiyong

    2016-04-04

    A comprehensive dynamics analysis of microsphere has been presented in a dual-beam fiber-optic trap with transverse offset. As the offset distance between two counterpropagating beams increases, the motion type of the microsphere starts with capture, then spiral motion, then orbital rotation, and ends with escape. We analyze the transformation process and mechanism of the four motion types based on ray optics approximation. Dynamic simulations show that the existence of critical offset distances at which different motion types transform. The result is an important step toward explaining physical phenomena in a dual-beam fiber-optic trap with transverse offset, and is generally applicable to achieving controllable motions of microspheres in integrated systems, such as microfluidic systems and lab-on-a-chip systems.

  7. Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response

    Energy Technology Data Exchange (ETDEWEB)

    Crnolatac, Ivo; Rogan, Iva; Majić, Boris; Tomić, Sanja [Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb (Croatia); Deligeorgiev, Todor [Faculty of Chemistry and Pharmacy, University of Sofia (Bulgaria); Horvat, Gordan [Department of Physical Chemistry, Faculty of Science/Chemistry, Horvatovac 102A, HR-10000 Zagreb (Croatia); Makuc, Damjan; Plavec, Janez [Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana (Slovenia); EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, Ljubljana (Slovenia); Pescitelli, Gennaro [Department of Chemistry, University of Pisa, Via Moruzzi 13, Pisa (Italy); Piantanida, Ivo, E-mail: pianta@irb.hr [Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb (Croatia)

    2016-10-12

    Two small molecules showed intriguing properties of analytical multipurpose probes, whereby one chromophore gives different signal for many different DNA/RNA by application of several highly sensitive spectroscopic methods. Dyes revealed pronounced fluorescence ratiomeric differentiation between ds-AU-RNA, AT-DNA and GC-DNA in approximate order 10:8:1. Particularly interesting, dyes showed specific fluorimetric response for poly rA even at 10-fold excess of any other ss-RNA, and moreover such emission selectivity is preserved in multicomponent ss-RNA mixtures. The dyes also showed specific chiral recognition of poly rU in respect to the other ss-RNA by induced CD (ICD) pattern in visible range (400–500 nm), which was attributed to the dye-side-chain contribution to binding (confirmed by absence of any ICD band for reference compound lacking side-chain). Most intriguingly, minor difference in the side-chain attached to dye chromophore resulted in opposite sign of dye-ICD pattern, whereby differences in NMR NOESY contacts and proton chemical shifts between two dye/oligo rU complexes combined with MD simulations and CD calculations attributed observed bisignate ICD to the dimeric dye aggregate within oligo rU. - Highlights: • Novel dyes emit fluorescence only for poly rA even at high excess of all other ss-RNA. • Fluorescence response for AT-DNA is 8 times stronger than for GC-DNA. • Florescence induced by ds-RNA is 20% stronger that emission induced by ds-DNA. • Intrinsically non-chiral, dyes show strong and characteristic ICD response for poly rU.

  8. Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

    Directory of Open Access Journals (Sweden)

    Gravelat Fabrice

    2010-09-01

    Full Text Available Abstract Background Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. Results First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality can be used to study a complex environment efficiently. Conclusions We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments

  9. A novel probe density controllable electrochemiluminescence biosensor for ultra-sensitive detection of Hg2+ based on DNA hybridization optimization with gold nanoparticles array patterned self-assembly platform.

    Science.gov (United States)

    Gao, Wenhua; Zhang, An; Chen, Yunsheng; Chen, Zixuan; Chen, Yaowen; Lu, Fushen; Chen, Zhanguang

    2013-11-15

    Biosensor based on DNA hybridization holds great potential to get higher sensitivity as the optimal DNA hybridization efficiency can be achieved by controlling the distribution and orientation of probe strands on the transducer surface. In this work, an innovative strategy is reported to tap the sensitivity potential of current electrochemiluminescence (ECL) biosensing system by dispersedly anchoring the DNA beacons on the gold nanoparticles (GNPs) array which was electrodeposited on the glassy carbon electrode surface, rather than simply sprawling the coil-like strands onto planar gold surface. The strategy was developed by designing a "signal-on" ECL biosensing switch fabricated on the GNPs nanopatterned electrode surface for enhanced ultra-sensitivity detection of Hg(2+). A 57-mer hairpin-DNA labeled with ferrocene as ECL quencher and a 13-mer DNA labeled with Ru(bpy)3(2+) as reporter were hybridized to construct the signal generator in off-state. A 31-mer thymine (T)-rich capture-DNA was introduced to form T-T mismatches with the loop sequence of the hairpin-DNA in the presence of Hg(2+) and induce the stem-loop open, meanwhile the ECL "signal-on" was triggered. The peak sensitivity with the lowest detection limit of 0.1 nM was achieved with the optimal GNPs number density while exorbitant GNPs deposition resulted in sensitivity deterioration for the biosensor. We expect the present strategy could lead the renovation of the existing probe-immobilized ECL genosensor design to get an even higher sensitivity in ultralow level of target detection such as the identification of genetic diseases and disorders in basic research and clinical application. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Probe design for expression arrays using OligoWiz

    DEFF Research Database (Denmark)

    Wernersson, Rasmus

    2014-01-01

    Since all measurements from a DNA microarray is dependant on the probes used, a good choice of probes is of vital importa nce when designing custom micro-arrays. This chapter describes how to de sign expression arrays using the “ OligoWiz ” software suite. The general desired features of good...... probes and the issues which probe design must address are introduced and a conceptual (rather than mathematical) description of how OligoWiz scores the quality of th e potential probes is presented. This is followed by a detailed step-by-step guide to designing expression arrays with OligoWiz....

  11. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies.

    Science.gov (United States)

    Kratochvílová, Irena; Vala, Martin; Weiter, Martin; Špérová, Miroslava; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    2013-01-01

    Oligonucleotides conduct electric charge via various mechanisms and their characterization and understanding is a very important and complicated task. In this work, experimental (temperature dependent steady state fluorescence spectroscopy, time-resolved fluorescence spectroscopy) and theoretical (Density Functional Theory) approaches were combined to study charge transfer processes in short DNA/DNA and RNA/DNA duplexes with virtually equivalent sequences. The experimental results were consistent with the theoretical model - the delocalized nature of HOMO orbitals and holes, base stacking, electronic coupling and conformational flexibility formed the conditions for more effective short distance charge transfer processes in RNA/DNA hybrids. RNA/DNA and DNA/DNA charge transfer properties were strongly connected with temperature affected structural changes of molecular systems - charge transfer could be used as a probe of even tiny changes of molecular structures and settings. © 2013. Published by Elsevier B.V. All rights reserved.

  12. Direct immobilization of DNA probes on non-modified plastics by UV irradiation and integration in microfluidic devices for rapid bioassay

    DEFF Research Database (Denmark)

    Yi, Sun; Perch-Nielsen, Ivan R.; Dufva, Martin

    2012-01-01

    that simple UV irradiation can be used to directly immobilize poly(T)poly(C)-tagged DNA oligonucleotide probes on many different types of plastics without any surface modification. On average, five- and fourfold improvement in immobilization and hybridization efficiency have been achieved compared to surface......DNA microarrays have become one of the most powerful tools in the field of genomics and medical diagnosis. Recently, there has been increased interest in combining microfluidics with microarrays since this approach offers advantages in terms of portability, reduced analysis time, low consumption...... of reagents, and increased system integration. Polymers are widely used for microfluidic systems, but fabrication of microarrays on such materials often requires complicated chemical surface modifications, which hinders the integration of microarrays into microfluidic systems. In this paper, we demonstrate...

  13. Cloning and characterization of BKV(MM) DNA and its use for detection of BKV DNA in human urine

    International Nuclear Information System (INIS)

    Harley, E.H.; Olliver, C.L.; Rhodes-Harrison, L.; Mew, R.T.; Lecatsas, G.; Naude, W. du T.

    1982-01-01

    The two fragments produced by restriction of BKV(MM) DNA with the endonucleases Pst I and Eco RI have been cloned separately into the vector pBR322 and amplified in E. coli HB101. Eight recombinant plasmids were characterized by gel electrophoresis of Pst I/Eco RI double digestions or Hind III digestions of the DNA and by hybridization of Southern gel blots to a nick-translated BKV(MM) DNA probe. Four of the recombinant plasmids contained the large Pst I/Eco RI BKV(MM) DNA fragment and four contained the small fragment. Two of these recombinant plasmids were then used to make a probe for the identification of BK DNA in a urine specimen from a patient known to be exreting particles with the morphological features of papovavirus [af

  14. Tools for Ultraspecific Probe/Primer Design

    National Research Council Canada - National Science Library

    Fofanov, Yurly

    2006-01-01

    .... Our approach will deliver DNA probes and PCR primers that have an unprecedentedly low probability of false positives or confusion by environmental background, and which resist evasion by threat agent engineering...

  15. Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients.

    Science.gov (United States)

    Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W

    2004-01-01

    Stable isotope probing (SIP) of nucleic acids allows the detection and identification of active members of natural microbial populations that are involved in the assimilation of an isotopically labelled compound into nucleic acids. SIP is based on the separation of isotopically labelled DNA or rRNA by isopycnic density gradient centrifugation. We have developed a highly sensitive protocol for the detection of 'light' and 'heavy' nucleic acids in fractions of centrifugation gradients. It involves the fluorometric quantification of total DNA or rRNA, and the quantification of either 16S rRNA genes or 16S rRNA in gradient fractions by real-time PCR with domain-specific primers. Using this approach, we found that fully 13C-labelled DNA or rRNA of Methylobacterium extorquens was quantitatively resolved from unlabelled DNA or rRNA of Methanosarcina barkeri by cesium chloride or cesium trifluoroacetate density gradient centrifugation respectively. However, a constant low background of unspecific nucleic acids was detected in all DNA or rRNA gradient fractions, which is important for the interpretation of environmental SIP results. Consequently, quantitative analysis of gradient fractions provides a higher precision and finer resolution for retrieval of isotopically enriched nucleic acids than possible using ethidium bromide or gradient fractionation combined with fingerprinting analyses. This is a prerequisite for the fine-scale tracing of microbial populations metabolizing 13C-labelled compounds in natural ecosystems.

  16. Sensitivity and Specificity of Cardiac Tissue Discrimination Using Fiber-Optics Confocal Microscopy.

    Science.gov (United States)

    Huang, Chao; Sachse, Frank B; Hitchcock, Robert W; Kaza, Aditya K

    2016-01-01

    Disturbances of the cardiac conduction system constitute a major risk after surgical repair of complex cases of congenital heart disease. Intraoperative identification of the conduction system may reduce the incidence of these disturbances. We previously developed an approach to identify cardiac tissue types using fiber-optics confocal microscopy and extracellular fluorophores. Here, we applied this approach to investigate sensitivity and specificity of human and automated classification in discriminating images of atrial working myocardium and specialized tissue of the conduction system. Two-dimensional image sequences from atrial working myocardium and nodal tissue of isolated perfused rodent hearts were acquired using a fiber-optics confocal microscope (Leica FCM1000). We compared two methods for local application of extracellular fluorophores: topical via pipette and with a dye carrier. Eight blinded examiners evaluated 162 randomly selected images of atrial working myocardium (n = 81) and nodal tissue (n = 81). In addition, we evaluated the images using automated classification. Blinded examiners achieved a sensitivity and specificity of 99.2 ± 0.3% and 98.0 ± 0.7%, respectively, with the dye carrier method of dye application. Sensitivity and specificity was similar for dye application via a pipette (99.2 ± 0.3% and 94.0 ± 2.4%, respectively). Sensitivity and specificity for automated methods of tissue discrimination were similarly high. Human and automated classification achieved high sensitivity and specificity in discriminating atrial working myocardium and nodal tissue. We suggest that our findings facilitate clinical translation of fiber-optics confocal microscopy as an intraoperative imaging modality to reduce the incidence of conduction disturbances during surgical correction of congenital heart disease.

  17. Identification of metabolically active methanogens in anaerobic digester by DNA Stable-Isotope Probing using 13C-acetate

    Directory of Open Access Journals (Sweden)

    V. Gowdaman

    2015-04-01

    Full Text Available Anaerobic digestion is gaining enormous attention due to the ability to covert organic wastes into biogas, an alternative sustainable energy. Methanogenic community plays a significant role in biogas production and also for proficient functioning of the anaerobic digester. Therefore, this study was carried out to investigate the methanogen diversity of a food waste anaerobic digester. After endogenous respiration, the digester samples were supplemented with isotopes of acetate to enrich methanogen population, and were analyzed using DNA-SIP (Stable-Isotope Probing. Following separation and fractionation of heavy (13C and light (12C DNA, PCR amplification was carried out using archaeal 16S rRNA gene followed by DGGE analysis. Sequencing of the prominent DGGE bands revealed the dominance of Methanocorpusculum labreanum species belonging to hydrogenotrophic Methanomicrobiales, which can produce methane in the presence of H2/CO2 and requires acetate for its growth. This is the first instance where Methanocorpusculum labreanum is being reported as a dominant species in an anaerobic digester operative on food waste.

  18. Toehold-mediated strand displacement reaction-dependent fluorescent strategy for sensitive detection of uracil-DNA glycosylase activity.

    Science.gov (United States)

    Wu, Yushu; Wang, Lei; Jiang, Wei

    2017-03-15

    Sensitive detection of uracil-DNA glycosylase (UDG) activity is beneficial for evaluating the repairing process of DNA lesions. Here, toehold-mediated strand displacement reaction (TSDR)-dependent fluorescent strategy was constructed for sensitive detection of UDG activity. A single-stranded DNA (ssDNA) probe with two uracil bases and a trigger sequence were designed. A hairpin probe with toehold domain was designed, and a reporter probe was also designed. Under the action of UDG, two uracil bases were removed from ssDNA probe, generating apurinic/apyrimidinic (AP) sites. Then, the AP sites could inhibit the TSDR between ssDNA probe and hairpin probe, leaving the trigger sequence in ssDNA probe still free. Subsequently, the trigger sequence was annealed with the reporter probe, initiating the polymerization and nicking amplification reaction. As a result, numerous G-quadruplex (G4) structures were formed, which could bind with N-methyl-mesoporphyrin IX (NMM) to generate enhanced fluorescent signal. In the absence of UDG, the ssDNA probe could hybridize with the toehold domain of the hairpin probe to initiate TSDR, blocking the trigger sequence, and then the subsequent amplification reaction would not occur. The proposed strategy was successfully implemented for detecting UDG activity with a detection limit of 2.7×10 -5 U/mL. Moreover, the strategy could distinguish UDG well from other interference enzymes. Furthermore, the strategy was also applied for detecting UDG activity in HeLa cells lysate with low effect of cellular components. These results indicated that the proposed strategy offered a promising tool for sensitive quantification of UDG activity in UDG-related function study and disease prognosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Fiberoptic endoscopic evaluation of swallowing (FEES): proposal for informed consent

    OpenAIRE

    Nacci, A; Ursino, F; La Vela, R; Matteucci, F; Mallardi, V; Fattori, B

    2008-01-01

    Fiberoptic endoscopic evaluation of swallowing (FEES) is now a first choice method for studying swallowing disorders on account of the various advantages it offers: easy to use, very well tolerated, allows bedside examination and is economic. Nevertheless, this diagnostic procedure is not without risks, the most probable consequences of which include discomfort, gagging and/or vomiting, vasovagal syncope, epistaxis, mucosal perforation, adverse reactions to topical anaesthetics and laryngospa...

  20. Development of species-specific rDNA probes for Giardia by multiple fluorescent in situ hybridization combined with immunocytochemical identification of cyst wall antigens.

    Science.gov (United States)

    Erlandsen, Stanley L; Jarroll, Edward; Wallis, Peter; van Keulen, Harry

    2005-08-01

    In this study, we describe the development of fluorescent oligonucleotide probes to variable regions in the small subunit of 16S rRNA in three distinct Giardia species. Sense and antisense probes (17-22 mer) to variable regions 1, 3, and 8 were labeled with digoxygenin or selected fluorochomes (FluorX, Cy3, or Cy5). Optimal results were obtained with fluorochome-labeled oligonucleotides for detection of rRNA in Giardia cysts. Specificity of fluorescent in situ hybridization (FISH) was shown using RNase digestion and high stringency to diminish the hybridization signal, and oligonucleotide probes for rRNA in Giardia lamblia, Giardia muris, and Giardia ardeae were shown to specifically stain rRNA only within cysts or trophozoites of those species. The fluorescent oligonucleotide specific for rRNA in human isolates of Giardia was positive for ten different strains. A method for simultaneous FISH detection of cysts using fluorescent antibody (genotype marker) and two oligonucleotide probes (species marker) permitted visualization of G. lamblia and G. muris cysts in the same preparation. Testing of an environmental water sample revealed the presence of FISH-positive G. lamblia cysts with a specific rDNA probe for rRNA, while negative cysts were presumed to be of animal or bird origin.

  1. A tilted fiber-optic plate coupled CCD detector for high resolution neutron imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jongyul; Cho, Gyuseong [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of); Kim, Jongyul; Hwy, Limchang; Kim, Taejoo; Lee, Kyehong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Lee, Seungwook [Pusan National Univ., Pusan (Korea, Republic of)

    2013-05-15

    One of these efforts is that a tilted scintillator geometry and lens coupled CCD detector for neutron imaging system were used to improve spatial resolution in one dimension. The increased spatial resolution in one dimension was applied to fuel cell study. However, a lens coupled CCD detector has lower sensitivity than a fiber-optic plate coupled CCD detector due to light loss. In this research, a tilted detector using fiber-optic plate coupled CCD detector was developed to improve resolution and sensitivity. In addition, a tilted detector can prevent an image sensor from direct radiation damage. Neutron imaging has been used for fuel cell study, lithium ion battery study, and many scientific applications. High quality neutron imaging is demanded for more detailed studies of applications, and spatial resolution should be considered to get high quality neutron imaging. Therefore, there were many efforts to improve spatial resolution.

  2. Molecular studies of fibroblasts transfected with hepatitis B virus DNA

    International Nuclear Information System (INIS)

    Chen, M.L.; Hood, A.; Thung, S.N.; Gerber, M.A.

    1987-01-01

    Two subclones (D7 and F8) derived from an NIH 3T3 mouse fibroblast cell line after transfection with hepatitis B virus (HBV) genomes, secreted significantly different amounts of HBsAg and HBeAg. DNA extracted from the subclones revealed only integrated and no extrachromosomal HBV DNA sequences as determined by the Southern blot technique with a /sup 32/P-labeled full length HBV DNA probe. The amount and integration sites of HBV sequences were significantly different in the two subclones. HBV DNA sequences coding for HBsAg and HBcAg were detected by alkaline phosphatase-conjugated, single-stranded synthetic gene-specific oligonucleotide probes revealing a larger number of copies in D7 DNA than in F8 DNA. Using a biotinylated probe for in situ hybridization, HBV DNA was found in the nuclei of all D7 cells with predominant localization to a single chromsome, but only in 10-20% of F8 cells. These observations demonstrate different integration patterns of HBV and DNA in two subclones derived from a transfected cell line and suggest that the amount of integrated HBV DNA is proportional to the amount of HBV antigens produced

  3. A combined approach of DNA probe and RFLP for family and species identification of larval stages of commercially important aquatic species: A study on the surfclam Spisula solidissima

    Digital Repository Service at National Institute of Oceanography (India)

    Achuthankutty, C.T.

    fragment length polymorphism (RFLP) analysis. An oilgonucleotide sequence designed from the 18S ribosomal RNA gene (nucleotide position 259-276) provided a sensitive probe for the Family Mactridae, to which S. solidissima belongs. DNA of unknown larvae...

  4. A Fast, Sensitive and Label Free Electrochemical DNA Sensor

    International Nuclear Information System (INIS)

    Chen Yu; Elling; Lee Yokeling; Chong Serchoong

    2006-01-01

    A label free and sensitive DNA/RNA silicon based electrochemical microsensor array was developed by using thin film of the conducting polymer polypyrrole doped with an oligonucleotide probe. The electrochemical potential pulse amperometry technique was used for a biowarfare pathogen target DNA detection. The electrical potential assistanted DNA hybridisation method was applied. The sensor signal was increased by increasing the electrical potential assistanted DNA hybridisation time. It was possible to detect 0.34pmol and 0.072fmol of complementary oligonucleotide target in 0.1ml in seconds by using unpolished and polished gold electrode respectively. The probe preparation was also in seconds time, comparing indirect electrochemical DNA sensor, it has a fast sensor preparation as well as sensor response and label free advantages. The silicon microfabrication technique was used for this sensor array fabrication, which holds the potential to integrate with sensor electrical circuits. The conducting polymer polypyrrole was electrochemically deposited on each electrode respectively which has a possibility to dope the different DNA probe into the individual electrode to form a sensor array

  5. DNA origami nanorobot fiber optic genosensor to TMV.

    Science.gov (United States)

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

    2018-01-15

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

  6. A 15-meter Multi-Gigabit W-band Bidirectional Wireless Bridge in Fiber-Optic Access Networks

    DEFF Research Database (Denmark)

    Pang, Xiaodan; Vegas Olmos, Juan José; Lebedev, Alexander

    2013-01-01

    . The down-converted signal is re-modulated on to the lightwave and transmit further through the fiber-optic system. In the uplink, both up-and down-conversion are performed by electrical means. Furthermore, we investigate both passive and active wireless transmitters in this work for both downlink......We present a bidirectional wireless bridge in the W-band enabling the seamless convergence between the wireless and fiber-optic access networks. In the downlink, a 16 Gbit/s QPSK signal is photonically up-converted at the wireless transmitter and electrically down-converted at the wireless receiver...... and uplink transmissions. With an active wireless transmitter, up to 15 meters wireless transmission is successfully achieved with a BER below the 7% FEC limit in the downlink....

  7. Fiber-optic sensor demonstrator (FSD) for the monitoring of spacecraft subsystems on ESA's PROBA-2

    Science.gov (United States)

    Kruzelecky, Roman V.; Zou, Jing; Mohammed, Najeeb; Haddad, Emile; Jamroz, Wes; Ricci, Francesco; Lamorie, Joshua; Edwards, Eric; McKenzie, Iain; Vuilleumier, Pierrik

    2017-11-01

    MPB Communications (MPBC) is developing solutions to the monitoring requirements of spacecraft based on its fiber-laser and Fiber Bragg Grating expertise. This is cumulating in the Fiber Sensor Demonstrator for ESA's Proba-2 that is scheduled for launch in 2007. The advantages of the MPBC approach include a central interrogation system that can be used to control a variety of different fiber-optic sensors including temperature, pressure, actuator status, and propellant leakage. This paper reviews the design and ground qualification of the FSD system in preparation for integration with Proba-2. The FSD will provide monitoring for various Proba-2 subsystems, including a hybrid propulsion system. Some of the challenges associated with using fiber-optics in space are discussed.

  8. Electrochemical DNA biosensor based on avidin-biotin conjugation for influenza virus (type A) detection

    Science.gov (United States)

    Chung, Da-Jung; Kim, Ki-Chul; Choi, Seong-Ho

    2011-09-01

    An electrochemical DNA biosensor (E-DNA biosensor) was fabricated by avidin-biotin conjugation of a biotinylated probe DNA, 5'-biotin-ATG AGT CTT CTA ACC GAG GTC GAA-3', and an avidin-modified glassy carbon electrode (GCE) to detect the influenza virus (type A). An avidin-modified GCE was prepared by the reaction of avidin and a carboxylic acid-modified GCE, which was synthesized by the electrochemical reduction of 4-carboxyphenyl diazonium salt. The current value of the E-DNA biosensor was evaluated after hybridization of the probe DNA and target DNA using cyclic voltammetry (CV). The current value decreased after the hybridization of the probe DNA and target DNA. The DNA that was used follows: complementary target DNA, 5'-TTC GAC CTC GGT TAG AAG ACT CAT-3' and two-base mismatched DNA, 5'-TTC GAC AGC GGT TAT AAG ACT CAT-3'.

  9. Importance of the efficiency of double-stranded DNA formation in cDNA synthesis for the imprecision of microarray expression analysis.

    Science.gov (United States)

    Thormar, Hans G; Gudmundsson, Bjarki; Eiriksdottir, Freyja; Kil, Siyoen; Gunnarsson, Gudmundur H; Magnusson, Magnus Karl; Hsu, Jason C; Jonsson, Jon J

    2013-04-01

    The causes of imprecision in microarray expression analysis are poorly understood, limiting the use of this technology in molecular diagnostics. Two-dimensional strandness-dependent electrophoresis (2D-SDE) separates nucleic acid molecules on the basis of length and strandness, i.e., double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA·DNA hybrids. We used 2D-SDE to measure the efficiency of cDNA synthesis and its importance for the imprecision of an in vitro transcription-based microarray expression analysis. The relative amount of double-stranded cDNA formed in replicate experiments that used the same RNA sample template was highly variable, ranging between 0% and 72% of the total DNA. Microarray experiments showed an inverse relationship between the difference between sample pairs in probe variance and the relative amount of dsDNA. Approximately 15% of probes showed between-sample variation (P cDNA synthesized can be an important component of the imprecision in T7 RNA polymerase-based microarray expression analysis. © 2013 American Association for Clinical Chemistry

  10. Fiber-optical accelerometers based on polymer optical fiber Bragg gratings

    DEFF Research Database (Denmark)

    Yuan, Scott Wu; Stefani, Alessio; Bang, Ole

    2010-01-01

    Fiber-optical accelerometers based on polymer optical fiber Bragg gratings (FBGs) are reported. We have written 3mm FBGs for 1550nm operation, characterized their temperature and strain response, and tested their performance in a prototype accelerometer.......Fiber-optical accelerometers based on polymer optical fiber Bragg gratings (FBGs) are reported. We have written 3mm FBGs for 1550nm operation, characterized their temperature and strain response, and tested their performance in a prototype accelerometer....

  11. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique.

    OpenAIRE

    Noll, W W; Collins, M

    1987-01-01

    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. We have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and th...

  12. Remote Raman microimaging using an AOTF and a spatially coherent microfiber optical probe

    International Nuclear Information System (INIS)

    Trey Skinner, H.; Cooney, T.F.; Sharma, S.K.; Angel, S.M.

    1996-01-01

    A fiber-optic Raman microimaging probe is described that is suitable for acquiring high-spatial-resolution Raman images in sampling situations with no clear line of sight. A high-power near-infrared diode laser combined with an acousto-optic tunable filter and a spatially coherent optical fiber bundle allow fluorescence-free Raman images of remotely located samples to be acquired at distances up to several meters. The feasibility of this technique is demonstrated with Raman images of (1) a pellet containing a mixture of a highly scattering sample, bis-methylstyrylbenzene (BMSB), KCl, and graphite, and (2) a partially graphitized diamond. These images clearly show phase boundaries over an area of approximately 0.1 mm 2 with ∼4-μm resolution. copyright 1996 Society for Applied Spectroscopy

  13. Engineering surface plasmon based fiber-optic sensors

    International Nuclear Information System (INIS)

    Dhawan, Anuj; Muth, John F.

    2008-01-01

    Ordered arrays of nanoholes with subwavelength diameters, and submicron array periodicity were fabricated on the tips of gold-coated optical fibers using focused ion beam (FIB) milling. This provided a convenient platform for evaluating extraordinary transmission of light through subwavelength apertures and allowed the implementation of nanostructures for surface plasmon engineered sensors. The fabrication procedure was straightforward and implemented on single mode and multimode optical fibers as well as etched and tapered fiber tips. Control of the periodicity and spacing of the nanoholes allowed the wavelength of operation to be tailored. Large changes in optical transmission were observed at the designed wavelengths, depending on the surrounding refractive index, allowing the devices to be used as fiber-optic sensors

  14. Engineering surface plasmon based fiber-optic sensors

    Energy Technology Data Exchange (ETDEWEB)

    Dhawan, Anuj [Department of Electrical and Computer Engineering, NC State University, Raleigh, NC 27606 (United States); Muth, John F. [Department of Electrical and Computer Engineering, NC State University, Raleigh, NC 27606 (United States)], E-mail: muth@unity.ncsu.edu

    2008-04-15

    Ordered arrays of nanoholes with subwavelength diameters, and submicron array periodicity were fabricated on the tips of gold-coated optical fibers using focused ion beam (FIB) milling. This provided a convenient platform for evaluating extraordinary transmission of light through subwavelength apertures and allowed the implementation of nanostructures for surface plasmon engineered sensors. The fabrication procedure was straightforward and implemented on single mode and multimode optical fibers as well as etched and tapered fiber tips. Control of the periodicity and spacing of the nanoholes allowed the wavelength of operation to be tailored. Large changes in optical transmission were observed at the designed wavelengths, depending on the surrounding refractive index, allowing the devices to be used as fiber-optic sensors.

  15. The use of radionuclide DNA probe technology in epidemiological studies of leishmaniasis

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Antero Silva Ribeiro de [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Belo Horizonte, MG (Brazil); Fernandes, Octavio [Fundacao Inst. Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ (Brazil). Dept. de Medicina Tropical; Gomes, Rosangela Fatima; Melo, Maria Norma de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Parasitologia]|[Cor Jesus Fontes Mato Grosso Univ., Cuiaba, MT (Brazil). Hospital Universitario Julio Muller

    2000-07-01

    Cutaneous and mucosal leishmaniasis are due to different species that belongs to Leishmania (Leishmania) mexicana complex and Leishmania (Viannia) braziliensis complex, respectively. Cutaneous leishmaniasis ulcers may persist for months to years but eventually they heal, while mucocutaneous leishmaniasis can result in destructive lesions on the nose, oral pharynx, lips or face. The specific diagnosis of the disease is important because of the high cost and toxicity of the treatment and the subsequent medical follow-up depends on the precise identification of the complex that causes the infection. The epidemiological information furnished by the identification of parasites of a given endemic region is also essential for the design of appropriate control measures. In this work we typed, using specific DNA probes labelled with {sup 32}P radionuclide, samples collected from patients living in endemic areas of Mato Grosso state. The results showed that L. braziliensis is the predominant group infecting human patients in the state. We have typed, up to the moment 68 samples. 64 samples (94.1%) belonged to the L. braziliensis complex and only 4 (5.9%) belonged to the L. mexicana complex. (author)

  16. A wideband connection to sperm whales: A fiber-optic, deep-sea hydrophone array

    DEFF Research Database (Denmark)

    Heerfordt, Anders; Møhl, Bertel; Wahlberg, Magnus

    2007-01-01

    A 10-element, 950 m long, vertical hydrophone array based on fiber-optic data transmission has been developed primarily for studying the beam pattern from deep diving cetaceans emitting sonar pulses. The array elements have a configurable sampling rate and resolution with a maximum signal bandwidth...

  17. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique

    International Nuclear Information System (INIS)

    Noll, W.W.; Collins, M.

    1987-01-01

    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. The authors have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and the reaction mixture is electrophoresed on a denaturing gradient gel. Only the genomic DNA probe hybrids migrate into the gel. Differences in hybrid mobility on the gel indicate base pair changes in the genomic DNA. They have used this technique to identify two polymorphic sites within a 1.2-kilobase region of human chromosome 20. This approach should greatly facilitate the identification of DNA polymorphisms useful for gene linkage studies and the diagnosis of genetic diseases

  18. Fiber-optic annular detector array for large depth of field photoacoustic macroscopy

    Directory of Open Access Journals (Sweden)

    Johannes Bauer-Marschallinger

    2017-03-01

    Full Text Available We report on a novel imaging system for large depth of field photoacoustic scanning macroscopy. Instead of commonly used piezoelectric transducers, fiber-optic based ultrasound detection is applied. The optical fibers are shaped into rings and mainly receive ultrasonic signals stemming from the ring symmetry axes. Four concentric fiber-optic rings with varying diameters are used in order to increase the image quality. Imaging artifacts, originating from the off-axis sensitivity of the rings, are reduced by coherence weighting. We discuss the working principle of the system and present experimental results on tissue mimicking phantoms. The lateral resolution is estimated to be below 200 μm at a depth of 1.5 cm and below 230 μm at a depth of 4.5 cm. The minimum detectable pressure is in the order of 3 Pa. The introduced method has the potential to provide larger imaging depths than acoustic resolution photoacoustic microscopy and an imaging resolution similar to that of photoacoustic computed tomography.

  19. Fiber-optic annular detector array for large depth of field photoacoustic macroscopy.

    Science.gov (United States)

    Bauer-Marschallinger, Johannes; Höllinger, Astrid; Jakoby, Bernhard; Burgholzer, Peter; Berer, Thomas

    2017-03-01

    We report on a novel imaging system for large depth of field photoacoustic scanning macroscopy. Instead of commonly used piezoelectric transducers, fiber-optic based ultrasound detection is applied. The optical fibers are shaped into rings and mainly receive ultrasonic signals stemming from the ring symmetry axes. Four concentric fiber-optic rings with varying diameters are used in order to increase the image quality. Imaging artifacts, originating from the off-axis sensitivity of the rings, are reduced by coherence weighting. We discuss the working principle of the system and present experimental results on tissue mimicking phantoms. The lateral resolution is estimated to be below 200 μm at a depth of 1.5 cm and below 230 μm at a depth of 4.5 cm. The minimum detectable pressure is in the order of 3 Pa. The introduced method has the potential to provide larger imaging depths than acoustic resolution photoacoustic microscopy and an imaging resolution similar to that of photoacoustic computed tomography.

  20. A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences

    Science.gov (United States)

    Mills, Dawn M.; Calvo-Marzal, Percy; Pinzon, Jeffer M.; Armas, Stephanie; Kolpashchikov, Dmitry M.; Chumbimuni-Torres, Karin Y.

    2017-01-01

    Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode’s surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode’s surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets. PMID:29371782

  1. Detection of Hepatitis B virus DNA and Hepatitis δ virus RNA

    International Nuclear Information System (INIS)

    Smedile, A.; Chiaberge, E.; Brunetto, M.R.; Negro, F.; Baldi, M.; Lavarini, C.; Maran, E.

    1987-01-01

    The recent availability of DNA probes of the Hepatitis B Virus DNA (HBV-DNA) and of Hepatitis Delta Virus RNA (HDV-RNA) allows the application of nucleic acid hybridization techniques to solve a variety of clinical problems. DNA probes of HBV-DNA and HDV-RNA are labeled by nick translation using 32 P or biotinylated nucleotides and hybridized to filters containing test nucleic acids. Complementary sequences are identified and the degree of blackening of the film at autoradiography or the enzymatic staining of the filter is proportional to the amount of viral nucleic acid hybridized to the probe and present in the sample. These procedures allow rapid examination of multiple specimens and are sensitive and reproducible. Viral nucleic acids can be measured quantitatively and their quantity correlates with the infectivity of sera titered in experimentally infected animals

  2. Sensitive electrochemical monitoring of nucleic acids coupling DNA nanostructures with hybridization chain reaction

    International Nuclear Information System (INIS)

    Zhuang, Junyang; Fu, Libing; Xu, Mingdi; Yang, Huanghao; Chen, Guonan; Tang, Dianping

    2013-01-01

    Graphical abstract: -- Highlights: •A new signal-on metallobioassay was developed for detection of nucleic acids. •Target-triggered long-range self-assembled DNA nanostructures are used for amplification of electronic signal. •Hybridization chain reaction is utilized for construction of long-range DNA nanostructures. -- Abstract: Methods based on metal nanotags have been developed for metallobioassay of nucleic acids, but most involve complicated labeling or stripping procedures and are unsuitable for routine use. Herein, we report the proof-of-concept of a novel and label-free metallobioassay for ultrasensitive electronic determination of human immunodeficiency virus (HIV)-related gene fragments at an ultralow concentration based on target-triggered long-range self-assembled DNA nanostructures and DNA-based hybridization chain reaction (HCR). The signal is amplified by silver nanotags on the DNA duplex. The assay mainly consists of capture probe, detection probe, and two different DNA hairpins. In the presence of target DNA, the capture probe immobilized on the sensor sandwiches target DNA with the 3′ end of detection probe. Another exposed part of detection probe at the 5′ end opens two alternating DNA hairpins in turn, and propagates a chain reaction of hybridization events to form a nicked double-helix. Finally, numerous silver nanotags are immobilized onto the long-range DNA nanostructures, each of which produces a strong electronic signal within the applied potentials. Under optimal conditions, the target-triggered long-range DNA nanostructures present good electrochemical behaviors for the detection of HIV DNA at a concentration as low as 0.5 fM. Importantly, the outstanding sensitivity can make this approach a promising scheme for development of next-generation DNA sensors without the need of enzyme labeling or fluorophore labeling

  3. Highly sensitive polymerase chain reaction-free quantum dot-based quantification of forensic genomic DNA

    International Nuclear Information System (INIS)

    Tak, Yu Kyung; Kim, Won Young; Kim, Min Jung; Han, Eunyoung; Han, Myun Soo; Kim, Jong Jin; Kim, Wook; Lee, Jong Eun; Song, Joon Myong

    2012-01-01

    Highlights: ► Genomic DNA quantification were performed using a quantum dot-labeled Alu sequence. ► This probe provided PCR-free determination of human genomic DNA. ► Qdot-labeled Alu probe-hybridized genomic DNAs had a 2.5-femtogram detection limit. ► Qdot-labeled Alu sequence was used to assess DNA samples for human identification. - Abstract: Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification.

  4. A duplex DNA-gold nanoparticle probe composed as a colorimetric biosensor for sequence-specific DNA-binding proteins.

    Science.gov (United States)

    Ahn, Junho; Choi, Yeonweon; Lee, Ae-Ree; Lee, Joon-Hwa; Jung, Jong Hwa

    2016-03-21

    Using duplex DNA-AuNP aggregates, a sequence-specific DNA-binding protein, SQUAMOSA Promoter-binding-Like protein 12 (SPL-12), was directly determined by SPL-12-duplex DNA interaction-based colorimetric actions of DNA-Au assemblies. In order to prepare duplex DNA-Au aggregates, thiol-modified DNA 1 and DNA 2 were attached onto the surface of AuNPs, respectively, by the salt-aging method and then the DNA-attached AuNPs were mixed. Duplex-DNA-Au aggregates having the average size of 160 nm diameter and the maximum absorption at 529 nm were able to recognize SPL-12 and reached the equivalent state by the addition of ∼30 equivalents of SPL-12 accompanying a color change from red to blue with a red shift of the maximum absorption at 570 nm. As a result, the aggregation size grew to about 247 nm. Also, at higher temperatures of the mixture of duplex-DNA-Au aggregate solution and SPL-12, the equivalent state was reached rapidly. On the contrary, in the control experiment using Bovine Serum Albumin (BSA), no absorption band shift of duplex-DNA-Au aggregates was observed.

  5. DNA probe for strain typing of Cryptococcus neoformans.

    OpenAIRE

    Varma, A; Kwon-Chung, K J

    1992-01-01

    A 7-kb linear plasmid, harbored by a URA5 transformant, hybridized to all the chromosomes of Cryptococcus neoformans separated by contour-clamped homogeneous electric field electrophoresis. Its linear maintenance was determined to have been facilitated by the presence of telomere-like sequences at its free ends. Hybridization of this plasmid to AccI-digested genomic DNAs of 26 C. neoformans strains generated 21 unique DNA fingerprints. The DNA fingerprints of isolates within the same serotype...

  6. Highly sensitive rotation sensing based on orthogonal fiber-optic structures

    Science.gov (United States)

    Yang, Yi; Wang, Zi-nan; Xu, Lian-yu; Wang, Cui-yun; Jia, Lei; Yu, Xiao-qi; Shao, Shan; Li, Zheng-bin

    2011-08-01

    In traditional fiber-optic gyroscopes (FOG), the polarization state of counter propagating waves is critically controlled, and only the mode polarized along one particular direction survives. This is important for a traditional single mode fiber gyroscope as the requirement of reciprocity. However, there are some fatal defects such as low accuracy and poor bias stability in traditional structures. In this paper, based on the idea of polarization multiplexing, a double-polarization structure is put forward and experimentally studied. In highly birefringent fibers or standard single mode fibers with induced anisotropy, two orthogonal polarization modes can be used at the same time. Therefore, in polarization maintaining fibers (PMF), each pair of counter propagating beams preserve reciprocity within their own polarization state. Two series of sensing results are gotten in the fast and slow axes in PMF. The two sensing results have their own systematic drifts and the correlation of random noise in them is approximately zero. So, beams in fast and slow axes work as two independent and orthogonal gyroscopes. In this way, amount of information is doubled, providing opportunity to eliminate noise and improve sensitivity. Theoretically, this double-polarization structure can achieve a sensitivity of 10-18 deg/h. Computer simulation demonstrates that random noise and systematic drifts are largely reduced in this novel structure. In experiment, a forty-hour stability test targeting the earth's rotation velocity is carried out. Experiment result shows that the orthogonal fiber-optic structure has two big advantages compared with traditional ones. Firstly, the structure gets true value without any bias correction in any axis and even time-varying bias does not affect the acquisition of true value. The unbiasedness makes the structure very attractive when sudden disturbances or temperature drifts existing in working environment. Secondly, the structure lowers bias for more than

  7. Sandwich nucleic acid hybridization: a method with a universally usable labeled probe for various specific tests

    International Nuclear Information System (INIS)

    Wolf, H.; Leser, U.; Haus, M.; Gu, S.Y.; Pathmanathan, R.

    1986-01-01

    The use of recombinant m13 phages as hybridization probes offers a considerable advantage over the commonly used recombinant plasmids as the preparation of the DNA probe is very simple and it can easily be labeled directly, e.g. with isotopes with long half-life like 125 I and used for hybridization. However, as the application of nucleic acid hybridization for diagnostic and epidemiological purposes becomes almost unavoidable, the logistic problems of keeping numerous individually labeled hybridization probes increase considerably and may reach prohibitory levels in less well-equipped laboratories. In a new sandwich technique, the first step involves hybridization with an unlabeled recombinant m13 DNA carrying an insert of the desired specificity. In a second step a universally usable labeled probe directed against the m13 part of the recombinant phage DNA is applied. This reduces considerably the problem of preparing and keeping multiple labeled probes in stock. (Auth.)

  8. Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Knudsen, Steen

    2002-01-01

    PROBEWIZ designs PCR primers for amplifying probes for cDNA arrays. The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3' end.......PROBEWIZ designs PCR primers for amplifying probes for cDNA arrays. The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3' end....

  9. Variability of chloroplast DNA and nuclear ribosomal DNA in cassava (Manihot esculenta Crantz) and its wild relatives.

    Science.gov (United States)

    Fregene, M A; Vargas, J; Ikea, J; Angel, F; Tohme, J; Asiedu, R A; Akoroda, M O; Roca, W M

    1994-11-01

    Chloroplast DNA (cp) and nuclear ribosomal DNA (rDNA) variation was investigated in 45 accessions of cultivated and wild Manihot species. Ten independent mutations, 8 point mutations and 2 length mutations were identified, using eight restriction enzymes and 12 heterologous cpDNA probes from mungbean. Restriction fragment length polymorphism analysis defined nine distinct chloroplast types, three of which were found among the cultivated accessions and six among the wild species. Cladistic analysis of the cpDNA data using parsimony yielded a hypothetical phylogeny of lineages among the cpDNAs of cassava and its wild relatives that is congruent with morphological evolutionary differentiation in the genus. The results of our survey of cpDNA, together with rDNA restriction site change at the intergenic spacer region and rDNA repeat unit length variation (using rDNA cloned fragments from taro as probe), suggest that cassava might have arisen from the domestication of wild tuberous accessions of some Manihot species, followed by intensive selection. M. esculenta subspp flabellifolia is probably a wild progenitor. Introgressive hybridization with wild forms and pressures to adapt to the widely varying climates and topography in which cassava is found might have enhanced the crop's present day variability.

  10. Theory and Application of DNA Histogram Analysis.

    Science.gov (United States)

    Bagwell, Charles Bruce

    The underlying principles and assumptions associated with DNA histograms are discussed along with the characteristics of fluorescent probes. Information theory was described and used to calculate the information content of a DNA histogram. Two major types of DNA histogram analyses are proposed: parametric and nonparametric analysis. Three levels…

  11. Mixed DNA/Oligo(ethylene glycol) Functionalized Gold Surface Improve DNA Hybridization in Complex Media

    International Nuclear Information System (INIS)

    Lee, C.; Gamble, L.; Grainger, D.; Castner, D.

    2006-01-01

    Reliable, direct 'sample-to-answer' capture of nucleic acid targets from complex media would greatly improve existing capabilities of DNA microarrays and biosensors. This goal has proven elusive for many current nucleic acid detection technologies attempting to produce assay results directly from complex real-world samples, including food, tissue, and environmental materials. In this study, we have investigated mixed self-assembled thiolated single-strand DNA (ssDNA) monolayers containing a short thiolated oligo(ethylene glycol) (OEG) surface diluent on gold surfaces to improve the specific capture of DNA targets from complex media. Both surface composition and orientation of these mixed DNA monolayers were characterized with x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS). XPS results from sequentially adsorbed ssDNA/OEG monolayers on gold indicate that thiolated OEG diluent molecules first incorporate into the thiolated ssDNA monolayer and, upon longer OEG exposures, competitively displace adsorbed ssDNA molecules from the gold surface. NEXAFS polarization dependence results (followed by monitoring the N 1s→π* transition) indicate that adsorbed thiolated ssDNA nucleotide base-ring structures in the mixed ssDNA monolayers are oriented more parallel to the gold surface compared to DNA bases in pure ssDNA monolayers. This supports ssDNA oligomer reorientation towards a more upright position upon OEG mixed adlayer incorporation. DNA target hybridization on mixed ssDNA probe/OEG monolayers was monitored by surface plasmon resonance (SPR). Improvements in specific target capture for these ssDNA probe surfaces due to incorporation of the OEG diluent were demonstrated using two model biosensing assays, DNA target capture from complete bovine serum and from salmon genomic DNA mixtures. SPR results demonstrate that OEG incorporation into the ssDNA adlayer improves surface resistance to both nonspecific DNA and protein

  12. Alpha-fetoprotein detection by using a localized surface plasmon coupled fluorescence fiber-optic biosensor

    Science.gov (United States)

    Chang, Ying-Feng; Chen, Ran-Chou; Li, Ying-Chang; Yu, Chih-Jen; Hsieh, Bao-Yu; Chou, Chien

    2007-11-01

    Alpha-fetoprotein (AFP) detection by using a localized surface plasmon coupled fluorescence (LSPCF) fiber-optic biosensor is setup and experimentally demonstrated. It is based on gold nanoparticle (GNP) and coupled with localized surface plasmon wave on the surface of GNP. In this experiment, the fluorophores are labeled on anti-AFP which are bound to protein A conjugated GNP. Thus, LSPCF is excited with high efficiency in the near field of localized surface plasmon wave. Therefore, not only the sensitivity of LSPCF biosensor is enhanced but also the specific selectivity of AFP is improved. Experimentally, the ability of real time measurement in the range of AFP concentration from 0.1ng/ml to 100ng/ml was detected. To compare with conventional methods such as enzyme-linked immunosorbent assay (ELISA) or radioimmunoassay (RIA), the LSPCF fiber-optic biosensor performs higher or comparable detection sensitivity, respectively.

  13. Persistence of microbial contamination on transvaginal ultrasound probes despite low-level disinfection procedure.

    Directory of Open Access Journals (Sweden)

    Fatima M'Zali

    Full Text Available AIM OF THE STUDY: In many countries, Low Level Disinfection (LLD of covered transvaginal ultrasound probes is recommended between patients' examinations. The aim of this study was to evaluate the antimicrobial efficacy of LLD under routine conditions on a range of microorganisms. MATERIALS AND METHODS: Samples were taken over a six month period in a private French Radiology Center. 300 specimens derived from endovaginal ultrasound probes were analyzed after disinfection of the probe with wipes impregnated with a quaternary ammonium compound and chlorhexidine. Human papillomavirus (HPV was sought in the first set of s100 samples, Chlamydia trachomatis and mycoplasmas were searched in the second set of 100 samples, bacteria and fungi in the third 100 set samples. HPV, C. trachomatis and mycoplasmas were detected by PCR amplification. PCR positive samples were subjected to a nuclease treatment before an additional PCR assay to assess the likely viable microorganisms. Bacteria and fungi were investigated by conventional methods. RESULTS: A substantial persistence of microorganisms was observed on the disinfected probes: HPV DNA was found on 13% of the samples and 7% in nuclease-resistant form. C. trachomatis DNA was detected on 20% of the probes by primary PCR but only 2% after nuclease treatment, while mycoplasma DNA was amplified in 8% and 4%, respectively. Commensal and/or environmental bacterial flora was present on 86% of the probes, occasionally in mixed culture, and at various levels (10->3000 CFU/probe; Staphylococcus aureus was cultured from 4% of the probes (10-560 CFU/probe. No fungi were isolated. CONCLUSION: Our findings raise concerns about the efficacy of impregnated towels as a sole mean for disinfection of ultrasound probes. Although the ultrasound probes are used with disposable covers, our results highlight the potential risk of cross contamination between patients during ultrasound examination and emphasize the need for reviewing

  14. Intra-Tissue Pressure Measurement in Ex Vivo Liver Undergoing Laser Ablation with Fiber-Optic Fabry-Perot Probe

    Directory of Open Access Journals (Sweden)

    Daniele Tosi

    2016-04-01

    Full Text Available We report the first-ever intra-tissue pressure measurement performed during 1064 nm laser ablation (LA of an ex vivo porcine liver. Pressure detection has been performed with a biocompatible, all-glass, temperature-insensitive Extrinsic Fabry-Perot Interferometry (EFPI miniature probe; the proposed methodology mimics in-vivo treatment. Four experiments have been performed, positioning the probe at different positions from the laser applicator tip (from 0.5 mm to 5 mm. Pressure levels increase during ablation time, and decrease with distance from applicator tip: the recorded peak parenchymal pressure levels range from 1.9 kPa to 71.6 kPa. Different pressure evolutions have been recorded, as pressure rises earlier in proximity of the tip. The present study is the first investigation of parenchymal pressure detection in liver undergoing LA: the successful detection of intra-tissue pressure may be a key asset for improving LA, as pressure levels have been correlated to scattered recurrences of tumors by different studies.

  15. Maximum-performance fiber-optic irradiation with nonimaging designs.

    Science.gov (United States)

    Fang, Y; Feuermann, D; Gordon, J M

    1997-10-01

    A range of practical nonimaging designs for optical fiber applications is presented. Rays emerging from a fiber over a restricted angular range (small numerical aperture) are needed to illuminate a small near-field detector at maximum radiative efficiency. These designs range from pure reflector (all-mirror), to pure dielectric (refractive and based on total internal reflection) to lens-mirror combinations. Sample designs are shown for a specific infrared fiber-optic irradiation problem of practical interest. Optical performance is checked with computer three-dimensional ray tracing. Compared with conventional imaging solutions, nonimaging units offer considerable practical advantages in compactness and ease of alignment as well as noticeably superior radiative efficiency.

  16. Effective immobilization of DNA for development of polypyrrole nanowires based biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Thi Luyen; Chu, Thi Xuan, E-mail: xuan@itims.edu.vn; Huynh, Dang Chinh; Pham, Duc Thanh; Luu, Thi Hoai Thuong; Mai, Anh Tuan, E-mail: tuan.maianh@hust.edu.vn

    2014-09-30

    Highlights: • Effective technique to immobilize probe DNA to the conducting polymer Polypyrrole nanowires (PPy NWs). • The PPy-NWs were electrochemically synthesized on the surface of the Pt electrodes using gelatin as the soft mold. • The DNA probe sequences were immobilized easily on the PPy NWs/Pt electrode using the adsorption method. • The DNA sensor has a low detection limit. - Abstract: This paper reports an easy technique for immobilization of the DNA to the conducting polymer polypyrrole nanowires (PPy NWs). The nanowires were electrochemically synthesized on the surface of working electrode in the presence of gelatin as a soft mold. The structure of obtained PPy NWs was investigated by Scanning Electron Microscopy (SEM), Fourier Transform Infrared (FTIR) spectroscopy and Surface Enhanced Raman Spectroscopy (SERS). The DNA strands were directly immobilized on the PPy NWs. The amino groups at the up-end of the PPy nanowires facilitate the linkage with the phosphate groups of the probe DNA. The DNA immobilization and hybridization were characterized by Electrochemical Impedance Spectroscopy (EIS). The initial results show that the sensor responses to 10 pM of DNA sequence in the solution.

  17. Direction of Intercalation of a bis-Ru(II) Complex to DNA Probed by a Minor Groove Binding Molecule 4',6-Diamidino-2-phenylindole

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Yoon Jung; Kim, Raeyeong; Chitrapriya, Nataraj; Kim, Seog K.; Bae, Inho [Yeungnam Univ., Gyeongsan (Korea, Republic of)

    2013-10-15

    Direction of intercalation to DNA of the planar dipyrido[3,2-a:2',3'-c]phenazine ligands (dppz) of a bis-Ru(II) complex namely, [Ru(1,10-phenanthroline){sub 2}dipyrido[3,2-a:2',3'-c]phenazine]{sup 2+} linkered by a 1,3-bis(4-pyridyl)propane, was investigated by probing the behavior of 4',6-diamidino-2-phenylindole (DAPI) that bound deep in the minor groove. Bis-intercalation of DPPZ resulted in a little blue shift and hyperchromism in DAPI absorption band, and a large decrease in DAPI fluorescence intensity which accompanied by an increase in the dppz emission intensity. Diminishing the intensity of the positive induced circular dichroism (CD) and linear dichroism (LD) were also observed. These spectral changes indicated that insertion of dppz ligand caused the change of the binding mode of DAPI, which probably moved to the exterior of DNA from the minor groove and interacted with the phospghate groups of DNA by electrostatic interaction. At the surface of DNA, DAPI binds at the phosphate groups of DNA by electrostatic attraction. Consequently, this observation indicated that the dppz ligand intercalated from the minor groove.

  18. THERMAL PROTECTION AND THERMAL STABILIZATION OF FIBER-OPTICAL GYROSCOPE INCLUDED IN STRAPDOWN INERTIAL NAVIGATION SYSTEM

    Directory of Open Access Journals (Sweden)

    D. S. Gromov

    2014-03-01

    Full Text Available It is known, that temperature perturbations and thermal modes have significant influence on the accuracy of a fiber-optical gyroscope. Nowadays, thermal perturbations are among the main problems in the field of navigation accuracy. Review of existing methods for decrease of temperature influences on the accuracy of a strapdown inertial navigation system with fiberoptical gyros showed, that the usage of constructive and compensation methods only is insufficient and, therefore, thermostabilization is required. Reversible thermostabilization system is offered, its main executive elements are thermoelectric modules (Peltier’s modules, heat transfer from which is provided by heatsinks at work surfaces of modules. This variant of thermostabilization maintenance is considered; Peltier’s modules and temperature sensors for the system are chosen. Parameters of heatsinks for heat transfer intensification are calculated. Fans for necessary air circulation in the device are chosen and thickness of thermal isolation is calculated. Calculations of thermal modes of navigation system with thermostabilization are made in modern software Autodesk Simulation CFD. Comparison of results for present and previous researches and calculations shows essential decrease in gradients of temperature on gyro surfaces and better uniformity of temperature field in the whole device. Conclusions about efficiency of the given method usage in view of accuracy improvement of navigation system are made. Thermostabilization provision of a strapdown inertial navigation system with fiberoptical gyros is proved. Thermostabilization application in combination with compensational methods can reach a necessary accuracy of navigation system.

  19. On-bead fluorescent DNA nanoprobes to analyze base excision repair activities

    International Nuclear Information System (INIS)

    Gines, Guillaume; Saint-Pierre, Christine; Gasparutto, Didier

    2014-01-01

    Graphical abstract: -- Highlights: •On magnetic beads fluorescent enzymatic assays. •Simple, easy, non-radioactive and electrophoresis-free functional assay. •Lesion-containing hairpin DNA probes are selective for repair enzymes. •The biosensing platform allows the measurement of DNA repair activities from purified enzymes or within cell free extracts. -- Abstract: DNA integrity is constantly threatened by endogenous and exogenous agents that can modify its physical and chemical structure. Changes in DNA sequence can cause mutations sparked by some genetic diseases or cancers. Organisms have developed efficient defense mechanisms able to specifically repair each kind of lesion (alkylation, oxidation, single or double strand break, mismatch, etc). Here we report the adjustment of an original assay to detect enzymes’ activity of base excision repair (BER), that supports a set of lesions including abasic sites, alkylation, oxidation or deamination products of bases. The biosensor is characterized by a set of fluorescent hairpin-shaped nucleic acid probes supported on magnetic beads, each containing a selective lesion targeting a specific BER enzyme. We have studied the DNA glycosylase alkyl-adenine glycosylase (AAG) and the human AP-endonuclease (APE1) by incorporating within the DNA probe a hypoxanthine lesion or an abasic site analog (tetrahydrofuran), respectively. Enzymatic repair activity induces the formation of a nick in the damaged strand, leading to probe's break, that is detected in the supernatant by fluorescence. The functional assay allows the measurement of DNA repair activities from purified enzymes or in cell-free extracts in a fast, specific, quantitative and sensitive way, using only 1 pmol of probe for a test. We recorded a detection limit of 1 μg mL −1 and 50 μg mL −1 of HeLa nuclear extracts for APE1 and AAG enzymes, respectively. Finally, the on-bead assay should be useful to screen inhibitors of DNA repair activities

  20. Multifunctional fiber-optic microwave links based on remote heterodyne detection

    DEFF Research Database (Denmark)

    Gliese, Ulrik Bo; Nielsen, Torben Nørskov; Nielsen, Søren Nørskov

    1998-01-01

    The multifunctionality of microwave links based on remote heterodyne detection (RHD) of signals from a dual-frequency laser transmitter is discussed and experimentally demonstrated in this paper. Typically, direct detection (DD) in conjunction with optical intensity modulation is used to implement...... fiber-optic microwave links. The resulting links are inherently transparent. As opposed to DD links, RHD links can perform radio-system functionalities such as modulation and frequency conversion in addition to transparency. All of these three functionalities are presented and experimentally...

  1. Eggshell membrane: A natural substrate for immobilization and detection of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Ray, Preetam Guha; Roy, Somenath, E-mail: sroy@cgcri.res.in

    2016-02-01

    Chemically modified eggshell membranes (ESM) have been explored as potentially novel platforms for immobilization of oligonucleotides and subsequent detection of target DNA. The fibrous network of the native ESM as well those functionalized with acetic acid or n-butyl acetate has been examined by field-emission scanning electron microscopy (FESEM). The formation of surface functional moieties has been confirmed by Fourier-transform infrared spectroscopy (FTIR). DNA molecules, with an end terminal − NH{sub 2} group (at 5′ end) have been immobilized on the chemically modified ESM surface. The effect of surface modification on the DNA immobilization efficiency has been investigated using fluorescence microscopy and atomic force microscopy (AFM). The above studies concurrently suggest that functionalization of ESM with n-butyl acetate causes a better homogeneity of the DNA probes on the membrane surface. On-chip hybridization of the target DNA with the surface bound capture probes has been performed on the functionalized membranes. It is observed that n-butyl acetate modification of ESM pushes the limit of detection (LOD) of the DNA sensors by at least an order of magnitude compared to the other modification method. - Graphical abstract: Eggshell membranes (ESM) have been chemically modified with acetic acid or n-butyl acetate for immobilization of aminated capture probes and subsequent detection of fluorophore-tagged target DNA molecules. n-Butyl acetate modified ESM exhibits superior homogeneity of capture probe immobilization and lower limit of detection for the target DNA molecules. - Highlights: • Eggshell membranes (ESM) have been explored as potentially novel platforms for immobilization of oligonucleotides. • Compared to native ESM, those modified with acetic acid or n-butyl acetate have shown more efficient loading of DNA probes. • ESM modified with n-butyl acetate pushed the lower limit of detection (LOD) of the sensor down to 10 nM of target DNA

  2. TaqMan probe real-time polymerase chain reaction assay for the quantification of canine DNA in chicken nugget.

    Science.gov (United States)

    Rahman, Md Mahfujur; Hamid, Sharifah Bee Abd; Basirun, Wan Jefrey; Bhassu, Subha; Rashid, Nur Raifana Abdul; Mustafa, Shuhaimi; Mohd Desa, Mohd Nasir; Ali, Md Eaqub

    2016-01-01

    This paper describes a short-amplicon-based TaqMan probe quantitative real-time PCR (qPCR) assay for the quantitative detection of canine meat in chicken nuggets, which are very popular across the world, including Malaysia. The assay targeted a 100-bp fragment of canine cytb gene using a canine-specific primer and TaqMan probe. Specificity against 10 different animals and plants species demonstrated threshold cycles (Ct) of 16.13 ± 0.12 to 16.25 ± 0.23 for canine DNA and negative results for the others in a 40-cycle reaction. The assay was tested for the quantification of up to 0.01% canine meat in deliberately spiked chicken nuggets with 99.7% PCR efficiency and 0.995 correlation coefficient. The analysis of the actual and qPCR predicted values showed a high recovery rate (from 87% ± 28% to 112% ± 19%) with a linear regression close to unity (R(2) = 0.999). Finally, samples of three halal-branded commercial chicken nuggets collected from different Malaysian outlets were screened for canine meat, but no contamination was demonstrated.

  3. 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.

  4. Establishment of a novel two-probe real-time PCR for simultaneously quantification of hepatitis B virus DNA and distinguishing genotype B from non-B genotypes.

    Science.gov (United States)

    Wang, Wei; Liang, Hongpin; Zeng, Yongbin; Lin, Jinpiao; Liu, Can; Jiang, Ling; Yang, Bin; Ou, Qishui

    2014-11-01

    Establishment of a simple, rapid and economical method for quantification and genotyping of hepatitis B virus (HBV) is of great importance for clinical diagnosis and treatment of chronic hepatitis B patients. We hereby aim to develop a novel two-probe real-time PCR for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes. Conserved primers and TaqMan probes for genotype B and non-B genotypes were designed. The linear range, detection sensitivity, specificity and repeatability of the method were assessed. 539 serum samples from HBV-infected patients were assayed, and the results were compared with commercial HBV quantification and HBV genotyping kits. The detection sensitivity of the two-probe real-time PCR was 500IU/ml; the linear range was 10(3)-10(9)IU/ml, and the intra-assay CVs and inter-assay CVs were between 0.84% and 2.80%. No cross-reaction was observed between genotypes B and non-B. Of the 539 detected samples, 509 samples were HBV DNA positive. The results showed that 54.0% (275/509) of the samples were genotype B, 39.5% (201/509) were genotype non-B and 6.5% (33/509) were mixed genotype. The coincidence rate between the method and a commercial HBV DNA genotyping kit was 95.9% (488/509, kappa=0.923, PDNA qPCR kit were achieved. A novel two-probe real-time PCR method for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes was established. The assay was sensitive, specific and reproducible which can be applied to areas prevalent with HBV genotypes B and C, especially in China. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. EXPERIMENTAL COMPARISON OF HOMODYNE DEMODULATION ALGORITHMS FOR PHASE FIBER-OPTIC SENSOR

    Directory of Open Access Journals (Sweden)

    M. N. Belikin

    2015-11-01

    Full Text Available Subject of Research. The paper presents the results of experimental comparative analysis of homodyne demodulation algorithms based on differential cross multiplying method and on arctangent method under the same conditions. The dependencies of parameters for the output signals on the optical radiation intensity are studied for the considered demodulation algorithms. Method. The prototype of single fiber optic phase interferometric sensor has been used for experimental comparison of signal demodulation algorithms. Main Results. We have found that homodyne demodulation based on arctangent method provides greater (by 7 dB at average signal-to-noise ratio of output signals over the frequency band of acoustic impact from 100 Hz to 500 Hz as compared to differential cross multiplying algorithms. We have demonstrated that no change in the output signal amplitude occurs for the studied range of values of the optical pulses amplitudes. Obtained results indicate that the homodyne demodulation based on arctangent method is most suitable for application in the phase fiber-optic sensors. It provides higher repeatability of their characteristics than the differential cross multiplying algorithm. Practical Significance. Algorithms of interferometric signals demodulation are widely used in phase fiber-optic sensors. Improvement of their characteristics has a positive effect on the performance of such sensors.

  6. Effect of midazolam on memory during fiberoptic gastroscopy under conscious sedation.

    Science.gov (United States)

    Hong, Yun Jeong; Jang, Eun Hye; Hwang, Jihye; Roh, Jee Hoon; Kwon, Miseon; Lee, Don; Lee, Jae-Hong

    2015-01-01

    As the fiberoptic gastroscopy using midazolam is being in widespread use, the exact nature of midazolam on memory should be clarified. We intended to examine whether midazolam causes selective anterograde amnesia and what impact it has on other aspects of memory and general cognitive function. We recruited healthy subjects undergoing fiberoptic gastroscopy under conscious sedation. At baseline, history taking for retrograde amnesia and the Korean version of the Montreal Cognitive Assessment were performed. A man's name and address were given immediately after intravenous midazolam administration. After gastroscopy, the subjects were asked to recall those items. By the time they had fully recovered consciousness, the same test was repeated along with the Korean version of the Montreal Cognitive Assessment and a test for retrograde amnesia. A total of 30 subjects were enrolled in this study. Subjects with high-dose midazolam showed lower scores in the immediate and delayed recall of "a man's name and address" compared with those with low-dose midazolam. The midazolam dose was inversely correlated with the delayed recall scores of "a man's name and address." On full recovery of consciousness, the subjects did not exhibit any of anterograde or retrograde amnesia. These findings suggest that midazolam causes transient selective anterograde amnesia in a dose-dependent manner.

  7. Development of Piezoelectric DNA-Based Biosensor for Direct Detection of Mycobacterium Tuberculosis in Clinical Specimens

    Directory of Open Access Journals (Sweden)

    Thongchai KAEWPHINIT

    2010-02-01

    Full Text Available This study was focused on establishment of piezoelectric biosensor for direct detection of Mycobacterium tuberculosis (MTB in clinical specimens. The quartz crystal immobilized via 3-mercaptopropionic acid (MPA/avidin/DNA biotinylated probe on gold surface and hybridization of the DNA target to DNA biotinylated probe. The optimal concentration of MPA, avidin and 5’-biotinylated DNA probe for immobilization of specific DNA probe on gold surface were 15 mM, 0.1 mg/ml and 1.5 μM, respectively. The detection of genomic DNA digestion in the range from 0.5 to 30 μg/ml. The fabricated biosensor was evaluated through an examination of 200 samples. No cross hybridization were observed against M. avium complex (MAC and other microorganism. This target DNA preparation without amplification will reduce time consuming, costs, and the tedious step of amplification. This study can be extended to develop the new method which is high sensitivity, specificity, cheap, easy to use, and rapid for detection of MTB in many fields.

  8. Single Molecule Screening of Disease DNA Without Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ji-Young [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The potential of single molecule detection as an analysis tool in biological and medical fields is well recognized today. This fast evolving technique will provide fundamental sensitivity to pick up individual pathogen molecules, and therefore contribute to a more accurate diagnosis and a better chance for a complete cure. Many studies are being carried out to successfully apply this technique in real screening fields. In this dissertation, several attempts are shown that have been made to test and refine the application of the single molecule technique as a clinical screening method. A basic applicability was tested with a 100% target content sample, using electrophoretic mobility and multiple colors as identification tools. Both electrophoretic and spectral information of individual molecule were collected within a second, while the molecule travels along the flow in a capillary. Insertion of a transmission grating made the recording of the whole spectrum of a dye-stained molecule possible without adding complicated instrumental components. Collecting two kinds of information simultaneously and combining them allowed more thorough identification, up to 98.8% accuracy. Probing mRNA molecules with fluorescently labeled cDNA via hybridization was also carried out. The spectral differences among target, probe, and hybrid were interpreted in terms of dispersion distances after transmission grating, and used for the identification of each molecule. The probes were designed to have the least background when they are free, but have strong fluorescence after hybridization via fluorescence resonance energy transfer. The mRNA-cDNA hybrids were further imaged in whole blood, plasma, and saliva, to test how far a crude preparation can be tolerated. Imaging was possible with up to 50% of clear bio-matrix contents, suggesting a simple lysis and dilution would be sufficient for imaging for some cells. Real pathogen DNA of human papillomavirus (HPV) type-I6 in human genomic DNA

  9. A direct detection of Escherichia coli genomic DNA using gold nanoprobes

    Directory of Open Access Journals (Sweden)

    Padmavathy

    2012-02-01

    Full Text Available Abstract Background In situation like diagnosis of clinical and forensic samples there exists a need for highly sensitive, rapid and specific DNA detection methods. Though conventional DNA amplification using PCR can provide fast results, it is not widely practised in diagnostic laboratories partially because it requires skilled personnel and expensive equipment. To overcome these limitations nanoparticles have been explored as signalling probes for ultrasensitive DNA detection that can be used in field applications. Among the nanomaterials, gold nanoparticles (AuNPs have been extensively used mainly because of its optical property and ability to get functionalized with a variety of biomolecules. Results We report a protocol for the use of gold nanoparticles functionalized with single stranded oligonucleotide (AuNP- oligo probe as visual detection probes for rapid and specific detection of Escherichia coli. The AuNP- oligo probe on hybridization with target DNA containing complementary sequences remains red whereas test samples without complementary DNA sequences to the probe turns purple due to acid induced aggregation of AuNP- oligo probes. The color change of the solution is observed visually by naked eye demonstrating direct and rapid detection of the pathogenic Escherichia coli from its genomic DNA without the need for PCR amplification. The limit of detection was ~54 ng for unamplified genomic DNA. The method requires less than 30 minutes to complete after genomic DNA extraction. However, by using unamplified enzymatic digested genomic DNA, the detection limit of 11.4 ng was attained. Results of UV-Vis spectroscopic measurement and AFM imaging further support the hypothesis of aggregation based visual discrimination. To elucidate its utility in medical diagnostic, the assay was validated on clinical strains of pathogenic Escherichia coli obtained from local hospitals and spiked urine samples. It was found to be 100% sensitive and proves to

  10. Probing DNA with micro- and nanocapillaries and optical tweezers

    International Nuclear Information System (INIS)

    Steinbock, L J; Otto, O; Skarstam, D R; Jahn, S; Chimerel, C; Gornall, J L; Keyser, U F

    2010-01-01

    We combine for the first time optical tweezer experiments with the resistive pulse technique based on capillaries. Quartz glass capillaries are pulled into a conical shape with tip diameters as small as 27 nm. Here, we discuss the translocation of λ-phage DNA which is driven by an electrophoretic force through the nanocapillary. The resulting change in ionic current indicates the folding state of single λ-phage DNA molecules. Our flow cell design allows for the straightforward incorporation of optical tweezers. We show that a DNA molecule attached to an optically trapped colloid is pulled into a capillary by electrophoretic forces. The detected electrophoretic force is in good agreement with measurements in solid-state nanopores.

  11. Rapid, highly sensitive and highly specific gene detection by combining enzymatic amplification and DNA chip detection simultaneously

    Directory of Open Access Journals (Sweden)

    Koji Hashimoto

    2016-05-01

    Full Text Available We have developed a novel gene detection method based on the loop-mediated isothermal amplification (LAMP reaction and the DNA dissociation reaction on the same DNA chip surface to achieve a lower detection limit, broader dynamic range and faster detection time than are attainable with a conventional DNA chip. Both FAM- and thiol-labeled DNA probe bound to the complementary sequence accompanying Dabcyl was immobilized on the gold surface via Au/thiol bond. The LAMP reaction was carried out on the DNA probe fixed gold surface. At first, Dabcyl molecules quenched the FAM fluorescence. According to the LAMP reaction, the complementary sequence with Dabcyl was competitively reacted with the amplified targeted sequence. As a result, the FAM fluorescence increased owing to dissociation of the complementary sequence from the DNA probe. The simultaneous reaction of LAMP and DNA chip detection was achieved, and 103 copies of the targeted gene were detected within an hour by measuring fluorescence intensity of the DNA probe. Keywords: Biosensor, DNA chip, Loop-mediated isothermal amplification (LAMP, Fluorescence detection, Gold substrate, Au/thiol bond

  12. Ultrafast Fabry-Perot fiber-optic pressure sensors for multimedia blast event measurements.

    Science.gov (United States)

    Zou, Xiaotian; Wu, Nan; Tian, Ye; Zhang, Yang; Fitek, John; Maffeo, Michael; Niezrecki, Christopher; Chen, Julie; Wang, Xingwei

    2013-02-20

    A shock wave (SW) is characterized as a large pressure fluctuation that typically lasts only a few milliseconds. On the battlefield, SWs pose a serious threat to soldiers who are exposed to explosions, which may lead to blast-induced traumatic brain injuries. SWs can also be used beneficially and have been applied to a variety of medical treatments due to their unique interaction with tissues and cells. Consequently, it is important to have sensors that can quantify SW dynamics in order to better understand the physical interaction between body tissue and the incident acoustic wave. In this paper, the ultrafast fiber-optic sensor based on the Fabry-Perot interferometric principle was designed and four such sensors were fabricated to quantify a blast event within different media, simultaneously. The compact design of the fiber-optic sensor allows for a high degree of spatial resolution when capturing the wavefront of the traveling SW. Several blast event experiments were conducted within different media (e.g., air, rubber membrane, and water) to evaluate the sensor's performance. This research revealed valuable knowledge for further study of SW behavior and SW-related applications.

  13. DNA Diagnostics: Optical or by Electronics?

    KAUST Repository

    Khan, Hadayat Ullah

    2016-01-15

    In this paper, we very briefly review DNA biosensors based on optical and electrical detection principles, referring mainly to our past work applying both techniques but here using nearly identical sensor chip surface architectures, i.e., capture probe layers that were prepared based on a pulsed plasma deposition protocol for maleic anhydride and subsequent wet-chemical attachment of the amine-functionalized peptide nucleic acid (PNA) probe oligonucleotides. 15 mer DNA target strands, labeled with Cy5-chromophores that were attached at the 5’ end were used for surface plasmon optical detection and the same target DNA but without label was used in OTFT sensor-based detection where the mere charge density of the bound (hybridized) DNA molecules modulate the source-drain current. The sensing mechanisms and the detection limits of the devices are described in some detail. Both techniques allow for the monitoring of surface hybridization reactions, and offer the capacity to quantitatively discriminate between targets with different degrees of mismatched sequences.

  14. Fiber-optic coupling based on nonimaging expanded-beam optics.

    Science.gov (United States)

    Moslehi, B; Ng, J; Kasimoff, I; Jannson, T

    1989-12-01

    We have fabricated and experimentally tested low-cost and mass-producible multimode fiber-optic couplers and connectors based on nonimaging beam-expanding optics and Liouville's theorem. Analysis indicates that a pair coupling loss of -0.25 dB can be achieved. Experimentally, we measured insertion losses as low as -0.38 dB. The beam expanders can be mass produced owing to the use of plastic injection-molding fabrication techniques and packaged in standard connector housings. This design is compatible with the fiber geometry and can yield highly stable coupling owing to its high tolerance for misalignments.

  15. Nonlinear fiber-optic strain sensor based on four-wave mixing in microstructured optical fiber

    DEFF Research Database (Denmark)

    Gu, Bobo; Yuan, Scott Wu; Frosz, Michael H.

    2012-01-01

    We demonstrate a nonlinear fiber-optic strain sensor, which uses the shifts of four-wave mixing Stokes and anti-Stokes peaks caused by the strain-induced changes in the structure and refractive index of a microstructured optical fiber. The sensor thus uses the inherent nonlinearity of the fiber a...

  16. A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

    Science.gov (United States)

    Narayanaswamy, Nagarjun; Kumar, Manoj; Das, Sadhan; Sharma, Rahul; Samanta, Pralok K.; Pati, Swapan K.; Dhar, Suman K.; Kundu, Tapas K.; Govindaraju, T.

    2014-01-01

    Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology. PMID:25252596

  17. Linking probe thermodynamics to microarray quantification

    International Nuclear Information System (INIS)

    Li, Shuzhao; Pozhitkov, Alexander; Brouwer, Marius

    2010-01-01

    Understanding the difference in probe properties holds the key to absolute quantification of DNA microarrays. So far, Langmuir-like models have failed to link sequence-specific properties to hybridization signals in the presence of a complex hybridization background. Data from washing experiments indicate that the post-hybridization washing has no major effect on the specifically bound targets, which give the final signals. Thus, the amount of specific targets bound to probes is likely determined before washing, by the competition against nonspecific binding. Our competitive hybridization model is a viable alternative to Langmuir-like models. (comment)

  18. Facile preparation of a DNA sensor for rapid herpes virus detection

    Energy Technology Data Exchange (ETDEWEB)

    Tam, Phuong Dinh, E-mail: tampd-hast@mail.hut.edu.vn [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Tuan, Mai Anh, E-mail: tuanma-itims@mail.hut.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam); Huy, Tran Quang [National Institute of Hygiene and Epidemiology (NIHE), 01 Yersin, Hai Ba Trung District, Hanoi (Viet Nam); Le, Anh-Tuan [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Hieu, Nguyen Van, E-mail: hieu@itims.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam)

    2010-10-12

    In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

  19. Facile preparation of a DNA sensor for rapid herpes virus detection

    International Nuclear Information System (INIS)

    Tam, Phuong Dinh; Tuan, Mai Anh; Huy, Tran Quang; Le, Anh-Tuan; Hieu, Nguyen Van

    2010-01-01

    In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

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

    Science.gov (United States)

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

    2009-08-01

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

  1. Recovery Based Nanowire Field-Effect Transistor Detection of Pathogenic Avian Influenza DNA

    Science.gov (United States)

    Lin, Chih-Heng; Chu, Chia-Jung; Teng, Kang-Ning; Su, Yi-Jr; Chen, Chii-Dong; Tsai, Li-Chu; Yang, Yuh-Shyong

    2012-02-01

    Fast and accurate diagnosis is critical in infectious disease surveillance and management. We proposed a DNA recovery system that can easily be adapted to DNA chip or DNA biosensor for fast identification and confirmation of target DNA. This method was based on the re-hybridization of DNA target with a recovery DNA to free the DNA probe. Functionalized silicon nanowire field-effect transistor (SiNW FET) was demonstrated to monitor such specific DNA-DNA interaction using high pathogenic strain virus hemagglutinin 1 (H1) DNA of avian influenza (AI) as target. Specific electric changes were observed in real-time for AI virus DNA sensing and device recovery when nanowire surface of SiNW FET was modified with complementary captured DNA probe. The recovery based SiNW FET biosensor can be further developed for fast identification and further confirmation of a variety of influenza virus strains and other infectious diseases.

  2. Assessment of detection limits of fiber-optic distributed temperature sensing for detection of illicit connections

    NARCIS (Netherlands)

    Nienhuis, J.; De Haan, C.; Langeveld, J.G.; Klootwijk, M.; Clemens, F.H.L.R.

    2012-01-01

    Distributed Temperature Sensing (DTS) with fiber-optic cables is a powerful tool to detect illicit connections in storm sewer systems. High frequency temperature measurements along the in-sewer cable create a detailed representation of temperature anomalies due to illicit discharges. The detection

  3. Coupling of an indicator-free electrochemical DNA biosensor with polymerase chain reaction for the detection of DNA sequences related to the apolipoprotein E

    Energy Technology Data Exchange (ETDEWEB)

    Lucarelli, Fausto; Marrazza, Giovanna; Palchetti, Ilaria; Cesaretti, S.; Mascini, Marco

    2002-09-26

    This paper describes a disposable indicator-free electrochemical DNA biosensor applied to the detection of apolipoprotein E (apoE) sequences in PCR samples. In the indicator-free assays, the duplex formation was detected by measuring the electrochemical signal of the guanine base of nucleic acids. The biosensor format involved the immobilisation of an inosine-modified (guanine-free) probe onto a screen-printed electrode (SPE) transducer and the detection of the duplex formation in connection with the square-wave voltammetric measurement of the oxidation peak of the guanine of the target sequence. The indicator-free scheme has been characterised using 23-mer oligonucleotides as model: parameters affecting the hybridisation assay such as probe immobilisation conditions, hybridisation time, use of hybridisation accelerators were examined and optimised. The analysis of PCR samples (244 bp DNA fragments, obtained by amplification of DNA extracted from human blood) required a further optimisation of the experimental procedure. In particular, a lower steric hyndrance of the probe modified surface was essential to allow an efficient hybridisation of the target DNA fragment. Negative controls have been performed using the PCR blank and amplicons unrelated to the immobilised probe. A 10 min hybridisation time allowed a full characterisation of each sample.

  4. Multifragment alleles in DNA fingerprints of the parrot, Amazona ventralis

    Science.gov (United States)

    Brock, M.K.; White, B.N.

    1991-01-01

    Human DNA probes that identify variable numbers of tandem repeat loci are being used to generate DNA fingerprints in many animal and plant species. In most species the majority of the sc rable autoradiographic bands of the DNA fingerprint represent alleles from numerous unlinked loci. This study was initiated to use DNA fingerprints to determine the amount of band-sharing among captive Hispaniolan parrots (Amazona ventralis) with known genetic relationships. This would form the data base to examine DNA fingerprints of the closely related and endangered Puerto Rican parrot (A. vittata) and to estimate the degree of inbreeding in the relic population. We found by segregation analysis of the bands scored in the DNA fingerprints of the Hispaniolan parrots that there may be as few as two to five loci identified by the human 33.15 probe. Furthermore, at one locus we identified seven alleles, one of which is represented by as many as 19 cosegregating bands. It is unknown how common multiband alleles might be in natural populations, and their existence will cause problems in the assessment of relatedness by band-sharing analysis. We believe, therefore, that a pedigree analysis should be included in all DNA fingerprinting studies, where possible, in order to estimate the number of loci identified by a minisatellite DNA probe and to examine the nature of their alleles.

  5. Detection of anthrax lef with DNA-based photonic crystal sensors

    Science.gov (United States)

    Zhang, Bailin; Dallo, Shatha; Peterson, Ralph; Hussain, Syed; Weitao, Tao; Ye, Jing Yong

    2011-12-01

    Bacillus anthracis has posed a threat of becoming biological weapons of mass destruction due to its virulence factors encoded by the plasmid-borne genes, such as lef for lethal factor. We report the development of a fast and sensitive anthrax DNA biosensor based on a photonic crystal structure used in a total-internal-reflection configuration. For the detection of the lef gene, a single-stranded DNA lef probe was biotinylated and immobilized onto the sensor via biotin-streptavidin interactions. A positive control, lef-com, was the complementary strand of the probe, while a negative control was an unrelated single-stranded DNA fragment from the 16S rRNA gene of Acinetobacter baumannii. After addition of the biotinylated lef probe onto the sensor, significant changes in the resonance wavelength of the sensor were observed, resulting from binding of the probe to streptavidin on the sensor. The addition of lef-com led to another significant increase as a result of hybridization between the two DNA strands. The detection sensitivity for the target DNA reached as low as 0.1 nM. In contrast, adding the unrelated DNAs did not cause an obvious shift in the resonant wavelength. These results demonstrate that detection of the anthrax lef by the photonic crystal structure in a total-internal-reflection sensor is highly specific and sensitive.

  6. Multiplexed microRNA detection using lanthanide-labeled DNA probes and laser ablation inductively coupled plasma mass spectrometry

    DEFF Research Database (Denmark)

    de Bang, Thomas Christian; Shah, Pratik; Cho, Seok Keun

    2014-01-01

    coupled plasma mass spectrometry (LA-ICPMS). Three miRNAs from Arabidopsis thaliana were analyzed simultaneously with high specificity, and the sensitivity of the method was comparable to radioactive detection (low femtomol range). The perspective of the developed method is highly multiplexed......In the past decade, microRNAs (miRNAs) have drawn increasing attention due to their role in regulation of gene expression. Especially, their potential as biomarkers in disease diagnostics has motivated miRNA research, including the development of simple, accurate, and sensitive detection methods....... The narrow size range of miRNAs (20-24 nucleotides) combined with the chemical properties of conventional reporter tags has hampered the development of multiplexed miRNA assays. In this study, we have used lanthanide-labeled DNA probes for the detection of miRNAs on membranes using laser ablation inductively...

  7. Aspiration in children and adolescents with neurogenic dysphagia: comparison of clinical judgment and fiberoptic endoscopic evaluation of swallowing.

    Science.gov (United States)

    Beer, Sabrina; Hartlieb, Till; Müller, Arnd; Granel, Michael; Staudt, Martin

    2014-12-01

    A total of 30 children and adolescents with dysphagia due to various chronic neurological disorders were assessed for their risk of aspiration. This assessment was performed clinically by experienced speech and swallowing therapists, and verified thereafter by fiberoptic endoscopy. We found the clinical judgment to be correct in only 70% (for aspiration of saliva), 55% (of puree), and 67% (of thin liquids). We conclude that, because of this unacceptably high error rate of clinical assessment, a fiberoptic evaluation of swallowing is a necessary diagnostic step both for the planning of therapy and for the development of feeding strategies in children and adolescents with neurogenic dysphagia. Georg Thieme Verlag KG Stuttgart · New York.

  8. Method for assessing damage to mitochondrial DNA caused by radiation and epichlorohydrin

    International Nuclear Information System (INIS)

    Singh, G.; Hauswirth, W.W.; Ross, W.E.; Neims, A.H.

    1985-01-01

    This paper describes a rapid and reliable method for quantification of damage to mitochondrial DNA (mtDNA), especially strand breaks. The degree of damage to mtDNA is assessed by the proportion of physical forms (i.e., supercoiled versus open-circular and linear forms) upon agarose gel electrophoresis, blotting, and visualization by hybridization with [ 32 P]mtDNA probes. The use of a radiolabeled probe is a crucial step in the procedure because it provides both a means to quantify by radioautography and to obtain the mtDNA specificity required to eliminate misinterpretation due to nuclear DNA contamination. To demonstrate the utility of this technique, X-irradiation and epichlorohydrin are shown to damage both isolated mtDNA and mtDNA in whole cells in a dose-dependent fashion

  9. Computational modeling of a carbon nanotube-based DNA nanosensor

    Energy Technology Data Exchange (ETDEWEB)

    Kalantari-Nejad, R; Bahrami, M [Mechanical Engineering Department, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Rafii-Tabar, H [Department of Medical Physics and Biomedical Engineering and Research Centre for Medical Nanotechnology and Tissue Engineering, Shahid Beheshti University of Medical Sciences, Evin, Tehran (Iran, Islamic Republic of); Rungger, I; Sanvito, S, E-mail: mbahrami@aut.ac.ir [School of Physics and CRANN, Trinity College, Dublin 2 (Ireland)

    2010-11-05

    During the last decade the design of biosensors, based on quantum transport in one-dimensional nanostructures, has developed as an active area of research. Here we investigate the sensing capabilities of a DNA nanosensor, designed as a semiconductor single walled carbon nanotube (SWCNT) connected to two gold electrodes and functionalized with a DNA strand acting as a bio-receptor probe. In particular, we have considered both covalent and non-covalent bonding between the DNA probe and the SWCNT. The optimized atomic structure of the sensor is computed both before and after the receptor attaches itself to the target, which consists of another DNA strand. The sensor's electrical conductance and transmission coefficients are calculated at the equilibrium geometries via the non-equilibrium Green's function scheme combined with the density functional theory in the linear response limit. We demonstrate a sensing efficiency of 70% for the covalently bonded bio-receptor probe, which drops to about 19% for the non-covalently bonded one. These results suggest that a SWCNT may be a promising candidate for a bio-molecular FET sensor.

  10. Computational modeling of a carbon nanotube-based DNA nanosensor

    International Nuclear Information System (INIS)

    Kalantari-Nejad, R; Bahrami, M; Rafii-Tabar, H; Rungger, I; Sanvito, S

    2010-01-01

    During the last decade the design of biosensors, based on quantum transport in one-dimensional nanostructures, has developed as an active area of research. Here we investigate the sensing capabilities of a DNA nanosensor, designed as a semiconductor single walled carbon nanotube (SWCNT) connected to two gold electrodes and functionalized with a DNA strand acting as a bio-receptor probe. In particular, we have considered both covalent and non-covalent bonding between the DNA probe and the SWCNT. The optimized atomic structure of the sensor is computed both before and after the receptor attaches itself to the target, which consists of another DNA strand. The sensor's electrical conductance and transmission coefficients are calculated at the equilibrium geometries via the non-equilibrium Green's function scheme combined with the density functional theory in the linear response limit. We demonstrate a sensing efficiency of 70% for the covalently bonded bio-receptor probe, which drops to about 19% for the non-covalently bonded one. These results suggest that a SWCNT may be a promising candidate for a bio-molecular FET sensor.

  11. ProbeZT: Simulation of transport coefficients of molecular electronic junctions under environmental effects using Büttiker's probes

    Science.gov (United States)

    Korol, Roman; Kilgour, Michael; Segal, Dvira

    2018-03-01

    We present our in-house quantum transport package, ProbeZT. This program provides linear response coefficients: electrical and electronic thermal conductances, as well as the thermopower of molecular junctions in which electrons interact with the surrounding thermal environment. Calculations are performed based on the Büttiker probe method, which introduces decoherence, energy exchange and dissipation effects phenomenologically using virtual electrode terminals called probes. The program can realize different types of probes, each introducing various environmental effects, including elastic and inelastic scattering of electrons. The molecular system is described by an arbitrary tight-binding Hamiltonian, allowing the study of different geometries beyond simple one-dimensional wires. Applications of the program to study the thermoelectric performance of molecular junctions are illustrated. The program also has a built-in functionality to simulate electron transport in double-stranded DNA molecules based on a tight-binding (ladder) description of the junction.

  12. Electrochemical DNA probe for Hg(2+) detection based on a triple-helix DNA and Multistage Signal Amplification Strategy.

    Science.gov (United States)

    Wang, Huan; Zhang, Yihe; Ma, Hongmin; Ren, Xiang; Wang, Yaoguang; Zhang, Yong; Wei, Qin

    2016-12-15

    In this work, an ultrasensitive electrochemical sensor was developed for detection of Hg(2+). Gold nanoparticles decorated bovine serum albumin reduction of graphene oxide (AuNP-BSA-rGO) were used as subsurface material for the immobilization of triple-helix DNA. The triple-helix DNA containing a thiol labelled single-stranded DNA (sDNA) and a thymine-rich DNA (T-rich DNA), which could be unwinded in the present of Hg(2+) to form more stable thymine-Hg(2+)-thymine (T-Hg(2+)-T) complex. T-Hg(2+)-T complex was then removed and the sDNA was left on the electrode. At this time, gold nanoparticle carrying thiol labelled cytosine-rich complementary DNA (cDNA-AuNP) could bind with the free sDNA. Meanwhile, the other free cDNA on AuNP could bind with each other in the present of Ag(+) to form the stable cytosine-Ag(+)-cytosine (C-Ag(+)-C) complex and circle amplification. Plenty of C-Ag(+)-C could form silver nanoclusters by electrochemical reduction and the striping signal of Ag could be measured for purpose of the final electrochemical detection of Hg(2+). This sensor could detect Hg(2+) over a wide concentration range from 0.1 to 130nM with a detection limit of 0.03nM. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration

    Directory of Open Access Journals (Sweden)

    Fasold Mario

    2010-04-01

    Full Text Available Abstract Background The brightness of the probe spots on expression microarrays intends to measure the abundance of specific mRNA targets. Probes with runs of at least three guanines (G in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis. Results Longer runs of three or more consecutive G along the probe sequence and in particular triple degenerated G at its solution end ((GGG1-effect are associated with exceptionally large probe intensities on GeneChip expression arrays. This intensity bias is related to non-specific hybridization and affects both perfect match and mismatch probes. The (GGG1-effect tends to increase gradually for microarrays of later GeneChip generations. It was found for DNA/RNA as well as for DNA/DNA probe/target-hybridization chemistries. Amplification of sample RNA using T7-primers is associated with strong positive amplitudes of the G-bias whereas alternative amplification protocols using random primers give rise to much smaller and partly even negative amplitudes. We applied positional dependent sensitivity models to analyze the specifics of probe intensities in the context of all possible short sequence motifs of one to four adjacent nucleotides along the 25meric probe sequence. Most of the longer motifs are adequately described using a nearest-neighbor (NN model. In contrast, runs of degenerated guanines require explicit consideration of next nearest neighbors (GGG terms. Preprocessing methods such as vsn, RMA, dChip, MAS5 and gcRMA only insufficiently remove the G-bias from data. Conclusions Positional and motif dependent sensitivity models accounts for sequence effects of oligonucleotide probe intensities. We propose a positional dependent NN+GGG hybrid model to correct the intensity bias associated with probes containing poly-G motifs. It is implemented as a single-chip based calibration

  14. Multicolour probes for sequence-specific DNA detection based on graphene oxide.

    Science.gov (United States)

    Zhu, Qing; Xiang, Dongshan; Zhang, Cuiling; Ji, Xinghu; He, Zhike

    2013-09-21

    The bifunctionality of graphene oxide (GO) which can highly adsorb single-stranded DNA (ssDNA) and effectively quench the emission of organic dyes is reasonably utilized in a multiplexed DNA detection system, achieving sensitive and selective detection of HIV, VV and EV, respectively.

  15. Detection of hepatitis A virus by hybridization with single-stranded RNA probes

    International Nuclear Information System (INIS)

    Xi, J.; Estes, M.K.; Metcalf, T.G.

    1987-01-01

    An improved method of dot-blot hybridization to detect hepatitis A virus (HAV) was developed with single-stranded RNA (ssRNA) probes. Radioactive and nonradioactive ssRNA probes were generated by in vitro transcription of HAV templates inserted into the plasmid pGEM-1. 32 P-labeled ssRNA probes were at least eightfold more sensitive than the 32 P-labeled double-stranded cDNA counterparts, whereas biotin-labeled ssRNA probes showed a sensitivity comparable with that of the 32 P-labeled double-stranded cDNA counterparts. Hybridization of HAV with the ssRNA probes at high stringency revealed specific reactions with a high signal-to-noise ratio. The differential hybridization reactions seen with probes of positive and negative sense (compared with HAV genomic RNA) were used to detect HAV in clinical and field samples. A positive/negative ratio was introduced as an indicator that permitted an semiquantitative expression of a positive HAV reaction. Good agreement of this indicator was observed with normal stool samples and with HAV-seeded samples. By using this system, HAV was detected in estuarine and freshwater samples collected from a sewage-polluted bayou in Houston and a saltwater tributary of Galveston Bay

  16. Cloning of the human androgen receptor cDNA

    International Nuclear Information System (INIS)

    Govindan, M.V.; Burelle, M.; Cantin, C.; Kabrie, C.; Labrie, F.; Lachance, Y.; Leblanc, G.; Lefebvre, C.; Patel, P.; Simard, J.

    1988-01-01

    The authors discuss how in order to define the functional domains of the human androgen receptor, complementary DNA (cDNA) clones encoding the human androgen receptor (hAR) have been isolated from a human testis λgtll cDNA library using synthetic oligonnucleotide probes, homologous to segments of the human glucocorticoid, estradiol and progesterone receptors. The cDNA clones corresponding to the human glucocorticoid, estradiol and progesterone receptors were eliminated after cross-hybridization with their respective cDNA probes and/or after restriction mapping of the cDNA clones. The remaining cDNA clones were classified into different groups after analysis by restriction digestion and cross-hybridization. Two of the largest cDNA clones from each group were inserted into an expression vector in both orientations. The linearized plasmids were used as templates in in vitro transcription with T7 RNA polymerase. Subsequent in vitro translation of the purified transcripts in rabbit reticulocyte lysate followed by sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) permitted the characterization of the encoded polyeptides. The expressed proteins larger than 30,000 Da were analyzed for their ability to bind tritium-labelled dihydrotestosterone ([ 3 H] DHT) with high affinity and specificity

  17. Technetium-99m labeled antisense probes uptake in vascular smooth muscle cells

    International Nuclear Information System (INIS)

    Zhang, Y.X.; Qin, G.M.; An, R.; Cao, G.X.; Cao, W.; Gao, Z.R.

    2002-01-01

    ex-cellular concentration between 0.05μg to 1.5μg. The SMC showed higher uptake for c-myc probe than bcl-2 probe. The normalized uptake per million cells was higher for the antisense than for the sense c-myc probe, it was also higher for the SMC in log rather than in plateau phase. Percentage uptake of bcl-2 antisense probe by the SMC was slightly lower in log phase than in plateau phase. Conclusion: These data suggested that 99m Tc- MAG 3 -DNA should be considered further as an early specific technique in noninvasive diagnosis of arteriosclerotic lesions. Increased uptake of c-myc antisense probe accompanied with diminished uptake of bcl-2 antisense probe may suggested a lesion of atherosclerosis at an early stage

  18. Chromosomal location of the human gene for DNA polymerase β

    International Nuclear Information System (INIS)

    McBride, O.W.; Zmudzka, B.Z.; Wilson, S.H.

    1987-01-01

    Inhibition studies indicate that DNA polymerase β has a synthetic role in DNA repair after exposure of mammalian cells to some types of DNA-damaging agents. The primary structure of the enzyme is highly conserved in vertebrates, and nearly full-length cDNAs for the enzyme were recently cloned from mammalian cDNA libraries. Southern blot analysis of DNA from a panel of human-rodent somatic cell hybrids, using portions of the cDNA as probe, indicates that the gene for human DNA polymerase β is single copy and located on the short arm or proximal long arm of chromosome 8 (8pter-8q22). A restriction fragment length polymorphism (RFLP) was detected in normal individuals by using a probe from the 5' end of the cDNA, and this RFLP probably is due to an insertion or duplication of DNA in 20-25% of the population. This restriction site can be used as one marker for chromosome 8 genetic linkage studies and for family studies of traits potentially involving this DNA repair gene

  19. Fiberoptic intubation through laryngeal mask airway for management of difficult airway in a child with Klippel-Feil syndrome

    Directory of Open Access Journals (Sweden)

    Ravi Bhat

    2014-01-01

    Full Text Available The ideal airway management modality in pediatric patients with syndromes like Klippel-Feil syndrome is a great challenge and is technically difficult for an anesthesiologist. Half of the patients present with the classic triad of short neck, low hairline, and fusion of cervical vertebra. Numerous associated anomalies like scoliosis or kyphosis, cleft palate, respiratory problems, deafness, genitourinary abnormalities, Sprengel′s deformity (wherein the scapulae ride high on the back, synkinesia, cervical ribs, and congenital heart diseases may further add to the difficulty. Fiberoptic bronchoscopy alone can be technically difficult and patient cooperation also becomes very important, which is difficult in pediatric patients. Fiberoptic bronchoscopy with the aid of supraglottic airway devices is a viable alternative in the management of difficult airway in children. We report a case of Klippel-Feil syndrome in an 18-month-old girl posted for cleft palate surgery. Imaging of spine revealed complete fusion of the cervical vertebrae with hypoplastic C3 and C6 vertebrae and thoracic kyphosis. We successfully managed airway in this patient by fiberoptic intubation through classic laryngeal mask airway (LMA. After intubation, we used second smaller endotracheal tube (ETT to stabilize and elongate the first ETT while removing the LMA.

  20. Nucleic acid probes as a diagnostic method for tick-borne hemoparasites of veterinary importance.

    Science.gov (United States)

    Figueroa, J V; Buening, G M

    1995-03-01

    An increased number of articles on the use of nucleic acid-based hybridization techniques for diagnostic purposes have been recently published. This article reviews nucleic acid-based hybridization as an assay to detect hemoparasite infections of economic relevance in veterinary medicine. By using recombinant DNA techniques, selected clones containing inserts of Anaplasma, Babesia, Cowdria or Theileria genomic DNA sequences have been obtained, and they are now available to be utilized as specific, highly sensitive DNA or RNA probes to detect the presence of the hemoparasite DNA in an infected animal. Either in an isotopic or non-isotopic detection system, probes have allowed scientists to test for--originally in samples collected from experimentally infected animals and later in samples collected in the field--the presence of hemoparasites during the prepatent, patent, convalescent, and chronic periods of the infection in the host. Nucleic acid probes have given researchers the opportunity to carry out genomic analysis of parasite DNA to differentiate hemoparasite species and to identify genetically distinct populations among and within isolates, strains and clonal populations. Prevalence of parasite infection in the tick vector can now be accomplished more specifically with the nucleic acid probes. Lately, with the advent of the polymerase chain reaction technique, small numbers of hemoparasites can be positively identified in the vertebrate host and tick vector. These techniques can be used to assess the veterinary epidemiological situation in a particular geographical region for the planning of control measures.

  1. Radioactive probes as diagnostic tools for rice tungro viruses

    International Nuclear Information System (INIS)

    Azzam, O.; Arboleda, M.; Reyes. J. de los

    1996-01-01

    Rice tungro bacilliform (RTBV) and rice tungro spherical viruses (RTSV) are the two viral components responsible for rice tungro disease which has seriously affected the irrigated rice ecosystem in Southeast Asia for the last 30 years. RTBV has an 8 Kb double-stranded DNA circular genome, and it is primarily responsible for induction of symptoms in infected plants. RTSV has a 12 kb single-stranded RNA genome. It does not induce any apparent symptoms in the infected plant, and it is transmitted by greenleafhopper. RTBV depends upon RTSV for its own transmission. The two viruses are limited to the vascular tissue of the rice plant and are present at a low titer. Most of the detection methods used for the identification of these viruses have relied on the virus protein properties and therefore, early detection of the virus activity was not possible. We were interested in evaluating tissue printing, dot blot, and southern techniques for early detection of virus nucleic acids in rice plant using radioactive and non radioactive probes. 32 P-labeled T7 or SP6 RNA polymerase transcripts complementary to the RTBV genome and RTSV coat protein genes were used as probes of the positive stand of both viruses. For nonradioactive probes, RTBV DNA genome was labeled using the ECL detection kit (Amersham). Preliminary results show that viral nucleic acids of RTBV and RTSV could be detected using both labelling systems. Non radioactive probes were comparable in their sensitivity to the radioactive probes. Less than 100 pg of viral DNA was detected in the dot-blot assays. More data will be presented to compare the efficiency and reliability of these two techniques in detecting early virus activity in the rice plant. (author)

  2. Rad-Tolerant, Thermally Stable, High-Speed Fiber-Optic Network for Harsh Environments

    Science.gov (United States)

    Leftwich, Matt; Hull, Tony; Leary, Michael; Leftwich, Marcus

    2013-01-01

    Future NASA destinations will be challenging to get to, have extreme environmental conditions, and may present difficulty in retrieving a spacecraft or its data. Space Photonics is developing a radiation-tolerant (rad-tolerant), high-speed, multi-channel fiber-optic transceiver, associated reconfigurable intelligent node communications architecture, and supporting hardware for intravehicular and ground-based optical networking applications. Data rates approaching 3.2 Gbps per channel will be achieved.

  3. A Novel Open Tubular Capillary Electrochromatographic Method for Differentiating the DNA Interaction Affinity of Environmental Contaminants.

    Directory of Open Access Journals (Sweden)

    Lucia D'Ulivo

    Full Text Available The interaction of chemicals with DNA may lead to genotoxicity, mutation or carcinogenicity. A simple open tubular capillary electrochromatographic method is proposed to rapidly assess the interaction affinity of three environmental contaminants (1,4-phenylenediamine, pyridine and 2,4-diaminotoluene to DNA by measuring their retention in the capillaries coated with DNA probes. DNA oligonucleotide probes were immobilized on the inner wall of a fused silica capillary that was first derivatized with 3-(aminopropyl-triethoxysilane (APTES. The difference in retention times and factors was considered as the difference in interaction affinity of the contaminants to the DNA probes. The interaction of the contaminants with both double-stranded (dsDNA and single-stranded DNA (ssDNA coatings was compared. Retention factors of 1,4-phenylenediamine, pyridine and 2,4-diaminotoluene in the capillary coated with ssDNA probe were 0.29, 0.42, and 0.44, respectively. A similar trend was observed in the capillary coated with dsDNA, indicating that 2,4-diaminotoluene has the highest affinity among the three contaminants. The relative standard deviation (RSD for the retention factors was in the range of 0.05-0.69% (n = 3. The results demonstrated that the developed technique could be applied for preliminary screening purpose to provide DNA interaction affinity information of various environmental contaminants.

  4. DNA nanotechnology-enabled biosensors.

    Science.gov (United States)

    Chao, Jie; Zhu, Dan; Zhang, Yinan; Wang, Lianhui; Fan, Chunhai

    2016-02-15

    Biosensors employ biological molecules to recognize the target and utilize output elements which can translate the biorecognition event into electrical, optical or mass-sensitive signals to determine the quantities of the target. DNA-based biosensors, as a sub-field to biosensor, utilize DNA strands with short oligonucleotides as probes for target recognition. Although DNA-based biosensors have offered a promising alternative for fast, simple and cheap detection of target molecules, there still exist key challenges including poor stability and reproducibility that hinder their competition with the current gold standard for DNA assays. By exploiting the self-recognition properties of DNA molecules, researchers have dedicated to make versatile DNA nanostructures in a highly rigid, controllable and functionalized manner, which offers unprecedented opportunities for developing DNA-based biosensors. In this review, we will briefly introduce the recent advances on design and fabrication of static and dynamic DNA nanostructures, and summarize their applications for fabrication and functionalization of DNA-based biosensors. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

    Science.gov (United States)

    Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

    2017-06-28

    Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

  6. Measurement of locus copy number by hybridisation with amplifiable probes

    Science.gov (United States)

    Armour, John A. L.; Sismani, Carolina; Patsalis, Philippos C.; Cross, Gareth

    2000-01-01

    Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicroscopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader–Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications. PMID:10606661

  7. Measurement of locus copy number by hybridisation with amplifiable probes.

    Science.gov (United States)

    Armour, J A; Sismani, C; Patsalis, P C; Cross, G

    2000-01-15

    Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicro-scopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader-Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications.

  8. Detection of hepatitis B virus DNA sequences in infected hepatocytes by in situ cytohybridisation

    International Nuclear Information System (INIS)

    Gowans, E.J.; Burrell, C.J.; Jilbert, A.R.; Marmion, B.P.

    1981-01-01

    Plasmid pHBV 114 DNA, which contains 73% of the genome of hepatitis B virus (HBV), was radiolabelled with tritium to 1-2 X 10(8) dpm/microgram by nick translation and used as a radioactive probe to detect HBV DNA present in sections of infected liver tissue by in situ hybridisation followed by autoradiography. Factors affecting the sensitivity of the reaction were examined, including different methods of fixation, hybridisation time, temperature, and buffers. The specificity of the reaction for detecting viral DNA was carefully established by the use of unrelated DNA probes, pretreatment of sections with DNAase, and comparing the stability of the binding of DNA probe at different temperatures, with the melting curve of double-stranded DNA in solution. In the one liver studied in detail, cells containing large amounts of viral DNA were distributed in foci corresponding to areas containing morphologically damaged hepatocytes. This observation suggested a relationship between active viral replication and cell damage. Viral DNA was found mainly in the cytoplasm, although a minority of nuclei in these foci were also positive

  9. Fiberoptic Applications in Sensors and Telemetry for the Electric Power Industry

    Science.gov (United States)

    Werneck, M. M.; Silva, A. V.; Souza, N. C. C.; Miguel, M. A. L.; Beres, C.; Yugue, E. S.; Carvalho, C. C.; Maciel, F. L.; Silva-Neto, J.; Guimarães, C. R. F.; Allil, R. C. S. B.; Baliosian, J. A. G.

    2008-10-01

    This presentation features the origin and the work of the Photonics and Instrumentation Laboratory (LIF) in instrumentation, fiberoptic sensors and POF technology. LIF started its work in 1986, twenty and two years ago, with only one lecturer and a few students. The first project was the development of the first Brazilian plotter with the purpose, at the time, to substitute expensive imported technology. LIF has today 25 people between students, technicians, scientists, engineers and teachers. We present here several successful projects of fiberoptic sensors using both silica and POF fibers, most of them applied on the field mainly for the electric power industry. Described are: a oil leakage sensor in petroleum hoses, PMMA evanescent sensors, temperature by the ruby fluorescence phenomenon, a current sensor calibrator for 500 kV current transformers, a leakage sensor to measure 500 kV insulators in extra-high voltage transmission line, etc. Many of the sensors presented here have been tested in the field, patented and transferred to the industry. We have also technical collaboration with several industries in Brazil, one of them a spin-off from LIF. Our objective is to become a reference centre in POF technology in Latin America and for this we are intended to keep producing "out of the shelves" POF technology and innovative industry solutions for many areas.

  10. Broadband light source for fiber-optic measurement system in spaceborne applications

    Science.gov (United States)

    Rößner, Max R.; Müller, Mathias S.; Buck, Thorbjörn C.; Koch, Alexander W.

    2012-01-01

    Measuring temperatures, mechanical loads and derived quantities precisely and reliably play an important role in spaceflight. With spacecraft becoming increasingly complex, upscaling of present telemetry techniques can become cumbersome. Additionally, there are entirely new sensory requirements, resulting from emerging technologies such as smart structures, active vibration damping and composite material health monitoring. It has been demonstrated in preceding studies that these measurements can be advantageously and efficiently carried out by means of fiber-optic systems. The most prominent fiber-optic strain and temperature sensor is the fiber Bragg grating. Typically, multiple fiber Bragg gratings are used to translate entire temperature and strain fields into an optical wavelength information. For the interrogation of these sensors, a broadband or scanning light source is required. Additional requirements with respect to the light source are high intensity and unpolarized illumination of the gratings. These constraints can be met by a light source that is based on amplified spontaneous emission in a rare-earth-doped fiber. In the presented work, a compact light source, adapted for measurement applications and targeted towards space applications, has been developed. The design of this light source is presented, as well as its implementation. The light source has been designed and tested for selected core aspects of space robustness and the results of these tests are summarized.

  11. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

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

  12. An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Takahashi, Norio; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-05-01

    We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32 P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

  13. On-bead fluorescent DNA nanoprobes to analyze base excision repair activities

    Energy Technology Data Exchange (ETDEWEB)

    Gines, Guillaume; Saint-Pierre, Christine; Gasparutto, Didier, E-mail: didier.gasparutto@cea.fr

    2014-02-17

    Graphical abstract: -- Highlights: •On magnetic beads fluorescent enzymatic assays. •Simple, easy, non-radioactive and electrophoresis-free functional assay. •Lesion-containing hairpin DNA probes are selective for repair enzymes. •The biosensing platform allows the measurement of DNA repair activities from purified enzymes or within cell free extracts. -- Abstract: DNA integrity is constantly threatened by endogenous and exogenous agents that can modify its physical and chemical structure. Changes in DNA sequence can cause mutations sparked by some genetic diseases or cancers. Organisms have developed efficient defense mechanisms able to specifically repair each kind of lesion (alkylation, oxidation, single or double strand break, mismatch, etc). Here we report the adjustment of an original assay to detect enzymes’ activity of base excision repair (BER), that supports a set of lesions including abasic sites, alkylation, oxidation or deamination products of bases. The biosensor is characterized by a set of fluorescent hairpin-shaped nucleic acid probes supported on magnetic beads, each containing a selective lesion targeting a specific BER enzyme. We have studied the DNA glycosylase alkyl-adenine glycosylase (AAG) and the human AP-endonuclease (APE1) by incorporating within the DNA probe a hypoxanthine lesion or an abasic site analog (tetrahydrofuran), respectively. Enzymatic repair activity induces the formation of a nick in the damaged strand, leading to probe's break, that is detected in the supernatant by fluorescence. The functional assay allows the measurement of DNA repair activities from purified enzymes or in cell-free extracts in a fast, specific, quantitative and sensitive way, using only 1 pmol of probe for a test. We recorded a detection limit of 1 μg mL{sup −1} and 50 μg mL{sup −1} of HeLa nuclear extracts for APE1 and AAG enzymes, respectively. Finally, the on-bead assay should be useful to screen inhibitors of DNA repair

  14. Laser-based ultrasonics by dual-probe interferometer detection and narrow-band ultrasound generation

    Science.gov (United States)

    Huang, Jin

    1993-01-01

    successfully applied to the detection of cracks emanating from rivet holes in aircraft fuselage panel samples. A compact fiber-optic dual-probe interferometer has also been developed and applied to the above mentioned problem of crack detection. Results agree well with those obtained with a bulk LBU system.

  15. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA...... structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

  16. DNA microarray technique for detecting food-borne pathogens

    Directory of Open Access Journals (Sweden)

    Xing GAO

    2012-08-01

    Full Text Available Objective To study the application of DNA microarray technique for screening and identifying multiple food-borne pathogens. Methods The oligonucleotide probes were designed by Clustal X and Oligo 6.0 at the conserved regions of specific genes of multiple food-borne pathogens, and then were validated by bioinformatic analyses. The 5' end of each probe was modified by amino-group and 10 Poly-T, and the optimized probes were synthesized and spotted on aldehyde-coated slides. The bacteria DNA template incubated with Klenow enzyme was amplified by arbitrarily primed PCR, and PCR products incorporated into Aminoallyl-dUTP were coupled with fluorescent dye. After hybridization of the purified PCR products with DNA microarray, the hybridization image and fluorescence intensity analysis was acquired by ScanArray and GenePix Pro 5.1 software. A series of detection conditions such as arbitrarily primed PCR and microarray hybridization were optimized. The specificity of this approach was evaluated by 16 different bacteria DNA, and the sensitivity and reproducibility were verified by 4 food-borne pathogens DNA. The samples of multiple bacteria DNA and simulated water samples of Shigella dysenteriae were detected. Results Nine different food-borne bacteria were successfully discriminated under the same condition. The sensitivity of genomic DNA was 102 -103pg/ μl, and the coefficient of variation (CV of the reproducibility of assay was less than 15%. The corresponding specific hybridization maps of the multiple bacteria DNA samples were obtained, and the detection limit of simulated water sample of Shigella dysenteriae was 3.54×105cfu/ml. Conclusions The DNA microarray detection system based on arbitrarily primed PCR can be employed for effective detection of multiple food-borne pathogens, and this assay may offer a new method for high-throughput platform for detecting bacteria.

  17. DAQ application of PC oscilloscope for chaos fiber-optic fence system based on LabVIEW

    Science.gov (United States)

    Lu, Manman; Fang, Nian; Wang, Lutang; Huang, Zhaoming; Sun, Xiaofei

    2011-12-01

    In order to obtain simultaneously high sample rate and large buffer in data acquisition (DAQ) for a chaos fiber-optic fence system, we developed a double-channel high-speed DAQ application of a digital oscilloscope of PicoScope 5203 based on LabVIEW. We accomplished it by creating call library function (CLF) nodes to call the DAQ functions in the two dynamic link libraries (DLLs) of PS5000.dll and PS5000wrap.dll provided by Pico Technology Company. The maximum real-time sample rate of the DAQ application can reach 1GS/s. We can control the resolutions of the application at the sample time and data amplitudes by changing their units in the block diagram, and also control the start and end times of the sampling operations. The experimental results show that the application has enough high sample rate and large buffer to meet the demanding DAQ requirements of the chaos fiber-optic fence system.

  18. DNA-based species detection capabilities using laser transmission spectroscopy.

    Science.gov (United States)

    Mahon, A R; Barnes, M A; Li, F; Egan, S P; Tanner, C E; Ruggiero, S T; Feder, J L; Lodge, D M

    2013-01-06

    Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.

  19. Gene probes : principles and protocols [Methods in molecular biology, v. 179

    National Research Council Canada - National Science Library

    Rapley, Ralph; Aquino de Muro, Marilena

    2002-01-01

    ... of labeled DNA has allowed genes to be mapped to single chromosomes and in many cases to a single chromosome band, promoting significant advance in human genome mapping. Gene Probes: Principles and Protocols presents the principles for gene probe design, labeling, detection, target format, and hybridization conditions together with detailed protocols, accom...

  20. Continuously tunable nucleic acid hybridization probes.

    Science.gov (United States)

    Wu, Lucia R; Wang, Juexiao Sherry; Fang, John Z; Evans, Emily R; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J; Beechem, Joseph; Zhang, David Yu

    2015-12-01

    In silico-designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.

  1. Fly-By-Light/Power-By-Wire Fault-Tolerant Fiber-Optic Backplane

    Science.gov (United States)

    Malekpour, Mahyar R.

    2002-01-01

    The design and development of a fault-tolerant fiber-optic backplane to demonstrate feasibility of such architecture is presented. The simulation results of test cases on the backplane in the advent of induced faults are presented, and the fault recovery capability of the architecture is demonstrated. The architecture was designed, developed, and implemented using the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL). The architecture was synthesized and implemented in hardware using Field Programmable Gate Arrays (FPGA) on multiple prototype boards.

  2. Synthetic LNA/DNA nano-scaffolds for highly efficient diagnostics of nucleic acids and autoimmune antibodies

    DEFF Research Database (Denmark)

    Astakhova, Irina Kira

    2014-01-01

    ) strands and a series of fluorescent azides. The multiply labeled fluorescent LNA/DNA probes prepared herein generally display high binding affinity to complementary DNA/RNA, high quantum yields and, hence, high fluorescence brightness values. With the novel fluorescent probes, specific sensing...

  3. Fiber-optic based instrumentation for water and air monitoring

    International Nuclear Information System (INIS)

    MacCraith, B.D.

    1991-01-01

    In this paper real-time in-situ water and air monitoring capabilities based on fiber-optic sensing technology are described. This relatively new technology combines advances in fiber optic and optoelectronics with chemical spectorscopic techniques to enable field environmental monitoring of sub ppm quantities of specific pollutants. The advantages of this technology over conventional sampling methods are outlined. As it is the more developed area the emphasis is on water quality monitoring rather than air. Examples of commercially available, soon-to be available and laboratory systems are presented. One such example is a system used to detect hydrocarbon spills and leaking of underground hydrocarbon storage tanks

  4. Preliminary field demonstration of a fiber-optic TCE sensor

    International Nuclear Information System (INIS)

    Angel, S.M.; Langry, K.; Roe, J.; Colston, B.W. Jr.; Daley, P.F.; Milanovich, F.P.

    1991-02-01

    We have developed a differential-absorption fiber-optic sensor for use in groundwater and vadose zone monitoring of certain volatile organochlorines. The principle of detection is a quantitative, irreversible chemical reaction that forms visible light-absorbing products. The sensor has been evaluated against gas chromatographic (GC) standard measurements and has demonstrated accuracy and sensitivity sufficient for the environmental monitoring of trace levels of trichloroethylene (TCE) and chloroform. This sensor is currently under evaluation in monitoring well and vadose zone applications. In this paper, we describe the principles of the existing single measurement sensor technology and show preliminary field-test results. 3 refs., 8 figs

  5. An Internalin A Probe-Based Genosensor for Listeria monocytogenes Detection and Differentiation

    Directory of Open Access Journals (Sweden)

    Laura Bifulco

    2013-01-01

    Full Text Available Internalin A (InlA, a protein required for Listeria monocytogenes virulence, is encoded by the inlA gene, which is only found in pathogenic strains of this genus. One of the best ways to detect and confirm the pathogenicity of the strain is the detection of one of the virulence factors produced by the microorganism. This paper focuses on the design of an electrochemical genosensor used to detect the inlA gene in Listeria strains without labelling the target DNA. The electrochemical sensor was obtained by immobilising an inlA gene probe (single-stranded oligonucleotide on the surfaces of screen-printed gold electrodes (Au-SPEs by means of a mercaptan-activated self-assembled monolayer (SAM. The hybridisation reaction occurring on the electrode surface was electrochemically transduced by differential pulse voltammetry (DPV using methylene blue (MB as an indicator. The covalently immobilised single-stranded DNA was able to selectively hybridise to its complementary DNA sequences in solution to form double-stranded DNA on the gold surface. A significant decrease of the peak current of the voltammogram (DPV upon hybridisation of immobilised ssDNA was recorded. Whole DNA samples of L. monocytogenes strains could be discriminated from other nonpathogenic Listeria species DNA with the inlA gene DNA probe genosensor.

  6. DNA-Based Applications in Nanobiotechnology

    Directory of Open Access Journals (Sweden)

    Khalid M. Abu-Salah

    2010-01-01

    Full Text Available Biological molecules such as deoxyribonucleic acid (DNA have shown great potential in fabrication and construction of nanostructures and devices. The very properties that make DNA so effective as genetic material also make it a very suitable molecule for programmed self-assembly. The use of DNA to assemble metals or semiconducting particles has been extended to construct metallic nanowires and functionalized nanotubes. This paper highlights some important aspects of conjugating the unique physical properties of dots or wires with the remarkable recognition capabilities of DNA which could lead to miniaturizing biological electronics and optical devices, including biosensors and probes. Attempts to use DNA-based nanocarriers for gene delivery are discussed. In addition, the ecological advantages and risks of nanotechnology including DNA-based nanobiotechnology are evaluated.

  7. 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

  8. A fiber-optic strain measurement and quench localization system for use in superconducting accelerator dipole magnets

    NARCIS (Netherlands)

    van Oort, J.M.; Scanlan, Ronald M.; ten Kate, Herman H.J.

    1995-01-01

    A novel fiber-optic measurement system for superconducting accelerator magnets is described. The principal component is an extrinsic Fabry-Perot interferometer to determine localized strain and stress in coil windings. The system can be used either as a sensitive relative strain measurement system

  9. Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray.

    Science.gov (United States)

    Kennedy, Laura; Vass, J Keith; Haggart, D Ross; Moore, Steve; Burczynski, Michael E; Crowther, Dan; Miele, Gino

    2008-08-25

    Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgene() RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2() enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgene() blood samples also advocate a short, fixed room temperature storage time for all PAXgene() blood samples collected for the purposes of global transcriptional profiling in clinical studies.

  10. Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene™ Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray

    Science.gov (United States)

    Kennedy, Laura; Vass, J. Keith; Haggart, D. Ross; Moore, Steve; Burczynski, Michael E.; Crowther, Dan; Miele, Gino

    2008-01-01

    Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgene™ RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2™ enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgene™ blood samples also advocate a short, fixed room temperature storage time for all PAXgene™ blood samples collected for the purposes of global transcriptional profiling in clinical studies. PMID:19578521

  11. Technical aspects of typing for HLA-DP alleles using allele-specific DNA in vitro amplification and sequence-specific oligonucleotide probes. Detection of single base mismatches

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P

    1990-01-01

    The polymerase chain reaction (PCR) is an effective method for in vitro DNA amplification which combined with probing with synthetic oligonucleotides can be used for, e.g., HLA-typing. We have studied the technical aspects of HLA-DP typing with the technique. DNA from mononuclear nucleated cells...... was extracted with either a simple salting out method or phenol/chloroform. Both DNAs could be readily used for PCR. The MgC2 concentration of the PCR buffer and the annealing temperature of the thermal cycle of the PCR were the two most important variables. The MgCl2 concentration and the temperature must...... be carefully titrated for each primer pair in the PCR. The influence of mismatches between the primer and the DNA template were studied and we found that, by using primers differing only from each other at the 3' end, cross-amplification of closely homologous alleles could be avoided. Thus, single base...

  12. Electrokinetic acceleration of DNA hybridization in microsystems.

    Science.gov (United States)

    Lei, Kin Fong; Wang, Yun-Hsiang; Chen, Huai-Yi; Sun, Jia-Hong; Cheng, Ji-Yen

    2015-06-01

    In this work, electrokinetic acceleration of DNA hybridization was investigated by different combinations of frequencies and amplitudes of actuating electric signals. Because the frequencies from low to high can induce different kinds of electrokinetic forces, i.e., electroosmotic to electrothermal forces, this work provides an in-depth investigation of electrokinetic enhanced hybridization. Concentric circular Cr/Au microelectrodes of 350 µm in diameter were fabricated on a glass substrate and probe DNA was immobilized on the electrode surface. Target DNA labeled with fluorescent dyes suspending in solution was then applied to the electrode. Different electrokinetic forces were induced by the application of different electric signals to the circular microelectrodes. Local microfluidic vortexes were generated to increase the collision efficiency between the target DNA suspending in solution and probe DNA immobilized on the electrode surface. DNA hybridization on the electrode surface could be accelerated by the electrokinetic forces. The level of hybridization was represented by the fluorescent signal intensity ratio. Results revealed that such 5-min dynamic hybridization increased 4.5 fold of signal intensity ratio as compared to a 1-h static hybridization. Moreover, dynamic hybridization was found to have better differentiation ability between specific and non-specific target DNA. This study provides a strategy to accelerate DNA hybridization in microsystems. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. One-by-one single-molecule detection of mutated nucleobases by monitoring tunneling current using a DNA tip.

    Science.gov (United States)

    Bui, Phuc Tan; Nishino, Tomoaki; Shiigi, Hiroshi; Nagaoka, Tsutomu

    2015-01-31

    A DNA molecule was utilized as a probe tip to achieve single-molecule genetic diagnoses. Hybridization of the probe and target DNAs resulted in electron tunneling along the emergent double-stranded DNA. Simple stationary monitoring of the tunneling current leads to single-molecule DNA detection and discovery of base mismatches and methylation.

  14. Mediated Electron Transfer at Vertically Aligned Single-Walled Carbon Nanotube Electrodes During Detection of DNA Hybridization

    Science.gov (United States)

    Wallen, Rachel; Gokarn, Nirmal; Bercea, Priscila; Grzincic, Elissa; Bandyopadhyay, Krisanu

    2015-06-01

    Vertically aligned single-walled carbon nanotube (VASWCNT) assemblies are generated on cysteamine and 2-mercaptoethanol (2-ME)-functionalized gold surfaces through amide bond formation between carboxylic groups generated at the end of acid-shortened single-walled carbon nanotubes (SWCNTs) and amine groups present on the gold surfaces. Atomic force microscopy (AFM) imaging confirms the vertical alignment mode of SWCNT attachment through significant changes in surface roughness compared to bare gold surfaces and the lack of any horizontally aligned SWCNTs present. These SWCNT assemblies are further modified with an amine-terminated single-stranded probe-DNA. Subsequent hybridization of the surface-bound probe-DNA in the presence of complementary strands in solution is followed using impedance measurements in the presence of Fe(CN)6 3-/4- as the redox probe in solution, which show changes in the interfacial electrochemical properties, specifically the charge-transfer resistance, due to hybridization. In addition, hybridization of the probe-DNA is also compared when it is attached directly to the gold surfaces without any intermediary SWCNTs. Contrary to our expectations, impedance measurements show a decrease in charge-transfer resistance with time due to hybridization with 300 nM complementary DNA in solution with the probe-DNA attached to SWCNTs. In contrast, an increase in charge-transfer resistance is observed with time during hybridization when the probe-DNA is attached directly to the gold surfaces. The decrease in charge-transfer resistance during hybridization in the presence of VASWCNTs indicates an enhancement in the electron transfer process of the redox probe at the VASWCNT-modified electrode. The results suggest that VASWCNTs are acting as mediators of electron transfer, which facilitate the charge transfer of the redox probe at the electrode-solution interface.

  15. Comparison of five DNA quantification methods

    DEFF Research Database (Denmark)

    Nielsen, Karsten; Mogensen, Helle Smidt; Hedman, Johannes

    2008-01-01

    Six commercial preparations of human genomic DNA were quantified using five quantification methods: UV spectrometry, SYBR-Green dye staining, slot blot hybridization with the probe D17Z1, Quantifiler Human DNA Quantification kit and RB1 rt-PCR. All methods measured higher DNA concentrations than...... Quantification kit in two experiments. The measured DNA concentrations with Quantifiler were 125 and 160% higher than expected based on the manufacturers' information. When the Quantifiler human DNA standard (Raji cell line) was replaced by the commercial human DNA preparation G147A (Promega) to generate the DNA...... standard curve in the Quantifiler Human DNA Quantification kit, the DNA quantification results of the human DNA preparations were 31% higher than expected based on the manufacturers' information. The results indicate a calibration problem with the Quantifiler human DNA standard for its use...

  16. Identification of nodal tissue in the living heart using rapid scanning fiber-optics confocal microscopy and extracellular fluorophores.

    Science.gov (United States)

    Huang, Chao; Kaza, Aditya K; Hitchcock, Robert W; Sachse, Frank B

    2013-09-01

    Risks associated with pediatric reconstructive heart surgery include injury of the sinoatrial node (SAN) and atrioventricular node (AVN), requiring cardiac rhythm management using implantable pacemakers. These injuries are the result of difficulties in identifying nodal tissues intraoperatively. Here we describe an approach based on confocal microscopy and extracellular fluorophores to quantify tissue microstructure and identify nodal tissue. Using conventional 3-dimensional confocal microscopy we investigated the microstructural arrangement of SAN, AVN, and atrial working myocardium (AWM) in fixed rat heart. AWM exhibited a regular striated arrangement of the extracellular space. In contrast, SAN and AVN had an irregular, reticulated arrangement. AWM, SAN, and AVN tissues were beneath a thin surface layer of tissue that did not obstruct confocal microscopic imaging. Subsequently, we imaged tissues in living rat hearts with real-time fiber-optics confocal microscopy. Fiber-optics confocal microscopy images resembled images acquired with conventional confocal microscopy. We investigated spatial regularity of tissue microstructure from Fourier analysis and second-order image moments. Fourier analysis of fiber-optics confocal microscopy images showed that the spatial regularity of AWM was greater than that of nodal tissues (37.5 ± 5.0% versus 24.3 ± 3.9% for SAN and 23.8 ± 3.7% for AVN; Pfiber-optics confocal microscopy. Application of the approach in pediatric reconstructive heart surgery may reduce risks of injuring nodal tissues.

  17. Fiber-optic transmission system information for the testing of active phased antenna arrays in an anechoic chamber.

    Science.gov (United States)

    Saveleiv, I. K.; Sharova, N. V.; Tarasenko, M. Yu; Yalunina, T. R.; Davydov, V. V.; Rud', V. Yu

    2017-11-01

    The results of the research of the developed fiber-optic transmission systems for analog high frequency signal are represented. On its basis, a new method to identify various structural defects in the active phased antenna arrays is elaborated.

  18. DNA Origami: Folded DNA-Nanodevices That Can Direct and Interpret Cell Behavior

    Science.gov (United States)

    Kearney, Cathal J.; Lucas, Christopher R.; O'Brien, Fergal J.; Castro, Carlos E.

    2016-01-01

    DNA origami is a DNA-based nanotechnology that utilizes programmed combinations of short complementary oligonucleotides to fold a large single strand of DNA into precise 2-D and 3-D shapes. The exquisite nanoscale shape control of this inherently biocompatible material is combined with the potential to spatially address the origami structures with diverse cargos including drugs, antibodies, nucleic acid sequences, small molecules and inorganic particles. This programmable flexibility enables the fabrication of precise nanoscale devices that have already shown great potential for biomedical applications such as: drug delivery, biosensing and synthetic nanopore formation. In this Progress Report, we will review the advances in the DNA origami field since its inception several years ago and then focus on how these DNA-nanodevices can be designed to interact with cells to direct or probe their behavior. PMID:26840503

  19. Cloning and sequencing of cDNA encoding human DNA topoisomerase II and localization of the gene to chromosome region 17q21-22

    International Nuclear Information System (INIS)

    Tsai-Pflugfelder, M.; Liu, L.F.; Liu, A.A.; Tewey, K.M.; Whang-Peng, J.; Knutsen, T.; Huebner, K.; Croce, C.M.; Wang, J.C.

    1988-01-01

    Two overlapping cDNA clones encoding human DNA topoisomerase II were identified by two independent methods. In one, a human cDNA library in phage λ was screened by hybridization with a mixed oligonucleotide probe encoding a stretch of seven amino acids found in yeast and Drosophila DNA topoisomerase II; in the other, a different human cDNA library in a λgt11 expression vector was screened for the expression of antigenic determinants that are recognized by rabbit antibodies specific to human DNA topoisomerase II. The entire coding sequences of the human DNA topoisomerase II gene were determined from these and several additional clones, identified through the use of the cloned human TOP2 gene sequences as probes. Hybridization between the cloned sequences and mRNA and genomic DNA indicates that the human enzyme is encoded by a single-copy gene. The location of the gene was mapped to chromosome 17q21-22 by in situ hybridization of a cloned fragment to metaphase chromosomes and by hybridization analysis with a panel of mouse-human hybrid cell lines, each retaining a subset of human chromosomes

  20. Rapid identification of DNA-binding proteins by mass spectrometry

    DEFF Research Database (Denmark)

    Nordhoff, E.; Korgsdam, A.-M.; Jørgensen, H.F.

    1999-01-01

    We report a protocol for the rapid identification of DNA-binding proteins. Immobilized DNA probes harboring a specific sequence motif are incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by matrix-assisted laser desorption/ionization time-of-flight mass...... was validated by the identification of known prokaryotic and eukaryotic DNA-binding proteins, and its use provided evidence that poly(ADP-ribose) polymerase exhibits DNA sequence-specific binding to DNA....

  1. Sub–100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA

    Science.gov (United States)

    Woehrstein, Johannes B.; Strauss, Maximilian T.; Ong, Luvena L.; Wei, Bryan; Zhang, David Y.; Jungmann, Ralf; Yin, Peng

    2017-01-01

    Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness. To address this challenge, we introduce metafluorophores, which are constructed as DNA nanostructure–based fluorescent probes with digitally tunable optical properties. Each metafluorophore is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact sub–100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 × 60 nm2, substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and photostability and demonstrated a palette of 124 virtual colors. Using these probes as fluorescent barcodes, we implemented an assay for multiplexed quantification of nucleic acids. Additionally, we demonstrated the triggered in situ self-assembly of fluorescent DNA nanostructures with prescribed brightness upon initial hybridization to a nucleic acid target. PMID:28691083

  2. Fiber-Optic Sensing System: Overview, Development and Deployment in Flight at NASA

    Science.gov (United States)

    Chan, Hon Man; Parker, Allen R.; Piazza, Anthony; Richards, W. Lance

    2015-01-01

    An overview of the research and technological development of the fiber-optic sensing system (FOSS) at the National Aeronautics and Space Administration Armstrong Flight Research Center (NASA AFRC) is presented. Theory behind fiber Bragg grating (FBG) sensors, as well as interrogation technique based on optical frequency domain reflectometry (OFDR) is discussed. Assessment and validation of FOSS as an accurate measurement tool for structural health monitoring is realized in the laboratory environment as well as large-scale flight deployment.

  3. Which Flexible Ureteroscopes (Digital vs. Fiber-Optic) Can Easily Reach the Difficult Lower Pole Calices and Have Better End-Tip Deflection: In Vitro Study on K-Box. A PETRA Evaluation.

    Science.gov (United States)

    Dragos, Laurian B; Somani, Bhaskar K; Sener, Emre T; Buttice, Salvatore; Proietti, Silvia; Ploumidis, Achilles; Iacoboaie, Catalin T; Doizi, Steeve; Traxer, Olivier

    2017-07-01

    Modern flexible ureteroscopes (fURSs) have good deflection, but despite this, approaching an acute angled calix can still be difficult. The goals of our in vitro study were to assess the ability of the available modern fURSs to effectively access the sharp angled calices and to compare the end-tip deflection of the various fiber-optic and digital fURSs. Using a bench-training model for FURS (K-Box, Porgès-Coloplast), we tried to access an acute angled calix with nine different fURSs (BOA vision, COBRA vision, R.Wolf; FLEX X 2 , FLEX Xc, K.Storz; LithoVue, Boston Scientific; URF-P5, URF-P6, URF-V, URF-V2, Olympus). Passing the fURSs through a ureteral access sheath (ReTrace, Porgès-Coloplast), the maximum end-tip deflection for every fURS was measured with the tip extended out from the sheath at 1, 2, 3, and 4 cm. Two ranking methods were designed for scoring the fURSs, one based on total ranking points and the other on total degrees of deflection. While all fiber-optic fURSs (except URF-P6) were able to access the sharp angled calix, none of the digital fURSs (except FLEX Xc) reached the difficult angled calix. Similarly, all fiber-optic fURSs had better end-tip deflection compared with the digital fURSs, except FLEX Xc, which was as deflectable as the fiber-optic fURSs. The fURSs showed an end-tip deflection (median difference of almost 21°) in favor of fiber-optic fURSs. Based on the scoring, the highest ranked fURS (best deflection) was FLEX X2 and the lowest ranked fURS (worst deflection) was URF-V2. Digital fURSs were less effective in accessing the sharp angled calix and they had lesser end-tip deflection compared with the fiber-optic counterparts. When approaching a difficult lower pole calix, it might be better to use a fiber-optic fURS.

  4. Diagnosis of canine visceral leishmaniasis with radiolabelled probes: comparison of the kDNA PCR-hybridization with three molecular methods in different clinical samples

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Aline Leandra C.; Ferreira, Sidney A.; Carregal, Virginia M.; Andrade, Antero Silva R., E-mail: antero@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil). Lab. de Radiobiologia; Melo, Maria N., E-mail: melo@icb.ufmg.br [Departamento de Parasitologia. Instituto de Ciencias Biologicas. Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil)

    2011-07-01

    Leishmania (Leishmania) chagasi is responsible for visceral leishmaniasis (VL) in Brazil and the dog is the main domestic reservoir. Disease control is based on the elimination of infected animals and the use of a sensitive and specific diagnostic test is necessary. The Brazilian VL control program emphasizes serologic surveys, mainly using the enzyme-linked immunosorbent assay (ELISA) and the immunofluorescence antibody test (IFAT), followed by the elimination of the seropositive dogs. However, these techniques present limitations in terms of sensitivity and specificity. The Polymerase Chain Reaction (PCR) associated to hybridization with DNA probes labeled with {sup 32}P has been recognized as a valuable tool for Leishmania identification. In this study, the sensitivity of kDNA PCR hybridization method was compared with three other molecular methods: Internal Transcribed Spacer 1 Nested PCR (ITS-1nPCR), Leishmania nested PCR (LnPCR) and Seminested kDNA PCR (kDNA snPCR). The comparison was performed in different clinical specimens: conjunctival swab, skin, blood and bone marrow. A group of thirty symptomatic dogs, positive in the parasitological and serological tests, was used. When. The techniques targeting kDNA mini-circles (kDNA snPCR and KDNA PCR-hybridization) showed the worst result for blood samples. The KDNA-PCR hybridization showed the best sensitivity for conjunctival swab. By comparing the samples on the basis of positivity obtained by the sum of all methods, the blood showed the worst outcome (71/120).The bone marrow showed the highest positivity (106/120), followed by conjunctival swab (100/120) and skin (89/120). Since the bone marrow samples are unsuitable for routine epidemiological surveys, the conjunctival swab was recommended because it allows high sensitivity, especially when associated with kDNA PCR hybridization method, and is a noninvasive sampling method. (author)

  5. Diagnosis of canine visceral leishmaniasis with radiolabelled probes: comparison of the kDNA PCR-hybridization with three molecular methods in different clinical samples

    International Nuclear Information System (INIS)

    Ferreira, Aline Leandra C.; Ferreira, Sidney A.; Carregal, Virginia M.; Andrade, Antero Silva R.

    2011-01-01

    Leishmania (Leishmania) chagasi is responsible for visceral leishmaniasis (VL) in Brazil and the dog is the main domestic reservoir. Disease control is based on the elimination of infected animals and the use of a sensitive and specific diagnostic test is necessary. The Brazilian VL control program emphasizes serologic surveys, mainly using the enzyme-linked immunosorbent assay (ELISA) and the immunofluorescence antibody test (IFAT), followed by the elimination of the seropositive dogs. However, these techniques present limitations in terms of sensitivity and specificity. The Polymerase Chain Reaction (PCR) associated to hybridization with DNA probes labeled with 32 P has been recognized as a valuable tool for Leishmania identification. In this study, the sensitivity of kDNA PCR hybridization method was compared with three other molecular methods: Internal Transcribed Spacer 1 Nested PCR (ITS-1nPCR), Leishmania nested PCR (LnPCR) and Seminested kDNA PCR (kDNA snPCR). The comparison was performed in different clinical specimens: conjunctival swab, skin, blood and bone marrow. A group of thirty symptomatic dogs, positive in the parasitological and serological tests, was used. When. The techniques targeting kDNA mini-circles (kDNA snPCR and KDNA PCR-hybridization) showed the worst result for blood samples. The KDNA-PCR hybridization showed the best sensitivity for conjunctival swab. By comparing the samples on the basis of positivity obtained by the sum of all methods, the blood showed the worst outcome (71/120).The bone marrow showed the highest positivity (106/120), followed by conjunctival swab (100/120) and skin (89/120). Since the bone marrow samples are unsuitable for routine epidemiological surveys, the conjunctival swab was recommended because it allows high sensitivity, especially when associated with kDNA PCR hybridization method, and is a noninvasive sampling method. (author)

  6. Development of a Fiber-Optics Microspatially Offset Raman Spectroscopy Sensor for Probing Layered Materials.

    Science.gov (United States)

    Vandenabeele, Peter; Conti, Claudia; Rousaki, Anastasia; Moens, Luc; Realini, Marco; Matousek, Pavel

    2017-09-05

    Microspatially offset Raman spectroscopy (micro-SORS) has been proposed as a valuable approach to sample molecular information from layers that are covered by a turbid (nontransparent) layer. However, when large magnifications are involved, the approach is not straightforward, as spatial constraints exist to position the laser beam and the objective lens with the external beam delivery or, with internal beam delivery, the maximum spatial offset achievable is restricted. To overcome these limitations, we propose here a prototype of a new micro-SORS sensor, which uses bare glass fibers to transfer the laser radiation to the sample and to collect the Raman signal from a spatially offset zone to the Raman spectrometer. The concept also renders itself amenable to remote delivery and to the miniaturization of the probe head which could be beneficial for special applications, e.g., where access to sample areas is restricted. The basic applicability of this approach was demonstrated by studying several layered structure systems. Apart from proving the feasibility of the technique, also, practical aspects of the use of the prototype sensor are discussed.

  7. Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

    Science.gov (United States)

    Oberstrass, Florian C.; Fernandes, Louis E.; Bryant, Zev

    2012-01-01

    B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC)n sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. “Bubble” templates containing 50–100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand–strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context. PMID:22474350

  8. Interaction between insulin and calf thymus DNA, and quantification of insulin and calf thymus DNA by a resonance Rayleigh scattering method

    International Nuclear Information System (INIS)

    Kong, L.; Liu, Z.; Hu, X.; Liu, S.; Li, W.

    2012-01-01

    The interaction of insulin with calf thymus deoxyribonucleic acid (ctDNA) leads to a complex that displays remarkably enhanced resonance Rayleigh scattering (RRS). The complex and its formation were investigated by atomic force microscopy and by absorption, fluorescence and circular dichroism spectroscopies. We show that the Tyr B16, Tyr B26 and Phe B24 amino acids near the active center (Phe B25) were influenced by the interaction, whereas Tyr A14, Tyr A19 and Phe B1 (which are located far away from the active center) were less influenced. The interaction provide a way in the quantitation of both ctDNA and insulin with high sensitivity. When ctDNA is used as a probe to quantify insulin, the detection limit (3σ) is 6.0 ng mL -1 . If, inversely, insulin is used as a probe to quantify ctDNA, the detection limit (3σ) is 7.2 ng mL -1 . The analysis of synthetic DNA samples and an insulin infection sample provided satisfactory results. (author)

  9. Multiple conformational states of DnaA protein regulate its interaction with DnaA boxes in the initiation of DNA replication.

    Science.gov (United States)

    Patel, Meera J; Bhatia, Lavesh; Yilmaz, Gulden; Biswas-Fiss, Esther E; Biswas, Subhasis B

    2017-09-01

    DnaA protein is the initiator of genomic DNA replication in prokaryotes. It binds to specific DNA sequences in the origin of DNA replication and unwinds small AT-rich sequences downstream for the assembly of the replisome. The mechanism of activation of DnaA that enables it to bind and organize the origin DNA and leads to replication initiation remains unclear. In this study, we have developed double-labeled fluorescent DnaA probes to analyze conformational states of DnaA protein upon binding DNA, nucleotide, and Soj sporulation protein using Fluorescence Resonance Energy Transfer (FRET). Our studies demonstrate that DnaA protein undergoes large conformational changes upon binding to substrates and there are multiple distinct conformational states that enable it to initiate DNA replication. DnaA protein adopted a relaxed conformation by expanding ~15Å upon binding ATP and DNA to form the ATP·DnaA·DNA complex. Hydrolysis of bound ATP to ADP led to a contraction of DnaA within the complex. The relaxed conformation of DnaA is likely required for the formation of the multi-protein ATP·DnaA·DNA complex. In the initiation of sporulation, Soj binding to DnaA prevented relaxation of its conformation. Soj·ADP appeared to block the activation of DnaA, suggesting a mechanism for Soj·ADP in switching initiation of DNA replication to sporulation. Our studies demonstrate that multiple conformational states of DnaA protein regulate its binding to DNA in the initiation of DNA replication. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Fiberoptic bronchoscopic treatment of blood aspiration and use of sugammadex in a patient with epistaxis

    Science.gov (United States)

    Ryu, Taeha; Kim, Dong Hyuck; Byun, Sung Hye

    2018-01-01

    Abstract Rationale: In patients with oropharyngeal and nasopharyngeal bleeding, blood aspiration can make airway management difficult and lead to severe pulmonary complications. Patient concerns: A 44-year-old male patient with recurrent epistaxis underwent surgery for hemostasis. The patient aspirated blood through the endotracheal tube when he hiccupped during the surgery. Diagnosis: The patient was diagnosed with blood aspiration after intraoperative fiberoptic bronchoscopy revealed a blood clot and viscous mucus in the airways, but no sign of active bleeding. Interventions: Tracheobronchial suctioning and irrigation with normal saline was performed through the bronchoscope to remove the aspirated blood clot. Prior to emergence from anesthesia, sugammadex was administered to induce complete neuromuscular recovery and enable the patient to cough up any blood remaining in the airways. Outcomes: The patient was successfully extubated and fully recovered with no complications. Lessons: Blood aspiration due to oropharyngeal or nasopharyngeal bleeding can be diagnosed and treated by tracheobronchial suctioning via fiberoptic bronchoscopy. In addition, sugammadex can enable patients to recover spontaneous breathing, facilitate extubation, and enable patients to cough up any blood remaining in the airways. PMID:29642212

  11. Detection of endonuclease III- and 8-oxoguanine glycosylase-sensitive base modifications in γ-irradiated DNA and cells by the aldehyde reactive probe (ARP) assay

    International Nuclear Information System (INIS)

    Mohsin Ali, M.; Kurisu, Satofumi; Yoshioka, Yoshihiro; Terato, Hiroaki; Ohyama, Yoshihiko; Ide Hiroshi; Kubo, Kihei

    2004-01-01

    Ionizing radiation generates diverse DNA lesions that differentially induce cell death and mutations. In the present study, calf thymus DNA (400 μg/ml) and HeLa cells were irradiated by 60 Co γ-rays, and abasic (AP) sites and endonuclease (Endo) III- and 8-oxoguanine glycosylase (hOGG1)-sensitive base modifications in DNA were quantitated by the aldehyde reactive probe (ARP) assay. The irradiation of calf thymus DNA in phosphate buffer generated 91 Endo III- and 100 hOGG1-sensitive base modifications and 110 AP sites per 10 6 base pairs (bp) per Gy. The yield of the lesions in Tris buffer was 41- to 91-fold lower than that in phosphate, demonstrating a radioprotective effect of Tris. The HeLa cell chromosomal DNA contained 12 Endo III- and 3.8 hOGG1-sensitive base modifications and less than 1 AP sites per 10 6 bp as endogenous damage, and their level was increased by irradiation. The yields of the damage at 1 Gy (roughly equivalent to the lethal dose of HeLa cells [1.6-1.8 Gy]) were 0.13 Endo III, 0.091 hOGG1, and 0.065 AP sites per 10 6 bp, showing that irradiation with a lethal dose brought about only a marginal increase in base damage relative to an endogenous one. A comparison of the present data with those reported for DNA strand breaks supports the primary importance of double-strand breaks and clustered lesions as lethal damages formed by ionizing radiation. (author)

  12. Modified surface of titanium dioxide nanoparticles-based biosensor for DNA detection

    Science.gov (United States)

    Nadzirah, Sh.; Hashim, U.; Rusop, M.

    2018-05-01

    A new technique was used to develop a simple and selective picoammeter DNA biosensor for identification of E. coli O157:H7. This biosensor was fabricated from titanium dioxide nanoparticles that was synthesized by sol-gel method and spin-coated on silicon dioxide substrate via spinner. 3-Aminopropyl triethoxy silane (APTES) was used to modify the surface of TiO2. Simple surface modification approach has been applied; which is single dropping of APTES onto the TiO2 nanoparticles surface. Carboxyl modified probe DNA has been bind onto the surface of APTES/TiO2 without any amplifier element. Electrical signal has been used as the indicator to differentiate each step (surface modification of TiO2 and probe DNA immobilization). The I-V measurements indicate extremely low current (pico-ampere) flow through the device which is 2.8138E-10 A for pure TiO2 nanoparticles, 2.8124E-10 A after APTES modification and 3.5949E-10 A after probe DNA immobilization.

  13. Use of fiberoptic endoscopic evaluation of swallowing (FEES) in the management of psychogenic dysphagia in children.

    Science.gov (United States)

    Thottam, Prasad John; Silva, Rodrigo C; McLevy, Jennifer D; Simons, Jeffrey P; Mehta, Deepak K

    2015-02-01

    To describe the use of fiberoptic endoscopic evaluation of swallowing (FEES) as an adjunct in the management of children presenting with psychogenic dysphagia, defined as food avoidance and excessive fear of eating without identifiable anatomic or functional swallowing abnormalities. Case series of patients presenting to the otolaryngology clinic of a tertiary pediatric teaching hospital between 2007 and 2008 that were evaluated and managed with the utilization of FEES. The outcomes measured were age, gender, duration of symptoms, findings of FEES, additional work-up and resolution of symptoms at follow-up. Five patients (4 males, 1 female) with ages ranging from 5 to 13 years old (mean=8.6). The median duration of symptoms before presentation was 3 weeks. Four families described refusal of solids starting after choking episode and variable estimated weight loss (mean 2.8kg). One child presented with vague complaints of intermittent odynophagia and food refusal. Fiberoptic endoscopic evaluation of swallowing was performed on all patients. No abnormalities of the oropharyngeal swallow were appreciated. Additional management included different combinations of modified barium swallow study, esophagastroduodenoscopy (EGD), upper GI series, antibiotics, and psychotherapy. Mean follow-up with clinic visit was 4.2 months. Three of the five children reported complete resolution of symptoms after FEES at follow-up visit. Fiberoptic endoscopic evaluation of swallowing can be a useful management tool in children with psychogenic dysphagia as it provides direct visualization of the oropharyngeal swallowing mechanism. This can be used to provide visual reassure and biofeedback to patients and parents. Additional workup should be decided on an individual basis. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  14. Hematopoietic Lineage Transcriptome Stability and Representation in PAXgeneTM Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray

    Directory of Open Access Journals (Sweden)

    Laura Kennedy

    2008-01-01

    Full Text Available Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgeneTM RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2TM enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgeneTM blood samples also advocate a short, fixed room temperature storage time for all PAXgeneTM blood samples collected for the purposes of global transcriptional profiling in clinical studies.

  15. Droplet-based microscale colorimetric biosensor for multiplexed DNA analysis via a graphene nanoprobe

    International Nuclear Information System (INIS)

    Xiang Xia; Luo Ming; Shi Liyang; Ji Xinghu; He Zhike

    2012-01-01

    Graphical abstract: With a microvalve manipulate technique combined with droplet platform, a microscale fluorescence-based colorimetric sensor for multiplexed DNA analysis is developed via a graphene nanoprobe. Highlights: ► A quantitative detection for multiplexed DNA is first realized on droplet platform. ► The DNA detection is relied on a simple fluorescence-based colorimetric method. ► GO is served as a quencher for two different DNA fluorescent probes. ► This present work provides a rapid, sensitive, visual and convenient detection tool for droplet biosensor. - Abstract: The development of simple and inexpensive DNA detection strategy is very significant for droplet-based microfluidic system. Here, a droplet-based biosensor for multiplexed DNA analysis is developed with a common imaging device by using fluorescence-based colorimetric method and a graphene nanoprobe. With the aid of droplet manipulation technique, droplet size adjustment, droplet fusion and droplet trap are realized accurately and precisely. Due to the high quenching efficiency of graphene oxide (GO), in the absence of target DNAs, the droplet containing two single-stranded DNA probes and GO shows dark color, in which the DNA probes are labeled carboxy fluorescein (FAM) and 6-carboxy-X-rhodamine (ROX), respectively. The droplet changes from dark to bright color when the DNA probes form double helix with the specific target DNAs leading to the dyes far away from GO. This colorimetric droplet biosensor exhibits a quantitative capability for simultaneous detection of two different target DNAs with the detection limits of 9.46 and 9.67 × 10 −8 M, respectively. It is also demonstrated that this biosensor platform can become a promising detection tool in high throughput applications with low consumption of reagents. Moreover, the incorporation of graphene nanoprobe and droplet technique can drive the biosensor field one more step to some extent.

  16. Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints.

    Science.gov (United States)

    Heuer, H; Hartung, K; Wieland, G; Kramer, I; Smalla, K

    1999-03-01

    Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5' exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.

  17. DNA-mediated strand displacement facilitates sensitive electronic detection of antibodies in human serums.

    Science.gov (United States)

    Dou, Baoting; Yang, Jianmei; Shi, Kai; Yuan, Ruo; Xiang, Yun

    2016-09-15

    We describe here the development of a sensitive and convenient electronic sensor for the detection of antibodies in human serums. The sensor is constructed by self-assembly formation of a mixed monolayer containing the small molecule epitope conjugated double stranded DNA probes on gold electrode. The target antibody binds the epitope on the dsDNA probe and lowers the melting temperature of the duplex, which facilitates the displacement of the antibody-linked strand of the duplex probe by an invading methylene blue-tagged single stranded DNA (MB-ssDNA) through the strand displacement reaction and leads to the capture of many MB-ssDNA on the sensor surface. Subsequent electrochemical oxidation of the methylene blue labels results in amplified current response for sensitive monitoring of the antibodies. The antibody assay conditions are optimized and the sensor exhibits a linear range between 1.0 and 25.0nM with a detection limit of 0.67nM for the target antibody. The sensor is also selective and can be employed to detect the target antibodies in human serum samples. With the advantages of using small molecule epitope as the antibody recognition element over traditional antigen, the versatile manipulability of the DNA probes and the unique properties of the electrochemical transduction technique, the developed sensor thus hold great potential for simple and sensitive detection of different antibodies and other proteins in real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Detection of DNA hybridization based on SnO2 nanomaterial enhanced fluorescence

    International Nuclear Information System (INIS)

    Gu Cuiping; Huang Jiarui; Ni Ning; Li Minqiang; Liu Jinhuai

    2008-01-01

    In this paper, enhanced fluorescence emissions were firstly investigated based on SnO 2 nanomaterial, and its application in the detection of DNA hybridization was also demonstrated. The microarray of SnO 2 nanomaterial was fabricated by the vapour phase transport method catalyzed by patterned Au nanoparticles on a silicon substrate. A probe DNA was immobilized on the substrate with patterned SnO 2 nanomaterial, respectively, by covalent and non-covalent linking schemes. When a fluorophore labelled target DNA was hybridized with a probe DNA on the substrate, fluorescence emissions were only observed on the surface of SnO 2 nanomaterial, which indicated the property of enhancing fluorescence signals from the SnO 2 nanomaterial. By comparing the different fluorescence images from covalent and non-covalent linking schemes, the covalent method was confirmed to be more effective for immobilizing a probe DNA. With the combined use of SnO 2 nanomaterial and the covalent linking scheme, the target DNA could be detected at a very low concentration of 10 fM. And the stability of SnO 2 nanomaterial under the experimental conditions was also compared with silicon nanowires. The findings strongly suggested that SnO 2 nanomaterial could be extensively applied in detections of biological samples with enhancing fluorescence property and high stability

  19. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

    Energy Technology Data Exchange (ETDEWEB)

    Song, Mengke [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Jiang, Longfei [College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 (China); Zhang, Dayi [Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ (United Kingdom); Luo, Chunling, E-mail: clluo@gig.ac.cn [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Wang, Yan [Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024 (China); Yu, Zhiqiang [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Yin, Hua [College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); Zhang, Gan [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China)

    2016-05-05

    Highlights: • Investigate PAHs degraders in forest carbon-rich soils via DNA-SIP. • Rhodanobacter is identified to metabolite anthracene for the first time. • The first fluoranthene degrader belongs to Acidobacteria. • Different functions of PAHs degraders in forest soils from contaminated soils. - Abstract: Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually {sup 13}C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

  20. Direct immobilization and hybridization of DNA on group III nitride semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Xu Xiaobin; Jindal, Vibhu; Shahedipour-Sandvik, Fatemeh; Bergkvist, Magnus [College of Nanoscale Science and Engineering, University at Albany (SUNY), 255 Fuller Road, Albany, NY 12203 (United States); Cady, Nathaniel C. [College of Nanoscale Science and Engineering, University at Albany (SUNY), 255 Fuller Road, Albany, NY 12203 (United States)], E-mail: ncady@uamail.albany.edu

    2009-03-15

    A key concern for group III-nitride high electron mobility transistor (HEMT) biosensors is the anchoring of specific capture molecules onto the gate surface. To this end, a direct immobilization strategy was developed to attach single-stranded DNA (ssDNA) to AlGaN surfaces using simple printing techniques without the need for cross-linking agents or complex surface pre-functionalization procedures. Immobilized DNA molecules were stably attached to the AlGaN surfaces and were able to withstand a range of pH and ionic strength conditions. The biological activity of surface-immobilized probe DNA was also retained, as demonstrated by sequence-specific hybridization experiments. Probe hybridization with target ssDNA could be detected by PicoGreen fluorescent dye labeling with a minimum detection limit of 2 nM. These experiments demonstrate a simple and effective immobilization approach for attaching nucleic acids to AlGaN surfaces which can further be used for the development of HEMT-based DNA biosensors.