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Sample records for situ hybridization techniques

  1. Implementation of the Fluorescent in Situ Hybridization technique in the Faculty of Medicine, UdelaR

    Directory of Open Access Journals (Sweden)

    Andrea Cairus

    2017-11-01

    Full Text Available The Cytogenetic Laboratory of the Faculty of Medicine processes, on average, 300 annual samples of public and private healthcare centers by conventional cytogenetics. It is essential to implement new techniques to improve the quality of the service offered. The purpose of this work was to implement the Fluorescent in situ Hybridization technique (FISH. An observational, cross-sectional, analytical study was performed. Peripheral blood samples from patients with sex chromosomopathies diagnosed by conventional cytogenetics were analyzed. Fluorescent in situ hybridization technique was applied, comparing results with FISH and with conventional cytogenetics. The percentage of mosaicism detected by conventional cytogenetics and Fluorescent in situ Hybridization was studied: 24 samples were analyzed; 19 presented numerical alterations, 3 structural and 2 both. Numerical alterations were Turner syndrome, Klinefelter syndrome, XXX syndrome and XYY syndrome. Concordance in diagnoses was found for both techniques. For Turner syndrome, 8 of 12 samples corresponded to mosaicism, and there were no significant differences between conventional cytogenetics and the technique studied (p0.05. Klinefelter syndrome and XYY were both presented in a non-mosaic karyotype. For XXX syndrome, a normal line (46, XX was observed in three of the samples, in a percentage close to the cut off. From this research, it will be possible to implement Fluorescent in situ Hybridization in this service, to extend it to other pathologies and to enable the training of human resources; consolidating this laboratory as a national academic reference center.

  2. In situ hybridization; principles and applications: review article

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    Zahra Nozhat

    2015-06-01

    Full Text Available In situ hybridization (ISH is a method that uses labeled complementary single strand DNA or RNA to localize specific DNA or RNA sequences in an intact cell or in a fixed tissue section. The main steps of ISH consist of: probe selection, tissue or sample preparation, pre-hybridization treatment, hybridization and washing, detection and control procedure. Probe selection is one of the important aspects of successful hybridization. ISH sensitivity and specificity can be influenced by: probe construct, efficiency of labeling, percentage of GC, probe length and signal detection systems. Different methods such as nick translation, random priming, end tailing and T4 DNA polymerase replacement are used for probe generation. Both radioactive and non-radioactive labels can be used in order to probe labeling. Nucleic acid maintenance in samples, prevention of morphological changes of samples and probe penetration into tissue section are the main aims of sample preparation step. Then, a small amount of solution containing probe, is added on slides containing tissue sections for hybridization process, then slides are incubated overnight. Next day, washes are carried out to remove the probes which are not bound to target DNA or RNA. Finally, in order to be sure that the observed labeling is specific to the target sequence, using several control procedures is very important. Various techniques based on ISH consist of: Fluorescence in situ hybridization (FISH, chromogenic in situ hybridization (CISH, genomic in situ hybridization (GISH, comparative genomic hybridization (CGH, spectral karyotyping (SKY and multiplex fluorescence in situ hybridization (MFISH. One of the most common techniques of ISH is fluorescence in situ hybridization. FISH can be used to: 1 detect small deletions and duplications that are not visible using microscope analysis, 2 detect how many chromosomes of a certain type are present in each cell and 3 confirm rearrangements that are

  3. Application of Genomic In Situ Hybridization in Horticultural Science

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    Fahad Ramzan

    2017-01-01

    Full Text Available Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH techniques in horticultural plants.

  4. A double labeling technique for performing immunocytochemistry and in situ hybridization in virus infected cell cultures and tissues

    International Nuclear Information System (INIS)

    Gendelman, H.E.; Moench, T.R.; Narayan, O.; Griffin, D.E.; Clements, J.E.

    1985-01-01

    This report describes a combined immunocytochemical and in situ hybridization procedure which allows visualization of cellular or viral antigens and viral RNA in the same cell. Cultures infected with visna or measles virus were fixed in periodate-lysine-paraformaldehyde-glutaraldehyde, stained by the avidin-biotin-peroxidase technique using antibodies to viral or cellular proteins and then incubated with radiolabeled specific DNA probes (in situ hybridization). This technique provides a new approach to the study of viral pathogenesis by: (1) identifying the types of cells which are infected in the host and (2) identifying points of blockade in the virus life cycle during persistent infections. (Auth.)

  5. Contribution of fluorescence in situ hybridization to biological dosimetry

    International Nuclear Information System (INIS)

    Sorokine-Durm, I.; Roy, L.; Durand, V.; Voisin, P.

    1995-01-01

    Fluorescence in situ hybridization with composite whole chromosome specific DNA probes for human chromosomes 2, 4 and 12 an α-satellite centromeric DNA probe labelled with biotin were used to measure symmetrical and terminal translocations (dose rate 0.5 Gy/min) and dicentrics (0.1 Gy/min) induced in vitro by 60 Co γ-irradiation (0-5 Gy). The suitability of fluorescence in situ hybridization (F.I.S.H.) technique for dicentrics detection is compared with the conventional technique. Dose-response curves for γ-rays ( 60 Co) for two dose rates are shown (dicentrics and translocations). (authors). 10 refs., 2 figs

  6. Application of Fluorescence In Situ Hybridization (FISH) Technique for the Detection of Genetic Aberration in Medical Science

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    Ratan, Zubair Ahmed; Zaman, Sojib Bin; Mehta, Varshil; Haidere, Mohammad Faisal; Runa, Nusrat Jahan; Akter, Nasrin

    2017-01-01

    Fluorescence in situ hybridization (FISH) is a macromolecule recognition technique, which is considered as a new advent in the field of cytology.?Initially, it was developed as a physical mapping tool to delineate genes within chromosomes. The accuracy and versatility of FISH were subsequently capitalized upon in biological and medical research. This visually appealing technique provides an intermediate degree of resolution between DNA analysis and chromosomal investigations. FISH consists of...

  7. A novel fluorescent in situ hybridization technique for detection of Rickettsia spp. in archival samples

    DEFF Research Database (Denmark)

    Svendsen, Claus Bo; Boye, Mette; Struve, Carsten

    2009-01-01

    A novel, sensitive and specific method for detecting Rickettsia spp. in archival samples is described. The method involves the use of fluorescently marked oligonucleotide probes for in situ hybridization. Specific hybridization of Ricekttsia was found without problems of cross-reactions with bact......A novel, sensitive and specific method for detecting Rickettsia spp. in archival samples is described. The method involves the use of fluorescently marked oligonucleotide probes for in situ hybridization. Specific hybridization of Ricekttsia was found without problems of cross...

  8. Comparison of Chromogenic In Situ Hybridization and Fluorescence In Situ Hybridization for the Evaluation of MDM2 Amplification in Adipocytic Tumors.

    Science.gov (United States)

    Mardekian, Stacey K; Solomides, Charalambos C; Gong, Jerald Z; Peiper, Stephen C; Wang, Zi-Xuan; Bajaj, Renu

    2015-11-01

    Atypical lipomatous tumor/well-differentiated liposarcoma (ALT-WDLPS) and dedifferentiated liposarcoma (DDLPS) are characterized cytogenetically by a 12q13-15 amplification involving the mouse double minute 2 (MDM2) oncogene. Fluorescence in situ hybridization (FISH) is used frequently to detect this amplification and aid with the diagnosis of these entities, which is difficult by morphology alone. Recently, bright-field in situ hybridization techniques such as chromogenic in situ hybridization (CISH) have been introduced for the determination of MDM2 amplification status. The present study compared the results of FISH and CISH for detecting MDM2 amplification in 41 cases of adipocytic tumors. Amplification was defined in both techniques as a MDM2/CEN12 ratio of 2 or greater. Eleven cases showed amplification with both FISH and CISH, and 26 cases showed no amplification with both methods. Two cases had discordant results between CISH and FISH, and two cases were not interpretable by CISH. CISH is advantageous for allowing pathologists to evaluate the histologic and molecular alterations occurring simultaneously in a specimen. Moreover, CISH is found to be more cost- and time-efficient when used with automation, and the signals do not quench over time. CISH technique is a reliable alternative to FISH in the evaluation of adipocytic tumors for MDM2 amplification. © 2014 Wiley Periodicals, Inc.

  9. Triplex in-situ hybridization

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    Fresco, Jacques R.; Johnson, Marion D.

    2002-01-01

    Disclosed are methods for detecting in situ the presence of a target sequence in a substantially double-stranded nucleic acid segment, which comprises: a) contacting in situ under conditions suitable for hybridization a substantially double-stranded nucleic acid segment with a detectable third strand, said third strand being capable of hybridizing to at least a portion of the target sequence to form a triple-stranded structure, if said target sequence is present; and b) detecting whether hybridization between the third strand and the target sequence has occured.

  10. The Use of Whole-Mount "in Situ" Hybridization to Illustrate Gene Expression Regulation

    Science.gov (United States)

    Llamusí, Beatriz; Muñoz-Soriano, Verónica; Paricio, Nuria; Artero, Rubén

    2014-01-01

    "In situ" hybridization is a widely used technique for studying gene expression. Here, we describe two experiments addressed to postgraduate genetics students in which the effect of transcription factors on gene expression is analyzed in "Drosophila embryos of different genotypes by whole-mount in situ hybridization. In one of the…

  11. Establishment of 60Co dose calibration curve using fluorescent in situ hybridization assay technique: Result of preliminary study

    International Nuclear Information System (INIS)

    Rahimah Abdul Rahim; Noriah Jamal; Noraisyah Mohd Yusof; Juliana Mahamad Napiah; Nelly Bo Nai Lee

    2010-01-01

    This study aims at establishing an in-vitro 60 Co dose calibration curve using Fluorescent In-Situ Hybridization assay technique for the Malaysian National Bio dosimetry Laboratory. Blood samples collected from a female healthy donor were irradiated with several doses of 60 Co radiation. Following culturing of lymphocytes, microscopic slides are prepared, denatured and hybridized. The frequencies of translocation are estimated in the metaphases. A calibration curve was then generated using a regression technique. It shows a good fit to a linear-quadratic model. The results of this study might be useful in estimating absorbed dose for the individual exposed to ionizing radiation retrospectively. This information may be useful as a guide for medical treatment for the assessment of possible health consequences. (author)

  12. In Situ Hybridization Pada Kanker Payudara

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    Diah Witari, Ni Putu

    2014-01-01

    Kesulitan yang dijumpai pada penanganan kanker payudara adalah terjadinya kekambuhan atau relaps. Deteksi status HER2 pada pasien merupakan salah satu upaya untuk mendeteksi terjadinya relaps dan juga untuk menentukan jenis terapi yang ada diberikan. Ekspresi protein HER2 dapat dideteksi dengan immunohistochemistry (IHC), sedangkan mutasi gen HER2 dapat dideteksi dengan teknik in situ hybridization baik berupa fluorescence in situ hybridization (FISH) ataupun chromogenic in situ hy...

  13. Design of Hybrid Steam-In Situ Combustion Bitumen Recovery Processes

    International Nuclear Information System (INIS)

    Yang Xiaomeng; Gates, Ian D.

    2009-01-01

    Given enormous capital costs, operating expenses, flue gas emissions, water treatment and handling costs of thermal in situ bitumen recovery processes, improving the overall efficiency by lowering energy requirements, environmental impact, and costs of these production techniques is a priority. Steam-assisted gravity drainage (SAGD) is the most widely used in situ recovery technique in Athabasca reservoirs. Steam generation is done on surface and consequently, because of heat losses, the energy efficiency of SAGD can never be ideal with respect to the energy delivered to the sandface. An alternative to surface steam generation is in situ combustion (ISC) where heat is generated within the formation through injection of oxygen at a sufficiently high pressure to initiate combustion of bitumen. In this manner, the heat from the combustion reactions can be used directly to mobilize the bitumen. As an alternative, the heat can be used to generate steam within the formation which then is the agent to move heat in the reservoir. In this research, alternative hybrid techniques with simultaneous and sequential steam-oxygen injection processes are examined to maximize the thermal efficiency of the recovery process. These hybrid processes have the advantage that during ISC, steam is generated within the reservoir from injected and formation water and as a product of oxidation. This implies that ex situ steam generation requirements are reduced and if there is in situ storage of combustion gases, that overall gas emissions are reduced. In this research, detailed reservoir simulations are done to examine the dynamics of hybrid processes to enable design of these processes. The results reveal that hybrid processes can lower emitted carbon dioxide-to-oil ratio by about 46%, decrease the consumed natural gas-to-oil ratio by about 73%, reduce the cumulative energy-to-oil ratio by between 40% and 70% compared to conventional SAGD, and drop water consumption per unit oil produced

  14. Double-staining chromogenic in situ hybridization as a useful alternative to split-signal fluorescence in situ hybridization in lymphoma diagnostics

    DEFF Research Database (Denmark)

    van Rijk, A.; Svenstroup-Poulsen, T.; Jones, M.

    2010-01-01

    within the reach of every pathology laboratory. Design and Methods Our study was initiated to determine the consistency between chromogenic in situ hybridization and fluorescence in situ hybridization, both using split-signal probes developed for the detection of chromosomal breaks. Five hundred...... and actual signal were compared to the original fluorescence hybridization results. In addition, hematoxylin background staining intensity and signal intensity of the double-staining chromogenic in situ hybridization procedure were analyzed. Results With respect to the presence or absence of chromosomal...

  15. Identification of bacteria used for microbial enhanced oil recovery process by fluorescence in situ hybridization technique

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, K.; Tanaka, S.; Otsuka, M. [Kansai Research Institute, Kyoto (Japan). Lifescience Lab.; Yonebayashi, H. [Japan National Oil Corp., Chiba (Japan). Tech. Research Center; Enomoto, H. [Tohoku University, Sendai (Japan). Dept. of Geoscience and Tech.

    2000-01-01

    A fluorescence in situ hybridization (FISH) technique using 16S rRNA-targeted oligonucleotide probes was developed for rapid detection of microorganisms for use in the microbial enhancement of oil recovery (MEOR) process. Two microorganisms, Enterobacter cloacae TRC-322 and Bacillus licheniformis TRC-18-2-a, were selected from a collection of Enterobacter sp. and Bacillus sp. which were screened in previous studies as candidate microorganisms for injection, and were used for this experiment. Oligonucleotide probes, design based on specific sequences in the 16S rRNA gene were labeled with either fluorescein isothiocyanate (FITC), or 6-car-boxy-X-rhodamine (ROX), and were allowed to hybridize with fixed cells of the two microorganisms noted above. The fluorescence signal emitted from each microorganism cells could clearly be detected by an epifluorescence microscope. Moreover, E. cloacae TRC-322 and B, licheniformis TRC-18-2-a, suspended in actual reservoir brine, including inorganic salts, oil and aboriginal cells of the reservoir brine, could be detected directly by this hybridization method, without the need for cultivation and isolation. (author)

  16. Fluorescence in situ hybridization on formalin-fixed and paraffin-embedded tissue

    DEFF Research Database (Denmark)

    Laub Petersen, Bodil; Zeuthen, Mette Christa; Pedersen, Sanni

    2004-01-01

    Fluorescence in situ hybridization (FISH) is widely used to study numerical and structural genetic abnormalities in both metaphase and interphase cells. The technique is based on the hybridization of labeled probes to complementary sequences in the DNA or RNA of the cells. Interphase FISH is most...... in time lapse between removal of tissue and fixation, duration of fixation, enzymatic pretreatment, hybridization conditions, and posthybridization washing conditions are important factors in the hybridization. In this study, we have listed the results of a systematic approach to improve FISH on isolated...

  17. Application of Fluorescence In Situ Hybridization (FISH) Technique for the Detection of Genetic Aberration in Medical Science

    Science.gov (United States)

    Ratan, Zubair Ahmed; Zaman, Sojib Bin; Haidere, Mohammad Faisal; Runa, Nusrat Jahan; Akter, Nasrin

    2017-01-01

    Fluorescence in situ hybridization (FISH) is a macromolecule recognition technique, which is considered as a new advent in the field of cytology. Initially, it was developed as a physical mapping tool to delineate genes within chromosomes. The accuracy and versatility of FISH were subsequently capitalized upon in biological and medical research. This visually appealing technique provides an intermediate degree of resolution between DNA analysis and chromosomal investigations. FISH consists of a hybridizing DNA probe, which can be labeled directly or indirectly. In the case of direct labeling, fluorescent nucleotides are used, while indirect labeling is incorporated with reporter molecules that are subsequently detected by fluorescent antibodies or other affinity molecules. FISH is applied to detect genetic abnormalities that include different characteristic gene fusions or the presence of an abnormal number of chromosomes in a cell or loss of a chromosomal region or a whole chromosome. It is also applied in different research applications, such as gene mapping or the identification of novel oncogenes. This article reviews the concept of FISH, its application, and its advantages in medical science.  PMID:28690958

  18. Design and optimization of hybrid ex situ/in situ steam generation recovery processes for heavy oil and bitumen

    Energy Technology Data Exchange (ETDEWEB)

    Yang, X.; Gates, I.D. [Calgary Univ., AB (Canada). Dept. of Chemical and Petroleum Engineering; Larter, S.R. [Calgary Univ., AB (Canada). Dept. of Geoscience]|[Alberta Ingenuity Centre for In Situ Energy, Edmonton, AB (Canada)

    2008-10-15

    Hybrid steam-air based oil recovery techniques were investigated using advanced 3-D reactive thermal reservoir simulations. The hybrid techniques combined ex situ steam and in situ steam generation processes in order to raise efficiency, lower natural gas consumption, and reduce gas emissions. The steam-air based processes used 70 per cent of the energy of conventional steam assisted gravity drainage (SAGD) techniques to recover the same amount of oil. The process used an SAGD wellpair arrangement, where steam and air were injected through the top injection well. The kinetic parameters used in the study were developed by history matching a combustion tube experiments with Athabasca bitumen conducted to predict cumulative bitumen and gas production volumes and compositions. A total of 6 SAGD and 6 in situ combustion simulations were conducted with steam oxygen volume ratios set at 50 per cent steam and 50 per cent oxygen. Various case studies were considered over a 5 year period. Carbon dioxide (CO{sub 2}) emissions were also measured as well as cumulative water and methane consumption rates. Results of the study were used to develop an optimized hybrid operation that consisted of a SAGD well pair arrangement operating with cyclic steam-oxygen injection at high pressures. It was concluded that the high pressure operation increased the steam partial pressure within the reservoir and enhanced combustion performance. A 29 per cent improvement in the cumulative energy to oil ratio was obtained. 23 refs., 2 tabs., 9 figs.

  19. Comparison of Fluorescence In Situ Hybridization and Chromogenic In Situ Hybridization for Low and High Throughput HER2 Genetic Testing

    DEFF Research Database (Denmark)

    Poulsen, Tim S; Espersen, Maiken Lise Marcker; Kofoed, Vibeke

    2013-01-01

    cancer patients with HER2 immunohistochemistry (IHC) results scored as 0/1+, 2+, and 3+. HER2 genetic status was analysed using chromogenic in situ hybridization (CISH) and fluorescence in situ hybridization (FISH). Scoring results were documented through digital image analysis. The cancer region...

  20. Genome reorganization in Nicotiana asymmetric somatic hybrids analysed by in situ hybridization

    International Nuclear Information System (INIS)

    Parokonny, A.S.; Kenton, A.Y.; Gleba, Y.Y.; Bennett, M.D.

    1992-01-01

    In situ hybridization was used to examine genome reorganization in asymmetric somatic hybrids between Nicotiana plumbaginifolia and Nicotiana sylvestris obtained by fusion of gamma-irradiated protoplasts from one of the parents (donor) with non-irradiated protoplasts from the other (recipient). Probing with biotinylated total genomic DNA from either the donor or the recipient species unequivocally identified genetic material from both parents in 31 regenerant plants, each originating from a different nuclear hybrid colony. This method, termed genomic in situ hybridization (GISH), allowed intergenomic translocations containing chromosome segments from both species to be recognized in four regenerants. A probe homologous to the consensus sequence of the Arabidopsis thaliana telomeric repeat (5'-TTTAGGG-3')n, identified telomeres on all chromosomes, including 'mini-chromosomes' originating from the irradiated donor genome. Genomic in situ hybridization to plant chromosomes provides a rapid and reliable means of screening for recombinant genotypes in asymmetric somatic hybrids. Used in combination with other DNA probes, it also contributes to a greater understanding of the events responsible for genomic recovery and restabilization following genetic manipulation in vitro

  1. Whole-slide imaging is a robust alternative to traditional fluorescent microscopy for fluorescence in situ hybridization imaging using break-apart DNA probes.

    Science.gov (United States)

    Laurent, Camille; Guérin, Maxime; Frenois, François-Xavier; Thuries, Valérie; Jalabert, Laurence; Brousset, Pierre; Valmary-Degano, Séverine

    2013-08-01

    Fluorescence in situ hybridization is an indispensable technique used in routine pathology and for theranostic purposes. Because fluorescence in situ hybridization techniques require sophisticated microscopic workstations and long procedures of image acquisition with sometimes subjective and poorly reproducible results, we decided to test a whole-slide imaging system as an alternative approach. In this study, we used the latest generation of Pannoramic 250 Flash digital microscopes (P250 Flash digital microscopes; 3DHISTECH, Budapest, Hungary) to digitize fluorescence in situ hybridization slides of diffuse large B cells lymphoma cases for detecting MYC rearrangement. The P250 Flash digital microscope was found to be precise with better definition of split signals in cells containing MYC rearrangement with fewer truncated signals as compared to traditional fluorescence microscopy. This digital technique is easier thanks to the preview function, which allows almost immediate identification of the tumor area, and the panning and zooming functionalities as well as a shorter acquisition time. Moreover, fluorescence in situ hybridization analyses using the digital technique appeared to be more reproducible between pathologists. Finally, the digital technique also allowed prolonged conservation of photos. In conclusion, whole-slide imaging technologies represent rapid, robust, and highly sensitive methods for interpreting fluorescence in situ hybridization slides with break-apart probes. In addition, these techniques offer an easier way to interpret the signals and allow definitive storage of the images for pathology expert networks or e-learning databases. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Common Fluorescence In Situ Hybridization Applications in Cytology.

    Science.gov (United States)

    Savic, Spasenija; Bubendorf, Lukas

    2016-12-01

    - Fluorescence in situ hybridization (FISH) is a well-established method for detection of genomic aberrations in diagnostic, prognostic, and predictive marker testing. - To review common applications of FISH in cytology. - The published literature was reviewed. - Cytology is particularly well suited for all kinds of FISH applications, which is highlighted in respiratory tract cytology with an increasing demand for predictive FISH testing in lung cancer. Fluorescence in situ hybridization is the gold standard for detection of predictive anaplastic lymphoma kinase gene (ALK) rearrangements, and the same evaluation criteria as in histology apply to cytology. Several other gene rearrangements, including ROS proto-oncogene 1 receptor tyrosine kinase (ROS1), are becoming clinically important and share the same underlining cytogenetic mechanisms with ALK. MET amplification is one of the most common mechanisms of acquired resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors and can be targeted by crizotinib. As genomic aberrations are a hallmark of malignant cells, FISH is a valuable objective ancillary diagnostic tool. In urinary tract cytology, atypical urothelial cells equivocal for malignancy are a common diagnostic dilemma and multitarget FISH can help clarify such cells. Diagnosis of malignant mesothelioma remains one of the most challenging fields in effusion cytology, and ancillary FISH is useful in establishing the diagnosis. Fluorescence in situ hybridization is a morphology-based technique, and the prerequisite for reliable FISH results is a targeted evaluation of the cells in question (eg, cancer or atypical cells). Cytopathologists and cytotechnicians should therefore be involved in molecular testing in order to select the best material and to provide their morphologic expertise.

  3. Applications of in situ hybridization to plant-improvement

    International Nuclear Information System (INIS)

    Abbasi, F.M.

    2004-01-01

    In situ hybridization is a powerful method for characteristic alien addition and substitution lines. RFLP analysis can identify the presence of a particular individual chromosome, but whether they are as a pair or as a single chromosome cannot be determined. In situ hybridization has become established as an essential method in cell and molecular biology. It is able to link DNA sequences with their organization and physical position. The rate of technology-development in the field of in situ hybridization has been rapid: radioactive probes are now rarely used, while labeling methods, fluorochromes, chromosomes and tissue-preparation methods, microscope and imaging technology have all useful in functional genomics and localization of transgenes on the chromosomes. (author)

  4. Detection and quantitative analysis of actin mRNA by in situ hybridization with an oligodeoxynucleotide probe

    International Nuclear Information System (INIS)

    Taneja, K.; Singer, R.

    1987-01-01

    In situ hybridization is a useful method for localizing specific nucleic acid sequences intracellularly and for studying regulation of gene expression. Recently synthetic oligonucleotides have been successfully used as probes in this technique. Since they can be made easily to specific nucleic acid regions, they may be the best approach for analysis of a gene family of highly conserved sequences. They have analyzed these probes for the development of an in situ hybridization method. Oligonucleotides were made to different regions of chick beta-actin mRNA and used for detection of these sequences in a culture of chicken fibroblasts and myoblasts. They found that synthetic DNAs have different efficiencies of hybridization, indicating that not all target sequences are equivalent. They have investigated in detail a particular probe to the actin mRNA coding region and have optimized hybridization parameters. When hybridization was quantitated it was found that an oligonucleotide end labelled with 35 S or 32 P was capable of detecting several thousand messages per cell with a signal-to-noise ratio of 10:1. In situ hybridization confirmed the specificity of the hybridization as well as the background level. Increase in the number of oligonucleotides used should increase the signal-to-noise ratio-proportionately. Under particular circumstances the specificity of oligonucleotides make them an important reagent for in situ hybridization

  5. The application of fluorescence in situ hybridization (FISH technique for studying the microbial communities in intestinal tissues of white shrimp (Penaeus vannamei

    Directory of Open Access Journals (Sweden)

    Supamattaya, K.

    2005-02-01

    Full Text Available Fluorescence in situ hybridization technique is very useful for the evaluation of microbial communities in various environments. It is possible to apply this technique to study the intestinal microflora in white shrimp (Penaeus vannamei. Different fixatives and storage temperature were tested in this technique. It was found that fixation with 10% buffered formalin for 12 hours and changed to 70% ethanol shown positive results when compared to the fixation with Davidson's fixative or RF fixative. The best signaling was obtainedfrom the samples which were stored in -20ºC. By using the DNA probe targeted to the Eubacteria domain (EUB338 probe, 5′-GCT GCC TCC CGT AGG AGT-3′ labeled with fluorescein as a hybridizing probe, it was found that most intestinal microflora were aggregated with the intestinal contents, or dispersed in the lumen. There was not evidence of the attachment of the microflora with the intestinal epithelium in this study.

  6. Biomarkers for ALK and ROS1 in Lung Cancer: Immunohistochemistry and Fluorescent In Situ Hybridization.

    Science.gov (United States)

    Luk, Peter P; Selinger, Christina I; Mahar, Annabelle; Cooper, Wendy A

    2018-06-14

    - A small proportion of non-small cell lung cancers harbor rearrangements of ALK or ROS1 genes, and these tumors are sensitive to targeted tyrosine kinase inhibitors. It is crucial for pathologists to accurately identify tumors with these genetic alterations to enable patients to access optimal treatments and avoid unnecessary side effects of less effective agents. Although a number of different techniques can be used to identify ALK- and ROS1-rearranged lung cancers, immunohistochemistry and fluorescence in situ hybridization are the mainstays. - To review the role of immunohistochemistry in assessment of ALK and ROS1 rearrangements in lung cancer, focusing on practical issues in comparison with other modalities such as fluorescence in situ hybridization. - This manuscript reviews the current literature on ALK and ROS1 detection using immunohistochemistry and fluorescence in situ hybridization as well as current recommendations. - Although fluorescence in situ hybridization remains the gold standard for detecting ALK and ROS1 rearrangement in non-small cell lung cancer, immunohistochemistry plays an important role and can be an effective screening method for detection of these genetic alterations, or a diagnostic test in the setting of ALK.

  7. 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...

  8. Fluorescence in situ hybridization: an improved method of quantitating chromosome damage and repair

    International Nuclear Information System (INIS)

    Brown, J.M.; Evans, J.W.

    1993-01-01

    The authors combined fluorescence in situ hybridization (FISH) with specific full-length chromosome probes using the premature chromosome condensation (PCC) technique chromosome condensation (PCC) technique to simplify scoring chromosome damage and its repair. They have shown the technique works well and enables breaks and exchanges to be readily detected and scored in individual chromosomes. A chromosome 4 full-length specific library has been used in initial studies. (UK)

  9. Using Whole Mount in situ Hybridization to Link Molecular and Organismal Biology

    OpenAIRE

    Jacobs, Nicole L.; Albertson, R. Craig; Wiles, Jason R.

    2011-01-01

    Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the ...

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

    Science.gov (United States)

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

    2015-10-19

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

  11. In situ hybridization at the electron microscope level: hybrid detection by autoradiography and colloidal gold.

    Science.gov (United States)

    Hutchison, N J; Langer-Safer, P R; Ward, D C; Hamkalo, B A

    1982-11-01

    In situ hybridization has become a standard method for localizing DNA or RNA sequences in cytological preparations. We developed two methods to extend this technique to the transmission electron microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope in situ hybridization. Radioactively labeled complementary RNA (cRNA) is hybridized to metaphase chromosomes deposited on electron microscope grids and fixed in 70 percent ethanol vapor; hybridixation site are detected by autoradiography. Specific and intense labeling of chromosomal centromeric regions is observed even after relatively short exposure times. Inerphase nuclei present in some of the metaphase chromosome preparations also show defined paatterms of satellite DNA labeling which suggests that satellite-containing regions are associate with each other during interphase. The sensitivity of this method is estimated to at least as good as that at the light microscope level while the resolution is improved at least threefold. The second method, which circumvents the use of autoradiogrphic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction is improved at least threefold. The second method, which circumvents the use of autoradiographic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction with an antibody against biotin and secondary antibody adsorbed to the surface of over centromeric heterochromatin and along the associated peripheral fibers. Labeling is on average

  12. Seven-hour fluorescence in situ hybridization technique for enumeration of Enterobacteriaceae in food and environmental water sample.

    Science.gov (United States)

    Ootsubo, M; Shimizu, T; Tanaka, R; Sawabe, T; Tajima, K; Ezura, Y

    2003-01-01

    A fluorescent in situ hybridization (FISH) technique using an Enterobacteriaceae-specific probe (probe D) to target 16S rRNA was improved in order to enumerate, within a single working day, Enterobacteriaceae present in food and environmental water samples. In order to minimize the time required for the FISH procedure, each step of FISH with probe D was re-evaluated using cultured Escherichia coli. Five minutes of ethanol treatment for cell fixation and hybridization were sufficient to visualize cultured E. coli, and FISH could be performed within 1 h. Because of the difficulties in detecting low levels of bacterial cells by FISH without cultivation, a FISH technique for detecting microcolonies on membrane filters was investigated to improve the bacterial detection limit. FISH with probe D following 6 h of cultivation to grow microcolonies on a 13 mm diameter membrane filter was performed, and whole Enterobacteriaceae microcolonies on the filter were then detected and enumerated by manual epifluorescence microscopic scanning at magnification of x100 in ca 5 min. The total time for FISH with probe D following cultivation (FISHFC) was reduced to within 7 h. FISHFC can be applied to enumerate cultivable Enterobacteriaceae in food (above 100 cells g-1) and environmental water samples (above 1 cell ml-1). Cultivable Enterobacteriaceae in food and water samples were enumerated accurately within 7 h using the FISHFC method. A FISHFC method capable of evaluating Enterobacteriaceae contamination in food and environmental water within a single working day was developed.

  13. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated fluorescence in situ hybridization (FISH... Laboratory Equipment and Reagents § 866.4700 Automated fluorescence in situ hybridization (FISH) enumeration... Hybridization (FISH) Enumeration Systems.” See § 866.1(e) for the availability of this guidance document. [70 FR...

  14. Fluorescence in situ hybridization on human metaphase chromosomes detected by near-field scanning optical microscopy

    NARCIS (Netherlands)

    Moers, M.H.P.; Moers, M.H.P.; Kalle, W.H.J.; Kalle, W.H.J.; Ruiter, A.G.T.; Wiegant, J.C.A.G.; Raap, A.K.; Greve, Jan; de Grooth, B.G.; van Hulst, N.F.

    1996-01-01

    Fluorescence in situ hybridization o­n human metaphase chromosomes is detected by near-field scanning optical microscopy. This combination of cytochemical and scanning probe techniques enables the localization and identification of several fluorescently labelled genomic DNA fragments o­n a single

  15. Chromogenic in situ hybridization compared with other approaches to evaluate HER2/neu status in breast carcinomas

    Energy Technology Data Exchange (ETDEWEB)

    Rosa, F.E.; Santos, R.M. [Departamento de Patologia, Hospital das Clínicas, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Rogatto, S.R. [Departamento de Urologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Hospital A.C. Camargo, CIPE, São Paulo, SP (Brazil); Domingues, M.A.C. [Departamento de Patologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil)

    2013-03-19

    Human epidermal growth factor receptor 2 (HER2) has been evaluated in breast cancer patients to identify those most likely to benefit from herceptin-targeted therapy. HER2 amplification, detected in 20-30% of invasive breast tumors, is associated with reduced survival and metastasis. The most frequently used technique for evaluating HER2 protein status as a routine procedure is immunohistochemistry (IHC). HER2 copy number alterations have also been evaluated by fluorescence in situ hybridization (FISH) in moderate immunoexpression (IHC 2+) cases. An alternative procedure to evaluate gene amplification is chromogenic in situ hybridization (CISH), which has some advantages over FISH, including the correlation between HER2 status and morphological features. Other methodologies have also been used, such as silver-enhanced in situ hybridization (SISH) and quantitative real-time RT-PCR, to determine the number of HER2 gene copies and expression, respectively. Here we will present a short and comprehensive review of the current advances concerning HER2 evaluation in human breast cancer.

  16. Chromogenic in situ hybridization compared with other approaches to evaluate HER2/neu status in breast carcinomas

    Science.gov (United States)

    Rosa, F.E.; Santos, R.M.; Rogatto, S.R.; Domingues, M.A.C.

    2013-01-01

    Human epidermal growth factor receptor 2 (HER2) has been evaluated in breast cancer patients to identify those most likely to benefit from herceptin-targeted therapy. HER2 amplification, detected in 20-30% of invasive breast tumors, is associated with reduced survival and metastasis. The most frequently used technique for evaluating HER2 protein status as a routine procedure is immunohistochemistry (IHC). HER2 copy number alterations have also been evaluated by fluorescence in situ hybridization (FISH) in moderate immunoexpression (IHC 2+) cases. An alternative procedure to evaluate gene amplification is chromogenic in situ hybridization (CISH), which has some advantages over FISH, including the correlation between HER2 status and morphological features. Other methodologies have also been used, such as silver-enhanced in situ hybridization (SISH) and quantitative real-time RT-PCR, to determine the number of HER2 gene copies and expression, respectively. Here we will present a short and comprehensive review of the current advances concerning HER2 evaluation in human breast cancer. PMID:23558859

  17. Chromogenic in situ hybridization compared with other approaches to evaluate HER2/neu status in breast carcinomas

    International Nuclear Information System (INIS)

    Rosa, F.E.; Santos, R.M.; Rogatto, S.R.; Domingues, M.A.C.

    2013-01-01

    Human epidermal growth factor receptor 2 (HER2) has been evaluated in breast cancer patients to identify those most likely to benefit from herceptin-targeted therapy. HER2 amplification, detected in 20-30% of invasive breast tumors, is associated with reduced survival and metastasis. The most frequently used technique for evaluating HER2 protein status as a routine procedure is immunohistochemistry (IHC). HER2 copy number alterations have also been evaluated by fluorescence in situ hybridization (FISH) in moderate immunoexpression (IHC 2+) cases. An alternative procedure to evaluate gene amplification is chromogenic in situ hybridization (CISH), which has some advantages over FISH, including the correlation between HER2 status and morphological features. Other methodologies have also been used, such as silver-enhanced in situ hybridization (SISH) and quantitative real-time RT-PCR, to determine the number of HER2 gene copies and expression, respectively. Here we will present a short and comprehensive review of the current advances concerning HER2 evaluation in human breast cancer

  18. [HER-2 oncogene amplification assessment in invasive breast cancer by dual-color in situ hybridization (dc-CISH): a comparative study with fluorescent in situ hybridization (FISH)].

    Science.gov (United States)

    Akhdar, Abbas; Bronsard, Marc; Lemieux, Renald; Geha, Sameh

    2011-12-01

    The amplification of the gene encoding for the human epidermal growth factor receptor 2 (HER-2 oncogene), located on chromosome 17 (17q21-q22), or the overexpression of this receptor have prognostic and therapeutic implications in invasive breast cancer. An evaluation of the HER-2 status by immunohistochemistry (IHC) is performed on all invasive breast cancer cases. Fluorescent in situ hybridization (FISH) is considered as the gold standard for the detection of HER-2 gene amplification for IHC equivocal cases (score 2+). A more recent in situ hybridization technique, the dual-color chromogenic in situ hybridization (dc-CISH), has been proposed as an alternative to FISH. The aim of this study was to measure the correlation between dc-CISH and FISH for HER-2 oncogene amplification assessment in invasive breast cancer. We built four tissue micro-array (TMA) blocs with 100 breast invasive cancer cases that had been previously tested by IHC for HER-2 detection: 10 score 0 cases, 10 score 3+cases, 39 score 1+and 41 score 2+cases. Both FISH and dc-CISH techniques were applied on all TMA cases as well as on two additional slides serving as controls. Interpretation of dc-CISH was carried out by a pathologist using an optical microscope. For FISH, the interpretation was done by a professional from the medical genetics department using a fluorescent microscope linked to a computer system for image capturing and analysis. The interpretation of the HER-2/CEN-17 ratio for both tests was in accordance with the values of the updated recommendations from the Canadian National Consensus Meeting on HER-2/neu testing in breast cancer and from the ASCO/CAP. Among the 100 cases initially included in the study, eight were excluded from the analysis due to sampling or technical flaws. From the 92 remaining cases, we obtained a concordance of 97.8% (90/92 cases) between the two techniques (Kappa coefficient 0.97, 95% confidence interval). The correlation coefficient (rho) between ratios

  19. High sensitive diagnostic technique for virus gene using radioisotope. Development of PCR in situ hybridization and its application

    Energy Technology Data Exchange (ETDEWEB)

    Iwasaki, Takuya; Sada, Tetsutaro; Terai, Masanori; Sato, Yuko; Kurata, Takeshi [National Inst. of Infectious Diseases, Tokyo (Japan); Yamaguchi, Kazuyoshi; Yanagisawa, Akio; Sakai, Yuzo

    1998-02-01

    An animal model, experimentally induced squamous cell carcinoma was produced in hamster mucosa to establish a carcinogenic system inducible by interaction of a virus and chemical(s). Human hydatid mole and cholioepithelioma were chosen as the target subjects. Several tumor cells and host cells were isolated under microscopy and DNA was extracted from these cells to indentify the respective origins (maternal, paternal or host origin). The base sequence of HLADRB region was analyzed by PCR using synthetic primer and the tissue localization was examined by PCR in situ hybridization. A PCR product of 82 bp was found in 15 of 17 samples and there were 2 samples in which the product was not detectable with the constructed primer and 6 samples were negative. While significant differences were not observed by in situ hybridization compared with the negative control. (M.N.)

  20. High sensitive diagnostic technique for virus gene using radioisotope. Development of PCR in situ hybridization and its application

    International Nuclear Information System (INIS)

    Iwasaki, Takuya; Sada, Tetsutaro; Terai, Masanori; Sato, Yuko; Kurata, Takeshi; Yamaguchi, Kazuyoshi; Yanagisawa, Akio; Sakai, Yuzo

    1998-01-01

    An animal model, experimentally induced squamous cell carcinoma was produced in hamster mucosa to establish a carcinogenic system inducible by interaction of a virus and chemical(s). Human hydatid mole and cholioepithelioma were chosen as the target subjects. Several tumor cells and host cells were isolated under microscopy and DNA was extracted from these cells to indentify the respective origins (maternal, paternal or host origin). The base sequence of HLADRB region was analyzed by PCR using synthetic primer and the tissue localization was examined by PCR in situ hybridization. A PCR product of 82 bp was found in 15 of 17 samples and there were 2 samples in which the product was not detectable with the constructed primer and 6 samples were negative. While significant differences were not observed by in situ hybridization compared with the negative control. (M.N.)

  1. Application of fluorescence in situ hybridization technique in the diagnosis of acute promyelocytic leukemia with abnormal immunophenotype

    International Nuclear Information System (INIS)

    Chen Leilei; Sun Xuemei; Chen Junhao; Zhang Le

    2005-01-01

    To evaluate the utilization of fluorescence in situ hybridization (FISH) technique in the diagnosis of acute promyelocytic leukemia(APL) with abnormal immunophenotype, flow cytometry was used to detect the immunophenotype of mononuclear cells in APL patients and PML/RARα fusion gene was detected by FISH. The mononuclear cells of several APL patients showed abnormal immunophenotype: CD13 + , CD33 + , CD34 - , HLA-DR + and PML/RARα fusion gene was also detected, which was different from the regular result of APL: HLA- DR - , PML/RARα + . Therefore, the detection of immunophenotype in APL patients should not be regarded as the sole accurate target for diagnosing leukemia. FISH ,associated with traditional FAB classification, is a simple, rapid, accurate and direct method. It can be used to help confirm the diagnosis, to guide the formulation of a reasonable chemotherapy scheme and to supervise the efficacy of the treatment in patients with leukemia. (authors)

  2. In Situ Synthesis of Metal Nanoparticle Embedded Hybrid Soft Nanomaterials.

    Science.gov (United States)

    Divya, Kizhmuri P; Miroshnikov, Mikhail; Dutta, Debjit; Vemula, Praveen Kumar; Ajayan, Pulickel M; John, George

    2016-09-20

    The allure of integrating the tunable properties of soft nanomaterials with the unique optical and electronic properties of metal nanoparticles has led to the development of organic-inorganic hybrid nanomaterials. A promising method for the synthesis of such organic-inorganic hybrid nanomaterials is afforded by the in situ generation of metal nanoparticles within a host organic template. Due to their tunable surface morphology and porosity, soft organic materials such as gels, liquid crystals, and polymers that are derived from various synthetic or natural compounds can act as templates for the synthesis of metal nanoparticles of different shapes and sizes. This method provides stabilization to the metal nanoparticles by the organic soft material and advantageously precludes the use of external reducing or capping agents in many instances. In this Account, we exemplify the green chemistry approach for synthesizing these materials, both in the choice of gelators as soft material frameworks and in the reduction mechanisms that generate the metal nanoparticles. Established herein is the core design principle centered on conceiving multifaceted amphiphilic soft materials that possess the ability to self-assemble and reduce metal ions into nanoparticles. Furthermore, these soft materials stabilize the in situ generated metal nanoparticles and retain their self-assembly ability to generate metal nanoparticle embedded homogeneous organic-inorganic hybrid materials. We discuss a remarkable example of vegetable-based drying oils as host templates for metal ions, resulting in the synthesis of novel hybrid nanomaterials. The synthesis of metal nanoparticles via polymers and self-assembled materials fabricated via cardanol (a bioorganic monomer derived from cashew nut shell liquid) are also explored in this Account. The organic-inorganic hybrid structures were characterized by several techniques such as UV-visible spectroscopy, scanning electron microscopy (SEM), and

  3. Chromogenic in situ hybridization compared with other approaches to evaluate HER2/neu status in breast carcinomas

    Directory of Open Access Journals (Sweden)

    F.E. Rosa

    Full Text Available Human epidermal growth factor receptor 2 (HER2 has been evaluated in breast cancer patients to identify those most likely to benefit from herceptin-targeted therapy. HER2 amplification, detected in 20-30% of invasive breast tumors, is associated with reduced survival and metastasis. The most frequently used technique for evaluating HER2 protein status as a routine procedure is immunohistochemistry (IHC. HER2 copy number alterations have also been evaluated by fluorescence in situ hybridization (FISH in moderate immunoexpression (IHC 2+ cases. An alternative procedure to evaluate gene amplification is chromogenic in situ hybridization (CISH, which has some advantages over FISH, including the correlation between HER2 status and morphological features. Other methodologies have also been used, such as silver-enhanced in situ hybridization (SISH and quantitative real-time RT-PCR, to determine the number of HER2 gene copies and expression, respectively. Here we will present a short and comprehensive review of the current advances concerning HER2 evaluation in human breast cancer.

  4. Chromogenic in situ hybridization compared with other approaches to evaluate HER2/neu status in breast carcinomas

    Directory of Open Access Journals (Sweden)

    F.E. Rosa

    2013-03-01

    Full Text Available Human epidermal growth factor receptor 2 (HER2 has been evaluated in breast cancer patients to identify those most likely to benefit from herceptin-targeted therapy. HER2 amplification, detected in 20-30% of invasive breast tumors, is associated with reduced survival and metastasis. The most frequently used technique for evaluating HER2 protein status as a routine procedure is immunohistochemistry (IHC. HER2 copy number alterations have also been evaluated by fluorescence in situ hybridization (FISH in moderate immunoexpression (IHC 2+ cases. An alternative procedure to evaluate gene amplification is chromogenic in situ hybridization (CISH, which has some advantages over FISH, including the correlation between HER2 status and morphological features. Other methodologies have also been used, such as silver-enhanced in situ hybridization (SISH and quantitative real-time RT-PCR, to determine the number of HER2 gene copies and expression, respectively. Here we will present a short and comprehensive review of the current advances concerning HER2 evaluation in human breast cancer.

  5. Fathead minnow whole-mount in situ hybridization (WISH)

    Data.gov (United States)

    U.S. Environmental Protection Agency — This study demonstrates the potential of whole-mount in situ hybridization (WISH), in conjunction with quantitative real-time polymerase chain reaction (QPCR)...

  6. [Molecular classification of breast cancer patients obtained through the technique of chromogenic in situ hybridization (CISH)].

    Science.gov (United States)

    Fernández, Angel; Reigosa, Aldo

    2013-12-01

    Breast cancer is a heterogeneous disease composed of a growing number of biological subtypes, with substantial variability of the disease progression within each category. The aim of this research was to classify the samples object of study according to the molecular classes of breast cancer: luminal A, luminal B, HER2 and triple negative, as a result of the state of HER2 amplification obtained by the technique of chromogenic in situ hybridization (CISH). The sample consisted of 200 biopsies fixed in 10% formalin, processed by standard techniques up to paraffin embedding, corresponding to patients diagnosed with invasive ductal carcinoma of the breast. These biopsies were obtained from patients from private practice and the Institute of Oncology "Dr. Miguel Pérez Carreño", for immunohistochemistry (IHC) of hormone receptors and HER2 made in the Hospital Metropolitano del Norte, Valencia, Venezuela. The molecular classification of the patient's tumors considering the expression of estrogen and progesterone receptors by IHC and HER2 amplification by CISH, allowed those cases originally classified as unknown, since they had an indeterminate (2+) outcome for HER2 expression by IHC, to be grouped into the different molecular classes. Also, this classification permitted that some cases, initially considered as belonging to a molecular class, were assigned to another class, after the revaluation of the HER2 status by CISH.

  7. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications.

    Science.gov (United States)

    Cui, Chenghua; Shu, Wei; Li, Peining

    2016-01-01

    Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH

  8. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

    Directory of Open Access Journals (Sweden)

    Chenghua Cui

    2016-09-01

    Full Text Available Fluorescence in situ hybridization (FISH is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbials and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells

  9. Human Papilloma Virus 16 and 18 Association in Cervical Intraepithelial Lesions and Cervical Cancers by In Situ Hybridization

    Directory of Open Access Journals (Sweden)

    Mohanty Manisa

    2017-03-01

    Full Text Available Objective: To correlate the association of high risk Human Papilloma Virus (HPV 16, 18 in cervical intraepithelial lesions and cervical cancers by in-situ hybridization (ISH technique. Study Group: Cervical biopsy and hysterectomy specimen of 78 young and adult women, attending Hi-Tech Medical College and Hospital, Bhubaneswar, who were clinically or cytologically suspected of cervical intraepithelial lesion or cervical cancer were taken as source of target viral DNA. Material: Formalin 10% as fixative H & E stain as routine staining agent In-situ hybridization kit for HPV 16 and 18 DNA. Method: After following standard protocol for surgical grossing, HPV 16, 18 In-situ hybridization kit was used on paraffin embedded tissue sections. Results: The percentage of positive cases was highest in cervical cancer patients followed by cervical intraepithelial lesions, high grade, and low grade. Conclusion: This study has been carried out for the first in our state and our results show high degree of positivity of HPV 16/18 in females with cervical intraepithelial lesions and cervical cancers attending our tertiary care hospital.

  10. Diagnosis, prognosis and disease management using in situ hybridization

    International Nuclear Information System (INIS)

    Kucheria, K.; Talwar, R.

    2002-01-01

    The year 2001 saw unveiling of anatomy of the human genome with sequencing of 90% of the euchromatic region. But the ultimate goal of the Human Genome Project to delineate the positions of all genes is yet to be achieved. In Situ Hybridization (ISH) is one of the methods that help in localizing genes on chromosomes. The present study aimed to use radioactive- and fluorescent-labeled probes for screening various congenital anomalies (sex chromosomal and autosomal), for prenatal diagnosis and cancer genetics. Standard techniques were used for hybridization with radioactively and fluorescent labeled probes. Sex chromosome aneuploidies (XXY, XO, XXX, XYY etc.) were analyzed using centromeric probes for chromosomes X and Y. The cases with ambiguous genitalia were further analyzed using probe specific for the sex-determining region (SRY) on the Y chromosome. Suspected cases of Down syndrome were analyzed using probe specific for centromeric region of chromosome 21 to confirm trisomy 21. Prenatal diagnosis included screening aneuploidies of chromosomes 13, 18, 21, X and Y on uncultured cells and metaphases obtained from amniotic fluid and chorionic villi samplings. Gene alterations were also studied in Retinoblastoma patients, Chronic Myeloid Leukemia (CML) and Acute Promyelocytic Leukemia (APML) using probes specific for Rb1, bcr/abl and PML/RARα genes respectively. Response to therapy was assessed by evaluating minimal residual disease (MRD) in leukemia patients. Attempts were also made to analyze cells obtained from buccal mucosa and bladder epithelium that could facilitate rapid screening of sex chromosome anomalies and bladder cancer without painful invasive techniques. Prenatal diagnosis using ISH on uncultured cells could provide an accurate and rapid result. These results of prenatal diagnosis were in conformation with results of conventional cytogenetics obtained after long-term cultures. Molecular rearrangements that could not be detected with conventional

  11. Novel in-situ lamella fabrication technique for in-situ TEM.

    Science.gov (United States)

    Canavan, Megan; Daly, Dermot; Rummel, Andreas; McCarthy, Eoin K; McAuley, Cathal; Nicolosi, Valeria

    2018-03-29

    In-situ transmission electron microscopy is rapidly emerging as the premier technique for characterising materials in a dynamic state on the atomic scale. The most important aspect of in-situ studies is specimen preparation. Specimens must be electron transparent and representative of the material in its operational state, amongst others. Here, a novel fabrication technique for the facile preparation of lamellae for in-situ transmission electron microscopy experimentation using focused ion beam milling is developed. This method involves the use of rotating microgrippers during the lift-out procedure, as opposed to the traditional micromanipulator needle and platinum weld. Using rotating grippers, and a unique adhesive substance, lamellae are mounted onto a MEMS device for in-situ TEM annealing experiments. We demonstrate how this technique can be used to avoid platinum deposition as well as minimising damage to the MEMS device during the thinning process. Our technique is both a cost effective and readily implementable alternative to the current generation of preparation methods for in-situ liquid, electrical, mechanical and thermal experimentation within the TEM as well as traditional cross-sectional lamella preparation. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Reliability of chromogenic in situ hybridization for epidermal growth factor receptor gene copy number detection in non-small-cell lung carcinomas: a comparison with fluorescence in situ hybridization study.

    Science.gov (United States)

    Yoo, Seol Bong; Lee, Hyun Ju; Park, Jung Ok; Choe, Gheeyoung; Chung, Doo Hyun; Seo, Jeong-Wook; Chung, Jin-Haeng

    2010-03-01

    Fluorescence in situ hybridization (FISH) has been known to be the most representative and standardized test for assessing gene amplification. However, FISH requires a fluorescence microscope, the signals are labile and rapidly fade over time. Recently, chromogenic in situ hybridization (CISH) has emerged as a potential alternative to FISH. The aim of this study is to test the reliability of CISH technique for the detection of epidermal growth factor receptor (EGFR) gene amplification in non-small-cell lung carcinomas (NSCLC), to compare CISH results with FISH. A total of 277 formalin-fixed and paraffin embedded NSCLC tissue samples were retrieved from the surgical pathology archives at Seoul National University Bundang Hospital. CISH and FISH examinations were performed to test EGFR gene amplification status. There was high concordance in the assessment of EGFR gene copy number between CISH and FISH tests (Kappa coefficient=0.83). Excellent concordance was shown between two observers on the interpretation of the CISH results (Kappa coefficient=0.90). In conclusion, CISH result is highly reproducible, accurate and practical method to determine EGFR gene amplification in NSCLC. In addition, CISH allows a concurrent analysis of histological features of the tumors and gene copy numbers.

  13. Detection of distribution of avian influenza H5N1 virus by immunohistochemistry, chromogenic in situ hybridization and real-time PCR techniques in experimentally infected chickens.

    Science.gov (United States)

    Chamnanpood, Chanpen; Sanguansermsri, Donruedee; Pongcharoen, Sutatip; Sanguansermsri, Phanchana

    2011-03-01

    Ten specific pathogen free (SPF) chickens were inoculated intranasally with avian influenza virus subtype H5N1. Evaluation revealed distribution of the virus in twelve organs: liver, intestine, bursa, lung, trachea, thymus, heart, pancreas, brain, spleen, kidney, and esophagus. Immunohistochemistry (IHC), chromogenic in situ hybridization (CISH), and real-time polymerase chain reaction (PCR) were developed and compared for detection of the virus from the organs. The distribution of avian influenza H5N1 in chickens varied by animal and detecting technique. The heart, kidneys, intestines, lungs, and pancreas were positive with all three techniques, while the others varied by techique. The three techniques can be used to detect avian influenza effectively, but the pros and cons of each technique need to be determined. The decision of which technique to use depends on the objective of the examination, budget, type and quality of samples, laboratory facilities and technician skills.

  14. A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species.

    Science.gov (United States)

    Sinigaglia, Chiara; Thiel, Daniel; Hejnol, Andreas; Houliston, Evelyn; Leclère, Lucas

    2018-02-01

    In situ hybridization is a widely employed technique allowing spatial visualization of gene expression in fixed specimens. It has greatly advanced our understanding of biological processes, including developmental regulation. In situ protocols are today routinely followed in numerous laboratories, and although details might change, they all include a hybridization step, where specific antisense RNA or DNA probes anneal to the target nucleic acid sequence. This step is generally carried out at high temperatures and in a denaturing solution, called hybridization buffer, commonly containing 50% (v/v) formamide - a hazardous chemical. When applied to the soft-bodied hydrozoan medusa Clytia hemisphaerica, we found that this traditional hybridization approach was not fully satisfactory, causing extensive deterioration of morphology and tissue texture which compromised our observation and interpretation of results. We thus tested alternative solutions for in situ detection of gene expression and, inspired by optimized protocols for Northern and Southern blot analysis, we substituted the 50% formamide with an equal volume of 8M urea solution in the hybridization buffer. Our new protocol not only yielded better morphologies and tissue consistency, but also notably improved the resolution of the signal, allowing more precise localization of gene expression and reducing aspecific staining associated with problematic areas. Given the improved results and reduced manipulation risks, we tested the urea protocol on other metazoans, two brachiopod species (Novocrania anomala and Terebratalia transversa) and the priapulid worm Priapulus caudatus, obtaining a similar reduction of aspecific probe binding. Overall, substitution of formamide by urea during in situ hybridization offers a safer alternative, potentially of widespread use in research, medical and teaching contexts. We encourage other workers to test this approach on their study organisms, and hope that they will also

  15. Image files of planarians analyzed by in situ hybridication and immunohistochemical staining - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Plabrain DB Image files of planarians analyzed by in situ hybridication and immunohistochemical... staining Data detail Data name Image files of planarians analyzed by in situ hybridication and immunohistochemical...sion patterns by whole-mount in situ hybridication and also protein distribution by immunohistochemical...Images are displayed in A list of image files of planarians analyzed by in situ hybridication and immunohistochemical...le search URL - Data acquisition method Whole-mount in situ hybridication, immunohistochemical staining Data

  16. Analysis of hepcidin expression: in situ hybridization and quantitative polymerase chain reaction from paraffin sections.

    Science.gov (United States)

    Sakuraoka, Yuhki; Sawada, Tokihiko; Shiraki, Takayuki; Park, Kyunghwa; Sakurai, Yuhichiro; Tomosugi, Naohisa; Kubota, Keiichi

    2012-07-28

    To establish methods for quantitative polymerase chain reaction (PCR) for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of hepatocellular carcinoma (HCC). Total RNA from paraffin-embedded sections was isolated from 68 paraffin-embedded samples of HCC. Samples came from 54 male and 14 female patients with a mean age of 66.8 ± 7.8 years. Quantitative PCR was performed. Immunohistochemistry and in situ hybridization for hepcidin were also performed. Quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections of HCC was performed successfully. The expression level of hepcidin mRNA in cancer tissues was significantly higher than that in non-cancer tissues. A method of in situ hybridization for hepcidin was established successfully, and this demonstrated that hepcidin mRNA was expressed in non-cancerous tissue but absent in cancerous tissue. We have established novel methods for quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of HCC.

  17. Heavy ion-induced chromosomal aberrations analyzed by fluorescence in situ hybridization

    International Nuclear Information System (INIS)

    Durante, M.; Gialanella, G.; Grossi, G.; Pugliese, M.; Cella, L.; Greco, O.; George, K.; Yang, T.C.

    1997-01-01

    We have investigated the effectiveness of heavy ions in the induction of chromosomal aberrations in mammalian cells by the recent technique of fluorescence in situ hybridization (FISH) with whole-chromosome probes. FISH-painting was used both in metaphase and interphase (prematurely condensed) chromosomes. The purpose of our experiments was to address the following problems: (a) the ratio of different types of aberrations as a function of radiation quality (search for biomarkers); (b) the ratio between aberrations scored in interphase and metaphase as a function of radiation quality (role of apoptosis); (c) differences between cytogenetic effects produced by different ions at the same LET (role of track structure). (orig./MG)

  18. Heavy ion-induced chromosomal aberrations analyzed by fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Durante, M; Gialanella, G; Grossi, G; Pugliese, M [Univ. ` ` Federico II` ` , Naples (Italy). Dept. of Physics; [INFN, Naples (Italy); Cella, L; Greco, O [Univ. ` ` Federico II` ` , Naples (Italy). Dept. of Physics; Furusawa, Y [NIRS, Chiba (Japan); George, K; Yang, T C [NASA Lyndon B. Johnson Space Center, Houston, TX (United States)

    1997-09-01

    We have investigated the effectiveness of heavy ions in the induction of chromosomal aberrations in mammalian cells by the recent technique of fluorescence in situ hybridization (FISH) with whole-chromosome probes. FISH-painting was used both in metaphase and interphase (prematurely condensed) chromosomes. The purpose of our experiments was to address the following problems: (a) the ratio of different types of aberrations as a function of radiation quality (search for biomarkers); (b) the ratio between aberrations scored in interphase and metaphase as a function of radiation quality (role of apoptosis); (c) differences between cytogenetic effects produced by different ions at the same LET (role of track structure). (orig./MG)

  19. 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)

  20. Fluorescence in situ hybridization with reference to biodosimetry: a review

    International Nuclear Information System (INIS)

    Venkatachalam, P.; Paul, S.F.D.; Jeevanram, R.K.

    1996-01-01

    Many advances have taken place in the field of radiation biodosimetry in the recent past. Measurement of dicentric chromosome aberrations, was first developed and followed by micronuclei scoring. These, however, are unstable type aberrations and the cells carrying such aberrations are eliminated from the body in few years. They are therefore of use primarily in case of accidental exposures. The challenge is to measure the cumulative radiation exposure resulting from normal operations by measuring stable chromosome aberrations. Banding technique can measure stable chromosome aberration but require long time to analyse the banding pattern to study translocations. On the other hand fluorescence in situ hybridization (FISH) technique is sensitive, fast and easy to identify the translocations as the chromosomes involved in translocation are painted with different colours. This review brings out the requirements of various materials, their preparations, method of detection of fluorescence etc. for carrying out FISH. The experience of various laboratories using FISH in the monitoring of radiation absorbed dose is discussed. (author)

  1. Evaluation of fluorescent in-situ hybridization technique for diagnosis of malaria in Ahero Sub-County hospital, Kenya.

    Science.gov (United States)

    Kandie, Regina; Ochola, Rachel; Njaanake, Kariuki

    2018-01-08

    Malaria is a major cause of morbidity and mortality. Treatment of malaria in a timely manner could avert deaths. Treatment ultimately relies on the rapid and accurate diagnosis. Fluorescence in situ hybridization (FISH), a cytogenetic technique based on detection of specific nucleic acid, has the potential to address the limitations of the current diagnostic approaches. This study investigates further the performance of FISH for the diagnosis of malaria in a rural setting in Western Kenya. Blood samples from 302 patients presenting with fever (temperature ≥ 37.5 °C) were examined for malaria using the Giemsa microscopy (GM), rapid diagnostic test (RDT), polymerase chain reaction (PCR) and FISH. The sensitivity and specificity of FISH was 85.6% and 96.2% respectively, while the corresponding values for GM were 82.2% and 100% respectively. RDT and PCR had sensitivities of 91.1% and 98.9%, respectively with their specificities being 89.6 and 100%, respectively. The positive predictive values for RDT, GM, FISH and PCR were 78.8%, 100%, 90.6% and 100%, respectively. The negative predictive values for RDT, GM, FISH and PCR were 96.0%, 93.0%, 94.0% and 99.5%, respectively. Their respective diagnostic accuracies were 90.1%, 94.7% 93.0% and 99.7%. The present study demonstrates that the specificity and reproducibility of FISH assays are high, thus adding to the growing evidence on the potential of the technique as an effective tool for the detection of malaria parasites in remote settings.

  2. Nerve growth factor mRNA in brain: localization by in situ hybridization

    International Nuclear Information System (INIS)

    Rennert, P.D.; Heinrich, G.

    1986-01-01

    Nerve Growth Factor is a 118 amino acid polypeptide that plays an important role in the differentiation and survival of neurons. The recent discovery that a mRNA that encodes beta Nerve Growth Factor is present in brain suggests that the Nerve Growth Factor gene may not only regulate gene expression of peripheral but also of central neurons. To identify the site(s) of Nerve Growth Factor mRNA production in the brain and to determine which cells express the Nerve Growth Factor gene, the technique of in situ hybridization was employed. A 32P-labeled RNA probe complementary to Nerve Growth Factor mRNA hybridized to cells in the stratum granulosum of the dentate gyrus and the stratum pyramidale of the hippocampus. These observations identify for the first time cellular sites of Nerve Growth Factor gene expression in the central nervous system, and suggest that Nerve Growth Factor mRNA is produced by neurons

  3. Chromosome identification by new molecular markers and genomic in situ hybridization in the Triticum-Secale-Thinopyrum trigeneric hybrids.

    Science.gov (United States)

    Dai, Yi; Duan, Yamei; Chi, Dawn; Liu, Huiping; Huang, Shuai; Cao, Wenguang; Gao, Yong; Fedak, George; Chen, Jianmin

    2017-08-01

    It is very important to use chromosome-specific markers for identifying alien chromosomes in advanced generations of distant hybridization. The chromosome-specific markers of rye and Thinopyrum elongatum, as well as genomic in situ hybridization, were used to identify the alien chromosomes in eight lines that were derived from the crossing between Triticum trititrigia (AABBEE) and triticale (AABBRR). The results showed that four lines contained all rye chromosomes but no Th. elongatum chromosomes. The line RE36-1 contained all of the rye chromosomes except for chromosome 2R. The lines RE33-2 and RE62-1 contained all rye chromosomes and 1E and 5E translocated chromosome, respectively. The line RE24-4 contained 12 rye chromosomes plus a 7E chromosome or 12 rye chromosomes plus one R-E translocated chromosome. Chromosome identification in the above lines was consistent using chromosome-specific markers and genomic in situ hybridization. These chromosome-specific markers provide useful tools for detecting alien chromosomes in trigeneric hybrids, and these lines could be utilized as valuable germplasm in wheat improvement.

  4. Tracking alien chromosome in sativa background by genomic in situ hybridization

    International Nuclear Information System (INIS)

    Abbasi, F.M.; Iqbal, M.; Salim, M.

    2004-01-01

    Genomic in situ hybridization (GISH) was used to look into the genomic constitution of monosomic alien -addition line derived from O. sativa x O. brachyantha. Biotin label genomic DNA from O. brachyantha was used as probe. The probe hybridized to the brachyantha chromosome. No detectable hybridization signal was observed on sativa chromosomes. This differential painting of chromosome enables us to unequivocally discriminate brachyantha chromosome from those of sativa. Results showed the usefulness of GISH in the identification of a single alien chromosome in the sativa background. (author)

  5. 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

  6. Oligonucleotide PIK3CA/Chromosome 3 Dual in Situ Hybridization Automated Assay with Improved Signals, One-Hour Hybridization, and No Use of Blocking DNA.

    Science.gov (United States)

    Zhang, Wenjun; Hubbard, Antony; Baca-Parkinson, Leslie; Stanislaw, Stacey; Vladich, Frank; Robida, Mark D; Grille, James G; Maxwell, Daniel; Tsao, Tsu-Shuen; Carroll, William; Gardner, Tracie; Clements, June; Singh, Shalini; Tang, Lei

    2015-09-01

    The PIK3CA gene at chromosome 3q26.32 was found to be amplified in up to 45% of patients with squamous cell carcinoma of the lung. The strong correlation between PIK3CA amplification and increased phosphatidylinositol 3-kinase (PI3K) pathway activities suggested that PIK3CA gene copy number is a potential predictive biomarker for PI3K inhibitors. Currently, all microscopic assessments of PIK3CA and chromosome 3 (CHR3) copy numbers use fluorescence in situ hybridization. PIK3CA probes are derived from bacterial artificial chromosomes whereas CHR3 probes are derived mainly from the plasmid pHS05. These manual fluorescence in situ hybridization assays mandate 12- to 18-hour hybridization and use of blocking DNA from human sources. Moreover, fluorescence in situ hybridization studies provide limited morphologic assessment and suffer from signal decay. We developed an oligonucleotide-based bright-field in situ hybridization assay that overcomes these shortcomings. This assay requires only a 1-hour hybridization with no need for blocking DNA followed by indirect chromogenic detection. Oligonucleotide probes produced discrete and uniform CHR3 stains superior to those from the pHS05 plasmid. This assay achieved successful staining in 100% of the 195 lung squamous cell carcinoma resections and in 94% of the 33 fine-needle aspirates. This robust automated bright-field dual in situ hybridization assay for the simultaneous detection of PIK3CA and CHR3 centromere provides a potential clinical diagnostic method to assess PIK3CA gene abnormality in lung tumors. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  7. Supernumerary ring chromosome 20 characterized by fluorescence in situ hybridization

    NARCIS (Netherlands)

    Van Langen, Irene M.; Otter, Mariëlle A.; Aronson, Daniël C.; Overweg-Plandsoen, W.C.G.; Hennekam, Raoul C.M.; Leschot, Nico J.; Hoovers, Jan M.N.

    1996-01-01

    We report on a boy with mild dysmorphic features and developmental delay, in whom karyotyping showed an additional minute ring chromosome in 60% of metaphases. Fluorescence in situ hybridization (FISH) with a centromere specific probe demonstrated that the ring chromosome contained the centromeric

  8. Comparison of Fluorescence In Situ Hybridization and Chromogenic In Situ Hybridization for Low and High Throughput HER2 Genetic Testing

    Science.gov (United States)

    Poulsen, Tim S.; Espersen, Maiken L. M.; Kofoed, Vibeke; Dabetic, Tanja; Høgdall, Estrid; Balslev, Eva

    2013-01-01

    The purpose was to evaluate and compare 5 different HER2 genetic assays with different characteristics that could affect the performance to analyze the human epidermal growth factor 2 (HER2) gene copy number under low and high throughput conditions. The study included 108 tissue samples from breast cancer patients with HER2 immunohistochemistry (IHC) results scored as 0/1+, 2+, and 3+. HER2 genetic status was analysed using chromogenic in situ hybridization (CISH) and fluorescence in situ hybridization (FISH). Scoring results were documented through digital image analysis. The cancer region of interest was identified from a serial H&E stained slide following tissue cores were transferred to a tissue microarrays (TMA). When using TMA in a routine flow, all patients will be tested for HER2 status with IHC followed by CISH or FISH, thereby providing individual HER2 results. In conclusion, our results show that the differences between the HER2 genetic assays do not have an effect on the analytic performance and the CISH technology is superior to high throughput HER2 genetic testing due to scanning speed, while the IQ-FISH may still be a choice for fast low throughput HER2 genetic testing. PMID:24383005

  9. Dual-colour chromogenic in-situ hybridization is a potential alternative to fluorescence in-situ hybridization in HER2 testing.

    Science.gov (United States)

    Hwang, Cheng-Cheng; Pintye, Mariann; Chang, Liang-Che; Chen, Huang-Yang; Yeh, Kun-Yan; Chein, Hui-Ping; Lee, Nin; Chen, Jim-Ray

    2011-11-01

    Dual-colour chromogenic in-situ hybridization (dc-CISH) is an emerging methodology for characterizing genomic alterations. This study was aimed at evaluating the performance of a dc-CISH kit (ZytoVision) in determining human epidermal growth factor receptor 2 (HER2) status in breast cancer. Two hundred and twenty-eight invasive breast carcinomas arranged in tissue microarrays were analysed in parallel with dc-CISH, fluorescence in-situ hybridization (FISH), and immunohistochemistry. Of 227 tumours with available FISH and dc-CISH results, HER2 amplification and non-amplification were detected in 49 (21.6%) and 178 (78.4%) tumours, respectively, by both assays. The concordance between dc-CISH and FISH results showed 100% agreement (κ-coefficient=1.00). Immunohistochemically, 162 (71%), 25 (11.0%) and 41 (18%) tumours were scored 0/1+, 2+, and 3+, respectively. The corresponding results with both FISH and dc-CISH demonstrated HER2 amplification in two (3.2%), nine (36%) and 38 (93%) tumours, respectively. Complete consensus among these three methods was observed in 197 cases, representing 98% of all 3+ and 0/1+ tumours (κ-coefficient=0.92). Confirmatory testing of 25 2+ tumours showed complete consensus between FISH and dc-CISH. dc-CISH is a promising alternative to FISH in HER2 testing, and the single-institute incidence of HER2 amplification in breast cancer in Taiwan is 21.2%. © 2011 Blackwell Publishing Limited.

  10. Specific identification of human papillomavirus type in cervical smears and paraffin sections by in situ hybridization with radioactive probes: a preliminary communication

    International Nuclear Information System (INIS)

    Gupta, J.; Gendelman, H.E.; Naghashfar, Z.; Gupta, P.; Rosenshein, N.; Sawada, E.; Woodruff, J.D.; Shah, K.

    1985-01-01

    Cervical Papanicolaou smears and paraffin sections of biopsy specimens obtained from women attending dysplasia clinics were examined for viral DNA sequences by in situ hybridization technique using 35 S-labeled cloned recombinant DNA probes of human papillomavirus (HPV) types 6, 11, and 16. These and one unrelated DNA probe complementary to measles virus RNA were labeled by nick translation using either one or two 35 S-labeled nucleotides. Paraffin sections and cervical smears were collected on pretreated slides, hybridized with the probes under stringent or nonstringent conditions for 50 h, and autoradiographed. Additional cervical specimens from the same women were examined for the presence of genus-specific papillomavirus capsid antigen by the immunoperoxidase technique. Preliminary results may be summarized as follows. The infecting virus could be identified in smears as well as in sections. Viral DNA sequences were detected only when there were condylomatous cells in the specimen and in only a proportion of the condylomatous cells. Even under stringent conditions, some specimens reacted with both HPV-6 and HPV-11. In some instances, the cells did not hybridize with any of the three probes even when duplicate specimens contained frankly condylomatous, capsid antigen-positive cells. In situ hybridization of Papanicolaou smears or of tissue sections is a practical method for diagnosis and follow-up of specific papillomavirus infection using routinely collected material

  11. Fluorescent In Situ Hybridization to Detect Transgene Integration into Plant Genomes

    Science.gov (United States)

    Schwarzacher, Trude

    Fluorescent chromosome analysis technologies have advanced our understanding of genome organization during the last 30 years and have enabled the investigation of DNA organization and structure as well as the evolution of chromosomes. Fluorescent chromosome staining allows even small chromosomes to be visualized, characterized by their composition and morphology, and counted. Aneuploidies and polyploidies can be established for species, breeding lines, and individuals, including changes occurring during hybridization or tissue culture and transformation protocols. Fluorescent in situ hybridization correlates molecular information of a DNA sequence with its physical location on chromosomes and genomes. It thus allows determination of the physical position of sequences and often is the only means to determine the abundance and distribution of DNA sequences that are difficult to map with any other molecular method or would require segregation analysis, in particular multicopy or repetitive DNA. Equally, it is often the best way to establish the incorporation of transgenes, their numbers, and physical organization along chromosomes. This chapter presents protocols for probe and chromosome preparation, fluorescent in situ hybridization, chromosome staining, and the analysis of results.

  12. Determination of HER2 amplification in primary breast cancer using dual-colour chromogenic in situ hybridization is comparable to fluorescence in situ hybridization: a European multicentre study involving 168 specimens

    Science.gov (United States)

    García-Caballero, Tomás; Grabau, Dorthe; Green, Andrew R; Gregory, John; Schad, Arno; Kohlwes, Elke; Ellis, Ian O; Watts, Sarah; Mollerup, Jens

    2010-01-01

    García-Caballero T, Grabau D, Green A R, Gregory J, Schad A, Kohlwes E, Ellis I O, Watts S & Mollerup J (2010) Histopathology56, 472–480 Determination of HER2 amplification in primary breast cancer using dual-colour chromogenic in situ hybridization is comparable to fluorescence in situ hybridization: a European multicentre study involving 168 specimens Aims: Fluorescence in situ hybridization (FISH) can be used to reveal several genomic imbalances relevant to proper cancer diagnosis and to the correct treatment regime. However, FISH requires expensive and advanced fluorescence microscopes in addition to expertise in fluorescence microscopy. To determine whether a newly developed dual-colour chromogenic in situ hybridization (CISH) method is a suitable alternative to FISH, we analysed the human epidermal growth factor receptor 2 gene (HER2) amplification level of 168 breast cancer specimens using dual-colour CISH and FISH and compared the results. Methods and results: We found 100% agreement between HER2 status determined by FISH and dual-colour CISH. Furthermore, we observed that the time used to score slides was significantly reduced by 28% in dual-colour CISH compared with the FISH protocol. Concordance between HER2 protein status and dual-colour CISH or FISH was equally good with an overall agreement of 96.8%. Correlation between the HER2/centromere 17 gene ratios obtained with dual-colour CISH and FISH was highly significant with an overall correlation coefficient (ρ) of 0.96. Conclusions: We conclude that dual-colour CISH and bright field microscopy are excellent alternatives to FISH when analysing the HER2 status of primary breast cancer. PMID:20459554

  13. Identification of MYCN gene amplification in neuroblastoma using chromogenic in situ hybridization (CISH): an alternative and practical method.

    Science.gov (United States)

    Bhargava, Rohit; Oppenheimer, Orit; Gerald, William; Jhanwar, Suresh C; Chen, Beiyun

    2005-06-01

    Chromogenic in situ hybridization (CISH) is a recently developed technique, which utilizes the general principles of in situ hybridization and a detection system similar to immunohistochemistry. To assess the utility of CISH for analysis of MYCN gene amplification, we compared this assay with established diagnostic assays such as Southern blot analysis (SB) and fluorescent in situ hybridization (FISH). CISH was performed on 67 cases of neuroblastoma using tissue microarray (65 cases) and whole tissue sections (2 cases). Unequivocal, high-level amplification (> or =10 gene copies per tumor nucleus) was identified in 19 of 67 (28.4%) tumors. Two (3%) tumors showed low-level amplification (6-9 gene copies per tumor nucleus). No amplification was seen in 46 of 67 (68.6%) tumors. SB data were available in 44 tumors. Forty-one of the 44 tumors (93%) showed concordant results between CISH and SB. Three tumors showed MYCN amplification by CISH but no amplification by SB, most likely due to dilution effect of nonneoplastic tissue in the test samples. Two of these three tumors also showed MYCN amplification by FISH, and the third tumor was not analyzed by FISH. FISH data were available in total of 30 tumors. All 30 tumors showed concordant results between CISH and FISH for classifying a tumor as MYCN amplified or not amplified. We conclude that CISH is an accurate method for determining MYCN gene amplification, with added advantages that make it a more practically useful method.

  14. Human cDNA mapping using fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-03-04

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

  15. A list of image files of planarians analyzed by in situ hybridication and immunohistochemical staining - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Plabrain DB A list of image files of planarians analyzed by in situ hybridication and immunohistochemical...tu hybridication and also protein distribution by immunohistochemical staining in intact planarians or plana...planarians analyzed by In situ hybridication and immunohistochemical staining . D..._image#en Data acquisition method Whole-mount in situ hybridication, immunohistochemical...te Policy | Contact Us A list of image files of planarians analyzed by in situ hybridication and immunohistochemical staining - Plabrain DB | LSDB Archive ...

  16. Identification of Cannabis sativa L. using the 1-kbTHCA synthase-fluorescence in situ hybridization probe.

    Science.gov (United States)

    Jeangkhwoa, Pattraporn; Bandhaya, Achirapa; Umpunjun, Puangpaka; Chuenboonngarm, Ngarmnij; Panvisavas, Nathinee

    2017-03-01

    This study reports a successful application of fluorescence in situ hybridization (FISH) technique in the identification of Cannabis sativa L. cells recovered from fresh and dried powdered plant materials. Two biotin-16-dUTP-labeled FISH probes were designed from the Cannabis-specific tetrahydrocannabinolic acid synthase (THCAS) gene and the ITS region of the 45S rRNA gene. Specificity of probe-target hybridization was tested against the target and 4 non-target plant species, i.e., Humulus lupulus, Mitragyna speciosa, Papaver sp., and Nicotiana tabacum. The 1-kb THCA synthase hybridization probe gave Cannabis-specific hybridization signals, unlike the 700-bp Cannabis-ITS hybridization probe. Probe-target hybridization was also confirmed against 20 individual Cannabis plant samples. The 1-kb THCA synthase and 700-bp Cannabis-ITS hybridization probes clearly showed 2 hybridization signals per cell with reproducibility. The 1-kb THCA synthase probe did not give any FISH signal when tested against H. lupulus, its closely related member of the Canabaceae family. It was also showed that 1-kb THCA synthase FISH probe can be applied to identify small amount of dried powdered Cannabis material with an addition of rehydration step prior to the experimental process. This study provided an alternative identification method for Cannabis trace. Copyright © 2016. Published by Elsevier B.V.

  17. RNA Imaging with Multiplexed Error Robust Fluorescence in situ Hybridization

    Science.gov (United States)

    Moffitt, Jeffrey R.; Zhuang, Xiaowei

    2016-01-01

    Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single-cells could revolutionize our understanding of a variety of cellular and tissue behaviors in both healthy and diseased states. Single-molecule Fluorescence In Situ Hybridization (smFISH)—an approach where individual RNAs are labeled with fluorescent probes and imaged in their native cellular and tissue context—provides both the copy number and spatial context of RNAs but has been limited in the number of RNA species that can be measured simultaneously. Here we describe Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH), a massively parallelized form of smFISH that can image and identify hundreds to thousands of different RNA species simultaneously with high accuracy in individual cells in their native spatial context. We provide detailed protocols on all aspects of MERFISH, including probe design, data collection, and data analysis to allow interested laboratories to perform MERFISH measurements themselves. PMID:27241748

  18. Fluorescence in situ hybridization techniques (FISH) to detect changes in CYP19a gene expression of Japanese medaka (Oryzias latipes)

    International Nuclear Information System (INIS)

    Park, June-Woo; Tompsett, Amber; Zhang, Xiaowei; Newsted, John L.; Jones, Paul D.; Au, Doris; Kong, Richard; Wu, Rudolf S.S.; Giesy, John P.; Hecker, Markus

    2008-01-01

    The aim of this study was to develop a sensitive in situ hybridization methodology using fluorescence-labeled riboprobes (FISH) that allows for the evaluation of gene expression profiles simultaneously in multiple target tissues of whole fish sections of Japanese medaka (Oryzias latipes). To date FISH methods have been limited in their application due to autofluorescence of tissues, fixatives or other components of the hybridization procedure. An optimized FISH method, based on confocal fluorescence microscopy was developed to reduce the autofluorescence signal. Because of its tissue- and gender-specific expression and relevance in studies of endocrine disruption, gonadal aromatase (CYP19a) was used as a model gene. The in situ hybridization (ISH) system was validated in a test exposure with the aromatase inhibitor fadrozole. The optimized FISH method revealed tissue-specific expression of the CYP19a gene. Furthermore, the assay could differentiate the abundance of CYP19a mRNA among cell types. Expression of CYP19a was primarily associated with early stage oocytes, and expression gradually decreased with increasing maturation. No expression of CYP19a mRNA was observed in other tissues such as brain, liver, or testes. Fadrozole (100 μg/L) caused up-regulation of CYP19a expression, a trend that was confirmed by RT-PCR analysis on excised tissues. In a combination approach with gonad histology, it could be shown that the increase in CYP19a expression as measured by RT-PCR on a whole tissue basis was due to a combination of both increases in numbers of CYP19a-containing cells and an increase in the amount of CYP19a mRNA present in the cells

  19. Chromogenic in situ hybridization for Her-2/neu-oncogene in breast cancer: comparison of a new dual-colour chromogenic in situ hybridization with immunohistochemistry and fluorescence in situ hybridization.

    Science.gov (United States)

    Mayr, Doris; Heim, Sibylle; Weyrauch, Kerstin; Zeindl-Eberhart, Evelyn; Kunz, Anne; Engel, Jutta; Kirchner, Thomas

    2009-12-01

    Her-2/neu testing is used as a marker for Herceptin therapy. The aim was to investigate new dual-colour chromogenic in situ hybridization (CISH), in a large number of breast carcinomas (n = 205) with DNA-specific dual-colour probes (ZytoVision, Bremerhaven, Germany) and to compare the results with immunohistochemistry (n = 205) and fluorescence in situ hybridization (FISH) (n = 129). Paraffin-embedded tissue of 205 patients was used. After immunohistochemistry with a focus on immunohistochemically uncertain cases, Her-2/neu amplification using dual-colour CISH (ZytoVision) was analysed. Validation by FISH was performed. The results were: immunohistochemistry, 27.8% with strong expression, 53.7% with uncertain overexpression and 18.5% with no expression; FISH, 25.6% amplified and 74.4% negative; CISH, 35.6% amplified, 62.9% negative and 1.5% not evaluable. Comparison of immunohistochemistry with CISH: CISH negative in 100% with immunohistochemistry 0/1+, amplified in 82.5% with immunohistochemistry 3+; 5.9% contradictory results: 4.4% immunohistochemistry 3+ and negative by CISH, 1.5% negative in immunohistochemistry but amplified by CISH; FISH (129 cases), 8.5% contradictory results to immunohistochemistry, 6.2% immunohistochemistry 3+ and negative by FISH, 2.3% negative by immunohistochemistry and amplified by FISH; comparison of CISH and FISH, 94.6% same results, 3.9% different ones, 1.6% CISH not analysable. CISH, using dual-colour probes (ZytoVision) is as good as FISH for Her-2/neu analysis. The few discrepant results are likely to be caused by polysomy or tumour heterogeneity.

  20. Erythrovirus B19 infection in acquired immunodeficiency syndrome: screening by histopathology, immunohistochemistry, and in situ hybridization

    Directory of Open Access Journals (Sweden)

    Sérgio Setúbal

    2006-06-01

    Full Text Available Erythrovirus B19 infects erythrocytic progenitors, transiently interrupting erythropoiesis. In AIDS patients it causes chronic anemia amenable to treatment. We looked for evidences of B19 infection in stored bone marrow material from patients with acquired immunodeficiency syndrome. Histological sections were made from stored paraffin blocks from 33 autopsies (39 blocks and 35 biopsies (45 blocks, 30 patients performed from 1988 to 2002. They were examined after hematoxylin-eosin (HE staining, immunohistochemical (IHC, and in situ hybridization. HE revealed intra-nuclear inclusion bodies ("lantern cells" suggesting B19 infection in 19 sections corresponding to 19 of 63 patients examined with this test. Seven of 78 sections subjected to immunohistochemistry were positive, corresponding to 7 of 58 patients examined with this test. Fourteen sections corresponding to 13 of the 20 HE and/or IHC positive patients were subjected to in situ hybridization, with six positives results. Among the 13 patients subjected to the three techniques, only one gave unequivocal positive results in all and was considered a true positive. The frequency of B19 infection (1/63 patients in the material examined can be deemed low.

  1. Comparative genomic and in situ hybridization of germ cell tumors of the infantile testis

    NARCIS (Netherlands)

    Mostert, M; Rosenberg, C; Stoop, H; Schuyer, M; Timmer, A; Oosterhuis, W; Looijenga, L

    Chromosomal information on germ cell tumors of the infantile testis, ie, teratomas and yolk sac tumors, is limited and controversial. We studied two teratomas and four yolk sac tumors using comparative genomic hybridization (CGH) and in situ hybridization. No chromosomal anomalies were found in the

  2. Weighted hybrid technique for recommender system

    Science.gov (United States)

    Suriati, S.; Dwiastuti, Meisyarah; Tulus, T.

    2017-12-01

    Recommender system becomes very popular and has important role in an information system or webpages nowadays. A recommender system tries to make a prediction of which item a user may like based on his activity on the system. There are some familiar techniques to build a recommender system, such as content-based filtering and collaborative filtering. Content-based filtering does not involve opinions from human to make the prediction, while collaborative filtering does, so collaborative filtering can predict more accurately. However, collaborative filtering cannot give prediction to items which have never been rated by any user. In order to cover the drawbacks of each approach with the advantages of other approach, both approaches can be combined with an approach known as hybrid technique. Hybrid technique used in this work is weighted technique in which the prediction score is combination linear of scores gained by techniques that are combined.The purpose of this work is to show how an approach of weighted hybrid technique combining content-based filtering and item-based collaborative filtering can work in a movie recommender system and to show the performance comparison when both approachare combined and when each approach works alone. There are three experiments done in this work, combining both techniques with different parameters. The result shows that the weighted hybrid technique that is done in this work does not really boost the performance up, but it helps to give prediction score for unrated movies that are impossible to be recommended by only using collaborative filtering.

  3. Determination of the ruminant origin of bone particles using fluorescence in situ hybridization (FISH).

    Science.gov (United States)

    Lecrenier, M C; Ledoux, Q; Berben, G; Fumière, O; Saegerman, C; Baeten, V; Veys, P

    2014-07-17

    Molecular biology techniques such as PCR constitute powerful tools for the determination of the taxonomic origin of bones. DNA degradation and contamination by exogenous DNA, however, jeopardise bone identification. Despite the vast array of techniques used to decontaminate bone fragments, the isolation and determination of bone DNA content are still problematic. Within the framework of the eradication of transmissible spongiform encephalopathies (including BSE, commonly known as "mad cow disease"), a fluorescence in situ hybridization (FISH) protocol was developed. Results from the described study showed that this method can be applied directly to bones without a demineralisation step and that it allows the identification of bovine and ruminant bones even after severe processing. The results also showed that the method is independent of exogenous contamination and that it is therefore entirely appropriate for this application.

  4. The effect of tissue decalcification on mRNA retention within bone for in-situ hybridization studies.

    Science.gov (United States)

    Walsh, L; Freemont, A J; Hoyland, J A

    1993-06-01

    Tissue decalcification is a routine part of the preparation of bone tissue for histological studies. Although in-situ hybridization has been employed to localize mRNA of collagenous and non-collagenous bone related proteins in skeletal tissue, little is known regarding the effects of decalcifying agents on mRNA retention within tissue. In this study in-situ hybridization using an oligonucleotide probe (i.e. a poly d(T) probe) to detect total messenger RNA has been employed to investigate the effects of the decalcifying agents nitric acid, formic acid and EDTA on mRNA retention compared to undeacalcified tissue. The results show that formalin fixation and EDTA decalcification preserve substantial amounts of mRNA within the tissue. In particular, this study illustrates that it is possible to perform in-situ hybridization on formalin fixed decalcified paraffin embedded tissue.

  5. Filter-Adapted Fluorescent In Situ Hybridization (FA-FISH) for Filtration-Enriched Circulating Tumor Cells.

    Science.gov (United States)

    Oulhen, Marianne; Pailler, Emma; Faugeroux, Vincent; Farace, Françoise

    2017-01-01

    Circulating tumor cells (CTCs) may represent an easily accessible source of tumor material to assess genetic aberrations such as gene-rearrangements or gene-amplifications and screen cancer patients eligible for targeted therapies. As the number of CTCs is a critical parameter to identify such biomarkers, we developed fluorescent in situ hybridization (FISH) for CTCs enriched on filters (filter-adapted-FISH, FA-FISH). Here, we describe the FA-FISH protocol, the combination of immunofluorescent staining (DAPI/CD45) and FA-FISH techniques, as well as the semi-automated microscopy method that we developed to improve the feasibility and reliability of FISH analyses in filtration-enriched CTC.

  6. EnVision+, a new dextran polymer-based signal enhancement technique for in situ hybridization (ISH).

    Science.gov (United States)

    Wiedorn, K H; Goldmann, T; Henne, C; Kühl, H; Vollmer, E

    2001-09-01

    Seventy paraffin-embedded cervical biopsy specimens and condylomata were tested for the presence of human papillomavirus (HPV) by conventional in situ hybridization (ISH) and ISH with subsequent signal amplification. Signal amplification was performed either by a commercial biotinyl-tyramide-based detection system [GenPoint (GP)] or by the novel two-layer dextran polymer visualization system EnVision+ (EV), in which both EV-horseradish peroxidase (EV-HRP) and EV-alkaline phosphatase (EV-AP) were applied. We could demonstrate for the first time, that EV in combination with preceding ISH results in a considerable increase in signal intensity and sensitivity without loss of specificity compared to conventional ISH. Compared to GP, EV revealed a somewhat lower sensitivity, as measured by determination of the integrated optical density (IOD) of the positively stained cells. However, EV is easier to perform, requires a shorter assay time, and does not raise the background problems that may be encountered with biotinyl-tyramide-based amplification systems. (J Histochem Cytochem 49:1067-1071, 2001)

  7. Hierarchically structured transparent hybrid membranes by in situ growth of mesostructured organosilica in host polymer

    Science.gov (United States)

    Vallé, Karine; Belleville, Philippe; Pereira, Franck; Sanchez, Clément

    2006-02-01

    The elaborate performances characterizing natural materials result from functional hierarchical constructions at scales ranging from nanometres to millimetres, each construction allowing the material to fit the physical or chemical demands occurring at these different levels. Hierarchically structured materials start to demonstrate a high input in numerous promising applied domains such as sensors, catalysis, optics, fuel cells, smart biologic and cosmetic vectors. In particular, hierarchical hybrid materials permit the accommodation of a maximum of elementary functions in a small volume, thereby optimizing complementary possibilities and properties between inorganic and organic components. The reported strategies combine sol-gel chemistry, self-assembly routes using templates that tune the material's architecture and texture with the use of larger inorganic, organic or biological templates such as latex, organogelator-derived fibres, nanolithographic techniques or controlled phase separation. We propose an approach to forming transparent hierarchical hybrid functionalized membranes using in situ generation of mesostructured hybrid phases inside a non-porogenic hydrophobic polymeric host matrix. We demonstrate that the control of the multiple affinities existing between organic and inorganic components allows us to design the length-scale partitioning of hybrid nanomaterials with tuned functionalities and desirable size organization from ångström to centimetre. After functionalization of the mesoporous hybrid silica component, the resulting membranes have good ionic conductivity offering interesting perspectives for the design of solid electrolytes, fuel cells and other ion-transport microdevices.

  8. Detection of c-myc amplification in formalin-fixed paraffin-embedded tumor tissue by chromogenic in situ hybridization (CISH).

    Science.gov (United States)

    Todorović-Raković, Nataša

    2013-01-01

    In situ hybridization (ISH) allows evaluation of genetic abnormalities, such as changes in chromosome number, chromosome translocations or gene amplifications, by hybridization of tagged DNA (or RNA) probes with complementary DNA (or RNA) sequences in interphase nuclei of target tissue. However, chromogenic in situ hybridization (CISH) is also applicable to formalin-fixed, paraffin-embedded (FFPE) tissues, besides metaphase chromosome spreads. CISH is similar to fluorescent in situ hybridization (FISH) regarding pretreatments and hybridization protocols but differs in the way of visualization. Indeed, CISH signal detection is similar to that used in immunohistochemistry, making use of a peroxidase-based chromogenic reaction instead of fluorescent dyes. In particular, tagged DNA probes are indirectly detected using an enzyme-conjugated antibody targeting the tags. The enzymatic reaction of the chromogenic substrate leads to the formation of strong permanent brown signals that can be visualized by bright-field microscopy at 40 × magnification. The advantage of CISH is that it allows the simultaneous observation of gene amplification and tissue morphology and the slides can be stored for a long time.

  9. In situ hybridization for the detection of infectious laryngotracheitis virus in sections of trachea from experimentally infected chickens

    DEFF Research Database (Denmark)

    Nielsen, O.L.; Handberg, Kurt; Jørgensen, Poul Henrik

    1998-01-01

    An in situ hybridization procedure for the detection of infectious laryngotracheitis virus (ILTV) in experimentally infected chickens is described. Formalin-fixed, paraffin-embedded sections of trachea, taken from chickens on days 3-10 post-inoculation (p.i.) with ILTV were hybridized with a mixt......An in situ hybridization procedure for the detection of infectious laryngotracheitis virus (ILTV) in experimentally infected chickens is described. Formalin-fixed, paraffin-embedded sections of trachea, taken from chickens on days 3-10 post-inoculation (p.i.) with ILTV were hybridized...... on day 5 p.i. No hybridization was observed in 3 out of 3 chickens examined on day 10 p.i. ILTV nucleic acid was detected in nuclei of degenerated tracheal epithelial cells and in intranuclear inclusion bodies of syncytia....

  10. Metaphase FISH on a Chip: Miniaturized Microfluidic Device for Fluorescence in situ Hybridization

    Directory of Open Access Journals (Sweden)

    Niels Tommerup

    2010-11-01

    Full Text Available Fluorescence in situ Hybridization (FISH is a major cytogenetic technique for clinical genetic diagnosis of both inherited and acquired chromosomal abnormalities. Although FISH techniques have evolved and are often used together with other cytogenetic methods like CGH, PRINS and PNA-FISH, the process continues to be a manual, labour intensive, expensive and time consuming technique, often taking over 3–5 days, even in dedicated labs. We have developed a novel microFISH device to perform metaphase FISH on a chip which overcomes many shortcomings of the current laboratory protocols. This work also introduces a novel splashing device for preparing metaphase spreads on a microscope glass slide, followed by a rapid adhesive tape-based bonding protocol leading to rapid fabrication of the microFISH device. The microFISH device allows for an optimized metaphase FISH protocol on a chip with over a 20-fold reduction in the reagent volume. This is the first demonstration of metaphase FISH on a microfluidic device and offers a possibility of automation and significant cost reduction of many routine diagnostic tests of genetic anomalies.

  11. Analysis of experimental mink enteritis virus infection in mink: in situ hybridization, serology, and histopathology

    DEFF Research Database (Denmark)

    Uttenthal, Åse; Larsen, S; Lund, E

    1990-01-01

    Strand-specific hybridization probes were used in in situ hybridization studies to localize cells containing mink enteritis virus (MEV) virion DNA or MEV replicative-form DNA and mRNA. Following the experimental MEV infection of 3-month-old unvaccinated mink, a significant increase in serum antib...

  12. Preparation of epoxy/zirconia hybrid materials via in situ polymerization using zirconium alkoxide coordinated with acid anhydride

    International Nuclear Information System (INIS)

    Ochi, Mitsukazu; Nii, Daisuke; Harada, Miyuki

    2011-01-01

    Highlights: → Novel epoxy/zirconia hybrid materials were synthesized via in situ polymerization using zirconium alkoxide coordinated with acid anhydride. → The half-ester compound of acid anhydride desorbed from zirconium played as curing agent of epoxy resin. → The zirconia was uniformly dispersed in the epoxy matrix on the nanometer or sub-nanometer scale by synchronizing the epoxy curing and sol-gel reactions. → The refractive indices of the hybrid materials significantly improved with an increase in the zirconia content. - Abstract: Novel epoxy/zirconia hybrid materials were synthesized using a bisphenol A epoxy resin (diglycidyl ether of bisphenol A; DGEBA), zirconium(IV)-n-propoxide (ZTNP), and hexahydrophthalic anhydride (HHPA) via in situ polymerization. HHPA played two roles in this system: it acted as a modifier to control the hydrolysis and condensation reactions of zirconium alkoxide and also as a curing agent - the half-ester compound of HHPA desorbed from zirconium reacted with the epoxy resin to form the epoxy network. As a result, both the sol-gel reaction and epoxy curing occurred simultaneously in a homogeneous solution, and organic-inorganic hybrid materials were readily obtained. Further, the zirconia produced by the in situ polymerization was uniformly dispersed in the epoxy matrix on the nanometer or sub-nanometer scale; thus, hybrid materials that exhibited excellent optical transparency were obtained. Furthermore, the heat resistance of the hybrid materials could be improved by hybridization with zirconia. And, the refractive indices of the hybrid materials significantly improved with an increase in the zirconia content.

  13. In situ biosynthesis of bacterial nanocellulose-CaCO3 hybrid bionanocomposite: One-step process

    International Nuclear Information System (INIS)

    Mohammadkazemi, Faranak; Faria, Marisa; Cordeiro, Nereida

    2016-01-01

    In this work, a simple and green route to the synthesis of the bacterial nanocellulose-calcium carbonate (BNC/CaCO 3 ) hybrid bionanocomposites using one-step in situ biosynthesis was studied. The CaCO 3 was incorporated in the bacterial nanocellulose structure during the cellulose biosynthesis by Gluconacetobacter xylinus PTCC 1734 bacteria. Hestrin-Schramm (HS) and Zhou (Z) culture media were used to the hybrid bionanocomposites production and the effect of ethanol addition was investigated. Attenuated total reflection Fourier transform infrared spectroscopy, field emission scanning electron microscopy, X-ray diffraction, energy-dispersive X-ray spectroscopy, inverse gas chromatography and thermogravimetric analysis were used to characterize the samples. The experimental results demonstrated that the ethanol and culture medium play an important role in the BNC/CaCO 3 hybrid bionanocomposites production, structure and properties. The BNC/CaCO 3 biosynthesized in Z culture medium revealed higher O/C ratio and amphoteric surface character, which justify the highest CaCO 3 content incorporation. The CaCO 3 was incorporated into the cellulosic matrix decreasing the bacterial nanocellulose crystallinity. This work reveals the high potential of in situ biosynthesis of BNC/CaCO 3 hybrid bionanocomposites and opens a new way to the high value-added applications of bacterial nanocellulose. - Graphical Abstract: Display Omitted - Highlights: • BNC/CaCO 3 hybrid bionanocomposites were produced using in situ biosynthesis process. • Ethanol and culture medium play an important role in the production and properties. • Z-BNC/CaCO 3 bionanocomposites revealed higher O/C ratio and amphoteric surface character. • CaCO 3 incorporated into the BNC decreased crystallinity.

  14. Dual color chromogenic in situ hybridization for determination of HER2 status in breast cancer: a large comparative study to current state of the art fluorescence in situ hybridization

    Directory of Open Access Journals (Sweden)

    Mollerup Jens

    2012-02-01

    Full Text Available Abstract Background Chromogenic in situ hybridization (CISH is fast becoming a well established technique for easy and sensitive determination of HER2 gene status in breast cancer. However, for the chromogenic method to achieve status as a safe and reliable technique, the method needs to be validated against already known and validated FISH techniques. Methods Here it is reported from a comparative study where HER2 gene status obtained by HER2 CISH pharmDx™ Kit was compared to HER2 gene status obtained by the FDA approved HER2 FISH pharmDx™ Kit and the PathVysion HER-2 DNA probe Kit. The study included 365 formalin fixed and paraffin-embedded invasive breast cancer tissue specimens collected consecutively at a US reference laboratory. Results The data obtained revealed an overall HER2 status concordance of approximately 98% for comparisons of HER2 CISH pharmDx™ Kit to both HER2 FISH pharmDx™ Kit and PathVysion HER-2 DNA Probe Kit. Conclusions The concordance between results obtained using the recently FDA approved HER2 CISH pharmDx™ Kit with previously FDA approved FISH techniques for HER2 gene status determination indicate that the HER2 CISH pharmDx™ Kit is a reliable chromogenic alternative to fluorescence-based methods.

  15. Dual color chromogenic in situ hybridization for determination of HER2 status in breast cancer: a large comparative study to current state of the art fluorescence in situ hybridization

    Science.gov (United States)

    2012-01-01

    Background Chromogenic in situ hybridization (CISH) is fast becoming a well established technique for easy and sensitive determination of HER2 gene status in breast cancer. However, for the chromogenic method to achieve status as a safe and reliable technique, the method needs to be validated against already known and validated FISH techniques. Methods Here it is reported from a comparative study where HER2 gene status obtained by HER2 CISH pharmDx™ Kit was compared to HER2 gene status obtained by the FDA approved HER2 FISH pharmDx™ Kit and the PathVysion HER-2 DNA probe Kit. The study included 365 formalin fixed and paraffin-embedded invasive breast cancer tissue specimens collected consecutively at a US reference laboratory. Results The data obtained revealed an overall HER2 status concordance of approximately 98% for comparisons of HER2 CISH pharmDx™ Kit to both HER2 FISH pharmDx™ Kit and PathVysion HER-2 DNA Probe Kit. Conclusions The concordance between results obtained using the recently FDA approved HER2 CISH pharmDx™ Kit with previously FDA approved FISH techniques for HER2 gene status determination indicate that the HER2 CISH pharmDx™ Kit is a reliable chromogenic alternative to fluorescence-based methods. PMID:22333181

  16. Novel RNA hybridization method for the in situ detection of ETV1, ETV4, and ETV5 gene fusions in prostate cancer.

    Science.gov (United States)

    Kunju, Lakshmi P; Carskadon, Shannon; Siddiqui, Javed; Tomlins, Scott A; Chinnaiyan, Arul M; Palanisamy, Nallasivam

    2014-09-01

    The genetic basis of 50% to 60% of prostate cancer (PCa) is attributable to rearrangements in E26 transformation-specific (ETS) (ERG, ETV1, ETV4, and ETV5), BRAF, and RAF1 genes and overexpression of SPINK1. The development and validation of reliable detection methods are warranted to classify various molecular subtypes of PCa for diagnostic and prognostic purposes. ETS gene rearrangements are typically detected by fluorescence in situ hybridization and reverse-transcription polymerase chain reaction methods. Recently, monoclonal antibodies against ERG have been developed that detect the truncated ERG protein in immunohistochemical assays where staining levels are strongly correlated with ERG rearrangement status by fluorescence in situ hybridization. However, specific antibodies for ETV1, ETV4, and ETV5 are unavailable, challenging their clinical use. We developed a novel RNA in situ hybridization-based assay for the in situ detection of ETV1, ETV4, and ETV5 in formalin-fixed paraffin-embedded tissues from prostate needle biopsies, prostatectomy, and metastatic PCa specimens using RNA probes. Further, with combined RNA in situ hybridization and immunohistochemistry we identified a rare subset of PCa with dual ETS gene rearrangements in collisions of independent tumor foci. The high specificity and sensitivity of RNA in situ hybridization provides an alternate method enabling bright-field in situ detection of ETS gene aberrations in routine clinically available PCa specimens.

  17. Modulation of tyrosine hydroxylase gene expression in the central nervous system visualized by in situ hybridization

    International Nuclear Information System (INIS)

    Berod, A.; Biguet, N.F.; Dumas, S.; Bloch, B.; Mallet, J.

    1987-01-01

    cDNA probe was used for in situ hybridization studies on histological sections through the locus coeruleus, substantia nigra, and the ventral tegmental area of the rat brain. Experimental conditions were established that yielded no background and no signal when pBR322 was used as control probe. Using the tyrosine hydroxylase probe, the authors ascertained the specificity of the labeling over catecholaminergic cells by denervation experiments and comparison of the hybridization pattern with that of immunoreactivity. The use of 35 S-labeled probe enabled the hybridization signal to be resolved at the cellular level. A single injection of reserpine into the rat led to an increase of the intensity of the autoradiographic signal over the locus coeruleus area, confirming an RNA gel blot analysis. The potential of in situ hybridization to analyze patterns of modulation of gene activity as a result of nervous activity is discussed

  18. In situ synthesis of silver benzene-dithiolate hybrid films

    Energy Technology Data Exchange (ETDEWEB)

    Brenier, Roger, E-mail: roger.brenier@univ-lyon1.fr [Institut Lumière Matière, UMR 5306, Université Lyon 1-CNRS, Université de Lyon, Domaine Scientifique de La Doua, Batiment Kastler, 10 rue Ada Byron, 69622 Villeurbanne, Cedex (France); Piednoir, Agnès, E-mail: agnes.piednoir@univ-lyon1.fr [Institut Lumière Matière, UMR 5306, Université Lyon 1-CNRS, Université de Lyon, Domaine Scientifique de La Doua, Batiment Kastler, 10 rue Ada Byron, 69622 Villeurbanne, Cedex (France); Bertorelle, Franck, E-mail: franck.bertorelle@univ-lyon1.fr [Institut Lumière Matière, UMR 5306, Université Lyon 1-CNRS, Université de Lyon, Domaine Scientifique de La Doua, Batiment Kastler, 10 rue Ada Byron, 69622 Villeurbanne, Cedex (France); Penuelas, José, E-mail: jose.penuelas@ec-lyon.fr [Université de Lyon, Institut des Nanotechnologies de Lyon, Ecole Centrale de Lyon, CNRS, UMR 5270, 36 rue Guy de Collongues, F69134 Ecully (France); Grenet, Geneviève, E-mail: genevieve.grenet@ec-lyon.fr [Université de Lyon, Institut des Nanotechnologies de Lyon, Ecole Centrale de Lyon, CNRS, UMR 5270, 36 rue Guy de Collongues, F69134 Ecully (France)

    2016-02-01

    In this article, a method for in situ synthesis of silver benzene-dithiolate hybrid films is presented. Silver nanoparticles, generated on ZrO{sub 2} films, are transformed into silver benzene 1,4-dithiolate or, partially, into silver benzene 1,2-dithiolate after sample immersion in the corresponding thiol solutions. These transformations occur at room temperature owing to the catalytic action of ZrO{sub 2}. It is also shown that TiO{sub 2} in place of ZrO{sub 2} is very efficient, both for the catalytic generation of silver nanoparticles and for their further transformation in benzene 1,4-dithiolate compound. This latter semiconductor has an optical bandgap of about 3 eV and the film is made of touching nanoparticles in an amorphous state. Our work has potential applications in the electronic and photovoltaic fields. - Highlights: • A method for in situ synthesis of silver benzene-dithiolate hybrid semiconductor films is presented. • Silver nanoparticles are, first, generated on ZrO{sub 2} or on TiO{sub 2} coated silica substrates. • The samples are immersed in benzene dithiol solution for two days at room temperature. • During the immersion, the silver nanoparticles are transformed into silver benzene dithiolate. • The silver benzene dithiolate film is made of amorphous nanoparticles with a banbgap of 3 eV.

  19. In situ hybridization of superparamagnetic iron-biomolecule nanoparticles.

    Science.gov (United States)

    Moghimi, Nafiseh; Donkor, Apraku David; Mohapatra, Mamata; Thomas, Joseph Palathinkal; Su, Zhengding; Tang, Xiaowu Shirley; Leung, Kam Tong

    2014-07-23

    The increase in interest in the integration of organic-inorganic nanostructures in recent years has promoted the use of hybrid nanoparticles (HNPs) in medicine, energy conversion, and other applications. Conventional hybridization methods are, however, often long, complicated, and multistepped, and they involve biomolecules and discrete nanostructures as separate entities, all of which hinder the practical use of the resulting HNPs. Here, we present a novel, in situ approach to synthesizing size-specific HNPs using Fe-biomolecule complexes as the building blocks. We choose an anticancer peptide (p53p, MW 1.8 kDa) and an enzyme (GOx, MW 160 kDa) as model molecules to demonstrate the versatility of the method toward different types of molecules over a large size range. We show that electrostatic interaction for complex formation of metal hydroxide ion with the partially charged side of biomolecule in the solution is the key to hybridization of metal-biomolecule materials. Electrochemical deposition is then used to produce hybrid NPs from these complexes. These HNPs with controllable sizes ranging from 30 nm to 3.5 μm are found to exhibit superparamagnetic behavior, which is a big challenge for particles in this size regime. As an example of greatly improved properties and functionality of the new hybrid material, in vitro toxicity assessment of Fe-GOx HNPs shows no adverse effect, and the Fe-p53p HNPs are found to selectively bind to cancer cells. The superparamagnetic nature of these HNPs (superparamagnetic even above the size regime of 15-20 nm!), their biocompatibility, and the direct integration approach are fundamentally important to biomineralization and general synthesis strategy for bioinspired functional materials.

  20. Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis

    Directory of Open Access Journals (Sweden)

    Botman Daniel

    2012-10-01

    Full Text Available Abstract Background Spatial gene expression quantification is required for modeling gene regulation in developing organisms. The fruit fly Drosophila melanogaster is the model system most widely applied for spatial gene expression analysis due to its unique embryonic properties: the shape does not change significantly during its early cleavage cycles and most genes are differentially expressed along a straight axis. This system of development is quite exceptional in the animal kingdom. In the sea anemone Nematostella vectensis the embryo changes its shape during early development; there are cell divisions and cell movement, like in most other metazoans. Nematostella is an attractive case study for spatial gene expression since its transparent body wall makes it accessible to various imaging techniques. Findings Our new quantification method produces standardized gene expression profiles from raw or annotated Nematostella in situ hybridizations by measuring the expression intensity along its cell layer. The procedure is based on digital morphologies derived from high-resolution fluorescence pictures. Additionally, complete descriptions of nonsymmetric expression patterns have been constructed by transforming the gene expression images into a three-dimensional representation. Conclusions We created a standard format for gene expression data, which enables quantitative analysis of in situ hybridizations from embryos with various shapes in different developmental stages. The obtained expression profiles are suitable as input for optimization of gene regulatory network models, and for correlation analysis of genes from dissimilar Nematostella morphologies. This approach is potentially applicable to many other metazoan model organisms and may also be suitable for processing data from three-dimensional imaging techniques.

  1. Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content.

    Science.gov (United States)

    Fazi, Stefano; Amalfitano, Stefano; Pizzetti, Ilaria; Pernthaler, Jakob

    2007-09-01

    We studied the efficiency of two hybridization techniques for the analysis of benthic bacterial community composition under varying sediment water content. Microcosms were set up with sediments from four European temporary rivers. Wet sediments were dried, and dry sediments were artificially rewetted. The percentage of bacterial cells detected by fluorescence in situ hybridization with fluorescently monolabeled probes (FISH) significantly increased from dry to wet sediments, showing a positive correlation with the community activity measured via incorporation of (3)H leucine. FISH and signal amplification by catalyzed reporter deposition (CARD-FISH) could significantly better detect cells with low activity in dried sediments. Through the application of an optimized cell permeabilization protocol, the percentage of hybridized cells by CARD-FISH showed comparable values in dry and wet conditions. This approach was unrelated to (3)H leucine incorporation rates. Moreover, the optimized protocol allowed a significantly better visualization of Gram-positive Actinobacteria in the studied samples. CARD-FISH is, therefore, proposed as an effective technique to compare bacterial communities residing in sediments with contrasting water content, irrespective of differences in the activity state of target cells. Considering the increasing frequencies of flood and drought cycles in European temporary rivers, our approach may help to better understand the dynamics of microbial communities in such systems.

  2. Detection of ALK gene rearrangement in non-small cell lung cancer: a comparison of fluorescence in situ hybridization and chromogenic in situ hybridization with correlation of ALK protein expression.

    Science.gov (United States)

    Kim, Hyojin; Yoo, Seol-Bong; Choe, Ji-Young; Paik, Jin Ho; Xu, Xianhua; Nitta, Hiroaki; Zhang, Wenjun; Grogan, Thomas M; Lee, Choon-Taek; Jheon, Sanghoon; Chung, Jin-Haeng

    2011-08-01

    Accurate determination of ALK rearrangement is important in lung cancer patients, especially in determining their eligibility for crizotinib therapy. Fluorescence in situ hybridization (FISH) has been regarded as the gold standard method for detecting ALK rearrangement. However, FISH requires a fluorescence microscope, and the signals are labile and rapidly fade over time. This study evaluates the concordance between ALK gene rearrangement in non-small cell lung cancer assessed by ALK FISH and a newly developed ALK chromogenic in situ hybridization (CISH) and correlates the results with ALK protein expression assessed by immunohistochemistry. A total of 465 formalin-fixed, paraffin-embedded non-small cell lung cancer samples were analyzed by ALK FISH (PathVysion, Vysis, Abbott) and ALK CISH. For comparison, all specimens were stained by immunohistochemistry (clone 5A4, Novocastra) and interobserver reproducibility was assessed. We found that agreement between the pathologists on the CISH-determined ALK status was achieved in 449 patients (96.6%), and ALK rearrangement was identified in 18 patients (4.0%) in CISH method. Among these cases, 443 cases (95.3%) had results matching the corresponding FISH results: 17 rearranged, 425 wild types, and 1 discordant case. There was high concordance in the assessment of ALK gene rearrangement between FISH and CISH techniques (κ = 0.92) and between observers (κ = 0.97). In addition, there was high concordance in the ALK gene status and ALK protein expression between CISH and IHC tests (κ = 0.82). CISH is a highly reproducible and practical method to detect ALK gene rearrangement and correlated well with ALK protein expression. Here, we present a diagnostic algorithm (Chung's SNUBH ALK protocol) to detect lung cancer with ALK rearrangements using IHC, FISH and CISH. Because CISH allows a concurrent analysis of histological features of the tumors and gene rearrangement, it appears to be a useful method in determining ALK gene

  3. Combination of microautoradiography and fluorescence in situ hybridization for identification of microorganisms degrading xenobiotic contaminants.

    Science.gov (United States)

    Yang, Yanru; Zarda, Annatina; Zeyer, Josef

    2003-12-01

    One of the central topics in environmental bioremediation research is to identify microorganisms that are capable of degrading the contaminants of interest. Here we report application of combined microautoradiography (MAR) and fluorescence in situ hybridization (FISH). The method has previously been used in a number of systems; however, here we demonstrate its feasibility in studying the degradation of xenobiotic compounds. With a model system (coculture of Pseudomonas putida B2 and Sphingomonas stygia incubated with [14C] o-nitrophenol), combination of MAR and FISH was shown to be able to successfully identify the microorganisms degrading o-nitrophenol. Compared with the conventional techniques, MAR-FISH allows fast and accurate identification of the microorganisms involved in environmental contaminant degradation.

  4. Accuracy Assessment of Interphase Fluorescence In-Situ Hybridization on Uncultured Amniotic Fluid Cells

    Directory of Open Access Journals (Sweden)

    Hamideh Karimi

    2007-01-01

    Full Text Available Background: Parental anxiety while waiting for the results of amniocentesis has been investigatedby many authors. It seems that the implementation of faster techniques such as fluorescence in-situhybridization (FISH will have some benefits in reducing this anxiety. Besides the patients' attitudesto choosing this method, gynecologists who are the persons responsible for treatment, must feelcomfortable about prescribing FISH techniques.Materials and Methods: This study, using a simple methodology, was undertaken to evaluate theresults of FISH tests on the amniotic fluid from 40 pregnant women undergoing cesarean surgery.Two sets of probes including X/Y cocktail and 13, 21 and 18 were applied on different slides.Results: The results of FISH tests were compared with the reports of the pediatrician about thehealth condition of the newborn. Complete conformity between the two sets of findings, haveconvinced our gynecologists of the benefit of prescribing this method to reduce the anxiety ofpatients at risk of having abnormal offspring due to chromosomal anuploidies.Conclusion: As has been documented by many authors, conventional chromosome analysis hasgreat advantages over fluorescence in situ hybridization of interphase amniocytes, but reducing theanxiety of parents is a good reason for employing the FISH technique.

  5. Fluorescence in situ hybridization evaluation of chromosome deletion patterns in prostate cancer.

    Science.gov (United States)

    Huang, S F; Xiao, S; Renshaw, A A; Loughlin, K R; Hudson, T J; Fletcher, J A

    1996-11-01

    Various nonrandom chromosomal aberrations have been identified in prostate carcinoma. These aberrations include deletions of several chromosome regions, particularly the chromosome 8 short arm. Large-scale numerical aberrations, reflected in aberrant DNA ploidy, are also found in a minority of cases. However, it is unclear whether prostate carcinomas contain aberrations of certain chromosome regions that are deleted frequently in other common types of cancer. In this study, we performed dual-color fluorescence in situ hybridization on intact nuclei from touch preparations of 16 prostate cancers. Chromosome copy number was determined using pericentromeric probes, whereas potential chromosome arm deletions were evaluated using yeast artificial chromosome (YAC) and P1 probes. Two YAC probes targeted chromosome 8 short arm regions known to be deleted frequently in prostate cancer. Other YACs and P1s were for chromosome regions, including 1p22, 3p14, 6q21, 9p21, and 22q12, that are deletion targets in a variety of cancers although not extensively studied in prostate cancer. Hybridization efficiencies and signal intensities were excellent for both repeat sequence (alpha-satellite) and single, copy (YAC and P1) fluorescence in situ hybridization probes. Of 16 prostate cancers, 11 had clonal aberrations of 1 or more of the 13 chromosome regions evaluated, and 10 cases (62.5%) had 8p deletions, including 4 cases with 8p deletion in virtually all cells and aneuploidy in only a subset of those deleted cells. Deletions at 3p14, 6q21, and 22q12 were identified in 2, 1, and 1 case, respectively, and each of those cases had a similarly sized cell population with 8p deletion. These studies confirm 8p deletion in the majority of prostate carcinomas. 8p deletions appear to be early events in prostate tumorigenesis, often antedating aneuploidy. Fluorescence in situ hybridization strategies incorporating pericentromeric and single-copy regional chromosome probes offer a powerful and

  6. In situ biosynthesis of bacterial nanocellulose-CaCO{sub 3} hybrid bionanocomposite: One-step process

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadkazemi, Faranak, E-mail: f_mkazemi@sbu.ac.ir [Department of Cellulose and Paper Technology, Faculty of New Technologies Engineering, Shahid Beheshti University, Science and Research Campus, Zirab, Savadkooh, Mazandaran (Iran, Islamic Republic of); Faria, Marisa; Cordeiro, Nereida [Faculty of Exact Science and Engineering, University of Madeira, Funchal (Portugal)

    2016-08-01

    In this work, a simple and green route to the synthesis of the bacterial nanocellulose-calcium carbonate (BNC/CaCO{sub 3}) hybrid bionanocomposites using one-step in situ biosynthesis was studied. The CaCO{sub 3} was incorporated in the bacterial nanocellulose structure during the cellulose biosynthesis by Gluconacetobacter xylinus PTCC 1734 bacteria. Hestrin-Schramm (HS) and Zhou (Z) culture media were used to the hybrid bionanocomposites production and the effect of ethanol addition was investigated. Attenuated total reflection Fourier transform infrared spectroscopy, field emission scanning electron microscopy, X-ray diffraction, energy-dispersive X-ray spectroscopy, inverse gas chromatography and thermogravimetric analysis were used to characterize the samples. The experimental results demonstrated that the ethanol and culture medium play an important role in the BNC/CaCO{sub 3} hybrid bionanocomposites production, structure and properties. The BNC/CaCO{sub 3} biosynthesized in Z culture medium revealed higher O/C ratio and amphoteric surface character, which justify the highest CaCO{sub 3} content incorporation. The CaCO{sub 3} was incorporated into the cellulosic matrix decreasing the bacterial nanocellulose crystallinity. This work reveals the high potential of in situ biosynthesis of BNC/CaCO{sub 3} hybrid bionanocomposites and opens a new way to the high value-added applications of bacterial nanocellulose. - Graphical Abstract: Display Omitted - Highlights: • BNC/CaCO{sub 3} hybrid bionanocomposites were produced using in situ biosynthesis process. • Ethanol and culture medium play an important role in the production and properties. • Z-BNC/CaCO{sub 3} bionanocomposites revealed higher O/C ratio and amphoteric surface character. • CaCO{sub 3} incorporated into the BNC decreased crystallinity.

  7. Utility of chromogenic in situ hybridization (CISH) for detection of EGFR amplification in glioblastoma: comparison with fluorescence in situ hybridization (FISH).

    Science.gov (United States)

    Fischer, Ingeborg; de la Cruz, Clarissa; Rivera, Andreana L; Aldape, Kenneth

    2008-12-01

    In this study, we test the reliability of chromogenic in situ hybridization (CISH) for the detection of epidermal growth factor receptor (EGFR) gene amplification in glioblastoma. Earlier reports have described EGFR CISH in glioblastoma multiforme, but a comparison of CISH with a "gold standard" testing method, such as fluorescence in situ hybridization (FISH), has not been described. Therapies targeting the EGFR-signaling pathway might increase the importance of assessment of EGFR-amplification status. CISH is a potential alternative to FISH as a testing method. To test its reliability, EGFR-amplification status by CISH was assessed in 89 cases of glioblastoma and compared with FISH results, and correlated with the protein expression using immunohistochemistry (IHC) for EGFR. FISH was scored as being EGFR-amplified in 47/89 tumors, CISH as being amplified in 43/89 tumors. The CISH and FISH results were in agreement in 83/89 cases (93%). Four glioblastomas were scored as being amplified by FISH, but not by CISH; whereas amplification was detected in 2 tumors by CISH that were not amplified using FISH. Forty-eight of the 89 cases were positive for EGFR expression by IHC. EGFR amplification was highly correlated with protein expression by IHC, as 40/48 (83%) EGFR IHC-positive cases were found to be EGFR-amplified. The high concordance of CISH and FISH for the assessment of EGFR gene-amplification status indicates that CISH is a viable alternative to FISH for the detection of EGFR gene amplification in glioblastoma. Detectable EGFR expression by IHC can occur in the absence of gene amplification, but is uncommon.

  8. Application of Pseudomurein Endoisopeptidase to Fluorescence In Situ Hybridization of Methanogens within the Family Methanobacteriaceae▿

    Science.gov (United States)

    Nakamura, Kohei ; Terada, Takeshi; Sekiguchi, Yuji; Shinzato, Naoya; Meng, Xian-Ying; Enoki, Miho; Kamagata, Yoichi

    2006-01-01

    In situ detection of methanogens within the family Methanobacteriaceae is sometimes known to be unsuccessful due to the difficulty in permeability of oligonucleotide probes. Pseudomurein endoisopeptidase (Pei), a lytic enzyme that specifically acts on their cell walls, was applied prior to 16S rRNA-targeting fluorescence in situ hybridization (FISH). For this purpose, pure cultured methanogens within this family, Methanobacterium bryantii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, and Methanothermobacter thermautotrophicus together with a Methanothermobacter thermautotrophicus-containing syntrophic acetate-oxidizing coculture, endosymbiotic Methanobrevibacter methanogens within an anaerobic ciliate, and an upflow anaerobic sludge blanket (UASB) granule were examined. Even without the Pei treatment, Methanobacterium bryantii and Methanothermobacter thermautotrophicus cells are relatively well hybridized with oligonucleotide probes. However, almost none of the cells of Methanobrevibacter ruminantium, Methanosphaera stadtmanae, cocultured Methanothermobacter thermautotrophicus, and the endosymbiotic methanogens and the cells within UASB granule were hybridized. Pei treatment was able to increase the probe hybridization ratio in every specimen, particularly in the specimen that had shown little hybridization. Interestingly, the hybridizing signal intensity of Methanothermobacter thermautotrophicus cells in coculture with an acetate-oxidizing H2-producing syntroph was significantly improved by Pei pretreatment, whereas the probe was well hybridized with the cells of pure culture of the same strain. We found that the difference is attributed to the differences in cell wall thicknesses between the two culture conditions. These results indicate that Pei treatment is effective for FISH analysis of methanogens that show impermeability to the probe. PMID:16950902

  9. Spatial Exploration and Characterization of Endozoicomonas spp. Bacteria in Stylophora pistillata Using Fluorescence In Situ Hybridization

    KAUST Repository

    Alsheikh-­Hussain, Areej

    2011-12-12

    Studies of coral-­associated bacterial communities have repeatedly demonstrated that the microbial assemblages of the coral host are highly specific and complex. In particular, bacterial community surveys of scleractinian and soft corals from geographically diverse reefs continually uncover a high abundance of sequences affiliated with the Gammaproteobacteria genus Endozoicomonas. The role of these bacteria within the complex coral holobiont is currently unknown. In order to localize these cells and gain an understanding of their potential interactions within the coral, we developed a fluorescence in situ hybridization(FISH) approach for reef-­building coral tissues. Using a custom small-­subunit ribosomal RNA gene database, we developed two Endozoicomonas-­specific probes that cover almost all known coral-­associated Endozoicomonas sequences. Probe hybridization conditions were quantitatively evaluated against target and non-­target bacterial cultures using fluorescence microscopy. Using these experimentally tested conditions, probes were then hybridized to the branching coral Stylophora pistillata, obtained from the Red Sea, using whole mount and paraffin embedding techniques. This study allowed preliminary spatial exploration and characterization of Endozoicomonas in coral, which has provided insight into their functional role and interactions within the coral holobiont.

  10. Frequency of reciprocal translocations and dicentrics induced in human blood lymphocytes by X-irradiation as determined by fluorescence in situ hybridization

    International Nuclear Information System (INIS)

    Nakano, M.; Nakashima, E.; Pawel, D.; Kodama, Y.; Awa, A.

    1993-01-01

    This study was designed to test the scoring efficiency of reciprocal translocations and dicentrics induced by X-irradiation in vitro using the fluorescence in situ hybridization (FISH) technique. An excess was found in the frequencies of reciprocal translocations relative to those of dicentrics by measurement with FISH at the first cell division after irradiation (translocation:dicentric ≅ 60:40). However, when the same metaphases were also evaluated sequentially by a conventional staining method, the ratio of about 50:50 was restored. This was due in part to misclassification of certain dicentrics as reciprocal translocations by the FISH technique. (author)

  11. SUPERSENSITIVE IN SITU HYBRIDIZATION BY TYRAMIDE SIGNAL AMPLIFICATION AND NANOGOLD SILVER STAINING: THE CONTRIBUTION OF AUTOMETALLOGRAPHY AND CATALYZED REPORTER DEPOSITION TO THE REJUVENATION OF IN SITU HYBRIDIZATION.

    Energy Technology Data Exchange (ETDEWEB)

    TUBBS,R.R.PETTAY,J.GROGAN,T.CHEUNG,A.L.M.POWELL,R.D.HAINFELD,J.HAUSER-KRONBERGER,C.HACKER,G.W.

    2002-04-17

    It is peculiar that in situ hybridization (ISH), a technique with many similarities to immunohistochemistry (IHC), has not enjoyed the phenomenal growth in both basic research and clinical applications as has its sister technique IHC. Since the late 1970s, when immunoperoxidase techniques began to be applied to routine diagnostic material and to numerous research applications, there has been a natural evolution of the IHC procedure. Namely, only a few primary antibodies were available commercially at the onset, and only one indirect and the peroxidase-antiperoxidase (PAP) technique detection systems were in place. With the advent of avidin-biotin detection systems and monoclonal antibodies, and a viable commercial market, extraordinary growth of the procedure's applications in clinical research and diagnostic pathology occurred during the subsequent two decades. Today, IHC is automated and widely used for research purposes and, to a large extent, has become a routine diagnostic ''special stain'' in most clinical laboratories. During the same period, ISH enjoyed very little growth in both research and diagnostic applications. What has accounted for this lack of maturation of the technique? The success of IHC is part of the reason measuring a gene's encoded protein routinely and inexpensively, particularly as automation evolved, rendered IHC a more viable choice in many instances. Inherent comparative sensitivity of the procedures has also clearly been a factor. Unfortunately, the chromogenic procedures in place are often insufficiently sensitive to detect the relatively low amounts of DNA and RNA levels at which the clinical utility is to be found.

  12. Protaper--hybrid technique.

    Science.gov (United States)

    Simon, Stephane; Lumley, Philip; Tomson, Phillip; Pertot, Wilhelm-Joseph; Machtou, Pierre

    2008-03-01

    Crown down preparation is the most known and described technique since the introduction of Nickel Titanium (NiTi) rotary instruments in endodontics. This technique gives good results but has limitations, such as not addressing the initial anatomy of oval or dumb-bell shaped canals. The specific design of the Protaper instruments allows use of them with a different technique and, specifically, with a brushing motion in the body of the canal. The recent introduction of hand Protaper files has expanded the range of application of this system, especially in curved canals. The 'hybrid technique', using rotary and hand files, and the advantages of the combination of both instruments, are clearly described in this article. Used with this technique, the Protaper is a very safe system to use, and more controllable, for both inexperienced and experienced practitioners alike, than other systems. To understand the precautions needed with rotary files, and how to use them to preserve the anatomy of the canal and get a tapered shaping, even in severely curved canals.

  13. In situ DNA-RNA hybridization using in vitro 125I-labeled ribosomal RNA of higher plant

    International Nuclear Information System (INIS)

    Sato, Seiichi; Kikuchi, Tadatoshi; Ishida, M.R.; Tanaka, Ryuso.

    1975-01-01

    In situ hybridization using 125 I-labeled ribosomal RNA was applied to plant cells. Cytoplasmic 25 s rRNA, which was eluted from acrylamide gels after electrophoretic separation, was labeled in vitro with carrier-free 125 I and hybridized with the interphase nuclei in root tips of Vicia faba. In most of the preparations, the nucleoli were more heavily labeled than the other regions within nuclei, and several types of grain distribution were observed on the nucleoli. From these results, it was confirmed that in situ hybridization using 125 I-labeled rRNA can be used very effectively to detect the annealing sites of different molecular species of rRNA within the nuclei of plant cells, for which it is not as easy to obtain high specific radioactive rRNA in vivo as it is in the case of cultured animal cells. (auth.)

  14. Chromosomal imbalances detected in primary bone tumors by comparative genomic hybridization and interphase fluorescence in situ hybridization

    Directory of Open Access Journals (Sweden)

    Marcelo Razera Baruffi

    2003-01-01

    Full Text Available We applied a combination of comparative genomic hybridization (CGH and fluorescence in situ hybridization (FISH, to characterize the genetic aberrations in three osteosarcomas (OS and one Ewing's sarcoma. CGH identified recurrent chromosomal losses at 10p14-pter and gains at 8q22.3-24.1 in OS. Interphase FISH allowed to confirm 8q gain in two cases. A high amplification level of 11q12-qter was detected in one OS. The Ewing's sarcoma showed gain at 1p32-36.1 as the sole chromosome alteration. These studies demonstrate the value of molecular cytogenetic methods in the characterization of recurrent genomic alterations in bone tumor tissue.

  15. Assignment of electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) to human chromosome 4q33 by fluorescence in situ hybridization and somatic cell hybridization.

    Science.gov (United States)

    Spector, E B; Seltzer, W K; Goodman, S I

    1999-08-01

    Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a nuclear-encoded protein located in the inner mitochondrial membrane. Inherited defects of ETF-QO cause glutaric acidemia type II. We here describe the localization of the ETF-QO gene to human chromosome 4q33 by somatic cell hybridization and fluorescence in situ hybridization. Copyright 1999 Academic Press.

  16. The correlation between dual-color chromogenic in situ hybridization and fluorescence in situ hybridization in assessing HER2 gene amplification in breast cancer.

    Science.gov (United States)

    Pedersen, Marianne; Rasmussen, Birgitte Bruun

    2009-06-01

    Fluorescence in situ hybridization (FISH) is regarded as the gold standard method for detecting HER2 gene amplification. Chromogenic in situ hybridization (CISH) is a promising alternative to FISH because CISH has the advantages of being a method evaluated by bright-field microscopy and the generated chromogenic signals are also stable. This study presents a dual color CISH for simultaneous detection of the HER2 gene and chromosome 17. The CISH method performs a chromogenic detection "on top" of the Food and Drug Administration (FDA)-approved HER2 FISH pharmDx method, where the fluorochrome-labeled probes are detected using enzyme-labeled antibodies and visualized by chromogenic enzymatic reactions. The HER2 status (amplified/not amplified and HER2 ratios) was evaluated by the CISH method and compared with results obtained by the FDA-approved FISH method. Of the 72 successfully investigated invasive breast carcinomas, both FISH and CISH detected HER2 amplification in 24 cases and nonamplification was detected in 47 cases. One case showed a discrepancy between FISH and CISH. The concordance between CISH and FISH was found to be almost perfect (98.6%). The correlation between the HER2 ratios obtained by the 2 methods showed excellent correlation (correlation coefficient 0.95). In conclusion, it is possible by dual-color CISH method to demonstrate HER2 genes and chromosome 17 genes, in the same tissue section and reliably assess HER2 status. The CISH method is a very promising alternative to the FISH method.

  17. Fluorescence in situ hybridization of old G-banded and mounted chromosome preparations

    DEFF Research Database (Denmark)

    Gerdes, A M; Pandis, N; Bomme, L

    1997-01-01

    the coverslips detach spontaneously; any mechanical manipulation will jeopardize the results. The success of chromosome painting is improved by excluding the regular RNase treatment step prior to hybridization. Additional changes compared with standard FISH protocols are that the 2 x SSC step is omitted......An improved method for fluorescence in situ hybridization (FISH) investigation of old, previously G-banded, mounted chromosome preparations with chromosome specific painting probes and centromere-specific probes is described. Before hybridization, the slides are incubated in xylene until......, that the amount of added probe is increased approximately 2.5 times, and that the amplification of signals is performed twice. The applicability of the method, which allows double painting with two differently labeled probes using two differently fluorescing colors, was tested on 11 cases involving different...

  18. Evaluation of Myc Gene Amplification in Prostate Cancer Using a Dual Color Chromogenic in-Situ Hybridization (Dual CISH) Assay

    OpenAIRE

    Daniel Lerda; Marta Cabrera; Jorge Flores; Luis Gutierrez; Armando Chierichetti; Martin Revol; Hernan Garcia Onto

    2013-01-01

    Objetive: The overall purpose of the study was to demonstrate applicability of the Dako dual-color chromogenic in situ hybridization (CISH) assay (DAKO Denmark, Glostrup) with respect to fluorescence in situ hybridization (FISH) probes MYC-C. Methods: MYC gene amplification by FISH and Dako dual-color CISH Results: The study showed that the dual-color CISH assay can convert Texas red and fluorescein isothiocyanate (FITC) signals into chromogenic signals. The dual –color CISH assay was p...

  19. Chromogenic in situ hybridization (CISH) to detect HER2 gene amplification in breast and gastric cancer: comparison with immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH).

    Science.gov (United States)

    Kiyose, Shinichiro; Igarashi, Hisaki; Nagura, Kiyoko; Kamo, Takaharu; Kawane, Kazunori; Mori, Hiroki; Ozawa, Takachika; Maeda, Matsuyoshi; Konno, Keisuke; Hoshino, Hideaki; Konno, Hiroyuki; Ogura, Hiroyuki; Shinmura, Kazuya; Hattori, Naohiko; Sugimura, Haruhiko

    2012-11-01

    The chromogenic in situ hybridization (CISH) assay, designed to detect the amplification of the HER2 gene in formalin-fixed, paraffin-embedded (FFPE) breast cancer (BC) and gastric cancer (GC) tissue specimens, was evaluated in 125 FFPE BC cases and 198 FFPE GC cases for which the HER2 status had been predetermined using immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). In the 125 BC cases and the 198 gastric cases, we found a very good concordance (98.4% and 99.0%, respectively) between CISH and FISH. In particular, we evaluated the polysomy cases, as these cases often have ambiguous treatment options in clinical practice. The polysomy of chromosome 17 was defined as the presence of three or more CEP17 signals in at least 10% of the tumor cells. In the 50 BC cases and 54 GC cases displaying chromosome 17 polysomy, the concordance between FISH and CISH was 98.0% and 98.1%, respectively. These results indicate that CISH could provide an accurate and practical alternative to FISH for the clinical diagnosis of HER2 gene amplification in FFPE BC and FFPE GC samples. © 2012 The Authors. Pathology International © 2012 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.

  20. Microstructure and wear of in-situ Ti/(TiN + TiB) hybrid composite layers produced using liquid phase process

    Energy Technology Data Exchange (ETDEWEB)

    Yazdi, R., E-mail: ryazdi@ut.ac.ir; Kashani-Bozorg, S.F.

    2015-02-15

    Tungsten inert gas (TIG) technique was conducted on commercially pure (CP)-Ti substrate, which was coated with h-BN-based powder mixture prior to the treatment. The treated surfaces were evaluated and characterized by means of scanning electron microscope (SEM), X-ray diffraction analysis, and electron dispersive spectrometry (EDS). The microhardness and wear experiment were also performed by using a microhardness machine and pin-on-disk tribometer. As h-BN reacted with titanium, an in-situ hybrid composite layer was formed showing near stoichiometric dendrites of TiN, platelets of TiB and interdendritic regions of α′-Ti martensite crystal structures. The population level of TiN and TiB regions were found to increase using a pre-placed powder mixture with greater h-BN content. However, the fabricated layers exhibited cracking and porosity; these were minimized by adjusting arc energy density and h-BN content of powder mixture. The microhardness value of the fabricated hybrid composite layers was found to be in the range of ∼650 HV{sub 0.2}–1000 HV{sub 0.2}; this is three to five times higher than that of the untreated CP-Ti substrate. In addition, the in-situ hybrid composite layers exhibited superior wear behavior over CP-Ti substrate; this is attributed to the formation of newly formed ceramic phases in the solidified surface layers and good coherent interface between the composite layer and CP-substrate. Meanwhile, severe adhesive wear mechanism of CP-titanium surface changed to mild abrasive one as a result of surface treatment. - Highlights: • In-situ Ti/(TiN + TiB) hybrid composite layers were synthesized by TIG processing on commercially pure titanium. • The microstructure features were characterized by several methods. • Microhardness enhanced three to five times higher than that of the CP-Ti substrate after surface modification. • The fabricated composite layers improved wear resistance of CP-titanium. • Severe adhesive wear mechanism of

  1. Detection of airborne Legionella while showering using liquid impingement and fluorescent in situ hybridization (FISH).

    Science.gov (United States)

    Deloge-Abarkan, Magali; Ha, Thi-Lan; Robine, Enric; Zmirou-Navier, Denis; Mathieu, Laurence

    2007-01-01

    Aerosols of water contaminated with Legionella bacteria constitute the only mode of exposure for humans. However, the prevention strategy against this pathogenic bacteria risk is managed through the survey of water contamination. No relationship linked the Legionella bacteria water concentration and their airborne abundance. Therefore, new approaches in the field of the metrological aspects of Legionella bioaerosols are required. This study was aimed at testing the main principles for bioaerosol collection (solid impaction, liquid impingement and filtration) and the in situ hybridization (FISH) method, both in laboratory and field assays, with the intention of applying such methodologies for airborne Legionella bacteria detection while showering. An aerosolization chamber was developed to generate controlled and reproducible L. pneumophila aerosols. This tool allowed the identification of the liquid impingement method as the most appropriate one for collecting airborne Legionella bacteria. The culturable fraction of airborne L. pneumophila recovered with the liquid impingement principle was 4 and 700 times higher compared to the impaction and filtration techniques, respectively. Moreover, the concentrations of airborne L. pneumophila in the impinger fluid were on average 7.0 x 10(5) FISH-cells m(-3) air with the fluorescent in situ hybridization (FISH) method versus 9.0 x 10(4) CFU m(-3) air with the culture method. These results, recorded under well-controlled conditions, were confirmed during the field experiments performed on aerosols generated by hot water showers in health institutions. This new approach may provide a more accurate characterization of aerobiocontamination by Legionella bacteria.

  2. In situ biosynthesis of bacterial nanocellulose-CaCO3 hybrid bionanocomposite: One-step process.

    Science.gov (United States)

    Mohammadkazemi, Faranak; Faria, Marisa; Cordeiro, Nereida

    2016-08-01

    In this work, a simple and green route to the synthesis of the bacterial nanocellulose-calcium carbonate (BNC/CaCO3) hybrid bionanocomposites using one-step in situ biosynthesis was studied. The CaCO3 was incorporated in the bacterial nanocellulose structure during the cellulose biosynthesis by Gluconacetobacter xylinus PTCC 1734 bacteria. Hestrin-Schramm (HS) and Zhou (Z) culture media were used to the hybrid bionanocomposites production and the effect of ethanol addition was investigated. Attenuated total reflection Fourier transform infrared spectroscopy, field emission scanning electron microscopy, X-ray diffraction, energy-dispersive X-ray spectroscopy, inverse gas chromatography and thermogravimetric analysis were used to characterize the samples. The experimental results demonstrated that the ethanol and culture medium play an important role in the BNC/CaCO3 hybrid bionanocomposites production, structure and properties. The BNC/CaCO3 biosynthesized in Z culture medium revealed higher O/C ratio and amphoteric surface character, which justify the highest CaCO3 content incorporation. The CaCO3 was incorporated into the cellulosic matrix decreasing the bacterial nanocellulose crystallinity. This work reveals the high potential of in situ biosynthesis of BNC/CaCO3 hybrid bionanocomposites and opens a new way to the high value-added applications of bacterial nanocellulose. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Chromogenic in situ hybridization (CISH): a novel alternative in screening archival breast cancer tissue samples for HER-2/neu status

    OpenAIRE

    Madrid, Manuelito A; Lo, Raymundo W

    2004-01-01

    Background Chromogenic in situ hybridization (CISH) is emerging as a practical, cost-effective, and valid alternative to fluorescent in situ hybridization in testing for gene alteration, especially in centers primarily working with immunohistochemistry (IHC). Methods We assessed Her-2/neu alteration using CISH on formalin-fixed paraffin-embedded primary invasive ductal carcinoma tumors in which IHC (CB11 antibody) had previously been performed, and we compared the results with IHC. The 160 se...

  4. Karyotypes and Distribution of Tandem Repeat Sequences in Brassica nigra Determined by Fluorescence in situ Hybridization

    Czech Academy of Sciences Publication Activity Database

    Wang, G.; He, Q.; Macas, Jiří; Novák, Petr; Neumann, Pavel; Meng, D.; Zhao, H.; Guo, N.; Han, S.; Zong, M.; Jin, W.; Liu, F.

    2017-01-01

    Roč. 152, č. 3 (2017), s. 158-165 ISSN 1424-8581 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : asymmetric somatic hybridization * Fluorescence in situ hybridization * Karyotype * (Peri) centromere Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.354, year: 2016

  5. Regulatory pathway analysis by high-throughput in situ hybridization.

    Directory of Open Access Journals (Sweden)

    Axel Visel

    2007-10-01

    Full Text Available Automated in situ hybridization enables the construction of comprehensive atlases of gene expression patterns in mammals. Such atlases can become Web-searchable digital expression maps of individual genes and thus offer an entryway to elucidate genetic interactions and signaling pathways. Towards this end, an atlas housing approximately 1,000 spatial gene expression patterns of the midgestation mouse embryo was generated. Patterns were textually annotated using a controlled vocabulary comprising >90 anatomical features. Hierarchical clustering of annotations was carried out using distance scores calculated from the similarity between pairs of patterns across all anatomical structures. This process ordered hundreds of complex expression patterns into a matrix that reflects the embryonic architecture and the relatedness of patterns of expression. Clustering yielded 12 distinct groups of expression patterns. Because of the similarity of expression patterns within a group, members of each group may be components of regulatory cascades. We focused on the group containing Pax6, an evolutionary conserved transcriptional master mediator of development. Seventeen of the 82 genes in this group showed a change of expression in the developing neocortex of Pax6-deficient embryos. Electromobility shift assays were used to test for the presence of Pax6-paired domain binding sites. This led to the identification of 12 genes not previously known as potential targets of Pax6 regulation. These findings suggest that cluster analysis of annotated gene expression patterns obtained by automated in situ hybridization is a novel approach for identifying components of signaling cascades.

  6. In situ hybridization studies of hepatitis A viral RNA in patients with acute hepatitis A

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, M; Goldin, R D; Ladva, S [Department of Histopathology, St. Mary' s Hospital Medical School, Imperial College of Science, Technology and Medicine, London (United Kingdom); Scheuer, P J [Department of Histopathology, Royal Free Hospital and School of Medicine, London (United Kingdom); Thomas, H C [Department of Medicine, St. Mary' s Hospital Medical School, Imperial College of Science, Technology and Medicine, London (United Kingdom)

    1994-01-01

    In situ hybridization with oligonucleotide probes has been used to localise hepatitis A virus RNA genomic sequences in formalin-fixed and routinely processed human liver biopsies from three patients. Using radiolabelled Sulphur-35 antisense probes, viral genomic sequences were found in all three cases, but signal intensity was greatest in cases 1 and 2 with fulminant hepatitis, and was minimal in the third case of resolving hepatitis biopsied 2 months after acute illness. Localisation showed the viral RNA to be present in hepatocytes, sinusoidal cells and inflammatory cells in and around the portal tracts. Both cases showed signal in similar cell types, but the distribution of staining was predominantly periportal in case 1, whereas lobular staining was more apparent in case 2. Hybridization with sense polarity probes failed to detect any evidence of replicative intermediates of antigenomic viral RNA. The presence of hepatitis A RNA in phagocytic cells was confirmed using immunohistochemistryfor a macrophage marker, CD68, combined with in situ hybridization. In all cases the signal was predominantly cytoplasmic, and this was confirmed with the use of tritiated probes. (au).

  7. In situ hybridization studies of hepatitis A viral RNA in patients with acute hepatitis A

    International Nuclear Information System (INIS)

    Taylor, M.; Goldin, R.D.; Ladva, S.; Scheuer, P.J.; Thomas, H.C.

    1994-01-01

    In situ hybridization with oligonucleotide probes has been used to localise hepatitis A virus RNA genomic sequences in formalin-fixed and routinely processed human liver biopsies from three patients. Using radiolabelled Sulphur-35 antisense probes, viral genomic sequences were found in all three cases, but signal intensity was greatest in cases 1 and 2 with fulminant hepatitis, and was minimal in the third case of resolving hepatitis biopsied 2 months after acute illness. Localisation showed the viral RNA to be present in hepatocytes, sinusoidal cells and inflammatory cells in and around the portal tracts. Both cases showed signal in similar cell types, but the distribution of staining was predominantly periportal in case 1, whereas lobular staining was more apparent in case 2. Hybridization with sense polarity probes failed to detect any evidence of replicative intermediates of antigenomic viral RNA. The presence of hepatitis A RNA in phagocytic cells was confirmed using immunohistochemistryfor a macrophage marker, CD68, combined with in situ hybridization. In all cases the signal was predominantly cytoplasmic, and this was confirmed with the use of tritiated probes. (au)

  8. Differential in situ hybridization for herpes simplex virus typing in routine skin biopsies

    NARCIS (Netherlands)

    Botma, H. J.; Dekker, H.; van Amstel, P.; Cairo, I.; van den Berg, F. M.

    1995-01-01

    A herpes simplex virus (HSV) type 2 specific recombinant plasmid probe designated pH2S3 was constructed from non-HSV-1 crossreactive regions of the HSV-2 genome. DNA in situ hybridization on in vitro reconstructed tissue samples of sheep collagen matrix impregnated with herpes virus-infected human

  9. 10p Duplication characterized by fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Wiktor, A.; Feldman, G.L.; Van Dyke, D.L.; Kratkoczki, P.; Ditmars, D.M. Jr. [Henry Ford Hospital, Detroit, MI (United States)

    1994-09-01

    We describe a patient with severe failure to thrive, mild-moderate developmental delay, cleft lip and palate, and other anomalies. Routine cytogenetic analysis documented a de novo chromosome rearrangement involving chromosome 4, but the origin of the derived material was unknown. Using chromosome specific painting probes, the karyotype was defined as 46,XY,der(4)t(4;10)(q35;p11.23). Characterization of the dup(10p) by fluorescence in situ hybridization (FISH) analysis provides another example of the usefulness of this technology in identifying small deletions, duplications, or supernumerary marker chromosomes. 19 refs., 4 figs.

  10. In situ protocol for butterfly pupal wings using riboprobes.

    Science.gov (United States)

    Ramos, Diane; Monteiro, Antonia

    2007-01-01

    Here we present, in video format, a protocol for in situ hybridizations in pupal wings of the butterfly Bicyclus anynana using riboprobes. In situ hybridizations, a mainstay of developmental biology, are useful to study the spatial and temporal patterns of gene expression in developing tissues at the level of transcription. If antibodies that target the protein products of gene transcription have not yet been developed, and/or there are multiple gene copies of a particular protein in the genome that cannot be differentiated using available antibodies, in situs can be used instead. While an in situ technique for larval wing discs has been available to the butterfly community for several years, the current protocol has been optimized for the larger and more fragile pupal wings.

  11. Multi-objective optimization of in-situ bioremediation of groundwater using a hybrid metaheuristic technique based on differential evolution, genetic algorithms and simulated annealing

    Directory of Open Access Journals (Sweden)

    Kumar Deepak

    2015-12-01

    Full Text Available Groundwater contamination due to leakage of gasoline is one of the several causes which affect the groundwater environment by polluting it. In the past few years, In-situ bioremediation has attracted researchers because of its ability to remediate the contaminant at its site with low cost of remediation. This paper proposed the use of a new hybrid algorithm to optimize a multi-objective function which includes the cost of remediation as the first objective and residual contaminant at the end of the remediation period as the second objective. The hybrid algorithm was formed by combining the methods of Differential Evolution, Genetic Algorithms and Simulated Annealing. Support Vector Machines (SVM was used as a virtual simulator for biodegradation of contaminants in the groundwater flow. The results obtained from the hybrid algorithm were compared with Differential Evolution (DE, Non Dominated Sorting Genetic Algorithm (NSGA II and Simulated Annealing (SA. It was found that the proposed hybrid algorithm was capable of providing the best solution. Fuzzy logic was used to find the best compromising solution and finally a pumping rate strategy for groundwater remediation was presented for the best compromising solution. The results show that the cost incurred for the best compromising solution is intermediate between the highest and lowest cost incurred for other non-dominated solutions.

  12. Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species.

    Science.gov (United States)

    Prado, E A; Faivre-Rampant, P; Schneider, C; Darmency, M A

    1996-10-01

    Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S-5.8S-25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.

  13. Fluorescence in situ hybridization for phytoplasma and endophytic bacteria localization in plant tissues.

    Science.gov (United States)

    Bulgari, Daniela; Casati, Paola; Faoro, Franco

    2011-11-01

    In the present study, we developed a rapid and efficient fluorescence in situ hybridization assay (FISH) in non-embedded tissues of the model plant Catharanthus roseus for co-localizing phytoplasmas and endophytic bacteria, opening new perspectives for studying the interaction between these microorganisms. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Actinobacillus pleuropneumoniae osteomyelitis in pigs demonstrated by fluorescent in situ hybridization

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Boye, Mette; Hagedorn-Olsen, T.

    1999-01-01

    Necrotizing osteomyelitis and fibrinopurulent arthritis with isolation of Actinobacillus pleuropneumoniae serotype 2 is reported in two pigs from a herd with lameness and mild coughing problems among 8 to 12-week-old pigs. Application of fluorescent in situ hybridization targeting 16S ribosomal R......, in joints with arthritis, and in bone necroses including lysis of growth plate and suppurative inflammation in the adjacent trabecular metaphysis, thus demonstrating that well-known infections manifest new, unusual lesions....

  15. Hard and transparent hybrid polyurethane coatings using in situ incorporation of calcium carbonate nanoparticles

    International Nuclear Information System (INIS)

    Yao Lu; Yang Jie; Sun Jing; Cai Lifang; He Linghao; Huang Hui; Song Rui; Hao Yongmei

    2011-01-01

    Highlights: → In situ mineralization via gas diffusion was adopted for a good dispersion of calcium carbonate nanoparticles in the polymeric PU matrix. → Hybrid films with high dispersion, transparency, robust and thermal stability can be obtained by controlling the CaCO 3 loading. → The hybrid films display a significant improvement in its water resistance, surface hardness, scratch resistance and flexibility, with the introduction of CaCO 3 , and all coatings exhibited excellent chemical resistance and adhesion. - Abstract: The combination of hardness, scratch resistance, and flexibility is a highly desired feature in many coating applications. The aim of this study is to achieve this goal through the in situ introduction of an unmodified calcium carbonate (CaCO 3 ) into a water-soluble polyurethane (PU) matrix. Smooth and (semi-) transparent films were prepared from both the neat PU and the CaCO 3 -filled composites. As evidenced by the measurements from scanning electron microscopy (SEM), optical microscopy, dynamic mechanical analysis (DMA) and thermogravimetric analysis (TGA), hybrid films with high dispersion, transparency, robustness and thermal stability could be obtained by controlling the CaCO 3 loading. The storage modulus could increase from 441 MPa of neat PU matrix to 1034 MPa of hybrid film containing 2% (w/w) CaCO 3 . In addition, the same hybrid films displayed a significant improvement in its water resistance. In this case, the water-uptake ratio decreased from 41.54% of PU to 2.21% of hybrid film containing 2% (w/w) CaCO 3 . Moreover, with the introduction of CaCO 3 , conventional coating characterization methods demonstrated an increase in the surface hardness, scratch resistance and flexibility, and all coatings exhibited excellent chemical resistance and adhesion.

  16. Detection of denitrification genes by in situ rolling circle amplification - fluorescence in situ hybridization (in situ RCA-FISH) to link metabolic potential with identity inside bacterial cells

    DEFF Research Database (Denmark)

    Hoshino, Tatsuhiko; Schramm, Andreas

    2010-01-01

    target site. Finally, the RCA product inside the cells was detected by standard fluorescence in situ hybridization (FISH). The optimized protocol showed high specificity and signal-to-noise ratio but low detection frequency (up to 15% for single-copy genes and up to 43% for the multi-copy 16S rRNA gene...... as Candidatus Accumulibacter phosphatis by combining in situ RCA-FISH with 16S rRNA-targeted FISH. While not suitable for quantification because of its low detection frequency, in situ RCA-FISH will allow to link metabolic potential with 16S rRNA (gene)-based identification of single microbial cells.......). Nevertheless, multiple genes (nirS and nosZ; nirS and the 16S rRNA gene) could be detected simultaneously in P. stutzeri. Environmental application of in situ RCA-FISH was demonstrated on activated sludge by the differential detection of two types of nirS-defined denitrifiers; one of them was identified...

  17. Fluorescence in situ hybridization in combination with the comet assay and micronucleus test in genetic toxicology

    Directory of Open Access Journals (Sweden)

    Hovhannisyan Galina G

    2010-09-01

    Full Text Available Abstract Comet assay and micronucleus (MN test are widely applied in genotoxicity testing and biomonitoring. While comet assay permits to measure direct DNA-strand breaking capacity of a tested agent MN test allows estimating the induced amount of chromosome and/or genome mutations. The potential of these two methods can be enhanced by the combination with fluorescence in situ hybridization (FISH techniques. FISH plus comet assay allows the recognition of targets of DNA damage and repairing directly. FISH combined with MN test is able to characterize the occurrence of different chromosomes in MN and to identify potential chromosomal targets of mutagenic substances. Thus, combination of FISH with the comet assay or MN test proved to be promising techniques for evaluation of the distribution of DNA and chromosome damage in the entire genome of individual cells. FISH technique also permits to study comet and MN formation, necessary for correct application of these methods. This paper reviews the relevant literature on advantages and limitations of Comet-FISH and MN-FISH assays application in genetic toxicology.

  18. Characterization of a de novo duplication of 11p14----p13, using fluorescent in situ hybridization and southern hybridization

    NARCIS (Netherlands)

    Speleman, F.; Mannens, M.; Redeker, B.; Vercruyssen, M.; van Oostveldt, P.; Leroy, J.; Slater, R.

    1991-01-01

    A de novo 11p+ chromosome was found in a child with mild mental retardation but no other remarkable dysmorphic characteristics. Banding studies suggested a duplication of regions 11p13 and 11p14 or regions 11p14 and 11p15. Using fluorescent in situ hybridization and digital imaging microscopy, we

  19. Presence and localization of bacteria in the bovine endometrium postpartum using fluorescence in situ hybridization

    DEFF Research Database (Denmark)

    Karstrup, C. C.; Agerholm, J. S.; Jensen, Tim Kåre

    2017-01-01

    The aim of this study was to investigate bacterial invasiveness of the bovine endometrium during the postpartum period. Fluorescence in situ hybridization was applied to endometrial biopsies using probes for Fusobacterium necrophorum, Porphyromonas levii, Trueperella pyogenes, Escherichia coli...

  20.   In situ identification of streptococci and other bacteria in initial dental biofilm by confocal laser scanning microscopy and fluorescence in situ hybridization

    DEFF Research Database (Denmark)

    Dige, Irene; Kilian, Mogens; Nilsson, Holger

    2007-01-01

    Confocal laser scanning microscopy (CLSM) has been employed as a method for studying intact natural biofilm. When combined with fluorescence in situ hybridization (FISH) it is possible to analyze spatial relationships and changes of specific members of microbial populations over time. The aim...

  1. Multicenter Evaluation of a New Shortened Peptide Nucleic Acid Fluorescence In Situ Hybridization Procedure for Species Identification of Select Gram-Negative Bacilli from Blood Cultures▿

    Science.gov (United States)

    Morgan, Margie; Marlowe, Elizabeth; Della-Latta, Phyllis; Salimnia, Hossein; Novak-Weekley, Susan; Wu, Fann; Crystal, Benjamin S.

    2010-01-01

    A shortened protocol for two peptide nucleic acid fluorescence in situ hybridization (PNA FISH) assays for the detection of Gram-negative bacilli from positive blood cultures was evaluated in a multicenter trial. There was 100% concordance between the two protocols for each assay (368 of 368 and 370 of 370 results) and 99.7% (367 of 368 and 369 of 370 results) agreement with routine laboratory techniques. PMID:20357212

  2. Hybridized centroid technique for 3D Molodensky-Badekas ...

    African Journals Online (AJOL)

    In view of this, the present study developed and tested two new hybrid centroid techniques known as the harmonic-quadratic mean and arithmetic-quadratic mean centroids. The proposed hybrid approaches were compared with the geometric mean, harmonic mean, median, quadratic mean and arithmetic mean. In addition ...

  3. Study of the frequency of translocations and dicentrics in human spermatozoid using fluorescent in situ hybridization

    International Nuclear Information System (INIS)

    Alvarez, R.; Ponsa, I.; Tusell, L.; Genesca, A.; Miro, R.; Egozcue, J.

    1998-01-01

    Present study has intended to analyze the induction translocations and dicentrics in human sperms irradiated in vitro to the dose 4Gy by means of the use technical in situ hybridization with probes marked fluorescently

  4. Bonding techniques for hybrid active pixel sensors (HAPS)

    Energy Technology Data Exchange (ETDEWEB)

    Bigas, M. [Centre Nacional de Microelectronica, CNM-IMB (CSIC), Campus Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)]. E-mail: Marc.Bigas@cnm.es; Cabruja, E. [Centre Nacional de Microelectronica, CNM-IMB (CSIC), Campus Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)]. E-mail: Enric.Cabruja@cnm.es; Lozano, M. [Centre Nacional de Microelectronica, CNM-IMB (CSIC), Campus Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)

    2007-05-01

    A hybrid active pixel sensor (HAPS) consists of an array of sensing elements which is connected to an electronic read-out unit. The most used way to connect these two different devices is bump bonding. This interconnection technique is very suitable for these systems because it allows a very fine pitch and a high number of I/Os. However, there are other interconnection techniques available such as direct bonding. This paper, as a continuation of a review [M. Lozano, E. Cabruja, A. Collado, J. Santander, M. Ullan, Nucl. Instr. and Meth. A 473 (1-2) (2001) 95-101] published in 2001, presents an update of the different advanced bonding techniques available for manufacturing a hybrid active pixel detector.

  5. Cytogenetic analysis using fluorescence in situ hybridization (FISH) to evaluate occupational exposure to carcinogens

    Czech Academy of Sciences Publication Activity Database

    Šrám, Radim; Beskid, Olena; Binková, Blanka; Rössner, P.; Šmerhovský, Zdeněk

    2004-01-01

    Roč. 149, - (2004), s. 335-344 ISSN 0378-4274 R&D Projects: GA MŽP SI/340/2/00 Institutional research plan: CEZ:AV0Z5039906 Keywords : Chromosomal aberrations * Fluorescence in situ hybridization Subject RIV: DN - Health Impact of the Environment Quality Impact factor: 2.571, year: 2004

  6. Detection of human papillomavirus in laryngeal lesions by in situ hybridization

    DEFF Research Database (Denmark)

    Multhaupt, H A; Fessler, J N; Warhol, M J

    1994-01-01

    Human papillomavirus (HPV) is associated with human neoplasms of squamous epithelium. Squamous papillomas and verrucous carcinomas are two types of squamous neoplasms of the larynx that present difficult problems in differential diagnosis. Using in situ hybridization with biotinylated DNA probes......, we examined benign squamous papillomas and verrucous squamous carcinomas of the larynx for the presence of HPV. Forty-two biopsy specimens from 18 patients with laryngeal papillomas and 11 biopsy specimens from seven patients with verrucous carcinomas were obtained from the files of Pennsylvania...... Hospital, Philadelphia, PA. Tissue sections were hybridized with an HPV DNA cocktail. The HPV-positive cases then were subtyped further with DNA probes specific for HPV subtypes 6/11, 16/18, and 31/33/35. All benign squamous papillomas (42 of 42) were positive for HPV subtype 6/11. None of the verrucous...

  7. Efficient in situ growth of enzyme-inorganic hybrids on paper strips for the visual detection of glucose.

    Science.gov (United States)

    Li, WanYun; Lu, ShiYu; Bao, ShuJuan; Shi, ZhuanZhuan; Lu, Zhisong; Li, ChangMing; Yu, Ling

    2018-01-15

    A visual colorimetric microfluidic paper-based analytical device (μPAD) was constructed following the direct synthesis of enzyme-inorganic hybrid nanomaterials on the paper matrix. An inorganic solution of MnSO 4 and KH 2 PO 4 containing a diluted enzyme (glucose oxidase, GOx) was subsequently pipetted onto cellulose paper for the in situ growth of GOx@Mn 3 (PO 4 ) 2 hybrid functional materials. The characterization of the morphology and chemical composition validated the presence of hybrid materials roots in the paper fiber, while the Mn 3 (PO 4 ) 2 of the hybrid provided both a surface for enzyme anchoring and a higher peroxidase-like catalytic activity as compared to the Mn 3 (PO 4 ) 2 crystal that was synthesized without enzyme modulation. This new approach for the in situ growth of an enzyme-inorganic hybrid on a paper matrix eliminates centrifugation and the dry process by casting the solution on paper. The sensing material loading was highly reproducible because of the accuracy and stability of pipetting, which eventually contributed to the reliability of the μPAD. The self-assembled natural and artificial enzyme hybrid on the μPADs specifically detected glucose from a group of interferences, which shows great specificity using this method. Moreover, the colorimetric signal exhibited detection limitation for glucose is 0.01mM, which lies in the physiological range of glucose in biological samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Treatment of critical lower limb ischemia using a hybrid technique

    Directory of Open Access Journals (Sweden)

    Ricardo Wagner da Costa Moreira

    2014-09-01

    Full Text Available Critical ischemia of a lower limb is a condition that threatens its viability and must be treated promptly to avoid major amputation. Revascularization is the most effective treatment method and is performed using surgical or endovascular techniques. For patients with thoracoabdominal aortic aneurysms, combining these two approaches into a "hybrid technique" makes it possible to treat patients who could not be adequately treated by either technique in isolation. We report on a case of lower limb critical ischemia treated using a combination of surgery and endovascular techniques, in an application of the hybrid technique in a different arterial bed.

  9. In-situ fabrication of hybrid polyoxometalate nanoparticles composite films

    International Nuclear Information System (INIS)

    Lan Yang; Mao Baodong; Wang Enbo; Song Yonghai; Kang Zhenhui; Wang Chunlei; Tian Chungui; Zhang Chao; Xu Lin; Li Zhuang

    2007-01-01

    Inorganic-organic hybrid nanoparticles multilayer films were fabricated by extending the method of nucleation and growth of particles in polymer assemblies. The polyelectrolyte matrix was constructed by layer-by-layer self-assembly method. Synthesis of polyoxometalate nanoparticles was achieved by alternately dipping the precursor polyelectrolyte matrix into AgNO 3 and H 4 SiW 12 O 40 aqueous solutions. Repeating the above synthesis process, Ag 4 SiW 12 O 40 nanoparticles with controllable diameters of 20 to 77 nm were synthesized in the multilayer films in-situ. UV-vis absorption spectra indicate that the nanoparticles grew gradually in the synthesis process. Transmission electron microscopy was used to observe the size and morphology of the nanoparticles

  10. Localization of insulin receptor mRNA in rat brain by in situ hybridization

    International Nuclear Information System (INIS)

    Marks, J.L.; Porte, D. Jr.; Stahl, W.L.; Baskin, D.G.

    1990-01-01

    Insulin receptor mRNA was demonstrated in rat brain slices by in situ hybridization with three 35 S-oligonucleotide probes and contact film autoradiography. Specificity was confirmed by showing that (a) excess unlabeled probe abolished the signal, (b) an oligonucleotide probe for rat neuropeptide Y mRNA showed a different distribution of hybridization signal, and (c) the distribution of insulin receptor binding was consistent with the distribution of insulin receptor mRNA. Insulin receptor mRNA was most abundant in the granule cell layers of the olfactory bulb, cerebellum and dentate gyrus, in the pyramidal cell body layers of the pyriform cortex and hippocampus, in the choroid plexus and in the arcuate nucleus of the hypothalamus

  11. In situ 3D nanoprinting of free-form coupling elements for hybrid photonic integration

    Science.gov (United States)

    Dietrich, P.-I.; Blaicher, M.; Reuter, I.; Billah, M.; Hoose, T.; Hofmann, A.; Caer, C.; Dangel, R.; Offrein, B.; Troppenz, U.; Moehrle, M.; Freude, W.; Koos, C.

    2018-04-01

    Hybrid photonic integration combines complementary advantages of different material platforms, offering superior performance and flexibility compared with monolithic approaches. This applies in particular to multi-chip concepts, where components can be individually optimized and tested. The assembly of such systems, however, requires expensive high-precision alignment and adaptation of optical mode profiles. We show that these challenges can be overcome by in situ printing of facet-attached beam-shaping elements. Our approach allows precise adaptation of vastly dissimilar mode profiles and permits alignment tolerances compatible with cost-efficient passive assembly techniques. We demonstrate a selection of beam-shaping elements at chip and fibre facets, achieving coupling efficiencies of up to 88% between edge-emitting lasers and single-mode fibres. We also realize printed free-form mirrors that simultaneously adapt beam shape and propagation direction, and we explore multi-lens systems for beam expansion. The concept paves the way to automated assembly of photonic multi-chip systems with unprecedented performance and versatility.

  12. Detection of human papillomavirus in oral warts using in situ hybridization

    Directory of Open Access Journals (Sweden)

    Suzana Orsini Machado de Sousa

    2008-01-01

    Full Text Available Objective: The human papillomavirus is a group of DNA epitheliotrophic viruses associated with the etiology of benign and malignant oral warts. More than 100 types have been identified and among them, 24 have been found into the oral cavity. The aim of this study was to analyze human papillomavirus prevalence and its subtypes in 50 oral warts, of which 20 were squamous papillomas, 17 condylomaacuminatum and 13 verruca vulgaris. Method: In situ hybridization was used with biotinylated DNA probes for wide-spectrum HPV and with specific probes for human papillomavirus 6/11, human papillomavirus 16/18 and human papillomavirus 31/33. Results: Human papillomavirus was present in ten (20% of the 50 oral wart cases, 03 (3/20 squamous papillomas, 05 (5/17 condyloma acuminatum and 02 (2/13 verruca vulgaris. Of these, 8 (16% were positive to the HPV probe 6/11 being 5 condyloma acuminatum, 1 squamous papilloma and 2 verruca vulgaris. Three cases (6% demonstrated positivity to the human papillomavirus probe 16/18, with 2 being cases of condyloma and the other a case of squamous papilloma. Of the six positive cases to the human papillomavirus probe 31/33, (12% 4 were condyloma acuminatum and 2 squamous papillomas. Conclusion: The human papillomavirus expression (20% found in this study was low, but within the average found in the literature. Nonetheless, in addition to in situ hybridization, other methods may be necessary for confirming the presence of human papillomavirus.

  13. Submicroscopic deletions at the WAGR locus, revealed by nonradioactive in situ hybridization.

    OpenAIRE

    Fantes, J A; Bickmore, W A; Fletcher, J M; Ballesta, F; Hanson, I M; van Heyningen, V

    1992-01-01

    Fluorescence in situ hybridization (FISH) with biotin-labeled probes mapping to 11p13 has been used for the molecular analysis of deletions of the WAGR (Wilms tumor, aniridia, genitourinary abnormalities, and mental retardation) locus. We have detected a submicroscopic 11p13 deletion in a child with inherited aniridia who subsequently presented with Wilms tumor in a horseshoe kidney, only revealed at surgery. The mother, who has aniridia, was also found to carry a deletion including both the ...

  14. Technique for in situ leach simulation of uranium ores

    International Nuclear Information System (INIS)

    Grant, D.C.; Seidel, D.C.; Nichols, I.L.

    1985-01-01

    In situ uranium mining offers the advantages of minimal environmental disturbance, low capital and operating costs, and reduced mining development time. It is becoming an increasingly attractive mining method for the recovery of uranium from secondary ore deposits. In order to better understand the process, a laboratory technique was developed and used to study and simulate both the chemical and physical phenomena occurring in ore bodies during in situ leaching. The laboratory simulation technique has been used to determine effects of leaching variables on permeability, uranium recovery, and post-leach aquifer restoration. This report describes the simulation system and testing procedure in sufficient detail to allow the construction of the system, and to perform the desired leaching tests. With construction of such a system, in situ leaching of a given ore using various leach conditions can be evaluated relatively rapidly in the laboratory. Not only could optimum leach conditions be selected for existing ore bodies, but also exploitation of new ore bodies could be accelerated. 8 references, 8 figures, 2 tables

  15. Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii

    OpenAIRE

    Zhao, Laibin; Ning, Shunzong; Yi, Yingjin; Zhang, Lianquan; Yuan, Zhongwei; Wang, Jirui; Zheng, Youliang; Hao, Ming; Liu, Dengcai

    2018-01-01

    Background Aegilops tauschii is the donor of the bread wheat D genome. Based on spike morphology, the taxon has conventionally been subdivided into ssp. tauschii and ssp. strangulata. The present study was intended to address the poor match between this whole plant morphology-based subdivision and genetic relationships inferred from genotyping by fluorescence in situ hybridization karyotyping a set of 31 Ae. tauschii accessions. Results The distribution of sites hybridizing to the two probes ...

  16. Automated Image Analysis for Quantitative Fluorescence In Situ Hybridization with Environmental Samples▿ †

    OpenAIRE

    Zhou, Zhi; Pons, Marie Noëlle; Raskin, Lutgarde; Zilles, Julie L.

    2007-01-01

    When fluorescence in situ hybridization (FISH) analyses are performed with complex environmental samples, difficulties related to the presence of microbial cell aggregates and nonuniform background fluorescence are often encountered. The objective of this study was to develop a robust and automated quantitative FISH method for complex environmental samples, such as manure and soil. The method and duration of sample dispersion were optimized to reduce the interference of cell aggregates. An au...

  17. Localization of introduced genes on the chromosomes of transgenic barley, wheat and triticale by fluorescence in situ hybridization

    DEFF Research Database (Denmark)

    Pedersen, C.; Zimny, J.; Becker, D.

    1997-01-01

    Using fluorescence in situ hybridization (FISH) we localized introduced genes on metaphase chromosomes of barley, wheat, and triticale transformed by microprojectile bombardment of microspores and scutellar tissue with the pDB1 plasmid containing the uidA and bar genes. Thirteen integration sites...... of single-copy integrations. There was a slight tendency towards the localization of transgenes in distal chromosome regions. Using the GAA-satellite sequence for chromosome banding, the chromosomes containing the inserted genes were identified in most cases. Two barley lines derived from the same...... transformant showed a totally different integration pattern. Southern analysis confirmed that the inserted genes were segregating independently, resulting in different integration patterns among the progeny lines. The application of the FISH technique for the analysis of transgenic plants is discussed....

  18. Modeling the effects of forest management on in situ and ex situ longleaf pine forest carbon stocks

    Science.gov (United States)

    C.A. Gonzalez-Benecke; L.J. Samuelson; T.A. Martin; W.P. Cropper Jr; Kurt Johnsen; T.A. Stokes; John Butnor; P.H. Anderson

    2015-01-01

    Assessment of forest carbon storage dynamics requires a variety of techniques including simulation models. We developed a hybrid model to assess the effects of silvicultural management systems on carbon (C) budgets in longleaf pine (Pinus palustris Mill.) plantations in the southeastern U.S. To simulate in situ C pools, the model integrates a growth and yield model...

  19. Development of an in situ hybridization assay for the detection of ostreid herpesvirus type 1 mRNAs in the Pacific oyster, Crassostrea gigas.

    Science.gov (United States)

    Corbeil, Serge; Faury, Nicole; Segarra, Amélie; Renault, Tristan

    2015-01-01

    An in situ hybridization protocol for detecting mRNAs of ostreid herpesvirus type 1 (OsHV-1) which infects Pacific oysters, Crassostrea gigas, was developed. Three RNA probes were synthesized by cloning three partial OsHV-1 genes into plasmids using three specific primer pairs, and performing a transcription in the presence of digoxigenin dUTP. The RNA probes were able to detect the virus mRNAs in paraffin sections of experimentally infected oysters 26 h post-injection. The in situ hybridization showed that the OsHV-1 mRNAs were mainly present in connective tissues in gills, mantle, adductor muscle, digestive gland and gonads. DNA detection by in situ hybridization using a DNA probe and viral DNA quantitation by real-time PCR were also performed and results were compared with those obtained using RNA probes. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Validation of interphase fluorescence in situ hybridization (iFISH for multiple myeloma using CD138 positive cells

    Directory of Open Access Journals (Sweden)

    Renata Kiyomi Kishimoto

    2016-06-01

    Full Text Available ABSTRACT BACKGROUND: Multiple myeloma is a plasma cell neoplasm with acquired genetic abnormalities of clinical and prognostic importance. Multiple myeloma differs from other hematologic malignancies due to a high fraction of low proliferating malignant plasma cells and the paucity of plasma cells in bone marrow aspiration samples, making cytogenetic analysis a challenge. An abnormal karyotype is found in only one-third of patients with multiple myeloma and interphase fluorescence in situ hybridization is the most useful test for studying the chromosomal abnormalities present in almost 90% of cases. However, it is necessary to study the genetic abnormalities in plasma cells after their identification or selection by morphology, immunophenotyping or sorting. Other challenges are the selection of the most informative FISH panel and determining cut-off levels for FISH probes. This study reports the validation of interphase fluorescence in situ hybridization using CD138 positive cells, according to proposed guidelines published by the European Myeloma Network (EMN in 2012. METHOD: Bone marrow samples from patients with multiple myeloma were used to standardize a panel of five probes [1q amplification, 13q14 deletion, 17p deletion, t(4;14, and t(14;16] in CD138+ cells purified by magnetic cell sorting. RESULTS: This test was validated with a low turnaround time and good reproducibility. Five of six samples showed genetic abnormalities. Monosomy/deletion 13 plus t(4;14 were found in two cases. CONCLUSION: This technique together with magnetic cell sorting is effective and can be used in the routine laboratory practice. In addition, magnetic cell sorting provides a pure plasma cell population that allows other molecular and genomic studies.

  1. Detection of genetic changes in Barrett's adenocarcinoma and Barrett's esophagus by DNA in situ hybridization and immunohistochemistry

    NARCIS (Netherlands)

    Krishnadath, K. K.; Tilanus, H. W.; Alers, J. C.; Mulder, A. H.; van Dekken, H.

    1994-01-01

    We have investigated the occurrence of chromosomal DNA and cell cycle-related protein changes in Barrett's epithelium and adenocarcinoma. The presence of numerical chromosomal aberrations was studied by applying nonisotopic in situ hybridization (ISH) with (peri-)centromeric DNA probes, specific for

  2. Demonstration of interleukin-1 beta transcripts in acute myeloblastic leukemic cells by in situ hybridization.

    Science.gov (United States)

    Nakamura, M; Kanakura, Y; Furukawa, Y; Ernst, T J; Griffin, J D

    1990-07-01

    The cells from some patients with acute myeloblastic leukemia will secrete autostimulatory cytokines in tissue culture without the addition of stimulators such as phorbol 12-myristate 13-acetate. Production of interleukin-1 beta (IL-1 beta), for example, has been observed in up to 50% of cases. In order to investigate the nature of the cell secreting IL-1 beta in AML, we used an antisense RNA probe to detect specific IL-1 beta transcripts in individual leukemic cells by in situ hybridization. In fresh, uncultured cells, IL-1 beta transcripts were observed in 1-40% of undifferentiated leukemic blast cells in 17 of 19 cases. In situ hybridization was at least as sensitive as Northern blot analysis in detecting IL-1 beta transcripts. No correlation of IL-1 beta transcript expression with FAB classification was observed. Normal blood and bone marrow mononuclear cells did not contain cells expressing IL-1 beta transcripts. These results support the concept that the regulation of cytokine genes in AML cells is aberrant.

  3. Synthesis and luminescence properties of hybrid organic-inorganic transparent titania thin film activated by in-situ formed lanthanide complexes

    International Nuclear Information System (INIS)

    Wang Yige; Wang Li; Li Huanrong; Liu Peng; Qin Dashan; Liu Binyuan; Zhang Wenjun; Deng Ruiping; Zhang Hongjie

    2008-01-01

    Stable transparent titania thin films were fabricated at room temperature by combining thenoyltrifluoroacetone (TTFA)-modified titanium precursors with amphiphilic triblock poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO, P123) copolymers. The obtained transparent titania thin films were systematically investigated by IR spectroscopy, PL emission and excitation spectroscopy and transmission electron microscopy. IR spectroscopy indicates that TTFA coordinates the titanium center during the process of hydrolysis and condensation. Luminescence spectroscopy confirms the in-situ formation of lanthanide complexes in the transparent titania thin film. TEM image shows that the in-situ formed lanthanide complexes were homogeneously distributed throughout the whole thin film. The quantum yield and the number of water coordinated to lanthanide metal center have been theoretically determined based on the luminescence data. - Graphical abstract: Novel stable luminescent organic-inorganic hybrid titania thin film with high transparency activated by in-situ formed lanthanide complexes have been obtained at room temperature via a simple one-pot synthesis approach by using TTFA-modified titanium precursor with amphiphilic triblock copolymer P123. The obtained hybrid thin film displays bright red (or green), near-monochromatic luminescence due to the in-situ formed lanthanide complex

  4. In situ observation techniques of protective oxide layer

    International Nuclear Information System (INIS)

    Doi, Takashi; Adachi, Takeharu; Usuki, Noriaki

    2015-01-01

    In situ analyzing techniques for investigating a surface and interface change during corrosion and oxidation of metals by using Raman scattering spectroscopy (Raman), X-ray diffraction (XRD) and X-ray photoemission spectroscopy (XPS) are present. The Raman spectra revealed that a crystal structure and distribution of corrosion products varied during corrosion progress at elevated temperature and high pressure electrolyte. Time dependent XRD measurements made clear the behavior of the electrochemical reduction of a rust and the iso thermal transformation of a scale on a steel. It was demonstrated that XPS was capable of the in-situ measurements for initial stage of high temperature oxidation. (author)

  5. Applications of ribosomal in situ hybridization for the study of bacterial cells in the mouse intestine

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Poulsen, Lars Kongsbak; Molin, Søren

    1997-01-01

    Localization of E. coli and S. typhimurium in the large and small intestine of streptomycin-treated mice was visualized by in situ hybridization with specific rRNA target probes and epi-fluorescence microscopy. Growth rates of E. coli BJ4 colonizing the large intestine of streptomycin-treated mic...

  6. Facile in situ synthesis of hierarchical porous Ni/Ni(OH)₂ hybrid sponges with excellent electrochemical energy-storage performances for supercapacitors.

    Science.gov (United States)

    Wang, Wanren; Wang, Wenhua; Wang, Mengjiao; Guo, Xiaohui

    2014-09-01

    Herein, we report the in situ growth of single-crystalline Ni(OH)2 nanoflakes on a Ni support by using facile hydrothermal processes. The as-prepared Ni/Ni(OH)2 sponges were well-characterized by using X-ray diffraction (XRD), SEM, TEM, and X-ray photoelectron spectroscopy (XPS) techniques. The results revealed that the nickel-skeleton-supported Ni(OH)2 rope-like aggregates were composed of numerous intercrossed single-crystal Ni(OH)2 flake-like units. The Ni/Ni(OH)2 hybrid sponges served as electrodes and displayed ultrahigh specific capacitance (SC=3247 F g(-1)) and excellent rate-capability performance, likely owing to fast electron and ion transport, sufficient Faradic redox reaction, and robust structural integrity of the Ni/Ni(OH)2 hybrid electrode. These results support the promising application of Ni(OH)2 nanoflakes as advanced pseudocapacitor materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Diagnostic and Prognostic Utility of Fluorescence In situ Hybridization (FISH) Analysis in Acute Myeloid Leukemia.

    Science.gov (United States)

    Gonzales, Patrick R; Mikhail, Fady M

    2017-12-01

    Acute myeloid leukemia (AML) is a hematologic neoplasia consisting of incompletely differentiated hematopoietic cells of the myeloid lineage that proliferate in the bone marrow, blood, and/or other tissues. Clinical implementation of fluorescence in situ hybridization (FISH) in cytogenetic laboratories allows for high-resolution analysis of recurrent structural chromosomal rearrangements specific to AML, especially in AML with normal karyotypes, which comprises approximately 33-50% of AML-positive specimens. Here, we review the use of several FISH probe strategies in the diagnosis of AML. We also review the standards and guidelines currently in place for use by clinical cytogenetic laboratories in the evaluation of AML. Updated standards and guidelines from the WHO, ACMG, and NCCN have further defined clinically significant, recurring cytogenetic anomalies in AML that are detectable by FISH. FISH continues to be a powerful technique in the diagnosis of AML, with higher resolution than conventional cytogenetic analysis, rapid turnaround time, and a considerable diagnostic and prognostic utility.

  8. 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.

  9. Detection of Methylobacterium radiotolerans IMBG290 in potato plants by in situ hybridization

    OpenAIRE

    Pirttila A. M.; Kozyrovska N. O.; Ovcharenko L. P.; Podolich O. V.

    2009-01-01

    A new bacterial strain of pink-pigmented facultative methylotroph (M. radiotolerans IMBG290) which was previously isolated from in vitro grown potato plantlets after their inoculation with Pseudomonas fluorescens IMBG163 was detected in tissues by in situ hybridization method (ISH/FISH). The presence of Methylobacterium rRNA was observed in leaves and stems of potato plantlets, whereas no signal was detected in potato roots. The signal was less abundant in the untreated plants than in the pla...

  10. Dealing with the problem of non-specific in situ mRNA hybridization signals associated with plant tissues undergoing programmed cell death

    Directory of Open Access Journals (Sweden)

    Jokela Anne

    2010-02-01

    Full Text Available Abstract Background In situ hybridization is a general molecular method typically used for the localization of mRNA transcripts in plants. The method provides a valuable tool to unravel the connection between gene expression and anatomy, especially in species such as pines which show large genome size and shortage of sequence information. Results In the present study, expression of the catalase gene (CAT related to the scavenging of reactive oxygen species (ROS and the polyamine metabolism related genes, diamine oxidase (DAO and arginine decarboxylase (ADC, were localized in developing Scots pine (Pinus sylvestris L. seeds. In addition to specific signals from target mRNAs, the probes continually hybridized non-specifically in the embryo surrounding region (ESR of the megagametophyte tissue, in the remnants of the degenerated suspensors as well as in the cells of the nucellar layers, i.e. tissues exposed to cell death processes and extensive nucleic acid fragmentation during Scots pine seed development. Conclusions In plants, cell death is an integral part of both development and defence, and hence it is a common phenomenon in all stages of the life cycle. Our results suggest that extensive nucleic acid fragmentation during cell death processes can be a considerable source of non-specific signals in traditional in situ mRNA hybridization. Thus, the visualization of potential nucleic acid fragmentation simultaneously with the in situ mRNA hybridization assay may be necessary to ensure the correct interpretation of the signals in the case of non-specific hybridization of probes in plant tissues.

  11. Localization of tRNAsup(asp)2 genes from Drosophila melanogaster by 'in situ' hybridization

    International Nuclear Information System (INIS)

    Schmidt, T.; Egg, A.H.; Kubli, E.

    1978-01-01

    Transfer RNAsup(asp) 2 delta was isolated from Drosophila melanogaster by affinity chromatography on concanavalin A-Sepharose. The tRNA was iodinated 'in vitro' with Na[ 125 I] and hybridized 'in situ' to salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNAsup(asp) 2 delta to the left arm of the second chromosome in the regions 29 D and E. (orig.) [de

  12. A hybrid perturbation-Galerkin technique for partial differential equations

    Science.gov (United States)

    Geer, James F.; Anderson, Carl M.

    1990-01-01

    A two-step hybrid perturbation-Galerkin technique for improving the usefulness of perturbation solutions to partial differential equations which contain a parameter is presented and discussed. In the first step of the method, the leading terms in the asymptotic expansion(s) of the solution about one or more values of the perturbation parameter are obtained using standard perturbation methods. In the second step, the perturbation functions obtained in the first step are used as trial functions in a Bubnov-Galerkin approximation. This semi-analytical, semi-numerical hybrid technique appears to overcome some of the drawbacks of the perturbation and Galerkin methods when they are applied by themselves, while combining some of the good features of each. The technique is illustrated first by a simple example. It is then applied to the problem of determining the flow of a slightly compressible fluid past a circular cylinder and to the problem of determining the shape of a free surface due to a sink above the surface. Solutions obtained by the hybrid method are compared with other approximate solutions, and its possible application to certain problems associated with domain decomposition is discussed.

  13. Distribution of 45S rDNA in Modern Rose Cultivars (Rosa hybrida), Rosa rugosa, and Their Interspecific Hybrids Revealed by Fluorescence in situ Hybridization.

    Science.gov (United States)

    Ding, Xiao-Liu; Xu, Ting-Liang; Wang, Jing; Luo, Le; Yu, Chao; Dong, Gui-Min; Pan, Hui-Tang; Zhang, Qi-Xiang

    2016-01-01

    To elucidate the evolutionary dynamics of the location and number of rDNA loci in the process of polyploidization in the genus Rosa, we examined 45S rDNA sites in the chromosomes of 6 modern rose cultivars (R. hybrida), 5 R. rugosa cultivars, and 20 hybrid progenies by fluorescence in situ hybridization. Variation in the number of rDNA sites in parents and their interspecific hybrids was detected. As expected, 4 rDNA sites were observed in the genomes of 4 modern rose cultivars, while 3 hybridization sites were observed in the 2 others. Two expected rDNA sites were found in 2 R. rugosa cultivars, while in the other 3 R. rugosa cultivars 4 sites were present. Among the 20 R. hybrida × R. rugosa offspring, 13 carried the expected number of rDNA sites, and 1 had 6 hybridization sites, which exceeded the expected number by far. The other 6 offspring had either 2 or 3 hybridization sites, which was less than expected. Differences in the number of rDNA loci were observed in interspecific offspring, indicating that rDNA loci exhibit instability after distant hybridization events. Abnormal chromosome pairing may be the main factor explaining the variation in rDNA sites during polyploidization. © 2016 S. Karger AG, Basel.

  14. Combined Confocal and Wide-Field High-Resolution Cytometry of Fluorescent In Situ Hybridization-Stained Cells

    Czech Academy of Sciences Publication Activity Database

    Kozubek, Michal; Kozubek, Stanislav; Lukášová, Emilie; Bártová, Eva; Skalníková, M.; Matula, Pa.; Matula, Pe.; Jirsová, Pavla; Cafourková, Alena; Koutná, Irena

    2001-01-01

    Roč. 45, č. 1 (2001), s. 1-12 ISSN 0196-4763 R&D Projects: GA MŠk VS97031; GA ČR GA202/99/P008; GA AV ČR IBS5004010 Institutional research plan: CEZ:AV0Z5004920 Keywords : high-resolution cytometry * fluorescence in situ hybridization * interphase nuclei Subject RIV: BO - Biophysics Impact factor: 2.220, year: 2001

  15. Fluorescence In Situ Hybridization for MicroRNA Detection in Archived Oral Cancer Tissues

    Directory of Open Access Journals (Sweden)

    Zonggao Shi

    2012-01-01

    Full Text Available The noncoding RNA designated as microRNA (miRNA is a large group of small single-stranded regulatory RNA and has generated wide-spread interest in human disease studies. To facilitate delineating the role of microRNAs in cancer pathology, we sought to explore the feasibility of detecting microRNA expression in formalin-fixed paraffin-embedded (FFPE tissues. Using FFPE materials, we have compared fluorescent in situ hybridization (FISH procedures to detect miR-146a with (a different synthetic probes: regular custom DNA oligonucleotides versus locked nucleic acid (LNA incorporated DNA oligonucleotides; (b different reporters for the probes: biotin versus digoxigenin (DIG; (c different visualization: traditional versus tyramide signal amplification (TSA system; (d different blocking reagents for endogenous peroxidase. Finally, we performed miR-146a FISH on a commercially available oral cancer tissue microarray, which contains 40 cases of oral squamous cell carcinoma (OSCC and 10 cases of normal epithelia from the human oral cavity. A sample FISH protocol for detecting miR-146a is provided. In summary, we have established reliable in situ hybridization procedures for detecting the expression of microRNA in FFPE oral cancer tissues. This method is an important tool for studies on the involvement of microRNA in oral cancer pathology and may have potential prognostic or diagnostic value.

  16. Techniques of DNA hybridization detect small numbers of mycobacteria with no cross-hybridization with non-mycobacterial respiratory organisms

    International Nuclear Information System (INIS)

    Shoemaker, S.A.; Fisher, J.H.; Scoggin, C.H.

    1985-01-01

    The traditional methods used in identifying mycobacteria, such as acid-fast bacillus stains and culture, are often time-consuming, insensitive, and nonspecific. As part of an ongoing program to improve diagnosis and characterization of mycobacteria, the authors have found that deoxyribonucleic acid (DNA) hybridization techniques using isotopically labeled, single-stranded, total DNA can be used to detect as little as 10(-4) micrograms of Mycobacterium tuberculosis (MTb) DNA. This amount of DNA represents approximately 2 X 10(4) genomes. They have also shown the MTb DNA is sufficiently different from the DNA of non-mycobacterial microorganisms such that cross-hybridization with MTb DNA does not occur under the hybridization conditions employed. The authors speculate that DNA hybridization techniques may allow the rapid, sensitive, and specific identification of mycobacteria

  17. New hybrid technique for impulsive noise suppression in OFDM systems

    International Nuclear Information System (INIS)

    Mirza, A.; Zeb, A.; Sheikh, S.A.

    2017-01-01

    In this paper, a new hybrid technique employing RS (Reed Solomon) coding and adaptive filter for impulsive noise suppression in OFDM (Orthogonal Frequency Division Multiplexing) systems is presented. Adaptive filter creates a more accurate estimate of the original OFDM signal after impulsive noise cancellation. The residual impulsive noise is further mitigated by RS decoder in the second stage of proposed technique. Three members of adaptive filters family i.e. NLMS (Normalized Least Mean Square) algorithm, RLS (Recursive Least Square) algorithm and Bhagyashri algorithm are tested with RS decoder in the proposed hybrid technique. Furthermore, the results in terms of steady state MSE (Mean Square Error) reduction, BER (Bit Error Rate) improvement and SNR (Signal to Noise Ratio) enhancement confirm the effectiveness of the proposed dual faceted technique when compared with the recently reported techniques in literature. (author)

  18. Development of an in situ calibration technique for combustible gas detectors

    Science.gov (United States)

    Shumar, J. W.; Wynveen, R. A.; Lance, N., Jr.; Lantz, J. B.

    1977-01-01

    This paper describes the development of an in situ calibration procedure for combustible gas detectors (CGD). The CGD will be a necessary device for future space vehicles as many subsystems in the Environmental Control/Life Support System utilize or produce hydrogen (H2) gas. Existing calibration techniques are time-consuming and require support equipment such as an environmental chamber and calibration gas supply. The in situ calibration procedure involves utilization of a water vapor electrolysis cell for the automatic in situ generation of a H2/air calibration mixture within the flame arrestor of the CGD. The development effort concluded with the successful demonstration of in situ span calibrations of a CGD.

  19. Ultrastructural localization of human papilloma virus by nonradioactive in situ hybridization on tissue of human cervical intraepithelial neoplasia

    DEFF Research Database (Denmark)

    Multhaupt, H A; Rafferty, P A; Warhol, M J

    1992-01-01

    BACKGROUND: A nonradioactive in situ hybridization was developed to localize human papilloma virus (HPV) at the ultrastructural level. EXPERIMENTAL DESIGN: Cervical biopsies from human uterine cervices clinically suspicious of condyloma were embedded in Lowicryl K4M at low temperature...

  20. Constrained Optimization Based on Hybrid Evolutionary Algorithm and Adaptive Constraint-Handling Technique

    DEFF Research Database (Denmark)

    Wang, Yong; Cai, Zixing; Zhou, Yuren

    2009-01-01

    A novel approach to deal with numerical and engineering constrained optimization problems, which incorporates a hybrid evolutionary algorithm and an adaptive constraint-handling technique, is presented in this paper. The hybrid evolutionary algorithm simultaneously uses simplex crossover and two...... mutation operators to generate the offspring population. Additionally, the adaptive constraint-handling technique consists of three main situations. In detail, at each situation, one constraint-handling mechanism is designed based on current population state. Experiments on 13 benchmark test functions...... and four well-known constrained design problems verify the effectiveness and efficiency of the proposed method. The experimental results show that integrating the hybrid evolutionary algorithm with the adaptive constraint-handling technique is beneficial, and the proposed method achieves competitive...

  1. In-situ preparation of NaA zeolite/chitosan porous hybrid beads for removal of ammonium from aqueous solution.

    Science.gov (United States)

    Yang, Kai; Zhang, Xiang; Chao, Cong; Zhang, Bing; Liu, Jindun

    2014-07-17

    Inorganic/organic hybrid materials play important roles in removal of contaminants from wastewater. Herein, we used the natural materials of halloysite and chitosan to prepare a new adsorbent of NaA zeolite/chitosan porous hybrid beads by in-situ hydrothermal synthesis method. SEM indicated that the porous hybrid beads were composed of 6-8 μm sized cubic NaA zeolite particles congregated together with chitosan. The adsorption behavior of NH4(+) from aqueous solution onto hybrid beads was investigated at different conditions. The Langmuir and Freundlich adsorption models were applied to describe the equilibrium isotherms. A maximum adsorption capacity of 47.62 mg/g at 298 K was achieved according to Langmuir model. The regenerated or reused experiments indicated that the adsorption capacity of the hybrid beads could maintain in 90% above after 10 successive adsorption-desorption cycles. The high adsorption and reusable ability implied potential application of the hybrid beads for removing NH4(+) pollutants from wastewater. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Detection of Alien Oryza punctata Kotschy Chromosomes in Rice, Oryza sativa L., by Genomic in situ Hybridization

    OpenAIRE

    Yasui, Hideshi; Nonomura, Ken-ichi; Iwata, Nobuo; 安井, 秀; 野々村, 賢一; 岩田, 伸夫

    1997-01-01

    Genomic in situ hybridization (GIS H) using total Oryza punctata Kotschy genomic DNA as a probe was applied to detect alien chromosomes transferred from O. punctata (W1514: 2n=2x=24: BB) to O. sativa Japonica cultivar, Nipponbare (2n=2x=24: AA). Only 12 chromosomes in the interspecific hybrids (2n=3x=36: AAB) between autotetraploid of O. sativa cultivar Nipponbare and a diploid strain of O. punctata (W1514) showed intense staining by FITC in mitotic metaphase spreads. Only one homologous pair...

  3. Putting the colours into chromogenic in situ hybridization (CISH).

    Science.gov (United States)

    Shipley, J

    2006-09-01

    Recurrent genomic alterations are the hallmarks of particular cancers. Application of molecular cytogenetic technologies to tumour material in order to detect these alterations has become important for molecular diagnostics and research. A dual-colour chromogenic in situ hybridization (dc-CISH) method described recently in the Journal of Pathology has the advantage of visualizing two probes simultaneously with the ability to discern morphological features. In addition, the bright field microscopy required is readily accessible to many laboratories. The approach has been validated by comparison of results with standard analyses for HER-2 amplification status in formalin-fixed, paraffin-embedded breast cancers and is applicable to the analysis of other clinically relevant genomic aberrations as well as of use in research investigations. Copyright (c) 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  4. Frequencies of X-ray induced chromosome aberrations in lymphocytes of xeroderma pigmentosum and Fanconi anemia patients estimated by Giemsa and fluorescence in situ hybridization staining techniques

    Directory of Open Access Journals (Sweden)

    Saraswathy Radha

    2000-01-01

    Full Text Available Blood lymphocytes from xeroderma pigmentosum (XP and Fanconi anemia (FA patients were assessed for their sensitivity to ionizing radiation by estimating the frequency of X-ray (1 and 2 Gy-induced chromosome aberrations (CA. The frequencies of aberrations in the whole genome were estimated in Giemsa-stained preparations of lymphocytes irradiated at G0 or G2 stages. The frequencies of translocations and dicentrics involving chromosomes 1 and 3 as well as the X-chromosome were determined in slides stained by fluorescence in situ hybridization (FISH technique. An increase in all types of CA was observed in XP and FA lymphocytes irradiated at G0 when compared to controls. The frequency of dicentrics and rings was 6 to 27% higher (at 1 and 2 Gy in XP lymphocytes and 37% higher (at 2 Gy in FA lymphocytes than in controls, while chromosome deletions were higher in irradiated (30% in 1 Gy and 72% in 2 Gy than in control XP lymphocytes and 28 to 102% higher in FA lymphocytes. In G2-irradiated lymphocytes the frequency of CA was 24 to 55% higher in XP lymphocytes than in controls. In most cases the translocation frequencies were higher than the frequencies of dicentrics (21/19.

  5. An Optimized Small Tissue Handling System for Immunohistochemistry and In Situ Hybridization.

    Directory of Open Access Journals (Sweden)

    Giovanni Anthony

    Full Text Available Recent development in 3D printing technology has opened an exciting possibility for manufacturing 3D devices on one's desktop. We used 3D modeling programs to design 3D models of a tissue-handling system and these models were "printed" in a stereolithography (SLA 3D printer to create precision histology devices that are particularly useful to handle multiple samples with small dimensions in parallel. Our system has been successfully tested for in situ hybridization of zebrafish embryos. Some of the notable features include: (1 A conveniently transferrable chamber with 6 mesh-bottomed wells, each of which can hold dozens of zebrafish embryos. This design allows up to 6 different samples to be treated per chamber. (2 Each chamber sits in a well of a standard 6-well tissue culture plate. Thus, up to 36 different samples can be processed in tandem using a single 6 well plate. (3 Precisely fitting lids prevent solution evaporation and condensation, even at high temperatures for an extended period of time: i.e., overnight riboprobe hybridization. (4 Flat bottom mesh maximizes the consistent treatment of individual tissue samples. (5 A magnet-based lifter was created to handle up to 6 chambers (= 36 samples in unison. (6 The largely transparent resin aids in convenient visual inspection both with eyes and using a stereomicroscope. (7 Surface engraved labeling enables an accurate tracking of different samples. (8 The dimension of wells and chambers minimizes the required amount of precious reagents. (9 Flexible parametric modeling enables an easy redesign of the 3D models to handle larger or more numerous samples. Precise dimensions of 3D models and demonstration of how we use our devices in whole mount in situ hybridization are presented. We also provide detailed information on the modeling software, 3D printing tips, as well as 3D files that can be used with any 3D printer.

  6. Hybrid Perovskite Thin-Film Photovoltaics: In Situ Diagnostics and Importance of the Precursor Solvate Phases

    KAUST Repository

    Munir, Rahim

    2016-11-07

    Solution-processed hybrid perovskite semiconductors attract a great deal of attention, but little is known about their formation process. The one-step spin-coating process of perovskites is investigated in situ, revealing that thin-film formation is mediated by solid-state precursor solvates and their nature. The stability of these intermediate phases directly impacts the quality and reproducibility of thermally converted perovskite films and their photovoltaic performance.

  7. Hybrid Perovskite Thin-Film Photovoltaics: In Situ Diagnostics and Importance of the Precursor Solvate Phases

    KAUST Repository

    Munir, Rahim; Sheikh, Arif D.; Abdelsamie, Maged; Hu, Hanlin; Yu, Liyang; Zhao, Kui; Kim, Taesoo; El Tall, Omar; Li, Ruipeng; Smilgies, Detlef M.; Amassian, Aram

    2016-01-01

    Solution-processed hybrid perovskite semiconductors attract a great deal of attention, but little is known about their formation process. The one-step spin-coating process of perovskites is investigated in situ, revealing that thin-film formation is mediated by solid-state precursor solvates and their nature. The stability of these intermediate phases directly impacts the quality and reproducibility of thermally converted perovskite films and their photovoltaic performance.

  8. Human chromosome-specific changes in a human-hamster hybrid cell line (AL) assessed by fluorescent in situ hybridization (fish)

    International Nuclear Information System (INIS)

    Geard, Charles R.; Jenkins, Gloria

    1995-01-01

    Purpose: To quantitatively assess all gamma-ray induced chromosomal changes confined to one human chromosome using fluorescence microscopy and in situ hybridization with a fluorescently labeled human chromosome specific nucleic acid probe. Methods and Materials: Synchronized human-hamster hybrid cells containing human chromosome 11 were obtained by a modified mitotic shake-off procedure. G1 phase cells (> 95%) were irradiated with 137 Cs gamma rays (0, 0.5, 1.0, 1.5, 2.0, 4.0, 6.0, 8.0, and 10.0 Gy) at a dose rate of 1.1 Gy/min and mitotic cells collected 16-20 h later; chromosomal spreads were prepared, denatured, and hybridized with a fluorescein-tagged nucleic acid probe against total human DNA. Chromosomes were examined by fluorescence microscopy and all categories of change involving the human chromosome 11 as target, recorded. Results: Overall, of the 3104 human-hamster hybrid cells examined, 82.1% were euploid, of which 88.6% contained one copy of human chromosome 11, 6.2% contained two copies, and 5.2% contained 0 copies. This is compatible with mitotic nondisjunction in a small fraction of cells. Of the remaining 17.9% of cells, 85.2% were tetraploid cells with two copies of human chromosome 11. For all aberrations involving human chromosome 11 there was a linear relationship between yield and absorbed dose of 0.1 aberrations per chromosome per Gy. The yield of dicentrics, translocations, and terminal deletions that involve one lesion on the human chromosome was linear, while the yield of interstitial deletions that arise from two interacting lesions on the human chromosome was curvilinear. The frequencies of dicentrics and translocations were about equal, while there was a high (40-60%) incidence of incomplete exchanges between human and hamster chromosomes. Conclusions: Fluorescent in situ hybridization (FISH) procedures allow for the efficient detection of a broad range of induced changes in target chromosomes. Symmetrical exchanges induced in G1

  9. Multicolor fluorescent in situ hybridization to define abutting and overlapping gene expression in the embryonic zebrafish brain

    Directory of Open Access Journals (Sweden)

    Hauptmann Giselbert

    2011-04-01

    Full Text Available Abstract Background In recent years, mapping of overlapping and abutting regulatory gene expression domains by chromogenic two-color in situ hybridization has helped define molecular subdivisions of the developing vertebrate brain and shed light on its basic organization. Despite the benefits of this technique, visualization of overlapping transcript distributions by differently colored precipitates remains difficult because of masking of lighter signals by darker color precipitates and lack of three-dimensional visualization properties. Fluorescent detection of transcript distributions may be able to solve these issues. However, despite the use of signal amplification systems for increasing sensitivity, fluorescent detection in whole-mounts suffers from rapid quenching of peroxidase (POD activity compared to alkaline phosphatase chromogenic reactions. Thus, less strongly expressed genes cannot be efficiently detected. Results We developed an optimized procedure for fluorescent detection of transcript distribution in whole-mount zebrafish embryos using tyramide signal amplification (TSA. Conditions for hybridization and POD-TSA reaction were optimized by the application of the viscosity-increasing polymer dextran sulfate and the use of the substituted phenol compounds 4-iodophenol and vanillin as enhancers of POD activity. In combination with highly effective bench-made tyramide substrates, these improvements resulted in dramatically increased signal-to-noise ratios. The strongly enhanced signal intensities permitted fluorescent visualization of less abundant transcripts of tissue-specific regulatory genes. When performing multicolor fluorescent in situ hybridization (FISH experiments, the highly sensitive POD reaction conditions required effective POD inactivation after each detection cycle by glycine-hydrochloric acid treatment. This optimized FISH procedure permitted the simultaneous fluorescent visualization of up to three unique transcripts

  10. Hybrid chemical and nondestructive-analysis technique

    International Nuclear Information System (INIS)

    Hsue, S.T.; Marsh, S.F.; Marks, T.

    1982-01-01

    A hybrid chemical/NDA technique has been applied at the Los Alamos National Laboratory to the assay of plutonium in ion-exchange effluents. Typical effluent solutions contain low concentrations of plutonium and high concentrations of americium. A simple trioctylphosphine oxide (TOPO) separation can remove 99.9% of the americium. The organic phase that contains the separated plutonium can be accurately assayed by monitoring the uranium L x-ray intensities

  11. Rapid-prenatal diagnosis through fluorescence in situ hybridization for preventing aneuploidy related birth defects.

    Science.gov (United States)

    Fauzdar, Ashish; Chowdhry, Mohit; Makroo, R N; Mishra, Manoj; Srivastava, Priyanka; Tyagi, Richa; Bhadauria, Preeti; Kaul, Anita

    2013-01-01

    Women with high-risk pregnancies are offered prenatal diagnosis through amniocentesis for cytogenetic analysis of fetal cells. The aim of this study was to evaluate the effectiveness of the rapid fluorescence in situ hybridization (FISH) technique for detecting numerical aberrations of chromosomes 13, 21, 18, X and Y in high-risk pregnancies in an Indian scenario. A total of 163 samples were received for a FISH and/or a full karyotype for prenatal diagnosis from high-risk pregnancies. In 116 samples both conventional culture techniques for getting karyotype through G-banding techniques were applied in conjunction to FISH test using the AneuVysion kit (Abbott Molecular, Inc.), following standard recommended protocol to compare the both the techniques in our setup. Out of 116 patients, we got 96 normal for the five major chromosome abnormality and seven patients were found to be abnormal (04 trisomy 21, 02 monosomy X, and 01 trisomy 13) and all the FISH results correlated with conventional cytogenetics. To summarize the results of total 163 patients for the major chromosomal abnormalities analyzed by both/or cytogenetics and FISH there were 140 (86%) normal, 9 (6%) cases were abnormal and another 4 (2.5%) cases were suspicious mosaic and 10 (6%) cases of culture failure. The diagnostic detection rate with FISH in 116 patients was 97.5%. There were no false-positive and false-negative autosomal or sex chromosomal results, within our established criteria for reporting FISH signals. Rapid FISH is a reliable and prompt method for detecting numerical chromosomal aberrations and has now been implemented as a routine diagnostic procedure for detection of fetal aneuploidy in India.

  12. Detection of Methylobacterium radiotolerans IMBG290 in potato plants by in situ hybridization

    Directory of Open Access Journals (Sweden)

    Pirttila A. M.

    2009-04-01

    Full Text Available A new bacterial strain of pink-pigmented facultative methylotroph (M. radiotolerans IMBG290 which was previously isolated from in vitro grown potato plantlets after their inoculation with Pseudomonas fluorescens IMBG163 was detected in tissues by in situ hybridization method (ISH/FISH. The presence of Methylobacterium rRNA was observed in leaves and stems of potato plantlets, whereas no signal was detected in potato roots. The signal was less abundant in the untreated plants than in the plantlets infected with M. radiotolerans IMBG290.

  13. Hybrid Technique of Lamellar Keratoplasty (DMEK-S

    Directory of Open Access Journals (Sweden)

    Pavel Studeny

    2013-01-01

    Full Text Available Purpose: To evaluate the outcomes of the hybrid technique of posterior lamellar keratoplasty (DMEK-S. Materials and Methods: 71 eyes of 55 patients enrolled in a single-center study underwent posterior lamellar keratoplasty with a hybrid lamella DMEK-S implanted using a solution implantation technique, owing to endothelial dysfunction. The outcome measures studied were visual acuity and endothelial cell density. Results: The rate of endothelial cell loss caused by surgery was 43.8%. During followups, we observed the stabilization of postoperative findings, or at minimum a very low rate of corneal endothelial cell loss. The UCDVA and BCDVA dramatically improved postoperatively. The rebubbling rate in our group of patients was 61.9%. We replaced the lamella due to its failure or malfunction in 17 patients (23.9%. Conclusion: In summary, DMEK-S combines the advantages of DSEK/DSAEK and DMEK. The central zone of bare Descemet’s membrane and endothelium allows for very good visual outcomes, and the peripheral rim allows for better manipulation of the lamella during implantation. It is an effective method of treating the endothelial dysfunction of various etiologies, but the high complication rate needs to be addressed before widespread implementation of the technique in the future.

  14. High performance technique for database applicationsusing a hybrid GPU/CPU platform

    KAUST Repository

    Zidan, Mohammed A.

    2012-07-28

    Many database applications, such as sequence comparing, sequence searching, and sequence matching, etc, process large database sequences. we introduce a novel and efficient technique to improve the performance of database applica- tions by using a Hybrid GPU/CPU platform. In particular, our technique solves the problem of the low efficiency result- ing from running short-length sequences in a database on a GPU. To verify our technique, we applied it to the widely used Smith-Waterman algorithm. The experimental results show that our Hybrid GPU/CPU technique improves the average performance by a factor of 2.2, and improves the peak performance by a factor of 2.8 when compared to earlier implementations. Copyright © 2011 by ASME.

  15. Localization of mRNA in vertebrate axonal compartments by in situ hybridization.

    Science.gov (United States)

    Sotelo-Silveira, José Roberto; Calliari, Aldo; Kun, Alejandra; Elizondo, Victoria; Canclini, Lucía; Sotelo, José Roberto

    2011-01-01

    The conclusive demonstration of RNA in vertebrate axons by in situ hybridization (ISH) has been elusive. We review the most important reasons for difficulties, including low concentration of axonal RNAs, localization in specific cortical domains, and the need to isolate axons. We demonstrate the importance of axon micro-dissection to obtain a whole mount perspective of mRNA distribution in the axonal territory. We describe a protocol to perform fluorescent ISH in isolated axons and guidelines for the preservation of structural and molecular integrity of cortical RNA-containing domains (e.g., Periaxoplasmic Ribosomal Plaques, or PARPs) in isolated axoplasm.

  16. Application of locked nucleic acid-based probes in fluorescence in situ hybridization

    DEFF Research Database (Denmark)

    Fontenete, Sílvia; Carvalho, Daniel R; Guimarães, Nuno

    2016-01-01

    of nucleic acid mimics used as mixmers in LNA-based probes strongly influence the efficiency of detection. LNA probes with 10 to 15 mers showed the highest efficiency. Additionally, the combination of 2′-OMe RNA with LNA allowed an increase on the fluorescence intensities of the probes. Overall......Fluorescence in situ hybridization (FISH) employing nucleic acid mimics as probes is becoming an emerging molecular tool in the microbiology area for the detection and visualization of microorganisms. However, the impact that locked nucleic acid (LNA) and 2′-O-methyl (2′-OMe) RNA modifications have...

  17. In situ hybridization of nucleus basalis neurons shows increased β-amyloid mRNA in Alzheimer disease

    International Nuclear Information System (INIS)

    Cohen, M.L.; Golde, T.E.; Usiak, M.F.; Younkin, L.H.; Younkin, S.G.

    1988-01-01

    To determine which cells within the brain produce β-amyloid mRNA and to assess expression of the β-amyloid gene in Alzheimer disease, the authors analyzed brain tissue from Alzheimer and control patients by in situ hybridization. The results demonstrate that β-amyloid mRNA is produced by neurons in the nucleus basalis of Meynert and cerebral cortex and that nuclues basalis perikarya from Alzheimer patients consistently hybridize more β-amyloid probe than those from controls. These observations support the hypothesis that increased expression of the β-amyloid gene plays an important role in the deposition of amyloid in the brains of patients with Alzheimer disease

  18. Structure and Optical Properties of Titania-PDMS Hybrid Nanocomposites Prepared by In Situ Non-Aqueous Synthesis

    Directory of Open Access Journals (Sweden)

    Antoine R. M. Dalod

    2017-12-01

    Full Text Available Organic-inorganic hybrid materials are attractive due to the combination of properties from the two distinct types of materials. In this work, transparent titania-polydimethylsiloxane hybrid materials with up to 15.5 vol. % TiO2 content were prepared by an in situ non-aqueous method using titanium (IV isopropoxide and hydroxy-terminated polydimethylsiloxane as precursors. Spectroscopy (Fourier transform infrared, Raman, Ultraviolet-visible, ellipsometry and small-angle X-ray scattering analysis allowed to describe in detail the structure and the optical properties of the nanocomposites. Titanium alkoxide was successfully used as a cross-linker and titania-like nanodomains with an average size of approximately 4 nm were shown to form during the process. The resulting hybrid nanocomposites exhibit high transparency and tunable refractive index from 1.42 up to 1.56, depending on the titania content.

  19. Polyaniline-coated halloysite nanotubes via in-situ chemical polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Long [State Key Laboratory of Applied Organic Chemistry and Institute of Polymer Science and Engineering, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000 (China); Wang Tingmei [State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Liu Peng [State Key Laboratory of Applied Organic Chemistry and Institute of Polymer Science and Engineering, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000 (China)], E-mail: pliu@lzu.edu.cn

    2008-12-30

    Polyaniline coated halloysite nanotubes (PANI/HNTs) were prepared by the in-situ soapless emulsion polymerization of the anilinium chloride adsorbed halloysite nanotubes (HNTs), obtained by the dispersion of HNTs in acidic aqueous solution of aniline with magnetic stirring and ultrasonic irradiation, by using ammonium persulfate (APS) as oxidant. The effect of the acidities of the polymerizing media on the crystal structure of the nanotubes was investigated with X-ray diffraction (XRD) technique. The surface conducting coatings of the hybrids were characterized with X-ray photoelectron spectroscopy (XPS). The morphological analyses showed that the polyaniline coated halloysite nanotubes via the in-situ chemical oxidation polymerization with ultrasonic irradiation had the better well-defined structures, by the transmission electron microscopy (TEM). The conductivities of the PANI/HNTs hybrids increased with the increasing of the amounts of HCl dopant added in the emulsion polymerization.

  20. Polyaniline-coated halloysite nanotubes via in-situ chemical polymerization

    International Nuclear Information System (INIS)

    Zhang Long; Wang Tingmei; Liu Peng

    2008-01-01

    Polyaniline coated halloysite nanotubes (PANI/HNTs) were prepared by the in-situ soapless emulsion polymerization of the anilinium chloride adsorbed halloysite nanotubes (HNTs), obtained by the dispersion of HNTs in acidic aqueous solution of aniline with magnetic stirring and ultrasonic irradiation, by using ammonium persulfate (APS) as oxidant. The effect of the acidities of the polymerizing media on the crystal structure of the nanotubes was investigated with X-ray diffraction (XRD) technique. The surface conducting coatings of the hybrids were characterized with X-ray photoelectron spectroscopy (XPS). The morphological analyses showed that the polyaniline coated halloysite nanotubes via the in-situ chemical oxidation polymerization with ultrasonic irradiation had the better well-defined structures, by the transmission electron microscopy (TEM). The conductivities of the PANI/HNTs hybrids increased with the increasing of the amounts of HCl dopant added in the emulsion polymerization.

  1. Next-generation in situ hybridization approaches to define and quantify HIV and SIV reservoirs in tissue microenvironments.

    Science.gov (United States)

    Deleage, Claire; Chan, Chi N; Busman-Sahay, Kathleen; Estes, Jacob D

    2018-01-09

    The development of increasingly safe and effective antiretroviral treatments for human immunodeficiency virus (HIV) over the past several decades has led to vastly improved patient survival when treatment is available and affordable, an outcome that relies on uninterrupted adherence to combination antiretroviral therapy for life. Looking to the future, the discovery of an elusive 'cure' for HIV will necessitate highly sensitive methods for detecting, understanding, and eliminating viral reservoirs. Next-generation, in situ hybridization (ISH) approaches offer unique and complementary insights into viral reservoirs within their native tissue environments with a high degree of specificity and sensitivity. In this review, we will discuss how modern ISH techniques can be used, either alone or in conjunction with phenotypic characterization, to probe viral reservoir establishment and maintenance. In addition to focusing on how these techniques have already furthered our understanding of HIV reservoirs, we discuss potential avenues for how high-throughput, next-generation ISH may be applied. Finally, we will review how ISH could allow deeper phenotypic and contextual insights into HIV reservoir biology that should prove instrumental in moving the field closer to viral reservoir elimination needed for an 'HIV cure' to be realized.

  2. Gene protein detection platform--a comparison of a new human epidermal growth factor receptor 2 assay with conventional immunohistochemistry and fluorescence in situ hybridization platforms.

    Science.gov (United States)

    Stålhammar, Gustav; Farrajota, Pedro; Olsson, Ann; Silva, Cristina; Hartman, Johan; Elmberger, Göran

    2015-08-01

    Human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are widely used semiquantitative assays for selecting breast cancer patients for HER2 antibody therapy. However, both techniques have been shown to have disadvantages. Our aim was to test a recent automated technique of combined IHC and brightfield dual in situ hybridization-gene protein detection platform (GPDP)-in breast cancer HER2 protein, gene, and chromosome 17 centromere status evaluations, comparing the results in accordance to the American Society of Clinical Oncology/College of American Pathologists recommendations for HER2 testing in breast cancer from both 2007 and 2013. The GPDP technique performance was evaluated on 52 consecutive whole slide invasive breast cancer cases with HER2 IHC 2/3+ scoring results. Applying in turns the American Society of Clinical Oncology/College of American Pathologists recommendations for HER2 testing in breast cancer from 2007 and 2013 to both FISH and GPDP DISH assays, the HER2 gene amplification results showed 100% concordance among amplified/nonamplified cases, but there was a shift in 4 cases toward positive from equivocal results and toward equivocal from negative results. This might be related to the emphasis on the average HER2 copy number in the 2013 criteria. HER2 expression by IVD market IHC kit (Pathway®) has a strong correlation with GPDP HER2 protein, including a full concordance for all cases scored as 3+ and a reduction from 2+ to 1+ in 7 cases corresponding to nonamplified cases. Gene protein detection platform HER2 protein "solo" could have spared the need for 7 FISH studies. In addition, the platform offered advantages on interpretation reassurance including selecting areas for counting gene signals paralleled with protein IHC expression, on heterogeneity detection, interpretation time, technical time, and tissue expense. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Facile In Situ Fabrication of Nanostructured Graphene–CuO Hybrid with Hydrogen Sulfide Removal Capacity

    Institute of Scientific and Technical Information of China (English)

    Sunil P.Lonkar; Vishnu V.Pillai; Samuel Stephen; Ahmed Abdala; Vikas Mittal

    2016-01-01

    A simple and scalable synthetic approach for one-step synthesis of graphene–Cu O(TRGC) nanocomposite by an in situ thermo-annealing method has been developed.Using graphene oxide(GO) and copper hydroxide as a precursors reagent,the reduction of GO and the uniform deposition of in situ formed Cu O nanoparticles on graphene was simultaneously achieved.The method employed no solvents,toxic-reducing agents,or organic modifiers.The resulting nanostructured hybrid exhibited improved H2 S sorption capacity of 1.5 mmol H2S/g-sorbent(3 g S/100 g-sorbent).Due to its highly dispersed sub-20 nm Cu O nanoparticles and large specific surface area,TRGC nanocomposite exhibits tremendous potential for energy and environment applications.

  4. Morphological spot counting from stacked images for automated analysis of gene copy numbers by fluorescence in situ hybridization.

    Science.gov (United States)

    Grigoryan, Artyom M; Dougherty, Edward R; Kononen, Juha; Bubendorf, Lukas; Hostetter, Galen; Kallioniemi, Olli

    2002-01-01

    Fluorescence in situ hybridization (FISH) is a molecular diagnostic technique in which a fluorescent labeled probe hybridizes to a target nucleotide sequence of deoxyribose nucleic acid. Upon excitation, each chromosome containing the target sequence produces a fluorescent signal (spot). Because fluorescent spot counting is tedious and often subjective, automated digital algorithms to count spots are desirable. New technology provides a stack of images on multiple focal planes throughout a tissue sample. Multiple-focal-plane imaging helps overcome the biases and imprecision inherent in single-focal-plane methods. This paper proposes an algorithm for global spot counting in stacked three-dimensional slice FISH images without the necessity of nuclei segmentation. It is designed to work in complex backgrounds, when there are agglomerated nuclei, and in the presence of illumination gradients. It is based on the morphological top-hat transform, which locates intensity spikes on irregular backgrounds. After finding signals in the slice images, the algorithm groups these together to form three-dimensional spots. Filters are employed to separate legitimate spots from fluorescent noise. The algorithm is set in a comprehensive toolbox that provides visualization and analytic facilities. It includes simulation software that allows examination of algorithm performance for various image and algorithm parameter settings, including signal size, signal density, and the number of slices.

  5. In Situ Techniques for Life Detection on Mars

    Science.gov (United States)

    Becker, L.; Brinckerhoff, W.; Cotter, R.

    2006-12-01

    The search for organic matter on Mars is rapidly emerging as a result of technological advancements and the study of early "life" on our own planet. As we learned from the Viking missions and the examination of martian meteorites, the criteria for establishing life require the appropriate strategy. One such approach would require careful mapping of the surface from orbit for the selection of the appropriate landing sites, robotic space missions equipped with several life detection in situ techniques for selection of samples, and sample return missions for additional verification of in situ results and laboratory measurements. It may, however, be possible to obtain critical information about the organic matter and associated mineral assemblages present on Mars, in situ, in a single measurement that is both capable of flight and is nondestructive to the sample. We discuss a new multi-source mass spectrometer, `MOMA' (Mars Organic Molecule Analyzer) that incorporates multiple methods of volatilizing and ionizing chemical compounds from intact samples without further processing or manipulation. Moreover, MOMA is capable of detecting a broad range of organics enabling the evaluation of the origin of the organics and the presence of terrestrial contaminants.

  6. Monosomy 3 by chromogenic in situ hybridization (CISH) in Iranian patients with uveal melanoma.

    Science.gov (United States)

    Naseripour, Masood; Mehrazma, Mitra; Pourmatin, Rama; Kashkouli, Mohsen Bahmani; Sedaghat, Ahad; Gheytanchi, Elmira

    2015-01-01

    The aim of this study was to investigate the rate of monosomy 3 by CISH technique in Iranian patients with uveal melanoma (UM) and its correlation with clinical and histopathological features. Archival formalin fixed, paraffin-embedded material from 50 patients who had undergone enucleation for large uveal melanomas was obtained. Monosomy of chromosome 3 alteration by chromogenic in situ hybridization (CISH) was investigated. Clinical and histopathological features of tumors were collected. The patients had a mean age of 56.6±7.6 years. Mean basal diameter and thickness of tumors were 14.1 mm and 10.2 mm, respectively. Four patients (8%) were identified to harbor monosomy of chromosome 3. In the mean follow-up of 5.3 years (range, 3.2-9.5 y), only one case with monosomy 3 died of UM metastasis. The most common type of cellularity was mixed cell (86%). There was not any statistically significant correlation between monosomy of chromosome 3 and type of cellularity, ciliary body involvement, and largest basal diameter. The low rate of monosomy chromosome 3 and the consequent low rate of mortality may be indicative of good prognosis in Iranian patients with uveal melanoma.

  7. One-step synthesis of graphene/polyaniline hybrids by in situ intercalation polymerization and their electromagnetic properties

    Science.gov (United States)

    Chen, Xiangnan; Meng, Fanchen; Zhou, Zuowan; Tian, Xin; Shan, Liming; Zhu, Shibu; Xu, Xiaoling; Jiang, Man; Wang, Li; Hui, David; Wang, Yong; Lu, Jun; Gou, Jihua

    2014-06-01

    A new method is introduced for the preparation of graphene/polyaniline hybrids using a one-step intercalation polymerization of aniline inside the expanded graphite. The structural and morphological characterizations were performed by X-ray diffraction analysis, transmission electron microscopy and field emission scanning electron microscopy. Both the experimental and first-principles simulated results show that the aniline cation formed by aniline and H+ tends to be drawn towards the electron-enriched zone and to intercalate into the interlayer of graphite. Subsequently, an in situ polymerization leads to the separation of graphite into graphene sheet, resulting from the exothermic effect and more vigorous movements of the chain molecules of polyaniline. The interactions between polyaniline and graphene were confirmed by Fourier transform infrared spectroscopy and Raman spectra. In addition, the graphene/polyaniline hybrid exhibited a breakthrough in the improvement of microwave absorption.A new method is introduced for the preparation of graphene/polyaniline hybrids using a one-step intercalation polymerization of aniline inside the expanded graphite. The structural and morphological characterizations were performed by X-ray diffraction analysis, transmission electron microscopy and field emission scanning electron microscopy. Both the experimental and first-principles simulated results show that the aniline cation formed by aniline and H+ tends to be drawn towards the electron-enriched zone and to intercalate into the interlayer of graphite. Subsequently, an in situ polymerization leads to the separation of graphite into graphene sheet, resulting from the exothermic effect and more vigorous movements of the chain molecules of polyaniline. The interactions between polyaniline and graphene were confirmed by Fourier transform infrared spectroscopy and Raman spectra. In addition, the graphene/polyaniline hybrid exhibited a breakthrough in the improvement of

  8. Exploring the origin of the D genome of oat by fluorescence in situ hybridization.

    Science.gov (United States)

    Luo, Xiaomei; Zhang, Haiqin; Kang, Houyang; Fan, Xing; Wang, Yi; Sha, Lina; Zhou, Yonghong

    2014-09-01

    Further understanding of the origin of cultivated oat would accelerate its genetic improvement. In particular, it would be useful to clarify which diploid progenitor contributed the D genome of this allohexaploid species. In this study, we demonstrate that the landmarks produced by fluorescence in situ hybridization (FISH) of species of Avena using probes derived from Avena sativa can be used to explore the origin of the D genome. Selected sets of probes were hybridized in several sequential experiments performed on exactly the same chromosome spreads, with multiple probes of cytological preparations. Probes pITS and A3-19 showed there might be a similar distribution of pITS between the Ac and D genomes. These results indicated that the Ac genome is closely related to the D genome, and that Avena canariensis (AcAc) could be the D-genome donor of cultivated oat.

  9. SU-E-T-16: A Hybrid VMAT/IMRT Technique for the Treatment of Nasopharyngeal Carcinoma

    International Nuclear Information System (INIS)

    Zhao, N; Yang, R; Wang, J

    2014-01-01

    Purpose: To investigate a Hybrid VMAT/IMRT technique which combines volumetric modulated arc therapy (VMAT) and intensity modulated radiation therapy (IMRT) for nasopharyngeal carcinoma (NPC). Methods: 2 full arcs VMAT, 9-field IMRT and Hybrid VMAT/IMRT plans were created for 10 patients with NPC. The Hybrid VMAT/IMRT technique consisted of 1 full VMAT arc and 7 IMRT fields. The dose distribution of planning target volume (PTV) and organs at risk (OARs) for Hybrid VMAT/IMRT was compared with IMRT and VMAT. The monitor units (MUs) were also evaluated. Results: The Hybrid VMAT/IMRT technique significantly improved target dose homogeneity compared with IMRT and VMAT for PTV70 and PTV54. For PTV70 and PTV60, the Hybrid VMAT/IMRT technique significantly improved target dose conformity compared with IMRT (0.62 vs 0.47; p<0.05 and 0.64 vs 0.58; p<0.05, respectively) and VMAT (0.62 vs 0.43; p<0.05 and 0.64 vs 0.6; p<0.05, respectively). The near maximum dose (D2%) of temporomandibular joint (TMJ), temporal lobe and mandible for Hybrid plans were 5.5%, 7.9% and 5.2% lower than IMRT plans (p<0.05). The mean dose of TMJ, temporal lobe, mandible and unspecified tissue for Hybrid plans were 12.8%, 11.4%, 4.2% and 4.1% lower than IMRT plans (p<0.05). The mean dose of right parotid, mandible and unspecified tissue for Hybrid plans were 3.3%, 2.4% and 3.1% lower than VMAT plans (p<0.05). The mean MUs needed for IMRT, VMAT and Hybrid plans were 2256, 507 and 1394, respectively. Conclusion: Hybrid VMAT/IMRT technique significantly improved the target dose homogeneity and conformity compared with IMRT and VMAT and reduced the dose of OARs and unspecified tissue compared with IMRT with fewer MUs. Compared with VMAT, Hybrid VMAT/IMRT technique can better protect parotid gland, mandible and unspecified tissue. Ruijie Yang was funded by the grant project: National Natural Science Foundation of China (No. 81071237). Other authors have no competing interest for this work

  10. SU-E-T-16: A Hybrid VMAT/IMRT Technique for the Treatment of Nasopharyngeal Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, N; Yang, R; Wang, J [Peking University Third Hospital, Beijing, Beijing (China)

    2014-06-01

    Purpose: To investigate a Hybrid VMAT/IMRT technique which combines volumetric modulated arc therapy (VMAT) and intensity modulated radiation therapy (IMRT) for nasopharyngeal carcinoma (NPC). Methods: 2 full arcs VMAT, 9-field IMRT and Hybrid VMAT/IMRT plans were created for 10 patients with NPC. The Hybrid VMAT/IMRT technique consisted of 1 full VMAT arc and 7 IMRT fields. The dose distribution of planning target volume (PTV) and organs at risk (OARs) for Hybrid VMAT/IMRT was compared with IMRT and VMAT. The monitor units (MUs) were also evaluated. Results: The Hybrid VMAT/IMRT technique significantly improved target dose homogeneity compared with IMRT and VMAT for PTV70 and PTV54. For PTV70 and PTV60, the Hybrid VMAT/IMRT technique significantly improved target dose conformity compared with IMRT (0.62 vs 0.47; p<0.05 and 0.64 vs 0.58; p<0.05, respectively) and VMAT (0.62 vs 0.43; p<0.05 and 0.64 vs 0.6; p<0.05, respectively). The near maximum dose (D2%) of temporomandibular joint (TMJ), temporal lobe and mandible for Hybrid plans were 5.5%, 7.9% and 5.2% lower than IMRT plans (p<0.05). The mean dose of TMJ, temporal lobe, mandible and unspecified tissue for Hybrid plans were 12.8%, 11.4%, 4.2% and 4.1% lower than IMRT plans (p<0.05). The mean dose of right parotid, mandible and unspecified tissue for Hybrid plans were 3.3%, 2.4% and 3.1% lower than VMAT plans (p<0.05). The mean MUs needed for IMRT, VMAT and Hybrid plans were 2256, 507 and 1394, respectively. Conclusion: Hybrid VMAT/IMRT technique significantly improved the target dose homogeneity and conformity compared with IMRT and VMAT and reduced the dose of OARs and unspecified tissue compared with IMRT with fewer MUs. Compared with VMAT, Hybrid VMAT/IMRT technique can better protect parotid gland, mandible and unspecified tissue. Ruijie Yang was funded by the grant project: National Natural Science Foundation of China (No. 81071237). Other authors have no competing interest for this work.

  11. Use of Hybridization Chain Reaction-Fluorescent In Situ Hybridization To Track Gene Expression by Both Partners during Initiation of Symbiosis.

    Science.gov (United States)

    Nikolakakis, K; Lehnert, E; McFall-Ngai, M J; Ruby, E G

    2015-07-01

    The establishment of a productive symbiosis between Euprymna scolopes, the Hawaiian bobtail squid, and its luminous bacterial symbiont, Vibrio fischeri, is mediated by transcriptional changes in both partners. A key challenge to unraveling the steps required to successfully initiate this and many other symbiotic associations is characterization of the timing and location of these changes. We report on the adaptation of hybridization chain reaction-fluorescent in situ hybridization (HCR-FISH) to simultaneously probe the spatiotemporal regulation of targeted genes in both E. scolopes and V. fischeri. This method revealed localized, transcriptionally coregulated epithelial cells within the light organ that responded directly to the presence of bacterial cells while, at the same time, provided a sensitive means to directly show regulated gene expression within the symbiont population. Thus, HCR-FISH provides a new approach for characterizing habitat transition in bacteria and for discovering host tissue responses to colonization. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-03-04

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

  13. FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy.

    Directory of Open Access Journals (Sweden)

    Debora Giorgi

    Full Text Available The large size and complex polyploid nature of many genomes has often hampered genomics development, as is the case for several plants of high agronomic value. Isolating single chromosomes or chromosome arms via flow sorting offers a clue to resolve such complexity by focusing sequencing to a discrete and self-consistent part of the whole genome. The occurrence of sufficient differences in the size and or base-pair composition of the individual chromosomes, which is uncommon in plants, is critical for the success of flow sorting. We overcome this limitation by developing a robust method for labeling isolated chromosomes, named Fluorescent In situ Hybridization In suspension (FISHIS. FISHIS employs fluorescently labeled synthetic repetitive DNA probes, which are hybridized, in a wash-less procedure, to chromosomes in suspension following DNA alkaline denaturation. All typical A, B and D genomes of wheat, as well as individual chromosomes from pasta (T. durum L. and bread (T. aestivum L. wheat, were flow-sorted, after FISHIS, at high purity. For the first time in eukaryotes, each individual chromosome of a diploid organism, Dasypyrum villosum (L. Candargy, was flow-sorted regardless of its size or base-pair related content. FISHIS-based chromosome sorting is a powerful and innovative flow cytogenetic tool which can develop new genomic resources from each plant species, where microsatellite DNA probes are available and high quality chromosome suspensions could be produced. The joining of FISHIS labeling and flow sorting with the Next Generation Sequencing methodology will enforce genomics for more species, and by this mightier chromosome approach it will be possible to increase our knowledge about structure, evolution and function of plant genome to be used for crop improvement. It is also anticipated that this technique could contribute to analyze and sort animal chromosomes with peculiar cytogenetic abnormalities, such as copy number variations

  14. FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy.

    Science.gov (United States)

    Giorgi, Debora; Farina, Anna; Grosso, Valentina; Gennaro, Andrea; Ceoloni, Carla; Lucretti, Sergio

    2013-01-01

    The large size and complex polyploid nature of many genomes has often hampered genomics development, as is the case for several plants of high agronomic value. Isolating single chromosomes or chromosome arms via flow sorting offers a clue to resolve such complexity by focusing sequencing to a discrete and self-consistent part of the whole genome. The occurrence of sufficient differences in the size and or base-pair composition of the individual chromosomes, which is uncommon in plants, is critical for the success of flow sorting. We overcome this limitation by developing a robust method for labeling isolated chromosomes, named Fluorescent In situ Hybridization In suspension (FISHIS). FISHIS employs fluorescently labeled synthetic repetitive DNA probes, which are hybridized, in a wash-less procedure, to chromosomes in suspension following DNA alkaline denaturation. All typical A, B and D genomes of wheat, as well as individual chromosomes from pasta (T. durum L.) and bread (T. aestivum L.) wheat, were flow-sorted, after FISHIS, at high purity. For the first time in eukaryotes, each individual chromosome of a diploid organism, Dasypyrum villosum (L.) Candargy, was flow-sorted regardless of its size or base-pair related content. FISHIS-based chromosome sorting is a powerful and innovative flow cytogenetic tool which can develop new genomic resources from each plant species, where microsatellite DNA probes are available and high quality chromosome suspensions could be produced. The joining of FISHIS labeling and flow sorting with the Next Generation Sequencing methodology will enforce genomics for more species, and by this mightier chromosome approach it will be possible to increase our knowledge about structure, evolution and function of plant genome to be used for crop improvement. It is also anticipated that this technique could contribute to analyze and sort animal chromosomes with peculiar cytogenetic abnormalities, such as copy number variations or cytogenetic

  15. Determination of HER2 gene amplification by chromogenic in situ hybridization (CISH) in archival breast carcinoma.

    Science.gov (United States)

    Zhao, Jianxin; Wu, Rina; Au, Alfred; Marquez, Abbey; Yu, Yibing; Shi, Zuorong

    2002-06-01

    To compare the efficacy of chromogenic in situ hybridization (CISH(TM)) with fluorescence in situ (FISH) hybridization and immunohistochemistry (IHC) in determination of the HER2 status in human breast cancer. HER2 gene amplification was determined on formalin-fixed paraffin-embedded (FFPE) sections of 62 invasive breast cancers by FISH and followed by CISH using a digoxigenin (DIG)-labeled HER2 DNA probe generated by Subtraction Probe Technology (SPT(TM)), and a biotin-labeled chromosome 17 centromeric (chr.17cen) probe. The sections were heat treated and enzyme digested. After in situ hybridization, the HER2 probe was detected with fluorescein (FITC)-anti-DIG for FISH, followed by peroxidase-anti-FITC and diaminobenzidine (DAB) for CISH. The chr.17cen probe was detected with peroxidase-streptavidin and DAB. For CISH application, HER2 gene copies or chromosome 17 centromeres and morphology of cells were easily visualized simultaneously with a 40x objective under bright-field microscope in hematoxylin-counterstained sections. IHC study of HER2 overexpression was performed on adjacent sections using a panel of three HER2 antibodies (TAB 250, CB11, A0485), and staining was scored according to the criteria specified in the HercepTest. HER2 gene amplification detected by CISH was visualized typically as large DAB-stained clusters or by many dots in the nucleus. FISH and CISH identified HER2 gene amplification in 19% of the tumors. Chromosome 17 polysomy was detected in 31% of the tumors. HER2 overexpression was demonstrated in 19% (TAB 250), 23% (CB11), and 36% (A0485) of the tumors. Complete concordance between the results of CISH with FISH, TAB 250, CB11, and A0485 was seen in 100%, 97%, 94%, and 84% of the cases, respectively. By permitting observation of morphology using a bright-field microscope, CISH is an accurate, practical, and economical approach to screen HER2 status in breast cancers. It is a useful methodology for confirming ambiguous IHC results.

  16. Hybrid aerogels and bioactive aerogels under uniaxial compression: an in situ SAXS study

    Directory of Open Access Journals (Sweden)

    Esquivias, L.

    2010-12-01

    Full Text Available The complex structure of hybrid organic/inorganic aerogels is composed by an inorganic phase covalently bonded to an organic chain forming a copolymer. Conventional hybrid aerogels were studied as well as bioactive hybrid aerogels, that is, aerogels with a calcium active phase added. In this work, the relationship between mechanical response and nanostructure was studied, using a specifically designed sample-holder for in situ uniaxial compression obtaining at the same time the small-angle X-ray pattern from synchrotron radiation (SAXS. Structural elements can be described as a particulated silica core surrounded by the organic chains. These chains are compressed on the direction parallel to the load, and a relationship between macroscopic uniaxial compression and particle and pore deformations can be established.

    La compleja estructura de los aerogeles híbridos orgánico/inorgánicos está compuesta por una fase inorgánica de sílice, unida mediante enlaces covalentes a una red de cadenas orgánicas. Se han estudiado composites híbridos convencionales y bioactivos, esto es, con una fase activa de calcio añadida. En este trabajo se ha investigado la relación entre la respuesta mecánica y la nanoestructura, con ayuda de un portamuestras específicamente diseñado para el estudio in situ de muestras bajo compresión uniaxial, a la vez que se obtiene el espectro de rayos-X a bajo-ángulo de radiación sincrotrón (SAXS. Los elementos estructurales se pueden describir como núcleos particulados de sílice rodeados de las cadenas orgánicas. Estas, se comprimen en la dirección paralela a la carga pudiéndose establecer una relación entre la compresión uniaxial macroscópica y la deformación de las partículas y poros que forman la estructura.

  17. HER-2 protein concentrations in breast cancer cells increase before immunohistochemical and fluorescence in situ hybridization analysis turn positive

    DEFF Research Database (Denmark)

    Olsen, Dorte A; Østergaard, Birthe; Bokmand, Susanne

    2007-01-01

    BACKGROUND: The level of HER-2/neu in breast cancer cells is normally measured by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH). It determines whether patients should be treated with trastuzumab (Herceptin). In this study, HER-2 protein in breast cancer tissue...

  18. Application of in situ x-ray diffraction techniques in heterogenous catalytic systems

    International Nuclear Information System (INIS)

    Sharifah Bee Abd Hamid

    2002-01-01

    A broad range of techniques is available today for the characterisation of catalysts and the investigation of catalyst reaction mechanisms. However, only a limited number of those are suitable for in situ studies, i.e experiments performed in conditions mimicking or close as possible to real operating conditions. Various commercially and in-house developed in situ X-Ray diffraction (XRD) cells have been used to obtain information on the phase and structure of materials at the initial formation stage, activation methodology, calcination, reduction and carburization. A major advantage of the in situ X-ray cells is that it allows direct observations on the decomposition of precursors leading to various phases in a controlled environment, i.e. controlled temperature and pressure under specified gases. The cells can be operated both at high temperatures and high pressures, equipped with Position Sensitive Detector (PSD), feature which was used to study phase transformation occurring during the activation of various solids. In MoO 3 , XRD results provide detailed information on the hydrogen insertion into its lattice, followed by carburization providing good understanding on the mechanism in the solid transformation leading to the metastable MoC 1 -x phase. For the Bi-SnO x systems, the environmental cell coupled with XRD and PSD allow the design of activation procedure to obtain the active Bi 2 Sn 2 O 7 . The in situ XRD technique reveals crucial information on the initial stage of oxides formations prior to condensation reaction shown in MCM-41 and titania systems. In this presentation, discussions on general achievements and problems relating to the use of in situ XRD techniques as well as of specific examples selected to illustrate the use and potential of in situ XRD are made. It is not intended to be a review of the art but a highlight of the challenges which the catalytic and material scientists face when entering the avenue. (Author)

  19. Transmission electron microscopic method for gene mapping on polytene chromosomes by in situ hybridization

    OpenAIRE

    Wu, Madeline; Davidson, Norman

    1981-01-01

    A transmission electron microscope method for gene mapping by in situ hybridization to Drosophila polytene chromosomes has been developed. As electron-opaque labels, we use colloidal gold spheres having a diameter of 25 nm. The spheres are coated with a layer of protein to which Escherichia coli single-stranded DNA is photochemically crosslinked. Poly(dT) tails are added to the 3' OH ends of these DNA strands, and poly(dA) tails are added to the 3' OH ends of a fragmented cloned Drosophila DN...

  20. PEAK-TO-AVERAGE POWER RATIO REDUCTION USING CODING AND HYBRID TECHNIQUES FOR OFDM SYSTEM

    OpenAIRE

    Bahubali K. Shiragapur; Uday Wali

    2016-01-01

    In this article, the research work investigated is based on an error correction coding techniques are used to reduce the undesirable Peak-to-Average Power Ratio (PAPR) quantity. The Golay Code (24, 12), Reed-Muller code (16, 11), Hamming code (7, 4) and Hybrid technique (Combination of Signal Scrambling and Signal Distortion) proposed by us are used as proposed coding techniques, the simulation results shows that performance of Hybrid technique, reduces PAPR significantly as compared to Conve...

  1. In situ hybridization of somatolactin transcripts in the pituitary glands from acclimatized carp (Cyprinus carpio

    Directory of Open Access Journals (Sweden)

    MAURICIO LÓPEZ

    2001-01-01

    Full Text Available We isolated and cloned a carp somatolactin SL DNA fragment, of which 78% of the nucleotides were identical to the corresponding salmon SL sequence. The results obtained upon Northern blot hybridization of carp pituitary RNA allowed the identification of two transcripts as described for other fish. When the content of SL transcripts in pituitary sections from summer- and winter- acclimatized carp was quantified by in situ hybridization assays, we found no significant differences between the two seasons. In salmonids, plasma SL reaches higher levels in summer than in winter in synchrony with the water temperature cycle; in the eurythermal carp, however, the complex adaptive responses imposed by seasonal environmental changes do not seem to include the regulation of the somatolactin detected with the probe used at the transcriptional level in pituitary glands

  2. Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples.

    Science.gov (United States)

    Tischer, Karolin; Zeder, Michael; Klug, Rebecca; Pernthaler, Jakob; Schattenhofer, Martha; Harms, Hauke; Wendeberg, Annelie

    2012-12-01

    Groundwater ecosystems are the most important sources of drinking water worldwide but they are threatened by contamination and overexploitation. Petroleum spills account for the most common source of contamination and the high carbon load results in anoxia and steep geochemical gradients. Microbes play a major role in the transformation of petroleum hydrocarbons into less toxic substances. To investigate microbial populations at the single cell level, fluorescence in situ hybridization (FISH) is now a well-established technique. Recently, however, catalyzed reporter deposition (CARD)-FISH has been introduced for the detection of microbes from oligotrophic environments. Nevertheless, petroleum contaminated aquifers present a worst case scenario for FISH techniques due to the combination of high background fluorescence of hydrocarbons and the presence of small microbial cells caused by the low turnover rates characteristic of groundwater ecosystems. It is therefore not surprising that studies of microorganisms from such sites are mostly based on cultivation techniques, fingerprinting, and amplicon sequencing. However, to reveal the population dynamics and interspecies relationships of the key participants of contaminant degradation, FISH is an indispensable tool. In this study, a protocol for FISH was developed in combination with cell quantification using an automated counting microscope. The protocol includes the separation and purification of microbial cells from sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave oven. As a proof of principle, the distribution of Archaea and Bacteria was shown in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, Germany), which has been heavily contaminated with several ten-thousand tonnes of petroleum hydrocarbons since World War II. Copyright © 2012 Elsevier GmbH. All rights reserved.

  3. In-situ fabrication of halloysite nanotubes/silica nano hybrid and its application in unsaturated polyester resin

    Science.gov (United States)

    Lin, Jing; Zhong, Bangchao; Jia, Zhixin; Hu, Dechao; Ding, Yong; Luo, Yuanfang; Jia, Demin

    2017-06-01

    Silica nanoparticles was in-situ grown on the surface of halloysite nanotubes (HNTs) by a facile one-step approach to prepare a unique nano-structured hybrid (HNTs-g-Silica). The structure, morphology and composition of HNTs-g-Silica were investigated. It was confirmed that silica nanoparticles with the diameter of 10-20 nm were chemically grafted through Sisbnd O bonds and uniformly dispersed onto the surface of HNTs, leading to the formation of nano-protrusions on the nanotube surface. Due to the significantly improved interface strength between HNTs-g-Silica and polymer matrix, HNTs-g-Silica effectively toughened unsaturated polyester resin (UPE) and endowed UPE with superior thermal stability compared to HNTs. Based on the unique hybrid architecture and the improved properties of UPE nanocomposites, it is envisioned that HNTs-g-Silica may be a promising filler for more high performance and functional polymers composites and the fabrication method may have implications in the synthesis of nano hybrid materials.

  4. Assessment of phytoremediation as an in-situ technique for cleaning oil-contaminated sites

    Energy Technology Data Exchange (ETDEWEB)

    Frick, C M; Germida, J J; Farrell, R E [Saskatchewan Univ., Saskatoon, SK (Canada). Dept. of Soil Science

    1999-01-01

    The effectiveness of phytoremediation as a tool for cleaning up hydrocarbon contaminated soil and groundwater was evaluated by reviewing relative literature. Phytoremediation is an emerging technology which consists of the use of plants for in situ treatment of contaminated soils. Grasses, herbs, shrubs and deciduous trees were the main types of plants considered in this study. A database is presently under construction to act as an inventory of plant species that tolerate or phytoremediate petroleum hydrocarbons. This paper focused on the main mechanisms and special considerations involved in the phytoremediation alkanes, aromatics, polycyclic aromatic hydrocarbons, and creosote. While phytoremediation does not require intensive engineering techniques, it does involve human intervention to establish appropriate plants and microorganisms to enhance natural degradation processes. Plants such as canola, oats barley have been shown to tolerate and accumulate metals such as selenium, copper, cadmium and zinc. Hybrid poplar trees reduce the concentration of nitrate in surficial groundwater and degrade the herbicide atrazine. Forage grasses inoculated with bacteria can degrade chlorinated benzoic acids. Various grasses and leguminous plants can increase the removal of petroleum hydrocarbons from contaminated soils. 66 refs., 3 tabs., 2 figs.

  5. Assessment of phytoremediation as an in-situ technique for cleaning oil-contaminated sites

    International Nuclear Information System (INIS)

    Frick, C.M.; Germida, J.J.; Farrell, R.E.

    1999-01-01

    The effectiveness of phytoremediation as a tool for cleaning up hydrocarbon contaminated soil and groundwater was evaluated by reviewing relative literature. Phytoremediation is an emerging technology which consists of the use of plants for in situ treatment of contaminated soils. Grasses, herbs, shrubs and deciduous trees were the main types of plants considered in this study. A database is presently under construction to act as an inventory of plant species that tolerate or phytoremediate petroleum hydrocarbons. This paper focused on the main mechanisms and special considerations involved in the phytoremediation alkanes, aromatics, polycyclic aromatic hydrocarbons, and creosote. While phytoremediation does not require intensive engineering techniques, it does involve human intervention to establish appropriate plants and microorganisms to enhance natural degradation processes. Plants such as canola, oats barley have been shown to tolerate and accumulate metals such as selenium, copper, cadmium and zinc. Hybrid poplar trees reduce the concentration of nitrate in surficial groundwater and degrade the herbicide atrazine. Forage grasses inoculated with bacteria can degrade chlorinated benzoic acids. Various grasses and leguminous plants can increase the removal of petroleum hydrocarbons from contaminated soils. 66 refs., 3 tabs., 2 figs

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

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-12-31

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

  7. mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.

    Science.gov (United States)

    Yilmaz, L Safak; Parnerkar, Shreyas; Noguera, Daniel R

    2011-02-01

    Mathematical models of RNA-targeted fluorescence in situ hybridization (FISH) for perfectly matched and mismatched probe/target pairs are organized and automated in web-based mathFISH (http://mathfish.cee.wisc.edu). Offering the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework, mathFISH is expected to maximize the probability of success during oligonucleotide probe design.

  8. A Hybrid Neural Network-Genetic Algorithm Technique for Aircraft Engine Performance Diagnostics

    Science.gov (United States)

    Kobayashi, Takahisa; Simon, Donald L.

    2001-01-01

    In this paper, a model-based diagnostic method, which utilizes Neural Networks and Genetic Algorithms, is investigated. Neural networks are applied to estimate the engine internal health, and Genetic Algorithms are applied for sensor bias detection and estimation. This hybrid approach takes advantage of the nonlinear estimation capability provided by neural networks while improving the robustness to measurement uncertainty through the application of Genetic Algorithms. The hybrid diagnostic technique also has the ability to rank multiple potential solutions for a given set of anomalous sensor measurements in order to reduce false alarms and missed detections. The performance of the hybrid diagnostic technique is evaluated through some case studies derived from a turbofan engine simulation. The results show this approach is promising for reliable diagnostics of aircraft engines.

  9. MicroRNA Detection by Whole-Mount In Situ Hybridization in C. elegans.

    Science.gov (United States)

    Andachi, Yoshiki; Kohara, Yuji

    2018-01-01

    MicroRNAs (miRNAs) loaded on argonaute proteins guide RNA-induced silencing complexes to target mRNAs. An excellent method to decipher the spatiotemporal expression patterns of miRNAs is whole-mount in situ hybridization (WISH), which has been successfully used in vertebrate embryos but still remains unavailable for many animal species. Here, we describe a WISH method for miRNA detection in Caenorhabditis elegans at both embryonic and post-embryonic stages. Strategies devised for detection include fixation of animals with carbodiimide at a high temperature and subsequent partial digestion of the fixed animals with an extremely high concentration of proteinase. WISH signals are visualized by staining with a chromogenic substrate or a fluorescent dye.

  10. Fluorescent whole-mount RNA in situ hybridization (F-WISH) in plant germ cells and the fertilized ovule.

    Science.gov (United States)

    Bleckmann, Andrea; Dresselhaus, Thomas

    2016-04-01

    First evidence on gene function and regulation is provided by the cellular expression pattern in complex tissues. However, to understand the activity of a specific gene, it is essential to analyze the regulatory network, which controls the spatio-temporal translation pattern during the entire life span of the transcribed mRNA. To explore mechanisms which control mRNA abundance and localization in space and time, it is necessary to visualize mRNAs quantitatively with a subcellular resolution, without sectioning the tissues. We have adapted and optimized a protocol for colorimetric whole-mount RNA in situ hybridization (WISH) using egg cell-specific digoxigenin (DIG) labeled probes (Hejátko et al., 2006) [1] on ovules and early seeds of Arabidopsis. Furthermore, we established a fluorescent whole-mount RNA in situ hybridization (F-WISH) protocol, which allows mRNA visualization on a subcellular level. The polar localized mRNA of SBT4.13, encoding a subtilase, was identified using this protocol. Both methods are described and discussed in detail. Additionally a (F)-WISH flow-chart is provided along with a troubleshooting table. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. High performance technique for database applicationsusing a hybrid GPU/CPU platform

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Hybrid GPU/CPU platform. In particular, our technique solves the problem of the low efficiency result- ing from running short-length sequences in a database on a GPU. To verify our technique, we applied it to the widely used Smith-Waterman algorithm

  12. Comparison of in situ polymerization and solution-dispersion techniques in the preparation of Polyimide/Montmorillonite (MMT) Nanocomposites.

    Science.gov (United States)

    Ahmad, Mansor Bin; Gharayebi, Yadollah; Salit, Mohd Sapuan; Hussein, Mohd Zobir; Shameli, Kamyar

    2011-01-01

    In this paper, Polyimide/Montmorillonite Nanocomposites (PI/MMT NCs), based on aromatic diamine (4-Aminophenyl sulfone) (APS) and aromatic dianhydride (3,3',4,4'-benzophenonetetracarboxylic dianhydride) (BTDA) were prepared using in situ polymerization and solution-dispersion techniques. The prepared PI/MMT NCs films were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM) and thermogravimetric analysis (TGA). The XRD results showed that at the content of 1.0 wt % Organo Montmorillonite (OMMT) for two techniques and 3.0 wt % OMMT for the in situ polymerization technique, the OMMT was well-intercalated, exfoliated and dispersed into polyimide matrix. The OMMT agglomerated when its amount exceeded 10 wt % and 3.0 wt % for solution-dispersion and in situ polymerization techniques respectively. These results were confirmed by the TEM images of the prepared PI/MMT NCs. The TGA thermograms indicated that thermal stability of prepared PI/MMT NCs were increased with the increase of loading that, the effect is higher for the samples prepared by in situ polymerization technique.

  13. Reliable cost effective technique for in situ ground stress measurements in deep gold mines.

    CSIR Research Space (South Africa)

    Stacey, TR

    1995-07-01

    Full Text Available on these requirements, an in situ stress measurement technique which will be practically applicable in the deep gold mines, has been developed conceptually. Referring to the figure on the following page, this method involves: • a borehole-based system, using... level mines have not been developed. 2 This is some of the background to the present SIMRAC research project, the title ofwhich is “Reliable cost effective technique for in-situ ground stress measurements in deep gold mines”. A copy of the research...

  14. Detection of dengue group viruses by fluorescence in situ hybridization

    Directory of Open Access Journals (Sweden)

    Raquin Vincent

    2012-10-01

    Full Text Available Abstract Background Dengue fever (DF and dengue hemorrhagic fever (DHF represent a global challenge in public health. It is estimated that 50 to 100 million infections occur each year causing approximately 20,000 deaths that are usually linked to severe cases like DHF and dengue shock syndrome. The causative agent of DF is dengue virus (genus Flavivirus that comprises four distinct serotypes (DENV-1 to DENV-4. Fluorescence in situ hybridization (FISH has been used successfully to detect pathogenic agents, but has not been implemented in detecting DENV. To improve our understanding of DENV infection and dissemination in host tissues, we designed specific probes to detect DENV in FISH assays. Methods Oligonucleotide probes were designed to hybridize with RNA from the broadest range of DENV isolates belonging to the four serotypes, but not to the closest Flavivirus genomes. Three probes that fit the criteria defined for FISH experiments were selected, targeting both coding and non-coding regions of the DENV genome. These probes were tested in FISH assays against the dengue vector Aedes albopictus (Diptera: Culicidae. The FISH experiments were led in vitro using the C6/36 cell line, and in vivo against dissected salivary glands, with epifluorescence and confocal microscopy. Results The three 60-nt oligonucleotides probes DENV-Probe A, B and C cover a broad range of DENV isolates from the four serotypes. When the three probes were used together, specific fluorescent signals were observed in C6/36 infected with each DENV serotypes. No signal was detected in either cells infected with close Flavivirus members West Nile virus or yellow fever virus. The same protocol was used on salivary glands of Ae. albopictus fed with a DENV-2 infectious blood-meal which showed positive signals in the lateral lobes of infected samples, with no significant signal in uninfected mosquitoes. Conclusion Based on the FISH technique, we propose a way to design and use

  15. Comparative review of techniques used for in situ remediation of contaminated soils

    International Nuclear Information System (INIS)

    Escusol Tomey, M.; Rodriguez Abad, R.

    2014-01-01

    Soil pollution may influence the geotechnical parameters of the soil itself, properties such as solid particle density or water within its pores. It may also vary its friction angle, modify its structure and texture, or change the properties of its constitutive minerals due to the inclusion of polluting components. For these reasons, soil decontamination is an important factor to consider in geotechnics. This work focuses on those soil decontamination techniques carried out in situ, since they allow to eliminate soil pollutants in a less invasive way than confinement, containment or ex situ remediation techniques, causing a minor soil alteration and, therefore, affecting less to its mechanical properties. These factors should be taken into account when carrying out a geotechnical performance on a previously decontaminated soil. (Author)

  16. Bright-field in situ hybridization for HER2 gene amplification in breast cancer using tissue microarrays: correlation between chromogenic (CISH) and automated silver-enhanced (SISH) methods with patient outcome.

    Science.gov (United States)

    Francis, Glenn D; Jones, Mark A; Beadle, Geoffrey F; Stein, Sandra R

    2009-06-01

    HER2 gene amplification or overexpression occurs in 15% to 25% of breast cancers and has implications for treatment and prognosis. The most commonly used methods for HER2 testing are fluorescence in situ hybridization (FISH) and immunohistochemistry. FISH is considered to be the reference standard and more accurately predicts response to trastuzumab, but is technically demanding, expensive, and requires specialized equipment. In situ hybridization is required to be eligible for adjuvant treatment with trastuzumab in Australia. Bright-field in situ hybridization is an alternative to FISH and uses a combination of in situ methodology and a peroxidase-mediated chromogenic substrate such as diaminobenzidine [chromogenic in situ hybridization (CISH)] or multimer technology coupled with enzyme metallography [silver-enhanced in situ hybridization (SISH)] to create a marker visible under bright-field microscopy. CISH was introduced into diagnostic testing in Australia in October 2006. SISH methodology is a more recent introduction into the testing repertoire. An evaluation of CISH and SISH performance to assess patient outcome were performed using tissue microarrays. Tissue microarrays were constructed in duplicate using material from 593 patients with invasive breast carcinoma and assessed using CISH and SISH. Gene amplification was assessed using the American Society of Clinical Oncology/College of American Pathologists guideline and Australian HER2 Advisory Board criteria (single probe: diploid, 1 to 2.5 copies/nucleus; polysomy >2.5 to 4 copies/nucleus; equivocal, >4 to 6 copies/nucleus; low-level amplification, >6 to 10 copies/nucleus and high-level amplification >10 copies/nucleus; dual probe HER2/CHR17 ratio: nonamplified 2.2). Results were informative for 337 tissue cores comprising 230 patient samples. Concordance rates were 96% for HER2 single probe CISH and SISH and 95.5% for single probe CISH and dual probe HER2/CHR17 SISH. Both bright-field methods correlated

  17. Mechanisms of induction of chromosomal aberrations and their detection by fluorescence in situ hybridization

    International Nuclear Information System (INIS)

    Natarajan, A.T.

    2002-01-01

    Recently introduced fluorescence in situ hybridization (FISH) technique employing chromosome specific DNA libraries as well as region specific DNA probes (e.g., centromere, telomere) have helped to analyse chromosomal aberrations in great detail and thus have given some new insights into the mechanisms of induction of chromosomal aberrations. The relative proportion of induction of translocations and dicentrics by ionising radiation was studied in human, mice and Chinese hamster cells. Many of the studies point to the differences between the mechanisms of induction of dicentrics and translocations. Preliminary results obtained in our laboratory using arm specific probes for human chromosomes 1 and 3 indicate that the aberrations between the arms appear to be more than expected on a random basis. By employing telomeric probes the frequencies of interstitial deletions were found to be high and similar to the frequencies of dicentrics both in human and mouse lymphocytes. A recent study with human chromosome specific probes clearly shows variation of sensitivity of chromosomes for the induction of exchange aberrations. Radiation response studies with Chinese hamster cells using telomeric probes, suggest that telomeric sequences, especially interstitial ones appear to be an important factor in the origin of both spontaneous and induced chromosomal aberrations

  18. Partial trisomy 13 in an infant with a mild phenotype: application of fluorescence in situ hybridization in cytogenetic syndromes.

    Science.gov (United States)

    Begovic, D; Hitrec, V; Lasan, R; Letica, L; Baric, I; Sarnavka, V; Galic, S

    1998-06-01

    We report on a month-old infant with dysmorphic face and several anomalies known to be associated with trisomy 13. Fluorescence in situ hybridization (FISH) studies performed on metaphase cells allowed us to identify an extra material on the short arm of the chromosome 13 as a duplication of 13q22-qter.

  19. Breeding of lilies and tulips—Interspecific hybridization and genetic background—

    Science.gov (United States)

    Marasek-Ciolakowska, Agnieszka; Nishikawa, Tomotaro; Shea, Daniel J.; Okazaki, Keiichi

    2018-01-01

    Lilies and tulips (Liliaceae family) are economically very important ornamental bulbous plants. Here, we summarize major breeding goals, the role of an integrated method of cut-style pollination and fertilization followed by embryo rescue and mitotic and meiotic polyploidization involved in new assortment development. Both crops have been subjected to extensive interspecific hybridization followed by selection. Additionally, spontaneous polyploidization has played a role in their evolution. In lilies, there is a tendency to replace diploids with polyploid cultivars, whereas in tulip a majority of the cultivars that exist today are still diploid except for triploid Darwin hybrid tulips. The introduction of molecular cytogenetic techniques such as genomic in situ hybridization (GISH) permitted the detailed studies of genome composition in lily and tulip interspecific hybrids and to follow the chromosome inheritance in interspecific crosses. In addition, this review presents the latest information on phylogenetic relationship in lily and tulip and recent developments in molecular mapping using different DNA molecular techniques. PMID:29681746

  20. Sugar Cane Genome Numbers Assumption by Ribosomal DNA FISH Techniques

    NARCIS (Netherlands)

    Thumjamras, S.; Jong, de H.; Iamtham, S.; Prammanee, S.

    2013-01-01

    Conventional cytological method is limited for polyploidy plant genome study, especially sugar cane chromosomes that show unstable numbers of each cultivar. Molecular cytogenetic as fluorescent in situ hybridization (FISH) techniques were used in this study. A basic chromosome number of sugar cane

  1. Expression and localization of ionotropic glutamate receptor subunits in the goldfish retina--an in situ hybridization and immunocytochemical study

    NARCIS (Netherlands)

    Vandenbranden, C. A.; Kamphuis, W.; Nunes Cardozo, B.; Kamermans, M.

    2000-01-01

    The expression and distribution of AMPA, kainate and NMDA glutamate receptor subunits was studied in the goldfish retina. For the immunocytochemical localization of the AMPA receptor antisera against GluR2, GluR2/3 and GluR4 were used, and for in situ hybridization rat specific probes for GluR1 and

  2. In Situ Hybridization Method Reveals (Pro)renin Receptor Expressing Cells in the Pituitary Gland of Rats: Correlation with Anterior Pituitary Hormones.

    Science.gov (United States)

    Takahashi, Kazuhiro; Yatabe, Megumi; Fujiwara, Ken; Hirose, Takuo; Totsune, Kazuhito; Yashiro, Takashi

    2013-02-28

    Expression of (pro)renin receptor ((P)RR), a specific receptor for renin and prorenin, was studied in rat pituitary gland. In situ hybridization showed that cells expressing (P)RR mRNA were widely distributed in the anterior lobe and intermediate lobe of the pituitary gland. Double-staining using in situ hybridization for (P)RR mRNA and immunohistochemistry for the pituitary hormones showed that (P)RR mRNA was expressed in most of the GH cells and ACTH cells in the anterior lobe. (P)RR mRNA was also expressed in a few prolactin cells and TSH cells, but not in LH cells. The present study has shown for the first time the distribution of (P)RR mRNA expressing cells in the rat pituitary gland. These findings suggest that (P)RR plays physiological roles in the pituitary gland, such as the modulation of the pituitary hormone secretion.

  3. In Situ Hybridization Method Reveals (Pro)renin Receptor Expressing Cells in the Pituitary Gland of Rats: Correlation with Anterior Pituitary Hormones

    International Nuclear Information System (INIS)

    Takahashi, Kazuhiro; Yatabe, Megumi; Fujiwara, Ken; Hirose, Takuo; Totsune, Kazuhito; Yashiro, Takashi

    2013-01-01

    Expression of (pro)renin receptor ((P)RR), a specific receptor for renin and prorenin, was studied in rat pituitary gland. In situ hybridization showed that cells expressing (P)RR mRNA were widely distributed in the anterior lobe and intermediate lobe of the pituitary gland. Double-staining using in situ hybridization for (P)RR mRNA and immunohistochemistry for the pituitary hormones showed that (P)RR mRNA was expressed in most of the GH cells and ACTH cells in the anterior lobe. (P)RR mRNA was also expressed in a few prolactin cells and TSH cells, but not in LH cells. The present study has shown for the first time the distribution of (P)RR mRNA expressing cells in the rat pituitary gland. These findings suggest that (P)RR plays physiological roles in the pituitary gland, such as the modulation of the pituitary hormone secretion

  4. Comparison of in situ hybridization methods for the assessment of HER-2/neu gene amplification status in breast cancer using a tissue microarray.

    Science.gov (United States)

    Malicka-Durczak, Anna; Korski, Konstanty; Ibbs, Matthew

    2012-01-01

    This project compared HER-2/neu gene status in breast cancers, as demonstrated by FISH (fluorescent in situ hybridization) and CISH (chromogenic in situ hybridization) and using a tissue microarray (TMA). The study also aimed to show whether the TMA technique could be used in clinical diagnostics, rather than remain a scientific tool. A TMA was constructed using 121 breast cancer specimens, 6 cores from each specimen. Demonstration and assessment of HER-2/neu gene status was by FISH (Vysis Path) and CISH (DAKO Duo CISH). The 121 breast cancer specimens were divided into 3 groups by HER-2 status, as determined by immunohistochemistry. In the HER-2 negative group no amplification was observed in 36 out of 40 cases. 3 cases showed amplification by both methods and one by CISH alone. The equivocal HER-2 group showed no amplification in 30 out of 41 cases and amplification in 9 cases. One case was FISH negative CISH positive and one was discarded. In the HER-2 positive group, amplification was confirmed in 37 of the 40 cases by both methods. 3 cases were unsuitable for assessment. This study indicated that CISH is a sensitive alternative to FISH in detecting HER2 gene amplification and may replace FISH in HER2 testing. Good agreement was observed between methods (98.5% - 119 out of 121 cases). Furthermore, as only 4 out of 121 cases were unsuitable for assessment (no signal or missing TMA cores) - it may be feasible to use TMA in diagnostics.

  5. Evaluation of Myc Gene Amplification in Prostate Cancer Using a Dual Color Chromogenic in-Situ Hybridization (Dual CISH Assay

    Directory of Open Access Journals (Sweden)

    Daniel Lerda

    2013-04-01

    Full Text Available Objetive: The overall purpose of the study was to demonstrate applicability of the Dako dual-color chromogenic in situ hybridization (CISH assay (DAKO Denmark, Glostrup with respect to fluorescence in situ hybridization (FISH probes MYC-C. Methods: MYC gene amplification by FISH and Dako dual-color CISH Results: The study showed that the dual-color CISH assay can convert Texas red and fluorescein isothiocyanate (FITC signals into chromogenic signals. The dual –color CISH assay was performed on 40 cases of prostate cancer. Amplification was identified in 12 of 40 (30% tumors. No amplification was seen in 28 of 40 (70% tumors. FISH data were available in total of 40 tumors. All tumors showed concordant results between dual-color CISH and FISH for classifying a tumor as MYC amplified or not amplified. Conclusions: We conclude that dual-color Dako CISH assay is an accurate method for determining MYC gene amplification with added advantages that make it a more practically useful method. [J Interdiscipl Histopathol 2013; 1(2.000: 81-84

  6. Correlation between HER2 gene amplification and protein overexpression through fluorescence in situ hybridization and immunohistochemistry in breast carcinoma patients.

    Science.gov (United States)

    Makroo, R N; Chowdhry, Mohit; Kumar, Manoj; Srivastava, Priyanka; Tyagi, Richa; Bhadauria, Preeti; Kaul, Sumaid; Sarin, Ramesh; Das, P K; Dua, Harsh

    2012-01-01

    In India, the incidence of breast cancer has increased in the urban population, with 1 in every 22 women diagnosed with breast cancer. It is important to know the HER2/neu gene status for a better prognostication of these patients. The aim of this study was to compare the efficacy of fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) for determining HER2/neu alteration in breast carcinoma. A total of 188 histologically proven breast carcinoma cases between the years 2007 and 2011 were retrospectively analyzed on the paraffin tissue sections by both IHC and FISH techniques. FISH for HER2/neu gene amplification was performed on cases where the IHC status was already known and the results were compared. A total of 64 (30%) patients were found to be amplified and the remaining 124 (65.9%) cases were found to be unamplified through FISH. Patients observed with 3+ reading on IHC were later confirmed as unamplified in 29.5% cases through FISH. It has been confirmed with the present study that IHC is a prudent first-step technique to screen tissue samples for HER2/neu gene status, but should be supplemented with the FISH technique especially in equivocal cases.

  7. Correlation between HER2 gene amplification and protein overexpression through fluorescence in situ hybridization and immunohistochemistry in breast carcinoma patients

    Directory of Open Access Journals (Sweden)

    R N Makroo

    2012-01-01

    Full Text Available Background : In India, the incidence of breast cancer has increased in the urban population, with 1 in every 22 women diagnosed with breast cancer. It is important to know the HER2/neu gene status for a better prognostication of these patients. Aim : The aim of this study was to compare the efficacy of fluorescence in situ hybridization (FISH and immunohistochemistry (IHC for determining HER2/neu alteration in breast carcinoma. Materials and Methods : A total of 188 histologically proven breast carcinoma cases between the years 2007 and 2011 were retrospectively analyzed on the paraffin tissue sections by both IHC and FISH techniques. FISH for HER2/neu gene amplification was performed on cases where the IHC status was already known and the results were compared. Results : A total of 64 (30% patients were found to be amplified and the remaining 124 (65.9% cases were found to be unamplified through FISH. Patients observed with 3+ reading on IHC were later confirmed as unamplified in 29.5% cases through FISH. Conclusion : It has been confirmed with the present study that IHC is a prudent first-step technique to screen tissue samples for HER2/neu gene status, but should be supplemented with the FISH technique especially in equivocal cases.

  8. In-situ measurement of mechanical properties of structural components using cyclic ball indentation technique

    International Nuclear Information System (INIS)

    Chatterjee, S.; Madhusoodanan, K.; Panwar, Sanjay; Rupani, B.B.

    2007-01-01

    Material properties of components change during service due to environmental conditions. Measurement of mechanical properties of the components is important for assessing their fitness for service. In many instances, it is not possible to remove sizable samples from the component for doing the measurement in laboratory. In-situ technique for measurement of mechanical properties has great significance in such cases. One of the nondestructive methods that can be adopted for in-situ application is based on cyclic ball indentation technique. It involves multiple indentation cycles (at the same penetration location) on a metallic surface by a spherical indenter. Each cycle consists of indentation, partial unload and reload sequences. Presently, commercial systems are available for doing indentation test on structural component for limited applications. But, there is a genuine need of remotely operable compact in-situ property measurement system. Considering the importance of such applications Reactor Engineering Division of BARC has developed an In-situ Property Measurement System (IProMS), which can be used for in-situ measurement of mechanical properties of a flat or tubular component. This paper highlights the basic theory of measurement, qualification tests on IProMS and results from tests done on flat specimens and tubular component. (author)

  9. Fluorescence photooxidation with eosin: a method for high resolution immunolocalization and in situ hybridization detection for light and electron microscopy

    Science.gov (United States)

    1994-01-01

    A simple method is described for high-resolution light and electron microscopic immunolocalization of proteins in cells and tissues by immunofluorescence and subsequent photooxidation of diaminobenzidine tetrahydrochloride into an insoluble osmiophilic polymer. By using eosin as the fluorescent marker, a substantial improvement in sensitivity is achieved in the photooxidation process over other conventional fluorescent compounds. The technique allows for precise correlative immunolocalization studies on the same sample using fluorescence, transmitted light and electron microscopy. Furthermore, because eosin is smaller in size than other conventional markers, this method results in improved penetration of labeling reagents compared to gold or enzyme based procedures. The improved penetration allows for three-dimensional immunolocalization using high voltage electron microscopy. Fluorescence photooxidation can also be used for high resolution light and electron microscopic localization of specific nucleic acid sequences by in situ hybridization utilizing biotinylated probes followed by an eosin-streptavidin conjugate. PMID:7519623

  10. Fluorescence in situ hybridization and molecular studies in infertile men with dysplasia of the fibrous sheath.

    Science.gov (United States)

    Baccetti, Baccio; Collodel, Giulia; Gambera, Laura; Moretti, Elena; Serafini, Francesca; Piomboni, Paola

    2005-07-01

    To perform fluorescence in situ hybridization (FISH) and molecular analysis in patients with the genetic sperm defect "dysplasia of the fibrous sheath" (DFS). Retrospective study. Regional Referral Center for Male Infertility, Siena, Italy. Twelve infertile patients with DFS sperm defects. Family history, lymphocytic karyotype, physical and hormonal assays, semen analysis. The DFS sperm phenotype was defined by light, fluorescent, and electron microscopy. Sperm chromosomal constitution was examined by FISH. Gene deletions were tested by polymerase chain reaction. The genetic sperm defect DFS was determined by transmission and scanning electron microscopy. Immunofluorescence staining of A-kinase anchoring protein 4 (AKAP4) showed a moderate and diffuse signal, revealing a disorganized and incompletely assembled fibrous sheath. In 11 of 12 DFS patients, polymerase chain reaction for detecting the presence of partial sequence of AKAP4/AKAP3 binding regions gave positive results. Fluorescence in situ hybridization was performed in decondensed sperm nuclei with probes for chromosomes 18, X, and Y. The mean disomy frequency of chromosome 18 was in the normal range, whereas the mean disomy frequencies of sex chromosomes and diploidies were twice those of controls. These results should be considered when DFS sperm are used in assisted reproductive technology, owing to the high risk of transmission of chromosomal unbalance and of DFS sperm defects to male offspring.

  11. Introduction to in situ leaching technique and facility at Smith Ranch uranium project in USA

    International Nuclear Information System (INIS)

    Xu Lechang; Wang Delin; Sun Xianrong; Gao Shangxiong

    2005-01-01

    The history of in situ leaching of uranium in USA is reviewed. Some techniques and parameters of alkaline in situ leach at Smith Ranch uranium project are introduced, including well field, sorption, elution, precipitation, filter and drying, automatic control, radiation protection, safety and environmental protection. (authors)

  12. Aquifer restoration techniques for in-situ leach uranium mines

    International Nuclear Information System (INIS)

    Deutsch, W.J.; Bell, N.E.; Mercer, B.W.; Serne, R.J.; Shade, J.W.; Tweeton, D.R.

    1984-02-01

    In-situ leach uranium mines and pilot-scale test facilities are currently operating in the states of Wyoming, Texas, New Mexico and Colorado. This report summarizes the technical considerations involved in restoring a leached ore zone and its aquifer to the required level. Background information is provided on the geology and geochemistry of mineralized roll-front deposits and on the leaching techniques used to extract the uranium. 13 references, 13 figures, 4 tables

  13. Preimplantation genetic diagnosis by fluorescence in situ hybridization of reciprocal and Robertsonian translocations.

    Science.gov (United States)

    Chen, Chun-Kai; Wu, Dennis; Yu, Hsing-Tse; Lin, Chieh-Yu; Wang, Mei-Li; Yeh, Hsin-Yi; Huang, Hong-Yuan; Wang, Hsin-Shin; Soong, Yung-Kuei; Lee, Chyi-Long

    2014-03-01

    The presence of reciprocal and Robertsonian chromosomal rearrangement is often related to recurrent miscarriage. Using preimplantation genetic diagnosis, the abortion rate can be decreased. Cases treated at our center were reviewed. A retrospective analysis for either Robertsonian or reciprocal translocations was performed on all completed cycles of preimplantation genetic diagnosis at our center since the first reported case in 2004 until the end of 2010. Day 3 embryo biopsies were carried out, and the biopsied cell was checked by fluorescent in situ hybridization using relevant informative probes. Embryos with a normal or balanced translocation karyotype were transferred on Day 4. Thirty-eight preimplantation genetic diagnosis cycles involving 17 couples were completed. A total of 450 (82.6%) of the total oocytes were MII oocytes, and 158 (60.0%) of the two-pronuclei embryos were biopsied. In 41.4% of the fluorescent in situ hybridization analyses, the results were either normal or balanced. Embryos were transferred back after 21 cycles. Three babies were born from Robertsonian translocation carriers and another two from reciprocal translocation carriers. The miscarriage rate was 0%. Among the reciprocal translocation group, the live delivery rate was 8.3% per ovum pick-up cycle and 18.2% per embryo transfer cycle. Among the Robertsonian translocation group, the live delivery rate was 14.3% per ovum pick-up cycle and 20.0% per embryo transfer cycle. There is a trend whereby the outcome for Robertsonian translocation group carriers is better than that for reciprocal translocation group carriers. Aneuploidy screening may possibly be added in order to improve the outcome, especially for individuals with an advanced maternal age. The emergence of an array-based technology should help improve this type of analysis. Copyright © 2014. Published by Elsevier B.V.

  14. Multi-technique hybrid imaging in PET/CT and PET/MR: what does the future hold?

    International Nuclear Information System (INIS)

    Galiza Barbosa, F. de; Delso, G.; Voert, E.E.G.W. ter; Huellner, M.W.; Herrmann, K.; Veit-Haibach, P.

    2016-01-01

    Integrated positron-emission tomography and computed tomography (PET/CT) is one of the most important imaging techniques to have emerged in oncological practice in the last decade. Hybrid imaging, in general, remains a rapidly growing field, not only in developing countries, but also in western industrialised healthcare systems. A great deal of technological development and research is focused on improving hybrid imaging technology further and introducing new techniques, e.g., integrated PET and magnetic resonance imaging (PET/MRI). Additionally, there are several new PET tracers on the horizon, which have the potential to broaden clinical applications in hybrid imaging for diagnosis as well as therapy. This article aims to highlight some of the major technical and clinical advances that are currently taking place in PET/CT and PET/MRI that will potentially maintain the position of hybrid techniques at the forefront of medical imaging technologies.

  15. Experimental Investigation on Mechanical and Turning Behavior of Al 7075/x% wt. TiB2-1% Gr In Situ Hybrid Composite

    Directory of Open Access Journals (Sweden)

    K. R. Ramkumar

    2015-01-01

    Full Text Available The present research work involves the study of AA 7075-TiB2-Gr in situ composite through stir casting route. This in situ method involves formation of reinforcements within the matrix by the chemical reaction of two or more compounds which also produces some changes in the matrix material within the vicinity. Titanium Diboride (TiB2 and graphite were the reinforcement in a matrix of AA 7075 alloy. The composite was prepared with the formation of the reinforcement inside the molten matrix by adding salts of Potassium Tetrafluoroborate (KBF4 and Potassium Hexafluorotitanate (K2TiF6. The samples were taken under casted condition and the properties of the composite were tested by conducting characterization using X-ray diffraction (XRD, hardness test, flexural strength by using three-point bend test, scanning electron microscope (SEM, optical microstructure, grain size analysis, and surface roughness. It was found that good/excellent mechanical properties were obtained in AA 7075-TiB2-Gr reinforced in situ hybrid composite compared to alloy due to particulate strengthening of ceramic particles of TiB2 in the matrix. Further, Al 7075-3% TiB2-1% Gr hybrid in situ composite exhibited improved machinability over the alloy and composites due to self-lubricating property given by the Gr particles in the materials.

  16. Two-dimensional in situ metrology of X-ray mirrors using the speckle scanning technique

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hongchang, E-mail: hongchang.wang@diamond.ac.uk; Kashyap, Yogesh; Laundy, David; Sawhney, Kawal [Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

    2015-06-06

    The two-dimensional slope error of an X-ray mirror has been retrieved by employing the speckle scanning technique, which will be valuable at synchrotron radiation facilities and in astronomical telescopes. In situ metrology overcomes many of the limitations of existing metrology techniques and is capable of exceeding the performance of present-day optics. A novel technique for precisely characterizing an X-ray bimorph mirror and deducing its two-dimensional (2D) slope error map is presented. This technique has also been used to perform fast optimization of a bimorph mirror using the derived 2D piezo response functions. The measured focused beam size was significantly reduced after the optimization, and the slope error map was then verified by using geometrical optics to simulate the focused beam profile. This proposed technique is expected to be valuable for in situ metrology of X-ray mirrors at synchrotron radiation facilities and in astronomical telescopes.

  17. Clinical application of fluorescence in situ hybridization for prenatal diagnosis

    Directory of Open Access Journals (Sweden)

    Shu-fang JIANG

    2012-07-01

    Full Text Available Objective To establish and optimize the procedures of fluorescence in situ hybridization(FISH), and evaluate its clinical value in rapid prenatal diagnosis of fetal numerical abnormality of chromosomes 21, 18, 13, X, Y. Methods Amniotic fluid or fetal blood was sampled by routine invasive procedures. After the amniotic fluid cells or fetal blood cells were separated and sequentially processed with hypotonic solution, fixation solution, smear and high temperature, they were hybridized in situ with two panels of specific fluorescence probes to detect numerical abnormality of chromosomes 21, 18, 13, X, Y. All the samples were also cultured and analyzed for their karyotype by conventional methods. Results When it was used as a diagnostic criterion of chromosomal number that the fluorescence signals were observed in ≥90% cells, GLP 13/GLP 21 probe panel showed 2 green/2 red fluorescence signals and CSP18/CSP X/CSP Y probe panel showed 2 blue/2 yellow (female or 2 blue/1 yellow/1 red fluorescence signals (male under normal condition. The test reports of all 196 cases were sent out in 72-96 hours, and 7 cases of Down syndrome, 2 cases of trisomy 18 and 1 case of sex chromosomal numerical abnormality were detected, which were accordant with karyotype analysis results reported one month later. Conclusions FISH has potential for clinical application, and is applicable to rapid prenatal diagnosis of fetal numerical abnormality of chromosomes 21, 18, 13, X, Y. The rapid FISH, together with conventional karyotyping, offer a valuable means for prenatal diagnosis of fetal aneuploidies.

  18. In situ green synthesis of antimicrobial carboxymethyl chitosan-nanosilver hybrids with controlled silver release.

    Science.gov (United States)

    Huang, Siqi; Yu, Zhiming; Zhang, Yang; Qi, Chusheng; Zhang, Shifeng

    2017-01-01

    In order to fabricate antimicrobial carboxymethyl chitosan-nanosilver (CMC-Ag) hybrids with controlled silver release, this study demonstrated comparable formation via three synthetic protocols: 1) carboxymethyl chitosan (CMC) and glucose (adding glucose after AgNO 3 ), 2) CMC and glucose (adding glucose before AgNO 3 ), and 3) CMC only. Under principles of green chemistry, the synthesis was conducted in an aqueous medium exposed to microwave irradiation for 10 minutes with nontoxic chemicals. The structure and formation mechanisms of the three CMC-Ag hybrids were explored using X-ray diffraction, ultraviolet-visible spectroscopy, transmission electron microscopy, and Fourier-transform infrared analyses. Additionally, antimicrobial activity and in vitro silver release of the three synthesized hybrids were investigated in detail. The results revealed that a large number of stable, uniform, and small silver nanoparticles (AgNPs) were synthesized in situ on CMC chains via protocol 1. AgNPs were well dispersed with narrow size distribution in the range of 6-20 nm, with mean diameter only 12.22±2.57 nm. The addition of glucose resulted in greater AgNP synthesis. The order of addition of glucose and AgNO 3 significantly affected particle size and size distribution of AgNPs. Compared to CMC alone and commercially available AgNPs, the antimicrobial activities of three hybrids were significantly improved. Of the three hybrids, CMC-Ag1 synthesized via protocol 1 exhibited better antimicrobial activity than CMC-Ag2 and CMC-Ag3, and showed more effective inhibition of Staphylococcus aureus than Escherichia coli . Due to strong coordination and electrostatic interactions between CMC and silver and good steric protection provided by CMC, CMC-Ag1 displayed stable and continuous silver release and better performance in retaining silver for prolonged periods than CMC-Ag2 and CMC-Ag3.

  19. In situ green synthesis of antimicrobial carboxymethyl chitosan–nanosilver hybrids with controlled silver release

    Science.gov (United States)

    Huang, Siqi; Yu, Zhiming; Zhang, Yang; Qi, Chusheng; Zhang, Shifeng

    2017-01-01

    In order to fabricate antimicrobial carboxymethyl chitosan–nanosilver (CMC-Ag) hybrids with controlled silver release, this study demonstrated comparable formation via three synthetic protocols: 1) carboxymethyl chitosan (CMC) and glucose (adding glucose after AgNO3), 2) CMC and glucose (adding glucose before AgNO3), and 3) CMC only. Under principles of green chemistry, the synthesis was conducted in an aqueous medium exposed to microwave irradiation for 10 minutes with nontoxic chemicals. The structure and formation mechanisms of the three CMC-Ag hybrids were explored using X-ray diffraction, ultraviolet-visible spectroscopy, transmission electron microscopy, and Fourier-transform infrared analyses. Additionally, antimicrobial activity and in vitro silver release of the three synthesized hybrids were investigated in detail. The results revealed that a large number of stable, uniform, and small silver nanoparticles (AgNPs) were synthesized in situ on CMC chains via protocol 1. AgNPs were well dispersed with narrow size distribution in the range of 6–20 nm, with mean diameter only 12.22±2.57 nm. The addition of glucose resulted in greater AgNP synthesis. The order of addition of glucose and AgNO3 significantly affected particle size and size distribution of AgNPs. Compared to CMC alone and commercially available AgNPs, the antimicrobial activities of three hybrids were significantly improved. Of the three hybrids, CMC-Ag1 synthesized via protocol 1 exhibited better antimicrobial activity than CMC-Ag2 and CMC-Ag3, and showed more effective inhibition of Staphylococcus aureus than Escherichia coli. Due to strong coordination and electrostatic interactions between CMC and silver and good steric protection provided by CMC, CMC-Ag1 displayed stable and continuous silver release and better performance in retaining silver for prolonged periods than CMC-Ag2 and CMC-Ag3. PMID:28458539

  20. Localization of the Norrie disease gene mRNA by in situ hybridization.

    Science.gov (United States)

    Hartzer, M K; Cheng, M; Liu, X; Shastry, B S

    1999-07-15

    Norrie disease is a rare X-linked recessive neurodevelopmental disorder. The affected males manifest congenital blindness, which is often associated with hearing loss, mental retardation and psychiatric problems. Genetic linkage studies have localized the gene to the short arm of the X-chromosome and the gene has been isolated recently. The encoded protein is a member of the superfamily of growth factors containing a cystine knot motif and may be involved in cell adhesion and neurodevelopment. Molecular genetic analysis revealed a large number of missense, nonsense, deletion, and splice-site mutations among Norrie patients. In order to further determine the role of the Norrie disease gene, we studied the distribution pattern of its mRNA in the retina and in brain by in situ hybridization. The results show abundant hybridization signals in outer nuclear, inner nuclear, and ganglion cell layers of the retina in all three species (mice, rabbit, and human) examined. There was no significant expression in the vitreous body, lens, and rod outer segment. High expression levels were also observed in the cerebellar granular layer, hippocampus, olfactory bulb, cortex, and epithelium of the rabbit brain. These data suggest that the Norrie disease gene could play a critical role in the differentiation or maintenance of the differentiated state of the retina.

  1. Novel Damage Detection Techniques for Structural Health Monitoring Using a Hybrid Sensor

    Directory of Open Access Journals (Sweden)

    Dengjiang Wang

    2016-01-01

    Full Text Available This study presents a technique for detecting fatigue cracks based on a hybrid sensor monitoring system consisting of a combination of intelligent coating monitoring (ICM and piezoelectric transducer (PZT sensors. An experimental procedure using this hybrid sensor system was designed to monitor the cracks generated by fatigue testing in plate structures. A probability of detection (POD model that quantifies the reliability of damage detection for a specific sensor or the nondestructive testing (NDT method was used to evaluate the weight factor for the ICM and PZT sensors. To estimate the uncertainty of model parameters in this study, the Bayesian method was employed. Realistic data from fatigue testing was used to validate the overall method, and the results show that the novel damage detection technique using a hybrid sensor can quantify fatigue cracks more accurately than results obtained by conventional sensor methods.

  2. Evidence for Integrity of Parental Genomes in the Diploid Hybridogenetic Water Frog Pelophylax esculentus by Genomic in situ Hybridization

    Czech Academy of Sciences Publication Activity Database

    Zalésna, A.; Choleva, Lukáš; Ogielska, M.; Rábová, Marie; Marec, František; Ráb, Petr

    2011-01-01

    Roč. 134, č. 3 (2011), s. 206-212 ISSN 1424-8581 R&D Projects: GA MŠk LC06073; GA ČR GA523/09/2106 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50070508 Keywords : Amphibia * Chromosomes * Genomic in situ hybridization (GISH) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.533, year: 2011

  3. Incorporating organizational factors into Probabilistic Risk Assessment (PRA) of complex socio-technical systems: A hybrid technique formalization

    International Nuclear Information System (INIS)

    Mohaghegh, Zahra; Kazemi, Reza; Mosleh, Ali

    2009-01-01

    This paper is a result of a research with the primary purpose of extending Probabilistic Risk Assessment (PRA) modeling frameworks to include the effects of organizational factors as the deeper, more fundamental causes of accidents and incidents. There have been significant improvements in the sophistication of quantitative methods of safety and risk assessment, but the progress on techniques most suitable for organizational safety risk frameworks has been limited. The focus of this paper is on the choice of 'representational schemes' and 'techniques.' A methodology for selecting appropriate candidate techniques and their integration in the form of a 'hybrid' approach is proposed. Then an example is given through an integration of System Dynamics (SD), Bayesian Belief Network (BBN), Event Sequence Diagram (ESD), and Fault Tree (FT) in order to demonstrate the feasibility and value of hybrid techniques. The proposed hybrid approach integrates deterministic and probabilistic modeling perspectives, and provides a flexible risk management tool for complex socio-technical systems. An application of the hybrid technique is provided in the aviation safety domain, focusing on airline maintenance systems. The example demonstrates how the hybrid method can be used to analyze the dynamic effects of organizational factors on system risk

  4. Chromosome translocations measured by fluorescence in-situ hybridization: A promising biomarker

    International Nuclear Information System (INIS)

    Lucas, J.N.; Straume, T.

    1995-10-01

    A biomarker for exposure and risk assessment would be most useful if it employs an endpoint that is highly quantitative, is stable with time, and is relevant to human risk. Recent advances in chromosome staining using fluorescence in situ hybridization (FISH) facilitate fast and reliable measurement of reciprocal translocations, a kind of DNA damage linked to both prior exposure and risk. In contrast to other biomarkers available, the frequency of reciprocal translocations in individuals exposed to whole-body radiation is stable with time post exposure, has a rather small inter-individual variability, and can be measured accurately at the low levels. Here, the authors discuss results from their studies demonstrating that chromosome painting can be used to reconstruct radiation dose for workers exposed within the dose limits, for individuals exposed a long time ago, and even for those who have been diagnosed with leukemia but not yet undergone therapy

  5. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections.

    Science.gov (United States)

    Ellison, Mitchell A; McMahon, Michael B; Bonde, Morris R; Palmer, Cristi L; Luster, Douglas G

    2016-01-01

    Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.

  6. Frequencies of X-ray and fast neutron induced chromosome translocations in human peripheral blood lymphocytes as detected by in situ hybridization using chromosome specific DNA libraries

    International Nuclear Information System (INIS)

    Natarajan, A.T.; Darroudi, F.; Vermeulen, S.; Wiegant, J.

    1992-01-01

    DNA libraries of six human chromosomes were used to detect translocations in human lymphocytes induced by different doses of X-rays and fast neutrons. Results show that with X-rays, one can detect about 1.5 to 2.0 fold more translocations in comparison to dicentrics, whereas following fast neutron irradiation, the difference between these two classes of aberrations are significantly different at high doses. In addition, triple fluorescent in situ hybridization technique was used to study the frequencies of radiation-induced translocations involving a specific chromosome. Chromosome number 1 was found to be involved in translocations more frequently than chromosomes number 2, 3, 4, 8 and X. (author). 10 refs., 1 fig., 2 tabs

  7. Analysis of the Ceratitis capitata y chromosome using in situ hybridization to mitotic chromosomes

    International Nuclear Information System (INIS)

    Willhoeft, U.; Franz, G.

    1998-01-01

    In Ceratitis capitata the Y chromosome is responsible for sex-determination. We used fluorescence in situ hybridization (FISH) for cytogenetic analysis of mitotic chromosomes. FISH with the wild-type strain EgyptII and two repetitive DNA probes enabled us to differentiate between the short and the long arm of the Y chromosome and gives a much better resolution than C-banding of mitotic chromosomes. We identified the Y-chromosomal breakpoints in Y-autosome translocations using FISH. Even more complex rearrangements i.e. deletions and insertions in some translocation strains were detected by this method. A strategy for mapping the primary sex determination factor in Ceratitis capitata by FISH is presented. (author)

  8. A simple protocol for attenuating the auto-fluorescence of cyanobacteria for optimized fluorescence in situ hybridization (FISH) imaging.

    Science.gov (United States)

    Zeller, Perrine; Ploux, Olivier; Méjean, Annick

    2016-03-01

    Cyanobacteria contain pigments, which generate auto-fluorescence that interferes with fluorescence in situ hybridization (FISH) imaging of cyanobacteria. We describe simple chemical treatments using CuSO4 or H2O2 that significantly reduce the auto-fluorescence of Microcystis strains. These protocols were successfully applied in FISH experiments using 16S rRNA specific probes and filamentous cyanobacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Developing new understanding of photoelectrochemical water splitting via in-situ techniques: A review on recent progress

    Directory of Open Access Journals (Sweden)

    Jiajie Cen

    2017-04-01

    Full Text Available Photoelectrochemical (PEC water splitting is a promising technology for solar hydrogen production to build a sustainable, renewable and clean energy economy. Given the complexity of the PEC water splitting processes, it is important to note that developing in-situ techniques for studying PEC water splitting presents a formidable challenge. This review is aimed at highlighting advantages and disadvantages of each technique, while offering a pathway of potentially combining several techniques to address different aspects of interfacial processes in PEC water splitting. We reviewed recent progress in various techniques and approaches utilized to study PEC water splitting, focusing on spectroscopic and scanning-probe methods. Keywords: In-situ, Water splitting, IMPS, TAS, SPM

  10. Correlation between Photoluminescence and Carrier Transport and a Simple In Situ Passivation Method for High-Bandgap Hybrid Perovskites.

    Science.gov (United States)

    Stoddard, Ryan J; Eickemeyer, Felix T; Katahara, John K; Hillhouse, Hugh W

    2017-07-20

    High-bandgap mixed-halide hybrid perovskites have higher open-circuit voltage deficits and lower carrier diffusion lengths than their lower-bandgap counterparts. We have developed a ligand-assisted crystallization (LAC) technique that introduces additives in situ during the solvent wash and developed a new method to dynamically measure the absolute intensity steady-state photoluminescence and the mean carrier diffusion length simultaneously. The measurements reveal four distinct regimes of material changes and show that photoluminescence brightening often coincides with losses in carrier transport, such as in degradation or phase segregation. Further, the measurements enabled optimization of LAC on the 1.75 eV bandgap FA 0.83 Cs 0.17 Pb(I 0.66 Br 0.34 ) 3 , resulting in an enhancement of the photoluminescence quantum yield (PLQY) of over an order of magnitude, an increase of 80 meV in the quasi-Fermi level splitting (to 1.29 eV), an increase in diffusion length by a factor of 3.5 (to over 1 μm), and enhanced open-circuit voltage and short-circuit current from photovoltaics fabricated from the LAC-treated films.

  11. Resizing Technique-Based Hybrid Genetic Algorithm for Optimal Drift Design of Multistory Steel Frame Buildings

    Directory of Open Access Journals (Sweden)

    Hyo Seon Park

    2014-01-01

    Full Text Available Since genetic algorithm-based optimization methods are computationally expensive for practical use in the field of structural optimization, a resizing technique-based hybrid genetic algorithm for the drift design of multistory steel frame buildings is proposed to increase the convergence speed of genetic algorithms. To reduce the number of structural analyses required for the convergence, a genetic algorithm is combined with a resizing technique that is an efficient optimal technique to control the drift of buildings without the repetitive structural analysis. The resizing technique-based hybrid genetic algorithm proposed in this paper is applied to the minimum weight design of three steel frame buildings. To evaluate the performance of the algorithm, optimum weights, computational times, and generation numbers from the proposed algorithm are compared with those from a genetic algorithm. Based on the comparisons, it is concluded that the hybrid genetic algorithm shows clear improvements in convergence properties.

  12. Fragrance composition of Dendrophylax lindenii (Orchidaceae using a novel technique applied in situ

    Directory of Open Access Journals (Sweden)

    James J. Sadler

    2012-02-01

    Full Text Available The ghost orchid, Dendrophylax lindenii (Lindley Bentham ex Rolfe (Orchidaceae, is one of North America’s rarest and well-known orchids. Native to Cuba and SW Florida where it frequents shaded swamps as an epiphyte, the species has experienced steady decline. Little information exists on D. lindenii’s biology in situ, raising conservation concerns. During the summer of 2009 at an undisclosed population in Collier County, FL, a substantial number (ca. 13 of plants initiated anthesis offering a unique opportunity to study this species in situ. We report a new technique aimed at capturing floral headspace of D. lindenii in situ, and identified volatile compounds using gas chromatography mass spectrometry (GC/MS. All components of the floral scent were identified as terpenoids with the exception of methyl salicylate. The most abundant compound was the sesquiterpene (E,E-α-farnesene (71% followed by (E-β-ocimene (9% and methyl salicylate (8%. Other compounds were: linalool (5%, sabinene (4%, (E-α-bergamotene (2%, α-pinene (1%, and 3-carene (1%. Interestingly, (E,E-α-farnesene has previously been associated with pestiferous insects (e.g., Hemiptera. The other compounds are common floral scent constituents in other angiosperms suggesting that our in situ technique was effective. Volatile capture was, therefore, possible without imposing physical harm (e.g., inflorescence detachment to this rare orchid.

  13. In situ hybridization of phytoplankton using fluorescently labeled rRNA probes

    OpenAIRE

    Groben, R.; Medlin, Linda

    2005-01-01

    Fluorescently-labelled molecular probes were used to identify and characterise phytoplankton species using in situ hybridisation coupled with fluorescence microscopy and flow cytometry. The application of this technique is sometimes problematic, because of the many different species with which this method is to be used. Problems that may occur are: probe penetration versus maintanance of cell stability, strong autofluorescence and/or cell lost during the sample processing. Here we present a m...

  14. In situ hybridization analysis of the temporospatial expression of the midkine/pleiotrophin family in rat embryonic pituitary gland.

    Science.gov (United States)

    Fujiwara, Ken; Maliza, Rita; Tofrizal, Alimuddin; Batchuluun, Khongorzul; Ramadhani, Dini; Tsukada, Takehiro; Azuma, Morio; Horiguchi, Kotaro; Kikuchi, Motoshi; Yashiro, Takashi

    2014-07-01

    Pituitary gland development is controlled by numerous signaling molecules, which are produced in the oral ectoderm and diencephalon. A newly described family of heparin-binding growth factors, namely midkine (MK)/pleiotrophin (PTN), is involved in regulating the growth and differentiation of many tissues and organs. Using in situ hybridization with digoxigenin-labeled cRNA probes, we detected cells expressing MK and PTN in the developing rat pituitary gland. At embryonic day 12.5 (E12.5), MK expression was localized in Rathke's pouch (derived from the oral ectoderm) and in the neurohypophyseal bud (derived from the diencephalon). From E12.5 to E19.5, MK mRNA was expressed in the developing neurohypophysis, and expression gradually decreased in the developing adenohypophysis. To characterize MK-expressing cells, we performed double-staining of MK mRNA and anterior pituitary hormones. At E19.5, no MK-expressing cells were stained with any hormone. In contrast, PTN was expressed only in the neurohypophysis primordium during all embryonic stages. In situ hybridization clearly showed that MK was expressed in primitive (immature/undifferentiated) adenohypophyseal cells and neurohypophyseal cells, whereas PTN was expressed only in neurohypophyseal cells. Thus, MK and PTN might play roles as signaling molecules during pituitary development.

  15. PEAK-TO-AVERAGE POWER RATIO REDUCTION USING CODING AND HYBRID TECHNIQUES FOR OFDM SYSTEM

    Directory of Open Access Journals (Sweden)

    Bahubali K. Shiragapur

    2016-03-01

    Full Text Available In this article, the research work investigated is based on an error correction coding techniques are used to reduce the undesirable Peak-to-Average Power Ratio (PAPR quantity. The Golay Code (24, 12, Reed-Muller code (16, 11, Hamming code (7, 4 and Hybrid technique (Combination of Signal Scrambling and Signal Distortion proposed by us are used as proposed coding techniques, the simulation results shows that performance of Hybrid technique, reduces PAPR significantly as compared to Conventional and Modified Selective mapping techniques. The simulation results are validated through statistical properties, for proposed technique’s autocorrelation value is maximum shows reduction in PAPR. The symbol preference is the key idea to reduce PAPR based on Hamming distance. The simulation results are discussed in detail, in this article.

  16. Fluorescence in situ hybridization and qPCR to detect Merkel cell polyomavirus physical status and load in Merkel cell carcinomas.

    Science.gov (United States)

    Haugg, Anke M; Rennspiess, Dorit; zur Hausen, Axel; Speel, Ernst-Jan M; Cathomas, Gieri; Becker, Jürgen C; Schrama, David

    2014-12-15

    The Merkel cell polyomavirus (MCPyV) is detected in 80% of Merkel cell carcinomas (MCC). Clonal integration and tumor-specific mutations in the large T antigen are strong arguments that MCPyV is a human tumor virus. However, the relationship between viral presence and cancer induction remains discussed controversially. Since almost all studies on virus prevalence are based on PCR techniques, we performed MCPyV fluorescence in situ hybridization (FISH) on MCC to gain information about the quality of the viral presence on the single cell level. MCPyV-FISH was performed on tissue microarrays containing 62 formalin-fixed and paraffin-embedded tissue samples including all tumor grades of 42 patients. The hybridization patterns were correlated to the qPCR data determined on corresponding whole tissue sections. Indeed, MCPyV-FISH and qPCR data were highly correlated, i.e. 83% for FISH-positive and 93% for FISH-negative cores. Accordingly, the mean of the qPCR values of all MCPyV-positive cores differed significantly from the mean of the negative cores (p = 0.0076). Importantly, two hybridization patterns were definable in the MCPyV-FISH: a punctate pattern (85%) indicating viral integration, which correlated with a moderate viral abundance and a combination of the punctate with a diffuse pattern (15%), suggesting a possible coexistence of integrated and episomal virus which was associated with very high viral load and VP1 expression. Thus, MCPyV-FISH adds important information on the single cell level within the histomorphological context and could therefore be an important tool to further elucidate MCPyV related carcinogenesis. © 2014 UICC.

  17. Incorporating organizational factors into Probabilistic Risk Assessment (PRA) of complex socio-technical systems: A hybrid technique formalization

    Energy Technology Data Exchange (ETDEWEB)

    Mohaghegh, Zahra [Center for Risk and Reliability, University of Maryland, College Park, MD 20742 (United States)], E-mail: mohagheg@umd.edu; Kazemi, Reza; Mosleh, Ali [Center for Risk and Reliability, University of Maryland, College Park, MD 20742 (United States)

    2009-05-15

    This paper is a result of a research with the primary purpose of extending Probabilistic Risk Assessment (PRA) modeling frameworks to include the effects of organizational factors as the deeper, more fundamental causes of accidents and incidents. There have been significant improvements in the sophistication of quantitative methods of safety and risk assessment, but the progress on techniques most suitable for organizational safety risk frameworks has been limited. The focus of this paper is on the choice of 'representational schemes' and 'techniques.' A methodology for selecting appropriate candidate techniques and their integration in the form of a 'hybrid' approach is proposed. Then an example is given through an integration of System Dynamics (SD), Bayesian Belief Network (BBN), Event Sequence Diagram (ESD), and Fault Tree (FT) in order to demonstrate the feasibility and value of hybrid techniques. The proposed hybrid approach integrates deterministic and probabilistic modeling perspectives, and provides a flexible risk management tool for complex socio-technical systems. An application of the hybrid technique is provided in the aviation safety domain, focusing on airline maintenance systems. The example demonstrates how the hybrid method can be used to analyze the dynamic effects of organizational factors on system risk.

  18. In Situ Hybridization of Pulp Fibers Using Mg-Al Layered Double Hydroxides

    Directory of Open Access Journals (Sweden)

    Carl-Erik Lange

    2015-04-01

    Full Text Available Inorganic Mg2+ and Al3+ containing layered double hydroxide (LDH particles were synthesised in situ from aqueous solution onto chemical pulp fibers of pine (Pinus sylvestris. High super saturated (hss solution with sodium carbonate produced LDH particles with an average diameter of 100–200 nm. Nano-size (70 nm LDH particles were found from fibers external surface and, to a lesser degree, from the S2 cell wall after synthesis via low super saturated (lss route. The synthesis via slow urea hydrolysis (Uhyd yielded micron and clay sized LDH (2–5 μm and enabled efficient fiber densification via mineralization of S2 fiber wall layer as indicated by TEM and compliance analysis. The Uhyd method decreased fiber compliance up to 50%. Reduction in the polymerisation degree of cellulose was observed with capillary viscometry. Thermogravimetric analysis showed that the hybridization with LDH reduced the exothermic heat, indicating, that this material can be incorporated in flame retardant applications. Fiber charge was assessed by Fibers 2015, 3 104 adsorption expermients with methylene blue (MB and metanil yellow (MY. Synthesis via lss route retained most of the fibres original charge and provided the highest capacity (10 μmol/g for anionic MY, indicating cationic character of hybrid fibers. Our results suggested that mineralized fibers can be potentially used in advanced applications such as biocomposites and adsorbent materials.

  19. Using the in situ lift-out technique to prepare TEM specimens on a single-beam FIB instrument

    International Nuclear Information System (INIS)

    Lekstrom, M; McLachlan, M A; Husain, S; McComb, D W; Shollock, B A

    2008-01-01

    Transmission electron microscope (TEM) specimens are today routinely prepared using focussed ion beam (FIB) instruments. Specifically, the lift-out method has become an increasingly popular technique and involves removing thin cross-sections from site-specific locations and transferring them to a TEM grid. This lift-out process can either be performed ex situ or in situ. The latter is mainly carried out on combined dual-beam FIB and scanning electron microscope (SEM) systems whereas conventional single-beam instruments often are limited to the traditional ex situ method. It is nevertheless desirable to enhance the capabilities of existing single-beam instruments to allow for in situ lift-out preparation to be performed since this technique offers a number of advantages over the older ex situ method. A single-beam FIB instrument was therefore modified to incorporate an in situ micromanipulator fitted with a tungsten needle, which can be attached to a cut-out FIB section using ion beam induced platinum deposition. This article addresses the issues of using an ion beam to monitor the in situ manipulation process as well as approaches that can be used to create stronger platinum welds between two objects, and finally, views on how to limit the extent of ion beam damage to the specimen surface.

  20. Visualization of mcr mRNA in a methanogen by fluorescence in situ hybridization with an oligonucleotide probe and two-pass tyramide signal amplification (two-pass TSA-FISH).

    Science.gov (United States)

    Kubota, Kengo; Ohashi, Akiyoshi; Imachi, Hiroyuki; Harada, Hideki

    2006-09-01

    Two-pass tyramide signal amplification-fluorescence in situ hybridization (two-pass TSA-FISH) with a horseradish peroxidase (HRP)-labeled oligonucleotide probe was applied to detect prokaryotic mRNA. In this study, mRNA of a key enzyme for methanogenesis, methyl coenzyme M reductase (mcr), in Methanococcus vannielii was targeted. Applicability of mRNA-targeted probes to in situ hybridization was verified by Clone-FISH. It was observed that sensitivity of two-pass TSA-FISH was significantly higher than that of TSA-FISH, which was further increased by the addition of dextran sulphate in TSA working solution. Signals from two-pass TSA-FISH were more reliable compared to the weak, spotty signals yielded by TSA-FISH.

  1. 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

  2. Automated processing of fluorescence in-situ hybridization slides for HER2 testing in breast and gastro-esophageal carcinomas.

    Science.gov (United States)

    Tafe, Laura J; Allen, Samantha F; Steinmetz, Heather B; Dokus, Betty A; Cook, Leanne J; Marotti, Jonathan D; Tsongalis, Gregory J

    2014-08-01

    HER2 fluorescence in-situ hybridization (FISH) is used in breast and gastro-esophageal carcinoma for determining HER2 gene amplification and patients' eligibility for HER2 targeted therapeutics. Traditional manual processing of the FISH slides is labor intensive because of multiple steps that require hands on manipulation of the slides and specifically timed intervals between steps. This highly manual processing also introduces inter-run and inter-operator variability that may affect the quality of the FISH result. Therefore, we sought to incorporate an automated processing instrument into our FISH workflow. Twenty-six cases including breast (20) and gastro-esophageal (6) cancer comprising 23 biopsies and three excision specimens were tested for HER2 FISH (Pathvysion, Abbott) using the Thermobrite Elite (TBE) system (Leica). Up to 12 slides can be run simultaneously. All cases were previously tested by the Pathvysion HER2 FISH assay with manual preparation. Twenty cells were counted by two observers for each case; five cases were tested on three separate runs by different operators to evaluate the precision and inter-operator variability. There was 100% concordance in the scoring between the manual and TBE methods as well as among the five cases that were tested on three runs. Only one case failed due to poor probe hybridization. In total, seven cases were positive for HER2 amplification (HER2:CEP17 ratio >2.2) and the remaining 19 were negative (HER2:CEP17 ratio <1.8) utilizing the 2007 ASCO/CAP scoring criteria. Due to the automated denaturation and hybridization, for each run, there was a reduction in labor of 3.5h which could then be dedicated to other lab functions. The TBE is a walk away pre- and post-hybridization system that automates FISH slide processing, improves work flow and consistency and saves approximately 3.5h of technologist time. The instrument has a small footprint thus occupying minimal counter space. TBE processed slides performed

  3. The ultrasonic technique for in situ investigations on stones: suggestions for uses

    Science.gov (United States)

    Bellopede, R.; Marini, P.

    2012-04-01

    The Ultrasound Pulse Velocity (UPV) is one of the main non destructive techniques to detect both in laboratory and in situ the stone decay and many international papers of the recent years deal with its application. This technique is often executed in laboratory, where the possibility to keep constant the environmental and test conditions are a guarantee of the reliability of the results. It is known in fact the UPV are mainly conditioned by the following factors: - the characteristics of the stone tested (not only petrographic properties such as texture and structure, but even specimen dimension and water content); - the transducers features such as frequency, divergence angle , near field and wavelength; - external climate factors such as environmental temperature, humidity. In spite of the many factors affecting the measurements, UPV performed in laboratory is well correlated with mechanical strength of the stone , with its porosity and, as consequence, it is a reliable technique to detect the durability of a stone. On the other side, for in situ UPV test it is important to take into account that the measurement uncertainty is affected by the unknown water content in the stone. From tests performed on different rocks (marble, limestones, travertines, granites, gneiss, schists , sandstones) , the ratios between UPV tested in dry and saturated conditions can be > 1 or stone in order to choose the suitable measurement frequency; the correct choice of transducers frequencies; the use of a reference slab, with a known UPV in dry conditions, to be exposed in the investigated site some days before the in situ tests, in order to appreciate the UPV variation due to climate factors.

  4. Combined amplification and hybridization techniques for genome scanning in vegetatively propagated crops

    International Nuclear Information System (INIS)

    Kahl, G.; Ramser, J.; Terauchi, R.; Lopez-Peralta, C.; Asemota, H.N.; Weising, K.

    1998-01-01

    A combination of PCR- and hybridization-based genome scanning techniques and sequence comparisons between non-coding chloroplast DNA flanking tRNA genes has been employed to screen Dioscorea species for intra- and interspecific genetic diversity. This methodology detected extensive polymorphisms within Dioscorea bulbifera L., and revealed taxonomic and phylogenetic relationships among cultivated Guinea yams varieties and their potential wild progenitors. Finally, screening of yam germplasm grown in Jamaica permitted reliable discrimination between all major cultivars. Genome scanning by micro satellite-primed PCR (MP-PCR) and random amplified polymorphic DNA (RAPD) analysis in combination with the novel random amplified micro satellite polymorphisms (RAMPO) hybridization technique has shown high potential for the genetic analysis of yams, and holds promise for other vegetatively propagated orphan crops. (author)

  5. Chromogenic in situ Hybridization Compared with Real time Quantitative Polymerase Chain Reaction to Evaluate HER2/neu Status in Breast Cancer.

    Science.gov (United States)

    Ayatollahi, Hossein; Fani, Azar; Ghayoor Karimiani, Ehsan; Homaee, Fateme; Shajiei, Arezoo; Sheikh, Maryam; Shakeri, Sepideh; Shams, Seyyede Fatemeh

    2017-01-01

    The assessment of human epidermal growth factor receptor 2 (HER2) status has become of great importance in the diagnosis of breast cancer. The aim of this study was to investigate the diagnostic value of quantitative Polymerase Chain Reaction (qPCR) and Chromogenic In Situ Hybridization (CISH) to assess HER2 status of biopsy specimens. To elucidate the status of HER2 gene amplification, biopsies of breast carcinoma from 120 patients with 2+ IHC status were analyzed by qPCR and CISH. The results of the two experiments were compared, and it was depicted that the concordance rate between CISH and qPCR assays was 88.1%.The quantification of HER2 gene with CISH and qPCR showed that there was a significant correlation (p value= 0.0001 and r= 0.808). The results of this research support the idea that qPCR is a precise and reproducible technique, which can be employed as a supplementary method to evaluate HER2 status.

  6. Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives.

    Science.gov (United States)

    Restrepo-Ortiz, C X; Merbt, S N; Barrero-Canossa, J; Fuchs, B M; Casamayor, E O

    2018-04-28

    The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N. devanaterra, as well as the non-target ammonia-oxidizing archaeon Nitrosopumilus maritimus. Probe specificity was improved with a competitor oligonucleotide, and fluorescence intensity and cell visualization were enhanced by the design and application of two adjacent helpers. Probe performance was tested in soil samples along a pH gradient, and counting results matched the expected in situ distributions. Probe SAG357 and the CARD-FISH protocol developed in the present study will help to improve the current understanding of the ecology and physiology of N. devanaterra and its relatives in natural environments. Copyright © 2018 Elsevier GmbH. All rights reserved.

  7. The effect of aging of formalin-fixed paraffin-embedded tissues on the in situ hybridization and immunohistochemistry signals in cervical lesions.

    Science.gov (United States)

    Nuovo, Allison J; Garofalo, Michela; Mikhail, Alexandria; Nicol, Alcina F; Vianna-Andrade, Cecilia; Nuovo, Gerard J

    2013-09-01

    Formalin-fixed, paraffin-embedded tissues are widely used in biomedical research but little is known about the effect of the age of the block or unstained slides on the in situ hybridization or immunohistochemistry signal. We compared the in situ-based and immunohistochemistry-based signals for cervical intraepithelial neoplasia samples that ranged from 0 to 15 years of age. There was a progressive and statistically significant decrease in the strength of the p16 signal when comparing tissues prepared from recent unstained slides (0 to 1 y old, mean score of 92%) to those of intermediate age (5 to 7 y old, mean score of 49%) to old unstained slides (cut 13 to 15 y ago, mean score of 10%). Equivalent, progressive, and significant decreases in the intensity of the signals for microRNAs, CD45, and human papillomavirus DNA were seen in tissues stored on slides from 5 to 7 years and 13 to 15 years, respectively. However, the diminution of signal was much less, although still statistically significant, if the sections from the 13- to 15-year-old paraffin blocks were prepared in 2012. The data likely does not represent degradation of the targets as extraction of several microRNA from the old blocks showed no detectable degradation, despite the markedly weakened in situ hybridization signal. It is concluded that in situ-based signal for DNA, microRNAs, and proteins in paraffin-embedded tissues are significantly reduced over time, especially when stored long term on glass slides which, in turn, can lead to a significant underestimation of the amount and presence of the nucleic acid or protein target.

  8. Outside-out "sniffer-patch" clamp technique for in situ measures of neurotransmitter release.

    Science.gov (United States)

    Muller-Chrétien, Emilie

    2014-01-01

    The mechanism underlying neurotransmitter release is a critical research domain for the understanding of neuronal network function; however, few techniques are available for the direct detection and measurement of neurotransmitter release. To date, the sniffer-patch clamp technique is mainly used to investigate these mechanisms from individual cultured cells. In this study, we propose to adapt the sniffer-patch clamp technique to in situ detection of neurosecretion. Using outside-out patches from donor cells as specific biosensors plunged in acute cerebral slices, this technique allows for proper detection and quantification of neurotransmitter release at the level of the neuronal network.

  9. Laser Based In Situ Techniques: Novel Methods for Generating Extreme Conditions in TEM Samples

    Energy Technology Data Exchange (ETDEWEB)

    Taheri, M; Lagrange, T; Reed, B; Armstrong, M; Campbell, G; DeHope, W; Kim, J; King, W; Masiel, D; Browning, N

    2008-02-25

    The Dynamic Transmission Electron Microscope (DTEM) is introduced as a novel tool for in situ processing of materials. Examples of various types of dynamic studies outline the advantages and differences of laser-based heating in the DTEM in comparison to conventional (resistive) heating in situ TEM methods. We demonstrate various unique capabilities of the drive laser, namely, in situ processing of nanoscale materials, rapid and high temperature phase transformations, and controlled thermal activation of materials. These experiments would otherwise be impossible without the use of the DTEM drive laser. Thus, the potential of the DTEM to as a new technique to process and characterize the growth of a myriad of micro and nanostructures is demonstrated.

  10. Identification of supernumerary ring chromosome 1 mosaicism using fluorescence in situ hybridization.

    Science.gov (United States)

    Chen, H; Tuck-Muller, C M; Batista, D A; Wertelecki, W

    1995-03-27

    We report on a 15-year-old black boy with severe mental retardation, multiple congenital anomalies, and a supernumerary ring chromosome mosaicism. Fluorescence in situ hybridization with a chromosome 1 painting probe (pBS1) identified the ring as derived from chromosome 1. The karyotype was 46,XY/47,XY,+r(1)(p13q23). A review showed 8 reports of ring chromosome 1. In 5 cases, the patients had a non-supernumerary ring chromosome 1 resulting in partial monosomies of the short and/or long arm of chromosome 1. In 3 cases, the presence of a supernumerary ring resulted in partial trisomy of different segments of chromosome 1. In one of these cases the supernumerary ring was composed primarily of the centromere and the heterochromatic region of chromosome 1, resulting in normal phenotype. Our patient represents the third report of a supernumerary ring chromosome 1 resulting in abnormal phenotype.

  11. Developing a hybrid dictionary-based bio-entity recognition technique

    Science.gov (United States)

    2015-01-01

    Background Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. Methods This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. Results The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. Conclusions The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall. PMID:26043907

  12. Developing a hybrid dictionary-based bio-entity recognition technique.

    Science.gov (United States)

    Song, Min; Yu, Hwanjo; Han, Wook-Shin

    2015-01-01

    Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall.

  13. Alternative technique to neutron probe calibration in situ

    International Nuclear Information System (INIS)

    Encarnacao, F.; Carneiro, C.; Dall'Olio, A.

    1990-01-01

    An alternative technique of neutron probe calibration in situ was applied for Podzolic soil. Under field condition, the neutron probe calibration was performed using a special arrangement that prevented the lateral movement of water around the access tube of the neutron probe. During the experiments, successive amounts of water were uniformly infiltrated through the soil profile. Two plots were set to study the effect of the plot dimension on the slope of the calibration curve. The results obtained shown that the amounts of water transferred to the soil profile were significantly correlated to the integrals of count ratio along the soil profile on both plots. In consequence, the slope of calibration curve in field condition was determined. (author)

  14. Assignment of Alzheimer's presenilin-2 (PS-2) gene to 1q42.1 by fluorescence in situ hybridization.

    Science.gov (United States)

    Takano, T; Sahara, N; Yamanouchi, Y; Mori, H

    1997-01-17

    Presenilin-2 (PS-2) was suggested to be localized on 1q31-42 based on linkage analysis and cDNA cloning. The final identification of PS-2 as the causal gene for early-onset familial Alzheimer's disease in Voga-German pedigrees was concluded based on the point mutation found in the candidate cDNA isolated from this familial AD. We present evidence of its physical genome mapping of PS-2 on chromosome 1q42.1 by fluorescence in situ hybridization method.

  15. Combined amplification and hybridization techniques for genome scanning in vegetatively propagated crops

    Energy Technology Data Exchange (ETDEWEB)

    Kahl, G; Ramser, J; Terauchi, R [Biocentre, University of Frankfurt, Frankfurt am Main (Germany); Lopez-Peralta, C [IRGP, Colegio de Postgraduados, Montecillo, Edo. de Mexico, Texcoco (Mexico); Asemota, H N [Biotechnology Centre, University of the West Indies, Mona, Kingston (Jamaica); Weising, K [School of Biological Sciences, University of Auckland, Auckland (New Zealand)

    1998-10-01

    A combination of PCR- and hybridization-based genome scanning techniques and sequence comparisons between non-coding chloroplast DNA flanking tRNA genes has been employed to screen Dioscorea species for intra- and interspecific genetic diversity. This methodology detected extensive polymorphisms within Dioscorea bulbifera L., and revealed taxonomic and phylogenetic relationships among cultivated Guinea yams varieties and their potential wild progenitors. Finally, screening of yam germplasm grown in Jamaica permitted reliable discrimination between all major cultivars. Genome scanning by micro satellite-primed PCR (MP-PCR) and random amplified polymorphic DNA (RAPD) analysis in combination with the novel random amplified micro satellite polymorphisms (RAMPO) hybridization technique has shown high potential for the genetic analysis of yams, and holds promise for other vegetatively propagated orphan crops. (author) 46 refs, 3 figs, 3 tabs

  16. Detection of chromosomal aberrations by fluorescence in situ hybridization in the first three postirradiation divisions of human lymphocytes

    International Nuclear Information System (INIS)

    Boei, J.J.W.A.; Vermeulen, S.; Natarajan, A.T.

    1996-01-01

    Chromosomal aberrations in human lymphocytes were analyzed by fluorescence in situ hybridization (FISH) in the first 3 postirradiation (0 and 2 Gy) divisions. Cells were grown in the presence of BrdU, collected at different sampling times (47, 70 and 91 h) and analyzed using an alphoid centromeric probe and PCR amplified DNA libraries for chromosomes 2 and 8. Following differential staining of sister chromatids, the analyzed cells were identified to be either in the first, second or third mitosis after irradiation. The frequencies of both dicentrics and fragments showed a reduction of about 50% after each cell generation, whereas translocations were more persistent. Cells within the same postirradiation division showed higher aberration frequencies when derived from later sampling times, indicating a delay in progression of aberrant cells. As a result, the frequencies for dicentrics and fragments remained rather constant at different sampling times if the cell cycle parameter was not taken into account. Thus, the average generation time of the lymphocytes had a clear effect on the obtained aberration frequencies. The described method allows the study of the persistence of chromosome damage using the FISH technique during 3 subsequent cell divisions in vitro

  17. Improved Image Encryption for Real-Time Application over Wireless Communication Networks using Hybrid Cryptography Technique

    Directory of Open Access Journals (Sweden)

    Kazeem B. Adedeji

    2016-12-01

    Full Text Available Advances in communication networks have enabled organization to send confidential data such as digital images over wireless networks. However, the broadcast nature of wireless communication channel has made it vulnerable to attack from eavesdroppers. We have developed a hybrid cryptography technique, and we present its application to digital images as a means of improving the security of digital image for transmission over wireless communication networks. The hybrid technique uses a combination of a symmetric (Data Encryption Standard and asymmetric (Rivest Shamir Adleman cryptographic algorithms to secure data to be transmitted between different nodes of a wireless network. Three different image samples of type jpeg, png and jpg were tested using this technique. The results obtained showed that the hybrid system encrypt the images with minimal simulation time, and high throughput. More importantly, there is no relation or information between the original images and their encrypted form, according to Shannon’s definition of perfect security, thereby making the system much more secure.

  18. Synthetic Strategies in the Preparation of Polymer/Inorganic Hybrid Nanoparticles

    Science.gov (United States)

    Hood, Matthew A.; Mari, Margherita; Muñoz-Espí, Rafael

    2014-01-01

    This article reviews the recent advances and challenges in the preparation of polymer/inorganic hybrid nanoparticles. We mainly focus on synthetic strategies, basing our classification on whether the inorganic and the polymer components have been formed in situ or ex situ, of the hybrid material. Accordingly, four types of strategies are identified and described, referring to recent examples: (i) ex situ formation of the components and subsequent attachment or integration, either by covalent or noncovalent bonding; (ii) in situ polymerization in the presence of ex situ formed inorganic nanoparticles; (iii) in situ precipitation of the inorganic components on or in polymer structures; and (iv) strategies in which both polymer and inorganic component are simultaneously formed in situ. PMID:28788665

  19. Safety Assessment of Two Hybrid Instrumentation Techniques in a Dental Student Endodontic Clinic: A Retrospective Study.

    Science.gov (United States)

    Coelho, Marcelo Santos; Card, Steven John; Tawil, Peter Zahi

    2017-03-01

    The aim of this study was to retrospectively assess the safety potential of a hybrid technique combining nickel-titanium (NiTi) reciprocating and rotary instruments by third- and fourth-year dental students in the predoctoral endodontics clinic at one U.S. dental school. For the study, 3,194 root canal treatments performed by 317 dental students from 2012 through 2015 were evaluated for incidence of ledge creation and instrument separation. The hybrid reciprocating and rotary technique (RRT) consisted of a glide path creation with stainless steel hand files up to size 15/02, a crown down preparation with a NiTi reciprocating instrument, and an apical preparation with NiTi rotary instruments. The control was a traditional rotary and hand technique (RHT) that consisted of the same glide path procedure followed by a crown down preparation with NiTi rotary instruments and an apical preparation with NiTi hand instruments. The results showed that the RHT technique presented a rate of ledge creation of 1.4% per root and the RRT technique was 0.5% per root (protary technique for root canal instrumentation by these dental students provided good safety. This hybrid technique offered a low rate of ledge creation along with no NiTi instrument separation.

  20. Novel Hybrid Scheduling Technique for Sensor Nodes with Mixed Criticality Tasks

    Directory of Open Access Journals (Sweden)

    Mihai-Victor Micea

    2017-06-01

    Full Text Available Sensor networks become increasingly a key technology for complex control applications. Their potential use in safety- and time-critical domains has raised the need for task scheduling mechanisms specially adapted to sensor node specific requirements, often materialized in predictable jitter-less execution of tasks characterized by different criticality levels. This paper offers an efficient scheduling solution, named Hybrid Hard Real-Time Scheduling (H2RTS, which combines a static, clock driven method with a dynamic, event driven scheduling technique, in order to provide high execution predictability, while keeping a high node Central Processing Unit (CPU utilization factor. From the detailed, integrated schedulability analysis of the H2RTS, a set of sufficiency tests are introduced and demonstrated based on the processor demand and linear upper bound metrics. The performance and correct behavior of the proposed hybrid scheduling technique have been extensively evaluated and validated both on a simulator and on a sensor mote equipped with ARM7 microcontroller.

  1. Novel Hybrid Scheduling Technique for Sensor Nodes with Mixed Criticality Tasks.

    Science.gov (United States)

    Micea, Mihai-Victor; Stangaciu, Cristina-Sorina; Stangaciu, Valentin; Curiac, Daniel-Ioan

    2017-06-26

    Sensor networks become increasingly a key technology for complex control applications. Their potential use in safety- and time-critical domains has raised the need for task scheduling mechanisms specially adapted to sensor node specific requirements, often materialized in predictable jitter-less execution of tasks characterized by different criticality levels. This paper offers an efficient scheduling solution, named Hybrid Hard Real-Time Scheduling (H²RTS), which combines a static, clock driven method with a dynamic, event driven scheduling technique, in order to provide high execution predictability, while keeping a high node Central Processing Unit (CPU) utilization factor. From the detailed, integrated schedulability analysis of the H²RTS, a set of sufficiency tests are introduced and demonstrated based on the processor demand and linear upper bound metrics. The performance and correct behavior of the proposed hybrid scheduling technique have been extensively evaluated and validated both on a simulator and on a sensor mote equipped with ARM7 microcontroller.

  2. Lithographically fabricated silicon microreactor for in situ characterization of heterogeneous catalysts—Enabling correlative characterization techniques

    Energy Technology Data Exchange (ETDEWEB)

    Baier, S.; Rochet, A.; Hofmann, G. [Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, D-76131 Karlsruhe (Germany); Kraut, M. [Institute for Micro Process Engineering, Karlsruhe Institute of Technology, D-76344 Eggenstein-Leopoldshafen (Germany); Grunwaldt, J.-D., E-mail: grunwaldt@kit.edu [Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, D-76131 Karlsruhe (Germany); Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, D-76344 Eggenstein-Leopoldshafen (Germany)

    2015-06-15

    We report on a new modular setup on a silicon-based microreactor designed for correlative spectroscopic, scattering, and analytic on-line gas investigations for in situ studies of heterogeneous catalysts. The silicon microreactor allows a combination of synchrotron radiation based techniques (e.g., X-ray diffraction and X-ray absorption spectroscopy) as well as infrared thermography and Raman spectroscopy. Catalytic performance can be determined simultaneously by on-line product analysis using mass spectrometry. We present the design of the reactor, the experimental setup, and as a first example for an in situ study, the catalytic partial oxidation of methane showing the applicability of this reactor for in situ studies.

  3. Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)

    DEFF Research Database (Denmark)

    Ronander, Elena; Bengtsson, Dominique C; Joergensen, Louise

    2012-01-01

    Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 protein variants encoded by the var genes. The haploid P. falciparum genome harbors approximately 60 different var genes of which only one has...... been believed to be transcribed per cell at a time during the blood stage of the infection. How such mutually exclusive regulation of var gene transcription is achieved is unclear, as is the identification of individual var genes or sub-groups of var genes associated with different receptors...... fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE(1). Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human...

  4. Fluorescence in situ hybridization detection of cytogenetic abnormalities and prognosis in multiple myeloma

    Directory of Open Access Journals (Sweden)

    Zhou Xu

    2015-01-01

    Full Text Available We evaluated the prognosis of patients with newly diagnosed multiple myeloma (MM and attempted to find a suitable treatment strategy for them. Interphase fluorescence in situ hybridization (FISH detection was performed on 57 patients with MM. The following probes: IgH, p53, 1q21, RB1, and D13S319 specific for the rearrangements of 14q32, 17p13, 1q21 and 13q14 were used. Fluorescent hybridization signals were observed using an Olympus BX60 epifluorescence microscope equipped with filters for detecting fluoroisothiocyanate (FITC, Texas red, and 4'-6-Diamidino-2-phenylindole (DAPI. Triple color clone-specific images were captured using a Quips XL genetic workstation. The mortalities in patients with moderate prognosis (66.7% and poor prognosis (50% were significantly higher compared with that in patients with good prognosis (15%, P<0.05. All the patients in good and moderate prognosis groups achieved complete remission (CR/very good partial remission (VGPR/partial remission (PR, whereas only half of the cases in the poor prognosis group reached this level. Patients 2 supported by autologous hematopoietic stem-cell transplantation presented CR/PR and long survival. For those with poor prognosis, a proper therapeutic regimen and timely transplantation, especially tandem transplantation, was necessary due to the rapid progression and complications.

  5. Correlation and comparison of immunohistochemistry for HER2/neu, using the antibody SP3 and chromogenic in situ hybridization in breast carcinomas samples

    Directory of Open Access Journals (Sweden)

    Franciele F. Wolf

    2015-12-01

    Full Text Available ABSTRACT Introduction: Advances in the field of molecular biology have provided the differentiation of molecular subtypes of breast tumors, providing better prognosis and important tools for the treatment of patients with breast cancer. Among these subtypes, the changes in the human epidermal growth factor receptor 2 gene (HER2/neu, increase its copy number and generating HER2 protein amplification. Studies show that patients with breast cancer HER2/neu amplified tend to relapse earlier and have shorter survival time, the monoclonal antibody Trastuzumab is the therapy indicated. The eligibility of patients for therapy is initially made by the immunohistochemistry (IHC technique, which evaluates the expression level of the HER2 protein. After this evaluation, the cases with equivocal diagnosis (score 2+, are referred to a more accurate technique, the chromogenic in situ hybridization (CISH. Objective: To analyze the sensitivity and specificity of the antibody SP3, and determine their level of agreement with the CISH technique. Material and methods: Retrospective study in the database of the anatomy-pathology laboratory, in CISH tests reports for HER2/neu. Conclusion: The results revealed that clone SP3 showed 100% specificity and 92% sensitivity. IHC reveals variability in its results; however, it is known that the technique is an important tool in the daily routine of laboratories, contributing to the initial screening of patients with breast cancer, which later showed satisfactory results when compared with the CISH technique.

  6. Detection of Bacteria by Fluorescence in Situ Hybridization in Culture-Negative Soft Tissue Filler Lesions

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

    2009-01-01

    BACKGROUND Adverse reactions to polyacrylamide gel occur as swellings or nodules, and controversy exists whether these are due to bacterial infection or an autoimmune reaction to the filler. OBJECTIVES Biopsies from culture-negative long-lasting nodules after injection with different types...... of polyacrylamide gel were examined with a combination of Gram stain and fluorescence in situ hybridization. RESULTS Bacteria were detected in biopsies from seven of eight patients. They inhabited gel and intervening tissue and tended to lie in aggregates. CONCLUSION This study supports the assumption...... that infection with bacteria in aggregates causes culture-negative late adverse reactions to polyacrylamide gel, suggesting a biofilm environment. The authors have indicated no significant interest with commercial supporters....

  7. Detection of MYCN Gene Amplification in Neuroblastoma by Fluorescence In Situ Hybridization: A Pediatric Oncology Group Study

    Directory of Open Access Journals (Sweden)

    Prasad Mathew

    2001-01-01

    Full Text Available To assess the utility of fluorescence in situ hybridization (FISH for analysis of MYCN gene amplification in neuroblastoma, we compared this assay with Southern blot analysis using tumor specimens collected from 232 patients with presenting characteristics typical of this disease. The FISH technique identified MYCN amplification in 47 cases, compared with 39 by Southern blotting, thus increasing the total number of positive cases by 21%. The major cause of discordancy was a low fraction of tumor cells (≤30% replacement in clinical specimens, which prevented an accurate estimate of MYCN copy number by Southern blotting. With FISH, by contrast, it was possible to analyze multiple interphase nuclei of tumor cells, regardless of the proportion of normal peripheral blood, bone marrow, or stromal cells in clinical samples. Thus, FISH could be performed accurately with very small numbers of tumor cells from touch preparations of needle biopsies. Moreover, this procedure allowed us to discern the heterogeneous pattern of MYCN amplification that is characteristic of neuroblastoma. We conclude that FISH improves the detection of MYCN gene amplification in childhood neuroblastomas in a clinical setting, thus facilitating therapeutic decisions based on the presence or absence of this prognostically important biologic marker.

  8. Incorporation of nano-clay saponite layers in the organo-clay hybrid films using anionic amphiphile stearic acid by Langmuir–Blodgett technique

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Syed Arshad, E-mail: sa_h153@hotmail.com [Department of Physics, Tripura University, Suryamaninagar-799022 (India); Chakraborty, S.; Bhattacharjee, D. [Department of Physics, Tripura University, Suryamaninagar-799022 (India); Schoonheydt, R.A. [Centres for Surface Chemistry and Catalysis, K.U. Leuven, Kasteelpark Arenberg 23, 3001 Leuven (Belgium)

    2013-06-01

    In general cationic amphiphiles are used to prepare organo-clay hybrid film in Langmuir–Blodgett (LB) technique. In this present communication we demonstrated a unique technique to prepare the organo–clay hybrid films using an anionic amphiphile. The T–O–T type clay saponite was incorporated onto a floating stearic acid monolayer via a divalent cation Mg{sup 2+}. Salt MgCl{sub 2} was mixed along with the clay dispersion in the LB trough and amphiphile solution was spread onto the subphase in order to make the organo-clay hybrid films. It was observed that salt (MgCl{sub 2}) concentration on the subphase affects the organization of nano-dimensional clay platelet (saponite) in organo-clay hybrid films at air–water interface as well as in LB films. Noticeable changes in area per molecule and shape of the isotherms were observed and measured at subphases with different salt concentrations. Infrared reflection absorption spectroscopy studies reveal that only an in-plane (996 cm{sup −1}) vibration of ν (Si-O) band occurred when the salt concentration was 10 mM. However, both in-plane (996 cm{sup −1}) and out-of-plane (1063 cm{sup −1}) vibrations of the ν (Si-O) band of saponite occurred when the subphase salt concentration was 100 mM. Also the out-of-plane vibration of ν (OH) of saponite was prominent at higher salt concentration. This is because at lower salt concentration clay sheets remain flat on the surface whereas; at higher MgCl{sub 2} concentration they aggregated and form stacks of saponite layers. Also they may be slightly tilted with a very small tilt angle at higher salt concentration making a favorable condition for both in-plane and out-of-plane vibrations of ν (Si-O) in the hybrid films. Observed decrease in starting area per molecule in the pressure area isotherm measured at higher salt concentration also supports the tilting of clay layers at air–clay dispersion interface. Attentuated total reflectance Fourier transform infrared

  9. PRINS and in situ PCR protocols

    National Research Council Canada - National Science Library

    Gosden, John R

    1997-01-01

    ... mapping of DNA sequences on chromosomes and location of gene expression followed the invention and refinement of in situ hybridization. Among the most recent technical developments has been the use of oligonucleotide primers to detect and amplify or extend complementary sequences in situ, and it is to this novel field that PRINS and In S...

  10. 5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH

    Directory of Open Access Journals (Sweden)

    Jaime Gosálvez

    2013-02-01

    Full Text Available We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH. A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL, 10 with high-grade SIL (HG-SIL, and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.

  11. 5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH).

    Science.gov (United States)

    Cortés-Gutiérrez, Elva I; Ortíz-Hernández, Brenda L; Dávila-Rodríguez, Martha I; Cerda-Flores, Ricardo M; Fernández, José Luis; López-Fernández, Carmen; Gosálvez, Jaime

    2013-02-19

    We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH). A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL), 10 with high-grade SIL (HG-SIL), and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.

  12. Development of in situ two-coil mutual inductance technique in a multifunctional scanning tunneling microscope.

    Science.gov (United States)

    Duan, Ming-Chao; Liu, Zhi-Long; Ge, Jian-Feng; Tang, Zhi-Jun; Wang, Guan-Yong; Wang, Zi-Xin; Guan, Dandan; Li, Yao-Yi; Qian, Dong; Liu, Canhua; Jia, Jin-Feng

    2017-07-01

    Superconducting thin films have been a focal point for intensive research efforts since their reduced dimension allows for a wide variety of quantum phenomena. Many of these films, fabricated in UHV chambers, are highly vulnerable to air exposure, making it difficult to measure intrinsic superconducting properties such as zero resistance and perfect diamagnetism with ex situ experimental techniques. Previously, we developed a multifunctional scanning tunneling microscope (MSTM) containing in situ four-point probe (4PP) electrical transport measurement capability in addition to the usual STM capabilities [Ge et al., Rev. Sci. Instrum. 86, 053903 (2015)]. Here we improve this MSTM via development of both transmission and reflection two-coil mutual inductance techniques for in situ measurement of the diamagnetic response of a superconductor. This addition does not alter the original STM and 4PP functions of the MSTM. We demonstrate the performance of the two-coil mutual inductance setup on a 10-nm-thick NbN thin film grown on a Nb-doped SrTiO 3 (111) substrate.

  13. Evaluation of HER2 gene amplification in invasive breast cancer using a dual-color chromogenic in situ hybridization (dual CISH).

    Science.gov (United States)

    Kato, Nobuaki; Itoh, Hitoshi; Serizawa, Akihiko; Hatanaka, Yutaka; Umemura, Shinobu; Osamura, R Yoshiyuki

    2010-07-01

    Fluorescence in situ hybridization (FISH) assay is considered the 'gold standard' for evaluation of HER2/neu (HER2) gene status, however, it is difficult to recognize morphologic features of tumors using fluorescence microscopy. Thus, chromogenic in situ hybridization (CISH) has been proposed as an alternative method to evaluate HER2 gene amplification. Here, we examined the dual color CISH (dual CISH) method which provides information regarding the copy number of the HER2 gene and chromosome 17 centromere from a single slide. We examined 40 cases of invasive ductal carcinomas of the breast that were resected surgically. HER2 gene status was assessed with FISH (Abbott) and dual CISH (Dako). HER2 gene amplification status was classified according to the guidelines of the American Society of Clinical Oncology and College of American Pathologists (ASCO/CAP). Comparison of the cut-off values for HER2/chromosome 17 centromere copy number ratio obtained by dual CISH and FISH showed that there was almost perfect agreement between two methods (Kappa coefficient 0.96). The results of the two commercial products were almost consistent for evaluation of HER2 gene counts on the sections. The current study proved that dual CISH is comparable with FISH for evaluating HER2 gene status.

  14. Subcellular localization of low-abundance human immunodeficiency virus nucleic acid sequences visualized by fluorescence in situ hybridization

    International Nuclear Information System (INIS)

    Lawrence, J.B.; Marselle, L.M.; Byron, K.S.; Johnson, C.V.; Sullivan, J.L.; Singer, R.H.

    1990-01-01

    Detection and subcellular localization of human immunodeficiency virus (HIV) were investigated using sensitive high-resolution in situ hybridization methodology. Lymphocytes infected with HIV in vitro or in vivo were detected by fluorescence after hybridization with either biotin or digoxigenin-labeled probes. At 12 hr after infection in vitro, a single intense signal appeared in the nuclei of individual cells. Later in infection, when cytoplasmic fluorescence became intense, multiple nuclear foci frequently appeared. The nuclear focus consisted of newly synthesized HIV RNA as shown by hybridization in the absence of denaturation and by susceptibility to RNase and actinomycin D. Virus was detected in patient lymphocytes and it was shown that a singular nuclear focus also characterizes cells infected in vivo. The cell line 8E5/LAV containing one defective integrated provirus revealed a similar focus of nuclear RNA, and the single integrated HIV genome was unequivocally visualized on a D-group chromosome. This demonstrates an extremely sensitive single-cell assay for the presence of a single site of HIV transcription in vitro and in vivo and suggests that it derives from one (or very few) viral genomes per cell. In contrast, productive Epstein-Barr virus infection exhibited many foci of nuclear RNA per cell

  15. Development of a hybrid strength training technique for paretic lower-limb muscles

    NARCIS (Netherlands)

    Bennett, T. L.; Glaser, R. M.; Janssen, T. W J; Couch, W. P.; Herr, C. J.; Almeyda, J. W.; Petrofsky, S. H.; Akuthota, P.

    1996-01-01

    A hybrid resistance exercise technique for strength training of patients with lower-limb paresis was developed. It consists of electrical stimulation-induced contractions (ESIC) superimposed on voluntary contractions to increase recruitment of motor units and the functional load capability of

  16. Supersonic impinging jet noise reduction using a hybrid control technique

    Science.gov (United States)

    Wiley, Alex; Kumar, Rajan

    2015-07-01

    Control of the highly resonant flowfield associated with supersonic impinging jet has been experimentally investigated. Measurements were made in the supersonic impinging jet facility at the Florida State University for a Mach 1.5 ideally expanded jet. Measurements included unsteady pressures on a surface plate near the nozzle exit, acoustics in the nearfield and beneath the impingement plane, and velocity field using particle image velocimetry. Both passive control using porous surface and active control with high momentum microjet injection are effective in reducing nearfield noise and flow unsteadiness over a range of geometrical parameters; however, the type of noise reduction achieved by the two techniques is different. The passive control reduces broadband noise whereas microjet injection attenuates high amplitude impinging tones. The hybrid control, a combination of two control methods, reduces both broadband and high amplitude impinging tones and surprisingly its effectiveness is more that the additive effect of the two control techniques. The flow field measurements show that with hybrid control the impinging jet is stabilized and the turbulence quantities such as streamwise turbulence intensity, transverse turbulence intensity and turbulent shear stress are significantly reduced.

  17. Nuclear techniques for in situ evaluation of coal and mineral deposits

    International Nuclear Information System (INIS)

    Borsaru, M.

    1993-01-01

    This paper reviews developments in in situ analysis of minerals and coal by nuclear borehole logging. Developments in the oil, gas and uranium industries are not discussed in the present paper unless they have direct applications in the mineral industry (e.g. multi-element analysis and development of spectral litho-density tools). The review covers techniques developed mostly in the last decade and is based on work published in North America, Europe and Australia. (author)

  18. Distribution and evolution of repeated sequences in genomes of Triatominae (Hemiptera-Reduviidae inferred from genomic in situ hybridization.

    Directory of Open Access Journals (Sweden)

    Sebastian Pita

    Full Text Available The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily.

  19. Electron microscopic in situ hybridization and autoradiography: Localization and transcription of rDNA in human lymphocyte nucleoli

    International Nuclear Information System (INIS)

    Wachtler, F.; Mosgoeller, W.S.; Schwarzacher, H.G.

    1990-01-01

    The distribution of ribosomal DNA (rDNA) in the nucleoli of human lymphocytes was revealed by in situ hybridization with a nonautoradiographic procedure at the electron microscopic level. rDNA is located in the dense fibrillar component of the nucleolus but not in the fibrillar centers. In the same cells the incorporation of tritiated uridine takes place in the dense fibrillar component of the nucleolus as seen by autoradiography followed by gold latensification. From these findings it can be concluded that the transcription of ribosomal DNA takes place in the dense fibrillar component of the nucleolus

  20. In situ hybridization of iodinated 5S and 18/25S RNA to Vicia faba metaphase chromosomes

    International Nuclear Information System (INIS)

    Schubert, I.; Baeumlein, H.; Wobus, U.

    1978-01-01

    In vitro labelled 125 I ribosomal RNA fractions (18/25S and 5S) were in situ hybridized to metaphase chromosomes of a reconstructed karyotype of Vicia faba (characterized by two translocations and one pericentric inversion, each being present homozygously). The sites of 18S and 25S RNA were found to be confined to the nucleolus organizing secondary constriction. Two loci of 5S RNA were recognized on the satellite of nucleolus bearing chromosome. Possible correlations between the location of ribosomal genes, heterochromatic G-bands and clusters of mutagen induced chromatid aberrations are discussed. (author)

  1. Review of in situ derivatization techniques for enhanced bioanalysis using liquid chromatography with mass spectrometry.

    Science.gov (United States)

    Baghdady, Yehia Z; Schug, Kevin A

    2016-01-01

    Accurate and specific analysis of target molecules in complex biological matrices remains a significant challenge, especially when ultra-trace detection limits are required. Liquid chromatography with mass spectrometry is often the method of choice for bioanalysis. Conventional sample preparation and clean-up methods prior to the analysis of biological fluids such as liquid-liquid extraction, solid-phase extraction, or protein precipitation are time-consuming, tedious, and can negatively affect target recovery and detection sensitivity. An alternative or complementary strategy is the use of an off-line or on-line in situ derivatization technique. In situ derivatization can be incorporated to directly derivatize target analytes in their native biological matrices, without any prior sample clean-up methods, to substitute or even enhance the extraction and preconcentration efficiency of these traditional sample preparation methods. Designed appropriately, it can reduce the number of sample preparation steps necessary prior to analysis. Moreover, in situ derivatization can be used to enhance the performance of the developed liquid chromatography with mass spectrometry-based bioanalysis methods regarding stability, chromatographic separation, selectivity, and ionization efficiency. This review presents an overview of the commonly used in situ derivatization techniques coupled to liquid chromatography with mass spectrometry-based bioanalysis to guide and to stimulate future research. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Small supernumerary marker chromosome derived from proximal p-arm of chromosome 2: identification by fluorescent in situ hybridization.

    Science.gov (United States)

    Lasan Trcić, Ruzica; Hitrec, Vlasta; Letica, Ljiljana; Cuk, Mario; Begović, Davor

    2003-08-01

    Conventional cytogenetics detected an interstitial deletion of proximal region of p-arm of chromosome 2 in a 6-month-old boy with a phenotype slightly resembling Down's syndrome. The deletion was inherited from the father, whose karyotype revealed a small ring-shaped marker chromosome, in addition to interstitial deletion. Fluorescence in situ hybridization identified the marker, which consisted of the proximal region of the p-arm of chromosome 2, including a part of its centromere. This case shows that molecular cytogenetic analysis can reveal the mechanism of the formation of the marker chromosome.

  3. Association of Serpulina hyodysenteriae with the colonic mucosa in experimental swine dysentery studied by fluorescent in situ hybridization

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Boye, Mette; Møller, Kristian

    1998-01-01

    The localization of Serpulina hyodysenteriae in experimental swine dysentery was studied by fluorescent in situ hybridization (FISH) using an oligonucleotide probe targeting the 23S rRNA of S. hyodysenteriae. Nine 8-week-old pigs were challenged. Seven of the pigs were intragastrically dosed with 1......x10(9) cfu S. hyodysenteriae for 3 consecutive days, whereas two pigs were infected by contact. Six non-challenged pigs served as negative controls. The challenged pigs developed clinical swine dysentery from 8 to 14 days postinfection with typical gross lesions. By FISH S. hyodysenteriae cells...

  4. Luminescent hybrid lanthanide sulfates and lanthanide sulfonate-carboxylates with 1,10-phenanthroline involving in-situ oxidation of 2-mercaptonbenzoic acid

    International Nuclear Information System (INIS)

    Zhong, Jie-Cen; Wan, Fang; Sun, Yan-Qiong; Chen, Yi-Ping

    2015-01-01

    A series of lanthanide sulfates and lanthanide sulfonate-carboxylates, [Ln 2 (phen) 2 (SO 4 ) 3 (H 2 O) 2 ] n (I:Ln=Nd(1a), Sm(1b), Eu(1c), phen=1,10-phenanthroline) and [Ln(phen)(2-SBA)(BZA)] n (II: Ln=Sm(2a), Eu(2b), Dy(2c), 2-SBA=2-sulfobenzoate, BZA=benzoate) have been hydrothermally synthesized from lanthanide oxide, 2-mercaptonbenzoic acid with phen as auxiliary ligand and characterized by single-crystal X-ray diffraction, elemental analyses, IR spectra, TG analyses and luminescence spectroscopy. Interestingly, SO 4 2− anions in I came from the in situ deep oxidation of thiol groups of 2-mercaptonbenzoic acid while 2-sulfobenzoate and benzoate ligands in II from the middle oxidation and desulfuration reactions of 2-mercaptonbenzoic acid. Compounds I are organic–inorganic hybrid lanthanide sulfates, which have rare one-dimensional column-like structures. Complexes II are binuclear lanthanide sulfonate-carboxylates with 2-sulfobenzoate and benzoate as bridges and 1,10-phenanthroline as terminal. Photoluminescence studies reveal that complexes I and II exhibit strong lanthanide characteristic emission bands in the solid state at room temperature. - Graphical abstract: Lanthanide sulfates and lanthanide sulfonate-carboxylates have been hydrothermally synthesized. Interestingly, sulfate anions, 2-sulfobenzoate and benzoate ligands came from the in situ oxidation and desulfuration reactions of 2-mercaptonbenzoic acid. - Highlights: • In situ oxidation and desulfuration reactions of 2-mercaptonbenzoic acid. • The organic–inorganic hybrid lanthanide sulfates with one-dimensional column-like structure. • The dinuclear lanthanide sulfonate-carboxylates. • The emission spectra exhibit the characteristic transition of 5 D 0 → 7 F J (J=0–4) of the Eu(III)

  5. Standardization and optimization of fluorescence in situ hybridization (FISH) for HER-2 assessment in breast cancer: A single center experience.

    Science.gov (United States)

    Bogdanovska-Todorovska, Magdalena; Petrushevska, Gordana; Janevska, Vesna; Spasevska, Liljana; Kostadinova-Kunovska, Slavica

    2018-05-20

    Accurate assessment of human epidermal growth factor receptor 2 (HER-2) is crucial in selecting patients for targeted therapy. Commonly used methods for HER-2 testing are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Here we presented the implementation, optimization and standardization of two FISH protocols using breast cancer samples and assessed the impact of pre-analytical and analytical factors on HER-2 testing. Formalin fixed paraffin embedded (FFPE) tissue samples from 70 breast cancer patients were tested for HER-2 using PathVysion™ HER-2 DNA Probe Kit and two different paraffin pretreatment kits, Vysis/Abbott Paraffin Pretreatment Reagent Kit (40 samples) and DAKO Histology FISH Accessory Kit (30 samples). The concordance between FISH and IHC results was determined. Pre-analytical and analytical factors (i.e., fixation, baking, digestion, and post-hybridization washing) affected the efficiency and quality of hybridization. The overall hybridization success in our study was 98.6% (69/70); the failure rate was 1.4%. The DAKO pretreatment kit was more time-efficient and resulted in more uniform signals that were easier to interpret, compared to the Vysis/Abbott kit. The overall concordance between IHC and FISH was 84.06%, kappa coefficient 0.5976 (p characteristics. Differences in the pre-analytical and analytical steps can affect the hybridization quality and efficiency. The use of DAKO pretreatment kit is time-saving and cost-effective.

  6. A New Technique for Deep in situ Measurements of the Soil Water Retention Behaviour

    DEFF Research Database (Denmark)

    Rocchi, Irene; Gragnano, Carmine Gerardo; Govoni, Laura

    2018-01-01

    In situ measurements of soil suction and water content in deep soil layers still represent an experimental challenge. Mostly developed within agriculture related disciplines, field techniques for the identification of soil retention behaviour have been so far employed in the geotechnical context ...

  7. Detection and quantification of Epstein-Barr virus EBER1 in EBV-infected cells by fluorescent in situ hybridization and flow cytometry

    Science.gov (United States)

    Stowe, R. P.; Cubbage, M. L.; Sams, C. F.; Pierson, D. L.; Barrett, A. D.

    1998-01-01

    A rapid and highly sensitive fluorescent in situ hybridization (FISH) assay was developed to detect Epstein Barr virus (EBV)-infected cells in peripheral blood. Multiple fluorescein-labeled antisense oligonucleotide probes were designed to hybridize to the EBER1 transcript, which is highly expressed in latently infected cells. After a rapid (30 min) hybridization, the cells were analyzed by flow cytometry. EBER1 was detected in several positive control cell lines that have variable numbers of EBV genome copies. No EBER1 was detected in two known EBV-negative cell lines. Northern blot analyses confirmed the presence and quantity of EBER1 transcripts in each cell line. This method was used to quantify the number of EBV-infected cells in peripheral blood from a patient with chronic mononucleosis. These results indicate that EBV-infected cells can be detected at the single cell level, and that this assay can be used to quantify the number of EBV-infected cells in clinical samples.

  8. A combination of direct viable count and fluorescence in situ hybridization for specific enumeration of viable Lactobacillus delbrueckii subsp.bulgaricus and Streptococcus thermophilus.

    Science.gov (United States)

    García-Hernández, J; Moreno, Y; Amorocho, C M; Hernández, M

    2012-03-01

    We have developed a direct viable count (DVC)-FISH procedure for quickly and easily discriminating between viable and nonviable cells of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus strains, the traditional yogurt bacteria. direct viable count method has been modified and adapted for Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus analysis by testing different times of incubation and concentrations of DNA-gyrase inhibitors. DVC procedure has been combined with fluorescent in situ hybridization (FISH) for the specific detection of viable cells of both bacteria with specific rRNA oligonucleotide probes (DVC-FISH). Of the four antibiotics tested (novobiocin, nalidixic acid, pipemidic acid and ciprofloxacin), novobiocin was the most effective for DVC method and the optimum incubation time was 7 h for both bacteria. The number of viable cells was obtained by the enumeration of specific hybridized cells that were elongated at least twice their original length for Lactobacillus and twice their original size for Streptococcus. This technique was successfully applied to detect viable cells in inoculated faeces. Results showed that this DVC-FISH procedure is a quick and culture-independent useful method to specifically detect viable Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus in different samples, being applied for the first time to lactic acid bacteria. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  9. Comparative review of techniques used for in situ remediation of contaminated soils; Revision comparativa de tecnicas empleadas para la descontaminacion in situ de suelos contaminados

    Energy Technology Data Exchange (ETDEWEB)

    Escusol Tomey, M.; Rodriguez Abad, R.

    2014-07-01

    Soil pollution may influence the geotechnical parameters of the soil itself, properties such as solid particle density or water within its pores. It may also vary its friction angle, modify its structure and texture, or change the properties of its constitutive minerals due to the inclusion of polluting components. For these reasons, soil decontamination is an important factor to consider in geotechnics. This work focuses on those soil decontamination techniques carried out in situ, since they allow to eliminate soil pollutants in a less invasive way than confinement, containment or ex situ remediation techniques, causing a minor soil alteration and, therefore, affecting less to its mechanical properties. These factors should be taken into account when carrying out a geotechnical performance on a previously decontaminated soil. (Author)

  10. Using whole mount in situ hybridization to link molecular and organismal biology.

    Science.gov (United States)

    Jacobs, Nicole L; Albertson, R Craig; Wiles, Jason R

    2011-03-31

    Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the embryology and gross anatomy of several organisms representing various chordate taxa primarily via traditional dissections and the use of models. The final portion of the course involved an innovative approach to teaching anatomy through observation of vertebrate development employing molecular techniques in which WISH was performed on zebrafish embryos. A heterozygous fibroblast growth factor 8 a (fgf8a) mutant line, ace, was used. Due to Mendelian inheritance, ace intercrosses produced wild type, heterozygous, and homozygous ace/fgf8a mutants in a 1:2:1 ratio. RNA probes with known expression patterns in the midline and in developing anatomical structures such as the heart, somites, tailbud, myotome, and brain were used. WISH was performed using zebrafish at the 13 somite and prim-6 stages, with students performing the staining reaction in class. The study of zebrafish embryos at different stages of development gave students the ability to observe how these anatomical structures changed over ontogeny. In addition, some ace/fgf8a mutants displayed improper heart looping, and defects in somite and brain development. The students in this lab observed the normal development of various organ systems using both external anatomy as well as gene expression patterns. They also identified and described embryos displaying improper anatomical development and gene expression (i.e., putative mutants). For instructors at institutions that do not already own the necessary equipment or where

  11. Study on biological dosimetry of premature chromosome condensation technique

    International Nuclear Information System (INIS)

    Jiang Bo

    2005-01-01

    The premature chromosome condensation technique has been applied for biological dosimetry purpose. Premature chromo-some condensation was induced by incubating unstimulated human peripheral blood lymphocytes in the presence of okadaic acid or calyculin A (a phosphatase inhibitor) which eliminated the need for fusion with mitotic cells. It is now possible to examine the early damage induced by radiation. It is simple, exact when it combines with fluorecence in situ hybridization. (authors)

  12. Determining the origin of cells in tissue engineered skin substitutes: a pilot study employing in situ hybridization.

    Science.gov (United States)

    Weber, Andreas Daniel; Pontiggia, Luca; Biedermann, Thomas; Schiestl, Clemens; Meuli, Martin; Reichmann, Ernst

    2011-03-01

    Definitive and high-quality coverage of large and, in particular, massive skin defects remains a significant challenge in burn as well as plastic and reconstructive surgery because of donor site shortage. A novel and promising approach to overcome these problems is tissue engineering of skin. Clearly, before eventual clinical application, engineered skin substitutes of human origin must be grafted and then evaluated in animal models. For the various tests to be conducted it is indispensable to be able to identify human cells as such in culture and also to distinguish between graft and recipient tissue after transplantation. Here we describe a tool to identify human cells in vitro and in vivo. In situ hybridization allows for the detection and localization of specific DNA or RNA sequences in morphologically preserved cells in culture or tissue sections, respectively. We used digoxigenin-labeled DNA probes corresponding to human-specific Alu repeats in order to identify human keratinocytes grown in culture together with rat cells, and also to label split and full thickness skin grafts of human origin after transplantation on immuno-incompetent rats. Digoxigenin-labeled DNA probing resulted in an intensive nuclear staining of human cells, both in culture and after transplantation onto recipient animals, while recipient animal cells (rat cells) did not stain. In situ hybridization using primate-specific Alu probes reliably allows distinguishing between cells of human and non-human origin both in culture as well as in histological sections. This method is an essential tool for those preclinical experiments (performed on non-primate animals) that must be conducted before novel tissue engineered skin substitutes might be introduced into clinical practice.

  13. Facile fabrication of ultrathin hybrid membrane for highly flexible supercapacitors via in-situ phase separation of polyethersulfone

    Science.gov (United States)

    Zhao, Xiaoning; Ran, Fen; Shen, Kuiwen; Yang, Yunlong; Wu, Jiayu; Niu, Xiaoqin; Kong, Lingbin; Kang, Long; Chen, Shaowei

    2016-10-01

    In this article, a facile method based on in-situ phase-separation was developed for the fabrication of ultrathin hybrid membranes for highly flexible supercapacitors. The structures and morphologies of the prepared electrodes were characterized by scanning electron microscopy (SEM), Fourier-transformed infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA) measurements; and the electrochemical behaviors were examined in 2 M KOH solution. SEM and FTIR characterizations reveal that activated carbon was imbedded into the polymer membrane of polyethersulfone to form a uniform and flexible hybrid membrane. When the thin polymer-carbon membrane (PCM) was used as an electrode material for supercapacitor, a high specific capacitance of 169.4 Fg-1 was obtained at a current density of 0.5 Ag-1 along with good long-term cycle life of 94.6% capacity retention after 2000 charging-discharging cycles. Benefiting from these merits, the as-fabricated PCM//PCM cell shows an excellent electrochemical property. These results suggest a promising route towards the fabrication of highly flexible electrodes for high-performance supercapacitors.

  14. A Standalone PV System with a Hybrid P&O MPPT Optimization Technique

    Directory of Open Access Journals (Sweden)

    S. Hota

    2017-12-01

    Full Text Available In this paper a maximum power point tracking (MPPT design for a photovoltaic (PV system using a hybrid optimization technique is proposed. For maximum power transfer, maximum harvestable power from a PV cell in a dynamically changing surrounding should be known. The proposed technique is compared with the conventional Perturb and Observe (P&O technique. A comparative analysis of power-voltage and current-voltage characteristics of a PV cell with and without the MPPT module when connected to the grid was performed in SIMULINK, to demonstrate the increment in the efficiency of the PV module after using the MPPT module.

  15. Intracellular distribution of histone mRNAs in human fibroblasts studied by in situ hybridization

    International Nuclear Information System (INIS)

    Lawrence, J.B.; Singer, R.H.; Villnave, C.A.; Stein, J.L.; Stein, G.S.

    1988-01-01

    We have used in situ hybridization to study the intracellular distribution of mRNAs for cell cycle-dependent core and H1 histone proteins in human WI-38 fibroblasts. Because histones are abundant nuclear proteins and histone mRNA expression is tightly coupled to DNA synthesis, it was of interest to determine whether histone mRNAs are localized near the nucleus. Cells were hybridized with tritiated DNA probes specific for either histone H1, histone H4, actin, or poly(A)+ mRNA and were processed for autoradiography. In exponentially growing cultures, the fraction of histone mRNA-positive cells correlated well with the fraction of cells in S phase and was eliminated by hydroxyurea inhibition of DNA synthesis. Within individual cells the label for histone mRNA was widely distributed throughout the cytoplasm and did not appear to be more heavily concentrated near the nucleus. However, histone mRNA appeared to exhibit patchy, nonhomogeneous localization, and a quantitative evaluation confirmed that grain distributions were not as uniform as they were after hybridizations to poly(A)+ mRNA. Actin mRNA in WI-38 cells was also widely distributed throughout the cytoplasm but differed from histone mRNA in that label for actin mRNA was frequently most dense at the outermost region of narrow cell extensions. The localization of actin mRNA was less pronounced but qualitatively very similar to that previously described for chicken embryonic myoblasts and fibroblasts. We conclude that localization of histones in WI-38 cells is not facilitated by localization of histone protein synthesis near the nucleus and that there are subtle but discrete and potentially functional differences in the distributions of histone, actin, and poly(A)+ mRNAs

  16. In situ solution mining technique

    International Nuclear Information System (INIS)

    Learmont, R.P.

    1978-01-01

    A method of in situ solution mining is disclosed in which a primary leaching process employing an array of 5-spot leaching patterns of production and injection wells is converted to a different pattern by converting to injection wells all the production wells in alternate rows

  17. Correlation between HER2 gene amplification and protein overexpression through fluorescence in situ hybridization and immunohistochemistry in breast carcinoma patients

    OpenAIRE

    R N Makroo; Mohit Chowdhry; Manoj Kumar; Priyanka Srivastava; Richa Tyagi; Preeti Bhadauria; Sumaid Kaul; Ramesh Sarin; P K Das; Harsh Dua

    2012-01-01

    Background : In India, the incidence of breast cancer has increased in the urban population, with 1 in every 22 women diagnosed with breast cancer. It is important to know the HER2/neu gene status for a better prognostication of these patients. Aim : The aim of this study was to compare the efficacy of fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) for determining HER2/neu alteration in breast carcinoma. Materials and Methods : A total of 188 histologically proven br...

  18. Detection of Epstein Barr Virus by Chromogenic In Situ Hybridization in cases of extra-hepatic biliary atresia

    Directory of Open Access Journals (Sweden)

    Farahmand Fatemeh

    2008-04-01

    Full Text Available Abstract Introduction Extra-hepatic biliary atresia (EHBA is an important cause of neonatal cholestasis. Several infectious agents have been proposed as etiologic factors such as Rotavirus and Reovirus. There is limited data on the role of Epstein Barr virus (EBV infection in EHBA, so we decided to study the presence of EBV virus in a series of 16 proven EHBA cases by Chromogenic in situ hybridization (CISH technique. Methods In the current study a total of 16 liver wedge biopsies of proven cases of EHBA were selected in a period of 4 years. CISH staining for EBV-encoded RNA (EBER transcript was performed. Results The review of H&E-stained slides of liver biopsies revealed fibrosis and marked ductular proliferation. In CISH-stained slides, EBV trace was observed in hepatocytes in two cases and in biliary epithelium in one case of EHBA. Discussion Considering the association of hepatitis with the Epstein-Barr virus in later life, it is likely that EBV hepatitis and its complications occur in the neonatal/perinatal period. Since EHBA is a relatively rare disease, a similar study on wedge biopsies of this number of proven cases of EHBA has not been performed to date. Current observation proposes the need for a study of larger series and employing other methods for confirming the etiologic role of EBV in EHBA cases.

  19. Electricity market price spike analysis by a hybrid data model and feature selection technique

    International Nuclear Information System (INIS)

    Amjady, Nima; Keynia, Farshid

    2010-01-01

    In a competitive electricity market, energy price forecasting is an important activity for both suppliers and consumers. For this reason, many techniques have been proposed to predict electricity market prices in the recent years. However, electricity price is a complex volatile signal owning many spikes. Most of electricity price forecast techniques focus on the normal price prediction, while price spike forecast is a different and more complex prediction process. Price spike forecasting has two main aspects: prediction of price spike occurrence and value. In this paper, a novel technique for price spike occurrence prediction is presented composed of a new hybrid data model, a novel feature selection technique and an efficient forecast engine. The hybrid data model includes both wavelet and time domain variables as well as calendar indicators, comprising a large candidate input set. The set is refined by the proposed feature selection technique evaluating both relevancy and redundancy of the candidate inputs. The forecast engine is a probabilistic neural network, which are fed by the selected candidate inputs of the feature selection technique and predict price spike occurrence. The efficiency of the whole proposed method for price spike occurrence forecasting is evaluated by means of real data from the Queensland and PJM electricity markets. (author)

  20. A Hybrid Islanding Detection Technique Using Average Rate of Voltage Change and Real Power Shift

    DEFF Research Database (Denmark)

    Mahat, Pukar; Chen, Zhe; Bak-Jensen, Birgitte

    2009-01-01

    The mainly used islanding detection techniques may be classified as active and passive techniques. Passive techniques don't perturb the system but they have larger nondetection znes, whereas active techniques have smaller nondetection zones but they perturb the system. In this paper, a new hybrid...... technique is proposed to solve this problem. An average rate of voltage change (passive technique) has been used to initiate a real power shift (active technique), which changes the eal power of distributed generation (DG), when the passive technique cannot have a clear discrimination between islanding...

  1. Cleaning capacity of hybrid instrumentation technique using reamer with alternating cutting edges system files: Histological analysis

    Directory of Open Access Journals (Sweden)

    Emilio Carlos Sponchiado Junior

    2014-01-01

    Full Text Available Aim: The aim of the following study is to evaluate the cleaning capacity of a hybrid instrumentation technique using Reamer with Alternating Cutting Edges (RaCe system files in the apical third of mesial roots of mandibular molars. Materials and Methods: Twenty teeth were selected and separated into two groups (n = 20 according to instrumentation technique as follows: BioRaCe - chemomechanical preparation with K-type files #10 and #15; and files BioRaCe BR0, BR1, BR2, BR3, and BR4; HybTec - hybrid instrumentation technique with K-type files #10 and #15 in the working length, #20 at 2 mm, #25 at 3 mm, cervical preparation with Largo burs #1 and #2; apical preparation with K-type files #15, #20, and #25 and RaCe files #25.04 and #30.04. The root canals were irrigated with 1 ml of 2.5% sodium hypochlorite at each change of instrument. The specimens were histologically processed and photographed under light optical microscope. The images were inserted onto an integration grid to count the amount of debris present in the root canal. Results: BioRaCe presented the highest percentage of debris in the apical third, however, with no statistically significant difference for HybTec (P > 0.05. Conclusions: The hybrid technique presented similar cleaning capacity as the technique recommended by the manufacturer.

  2. In-situ fluorescence hybridization applied to biological dosimetry: contribution of automation to the counting of radio-induced chromosome aberrations

    International Nuclear Information System (INIS)

    Germain Thomas Roy, Laurence

    1999-01-01

    The frequency of chromosome aberrations on peripheral blood lymphocytes is a dose indicator in the case of ionizing radiations over-exposure. Stable chromosome aberrations (translocations, insertions) are visualized after labelling of some chromosomes using the fluorescence in-situ hybridization (FISH). The study of the use of the FISH technique in biological dosimetry is done with dose-effect curves. It seems that a bias is introduced during the observation of chromosome aberrations involving only 3 pairs of chromosomes. In order to avoid this bias, it would be useful to test the feasibility of using the multi-FISH technique in biological dosimetry. Moreover, this type of chromosome aberration changes with the type of irradiation. It is thus important to define the aberrations to be considered when the FISH technique is used. In order to reduce the time of image analysis, the CYTOGEN system, developed by IMSTAR company (Paris, France) has been adapted to the needs of biological dosimetry. This system allows to localize automatically the metaphases on the slide, which reduces the observation time by 2 or 4. An automatic detection protocol for chromosome aberrations has been implemented. It comprises the image capture, the contours detection and the classification of some chromosome aberrations. The different steps of this protocol have been tested in order to check that no bias is introduced by the automation. However, because radio-induced aberrations are rare events, it seems that a totally automatic system is not foreseeable. A semi-automatic analysis is more suitable. The use of the Slit-Scan technology (Laboratory of applied physics, Heidelberg, Germany) in biological dosimetry has been studied too. This technique allows to analyze rapidly a huge number of chromosomes. A good correlation has been observed between the dicentric frequency measured automatically and by manual counting. The system is under development and should be adapted to the detection of

  3. Chromogenic in situ hybridization to detect EGFR gene copy number in cell blocks from fine-needle aspirates of non small cell lung carcinomas and lung metastases from colo-rectal cancer

    Directory of Open Access Journals (Sweden)

    Terrenato Irene

    2010-09-01

    Full Text Available Abstract Background Several studies demonstrated that epidermal growth factor receptor (EGFR gene copy number (GCN correlates to the response to tyrosine kinase inhibitors in non small cell lung cancer (NSCLC and to anti-EGFR monoclonal antibodies (MoAbs in metastatic colorectal cancer (CRC. In the presence of lung nodules, cytology is often the only possible diagnostic approach. Chromogenic in situ hybridization (CISH is an alternative technique to fluorescence in situ hybridization (FISH, but its feasibility in detecting EGFR GCN in cell blocks from fine-needle aspiration cytology (FNAC of lung nodules has not yet been established. Methods We evaluated the feasibility of CISH on 33 FNAC from 20 primary NSCLC (5 squamous carcinomas, 8 large cell carcinomas and 7 adenocarcinomas and 13 lung metastases from CRC. Results Of the 33 FNAC analyzed by CISH, 27 (82% presented a balanced increase in EGFR gene and chromosome 7 number: 10 cases (30% showed a low polysomy, 15 (45% a high polysomy and 2 (6% NSCLC were amplified. No significant differences between NSCLC and CRC lung metastases were found in relation to disomic or polysomic status. In addition, no correlation between EGFR GCN and EGFR immunohistochemical overexpression was found. Furthermore, we compared CISH results with those obtained by FISH on the same samples and we found 97% overall agreement between the two assays (k = 0.78, p Conclusions Our study shows that CISH is a valid method to detect EGFR GCN in cell blocks from FNAC of primary NSCLC or metastatic CRC to the lung.

  4. The development of an electrochemical technique for in situ calibrating of combustible gas detectors

    Science.gov (United States)

    Shumar, J. W.; Lantz, J. B.; Schubert, F. H.

    1976-01-01

    A program to determine the feasibility of performing in situ calibration of combustible gas detectors was successfully completed. Several possible techniques for performing the in situ calibration were proposed. The approach that showed the most promise involved the use of a miniature water vapor electrolysis cell for the generation of hydrogen within the flame arrestor of a combustible gas detector to be used for the purpose of calibrating the combustible gas detectors. A preliminary breadboard of the in situ calibration hardware was designed, fabricated and assembled. The breadboard equipment consisted of a commercially available combustible gas detector, modified to incorporate a water vapor electrolysis cell, and the instrumentation required for controlling the water vapor electrolysis and controlling and calibrating the combustible gas detector. The results showed that operation of the water vapor electrolysis at a given current density for a specific time period resulted in the attainment of a hydrogen concentration plateau within the flame arrestor of the combustible gas detector.

  5. Standardization and optimization of fluorescence in situ hybridization (FISH for HER-2 assessment in breast cancer: A single center experience

    Directory of Open Access Journals (Sweden)

    Magdalena Bogdanovska-Todorovska

    2018-05-01

    Full Text Available Accurate assessment of human epidermal growth factor receptor 2 (HER-2 is crucial in selecting patients for targeted therapy. Commonly used methods for HER-2 testing are immunohistochemistry (IHC and fluorescence in situ hybridization (FISH. Here we presented the implementation, optimization and standardization of two FISH protocols using breast cancer samples and assessed the impact of pre-analytical and analytical factors on HER-2 testing. Formalin fixed paraffin embedded (FFPE tissue samples from 70 breast cancer patients were tested for HER-2 using PathVysion™ HER-2 DNA Probe Kit and two different paraffin pretreatment kits, Vysis/Abbott Paraffin Pretreatment Reagent Kit (40 samples and DAKO Histology FISH Accessory Kit (30 samples. The concordance between FISH and IHC results was determined. Pre-analytical and analytical factors (i.e., fixation, baking, digestion, and post-hybridization washing affected the efficiency and quality of hybridization. The overall hybridization success in our study was 98.6% (69/70; the failure rate was 1.4%. The DAKO pretreatment kit was more time-efficient and resulted in more uniform signals that were easier to interpret, compared to the Vysis/Abbott kit. The overall concordance between IHC and FISH was 84.06%, kappa coefficient 0.5976 (p < 0.0001. The greatest discordance (82% between IHC and FISH was observed in IHC 2+ group. A standardized FISH protocol for HER-2 assessment, with high hybridization efficiency, is necessary due to variability in tissue processing and individual tissue characteristics. Differences in the pre-analytical and analytical steps can affect the hybridization quality and efficiency. The use of DAKO pretreatment kit is time-saving and cost-effective.

  6. Synthesis of ZnO nanorods-Au nanoparticles hybrids via in-situ plasma sputtering-assisted method for simultaneous electrochemical sensing of ascorbic acid and uric acid

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Chao [College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China); Liu, Hongying, E-mail: liuhongying@hdu.edu.cn [College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China); State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210093 (China); Zhang, Dan; Yang, Chi [Department of Pharmacy, Nantong University, Nantong 226001 (China); Zhang, Mingzhen [College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China)

    2016-05-05

    In this study, ZnO nanorods-Au nanoparticles (ZnO NRs-Au NPs) hybrids were prepared using an in-situ plasma sputtering-assisted method without any template. Characterization results from scanning electron microscopy, high-resolution transmission electron microscopy, and energy dispersive X-ray spectroscopy showed that Au NPs are highly dispersed and tightly anchored on the surface of ZnO NRs. The size and surface coverage of Au NPs were well controlled by plasma sputtering time. Moreover, the hybrids exhibited excellent electrocatalytic properties towards oxidation of ascorbic acid (AA) and uric acid (UA) due to large surface area of Au NPs and ZnO NRs, and thus can be used as electrochemical sensors. Differential pulse voltammetry results showed that AA and UA could be detected simultaneously by ZnO NRs-Au NPs hybrids modified glassy carbon electrode. The linear ranges for AA and UA are 0.1 to 4 mM and 0.01 to 0.4 mM, respectively. The results suggest promising future applications in clinical diagnosis. - Highlights: • ZnO nanorods-Au nanoparticles were synthesized by in-situ plasma sputtering method. • Influence of sputtering time on the formation of Au nanoparticles was studied. • It exhibited a strong electrocatalytic activity toward the oxidation of ascorbic acid and uric acid. • A portable and cheap approach for simultaneous detection of ascorbic acid and uric acid was developed.

  7. Synthesis of ZnO nanorods-Au nanoparticles hybrids via in-situ plasma sputtering-assisted method for simultaneous electrochemical sensing of ascorbic acid and uric acid

    International Nuclear Information System (INIS)

    Hou, Chao; Liu, Hongying; Zhang, Dan; Yang, Chi; Zhang, Mingzhen

    2016-01-01

    In this study, ZnO nanorods-Au nanoparticles (ZnO NRs-Au NPs) hybrids were prepared using an in-situ plasma sputtering-assisted method without any template. Characterization results from scanning electron microscopy, high-resolution transmission electron microscopy, and energy dispersive X-ray spectroscopy showed that Au NPs are highly dispersed and tightly anchored on the surface of ZnO NRs. The size and surface coverage of Au NPs were well controlled by plasma sputtering time. Moreover, the hybrids exhibited excellent electrocatalytic properties towards oxidation of ascorbic acid (AA) and uric acid (UA) due to large surface area of Au NPs and ZnO NRs, and thus can be used as electrochemical sensors. Differential pulse voltammetry results showed that AA and UA could be detected simultaneously by ZnO NRs-Au NPs hybrids modified glassy carbon electrode. The linear ranges for AA and UA are 0.1 to 4 mM and 0.01 to 0.4 mM, respectively. The results suggest promising future applications in clinical diagnosis. - Highlights: • ZnO nanorods-Au nanoparticles were synthesized by in-situ plasma sputtering method. • Influence of sputtering time on the formation of Au nanoparticles was studied. • It exhibited a strong electrocatalytic activity toward the oxidation of ascorbic acid and uric acid. • A portable and cheap approach for simultaneous detection of ascorbic acid and uric acid was developed.

  8. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal

    2012-07-28

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we introduce our Adaptive Hybrid Multiprocessor technique to accelerate the implementation of the Smith-Waterman algorithm. Our technique utilizes both the graphics processing unit (GPU) and the central processing unit (CPU). It adapts to the implementation according to the number of CPUs given as input by efficiently distributing the workload between the processing units. Using existing resources (GPU and CPU) in an efficient way is a novel approach. The peak performance achieved for the platforms GPU + CPU, GPU + 2CPUs, and GPU + 3CPUs is 10.4 GCUPS, 13.7 GCUPS, and 18.6 GCUPS, respectively (with the query length of 511 amino acid). © 2010 IEEE.

  9. Rapid detection of rRNA group I pseudomonads in contaminated metalworking fluids and biofilm formation by fluorescent in situ hybridization.

    Science.gov (United States)

    Saha, Ratul; Donofrio, Robert S; Goeres, Darla M; Bagley, Susan T

    2012-05-01

    Metalworking fluids (MWFs), used in different machining operations, are highly prone to microbial degradation. Microbial communities present in MWFs lead to biofilm formation in the MWF systems, which act as a continuous source of contamination. Species of rRNA group I Pseudomonas dominate in contaminated MWFs. However, their actual distribution is typically underestimated when using standard culturing techniques as most fail to grow on the commonly used Pseudomonas Isolation Agar. To overcome this, fluorescent in situ hybridization (FISH) was used to study their abundance along with biofilm formation by two species recovered from MWFs, Pseudomonas fluorescens MWF-1 and the newly described Pseudomonas oleovorans subsp. lubricantis. Based on 16S rRNA sequences, a unique fluorescent molecular probe (Pseudo120) was designed targeting a conserved signature sequence common to all rRNA group I Pseudomonas. The specificity of the probe was evaluated using hybridization experiments with whole cells of different Pseudomonas species. The probe's sensitivity was determined to be 10(3) cells/ml. It successfully detected and enumerated the abundance and distribution of Pseudomonas indicating levels between 3.2 (± 1.1) × 10(6) and 5.0 (± 2.3) × 10(6) cells/ml in four different industrial MWF samples collected from three different locations. Biofilm formation was visualized under stagnant conditions using high and low concentrations of cells for both P. fluorescens MWF-1 and P. oleovorans subsp. lubricantis stained with methylene blue and Pseudo120. On the basis of these observations, this molecular probe can be successfully be used in the management of MWF systems to monitor the levels and biofilm formation of rRNA group I pseudomonads.

  10. Measurement techniques for in situ stresses around underground constructions in a deep clay formation

    Directory of Open Access Journals (Sweden)

    Li X.L.

    2010-06-01

    Full Text Available Disposal in deep underground geological formations is internationally recognized as the most viable option for the long-term management of high-level radioactive waste. In Belgium, the Boom clay formation is extensively studied in this context, in particular at the 225 m deep HADES Underground Research Facility in Mol. A cost-effective design of deep underground structures requires an accurate assessment of the in situ stresses; a good estimation of these stresses is also essential when interpreting in situ experiments regarding the hydro-mechanical behaviour of the host formation. Different measurement techniques are available to provide data on the stress evolution and other mechanical properties of the geological formation. The measurement can be direct (measurement of total pressure, or it can be an indirect technique, deriving the stress from related quantities such as strain (changes in structural members. Most total stress measurements are performed through permanently installed sensors; also once-only measurements are performed through specific methods (e.g. pressuremeter. Direct measurement of the stress state is challenging due to the complex mechanical behaviour of the clay, and the fact that the sensor installation inevitably disturbs the original stress field. This paper describes ways to deal with these problems and presents the results obtained using different techniques at HADES.

  11. 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.

  12. Adaptation of Hybrid FSO/RF Communication System Using Puncturing Technique

    Directory of Open Access Journals (Sweden)

    M. N. Khan

    2016-12-01

    Full Text Available Spectrum of radio frequency (RF communications is limited and expensive to install new applications. Free space optical (FSO communication is a viable technology which offers enormous bandwidth, license free installation, inexpensive deployment and error prone links. The FSO links degrade significantly due to the varying atmospheric and weather conditions (fog, cloud, snow, haze and combination of these. We propose a hybrid FSO/RF communication system which adapts the varying nature of atmosphere and weather. For the adaption of varying atmosphere and weather scenarios, we develop a novel optimization algorithm. The proposed algorithm is based on the well-known puncturing technique. We provide an extrinsic information transfer (EXIT chart for the binary and quaternary mapping scheme for the proposed communication system. We simulate the proposed algorithm for the hybrid communication system and analyze the system performance. The proposed algorithm is computationally less expensive and provide better performance gains over varying atmosphere and weather conditions. The algorithm is suitable for fast speed applications.

  13. A hybrid Pade-Galerkin technique for differential equations

    Science.gov (United States)

    Geer, James F.; Andersen, Carl M.

    1993-01-01

    A three-step hybrid analysis technique, which successively uses the regular perturbation expansion method, the Pade expansion method, and then a Galerkin approximation, is presented and applied to some model boundary value problems. In the first step of the method, the regular perturbation method is used to construct an approximation to the solution in the form of a finite power series in a small parameter epsilon associated with the problem. In the second step of the method, the series approximation obtained in step one is used to construct a Pade approximation in the form of a rational function in the parameter epsilon. In the third step, the various powers of epsilon which appear in the Pade approximation are replaced by new (unknown) parameters (delta(sub j)). These new parameters are determined by requiring that the residual formed by substituting the new approximation into the governing differential equation is orthogonal to each of the perturbation coordinate functions used in step one. The technique is applied to model problems involving ordinary or partial differential equations. In general, the technique appears to provide good approximations to the solution even when the perturbation and Pade approximations fail to do so. The method is discussed and topics for future investigations are indicated.

  14. In Situ Analytical Characterization of Contaminated Sites Using Nuclear Spectrometry Techniques. Review of Methodologies and Measurements

    International Nuclear Information System (INIS)

    2017-01-01

    Past and current human activities can result in the contamination of sites by radionuclides and heavy metals. The sources of contamination are various. The most important sources for radionuclide release include global fallout from nuclear testing, nuclear and radiological accidents, waste production from nuclear facilities, and activities involving naturally occurring radioactive material (NORM). Contamination of the environment by heavy metals mainly originates from industrial applications and mineralogical background concentration. Contamination of sites by radionuclides and heavy metals can present a risk to people and the environment. Therefore, the estimation of the contamination level and the identification of the source constitute important information for the national authorities with the responsibility to protect people and the environment from adverse health effects. In situ analytical techniques based on nuclear spectrometry are important tools for the characterization of contaminated sites. Much progress has been made in the design and implementation of portable systems for efficient and effective monitoring of radioactivity and heavy metals in the environment directly on-site. Accordingly, the IAEA organized a Technical Meeting to review the current status and trends of various applications of in situ nuclear spectrometry techniques for analytical characterization of contaminated sites and to support Member States in their national environmental monitoring programmes applying portable instrumentation. This publication represents a comprehensive review of the in situ gamma ray spectrometry and field portable X ray fluorescence analysis techniques for the characterization of contaminated sites. It includes papers on the use of these techniques, which provide useful background information for conducting similar studies, in the following Member States: Argentina, Australia, Brazil, Czech Republic, Egypt, France, Greece, Hungary, Italy, Lithuania

  15. Third-order nonlinear optical response of Ag-CdSe/PVA hybrid nanocomposite

    Energy Technology Data Exchange (ETDEWEB)

    Tripathi, S.K.; Kaur, Ramneek; Kaur, Jaspreet; Sharma, Mamta [Panjab University, Department of Physics, Center of Advanced Study in Physics, Chandigarh (India)

    2015-09-15

    Hybrid nanocomposites of II-VI semiconductor nanoparticles are gaining great interest in nonlinear optoelectronic devices. Present work includes the characterization of CdSe polymer nanocomposite prepared by chemical in situ technique. From X-ray diffraction, the hexagonal wurtzite structure of nanoparticles has been confirmed with spherical morphology from transmission electron microscopy. Ag-CdSe hybrid polymer nanocomposite has been prepared chemically at different Ag concentrations. The presence of Ag in hybrid nanocomposite has been confirmed with energy-dispersive X-ray spectroscopy. The effect of varying Ag concentration on the linear and nonlinear optical properties of the nanocomposites has been studied. In linear optical parameters, the linear absorption coefficient, refractive index, extinction coefficient and optical conductivity have been calculated. The third-order nonlinear optical properties have been observed with open- and closed-aperture Z-scan technique. The large nonlinear refractive index ∝10{sup -5} cm{sup 2}/W with self-focusing behaviour is due to the combined effect of quantum confinement and thermo-optical effects. The enhanced nonlinearity with increasing Ag content is due to the surface plasmon resonance, which enhances the local electric field near the nanoparticle surface. Thus, Ag-CdSe hybrid polymer nanocomposite has favourable nonlinear optical properties for various optoelectronic applications. (orig.)

  16. Third-order nonlinear optical response of Ag-CdSe/PVA hybrid nanocomposite

    International Nuclear Information System (INIS)

    Tripathi, S.K.; Kaur, Ramneek; Kaur, Jaspreet; Sharma, Mamta

    2015-01-01

    Hybrid nanocomposites of II-VI semiconductor nanoparticles are gaining great interest in nonlinear optoelectronic devices. Present work includes the characterization of CdSe polymer nanocomposite prepared by chemical in situ technique. From X-ray diffraction, the hexagonal wurtzite structure of nanoparticles has been confirmed with spherical morphology from transmission electron microscopy. Ag-CdSe hybrid polymer nanocomposite has been prepared chemically at different Ag concentrations. The presence of Ag in hybrid nanocomposite has been confirmed with energy-dispersive X-ray spectroscopy. The effect of varying Ag concentration on the linear and nonlinear optical properties of the nanocomposites has been studied. In linear optical parameters, the linear absorption coefficient, refractive index, extinction coefficient and optical conductivity have been calculated. The third-order nonlinear optical properties have been observed with open- and closed-aperture Z-scan technique. The large nonlinear refractive index ∝10 -5 cm 2 /W with self-focusing behaviour is due to the combined effect of quantum confinement and thermo-optical effects. The enhanced nonlinearity with increasing Ag content is due to the surface plasmon resonance, which enhances the local electric field near the nanoparticle surface. Thus, Ag-CdSe hybrid polymer nanocomposite has favourable nonlinear optical properties for various optoelectronic applications. (orig.)

  17. Thermoelectric properties of graphene nanosheets-modified polyaniline hybrid nanocomposites by an in situ chemical polymerization

    International Nuclear Information System (INIS)

    Lu, Yan; Song, Ying; Wang, Fuping

    2013-01-01

    A hybrid material of polyaniline protonated with hydrochloric acid and conductive graphene nanosheets (PANi/GNs) has been prepared by an in situ chemical polymerization method. The interactions between PANi and GNs in the hybrid composites are investigated by utilizing XRD, FT-IR, UV–vis and Raman. It is found that the PANi are adsorbed on the surface of the GNs, and the morphology of PANi transforms from twist structure to extended structure after the GNs are introduced. The thermoelectric (TE) properties of PANi/GNs composites have been investigated in the range from 323 K to 453 K. The electrical conductivity and the Seebeck coefficient of PANi/GNs composites are obviously higher than those of the PANi, while the thermal conductivity of the composites still keeps relatively low values even with high GNs content, resulting in the increase in dimensionless figure of merit (ZT). A highest ZT value of 1.95 × 10 −3 has been obtained for the composite containing 30 wt % GNs at 453 K, which is about 70 times higher than that obtained from the PANi. - Highlights: ► PANi adsorbed on the surface of the GNs possesses more extended structure. ► Electrical conductivity and Seebeck coefficient of PANi/GNs composites are superior to those of PANi. ► Thermal conductivity of the composites still keeps relatively low values

  18. Biofilm biodiversity presented by fluorescent in situ hybridisation

    Directory of Open Access Journals (Sweden)

    Wolf Mirela

    2017-01-01

    Full Text Available Numerous microorganisms may be present in the water distribution system. This is associated with the imperfection of purification processes, or secondary water pollution. Not only it results in the deterioration of water quality parameters, but it also increases threat of epidemiological problems. The water that is biologically unstable creates ideal conditions for colonization of the microorganisms to the inner surface of pipelines which may form biofilm. The key issue, enabling prevention and control of the impact of the development of biofilms, is to assess the biodiversity of microbiocenosis. In order to obtain comprehensive characteristics of microorganisms communities on a particular substrate, it is necessary to combine several techniques. Further analysis using molecular biology methods are usually after traditional methods of assessing the microbiological quality of water. Standard methods do not reflect the actual species composition, because they are targeted at the bacteria that can be isolated and cultured in the laboratory. Conventional methods are capable of detecting less than 10% of the organisms in the sample. In order to study the biodiversity of organisms inhabiting a biofilm (apart from the conventional methods analyses of the diversity of nucleic acids should be used. The first method could be the polymerase chain reaction (PCR and denaturing gradient gel electrophoresis (DGGE. Another way may be fluorescence in situ hybridization, which allows to detect determined DNA sequence using specially labeled oligonucleotide probes. Visualization of the material is performed using a fluorescence microscope. The main purpose of this article is to present rapid and precise identification groups of microorganisms in their natural habitat in biofilm using fluorescent in situ hybridization method (FISH . FISH method can be successfully used to visualize these microorganisms, which show difficulties in culturing, as well as to provide

  19. Deformation processes in functional materials studied by in situ neutron diffraction and ultrasonic techniques

    International Nuclear Information System (INIS)

    Sittner, P.; Novak, V.; Landa, M.; Lukas, P.

    2007-01-01

    The unique thermomechanical functions of shape memory alloys (hysteretic stress-strain-temperature responses) not their structural properties (as strength, fatigue, corrosion resistance, etc.) are primarily utilized in engineering applications. In order to better understand and predict the functional behavior, we have recently employed two dedicated non-invasive in situ experimental methods capable to follow the deformation/transformation processes in thermomechanically loaded polycrystalline samples. The in situ neutron diffraction method takes advantage of the ability of thermal neutrons to penetrate bulk samples. As a diffraction technique sensitive to interplanar spacings in crystalline solids, it provides in situ information on the changes in crystal structure, phase composition, phase stress and texture in the transforming samples. The combined in situ ultrasonic and electric resistance method follows variations of the electric resistance as well as speed and attenuation of acoustic waves propagating through the transforming sample. The acoustic waves are mainly sensitive to changes of elastic properties accompanying the deformation/transformation processes. The latter method thus follows the changes in interatomic bonds rather than changes in the interplanar lattice spacings focused in the neutron diffraction method. The methods are thus complementary. They are briefly described and selected experimental results obtained recently on NiTi alloys are presented and discussed

  20. Homology of polytene elements between Drosophila and Zaprionus determined by in situ hybridization in Zaprionus indianus.

    Science.gov (United States)

    Campos, S R C; Rieger, T T; Santos, J F

    2007-05-09

    The drosophilid Zaprionus indianus due to its economical importance as an insect pest in Brazil deserves more investigation into its genetics. Its mitotic karyotype and a line-drawing map of its polytene chromosomes are already available. This paper presents a photomap of Z. indianus polytene chromosomes, which was used as the reference map for identification of sections marked by in situ hybridization with gene probes. Hybridization signals for Hsp70 and Hsr-omega were detected, respectively, in sections 34B and 32C of chromosome V of Z. indianus, which indicates its homology to the chromosomal arm 3R of Drosophila melanogaster and, therefore, to Muller's element E. The main signal for Hsp83 gene probe hybridization was in section 17C of Z. indianus chromosome III, suggesting its homology to arm 3L of D. melanogaster and to element D of Muller. The Ubi probe hybridized in sections 10C of chromosome II and 17A of chromosome III. Probably the 17A is the polyubiquitin locus, with homology to arm 3L of D. melanogaster and to the mullerian D element, as suggested also by Hsp83 gene location. The Br-C gene was mapped in section 1D, near the tip of the X chromosome, indicating its homology to the X chromosome of D. melanogaster and to mullerian element A. The Dpp gene probe hybridized mainly in the section 32A of chromosome V and, at lower frequencies to other sections, although no signal was observed as expected in the correspondent mullerian B element. This result led to the suggestion of a rearrangement including the Dpp locus in Z. indianus, the secondary signals possibly pointing to related genes of the TGF-beta family. In conclusion, the results indicate that chromosomes X, III, V of Z. indianus are respectively correspondents to elements A, D, and E of Muller. At least chromosome V of Z. indianus seems to share synteny with the 3R arm of D. melanogaster, as indicated by the relative positions of Hsp70 and Hsr-omega, although the Dpp gene indicates a disruption of

  1. Comparative cytogenetics of six Indo-Pacific moray eels (Anguilliformes: Muraenidae) by chromosomal banding and fluorescence in situ hybridization.

    Science.gov (United States)

    Coluccia, E; Deidda, F; Cannas, R; Lobina, C; Cuccu, D; Deiana, A M; Salvadori, S

    2015-09-01

    A comparative cytogenetic analysis, using both conventional staining techniques and fluorescence in situ hybridization, of six Indo-Pacific moray eels from three different genera (Gymnothorax fimbriatus, Gymnothorax flavimarginatus, Gymnothorax javanicus, Gymnothorax undulatus, Echidna nebulosa and Gymnomuraena zebra), was carried out to investigate the chromosomal differentiation in the family Muraenidae. Four species displayed a diploid chromosome number 2n = 42, which is common among the Muraenidae. Two other species, G. javanicus and G. flavimarginatus, were characterized by different chromosome numbers (2n = 40 and 2n = 36). For most species, a large amount of constitutive heterochromatin was detected in the chromosomes, with species-specific C-banding patterns that enabled pairing of the homologous chromosomes. In all species, the major ribosomal genes were localized in the guanine-cytosine-rich region of one chromosome pair, but in different chromosomal locations. The (TTAGGG)n telomeric sequences were mapped onto chromosomal ends in all muraenid species studied. The comparison of the results derived from this study with those available in the literature confirms a substantial conservation of the diploid chromosome number in the Muraenidae and supports the hypothesis that rearrangements have occurred that have diversified their karyotypes. Furthermore, the finding of two species with different diploid chromosome numbers suggests that additional chromosomal rearrangements, such as Robertsonian fusions, have occurred in the karyotype evolution of the Muraenidae. © 2015 The Fisheries Society of the British Isles.

  2. Sintering process optimization for multi-layer CGO membranes by in situ techniques

    DEFF Research Database (Denmark)

    Kaiser, Andreas; Prasad, A.S.; Foghmoes, Søren Preben Vagn

    2013-01-01

    The sintering of asymmetric CGO bi-layers (thin dense membrane on a porous support; Ce0.9Gd0.1O1.95-delta = CGO) with Co3O4 as sintering additive has been optimized by combination of two in situ techniques. Optical dilatometry revealed that bi-layer shape and microstructure are dramatically...... changing in a narrow temperature range of less than 100 degrees C. Below 1030 degrees C, a higher densification rate in the dense membrane layer than in the porous support leads to concave shape, whereas the densification rate of the support is dominant above 1030 degrees C, leading to convex shape. A fiat...... bi-layer could be prepared at 1030 degrees C, when shrinkage rates were similar. In situ van der Pauw measurements on tape cast layers during sintering allowed following the conductivity during sintering. A strong increase in conductivity and in activation energy E-a for conduction was observed...

  3. Anatomic and Pathologic Variability During Radiotherapy for a Hybrid Active Breath-Hold Gating Technique

    International Nuclear Information System (INIS)

    Glide-Hurst, Carri K.; Gopan, Ellen; Hugo, Geoffrey D.

    2010-01-01

    Purpose: To evaluate intra- and interfraction variability of tumor and lung volume and position using a hybrid active breath-hold gating technique. Methods and Materials: A total of 159 repeat normal inspiration active breath-hold CTs were acquired weekly during radiotherapy for 9 lung cancer patients (12-21 scans per patient). A physician delineated the gross tumor volume (GTV), lungs, and spinal cord on the first breath-hold CT, and contours were propagated semiautomatically. Intra- and interfraction variability of tumor and lung position and volume were evaluated. Tumor centroid and border variability were quantified. Results: On average, intrafraction variability of lung and GTV centroid position was 0.1). Increases in free-breathing tidal volume were associated with increases in breath-hold ipsilateral lung volume (p < 0.05). Conclusions: The breath-hold technique was reproducible within 2 mm during each fraction. Interfraction variability of GTV position and shape was substantial because of tumor volume and breath-hold lung volume change during therapy. These results support the feasibility of a hybrid breath-hold gating technique and suggest that online image guidance would be beneficial.

  4. In situ analytical techniques for battery interface analysis.

    Science.gov (United States)

    Tripathi, Alok M; Su, Wei-Nien; Hwang, Bing Joe

    2018-02-05

    Lithium-ion batteries, simply known as lithium batteries, are distinct among high energy density charge-storage devices. The power delivery of batteries depends upon the electrochemical performances and the stability of the electrode, electrolytes and their interface. Interfacial phenomena of the electrode/electrolyte involve lithium dendrite formation, electrolyte degradation and gas evolution, and a semi-solid protective layer formation at the electrode-electrolyte interface, also known as the solid-electrolyte interface (SEI). The SEI protects electrodes from further exfoliation or corrosion and suppresses lithium dendrite formation, which are crucial needs for enhancing the cell performance. This review covers the compositional, structural and morphological aspects of SEI, both artificially and naturally formed, and metallic dendrites using in situ/in operando cells and various in situ analytical tools. Critical challenges and the historical legacy in the development of in situ/in operando electrochemical cells with some reports on state-of-the-art progress are particularly highlighted. The present compilation pinpoints the emerging research opportunities in advancing this field and concludes on the future directions and strategies for in situ/in operando analysis.

  5. In situ gold nanoparticles formation: contrast agent for dental optical coherence tomography

    Science.gov (United States)

    Braz, Ana K. S.; Araujo, Renato E. de; Ohulchanskyy, Tymish Y.; Shukla, Shoba; Bergey, Earl J.; Gomes, Anderson S. L.; Prasad, Paras N.

    2012-06-01

    In this work we demonstrate the potential use of gold nanoparticles as contrast agents for the optical coherence tomography (OCT) imaging technique in dentistry. Here, a new in situ photothermal reduction procedure was developed, producing spherical gold nanoparticles inside dentinal layers and tubules. Gold ions were dispersed in the primer of commercially available dental bonding systems. After the application and permeation in dentin by the modified adhesive systems, the dental bonding materials were photopolymerized concurrently with the formation of gold nanoparticles. The gold nanoparticles were visualized by scanning electron microscopy (SEM). The SEM images show the presence of gold nanospheres in the hybrid layer and dentinal tubules. The diameter of the gold nanoparticles was determined to be in the range of 40 to 120 nm. Optical coherence tomography images were obtained in two- and three-dimensions. The distribution of nanoparticles was analyzed and the extended depth of nanosphere production was determined. The results show that the OCT technique, using in situ formed gold nanoparticles as contrast enhancers, can be used to visualize dentin structures in a non-invasive and non-destructive way.

  6. ProTaper rotary instrument fracture during root canal preparation: a comparison between rotary and hybrid techniques.

    Science.gov (United States)

    Farid, Huma; Khan, Farhan Raza; Rahman, Munawar

    2013-03-01

    This study aimed to compare the frequency of ProTaper rotary instrument fracture with rotary (conventional) and hybrid (rotary and hand files) canal preparation techniques. Secondary objectives were to determine whether there was an association of ProTaper file fracture with the canal curvature and to compare the mean time required for canal preparation in the two techniques. An in vitro experiment was conducted on 216 buccal canals of extracted maxillary and mandibular first molars. After creating an access cavity and a glide path for each canal, a periapical radiograph was taken and the canal curvature was measured with Schneider's technique. The canals were then randomly divided into Group A (rotary technique) and Group B (hybrid technique). The length of ProTaper files were measured before and after each canal preparation. Time taken for each canal preparation was recorded. A total of seven ProTaper files fractured in Group A (P=0.014) in canals with a curvature >25 degrees (PProTaper rotary files, although time consuming, was safer in canals having a curvature greater than 25 degrees.

  7. Fluorescent in situ hybridization (FISH as a diagnostic tool for Williams-Beuren syndrome

    Directory of Open Access Journals (Sweden)

    Deise Helena de Souza

    2007-01-01

    Full Text Available Fluorescent in situ hybridization (FISH with commercial probes covering the elastin gene (ELN was used to determine the frequency of the 7q11.23 deletion in 18 children clinically diagnosed with Williams-Beuren syndrome (WBS. A de novo deletion was detected in 15 of the children (83%. Diagnostic investigation for WBS started late in childhood (median = 5.8 years. All the children showed facial features typical of the syndrome, mental retardation and developmental delay. Over-friendliness was observed in the majority of cases. Clinodactyly of the 5th finger (n = 13, cardiovascular disease (n = 9, loquacity (n = 9, low birthweight (n = 8, and failure to thrive (n = 9 were observed only in those children with the deletion. Respiratory problems (n = 9, though not previously reported in the literature, was a common finding in the group studied. Our results confirmed that FISH is useful in identifying 7q11.23 deletions in cases of WBS. Clinical manifestations were more evident in the deletion-positive children.

  8. A Case of Renal Primitive Neuroectodermal Tumor Confirmed by Fluorescence in situ Hybridization

    Directory of Open Access Journals (Sweden)

    Toshiki Etani

    2015-04-01

    Full Text Available Primitive neuroectodermal tumor (PNET is a member of the Ewing's sarcoma family of tumors (ESFT. We report a case of PNET in a 66-year-old male who presented with a large solid tumor within the parenchyma of the middle pole of the left kidney with metastases to the left adrenal gland and right ischium. A fine-needle biopsy was performed and showed a small round cell tumor. Results of immunohistochemical staining suggested this tumor belonged to ESFT. Preoperative VDC-IE (combined vincristine, doxorubicin and cyclophosphamide followed by another combination of ifosfamide and etoposide chemotherapy and left radical nephrectomy and adrenalectomy were performed. The histopathological findings of the resected tumor were similar to those in the biopsy specimen, but the results of AE1/AE3 were different. For the diagnosis, fluorescence in situ hybridization was performed. Split signals of the EWSR1 gene were detected, and transmission electron microscopy showed neuroendocrine granules and microtubules. The final diagnosis of this tumor was PNET of the kidney.

  9. Ternary hybrid polymeric nanocomposites through grafting of polystyrene on graphene oxide-TiO_2 by surface initiated atom transfer radical polymerization (SI-ATRP)

    International Nuclear Information System (INIS)

    Kumar, Arvind; Bansal, Ankushi; Behera, Babita; Jain, Suman L.; Ray, Siddharth S.

    2016-01-01

    A ternary hybrid of graphene oxide-titania-polystyrene (GO-TiO_2-PS) nanocomposite is developed where polystyrene composition is regulated by controlling growth of polymer chains and nanoarchitectonics is discussed. Graphene Oxide-TiO_2 (GO-TiO_2) nanocomposite is prepared by in-situ hydrothermal method and the surface is anchored with α-bromoisobutyryl bromide to activate GO-TiO_2 as initiator for polymerization. In-situ grafting of polystyrene through surface initiated atom transfer radical polymerization (SI- ATRP) on this Br-functionalized nano-composite initiator yields GO-TiO_2-PS ternary hybrid. Varying the monomer amount and keeping the concentration of initiator constant, polystyrene chain growth is regulated with narrow poly-dispersivity to achieve desired composition. This composite is well characterized by various analytical techniques like FTIR, XRD, DSC, SEM, TEM, and TGA. - Highlights: • Nanocomposite of ternary hybrid of GO-TiO_2 with polystyrene. • PS is surface grafted on GO-TiO_2. • Polymer chain lengths are well regulated by SI-ATRP living polymerization. • Thermal stability of this hybrid is relatively high.

  10. Single molecule localization imaging of telomeres and centromeres using fluorescence in situ hybridization and semiconductor quantum dots.

    Science.gov (United States)

    Wang, Le; Zong, Shenfei; Wang, Zhuyuan; Lu, Ju; Chen, Chen; Zhang, Ruohu; Cui, Yiping

    2018-07-13

    Single molecule localization microscopy (SMLM) is a powerful tool for imaging biological targets at the nanoscale. In this report, we present SMLM imaging of telomeres and centromeres using fluorescence in situ hybridization (FISH). The FISH probes were fabricated by decorating CdSSe/ZnS quantum dots (QDs) with telomere or centromere complementary DNA strands. SMLM imaging experiments using commercially available peptide nucleic acid (PNA) probes labeled with organic fluorophores were also conducted to demonstrate the advantages of using QDs FISH probes. Compared with the PNA probes, the QDs probes have the following merits. First, the fluorescence blinking of QDs can be realized in aqueous solution or PBS buffer without thiol, which is a key buffer component for organic fluorophores' blinking. Second, fluorescence blinking of the QDs probe needs only one excitation light (i.e. 405 nm). While fluorescence blinking of the organic fluorophores usually requires two illumination lights, that is, the activation light (i.e. 405 nm) and the imaging light. Third, the high quantum yield, multiple switching times and a good optical stability make the QDs more suitable for long-term imaging. The localization precision achieved in telomeres and centromeres imaging experiments is about 30 nm, which is far beyond the diffraction limit. SMLM has enabled new insights into telomeres or centromeres on the molecular level, and it is even possible to determine the length of telomere and become a potential technique for telomere-related investigation.

  11. New application technology for 'in situ' pipeline protection using pigging techniques

    Energy Technology Data Exchange (ETDEWEB)

    Pretorius, Louis Charles [Corrocoat SA (PTY) Ltd., Durban (South Africa)

    2005-07-01

    Pigging of long pipelines is a technique for in situ (field) coating, creating seamless internal structural linings. Originally developed for cleaning pipes, the system was adapted to apply internal anti-corrosion protection to pipes using a thin epoxy layer, which had some problems in weld coverage, stress cracking, poor cold weather curing and the inability to fill pitting corrosion metal loss. New coating materials, revised application methods and modified pigging equipment have made it possible to apply in situ liquid film coatings up to 1 mm thick, as an internal corrosion barrier to pipes, in a single application (similar to continuous screeding) resulting in a bonded 'GRP pipe within a steel pipe'. The method can be used for new projects on fully welded pipe lines avoiding coating problems associated with flange joints and/or couplings, or for refurbishment of old pipelines, varying from 150-900 mm diameter, up to 12 km long. Pipes can be buried, submerged, continuously welded or flanged. Many different pipes, such as oil platform to shore based pipelines, can all be treated using this method. Thick film polymer pigging techniques create new possibilities for Engineers to extend the life of pipeline systems, with significant cost savings compared to replacement pipe. (author)

  12. Chromosomal instability detected by interphase fluorescence in situ hybridization and its relation to p3 alteration in prostate carcinoma in Saudi patients

    International Nuclear Information System (INIS)

    Al-Maghrabi, Jaudah A.

    2005-01-01

    Chromosomal instability (CIN) is a feature of human neoplasm. The p53 mutation has been shown to be associated with CIN in many human dysplastic and neoplastic lesions. The objective of this study was to examine CIN and p53 mutations in prostate carcinoma (Pca) resected from Saudi patients. Testing of p53 alterations using immunohistochemistry was performed on 28 archived prostatic carcinoma specimens containing Pca foci from Saudi patients seen at King Abdul-Aziz University Hospital, Jeddah, Kingdom of Saudi Arabia. Chrosomal instability was evaluated in the same tissues by interphase in situ hybridization (IFISH) using centromere probes for chromosomes 7 and 8. Immunochemistry and IFISH were performed at Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada in 2001. The p53 immunoreactivity was found in 29% in Pca and 0% in benign epithelium. Interphase in situ hybridization revealed numerical chromosomal alterations in keeping with CIN in 63% of p53 positive and 20% p53 negative Pca. No evidence of CIN was seen in non-neoplastic epithelium. We concluded that CIN as determined by IFISH is present in Pca from Saudi patients similarly to those reported in western countries. The p53 mutation occurs relatively infrequently in Pca and associated with the presence of CIN at least in a subset of Pca. (author)

  13. Detection and quantitation of HER-2/neu gene amplification in human breast cancer archival material using fluorescence in situ hybridization.

    Science.gov (United States)

    Pauletti, G; Godolphin, W; Press, M F; Slamon, D J

    1996-07-04

    Amplification and overexpression of the HER-2/neu gene occurs in 25-30% of human breast cancers. This genetic alteration is associated with a poor clinical prognosis in women with either node negative or node positive breast cancers. The initial studies testing this association were somewhat controversial and this controversy was due in large part to significant heterogeneity in both the methods and/or reagents used in testing archival material for the presence of the alteration. These methods included a number of solid matrix blotting techniques for DNA, RNA and protein as well as immunohistochemistry. Fluorescence in situ hybridization (FISH) represents the newest methodologic approach for testing for this genetic alteration. In this study, FISH is compared to Southern, Northern and Western blot analyses as well as immunohistochemistry in a large cohort of archival human breast cancer specimens. FISH was found to be superior to all other methodologies tested in assessing formalin fixed, paraffin embedded material for HER-2/neu amplification. The results from this study also confirm that overexpression of HER-2/neu rarely occurs in the absence of gene amplification in breast cancer (approximately 3% of cases). This method of analysis is rapid, reproducible and extremely reliable in detecting presence of HER-2/neu gene amplification and should have clinical utility.

  14. Effect of Graphene Oxide on the Reaction Kinetics of Methyl Methacrylate In Situ Radical Polymerization via the Bulk or Solution Technique

    Directory of Open Access Journals (Sweden)

    Ioannis S. Tsagkalias

    2017-09-01

    Full Text Available The synthesis of nanocomposite materials based on poly(methyl methacrylate and graphene oxide (GO is presented using the in situ polymerization technique, starting from methyl methacrylate, graphite oxide, and an initiator, and carried out either with (solution or without (bulk in the presence of a suitable solvent. Reaction kinetics was followed gravimetrically and the appropriate characterization of the products took place using several experimental techniques. X-ray diffraction (XRD data showed that graphite oxide had been transformed to graphene oxide during polymerization, whereas FTIR spectra revealed no significant interactions between the polymer matrix and GO. It appears that during polymerization, the initiator efficiency was reduced by the presence of GO, resulting in a reduction of the reaction rate and a slight increase in the average molecular weight of the polymer formed, measured by gel permeation chromatography (GPC, along with an increase in the glass transition temperature obtained from differential scanning calorimetry (DSC. The presence of the solvent results in the suppression of the gel-effect in the reaction rate curves, the synthesis of polymers with lower average molecular weights and polydispersities of the Molecular Weight Distribution, and lower glass transition temperatures. Finally, from thermogravimetric analysis (TG, it was verified that the presence of GO slightly enhances the thermal stability of the nano-hybrids formed.

  15. Enumeration of Vibrio parahaemolyticus in the viable but nonculturable state using direct plate counts and recognition of individual gene fluorescence in situ hybridization.

    Science.gov (United States)

    Griffitt, Kimberly J; Noriea, Nicholas F; Johnson, Crystal N; Grimes, D Jay

    2011-05-01

    Vibrio parahaemolyticus is a gram-negative, halophilic bacterium indigenous to marine and estuarine environments and it is capable of causing food and water-borne illness in humans. It can also cause disease in marine animals, including cultured species. Currently, culture-based techniques are used for quantification of V. parahaemolyticus in environmental samples; however, these can be misleading as they fail to detect V. parahaemolyticus in a viable but nonculturable (VBNC) state which leads to an underestimation of the population density. In this study, we used a novel fluorescence visualization technique, called recognition of individual gene fluorescence in situ hybridization (RING-FISH), which targets chromosomal DNA for enumeration. A polynucleotide probe labeled with Cyanine 3 (Cy3) was created corresponding to the ubiquitous V. parahaemolyticus gene that codes for thermolabile hemolysin (tlh). When coupled with the Kogure method to distinguish viable from dead cells, RING-FISH probes reliably enumerated total, viable V. parahaemolyticus. The probe was tested for sensitivity and specificity against a pure culture of tlh(+), tdh(-), trh(-)V. parahaemolyticus, pure cultures of Vibrio vulnificus, Vibrio harveyi, Vibrio alginolyticus and Vibrio fischeri, and a mixed environmental sample. This research will provide additional tools for a better understanding of the risk these environmental organisms pose to human health. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. In Situ Integration of Anisotropic SnO₂ Heterostructures inside Three-Dimensional Graphene Aerogel for Enhanced Lithium Storage.

    Science.gov (United States)

    Yao, Xin; Guo, Guilue; Ma, Xing; Zhao, Yang; Ang, Chung Yen; Luo, Zhong; Nguyen, Kim Truc; Li, Pei-Zhou; Yan, Qingyu; Zhao, Yanli

    2015-12-02

    Three-dimensional (3D) graphene aerogel (GA) has emerged as an outstanding support for metal oxides to enhance the overall energy-storage performance of the resulting hybrid materials. In the current stage of the studies, metals/metal oxides inside GA are in uncrafted geometries. Introducing structure-controlled metal oxides into GA may further push electrochemical properties of metal oxide-GA hybrids. Using rutile SnO2 as an example, we demonstrated here a facile hydrothermal strategy combined with a preconditioning technique named vacuum-assisted impregnation for in situ construction of controlled anisotropic SnO2 heterostructures inside GA. The obtained hybrid material was fully characterized in detail, and its formation mechanism was investigated by monitoring the phase-transformation process. Rational integration of the two advanced structures, anisotropic SnO2 and 3D GA, synergistically led to enhanced lithium-storage properties (1176 mAh/g for the first cycle and 872 mAh/g for the 50th cycle at 100 mA/g) as compared with its two counterparts, namely, rough nanoparticles@3D GA and anisotropic SnO2@2D graphene sheets (618 and 751 mAh/g for the 50th cycle at 100 mA/g, respectively). It was also well-demonstrated that this hybrid material was capable of delivering high specific capacity at rapid charge/discharge cycles (1044 mAh/g at 100 mA/g, 847 mAh/g at 200 mA/g, 698 mAh/g at 500 mA/g, and 584 mAh/g at 1000 mA/g). The in situ integration strategy along with vacuum-assisted impregnation technique presented here shows great potential as a versatile tool for accessing a variety of sophisticated smart structures in the form of anisotropic metals/metal oxides within 3D GA toward useful applications.

  17. Chromogenic in situ hybridization is a reliable assay for detection of ALK rearrangements in adenocarcinomas of the lung.

    Science.gov (United States)

    Schildhaus, Hans-Ulrich; Deml, Karl-Friedrich; Schmitz, Katja; Meiboom, Maren; Binot, Elke; Hauke, Sven; Merkelbach-Bruse, Sabine; Büttner, Reinhard

    2013-11-01

    Reliable detection of anaplastic lymphoma kinase (ALK) rearrangements is a prerequisite for personalized treatment of lung cancer patients, as ALK rearrangements represent a predictive biomarker for the therapy with specific tyrosine kinase inhibitors. Currently, fluorescent in situ hybridization (FISH) is considered to be the standard method for assessing formalin-fixed and paraffin-embedded tissue for ALK inversions and translocations. However, FISH requires a specialized equipment, the signals fade rapidly and it is difficult to detect overall morphology and tumor heterogeneity. Chromogenic in situ hybridization (CISH) has been successfully introduced as an alternative test for the detection of several genetic aberrations. This study validates a newly developed ALK CISH assay by comparing FISH and CISH signal patterns in lung cancer samples with and without ALK rearrangements. One hundred adenocarcinomas of the lung were included in this study, among them 17 with known ALK rearrangement. FISH and CISH were carried out and evaluated according to the manufacturers' recommendations. For both assays, tumors were considered positive if ≥15% of tumor cells showed either isolated 3' signals or break-apart patterns or a combination of both. A subset of tumors was exemplarily examined by using a novel EML4 (echinoderm microtubule-associated protein-like 4) CISH probe. Red, green and fusion CISH signals were clearcut and different signal patterns were easily recognized. The percentage of aberrant tumor cells was statistically highly correlated (PCISH. On the basis of 86 samples that were evaluable by ALK CISH, we found a 100% sensitivity and 100% specificity of this assay. Furthermore, EML4 rearrangements could be recognized by CISH. CISH is a highly reliable, sensitive and specific method for the detection of ALK gene rearrangements in pulmonary adenocarcinomas. Our results suggest that CISH might serve as a suitable alternative to FISH, which is the current gold

  18. Evaluating Acoustic Emission Signals as an in situ process monitoring technique for Selective Laser Melting (SLM)

    Energy Technology Data Exchange (ETDEWEB)

    Fisher, Karl A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Candy, Jim V. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Guss, Gabe [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mathews, M. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-10-14

    In situ real-time monitoring of the Selective Laser Melting (SLM) process has significant implications for the AM community. The ability to adjust the SLM process parameters during a build (in real-time) can save time, money and eliminate expensive material waste. Having a feedback loop in the process would allow the system to potentially ‘fix’ problem regions before a next powder layer is added. In this study we have investigated acoustic emission (AE) phenomena generated during the SLM process, and evaluated the results in terms of a single process parameter, of an in situ process monitoring technique.

  19. Development and use of fluorescent 16S rRNA-targeted probes for the specific detection of Methylophaga species by in situ hybridization in marine sediments.

    Science.gov (United States)

    Janvier, Monique; Regnault, Béatrice; Grimont, Patrick

    2003-09-01

    Methylotrophic bacteria are widespread in nature. They may play an important role in the cycling of carbon and in the metabolism of dimethylsulfide in a marine environment. Bacteria belonging to the genus Methylophaga are a unique group of aerobic, halophilic, non-methane-utilizing methylotrophs. Two 16S rRNA-targeted oligonucleotide probes were developed for the specific detection of Methylophaga species, marine methylobacteria, by fluorescence in situ hybridization. Probe MPH-730 was highly specific for all members of the genus Methylophaga while probe MPHm-994 targeted exclusively M. marina. The application of these probes were demonstrated by the detection of Methylophaga species in enrichment cultures from various marine sediments. All isolates recovered were visualized by using the genus specific probe MPH-730. The results were confirmed by 16S rDNA sequencing which demonstrated that all selected isolates belong to Methylophaga. Five isolates could be detected by the M. marina-specific probe MPHm-994 and were confirmed by rRNA gene restriction pattern (ribotyping). With the development of these specific probes, fluorescence in situ hybridization shows that the genus Methylophaga is widespread in marine samples.

  20. Polymer-Based Black Phosphorus (bP) Hybrid Materials by in Situ Radical Polymerization: An Effective Tool To Exfoliate bP and Stabilize bP Nanoflakes

    Science.gov (United States)

    2018-01-01

    Black phosphorus (bP) has been recently investigated for next generation nanoelectronic multifunctional devices. However, the intrinsic instability of exfoliated bP (the bP nanoflakes) toward both moisture and air has so far overshadowed its practical implementation. In order to contribute to fill this gap, we report here the preparation of new hybrid polymer-based materials where bP nanoflakes (bPn) exhibit a significantly improved stability. The new materials have been prepared by different synthetic paths including: (i) the mixing of conventionally liquid-phase exfoliated bP (in dimethyl sulfoxide, DMSO) with poly(methyl methacrylate) (PMMA) solution; (ii) the direct exfoliation of bP in a polymeric solution; (iii) the in situ radical polymerization after exfoliating bP in the liquid monomer (methyl methacrylate, MMA). This last methodology concerns the preparation of stable suspensions of bPn–MMA by sonication-assisted liquid-phase exfoliation (LPE) of bP in the presence of MMA followed by radical polymerization. The hybrids characteristics have been compared in order to evaluate the bP dispersion and the effectiveness of the bPn interfacial interactions with polymer chains aimed at their long-term environmental stabilization. The passivation of the bPn is particularly effective when the hybrid material is prepared by in situ polymerization. By using this synthetic methodology, the nanoflakes, even if with a gradient of dispersion (size of aggregates), preserve their chemical structure from oxidation (as proved by both Raman and 31P-solid state NMR studies) and are particularly stable to air and UV light exposure. The feasibility of this approach, capable of efficiently exfoliating bP while protecting the bPn, has been then verified by using different vinyl monomers (styrene and N-vinylpyrrolidone), thus obtaining hybrids where the nanoflakes are embedded in polymer matrices with a variety of intriguing thermal, mechanical, and solubility characteristics.

  1. Fabrication of ridge waveguide structure from photosensitive TiO2/ormosil hybrid films by using an ultraviolet soft imprint technique

    International Nuclear Information System (INIS)

    Zhang, Xuehua; Que, Wenxiu; Chen, Jing; Gao, Tianxi; Hu, Jiaxing; Liu, Weiguo

    2013-01-01

    Photosensitive TiO 2 /organically modified silane hybrid films were prepared by combining a low-temperature sol–gel process with a spin-coating technique. Optical properties and photochemical activities of the as-prepared hybrid sol–gel films under different UV irradiation time were characterized and monitored by prism coupling technique, UV–visible spectroscopy, and Fourier transform infrared spectroscopy. Surface morphology of the hybrid films was also observed by an atomic force microscopy. Advantages for fabrication of ridge waveguide structure based on the photosensitive hybrid films were demonstrated by an ultraviolet soft imprint technique. Effects of imprint force, imprint time, and UV irradiation time on high replication fidelity of the ridge waveguide structure were also investigated. An altitude replication fidelity of 99.7% can be obtained when the imprint force of 2 MPa, imprint time of 30 min and UV irradiation time of 45 min were chosen. Scanning electron microscopy and surface profiler were used to characterize the morphological and surface profile properties of the as fabricated ridge waveguide structure. Results indicate that the as-prepared photosensitive hybrid materials have great applicability for the fabrication of micro-optical elements and advantage as the imprint layer under the ultraviolet soft imprint technique. - Highlights: ► Photosensitive TiO 2 /ormosil hybrid film is prepared by a sol–gel process. ► Optical properties of the films change a little with UV exposure time. ► Photo-chemical property of the film changes a lot with UV exposure time. ► The imprint force and time, and the UV exposure time affect the imprint fidelity. ► A fidelity value of 99.7% is obtained under an optimized condition

  2. Heart dose reduction in breast cancer treatment with simultaneous integrated boost. Comparison of treatment planning and dosimetry for a novel hybrid technique and 3D-CRT

    International Nuclear Information System (INIS)

    Joest, Vincent; Kretschmer, Matthias; Sabatino, Marcello; Wuerschmidt, Florian; Dahle, Joerg; Lorenzen, Joern; Ueberle, Friedrich

    2015-01-01

    The present study compares in silico treatment plans of clinically established three-dimensional conformal radiotherapy (3D-CRT) with a hybrid technique consisting of intensity-modulated radiotherapy (IMRT) and volumetric modulated arc radiotherapy (VMAT) during normally fractionated radiation of mammary carcinomas with simultaneous integrated boost on the basis of dose-volume histogram (DVH) parameters. Radiation treatment planning was performed with a hybrid and a 3D-CRT treatment plan for 20 patients. Hybrid plans were implemented with two tangential IMRT fields and a VMAT field in the angular range of the tangents. Verification of the plan was performed with a manufacturer-independent measurement system consisting of a detector array and rotation unit. The mean values of the heart dose for the entire patient collective were 3.6 ± 2.5 Gy for 3D-CRT and 2.9 ± 2.1 Gy for the hybrid technique (p < 0.01). For the left side (n = 10), the mean values for the left anterior descending artery were 21.8 ± 7.4 Gy for 3D-CRT and 17.6 ± 7.4 Gy for the hybrid technique (p < 0.01). The mean values of the ipsilateral lung were 11.9 ± 1.6 Gy for 3D-CRT and 10.5 ± 1.3 Gy for the hybrid technique (p < 0.01). Calculated dose distributions in the hybrid arm were in good accordance with measured dose (on average 95.6 ± 0.5 % for γ < 1 and 3 %/3 mm). The difference of the mean treatment time per fraction was 7 s in favor of 3D-CRT. Compared with the established 3D-CRT technique, the hybrid technique allows for a decrease in dose, particularly of the mean heart and lung dose with comparable target volume acquisition and without disadvantageous low-dose load of contralateral structures. Uncomplicated implementation of the hybrid technique was demonstrated in this context. The hybrid technique combines the advantages of tangential IMRT with the superior sparing of organs at risk by VMAT. (orig.) [de

  3. Genetic analysis of tumorigenesis: XXXII. Localization of constitutionally amplified KRAS sequences to Chinese hamster chromosomes X and Y by in situ hybridization.

    Science.gov (United States)

    Stenman, G; Anisowicz, A; Sager, R

    1988-11-01

    The KRAS gene is constitutionally amplified in the Chinese hamster. We have mapped the amplified sequences by in situ hybridization to two major sites on the X and Y chromosomes, Xq4 and Yp2. No autosomal site was detected despite a search under relaxed hybridization conditions. KRAS DNA is amplified about 50-fold compared to a human cell line known to have a diploid number of KRAS sequences, whereas mRNA expression is 5- to 10-fold lower than in normal human cells. While mRNA expression levels do not necessarily parallel gene copy number, the low expression level strongly suggests that the amplified sequences are transcriptionally silent. It is suggested that the amplified sequences arose from the original KRAS gene on chromosome 8 and that the KRAS sequences on the Y chromosome arose by X-Y recombination.

  4. Linkage of cDNA expression profiles of mesencephalic dopaminergic neurons to a genome-wide in situ hybridization database

    Directory of Open Access Journals (Sweden)

    Simon Horst H

    2009-01-01

    Full Text Available Abstract Midbrain dopaminergic neurons are involved in control of emotion, motivation and motor behavior. The loss of one of the subpopulations, substantia nigra pars compacta, is the pathological hallmark of one of the most prominent neurological disorders, Parkinson's disease. Several groups have looked at the molecular identity of midbrain dopaminergic neurons and have suggested the gene expression profile of these neurons. Here, after determining the efficiency of each screen, we provide a linked database of the genes, expressed in this neuronal population, by combining and comparing the results of six previous studies and verification of expression of each gene in dopaminergic neurons, using the collection of in situ hybridization in the Allen Brain Atlas.

  5. Mapping 3D genome architecture through in situ DNase Hi-C.

    Science.gov (United States)

    Ramani, Vijay; Cusanovich, Darren A; Hause, Ronald J; Ma, Wenxiu; Qiu, Ruolan; Deng, Xinxian; Blau, C Anthony; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, Zhijun

    2016-11-01

    With the advent of massively parallel sequencing, considerable work has gone into adapting chromosome conformation capture (3C) techniques to study chromosomal architecture at a genome-wide scale. We recently demonstrated that the inactive murine X chromosome adopts a bipartite structure using a novel 3C protocol, termed in situ DNase Hi-C. Like traditional Hi-C protocols, in situ DNase Hi-C requires that chromatin be chemically cross-linked, digested, end-repaired, and proximity-ligated with a biotinylated bridge adaptor. The resulting ligation products are optionally sheared, affinity-purified via streptavidin bead immobilization, and subjected to traditional next-generation library preparation for Illumina paired-end sequencing. Importantly, in situ DNase Hi-C obviates the dependence on a restriction enzyme to digest chromatin, instead relying on the endonuclease DNase I. Libraries generated by in situ DNase Hi-C have a higher effective resolution than traditional Hi-C libraries, which makes them valuable in cases in which high sequencing depth is allowed for, or when hybrid capture technologies are expected to be used. The protocol described here, which involves ∼4 d of bench work, is optimized for the study of mammalian cells, but it can be broadly applicable to any cell or tissue of interest, given experimental parameter optimization.

  6. MMP activity in the hybrid layer detected with in situ zymography.

    Science.gov (United States)

    Mazzoni, A; Nascimento, F D; Carrilho, M; Tersariol, I; Papa, V; Tjäderhane, L; Di Lenarda, R; Tay, F R; Pashley, D H; Breschi, L

    2012-05-01

    Dentinal proteases are believed to play an important role in the degradation of hybrid layers (HL). This study investigated the HL gelatinolytic activity by in situ zymography and functional enzyme activity assay. The hypotheses were that HLs created by an etch-and-rinse adhesive exhibit active gelatinolytic activity, and MMP-2 and -9 activities in dentin increase during adhesive procedures. Etched-dentin specimens were bonded with Adper Scotchbond 1XT and restored with composite. Adhesive/dentin interface slices were placed on microscope slides, covered with fluorescein-conjugated gelatin, and observed with a multi-photon confocal microscope after 24 hrs. Human dentin powder aliquots were prepared and assigned to the following treatments: A, untreated; B, etched with 10% phosphoric acid; or C, etched with 10% phosphoric acid and mixed with Scotchbond 1XT. The MMP-2 and -9 activities of extracts of dentin powder were measured with functional enzyme assays. Intense and continuous enzyme activity was detected at the bottom of the HL, while that activity was more irregular in the upper HL. Both acid-etching and subsequent adhesive application significantly increased MMP-2 and -9 activities (p < 0.05). The results demonstrate, for the first time, intrinsic MMP activity in the HL, and intense activation of matrix-bound MMP activity with both etching and adhesive application.

  7. The Diagnosis of Gastric Mucosa-associated Lymphoid Tissue Lymphoma by Flow Cytometry and Fluorescence in situ Hybridization of Biopsy Specimens.

    Science.gov (United States)

    Matsueda, Katsunori; Omote, Sizuma; Sakata, Masahiro; Fujita, Isao; Horii, Jouichiro; Toyokawa, Tatsuya

    2018-04-15

    Mucosa-associated lymphoid tissue (MALT) lymphoma and reactive inflammatory lymphoid changes are frequently difficult to distinguish based on a routine histological differential diagnosis. We were unable to diagnose gastric MALT lymphoma histologically using specimens obtained by endoscopy, although a flow cytometry (FCM) analysis demonstrated clonality of neoplastic cells by separating cells by CD45 gating. Furthermore, a fluorescence in situ hybridization (FISH) analysis showed trisomy 18. We therefore diagnosed gastric MALT lymphoma with trisomy 18. We recommend that FCM and FISH analyses of biopsy specimens be considered for diagnosing gastric MALT lymphoma if this diagnosis is suspected based on endoscopic findings.

  8. Whole-mount in situ hybridization in the rotifer Brachionus plicatilis representing a basal branch of lophotrochozoans.

    Science.gov (United States)

    Boell, Louis A; Bucher, Gregor

    2008-08-01

    In order to broaden the comparative scope of evolutionary developmental biology and to refine our picture of animal macroevolution, it is necessary to establish new model organisms, especially from previously underrepresented groups, like the Lophotrochozoa. We have established the culture and protocols for molecular developmental biology in the rotifer species Brachionus plicatilis Müller (Rotifera, Monogononta). Rotifers are nonsegmented animals with enigmatic basal position within the lophotrochozoans and marked by several evolutionary novelties like the wheel organ (corona), the median eye, and the nonpaired posterior foot. The expression of Bp-Pax-6 is shown using whole-mount in situ hybridization. The inexpensive easy culture and experimental tractability of Brachionus as well as the range of interesting questions to which it holds the key make it a promising addition to the "zoo" of evo-devo model organisms.

  9. Hybrid machine learning technique for forecasting Dhaka stock market timing decisions.

    Science.gov (United States)

    Banik, Shipra; Khodadad Khan, A F M; Anwer, Mohammad

    2014-01-01

    Forecasting stock market has been a difficult job for applied researchers owing to nature of facts which is very noisy and time varying. However, this hypothesis has been featured by several empirical experiential studies and a number of researchers have efficiently applied machine learning techniques to forecast stock market. This paper studied stock prediction for the use of investors. It is always true that investors typically obtain loss because of uncertain investment purposes and unsighted assets. This paper proposes a rough set model, a neural network model, and a hybrid neural network and rough set model to find optimal buy and sell of a share on Dhaka stock exchange. Investigational findings demonstrate that our proposed hybrid model has higher precision than the single rough set model and the neural network model. We believe this paper findings will help stock investors to decide about optimal buy and/or sell time on Dhaka stock exchange.

  10. Novel hybrid (magnet plus curve grasper) technique during transumbilical cholecystectomy: initial experience of a promising approach.

    Science.gov (United States)

    Millan, Carolina; Bignon, Horacion; Bellia, Gaston; Buela, Enrique; Rabinovich, Fernando; Albertal, Mariano; Martinez Ferro, Marcelo

    2013-10-01

    The use of magnets in transumbilical cholecystectomy (TUC) improves triangulation and achieves an optimal critical view. Nonetheless, the tendency of the magnets to collide hinders the process. In order to simplify the surgical technique, we developed a hybrid model with a single magnet and a curved grasper. All TUCs performed with a hybrid strategy in our pediatric population between September 2009 and July 2012 were retrospectively reviewed. Of 260 surgical procedures in which at least one magnet was used, 87 were TUCs. Of those, 62 were hybrid: 33 in adults and 29 in pediatric patients. The technique combines a magnet and a curved grasper. Through a transumbilical incision, we placed a 12-mm trocar and another flexible 5-mm trocar. The laparoscope with the working channel used the 12-mm trocar. The magnetic grasper was introduced to the abdominal cavity using the working channel to provide cephalic retraction of the gallbladder fundus. Across the flexible trocar, the assistant manipulated the curved grasper to mobilize the infundibulum. The surgeon operated through the working channel of the laparoscope. In this pediatric population, the mean age was 14 years (range, 4-17 years), and mean weight was 50 kg (range, 18-90 kg); 65% were girls. Mean operative time was 62 minutes. All procedures achieved a critical view of safety with no instrumental collision. There were no intraoperative or postoperative complications. The hospital stay was 1.4±0.6 days, and the median follow-up was 201 days. A hybrid technique, combining magnets and a curved grasper, simplifies transumbilical surgery. It seems feasible and safe for TUC and potentially reproducible.

  11. In situ tagging technique for fishes provides insight into growth and movement of invasive lionfish.

    Science.gov (United States)

    Akins, John L; Morris, James A; Green, Stephanie J

    2014-10-01

    Information on fish movement and growth is primarily obtained through the marking and tracking of individuals with external tags, which are usually affixed to anesthetized individuals at the surface. However, the quantity and quality of data obtained by this method is often limited by small sample sizes owing to the time associated with the tagging process, high rates of tagging-related mortality, and displacement of tagged individuals from the initial capture location. To address these issues, we describe a technique for applying external streamer and dart tags in situ, which uses SCUBA divers to capture and tag individual fish on the sea floor without the use of anesthetic. We demonstrate this method for Indo-Pacific lionfish (Pterois volitans/P. miles), species which are particularly vulnerable to barotrauma when transported to and handled at the surface. To test our method, we tagged 161 individuals inhabiting 26 coral reef locations in the Bahamas over a period of 3 years. Our method resulted in no instances of barotrauma, reduced handling and recovery time, and minimal post-tagging release displacement compared with conventional ex situ tag application. Opportunistic resighting and recapture of tagged individuals reveals that lionfish exhibit highly variable site fidelity, movement patterns, and growth rates on invaded coral reef habitats. In total, 24% of lionfish were resighted between 29 and 188 days after tagging. Of these, 90% were located at the site of capture, while the remaining individuals were resighted between 200 m and 1.1 km from initial site of capture over 29 days later. In situ growth rates ranged between 0.1 and 0.6 mm/day. While individuals tagged with streamer tags posted slower growth rates with increasing size, as expected, there was no relationship between growth rate and fish size for individuals marked with dart tags, potentially because of large effects of tag presence on the activities of small bodied lionfish (i.e., lionfish

  12. Preparation of Transparent Bulk TiO2/PMMA Hybrids with Improved Refractive Indices via an in Situ Polymerization Process Using TiO2 Nanoparticles Bearing PMMA Chains Grown by Surface-Initiated Atom Transfer Radical Polymerization.

    Science.gov (United States)

    Maeda, Satoshi; Fujita, Masato; Idota, Naokazu; Matsukawa, Kimihiro; Sugahara, Yoshiyuki

    2016-12-21

    Transparent TiO 2 /PMMA hybrids with a thickness of 5 mm and improved refractive indices were prepared by in situ polymerization of methyl methacrylate (MMA) in the presence of TiO 2 nanoparticles bearing poly(methyl methacrylate) (PMMA) chains grown using surface-initiated atom transfer radical polymerization (SI-ATRP), and the effect of the chain length of modified PMMA on the dispersibility of modified TiO 2 nanoparticles in the bulk hybrids was investigated. The surfaces of TiO 2 nanoparticles were modified with both m-(chloromethyl)phenylmethanoyloxymethylphosphonic acid bearing a terminal ATRP initiator and isodecyl phosphate with a high affinity for common organic solvents, leading to sufficient dispersibility of the surface-modified particles in toluene. Subsequently, SI-ATRP of MMA was achieved from the modified surfaces of the TiO 2 nanoparticles without aggregation of the nanoparticles in toluene. The molecular weights of the PMMA chains cleaved from the modified TiO 2 nanoparticles increased with increases in the prolonging of the polymerization period, and these exhibited a narrow distribution, indicating chain growth controlled by SI-ATRP. The nanoparticles bearing PMMA chains were well-dispersed in MMA regardless of the polymerization period. Bulk PMMA hybrids containing modified TiO 2 nanoparticles with a thickness of 5 mm were prepared by in situ polymerization of the MMA dispersion. The transparency of the hybrids depended significantly on the chain length of the modified PMMA on the nanoparticles, because the modified PMMA of low molecular weight induced aggregation of the TiO 2 nanoparticles during the in situ polymerization process. The refractive indices of the bulk hybrids could be controlled by adjusting the TiO 2 content and could be increased up to 1.566 for 6.3 vol % TiO 2 content (1.492 for pristine PMMA).

  13. JC virus chromogenic in situ hybridization in brain biopsies from patients with and without PML.

    Science.gov (United States)

    Procop, Gary W; Beck, Rose C; Pettay, James D; Kohn, Debra J; Tuohy, Marion J; Yen-Lieberman, Belinda; Prayson, Richard A; Tubbs, Raymond R

    2006-06-01

    Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease of the central nervous system caused by the JC polyoma virus. Electron microscopy and immunohistochemistry are the traditional methods of confirming the presence of the virus in brain biopsies from these patients. We studied the brain biopsies from 7 patients with PML and 6 patients without PML with chromogenic in situ hybridization (CISH) for the JC polyoma virus using a commercially available probe. The biopsies from the patients with the PML cases were proven to contain the JC polyoma virus by traditional and molecular methods. The CISH findings were compared with the known state of infection. All (7/7) of the biopsies from patients with PML were positive for the presence of polyoma virus by CISH, whereas the biopsies from patients without PML were uniformly negative. CISH seems to be a useful tool for the detection of the JC virus in brain biopsies from patients with PML, and is more accessible because a commercial probe is available.

  14. Surgical technique for en bloc transurethral resection of bladder tumour with a Hybrid Knife(®).

    Science.gov (United States)

    Islas-García, J J O; Campos-Salcedo, J G; López-Benjume, B I; Torres-Gómez, J J; Aguilar-Colmenero, J; Martínez-Alonso, I A; Gil-Villa, S A

    2016-05-01

    Bladder cancer is the second most common malignancy of the urinary tract and the 9th worldwide. Latin American has an incidence of 5.6 per 100,000 inhabitants per year. Seventy-five percent of newly diagnosed cases are nonmuscle invasive bladder cancer, and 25% of cases present as muscle invasive. The mainstay of treatment for nonmuscle invasive bladder cancer is loop transurethral resection. In 2013, the group led by Dr Mundhenk of the University Hospital of Tübingen, Germany, was the first to describe the Hybrid Knife(®) equipment for performing en bloc bladder tumour resection, with favourable functional and oncological results. To describe the surgical technique of en bloc bladder tumour resection with a Hybrid Knife(®) as an alternative treatment for nonmuscle invasive bladder tumours. A male patient was diagnosed by urotomography and urethrocystoscopy with a bladder tumour measuring 2×1cm on the floor. En bloc transurethral resection of the bladder tumour was performed with a Hybrid Knife(®). Surgery was performed for 35min, with 70 watts for cutting and 50 watts for coagulation, resecting and evacuating en bloc the bladder tumour, which macroscopically included the muscle layer of the bladder. There were no complications. The technique of en bloc bladder tumour resection with Hybrid Knife(®) is an effective alternative to bipolar loop transurethral resection. Resection with a Hybrid Knife(®) is a procedure with little bleeding and good surgical vision and minimises the risk of bladder perforation and tumour implants. The procedure facilitates determining the positivity of the neoplastic process, vascular infiltration and bladder muscle invasion in the histopathology study. Copyright © 2015 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

  15. The Metal-Zirconia Implant Fixed Hybrid Full-Arch Prosthesis: An Alternative Technique for Fabrication.

    Science.gov (United States)

    Stumpel, Lambert J; Haechler, Walter

    2018-03-01

    The metal-resin hybrid full-arch prosthesis has been a traditionally used type of restoration for full-arch implant fixed dentures. A newer development has centered around the use of monolithic zirconia or zirconia veneered with porcelain. Being a ceramic, zirconia has the potential for fracture. This article describes a technique that utilizes a metal substructure to support a chemically and mechanically resinbonded shell of zirconia. The workflow is discussed, ranging from in-office master cast fabrication to the CAD/ CAM production of the provisional and the definitive metal-zirconia prosthesis. The article also highlights the advantages and disadvantages of various materials used for hybrid prostheses.

  16. Solving Linear Equations by Classical Jacobi-SR Based Hybrid Evolutionary Algorithm with Uniform Adaptation Technique

    OpenAIRE

    Jamali, R. M. Jalal Uddin; Hashem, M. M. A.; Hasan, M. Mahfuz; Rahman, Md. Bazlar

    2013-01-01

    Solving a set of simultaneous linear equations is probably the most important topic in numerical methods. For solving linear equations, iterative methods are preferred over the direct methods especially when the coefficient matrix is sparse. The rate of convergence of iteration method is increased by using Successive Relaxation (SR) technique. But SR technique is very much sensitive to relaxation factor, {\\omega}. Recently, hybridization of classical Gauss-Seidel based successive relaxation t...

  17. Scanning electron microscopy and fluorescent in situ hybridization of experimental Brachyspira (Serpulina) pilosicoli infection in growing pigs

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Møller, Kristian; Boye, Mette

    2000-01-01

    Two groups of six 8-week-old pigs were challenged with 1X10(9) cfu Brachyspira (Serpulina) pilosicoli or Serpulina intermedia daily for 3 consecutive days to study the pathology of porcine colonic spirochetosis by scanning electron microscopy (SEM) and fluorescent in situ hybridization (FISH......; however, only two pigs developed transient watery diarrhea. S. intermedia was reisolated from four of the inoculated pigs, but clinical signs were not observed. Gross examination of the B. pilosicoli-infected pigs revealed dilated large intestines with a hyperemic mucosa, whereas the large intestines...... of the S. intermedia-inoculated pigs and the control pigs appeared normal. SEM examination of B. pilosicoli-infected pigs revealed degenerated epithelial cells and spirochetal colonization of the colonic mucosa in four pigs. By FISH, B. pilosicoli cells were found colonizing and invading the surface...

  18. Implementation and importance of fluorescence in situ hybridization (fish) in paraffin tissues for categorization of B-cell lymphoma unclassifiable, with features intermediate between Burkitt lymphoma and diffuse large B-cell lymphoma

    International Nuclear Information System (INIS)

    Carvajal Cuenca, Alejandra

    2011-01-01

    The diagnostic criteria have been defined based on the tools that the country has acquired and international guidelines for pure entities: the LB, LDCGB, and the new entity of B lymphoma unclassifiable with features intermediate LDCGB and LB. The fluorescence in situ hybridization for the translocation (8;14) has been implemented in paraffin tissues for proper categorization. A total of 21 cases have been studied: the characteristics of patients, morphology, immunohistochemistry and the presence or absence of the translocation (8;14). Twelve of the cases have been classified as B-cell lymphoma unclassifiable with features intermediate between LDCGB and LB. Furthermore, nine of the cases were classified in LB. Fluorescence in situ hybridization (FISH) has been negative in 5 of the 21 cases. The diagnosis of lymphoma with features bordering between the LB and the LDCGB has been imperative for the survival of the patient and the corresponding treatment [es

  19. In Silico and Fluorescence In Situ Hybridization Mapping Reveals Collinearity between the Pennisetum squamulatum Apomixis Carrier-Chromosome and Chromosome 2 of Sorghum and Foxtail Millet

    OpenAIRE

    Sapkota, Sirjan; Conner, Joann A.; Hanna, Wayne W.; Simon, Bindu; Fengler, Kevin; Deschamps, St?phane; Cigan, Mark; Ozias-Akins, Peggy

    2016-01-01

    Apomixis, or clonal propagation through seed, is a trait identified within multiple species of the grass family (Poaceae). The genetic locus controlling apomixis in Pennisetum squamulatum (syn Cenchrus squamulatus) and Cenchrus ciliaris (syn Pennisetum ciliare, buffelgrass) is the apospory-specific genomic region (ASGR). Previously, the ASGR was shown to be highly conserved but inverted in marker order between P. squamulatum and C. ciliaris based on fluorescence in situ hybridization (FISH) a...

  20. Cytogenetic, genomic in situ hybridization (GISH) and agronomic ...

    African Journals Online (AJOL)

    F3 generations of a wheat-Psathyrostachys huashanica intergeneric cross. Their agronomic traits were evaluated in the field and their meiotic behaviors and chromosome composition were analyzed by cytogenetic and GISH (genomic in situ ...

  1. Chromosome translocations in chinese medical X-ray workers analyzed by fluorescence in situ hybridization

    International Nuclear Information System (INIS)

    Sun Yuanming; Li Jin; Wang Qin; Tang Weisheng; Wang Zhiquan

    2002-01-01

    Objective: To study long-term radiation effect in occupational workers exposed to low dose X-rays using the method of fluorescence in situ hybridization (FISH). Method: Chromosome translocations of 25 medical X-ray workers were analyzed by FISH with chromosome No. 4 and No. 7 probes according to PAINT (The Protocol for Aberration Identification and Nomenclature Terminology) system. Results: The frequency of genome translocation in X-ray workers was (13.14 ± 1.23)/1000 cells. The rate of complete and incomplete translocation was 1:1.7. According to the calendar year of entry before/after the year of 1965 as the border, the data showed that the incomplete translocation of the after 1965 group was obviously higher than those of the controls (P < 0.01 and P < 0.05, respectively). Conclusion: The chromosome translocation in early Chinese medical X-ray workers is mainly the incomplete one, the frequency of translocation does not dependent on chromosomal DNA content, and incomplete and complete ones increase along with prolongation of working years in their position

  2. Fabrication of ridge waveguide structure from photosensitive TiO{sub 2}/ormosil hybrid films by using an ultraviolet soft imprint technique

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xuehua [Electronic Materials Research Laboratory, International Center for Dielectric Research, Xi' an Jiaotong University, Xi' an 710049, Shaanxi (China); Que, Wenxiu, E-mail: wxque@mail.xjtu.edu.cn [Electronic Materials Research Laboratory, International Center for Dielectric Research, Xi' an Jiaotong University, Xi' an 710049, Shaanxi (China); Chen, Jing; Gao, Tianxi; Hu, Jiaxing [Electronic Materials Research Laboratory, International Center for Dielectric Research, Xi' an Jiaotong University, Xi' an 710049, Shaanxi (China); Liu, Weiguo [Micro-optoelectronic Systems Laboratories, Xi' an Technological University, Xi' an 710032, Shaanxi (China)

    2013-03-01

    Photosensitive TiO{sub 2}/organically modified silane hybrid films were prepared by combining a low-temperature sol–gel process with a spin-coating technique. Optical properties and photochemical activities of the as-prepared hybrid sol–gel films under different UV irradiation time were characterized and monitored by prism coupling technique, UV–visible spectroscopy, and Fourier transform infrared spectroscopy. Surface morphology of the hybrid films was also observed by an atomic force microscopy. Advantages for fabrication of ridge waveguide structure based on the photosensitive hybrid films were demonstrated by an ultraviolet soft imprint technique. Effects of imprint force, imprint time, and UV irradiation time on high replication fidelity of the ridge waveguide structure were also investigated. An altitude replication fidelity of 99.7% can be obtained when the imprint force of 2 MPa, imprint time of 30 min and UV irradiation time of 45 min were chosen. Scanning electron microscopy and surface profiler were used to characterize the morphological and surface profile properties of the as fabricated ridge waveguide structure. Results indicate that the as-prepared photosensitive hybrid materials have great applicability for the fabrication of micro-optical elements and advantage as the imprint layer under the ultraviolet soft imprint technique. - Highlights: ► Photosensitive TiO{sub 2}/ormosil hybrid film is prepared by a sol–gel process. ► Optical properties of the films change a little with UV exposure time. ► Photo-chemical property of the film changes a lot with UV exposure time. ► The imprint force and time, and the UV exposure time affect the imprint fidelity. ► A fidelity value of 99.7% is obtained under an optimized condition.

  3. Automated brightfield dual-color in situ hybridization for detection of mouse double minute 2 gene amplification in sarcomas.

    Science.gov (United States)

    Zhang, Wenjun; McElhinny, Abigail; Nielsen, Alma; Wang, Maria; Miller, Melanie; Singh, Shalini; Rueger, Ruediger; Rubin, Brian P; Wang, Zhen; Tubbs, Raymond R; Nagle, Raymond B; Roche, Pat; Wu, Ping; Pestic-Dragovich, Lidija

    2011-01-01

    The human homolog of the mouse double minute 2 (MDM2) oncogene is amplified in about 20% of sarcomas. The measurement of the MDM2 amplification can aid in classification and may provide a predictive value for recently formulated therapies targeting MDM2. We have developed and validated an automated bright field dual-color in situ hybridization application to detect MDM2 gene amplification. A repeat-depleted MDM2 probe was constructed to target the MDM2 gene region at 12q15. A chromosome 12-specific probe (CHR12) was generated from a pα12H8 plasmid. The in situ hybridization assay was developed by using a dinitrophenyl-labeled MDM2 probe and a digoxigenin-labeled CHR12 probe on the Ventana Medical Systems' automated slide-staining platforms. The specificity of the MDM2 and CHR12 probes was shown on metaphase spreads and further validated against controls, including normal human tonsil and known MDM2-amplified samples. The assay performance was evaluated on a cohort of 100 formalin-fixed, paraffin-embedded specimens by using a conventional bright field microscope. Simultaneous hybridization and signal detection for MDM2 and CHR12 showed that both DNA targets were present in the same cells. One hundred soft tissue specimens were stained for MDM2 and CHR12. Although 26 of 29 lipomas were nonamplified and eusomic, MDM2 amplification was noted in 78% of atypical lipomatous tumors or well-differentiated liposarcomas. Five of 6 dedifferentiated liposarcoma cases were amplified for MDM2. MDM2 amplification was observed in 1 of 8 osteosarcomas; 3 showed CHR12 aneusomy. MDM2 amplification was present in 1 of 4 chondrosarcomas. Nine of 10 synovial sarcomas displayed no evidence of MDM2 amplification in most tumor cells. In pleomorphic sarcoma, not otherwise specified (pleomorphic malignant fibrous histiocytoma), MDM2 was amplified in 38% of cases, whereas 92% were aneusomic for CHR12. One alveolar rhabdomyosarcoma and 2 embryonal rhabdomyosarcomas displayed low-level aneusomy

  4. Combustion synthesis of advanced materials. [using in-situ infiltration technique

    Science.gov (United States)

    Moore, J. J.; Feng, H. J.; Perkins, N.; Readey, D. W.

    1992-01-01

    The combustion synthesis of ceramic-metal composites using an in-situ liquid infiltration technique is described. The effect of varying the reactants and their stoichiometry to provide a range of reactant and product species i.e. solids, liquids and gases, with varying physical properties e.g. thermal conductivity, on the microstructure and morphology of synthesized products is also described. Alternatively, conducting the combustion synthesis reaction in a reactive gas environment is also discussed, in which advantages can be gained from the synergistic effects of combustion synthesis and vapor phase transport. In each case, the effect of the presence or absence of gravity (density) driven fluid flow and vapor transport is discussed as is the potential for producing new and perhaps unique materials by conducting these SHS reactions under microgravity conditions.

  5. Facile approach to prepare Pt decorated SWNT/graphene hybrid catalytic ink

    Energy Technology Data Exchange (ETDEWEB)

    Mayavan, Sundar, E-mail: sundarmayavan@cecri.res.in [Centre for Innovation in Energy Research, CSIR–Central Electrochemical Research Institute, Karaikudi 630006, Tamil Nadu (India); Department of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 305-701 (Korea, Republic of); Mandalam, Aditya; Balasubramanian, M. [Centre for Innovation in Energy Research, CSIR–Central Electrochemical Research Institute, Karaikudi 630006, Tamil Nadu (India); Sim, Jun-Bo [Department of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 305-701 (Korea, Republic of); Choi, Sung-Min, E-mail: sungmin@kaist.ac.kr [Department of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 305-701 (Korea, Republic of)

    2015-07-15

    Highlights: • Pt NPs were in situ synthesized onto CNT–graphene support in aqueous solution. • The as-prepared material was used directly as a catalyst ink without further treatment. • Catalyst ink is active toward methanol oxidation. • This approach realizes both scalable and greener production of hybrid catalysts. - Abstract: Platinum nanoparticles were in situ synthesized onto hybrid support involving graphene and single walled carbon nanotube in aqueous solution. We investigate the reduction of graphene oxide, and platinum nanoparticle functionalization on hybrid support by X-ray photoelectron spectroscopy, Raman spectroscopy, X-ray diffraction, scanning electron microscopy and transmission electron microscopy. The as-prepared platinum on hybrid support was used directly as a catalyst ink without further treatment and is active toward methanol oxidation. This work realizes both scalable and greener production of highly efficient hybrid catalysts, and would be valuable for practical applications of graphene based fuel cell catalysts.

  6. Hybrid 3D printing by bridging micro/nano processes

    International Nuclear Information System (INIS)

    Yoon, Hae-Sung; Jang, Ki-Hwan; Kim, Eunseob; Lee, Hyun-Taek; Ahn, Sung-Hoon

    2017-01-01

    A hybrid 3D printing process was developed for multiple-material/freeform nano-scale manufacturing. The process consisted of aerodynamically focused nanoparticle (AFN) printing, micro-machining, focused ion beam milling, and spin-coating. Theoretical and experimental investigations were carried out to improve the compatibility of each of the processes, enabling bridging of various different techniques. The resulting hybrid process could address the limitations of individual processes, enabling improved process scaling and dimensional degrees of freedom, without losing the advantages of the existing processes. The minimum structure width can be reduced to 50 nm using undercut structures. In addition, AFN printing employs particle impact for adhesion, and various inorganic materials are suitable for printing, including metals and functional ceramics. Using the developed system, we fabricated bi-material cantilevers for applications as a thermal actuator. The mechanical and thermal properties of the structure were investigated using an in situ measurement system, and irregular thermal phenomena due to the fabrication process were analyzed. We expect that this work will lead to improvements in the area of customized nano-scale manufacturing, as well as further improvements in manufacturing technology by combining different fabrication techniques. (paper)

  7. Hybrid 3D printing by bridging micro/nano processes

    Science.gov (United States)

    Yoon, Hae-Sung; Jang, Ki-Hwan; Kim, Eunseob; Lee, Hyun-Taek; Ahn, Sung-Hoon

    2017-06-01

    A hybrid 3D printing process was developed for multiple-material/freeform nano-scale manufacturing. The process consisted of aerodynamically focused nanoparticle (AFN) printing, micro-machining, focused ion beam milling, and spin-coating. Theoretical and experimental investigations were carried out to improve the compatibility of each of the processes, enabling bridging of various different techniques. The resulting hybrid process could address the limitations of individual processes, enabling improved process scaling and dimensional degrees of freedom, without losing the advantages of the existing processes. The minimum structure width can be reduced to 50 nm using undercut structures. In addition, AFN printing employs particle impact for adhesion, and various inorganic materials are suitable for printing, including metals and functional ceramics. Using the developed system, we fabricated bi-material cantilevers for applications as a thermal actuator. The mechanical and thermal properties of the structure were investigated using an in situ measurement system, and irregular thermal phenomena due to the fabrication process were analyzed. We expect that this work will lead to improvements in the area of customized nano-scale manufacturing, as well as further improvements in manufacturing technology by combining different fabrication techniques.

  8. The in situ side-to-side bypass technique: a comprehensive review of the technical characteristics, current anastomosis approaches and surgical experience.

    Science.gov (United States)

    Wang, Long; Cai, Li; Qian, Hai; Lawton, Michael T; Shi, Xiang'en

    2018-05-02

    In situ side-to-side (STS) revascularization is an intracranial-intracranial (IC-IC) bypass technique that is increasingly used to treat complex aneurysms and cerebral ischemia. This sophisticated technique involves connecting two proximal parallel vessels to create an artificial conduit for blood flow. This study aims to provide a detailed description of the configuration of the STS bypass technique and extensive information regarding its technical characteristics, current anastomosis approaches and surgical significance. A literature search was performed using the PubMed, Medline, ScienceDirect, Embase, Wiley Online Library, Cambridge Journals, SAGE Journals, Oxford Journals, Research Gate, and Google Scholar databases. The terms "intracranial-intracranial bypass", "in situ bypass", "communicating bypass" and "STS anastomosis" were searched to identify pertinent articles. Articles involving in situ STS anastomosis combined with other bypass methods were excluded. Computer tablet-drawn illustrations of this technique are provided to enhance comprehension. In total, seventy articles that met our search and inclusion criteria were identified. Overall, the radiographical and clinical outcomes of one-hundred and thirty-two (125 aneurysm and 7 cerebral ischemia) patients who underwent in situ STS revascularization were analyzed. IC-IC bypass in the STS fashion can be a safe and effective strategy for the management of complex intracranial aneurysms and cerebral ischemia and is particularly attractive in rescue, anticipated and troubleshooting cases. Despite its extreme rarity, a de novo aneurysm may be observed following STS anastomosis; thus, long-term follow-up is mandatory. Vascular neurosurgeons should consider including this procedure in their treatment armamentarium. Copyright © 2018. Published by Elsevier Inc.

  9. Y-chromosome status identification suggests a recipient origin of posttransplant non-small cell lung carcinomas: chromogenic in situ hybridization analysis.

    Science.gov (United States)

    Chen, Wei; Brodsky, Sergey V; Zhao, Weiqiang; Otterson, Gregory A; Villalona-Calero, Miguel; Satoskar, Anjali A; Hasan, Ayesha; Pelletier, Ronald; Ivanov, Iouri; Ross, Patrick; Nadasdy, Tibor; Shilo, Konstantin

    2014-05-01

    Owing to the need of lifelong immunosuppression, solid-organ transplant recipients are known to have an increased risk of posttransplant malignancies including lung cancer. Posttransplant neoplastic transformation of donor-derived cells giving rise to hematopoietic malignancies, Kaposi sarcoma, and basal cell carcinoma in nongraft tissues has been reported. The goal of this study was to assess the cell origin (donor versus recipient derived) of posttransplant non-small cell lung carcinomas (NSCLCs) in kidney and heart transplant recipients. An institutional database search identified 2557 kidney and heart transplant recipients in 8 consecutive years. Among this cohort, 20 (0.8%) renal and 18 (0.7%) heart transplant recipients developed NSCLC. The study cohort comprised 6 of 38 NSCLCs arising in donor-recipient sex-mismatched transplant patients. The tumor cell origin was evaluated by chromogenic in situ hybridization with Y-chromosome probe on formalin-fixed, paraffin-embedded tissues. Y-chromosome was identified in 97% ± 1% (range from 92% to 99%) of all types of nucleated cells in male control tissues. In all 5 NSCLCs from male recipients of female donor organ, Y-chromosome was identified in 97% ± 2% (range from 92% to 100%) of tumor cells, statistically equivalent to normal control (P recipient of male kidney. These findings suggest a recipient derivation of NSCLC arising in kidney and heart transplant recipients. A combination of histologic evaluation and chromogenic in situ hybridization with Y-chromosome analysis allows reliable determination of tissue origin in sex-mismatched solid-organ transplant recipients and may aid in management of posttransplant malignancy in such cases. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Experimental and mathematical simulation techniques for determining an in-situ response testing method for neutron sensors used in reactor power plant protection systems

    International Nuclear Information System (INIS)

    Behbahani, A.

    1983-01-01

    An analytical neutron sensor response model and methods for transient response measurements of neutron sensors (compensated ionization chamber), including possible in-situ techniques have been developed and evaluated to meet the provisions of Draft Standard ISA Sd67.06, IEEE 338-1977, and NRC Guide 1.118. One in-situ method requires the perturbation of the high voltage detector (sensor) power supply and measurement of the sensor response. The response to a perturbation of the power supply is related to the response of the sensor to a transient change in neutron flux. Random signal analysis is another in-situ technique to monitor the neutron sensor response. In this method the power spectrum of the inherent fluctuations from the neutron sensor output (current in CIC) are measured and evaluated. Transient response techniques (including in-situ methods) are experimentally and analytically evaluated to identify the mechanisms which may cause degradation in the response of the neutron sensors. The objective of the experimental evaluation was to correlate the measured response time using transient radiation flux changes and power supply perturbation. The objective of the analytical model of the different sensor response was to predict response time and degradation mechanisms

  11. Innovative hybrid pile oscillator technique in the Minerve reactor: open loop vs. closed loop

    Science.gov (United States)

    Geslot, Benoit; Gruel, Adrien; Bréaud, Stéphane; Leconte, Pierre; Blaise, Patrick

    2018-01-01

    Pile oscillator techniques are powerful methods to measure small reactivity worth of isotopes of interest for nuclear data improvement. This kind of experiments has long been implemented in the Mineve experimental reactor, operated by CEA Cadarache. A hybrid technique, mixing reactivity worth estimation and measurement of small changes around test samples is presented here. It was made possible after the development of high sensitivity miniature fission chambers introduced next to the irradiation channel. A test campaign, called MAESTRO-SL, took place in 2015. Its objective was to assess the feasibility of the hybrid method and investigate the possibility to separate mixed neutron effects, such as fission/capture or scattering/capture. Experimental results are presented and discussed in this paper, which focus on comparing two measurements setups, one using a power control system (closed loop) and another one where the power is free to drift (open loop). First, it is demonstrated that open loop is equivalent to closed loop. Uncertainty management and methods reproducibility are discussed. Second, results show that measuring the flux depression around oscillated samples provides valuable information regarding partial neutron cross sections. The technique is found to be very sensitive to the capture cross section at the expense of scattering, making it very useful to measure small capture effects of highly scattering samples.

  12. In Situ Production of Graphene-Fiber Hybrid Structures

    DEFF Research Database (Denmark)

    Akia, Mandana; Cremar, Lee; Chipara, Mircea

    2017-01-01

    We report a scalable method to obtain a new material where large graphene sheets form webs linking carbon fibers. Film-fiber hybrid nonwoven mats are formed during fiber processing and converted to carbon structures after a simple thermal treatment. This contrasts with multistep methods...... that attempt to mix previously prepared graphene and fibers, or require complicated and costly processes for deposition of graphene over carbon fibers. The developed graphene-fiber hybrid structures have seamless connections between graphene and fibers, and in fact the graphene "veils" extend directly from one...... a capillarity effect that promoted the formation of thin veils, which become graphene sheets upon dehydration by sulfuric acid vapor followed by carbonization (at relatively low temperatures, below 800 °C). These veils extend over several micrometers within the pores of the fiber network, and consist...

  13. Development of Advanced In-Situ Techniques for Chemistry Monitoring and Corrosion Mitigation in SCWO Environments

    International Nuclear Information System (INIS)

    Macdonald, D. D.; Lvov, S. N.

    2000-01-01

    This project is developing sensing technologies and corrosion monitoring techniques for use in super critical water oxidation (SCWO) systems to reduce the volume of mixed low-level nuclear waste by oxidizing organic components in a closed cycle system where CO2 and other gaseous oxides are produced, leaving the radioactive elements concentrated in ash. The technique uses water at supercritical temperatures under highly oxidized conditions by maintaining a high fugacity of molecular oxygen in the system, which causes high corrosion rates of even the most corrosive resistant reactor materials. This project significantly addresses the high corrosion shortcoming through development of (a) advanced electrodes and sensors for in situ potentiometric monitoring of pH in high subcritical and supercritical aqueous solutions, (b) an approach for evaluating the association constants for 1-1 aqueous electrolytes using a flow-through electrochemical thermocell; (c) an electrochemical noise sensor for the in situ measurement of corrosion rate in subcritical and supercritical aqueous systems; (d) a model for estimating the effect of pressure on reaction rates, including corrosion reactions, in high subcritical and supercritical aqueous systems. The project achieved all objectives, except for installing some of the sensors into a fully operating SCWO system

  14. Development of Advanced In-Situ Techniques for Chemistry Monitoring and Corrosion Mitigation in SCWO Environments

    Energy Technology Data Exchange (ETDEWEB)

    Macdonald, D. D.; Lvov, S. N.

    2000-03-31

    This project is developing sensing technologies and corrosion monitoring techniques for use in super critical water oxidation (SCWO) systems to reduce the volume of mixed low-level nuclear waste by oxidizing organic components in a closed cycle system where CO2 and other gaseous oxides are produced, leaving the radioactive elements concentrated in ash. The technique uses water at supercritical temperatures under highly oxidized conditions by maintaining a high fugacity of molecular oxygen in the system, which causes high corrosion rates of even the most corrosive resistant reactor materials. This project significantly addresses the high corrosion shortcoming through development of (a) advanced electrodes and sensors for in situ potentiometric monitoring of pH in high subcritical and supercritical aqueous solutions, (b) an approach for evaluating the association constants for 1-1 aqueous electrolytes using a flow-through electrochemical thermocell; (c) an electrochemical noise sensor for the in situ measurement of corrosion rate in subcritical and supercritical aqueous systems; (d) a model for estimating the effect of pressure on reaction rates, including corrosion reactions, in high subcritical and supercritical aqueous systems. The project achieved all objectives, except for installing some of the sensors into a fully operating SCWO system.

  15. [Chromosomal localization of foreign genes in transgenic mice using dual-color fluorescence in situ hybridization].

    Science.gov (United States)

    Lin, Dan; Gong, Xiu-li; Li, Wei; Guo, Xin-bing; Zhu, Yi-wen; Huang, Ying

    2008-02-01

    To establish a highly sensitive and specific dual-color fluorescence in situ hybridization (D-FISH) method used for chromosomal localization of foreign genes in double transgenic mice. Two strains of double transgenic mice were used in this experiment, one was integrated with the herpes simplex virus thymidine kinase (HSV-tk) and the enhanced green fluorescence protein (eGFP), the other was with the short hairpin RNA interference(RNAi) and beta(654). Splenic cells cultured in vitro were arrested in metaphase by colchicine and hybridized with digoxigenin-labeled and biotinylated DNA probes, then detected by rhodamine-conjugated avidin and FITC-conjugated anti-digoxigenin. Dual-color fluorescence signals were detected on the same metaphase in both transgenic mice strains. In HSV-tk/eGFP double transgenic mice, strong green fluorescence for HSV-tk and red for eGFP were observed and localized at 2E5-G3 and 8A2-A4 respectively. In beta(654)/RNAi mice, beta(654) was detected as red fluorescence on chromosome 7D3-E2, and RNAi showed random integration on chromosomes. It was detected as green fluorescence on chromosome 12B1 in one mouse, while on 1E2.3-1F and 3A3 in the other. Highly sensitive and specific D-FISH method was established using the self-prepared DNA probes, and chromosomal localization of the foreign genes was also performed in combination with G-banding in double transgenic mice. This technology will facilitate the researches in transgenic animals and gene therapy models.

  16. In Situ Detection of MicroRNA Expression with RNAscope Probes.

    Science.gov (United States)

    Yin, Viravuth P

    2018-01-01

    Elucidating the spatial resolution of gene transcripts provides important insight into potential gene function. MicroRNAs are short, singled-stranded noncoding RNAs that control gene expression through base-pair complementarity with target mRNAs in the 3' untranslated region (UTR) and inhibiting protein expression. However, given their small size of ~22- to 24-nt and low expression levels, standard in situ hybridization detection methods are not amendable for microRNA spatial resolution. Here, I describe a technique that employs RNAscope probe design and propriety amplification technology that provides simultaneous single molecule detection of individual microRNA and its target gene. This method allows for rapid and sensitive detection of noncoding RNA transcripts in frozen tissue sections.

  17. Ternary hybrid polymeric nanocomposites through grafting of polystyrene on graphene oxide-TiO{sub 2} by surface initiated atom transfer radical polymerization (SI-ATRP)

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Arvind; Bansal, Ankushi; Behera, Babita; Jain, Suman L.; Ray, Siddharth S., E-mail: ssray@iip.res.in

    2016-04-01

    A ternary hybrid of graphene oxide-titania-polystyrene (GO-TiO{sub 2}-PS) nanocomposite is developed where polystyrene composition is regulated by controlling growth of polymer chains and nanoarchitectonics is discussed. Graphene Oxide-TiO{sub 2} (GO-TiO{sub 2}) nanocomposite is prepared by in-situ hydrothermal method and the surface is anchored with α-bromoisobutyryl bromide to activate GO-TiO{sub 2} as initiator for polymerization. In-situ grafting of polystyrene through surface initiated atom transfer radical polymerization (SI- ATRP) on this Br-functionalized nano-composite initiator yields GO-TiO{sub 2}-PS ternary hybrid. Varying the monomer amount and keeping the concentration of initiator constant, polystyrene chain growth is regulated with narrow poly-dispersivity to achieve desired composition. This composite is well characterized by various analytical techniques like FTIR, XRD, DSC, SEM, TEM, and TGA. - Highlights: • Nanocomposite of ternary hybrid of GO-TiO{sub 2} with polystyrene. • PS is surface grafted on GO-TiO{sub 2}. • Polymer chain lengths are well regulated by SI-ATRP living polymerization. • Thermal stability of this hybrid is relatively high.

  18. Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

    Science.gov (United States)

    Cara, Nicolás; Marfil, Carlos F; Masuelli, Ricardo W

    2013-01-01

    Interspecific hybridization is known for triggering genetic and epigenetic changes, such as modifications on DNA methylation patterns and impact on phenotypic plasticity and ecological adaptation. Wild potatoes (Solanum, section Petota) are adapted to multiple habitats along the Andes, and natural hybridizations have proven to be a common feature among species of this group. Solanum × rechei, a recently formed hybrid that grows sympatrically with the parental species S. kurtzianum and S. microdontum, represents an ideal model for studying the ecologically and evolutionary importance of hybridization in generating of epigenetic variability. Genetic and epigenetic variability and their correlation with morphological variation were investigated in wild and ex situ conserved populations of these three wild potato species using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques. We observed that novel methylation patterns doubled the number of novel genetic patterns in the hybrid and that the morphological variability measured on 30 characters had a higher correlation with the epigenetic than with the genetic variability. Statistical comparison of methylation levels suggested that the interspecific hybridization induces genome demethylation in the hybrids. A Bayesian analysis of the genetic data reveled the hybrid nature of S. × rechei, with genotypes displaying high levels of admixture with the parental species, while the epigenetic information assigned S. × rechei to its own cluster with low admixture. These findings suggested that after the hybridization event, a novel epigenetic pattern was rapidly established, which might influence the phenotypic plasticity and adaptation of the hybrid to new environments. PMID:24198938

  19. A hybrid lightwave transmission system based on light injection/optoelectronic feedback techniques and fiber-VLLC integration

    International Nuclear Information System (INIS)

    Tsai, Wen-Shing; Lu, Hai-Han; Li, Chung-Yi; Chen, Bo-Rui; Lin, Hung-Hsien; Lin, Dai-Hua

    2016-01-01

    A hybrid lightwave transmission system based on light injection/optoelectronic feedback techniques and fiber-visible laser light communication (VLLC) integration is proposed and experimentally demonstrated. To be the first one of its kind in employing light injection and optoelectronic feedback techniques in a fiber-VLLC integration lightwave transmission system, the light is successfully directly modulated with Community Access Television (CATV), 16-QAM, and 16-QAM-OFDM signals. Over a 40 km SMF and a 10 m free-space VLLC transport, good performances of carrier-to-noise ratio (CNR)/composite second-order (CSO)/composite triple-beat (CTB)/bit error rate (BER) are achieved for CATV/16-QAM/16-QAM-OFDM signals transmission. Such a hybrid lightwave transmission system would be very useful since it can provide broadband integrated services including CATV, Internet, and telecommunication services over both distribute fiber and in-building networks. (letter)

  20. Performance of the In Situ Microcosm Technique for Measuring the Degradation of Organic Chemicals in Aquifers

    DEFF Research Database (Denmark)

    Nielsen, Per H.; Christensen, Thomas Højlund; Albrechtsen, Hans-Jørgen

    1996-01-01

    chemicals in polluted and pristine aquifers representing different redox environments. The ISM technique has great potential for providing field-relevant degradation potentials and rate constants, but care must be taken in using the equipment and interpreting the results. This paper provides details......An in situ microcosm (ISM) consists of a stainless steel cylinder isolating about 2 L of the aquifer and is equipped with valves allowing for loading and sampling from the ground surface. During the last five years, this technique has been used frequently to study the degradation of organic...

  1. Development of in-situ laser based cutting technique for shock absorber rear nut in pressurized heavy water reactors. CP-2.1

    International Nuclear Information System (INIS)

    Vishwakarma, S.C.; Jain, R.K.; Upadhyaya, B.N.; Choubey, Ambar; Agrawal, D.K.; Oak, S.M.

    2007-01-01

    We have developed a laser based cutting technique for shock absorber rear nuts in pressurized heavy water reactors (PHWRs). This technique has been successfully used for in-situ laser cutting at RAPS-3 reactor. The technique consists of a motorized compact fixture, which holds a fiber optic beam delivery cutting nozzle and can be operated remotely

  2. Two-dimensional Semiconductor-Superconductor Hybrids

    DEFF Research Database (Denmark)

    Suominen, Henri Juhani

    This thesis investigates hybrid two-dimensional semiconductor-superconductor (Sm-S) devices and presents a new material platform exhibiting intimate Sm-S coupling straight out of the box. Starting with the conventional approach, we investigate coupling superconductors to buried quantum well....... To overcome these issues we integrate the superconductor directly into the semiconducting material growth stack, depositing it in-situ in a molecular beam epitaxy system under high vacuum. We present a number of experiments on these hybrid heterostructures, demonstrating near unity interface transparency...

  3. In-situ, real-time, studies of film growth processes using ion scattering and direct recoil spectroscopy techniques.

    Energy Technology Data Exchange (ETDEWEB)

    Smentkowski, V. S.

    1999-04-22

    Time-of-flight ion scattering and recoil spectroscopy (TOF-ISARS) enables the characterization of the composition and structure of surfaces with 1-2 monolayer specificity. It will be shown that surface analysis is possible at ambient pressures greater than 3 mTorr using TOF-ISARS techniques; allowing for real-time, in situ studies of film growth processes. TOF-ISARS comprises three analytical techniques: ion scattering spectroscopy (ISS), which detects the backscattered primary ion beam; direct recoil spectroscopy (DRS), which detects the surface species recoiled into the forward scattering direction; and mass spectroscopy of recoiled ions (MSRI), which is 3 variant of DRS capable of isotopic resolution for all surface species--including H and He. The advantages and limitations of each of these techniques will be discussed. The use of the three TOF-ISARS methods for real-time, in situ film growth studies at high ambient pressures will be illustrated. It will be shown that MSRI analysis is possible during sputter deposition. It will be also be demonstrated that the analyzer used for MSRI can also be used for time of flight secondary ion mass spectroscopy (TOF-SIMS) under high vacuum conditions. The use of a single analyzer to perform the complimentary surface analytical techniques of MSRI and SIMS is unique. The dwd functionality of the MSRI analyzer provides surface information not obtained when either MSRI or SIMS is used independently.

  4. Hybrid image classification technique for land-cover mapping in the Arctic tundra, North Slope, Alaska

    Science.gov (United States)

    Chaudhuri, Debasish

    Remotely sensed image classification techniques are very useful to understand vegetation patterns and species combination in the vast and mostly inaccessible arctic region. Previous researches that were done for mapping of land cover and vegetation in the remote areas of northern Alaska have considerably low accuracies compared to other biomes. The unique arctic tundra environment with short growing season length, cloud cover, low sun angles, snow and ice cover hinders the effectiveness of remote sensing studies. The majority of image classification research done in this area as reported in the literature used traditional unsupervised clustering technique with Landsat MSS data. It was also emphasized by previous researchers that SPOT/HRV-XS data lacked the spectral resolution to identify the small arctic tundra vegetation parcels. Thus, there is a motivation and research need to apply a new classification technique to develop an updated, detailed and accurate vegetation map at a higher spatial resolution i.e. SPOT-5 data. Traditional classification techniques in remotely sensed image interpretation are based on spectral reflectance values with an assumption of the training data being normally distributed. Hence it is difficult to add ancillary data in classification procedures to improve accuracy. The purpose of this dissertation was to develop a hybrid image classification approach that effectively integrates ancillary information into the classification process and combines ISODATA clustering, rule-based classifier and the Multilayer Perceptron (MLP) classifier which uses artificial neural network (ANN). The main goal was to find out the best possible combination or sequence of classifiers for typically classifying tundra type vegetation that yields higher accuracy than the existing classified vegetation map from SPOT data. Unsupervised ISODATA clustering and rule-based classification techniques were combined to produce an intermediate classified map which was

  5. N-isopropylacrylamide-based fine-dispersed thermosensitive ferrogels obtained via in-situ technique.

    Science.gov (United States)

    Korotych, O; Samchenko, Yu; Boldeskul, I; Ulberg, Z; Zholobak, N; Sukhodub, L

    2013-03-01

    Thermosensitive hydrogels with magnetic properties (ferrogels) are very promising for medical application, first of all, for the design of targeted delivery systems with controlled release of drugs and for magnetic hyperthermia and chemotherapy treatment of cancer. These magnetic hydrogels could be obtained using diverse techniques: ex- and in-situ syntheses. The present work is devoted to the study of magnetite (Fe(3)O(4)) formation inside the nanoreactors of (co)polymeric hydrogels. Polymeric templates (hydrogel films and fine-dispersed hydrogels) used for obtaining ferrogels were based on acrylic monomers: thermosensitive N-isopropylacrylamide, and hydrophilic acrylamide. Covalent cross-linking was accomplished using bifunctional monomer N,N'-methylenebisacrylamide. Influence of hydrophilic-lipophilic balance of polymeric templates and concentration of iron cations on the magnetite formation were investigated along with the development of ferrogel preparation technique. Cytotoxicity, physical and chemical properties of obtained magnetic hydrogels have been studied in this work. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Radiation induced wheat-rye chromosomal translocations in triticale. Optimizing the dose using fluorescence in situ hybridization

    International Nuclear Information System (INIS)

    Ahmad, F.; Comeau, A.; Chen, Q.; Collin, J.; St-Pierre, C.A.

    2000-01-01

    Fluorescent in situ hybridization (FISH) was utilized to monitor the level of ionizing radiation ( 60 Co source) in their ability to cause intra- and intergeneric chromosomal aberrations in triticale seeds. Seeds were irradiated with 0, 20, 50, 100, 200, 300, 400, 500 and 1000 Gy doses. The root growth of irradiated seeds was greatly inhibited at 200 Gy and above. Various types of aberrations including wheat-rye, wheat-wheat, rye-rye, wheat-rye-wheat, rye-wheat-rye translocations and acentric fragments with or without translocations were observed. There was a consistent increase in proportion of aberrations per cell with an increase in radiation dose. It was concluded that for an optimal level of chromosomal translocation and least number of acentric fragments, a 20 Gy dose was quite sufficient for inducing a desirable level of wheat-rye chromosomal translocations. The excellent efficiency and importance of utilizing FISH in such studies of alien-introgression via chromosomal translocations are discussed. (author)

  7. Radiation induced wheat-rye chromosomal translocations in triticale. Optimizing the dose using fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Ahmad, F. [Brandon Univ., Manitoba (Canada); Comeau, A.; Chen, Q.; Collin, J.; St-Pierre, C.A.

    2000-03-01

    Fluorescent in situ hybridization (FISH) was utilized to monitor the level of ionizing radiation ({sup 60}Co source) in their ability to cause intra- and intergeneric chromosomal aberrations in triticale seeds. Seeds were irradiated with 0, 20, 50, 100, 200, 300, 400, 500 and 1000 Gy doses. The root growth of irradiated seeds was greatly inhibited at 200 Gy and above. Various types of aberrations including wheat-rye, wheat-wheat, rye-rye, wheat-rye-wheat, rye-wheat-rye translocations and acentric fragments with or without translocations were observed. There was a consistent increase in proportion of aberrations per cell with an increase in radiation dose. It was concluded that for an optimal level of chromosomal translocation and least number of acentric fragments, a 20 Gy dose was quite sufficient for inducing a desirable level of wheat-rye chromosomal translocations. The excellent efficiency and importance of utilizing FISH in such studies of alien-introgression via chromosomal translocations are discussed. (author)

  8. Chromogenic in situ hybridization (CISH): a novel alternative in screening archival breast cancer tissue samples for HER-2/neu status.

    Science.gov (United States)

    Madrid, Manuelito A; Lo, Raymundo W

    2004-01-01

    Chromogenic in situ hybridization (CISH) is emerging as a practical, cost-effective, and valid alternative to fluorescent in situ hybridization in testing for gene alteration, especially in centers primarily working with immunohistochemistry (IHC). We assessed Her-2/neu alteration using CISH on formalin-fixed paraffin-embedded primary invasive ductal carcinoma tumors in which IHC (CB11 antibody) had previously been performed, and we compared the results with IHC. The 160 selected cases were equally stratified randomly into the four IHC categories (scores of 0, 1+, 2+, and 3+). We also compared age at diagnosis and tumor histologic grade with IHC and CISH Her-2/neu. We were able to perform and evaluate CISH successfully on all cases. The agreement between 3+ IHC and CISH-amplified cases as well as between all IHC and CISH Her-2/neu negative cases was 100%, and the concordance on all positive cases was 72.50%, with an overall agreement of 86.25%. All the discordant cases had 2+ IHC scores. Although we noted Her-2/neu positivity more in premenopausal women, the age at diagnosis was not significantly associated with IHC or CISH results. Similarly, although the small group of well-differentiated tumors was apparently Her-2/neu negative in both tests, no significant association was noted between any tumor histologic grade and either IHC or CISH results. CISH is easily integrated into routine testing in our laboratory. It is a necessary adjunct in determining the subset of non-amplified IHC-positive invasive tumors that will not benefit from trastuzumab therapy. Those cases with 2+ IHC results will be triaged and subjected to CISH. Her-2/neu testing should be done on all breast cancer cases regardless of age at presentation and tumor histologic grade.

  9. Chromogenic in situ hybridization (CISH): a novel alternative in screening archival breast cancer tissue samples for HER-2/neu status

    International Nuclear Information System (INIS)

    Madrid, Manuelito A; Lo, Raymundo W

    2004-01-01

    Chromogenic in situ hybridization (CISH) is emerging as a practical, cost-effective, and valid alternative to fluorescent in situ hybridization in testing for gene alteration, especially in centers primarily working with immunohistochemistry (IHC). We assessed Her-2/neu alteration using CISH on formalin-fixed paraffin-embedded primary invasive ductal carcinoma tumors in which IHC (CB11 antibody) had previously been performed, and we compared the results with IHC. The 160 selected cases were equally stratified randomly into the four IHC categories (scores of 0, 1+, 2+, and 3+). We also compared age at diagnosis and tumor histologic grade with IHC and CISH Her-2/neu. We were able to perform and evaluate CISH successfully on all cases. The agreement between 3+ IHC and CISH-amplified cases as well as between all IHC and CISH Her-2/neu negative cases was 100%, and the concordance on all positive cases was 72.50%, with an overall agreement of 86.25%. All the discordant cases had 2+ IHC scores. Although we noted Her-2/neu positivity more in premenopausal women, the age at diagnosis was not significantly associated with IHC or CISH results. Similarly, although the small group of well-differentiated tumors was apparently Her-2/neu negative in both tests, no significant association was noted between any tumor histologic grade and either IHC or CISH results. CISH is easily integrated into routine testing in our laboratory. It is a necessary adjunct in determining the subset of non-amplified IHC-positive invasive tumors that will not benefit from trastuzumab therapy. Those cases with 2+ IHC results will be triaged and subjected to CISH. Her-2/neu testing should be done on all breast cancer cases regardless of age at presentation and tumor histologic grade

  10. Quantitative real-time RT-PCR and chromogenic in situ hybridization: precise methods to detect HER-2 status in breast carcinoma

    International Nuclear Information System (INIS)

    Rosa, Fabíola E; Silveira, Sara M; Silveira, Cássia GT; Bérgamo, Nádia A; Neto, Francisco A Moraes; Domingues, Maria AC; Soares, Fernando A; Caldeira, José RF; Rogatto, Silvia R

    2009-01-01

    HER-2 gene testing has become an integral part of breast cancer patient diagnosis. The most commonly used assay in the clinical setting for evaluating HER-2 status is immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). These procedures permit correlation between HER-2 expression and morphological features. However, FISH signals are labile and fade over time, making post-revision of the tumor difficult. CISH (chromogenic in situ hybridization) is an alternative procedure, with certain advantages, although still limited as a diagnostic tool in breast carcinomas. To elucidate the molecular profile of HER-2 status, mRNA and protein expression in 75 invasive breast carcinomas were analyzed by real time quantitative RT-PCR (qRT-PCR) and IHC, respectively. Amplifications were evaluated in 43 of these cases by CISH and in 11 by FISH. The concordance rate between IHC and qRT-PCR results was 78.9%, and 94.6% for qRT-PCR and CISH. Intratumoral heterogeneity of HER-2 status was identified in three cases by CISH. The results of the three procedures were compared and showed a concordance rate of 83.8%; higher discordances were observed in 0 or 1+ immunostaining cases, which showed high-level amplification (15.4%) and HER-2 transcript overexpression (20%). Moreover, 2+ immunostaining cases presented nonamplified status (50%) by CISH and HER-2 downexpression (38.5%) by qRT-PCR. In general, concordance occurred between qRT-PCR and CISH results. A high concordance was observed between CISH/qRT-PCR and FISH. Comparisons with clinicopathological data revealed a significant association between HER-2 downexpression and the involvement of less than four lymph nodes (P = 0.0350). Based on these findings, qRT-PCR was more precise and reproducible than IHC. Furthermore, CISH was revealed as an alternative and useful procedure for investigating amplifications involving the HER-2 gene

  11. High capacity fiber optic sensor networks using hybrid multiplexing techniques and their applications

    Science.gov (United States)

    Sun, Qizhen; Li, Xiaolei; Zhang, Manliang; Liu, Qi; Liu, Hai; Liu, Deming

    2013-12-01

    Fiber optic sensor network is the development trend of fiber senor technologies and industries. In this paper, I will discuss recent research progress on high capacity fiber sensor networks with hybrid multiplexing techniques and their applications in the fields of security monitoring, environment monitoring, Smart eHome, etc. Firstly, I will present the architecture of hybrid multiplexing sensor passive optical network (HSPON), and the key technologies for integrated access and intelligent management of massive fiber sensor units. Two typical hybrid WDM/TDM fiber sensor networks for perimeter intrusion monitor and cultural relics security are introduced. Secondly, we propose the concept of "Microstructure-Optical X Domin Refecltor (M-OXDR)" for fiber sensor network expansion. By fabricating smart micro-structures with the ability of multidimensional encoded and low insertion loss along the fiber, the fiber sensor network of simple structure and huge capacity more than one thousand could be achieved. Assisted by the WDM/TDM and WDM/FDM decoding methods respectively, we built the verification systems for long-haul and real-time temperature sensing. Finally, I will show the high capacity and flexible fiber sensor network with IPv6 protocol based hybrid fiber/wireless access. By developing the fiber optic sensor with embedded IPv6 protocol conversion module and IPv6 router, huge amounts of fiber optic sensor nodes can be uniquely addressed. Meanwhile, various sensing information could be integrated and accessed to the Next Generation Internet.

  12. Unexpected structural complexity of supernumerary marker chromosomes characterized by microarray comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Hing Anne V

    2008-04-01

    Full Text Available Abstract Background Supernumerary marker chromosomes (SMCs are structurally abnormal extra chromosomes that cannot be unambiguously identified by conventional banding techniques. In the past, SMCs have been characterized using a variety of different molecular cytogenetic techniques. Although these techniques can sometimes identify the chromosome of origin of SMCs, they are cumbersome to perform and are not available in many clinical cytogenetic laboratories. Furthermore, they cannot precisely determine the region or breakpoints of the chromosome(s involved. In this study, we describe four patients who possess one or more SMCs (a total of eight SMCs in all four patients that were characterized by microarray comparative genomic hybridization (array CGH. Results In at least one SMC from all four patients, array CGH uncovered unexpected complexity, in the form of complex rearrangements, that could have gone undetected using other molecular cytogenetic techniques. Although array CGH accurately defined the chromosome content of all but two minute SMCs, fluorescence in situ hybridization was necessary to determine the structure of the markers. Conclusion The increasing use of array CGH in clinical cytogenetic laboratories will provide an efficient method for more comprehensive characterization of SMCs. Improved SMC characterization, facilitated by array CGH, will allow for more accurate SMC/phenotype correlation.

  13. Contrast-Enhanced MR Angiography (CEMRA) in Peripheral Arterial Occlusive Disease (PAOD): conventional moving table technique versus hybrid technique

    International Nuclear Information System (INIS)

    Kalle, T. von; Gerlach, A.; Hatopp, A.; Klinger, S.; Prodehl, P.; Arlat, I.P.

    2004-01-01

    Patients and Methods: 80 patients (males n = 60, females n = 20, median age = 70 years, diabetics n = 27) with PAOD were examined with a 1,5T system (40 mT/m) using a dedicated phased array peripheral vascular coil. Protocol A consisted of a single injection of Gd-BOPTA with consecutive craniocaudal image acquisition and protocol B of two injections, with the first injection of Gd-BOPTA followed by image acquisition of the popliteocrural and pedal segments and the second injection followed by acquiring the aortoiliac and femoral segments (hybrid technique). The evaluation of the arterial system was directed to the iliac, femoral, popliteocrural and pedal arteries. Results: The visualization of the entire aortopedal vascular system was of diagnostically good or satisfactory quality in 16 of 40 patients using protocol A and in 29 of 40 patients using protocol B (iliac 40 vs. 37, femoral 40 vs. 40, popliteocrural 35 vs. 37, pedal 16 vs. 29); without the pedal station the number increased to 35 of 40 patients for both protocols. The reason of diagnostic limitations was an arteriovenous overlap in 24 of 80 cases, with 19 of 40 cases for protocol A and 5 of 40 for protocol B, located exclusively in the cruropedal region. Conclusion: Moving table hybrid CEMRA is superior to conventional technique in craniocaudal direction by producing less venous overlap of arteries and is especially more suitable for the diagnostic evaluation of the cruropedal region. (orig.) [de

  14. Innovative hybrid pile oscillator technique in the Minerve reactor: open loop vs. closed loop

    Directory of Open Access Journals (Sweden)

    Geslot Benoit

    2018-01-01

    Full Text Available Pile oscillator techniques are powerful methods to measure small reactivity worth of isotopes of interest for nuclear data improvement. This kind of experiments has long been implemented in the Mineve experimental reactor, operated by CEA Cadarache. A hybrid technique, mixing reactivity worth estimation and measurement of small changes around test samples is presented here. It was made possible after the development of high sensitivity miniature fission chambers introduced next to the irradiation channel. A test campaign, called MAESTRO-SL, took place in 2015. Its objective was to assess the feasibility of the hybrid method and investigate the possibility to separate mixed neutron effects, such as fission/capture or scattering/capture. Experimental results are presented and discussed in this paper, which focus on comparing two measurements setups, one using a power control system (closed loop and another one where the power is free to drift (open loop. First, it is demonstrated that open loop is equivalent to closed loop. Uncertainty management and methods reproducibility are discussed. Second, results show that measuring the flux depression around oscillated samples provides valuable information regarding partial neutron cross sections. The technique is found to be very sensitive to the capture cross section at the expense of scattering, making it very useful to measure small capture effects of highly scattering samples.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-03-01

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

  16. In-situ thermoelectric temperature monitoring and "Closed-loop integrated control" system for concentrator photovoltaic-thermoelectric hybrid receivers

    Science.gov (United States)

    Rolley, Matthew H.; Sweet, Tracy K. N.; Min, Gao

    2017-09-01

    This work demonstrates a new technique that capitalizes on the inherent flexibility of the thermoelectric module to provide a multifunctional platform, and exhibits a unique advantage only available within CPV-TE hybrid architectures. This system is the first to use the thermoelectric itself for hot-side temperature feedback to a PID control system, needing no additional thermocouple or thermistor to be attached to the cell - eliminating shading, and complex mechanical designs for mounting. Temperature measurement accuracy and thermoelectric active cooling functionality is preserved. Dynamic "per-cell" condition monitoring and protection is feasible using this technique, with direct cell-specific temperature measurement accurate to 1°C demonstrated over the entire experimental range. The extrapolation accuracy potential of the technique was also evaluated.

  17. Hybrid Electrodes by In-Situ Integration of Graphene and Carbon-Nanotubes in Polypyrrole for Supercapacitors

    Science.gov (United States)

    Aphale, Ashish; Maisuria, Krushangi; Mahapatra, Manoj K.; Santiago, Angela; Singh, Prabhakar; Patra, Prabir

    2015-09-01

    Supercapacitors also known as electrochemical capacitors, that store energy via either Faradaic or non-Faradaic processes, have recently grown popularity mainly because they complement, and can even replace, conventional energy storage systems in variety of applications. Supercapacitor performance can be improved significantly by developing new nanocomposite electrodes which utilizes both the energy storage processes simultaneously. Here we report, fabrication of the freestanding hybrid electrodes, by incorporating graphene and carbon nanotubes (CNT) in pyrrole monomer via its in-situ polymerization. At the scan rate of 5 mV s-1, the specific capacitance of the polypyrrole-CNT-graphene (PCG) electrode film was 453 F g-1 with ultrahigh energy and power density of 62.96 W h kg-1 and 566.66 W kg-1 respectively, as shown in the Ragone plot. A nanofibrous membrane was electrospun and effectively used as a separator in the supercapacitor. Four supercapacitors were assembled in series to demonstrate the device performance by lighting a 2.2 V LED.

  18. Hybrid Electrodes by In-Situ Integration of Graphene and Carbon-Nanotubes in Polypyrrole for Supercapacitors.

    Science.gov (United States)

    Aphale, Ashish; Maisuria, Krushangi; Mahapatra, Manoj K; Santiago, Angela; Singh, Prabhakar; Patra, Prabir

    2015-09-23

    Supercapacitors also known as electrochemical capacitors, that store energy via either Faradaic or non-Faradaic processes, have recently grown popularity mainly because they complement, and can even replace, conventional energy storage systems in variety of applications. Supercapacitor performance can be improved significantly by developing new nanocomposite electrodes which utilizes both the energy storage processes simultaneously. Here we report, fabrication of the freestanding hybrid electrodes, by incorporating graphene and carbon nanotubes (CNT) in pyrrole monomer via its in-situ polymerization. At the scan rate of 5 mV s(-1), the specific capacitance of the polypyrrole-CNT-graphene (PCG) electrode film was 453 F g(-1) with ultrahigh energy and power density of 62.96 W h kg(-1) and 566.66 W kg(-1) respectively, as shown in the Ragone plot. A nanofibrous membrane was electrospun and effectively used as a separator in the supercapacitor. Four supercapacitors were assembled in series to demonstrate the device performance by lighting a 2.2 V LED.

  19. An efficient hybrid technique in RCS predictions of complex targets at high frequencies

    Science.gov (United States)

    Algar, María-Jesús; Lozano, Lorena; Moreno, Javier; González, Iván; Cátedra, Felipe

    2017-09-01

    Most computer codes in Radar Cross Section (RCS) prediction use Physical Optics (PO) and Physical theory of Diffraction (PTD) combined with Geometrical Optics (GO) and Geometrical Theory of Diffraction (GTD). The latter approaches are computationally cheaper and much more accurate for curved surfaces, but not applicable for the computation of the RCS of all surfaces of a complex object due to the presence of caustic problems in the analysis of concave surfaces or flat surfaces in the far field. The main contribution of this paper is the development of a hybrid method based on a new combination of two asymptotic techniques: GTD and PO, considering the advantages and avoiding the disadvantages of each of them. A very efficient and accurate method to analyze the RCS of complex structures at high frequencies is obtained with the new combination. The proposed new method has been validated comparing RCS results obtained for some simple cases using the proposed approach and RCS using the rigorous technique of Method of Moments (MoM). Some complex cases have been examined at high frequencies contrasting the results with PO. This study shows the accuracy and the efficiency of the hybrid method and its suitability for the computation of the RCS at really large and complex targets at high frequencies.

  20. Interphase fluorescent in situ hybridization deletion analysis of the 9p21 region and prognosis in childhood acute lymphoblastic leukaemia (ALL)

    DEFF Research Database (Denmark)

    Kuchinskaya, Ekaterina; Heyman, Mats; Nordgren, Ann

    2011-01-01

    Interphase fluorescent in situ hybridization (FISH) was applied on diagnostic BM smears from 519 children with acute lymphoblastic leukaemia (ALL) in order to establish the frequency and prognostic importance of 9p21 deletion in children enrolled in the Nordic Society of Paediatric Haematology...... and Oncology (NOPHO) - 2000 treatment protocol. Among the patients, 452 were diagnosed with B-cell precursor (BCP)-ALL and 66 with T-ALL. A higher incidence of 9p21 deletions was found in T-ALL (38%) compared to BCP-ALL (15·7%). Homozygous deletions were found in 19·7% of T-ALL and 4·0% of BCP-ALL; hemizygous...

  1. Genetic Relationships among Hylocereus and Selenicereus Vine Cacti (Cactaceae): Evidence from Hybridization and Cytological Studies

    Science.gov (United States)

    TEL-ZUR, NOEMI; ABBO, SHAHAL; BAR-ZVI, DUDY; MIZRAHI, YOSEF

    2004-01-01

    • Background and Aims Hylocereus and Selenicereus are native to tropical and sub-tropical America. Based on its taxonomic status and crossability relations it was postulated that H. megalanthus (syn. S. megalanthus) is an allotetraploid (2n = 4x = 44) derived from natural hybridization between two closely related diploid taxa. The present work aimed at elucidating the genetic relationships between species of the two genera. • Methods Crosses were performed and the putative hybrids were analysed by chromosome counts and morphological traits. The ploidy level of hybrids was confirmed by fluorescent in situ hybridization (FISH) of rDNA sites. Genomic in situ hybridization (GISH) was used in an attempt to identify the putative diploid genome donors of H. megalanthus and an artificial interploid hybrid. • Key Results Reciprocal crosses among four diploid Hylocereus species (H. costaricensis, H. monacanthus (syn. H. polyrhizus), H. undatus and Hylocereus sp.) yielded viable diploid hybrids, with regular chromosome pairing. Reciprocal crosses between these Hylocereus spp. and H. megalanthus yielded viable triploid, pentaploid, hexaploid and aneuploid hybrids. Morphological and phenological traits confirm the hybrid origin. In situ detection of rDNA sites was in accord with the ploidy status of the species and hybrid studied. GISH results indicated that overall sequence composition of H. megalanthus is similar to that of H. ocamponis and S. grandiflorus. High sequence similarity was also found between the parental genomes of H. monacanthus and H. megalanthus in one triploid hybrid. • Conclusions The ease of obtaining partially fertile F1 hybrids and the relative sequence similarity (in GISH study) suggest close genetic relationships among the taxa analysed. PMID:15329334

  2. RNA detection in situ with FISH-STICs.

    Science.gov (United States)

    Sinnamon, John R; Czaplinski, Kevin

    2014-02-01

    The ability to detect RNA molecules in situ has long had important applications for molecular biological studies. Enzyme or dye-labeled antisense in vitro runoff transcripts and synthetic oligodeoxynucleotides (ODN) both have a proven track record of success, but each of these also has scientific and practical drawbacks and limitations to its use. We devised a means to use commercially synthesized oligonucleotides as RNA-FISH probes without further modification and show that such probes work well for detection of RNA in cultured cells. This approach can bind a high concentration of fluorescent ODN to a short stretch of an RNA using commercial DNA synthesis outlets available to any laboratory. We call this approach for creating in situ hybridization probes Fluorescence In Situ Hybridization with Sequential Tethered and Intertwined ODN Complexes (FISH-STICs). We demonstrate that one FISH-STIC probe can detect mRNA molecules in culture, and that probe detection can be improved by the addition of multiple probes that can be easily adapted for robust mRNA quantification. Using FISH-STICs, we demonstrate a nonoverlapping distribution for β-actin and γ-actin mRNA in cultured fibroblasts, and the detection of neuron-specific transcripts within cultured primary hippocampal neurons.

  3. In Situ Formation of Carbon Nanomaterials on Bulk Metallic Materials

    Directory of Open Access Journals (Sweden)

    J. Y. Xu

    2014-01-01

    Full Text Available Carbon nanomaterials were synthesized in situ on bulk 316L stainless steel, pure cobalt, and pure nickel by hybrid surface mechanical attrition treatment (SMAT. The microstructures of the treated samples and the resulted carbon nanomaterials were investigated by SEM and TEM characterizations. Different substrates resulted in different morphologies of products. The diameter of carbon nanomaterials is related to the size of the nanograins on the surface layer of substrates. The possible growth mechanism was discussed. Effects of the main parameters of the synthesis, including the carbon source and gas reactant composition, hydrogen, and the reaction temperature, were studied. Using hybrid SMAT is proved to be an effective way to synthesize carbon nanomaterials in situ on surfaces of metallic materials.

  4. Texture evolution and microstructural changes during solid-state dewetting: A correlative study by complementary in situ TEM techniques

    International Nuclear Information System (INIS)

    Niekiel, Florian; Kraschewski, Simon M.; Schweizer, Peter; Butz, Benjamin; Spiecker, Erdmann

    2016-01-01

    The transition of a thin film into an energetically favorable set of particles at temperatures below the melting point of the bulk material is known as solid-state dewetting. In this work the dewetting behavior of 16 nm thick discontinuous Au thin films on amorphous silicon nitride membranes is quantitatively studied by complementary in situ transmission electron microscopy techniques taking advantage of the unique capabilities of a chip-based heating system. The combination of dedicated imaging and diffraction techniques is used to investigate the interplay of grain growth and texture evolution with the process of dewetting. The results show an initial coarsening of the microstructure preceding the other processes. Texture evolution is highly correlated to material retraction and agglomeration during the following dewetting process. In-plane grain rotation has been observed, acting as an additional mechanism for orientation changes. From a methodological perspective this work demonstrates the capabilities of today’s transmission electron microscopy in combination with state-of-the-art in situ instrumentation. In particular the combination of complementary information from different dedicated techniques in one and the same setup is demonstrated to be highly beneficial.

  5. Hybrid technologies for the remediation of Diesel fuel polluted soil

    Energy Technology Data Exchange (ETDEWEB)

    Pazos, M.; Alcantara, M.T.; Rosales, E.; Sanroman, M.A. [Department of Chemical Engineering, University of Vigo (Spain)

    2011-12-15

    Diesel fuel may be released into soil due to anthropogenic activities, such as accidental spills or leaks in underground storage tanks or pipelines. Since diesel fuel is mainly composed of hydrophobic organic compounds, it has low water solubility. Therefore, treating contaminated areas with conventional techniques is difficult. In this study, electrokinetic treatment of soil contaminated with diesel fuel was carried out. Two different hybrid approaches to pollutant removal were tested. A surfactant was used as a processing fluid during electrokinetic treatment to increase desorption and the solubility of diesel fuel. Additionally, a hybrid technology combining a Fenton reaction and electrokinetic remediation (EK-Fenton) was tested in an attempt to generate favorable in situ degradation of pollutants. The efficiency of each treatment was determined based on diesel fuel removal. After 30 days of treatment, the highest removal of diesel fuel was found to be achieved with the EK-Fenton process. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization.

    Science.gov (United States)

    Poorman, Kelsey; Borst, Luke; Moroff, Scott; Roy, Siddharth; Labelle, Philippe; Motsinger-Reif, Alison; Breen, Matthew

    2015-06-01

    Melanocytic lesions originating from the oral mucosa or cutaneous epithelium are common in the general dog population, with up to 100,000 diagnoses each year in the USA. Oral melanoma is the most frequent canine neoplasm of the oral cavity, exhibiting a highly aggressive course. Cutaneous melanocytomas occur frequently, but rarely develop into a malignant form. Despite the differential prognosis, it has been assumed that subtypes of melanocytic lesions represent the same disease. To address the relative paucity of information about their genomic status, molecular cytogenetic analysis was performed on the three recognized subtypes of canine melanocytic lesions. Using array comparative genomic hybridization (aCGH) analysis, highly aberrant distinct copy number status across the tumor genome for both of the malignant melanoma subtypes was revealed. The most frequent aberrations included gain of dog chromosome (CFA) 13 and 17 and loss of CFA 22. Melanocytomas possessed fewer genome wide aberrations, yet showed a recurrent gain of CFA 20q15.3-17. A distinctive copy number profile, evident only in oral melanomas, displayed a sigmoidal pattern of copy number loss followed immediately by a gain, around CFA 30q14. Moreover, when assessed by fluorescence in situ hybridization (FISH), copy number aberrations of targeted genes, such as gain of c-MYC (80 % of cases) and loss of CDKN2A (68 % of cases), were observed. This study suggests that in concordance with what is known for human melanomas, canine melanomas of the oral mucosa and cutaneous epithelium are discrete and initiated by different molecular pathways.

  7. REVIEW OF HEART DISEASE PREDICTION SYSTEM USING DATA MINING AND HYBRID INTELLIGENT TECHNIQUES

    Directory of Open Access Journals (Sweden)

    R. Chitra

    2013-07-01

    Full Text Available The Healthcare industry generally clinical diagnosis is done mostly by doctor’s expertise and experience. Computer Aided Decision Support System plays a major role in medical field. With the growing research on heart disease predicting system, it has become important to categories the research outcomes and provides readers with an overview of the existing heart disease prediction techniques in each category. Neural Networks are one of many data mining analytical tools that can be utilized to make predictions for medical data. From the study it is observed that Hybrid Intelligent Algorithm improves the accuracy of the heart disease prediction system. The commonly used techniques for Heart Disease Prediction and their complexities are summarized in this paper.

  8. Engine Yaw Augmentation for Hybrid-Wing-Body Aircraft via Optimal Control Allocation Techniques

    Science.gov (United States)

    Taylor, Brian R.; Yoo, Seung Yeun

    2011-01-01

    Asymmetric engine thrust was implemented in a hybrid-wing-body non-linear simulation to reduce the amount of aerodynamic surface deflection required for yaw stability and control. Hybrid-wing-body aircraft are especially susceptible to yaw surface deflection due to their decreased bare airframe yaw stability resulting from the lack of a large vertical tail aft of the center of gravity. Reduced surface deflection, especially for trim during cruise flight, could reduce the fuel consumption of future aircraft. Designed as an add-on, optimal control allocation techniques were used to create a control law that tracks total thrust and yaw moment commands with an emphasis on not degrading the baseline system. Implementation of engine yaw augmentation is shown and feasibility is demonstrated in simulation with a potential drag reduction of 2 to 4 percent. Future flight tests are planned to demonstrate feasibility in a flight environment.

  9. A hybrid technique for private location-based queries with database protection

    KAUST Repository

    Ghinita, Gabriel

    2009-01-01

    Mobile devices with global positioning capabilities allow users to retrieve points of interest (POI) in their proximity. To protect user privacy, it is important not to disclose exact user coordinates to un-trusted entities that provide location-based services. Currently, there are two main approaches to protect the location privacy of users: (i) hiding locations inside cloaking regions (CRs) and (ii) encrypting location data using private information retrieval (PIR) protocols. Previous work focused on finding good trade-offs between privacy and performance of user protection techniques, but disregarded the important issue of protecting the POI dataset D. For instance, location cloaking requires large-sized CRs, leading to excessive disclosure of POIs (O(|D|) in the worst case). PIR, on the other hand, reduces this bound to , but at the expense of high processing and communication overhead. We propose a hybrid, two-step approach to private location-based queries, which provides protection for both the users and the database. In the first step, user locations are generalized to coarse-grained CRs which provide strong privacy. Next, a PIR protocol is applied with respect to the obtained query CR. To protect excessive disclosure of POI locations, we devise a cryptographic protocol that privately evaluates whether a point is enclosed inside a rectangular region. We also introduce an algorithm to efficiently support PIR on dynamic POI sub-sets. Our method discloses O(1) POI, orders of magnitude fewer than CR- or PIR-based techniques. Experimental results show that the hybrid approach is scalable in practice, and clearly outperforms the pure-PIR approach in terms of computational and communication overhead. © 2009 Springer Berlin Heidelberg.

  10. Techniques for sampling nuclear waste tank contents and in situ measurement of activity

    International Nuclear Information System (INIS)

    Lawrence, R.C.

    1978-04-01

    A study was conducted to develop suitable sampling equipment and techniques for characterizing the mechanical properties of nuclear wastes; identifying effective means of measuring radiation levels, temperatures, and neutron fluxes in situ in wastes; and developing a waste core sampler. A portable, stainless steel probe was developed which is placed in the tank through a riser. This probe is built for the insertion of instrumentation that can measure the contents of the tank at any level and take temperature, radiation, and neutron activation readings with reliable accuracy. A simple and reliable instrument for the in situ extraction of waste materials ranging from liquid to concrete-like substances was also developed. This portable, stainless steel waste core sampler can remove up to one liter of radioactive waste from tanks for transportation to hot cell laboratories for analysis of hardness, chemical form, and isotopic content. A cask for transporting the waste samples from the tanks to the laboratory under radiation-protected conditions was also fabricated. This cask was designed with a ''boot'' or inner-seal liner to contain any radioactive wastes that might remain on the outside of the waste core sampling device

  11. High-Temperature Tensile and Tribological Behavior of Hybrid (ZrB2+Al3Zr)/AA5052 In Situ Composite

    Science.gov (United States)

    Gautam, G.; Kumar, N.; Mohan, A.; Gautam, R. K.; Mohan, S.

    2016-09-01

    During service life, components such as piston, cylinder blocks, brakes, and discs/drums, have to work under high-temperature conditions. In order to have appropriate material for such applications high-temperature studies are important. Hybrid (ZrB2+Al3Zr)/AA5052 in situ composite has been investigated from ambient to 523 K (250 °C) at an interval of 50 deg. (ZrB2+Al3Zr)/AA5052 in situ composite has been fabricated by the direct melt reaction of AA5052 alloy with zirconium and boron salts. Microstructure studies show refinement in the grain size of base alloy on in situ formation of reinforcement particles. Al3Zr particles are observed in rectangular and polyhedron shapes. It is observed from the tensile studies that ultimate tensile strength, yield strength, and percentage elongation decrease with increase in test temperature. Similar kind of behavior is also observed for flow curve properties. The tensile results have also been correlated with fractography. Wear and friction results indicate that the wear rate increases with increase in normal load, whereas coefficient of friction shows decreasing trend. With increasing test temperature, wear rate exhibits a typical phenomenon. After an initial increase, wear rate follows a decreasing trend up to 423 K (150 °C), and finally a rapid increase is observed, whereas coefficient of friction increases continuously with increase in test temperature. The mechanisms responsible for the variation of wear and friction with different temperatures have been discussed in detail with the help of worn surfaces studies under scanning electron microscope (SEM) & 3D-profilometer and debris analysis by XRD.

  12. In Situ Techniques for the Investigation of the Kinetics of Austenitization of Supermartensitic Stainless Steel

    DEFF Research Database (Denmark)

    Nießen, Frank; Villa, Matteo; Apel, Daniel

    2016-01-01

    The austenitization and inter-critical annealing of X4CrNiMo16-5-1 (1.4418) supermartensitic stainless steel were investigated in-situ with synchrotron X-ray diffraction (XRD), dilatometry and differential scanning calorimetry (DSC) under isochronal heating conditions. Austenitization occurred...... of surface martensite formation on the XRD measurement. The applicable temperature range for DSC as well as the close proximity of the Ac1- and the Curietemperature limited the usage of the technique in the present case....

  13. Towards Fluorescence In Vivo Hybridization (FIVH) Detection of H. pylori in Gastric Mucosa Using Advanced LNA Probes

    DEFF Research Database (Denmark)

    Fontenete, Sílvia; Leite, Marina; Guimarães, Nuno

    2015-01-01

    acid (LNA)/ 2' O-methyl RNA (2'OMe) probe using standard phosphoramidite chemistry and FISH hybridization was then successfully performed both on adhered and suspended bacteria at 37°C. In this work we simplified, shortened and adapted FISH to work at gastric pH values, meaning that the hybridization...... step now takes only 30 minutes and, in addition to the buffer, uses only urea and probe at non-toxic concentrations. Importantly, the sensitivity and specificity of the FISH method was maintained in the range of conditions tested, even at low stringency conditions (e.g., low pH). In conclusion......In recent years, there have been several attempts to improve the diagnosis of infection caused by Helicobacter pylori. Fluorescence in situ hybridization (FISH) is a commonly used technique to detect H. pylori infection but it requires biopsies from the stomach. Thus, the development of an in vivo...

  14. Cross-check of ex-situ and in-situ metrology of a bendable temperature stabilized KB mirror

    International Nuclear Information System (INIS)

    Yuan Sheng; Goldberg, Kenneth A.; Yashchuk, Valeriy V.; Celestre, Richard; McKinney, Wayne R.; Morrison, Gregory; Macdougall, James; Mochi, Iacopo; Warwick, Tony

    2011-01-01

    At the Advanced Light Source (ALS), we are developing broadly applicable, high-accuracy, in-situ, at-wavelength wavefront slope measurement techniques for Kirkpatrick-Baez (KB) mirror nano-focusing. In this paper, we report an initial cross-check of ex-situ and in-situ metrology of a bendable temperature stabilized KB mirror. This cross-check provides a validation of the in-situ shearing interferometry, currently under development at the ALS.

  15. Locked Nucleic Acid-Based In Situ Hybridization Reveals miR-7a as a Hypothalamus-Enriched MicroRNA with a Distinct Expression Pattern

    DEFF Research Database (Denmark)

    Herzer, S; Silahtaroglu, A; Meister, B

    2012-01-01

    , a part of the brain that controls vital bodily functions, we employed locked nucleic acid (LNA) - fluorescent in situ hybridization (FISH). The expression pattern of the mature miRNAs miR-7a, miR-7b, miR-137 and miR-153 in mouse brain tissue sections was investigated. Whereas all studied miRNAs were......R-7a expression was particularly prominent in the subfornical organ, suprachiasmatic, paraventricular, periventricular, supraoptic, dorsomedial and arcuate nuclei. Identical expression patterns for miR-7a was seen in mouse and rat hypothalamus. By combining LNA-FISH with immunohistochemistry...

  16. In situ nonlinear ultrasonic technique for monitoring microcracking in concrete subjected to creep and cyclic loading.

    Science.gov (United States)

    Kim, Gun; Loreto, Giovanni; Kim, Jin-Yeon; Kurtis, Kimberly E; Wall, James J; Jacobs, Laurence J

    2018-08-01

    This research conducts in situ nonlinear ultrasonic (NLU) measurements for real time monitoring of load-induced damage in concrete. For the in situ measurements on a cylindrical specimen under sustained load, a previously developed second harmonic generation (SHG) technique with non-contact detection is adapted to a cylindrical specimen geometry. This new setup is validated by demonstrating that the measured nonlinear Rayleigh wave signals are equivalent to those in a flat half space, and thus the acoustic nonlinearity parameter, β can be defined and interpreted in the same way. Both the acoustic nonlinearity parameter and strain are measured to quantitatively assess the early-age damage in a set of concrete specimens subjected to either 25 days of creep, or 11 cycles of cyclic loading at room temperature. The experimental results show that the acoustic nonlinearity parameter is sensitive to early-stage microcrack formation under both loading conditions - the measured β can be directly linked to the accumulated microscale damage. This paper demonstrates the potential of NLU for the in situ monitoring of mechanical load-induced microscale damage in concrete components. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Rapid detection of chromosome rearrangement in medical diagnostic X-ray workers by using fluorescence in situ hybridization and study on dose estimation

    International Nuclear Information System (INIS)

    Wang Zhiquan; Sun Yuanming; Li Jin

    1998-01-01

    Objective: Biological doses were estimated for medical diagnostic X-ray workers. Methods: Chromosome rearrangements in X-ray workers were analysed by fluorescence in situ hybridization (FISH) with composite whole chromosome paintings number 4 and number 7. Results: The frequency of translocation in medical diagnostic X-ray workers was much higher than that in control group (P<0.01). The biological doses to individual X-ray workers were calculated by their translocation frequency. The translocation frequencies of both FISH and G-banding were in good agreement. Conclusion: The biological doses to X-ray workers are estimated by FISH first when their dosimetry records are not documented

  18. SU-E-T-451: Hybrid-VMAT: A Novel Technique Combining VMAT and 3D in Planning Whole Breast Radiotherapy with a Simultaneously-Integrated Boost (WBRT+SIB)

    International Nuclear Information System (INIS)

    Guida, K; Qamar, K; Thompson, M

    2015-01-01

    Purpose: The RTOG 1005 trial offered a hypofractionated arm in delivering WBRT+SIB. Traditionally, treatments were planned at our institution using field-in-field (FiF) tangents with a concurrent 3D conformal boost. With the availability of VMAT, it is possible that a hybrid VMAT-3D planning technique could provide another avenue in treating WBRT+SIB. Methods: A retrospective study of nine patients previously treated using RTOG 1005 guidelines was performed to compare FiF+3D plans with the hybrid technique. A combination of static tangents and partial VMAT arcs were used in base-dose optimization. The hybrid plans were optimized to deliver 4005cGy to the breast PTVeval and 4800cGy to the lumpectomy PTVeval over 15 fractions. Plans were optimized to meet the planning goals dictated by RTOG 1005. Results: Hybrid plans yielded similar coverage of breast and lumpectomy PTVs (average D95 of 4013cGy compared to 3990cGy for conventional), while reducing the volume of high dose within the breast; the average D30 and D50 for the hybrid technique were 4517cGy and 4288cGy, compared to 4704cGy and 4377cGy for conventional planning. Hybrid plans increased conformity as well, yielding CI95% values of 1.22 and 1.54 for breast and lumpectomy PTVeval volumes; in contrast, conventional plans averaged 1.49 and 2.27, respectively. The nearby organs at risk (OARs) received more low dose with the hybrid plans due to low dose spray from the partial arcs, but all hybrid plans did meet the acceptable constraints, at a minimum, from the protocol. Treatment planning time was also reduced, as plans were inversely optimized (VMAT) rather than forward optimized. Conclusion: Hybrid-VMAT could be a solution in delivering WB+SIB, as plans yield very conformal treatment plans and maintain clinical standards in OAR sparing. For treating breast cancer patients with a simultaneously-integrated boost, Hybrid-VMAT offers superiority in dosimetric conformity and planning time as compared to FIF

  19. SU-E-T-451: Hybrid-VMAT: A Novel Technique Combining VMAT and 3D in Planning Whole Breast Radiotherapy with a Simultaneously-Integrated Boost (WBRT+SIB)

    Energy Technology Data Exchange (ETDEWEB)

    Guida, K; Qamar, K; Thompson, M [University of Kansas Hospital, Kansas City, MO (United States)

    2015-06-15

    Purpose: The RTOG 1005 trial offered a hypofractionated arm in delivering WBRT+SIB. Traditionally, treatments were planned at our institution using field-in-field (FiF) tangents with a concurrent 3D conformal boost. With the availability of VMAT, it is possible that a hybrid VMAT-3D planning technique could provide another avenue in treating WBRT+SIB. Methods: A retrospective study of nine patients previously treated using RTOG 1005 guidelines was performed to compare FiF+3D plans with the hybrid technique. A combination of static tangents and partial VMAT arcs were used in base-dose optimization. The hybrid plans were optimized to deliver 4005cGy to the breast PTVeval and 4800cGy to the lumpectomy PTVeval over 15 fractions. Plans were optimized to meet the planning goals dictated by RTOG 1005. Results: Hybrid plans yielded similar coverage of breast and lumpectomy PTVs (average D95 of 4013cGy compared to 3990cGy for conventional), while reducing the volume of high dose within the breast; the average D30 and D50 for the hybrid technique were 4517cGy and 4288cGy, compared to 4704cGy and 4377cGy for conventional planning. Hybrid plans increased conformity as well, yielding CI95% values of 1.22 and 1.54 for breast and lumpectomy PTVeval volumes; in contrast, conventional plans averaged 1.49 and 2.27, respectively. The nearby organs at risk (OARs) received more low dose with the hybrid plans due to low dose spray from the partial arcs, but all hybrid plans did meet the acceptable constraints, at a minimum, from the protocol. Treatment planning time was also reduced, as plans were inversely optimized (VMAT) rather than forward optimized. Conclusion: Hybrid-VMAT could be a solution in delivering WB+SIB, as plans yield very conformal treatment plans and maintain clinical standards in OAR sparing. For treating breast cancer patients with a simultaneously-integrated boost, Hybrid-VMAT offers superiority in dosimetric conformity and planning time as compared to FIF

  20. Oriented Arrays of Graphene in a Polymer Matrix by in situ Reduction of Graphite Oxide Nanosheets

    KAUST Repository

    Ansari, Seema; Kelarakis, Antonios; Estevez, Luis; Giannelis, Emmanuel P.

    2010-01-01

    Graphite oxide-Nafion hybrids with a high degree of alignment are cast from aqueous solution in the absence of any external field and reduced in situ by exposure to hydrazine to produce graphene-Nafion hybrids. Dramatic enhancement of electrical

  1. In situ characterization of natural pyrite bioleaching using electrochemical noise technique

    Science.gov (United States)

    Chen, Guo-bao; Yang, Hong-ying; Li, Hai-jun

    2016-02-01

    An in situ characterization technique called electrochemical noise (ECN) was used to investigate the bioleaching of natural pyrite. ECN experiments were conducted in four active systems (sulfuric acid, ferric-ion, 9k culture medium, and bioleaching solutions). The ECN data were analyzed in both the time and frequency domains. Spectral noise impedance spectra obtained from power spectral density (PSD) plots for different systems were compared. A reaction mechanism was also proposed on the basis of the experimental data analysis. The bioleaching system exhibits the lowest noise resistance of 0.101 MΩ. The bioleaching of natural pyrite is considered to be a bio-battery reaction, which distinguishes it from chemical oxidation reactions in ferric-ion and culture-medium (9k) solutions. The corrosion of pyrite becomes more severe over time after the long-term testing of bioleaching.

  2. Immobilization of Mo(IV) complex in hybrid matrix obtained via sol-gel technique

    Energy Technology Data Exchange (ETDEWEB)

    Marques, C.; Sousa, A.M.; Freire, C.; Neves, I.C.; Fonseca, A.M.; Silva, C.J.R

    2003-10-06

    A molybdenum(IV) complex, trans-bis-[1,2-bis(diphenylphosphino)ethane]-fluoro-(diazopropano) -molybdenum tetraphenylborate, [MoF(DIAZO)(dppe){sub 2}][BPh{sub 4}], was prepared and immobilized in a hybrid matrix synthesized by the sol-gel process. The host matrix, designated as U(500), is an organic-inorganic network material, classed as ureasil, that combines a reticulated siliceous backbone linked by short polyether-based segments. Urea bridges make the link between these two components, and the polymerization of silicate substituted terminal groups generates the inorganic network. The free Mo(IV) complex and all new materials were characterized by spectroscopic techniques (FT-IR and UV-Vis) and thermal analysis (DSC). The ionic conductivity of the resulting material was also studied. The results indicate that immobilized Mo(IV) complex has kept its solid-state structure, although there is evidence of inter-molecular interactions between the Mo(IV) complex and some groups/atoms of the hybrid host matrix.

  3. Hybrid PIV-PTV technique for measuring blood flow in rat mesenteric vessels.

    Science.gov (United States)

    Ha, Hojin; Nam, Kweon-Ho; Lee, Sang Joon

    2012-11-01

    The micro-particle tracking velocimetry (μ-PTV) technique is used to obtain the velocity fields of blood flow in the microvasculature under in vivo conditions because it can provide the blood velocity distribution in microvessels with high spatial resolution. The in vivo μ-PTV technique usually requires a few to tens of seconds to obtain a whole velocity profile across the vessel diameter because of the limited number density of tracer particles under in vivo conditions. Thus, the μ-PTV technique alone is limited in measuring unsteady blood flows that fluctuate irregularly due to the heart beating and muscle movement in surrounding tissues. In this study, a new hybrid PIV-PTV technique was established by combining PTV and particle image velocimetry (PIV) techniques to resolve the drawbacks of the μ-PTV method in measuring blood flow in microvessels under in vivo conditions. Images of red blood cells (RBCs) and fluorescent particles in rat mesenteric vessels were obtained simultaneously. Temporal variations of the centerline blood velocity were monitored using a fast Fourier transform-based cross-correlation PIV method. The fluorescence particle images were analyzed using the μ-PTV technique to extract the spatial distribution of the velocity vectors. Data from the μ-PTV and PIV methods were combined to obtain a better estimate of the velocity profile in actual blood flow. This technique will be useful in investigating hemodynamics in microcirculation by measuring unsteady irregular blood flows more accurately. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Flat mount preparation for observation and analysis of zebrafish embryo specimens stained by whole mount in situ hybridization.

    Science.gov (United States)

    Cheng, Christina N; Li, Yue; Marra, Amanda N; Verdun, Valerie; Wingert, Rebecca A

    2014-07-17

    The zebrafish embryo is now commonly used for basic and biomedical research to investigate the genetic control of developmental processes and to model congenital abnormalities. During the first day of life, the zebrafish embryo progresses through many developmental stages including fertilization, cleavage, gastrulation, segmentation, and the organogenesis of structures such as the kidney, heart, and central nervous system. The anatomy of a young zebrafish embryo presents several challenges for the visualization and analysis of the tissues involved in many of these events because the embryo develops in association with a round yolk mass. Thus, for accurate analysis and imaging of experimental phenotypes in fixed embryonic specimens between the tailbud and 20 somite stage (10 and 19 hours post fertilization (hpf), respectively), such as those stained using whole mount in situ hybridization (WISH), it is often desirable to remove the embryo from the yolk ball and to position it flat on a glass slide. However, performing a flat mount procedure can be tedious. Therefore, successful and efficient flat mount preparation is greatly facilitated through the visual demonstration of the dissection technique, and also helped by using reagents that assist in optimal tissue handling. Here, we provide our WISH protocol for one or two-color detection of gene expression in the zebrafish embryo, and demonstrate how the flat mounting procedure can be performed on this example of a stained fixed specimen. This flat mounting protocol is broadly applicable to the study of many embryonic structures that emerge during early zebrafish development, and can be implemented in conjunction with other staining methods performed on fixed embryo samples.

  5. Utility and impact of early t(15;17) identification by Fluorescence In Situ Hybridization (FISH) in clinical decision making for patients in Acute Promyelocytic Leukemia (APL).

    Science.gov (United States)

    Kolhe, R; Mangaonkar, A; Mansour, J; Clemmons, A; Shaw, J; Dupont, B; Walczak, L; Mondal, A; Rojiani, A; Jillella, A; Kota, V

    2015-08-01

    Acute Promyelocytic Leukemia (APL) is a curable malignancy with studies showing above 90% survival. However, population-based studies looking at survival suggest that approximately 30% of patients with APL die during induction. Early demonstration of t(15;17) will lead to accurate decision making regarding treatment. The aim of this project was to validate earlier time frames for the Abbott Molecular Vysis LSI promyelocytic leukemia (PML)/ retinoic acid receptor alpha (RARA) fluorescence in situ hybridization (FISH) probe (ASR 6-16 h). Twenty patients (15 APL cases and five non-APL cases) were selected for validating various hybridization times for the FISH probe. Expected normal signal pattern was two red and two green signals (2R2G), and the most common expected abnormal signal pattern was two fusion (yellow) signals, one red and one green (2F1R1G) and/or one fusion, one red and one green (1F1R1G). The specificity of the probe ranged from 84% at 2 h, 86% at 4 h, 84% at 6 h, and 87% for overnight hybridization. The sensitivity increased from 79% at 2 h, 80% at 4 h, 81% at 6 h to 87% for overnight hybridization. Based on the validation studies, we recommend reading of FISH results at the 4-h incubation mark for a preliminary diagnosis and confirmation with overnight hybridization. © 2015 John Wiley & Sons Ltd.

  6. Distribution of herpes simplex virus types 1 and 2 genomes in human spinal ganglia studied by PCR and in situ hybridization.

    Science.gov (United States)

    Obara, Y; Furuta, Y; Takasu, T; Suzuki, S; Suzuki, H; Matsukawa, S; Fujioka, Y; Takahashi, H; Kurata, T; Nagashima, K

    1997-06-01

    Clinical data indicate that the recurring herpes simplex virus (HSV) from oro-labial lesions is HSV subtype 1 and that the virus from genital lesions is HSV-2. This suggests that HSV-1 and HSV-2 reside in latent forms in the trigeminal ganglia and sacral ganglia, respectively. However, the distribution of latent HSV-1 and HSV-2 infections in human spinal ganglia has not been fully examined. This report concerns the application of polymerase chain reaction (PCR) and in situ hybridization (ISH) to such a study. By using PCR and employing the respective primers, HSV-1 and HSV-2 DNAs were detected in 207 of 524 samples from 262 spinal ganglia (from the cervical to the sacral ganglia) examined on both sides. The percentages of HSV-1 and HSV-2 detected in a given set of ganglia were similar, indicating an absence of site preference. By ISH, few but positive hybridization signals were detected evenly in sacral ganglia sections. The data suggest that regional specificity of recurrent HSV infections is not due to regional distribution of latent virus, but that local host factors may be important for recurrences.

  7. Starch degradability of dry and ensiled high-moisture grains of corn hybrids with different textures at different grinding degrees

    OpenAIRE

    Wagner dos Reis; Ciniro Costa; Paulo Roberto de Lima Meirelles; Marina Gabriela Berchiol da Silva; Marco Aurélio Factori; Cristiano Magalhães Pariz; Simony Alves Mendonça; Erikelly Aline Ribeiro de Santana

    2011-01-01

    This research evaluated corn grains with flint and dent texture (ensiled high-moisture or dried), submitted to grinding degrees, using the in situ ruminal degradation technique. Three rumen canulated adult sheeps were used in a complete randomized design, using a factorial outline 2 x 2 x 3, with two corn hybrids (flint and dent texture), two conservation methods (ensiled high-moisture and dry) and three grinding degress (whole, coarsely and finely ground, corresponding to the sieve of 12; 10...

  8. Analysis of methanogenic activity in a thermophilic-dry anaerobic reactor: Use of fluorescent in situ hybridization

    International Nuclear Information System (INIS)

    Montero, B.; Garcia-Morales, J.L.; Sales, D.; Solera, R.

    2009-01-01

    Methanogenic activity in a thermophilic-dry anaerobic reactor was determined by comparing the amount of methane generated for each of the organic loading rates with the size of the total and specific methanogenic population, as determined by fluorescent in situ hybridization. A high correlation was evident between the total methanogenic activity and retention time [-0.6988Ln(x) + 2.667] (R 2 0.8866). The total methanogenic activity increased from 0.04 x 10 -8 mLCH 4 cell -1 day -1 to 0.38 x 10 -8 mLCH 4 cell -1 day -1 while the retention time decreased, augmenting the organic loading rates. The specific methanogenic activities of H 2 -utilizing methanogens and acetate-utilizing methanogens increased until they stabilised at 0.64 x 10 -8 mLCH 4 cell -1 day -1 and 0.33 x 10 -8 mLCH 4 cell -1 day -1 , respectively. The methanogenic activity of H 2 -utilizing methanogens was higher than acetate-utilizing methanogens, indicating that maintaining a low partial pressure of hydrogen does not inhibit the acetoclastic methanogenesis or the anaerobic process

  9. Hybrid strategies in nanolithography

    Energy Technology Data Exchange (ETDEWEB)

    Saavedra, Hector M; Mullen, Thomas J; Zhang Pengpeng; Dewey, Daniel C; Claridge, Shelley A; Weiss, Paul S [Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 (United States)], E-mail: psw@cnsi.ucla.edu

    2010-03-15

    Hybrid nanoscale patterning strategies combine the registration and addressability of conventional lithographic techniques with the chemical and physical functionality enabled by intermolecular, electrostatic and/or biological interactions. This review aims to highlight and to provide a comprehensive description of recent developments in hybrid nanoscale patterning strategies that enhance existing lithographic techniques or can be used to fabricate functional chemical patterns that interact with their environment. These functional structures create new capabilities, such as the fabrication of physicochemical surfaces that can recognize and capture analytes from complex liquid or gaseous mixtures. The nanolithographic techniques we describe can be classified into three general areas: traditional lithography, soft lithography and scanning-probe lithography. The strengths and limitations of each hybrid patterning technique will be discussed, along with the current and potential applications of the resulting patterned, functional surfaces.

  10. A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans.

    Science.gov (United States)

    Andachi, Yoshiki; Kohara, Yuji

    2016-07-01

    Whole-mount in situ hybridization (WISH) is an outstanding method to decipher the spatiotemporal expression patterns of microRNAs (miRNAs) and provides important clues for elucidating their functions. The first WISH method for miRNA detection was developed in zebrafish. Although this method was quickly adapted for other vertebrates and fruit flies, WISH analysis has not been successfully used to detect miRNAs in Caenorhabditis elegans Here, we show a novel WISH method for miRNA detection in C. elegans Using this method, mir-1 miRNA was detected in the body-wall muscle where the expression and roles of mir-1 miRNA have been previously elucidated. Application of the method to let-7 family miRNAs, let-7, mir-48, mir-84, and mir-241, revealed their distinct but partially overlapping expression patterns, indicating that miRNAs sharing a short common sequence were distinguishably detected. In pash-1 mutants that were depleted of mature miRNAs, signals of mir-48 miRNA were greatly reduced, suggesting that mature miRNAs were detected by the method. These results demonstrate the validity of WISH to detect mature miRNAs in C. elegans. © 2016 Andachi and Kohara; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  11. Speed control with torque ripple reduction of switched reluctance motor by Hybrid Many Optimizing Liaison Gravitational Search technique

    Directory of Open Access Journals (Sweden)

    Nutan Saha

    2017-06-01

    Full Text Available This paper presents a control scheme for simultaneous control of the speed of Switched Reluctance Motor (SRM and minimizing the torque ripple employing Hybrid Many Optimizing Liaison Gravitational Search Algorithm (Hybrid MOLGSA technique. The control mechanism includes two controlling loops, the outer loop is governed for speed control and a current controller for the inner loop, intelligent selection of turn on and turn off angle for a 60 KW, 3-phase 6/8 SRM. It is noticed that the torque ripple coefficient, ISE of speed & current are reduced by 12.81%, 38.60%, 16.74% respectively by Hybrid MOLGSA algorithm compared to Gravitational Search Algorithm (GSA algorithm. It is also observed that the settling times for the controller using the parameter values for obtaining best values of torque ripple, Integral square error of speed and current are reduced by 51.25%, 58.04% and 59.375% by proposed Hybrid MOLGSA algorithm compared to the GSA algorithm.

  12. Considerations in the use of fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy to characterize rumen methanogens and define their spatial distributions.

    Science.gov (United States)

    Valle, Edith R; Henderson, Gemma; Janssen, Peter H; Cox, Faith; Alexander, Trevor W; McAllister, Tim A

    2015-06-01

    In this study, methanogen-specific coenzyme F420 autofluorescence and confocal laser scanning microscopy were used to identify rumen methanogens and define their spatial distribution in free-living, biofilm-, and protozoa-associated microenvironments. Fluorescence in situ hybridization (FISH) with temperature-controlled hybridization was used in an attempt to describe methanogen diversity. A heat pretreatment (65 °C, 1 h) was found to be a noninvasive method to increase probe access to methanogen RNA targets. Despite efforts to optimize FISH, 16S rRNA methanogen-specific probes, including Arch915, bound to some cells that lacked F420, possibly identifying uncharacterized Methanomassiliicoccales or reflecting nonspecific binding to other members of the rumen bacterial community. A probe targeting RNA from the methanogenesis-specific methyl coenzyme M reductase (mcr) gene was shown to detect cultured Methanosarcina cells with signal intensities comparable to those of 16S rRNA probes. However, the probe failed to hybridize with the majority of F420-emitting rumen methanogens, possibly because of differences in cell wall permeability among methanogen species. Methanogens were shown to integrate into microbial biofilms and to exist as ecto- and endosymbionts with rumen protozoa. Characterizing rumen methanogens and defining their spatial distribution may provide insight into mitigation strategies for ruminal methanogenesis.

  13. Investigations of inorganic and hybrid inorganic-organic nanostructures

    Science.gov (United States)

    Kam, Kinson Chihang

    This thesis focuses on the exploratory synthesis and characterization of inorganic and hybrid inorganic-organic nanomaterials. In particular, nanostructures of semiconducting nitrides and oxides, and hybrid systems of nanowire-polymer composites and framework materials, are investigated. These materials are characterized by a variety of techniques for structure, composition, morphology, surface area, optical properties, and electrical properties. In the study of inorganic nanomaterials, gallium nitride (GaN), indium oxide (In2O3), and vanadium dioxide (VO2) nanostructures were synthesized using different strategies and their physical properties were examined. GaN nanostructures were obtained from various synthetic routes. Solid-state ammonolysis of metastable gamma-Ga2O 3 nanoparticles was found to be particularly successful; they achieved high surface areas and photoluminescent study showed a blue shift in emission as a result of surface and size defects. Similarly, In2O3 nanostructures were obtained by carbon-assisted solid-state syntheses. The sub-oxidic species, which are generated via a self-catalyzed vapor-liquid-solid mechanism, resulted in 1D nanostructures including nanowires, nanotrees, and nanobouquets upon oxidation. On the other hand, hydrothermal methods were used to obtain VO2 nanorods. After post-thermal treatment, infrared spectroscopy demonstrated that these nanorods exhibit a thermochromic transition with temperature that is higher by ˜10°C compared to the parent material. The thermochromic behavior indicated a semiconductor-to-metal transition associated with a structural transformation from monoclinic to rutile. The hybrid systems, on the other hand, enabled their properties to be tunable. In nanowire-polymer composites, zinc oxide (ZnO) and silver (Ag) nanowires were synthesized and incorporated into polyaniline (PANI) and polypyrrole (PPy) via in-situ and ex-situ polymerization method. The electrical properties of these composites are

  14. A comprehensive overview of hybrid electric vehicle: Powertrain configurations, powertrain control techniques and electronic control units

    Energy Technology Data Exchange (ETDEWEB)

    Cagatay Bayindir, Kamil; Goezuekuecuek, Mehmet Ali; Teke, Ahmet [Cukurova University, Department of Electrical and Electronics Engineering, Balcali, Saricam, Adana (Turkey)

    2011-02-15

    The studies for hybrid electrical vehicle (HEV) have attracted considerable attention because of the necessity of developing alternative methods to generate energy for vehicles due to limited fuel based energy, global warming and exhaust emission limits in the last century. HEV incorporates internal composition engine, electric machines and power electronic equipments. In this study, overview of HEVs with a focus on hybrid configurations, energy management strategies and electronic control units are presented. Advantages and disadvantages of each configuration are clearly emphasized. The existing powertrain control techniques for HEVs are classified and comprehensively described. Electronic control units used in HEV configuration are also elaborated. The latest trends and technological challenges in the near future for HEVs are discussed. (author)

  15. Multi-Wave and Hybrid Imaging Techniques: A New Direction for Nondestructive Testing and Structural Health Monitoring

    Directory of Open Access Journals (Sweden)

    Yuhua Cheng

    2013-11-01

    Full Text Available In this article, the state-of-the-art multi-wave and hybrid imaging techniques in the field of nondestructive evaluation and structural health monitoring were comprehensively reviewed. A new direction for assessment and health monitoring of various structures by capitalizing the advantages of those imaging methods was discussed. Although sharing similar system configurations, the imaging physics and principles of multi-wave phenomena and hybrid imaging methods are inherently different. After a brief introduction of nondestructive evaluation (NDE , structure health monitoring (SHM and their related challenges, several recent advances that have significantly extended imaging methods from laboratory development into practical applications were summarized, followed by conclusions and discussion on future directions.

  16. Persistence of translocations detected by means of fluorescence in situ hybridization in peripheral lymphocytes of accidentally exposed radiation workers

    International Nuclear Information System (INIS)

    Pressl, S.; Stephan, G.

    1997-01-01

    The translocation frequency in lymphocytes of radiation workers accidentally exposed a number of years earlier was determined by means of fluorescence in situ hybridization. Chromosomes 2, 4 and 8 were painted, and simultaneously the centromeres. The genomic frequency of translocations is between 1.7 and 17.9 per 1000 cells. This variation is not significantly different from the level in healthy control subjects. Therefore, no radiation exposure could be detected retrospectively. On the other hand, the frequency of dicentrics in these radiation workers measured by means of fluorescence plus Giemsa staining shortly after the exposure was significantly increased, and whole body doses between 0.2 and 0.3 Gy could be calculated. Consequently, it would seem that dicentrics measured shortly after an exposure are a more sensitive indicator than translocations which are determined years later. (author)

  17. Rumen escape nitrogen from forages in sheep: comparison of in situ and in vitro techniques using in vivo data

    NARCIS (Netherlands)

    Gosselink, J.M.J.; Dulphy, J.P.; Poncet, C.; Aufrère, J.; Tamminga, S.; Cone, J.W.

    2004-01-01

    The objective of this study was to relate in vivo data of rumen escape N (REN) of forages with REN estimated from models and with determinations of rumen undegradable N. For these determinations and models measurements from in situ and in vitro techniques were used. Eleven forages were investigated

  18. Quantitative real-time RT-PCR and chromogenic in situ hybridization: precise methods to detect HER-2 status in breast carcinoma

    Directory of Open Access Journals (Sweden)

    Soares Fernando A

    2009-03-01

    Full Text Available Abstract Background HER-2 gene testing has become an integral part of breast cancer patient diagnosis. The most commonly used assay in the clinical setting for evaluating HER-2 status is immunohistochemistry (IHC and fluorescence in situ hybridization (FISH. These procedures permit correlation between HER-2 expression and morphological features. However, FISH signals are labile and fade over time, making post-revision of the tumor difficult. CISH (chromogenic in situ hybridization is an alternative procedure, with certain advantages, although still limited as a diagnostic tool in breast carcinomas. Methods To elucidate the molecular profile of HER-2 status, mRNA and protein expression in 75 invasive breast carcinomas were analyzed by real time quantitative RT-PCR (qRT-PCR and IHC, respectively. Amplifications were evaluated in 43 of these cases by CISH and in 11 by FISH. Results The concordance rate between IHC and qRT-PCR results was 78.9%, and 94.6% for qRT-PCR and CISH. Intratumoral heterogeneity of HER-2 status was identified in three cases by CISH. The results of the three procedures were compared and showed a concordance rate of 83.8%; higher discordances were observed in 0 or 1+ immunostaining cases, which showed high-level amplification (15.4% and HER-2 transcript overexpression (20%. Moreover, 2+ immunostaining cases presented nonamplified status (50% by CISH and HER-2 downexpression (38.5% by qRT-PCR. In general, concordance occurred between qRT-PCR and CISH results. A high concordance was observed between CISH/qRT-PCR and FISH. Comparisons with clinicopathological data revealed a significant association between HER-2 downexpression and the involvement of less than four lymph nodes (P = 0.0350. Conclusion Based on these findings, qRT-PCR was more precise and reproducible than IHC. Furthermore, CISH was revealed as an alternative and useful procedure for investigating amplifications involving the HER-2 gene.

  19. Fluorescence in situ hybridization as adjunct to cytology improves the diagnosis and directs estimation of prognosis of malignant pleural effusions

    Directory of Open Access Journals (Sweden)

    Han Jingquan

    2012-11-01

    Full Text Available Abstract Background The identification of malignant cells in effusions by conventional cytology is hampered by its limited sensitivity and specificity. The aim of this study was to investigate the value of fluorescence in situ hybridization (FISH as adjuncts to conventional cytologic examination in patients with malignant pleural effusions. Methods We conducted a retrospective cohort study of 93 inpatients with pleural effusions (72 malignant pleural effusions metastatic from 11 different organs and 21 benign over 23 months. All the patients came from Chinese northeast areas. Aspirated pleural fluid underwent cytologic examination and fluorescence in situ hybridization (FISH for aneuploidy. We used FISH in single-colour or if appropriate in dual-colour evaluation to detect chromosomal aberrations (chromosomes 7, 11, and 17 in effusion cells as markers of malignancy, to raise the diagnostic yield and identified the efficiency by diagnostic biopsy. Predominant cytogenetic anomalies and patterns of intratumor cytogenetic heterogeneity were brought in relation to overall survival rate. Results Cytology alone confirmed malignant pleural effusions in 45 of 72 patients (sensitivity 63%, whereas FISH alone positively identified 48 of 72 patients (sensitivity 67%. Both tests had high specificity in predicting benign effusions. If cytology and FISH were considered together, they exhibited 88% sensitivity and 94.5% specificity in discriminating benign and malignant effusions. Combined, the two assays were more sensitive than either test alone. Although the positive predictive value of each test was 94.5%, the negative predictive value of cytology and FISH combined was 78%, better than 47% and 44% for FISH and cytology alone, respectively. There was a significantly prolonged survival rate for patients with aneuploidy for chromosome 17. Conclusions FISH in combination with conventional cytology is a highly sensitive and specific diagnostic tool for detecting

  20. Construction of g-C_3N_4/Al_2O_3 hybrids via in-situ acidification and exfoliation with enhanced photocatalytic activity

    International Nuclear Information System (INIS)

    Wang, Xiao-jing; Liu, Chao; Li, Xu-li; Li, Fa-tang; Li, Yu-pei; Zhao, Jun; Liu, Rui-hong

    2017-01-01

    Highlights: • Ultrathin g-C_3N_4/Al_2O_3 hybrids are prepared via in-situ reaction. • The structure modification role of in-situ formed HNO_3 for g-C_3N_4 is found. • The ultrathin g-C_3N_4 nanosheets are formed by the acidified melamine and Al(OH)_3. • In-situ calcination of melamine and Al(OH)_3 benefits the contact of C_3N_4 and Al_2O_3. • The activity of g-C_3N_4/Al_2O_3 is 16.6 times that of pristine g-C_3N_4 in degrading RhB. - Abstract: Homogeneous ultrathin g-C_3N_4 nanosheets/Al_2O_3 heterojunctions are synthesized using melamine and Al(NO_3)_3 via in-situ reaction and the following thermal polymerization approach. The in-situ reaction between melamine and Al(NO_3)_3 results in the existence of HNO_3-acidified melamine and Al(OH)_3 aggregates via the hydrolysis of Al(NO_3)_3. After thermal polymerization, the aggregates are converted to g-C_3N_4/Al_2O_3 composites. The thermal polymerization of acidified melamine and the support effect of aluminum hydroxide for g-C_3N_4 during the calcination process lead to highly dispersed amrophous Al_2O_3 on ultrathin g-C_3N_4 nanosheets, which is beneficial for the separation of photogenerated electron-hole pairs in the heterojunction. The degradation rate for Rhodamine B (RhB) over the most activie sample is 16.6 times than that of pristine g-C_3N_4 under visible light irradiation, which can be attributed to the high specific surface area, highly dispersion of amorphous Al_2O_3 on ultrathin g-C_3N_4 nanosheet, and the effective electrons transfer from g-C_3N_4 to the amorphous Al_2O_3.

  1. Detection of group B streptococci in Lim broth by use of group B streptococcus peptide nucleic acid fluorescent in situ hybridization and selective and nonselective agars.

    Science.gov (United States)

    Montague, Naomi S; Cleary, Timothy J; Martinez, Octavio V; Procop, Gary W

    2008-10-01

    The sensitivity, specificity, and positive and negative predictive values for the detection of group B streptococci from Lim enrichment broth with sheep blood agar (SBA), with selective Streptococcus agar (SSA), and by a peptide nucleic acid fluorescent in situ hybridization (PNA FISH) assay were as follows: for culture on SBA, 68.4%, 100%, 100%, and 87.9%, respectively; for culture on SSA, 85.5%, 100%, 100%, and 94.1%, respectively; and for the PNA FISH assay, 97.4%, 98.3%, 96.1%, and 98.9%, respectively.

  2. In situ study of Li-ions diffusion and deformation in Li-rich cathode materials by using scanning probe microscopy techniques

    Science.gov (United States)

    Zeng, Kaiyang; Li, Tao; Tian, Tian

    2017-08-01

    In this paper, the scanning probe microscopy (SPM) based techniques, namely, conductive-AFM, electrochemical strain microscopy (ESM) and AM-FM (amplitude modulation-frequency modulation) techniques, are used to in situ characterize the changes in topography, conductivity and elastic properties of Li-rich layered oxide cathode (Li1.2Mn0.54Ni0.13Co0.13O2) materials, in the form of nanoparticles, when subject to the external electric field. Nanoparticles are the basic building blocks for composite cathode in a Li-ion rechargeable battery. Characterization of the structure and electrochemical properties of the nanoparticles is very important to understand the performance and reliability of the battery materials and devices. In this study, the conductivity, deformation and mechanical properties of the Li-rich oxide nanoparticles under different polarities of biases are studied using the above-mentioned SPM techniques. This information can be correlated with the Li+-ion diffusion and migration in the particles under external electrical field. The results also confirm that the SPM techniques are ideal tools to study the changes in various properties of electrode materials at nano- to micro-scales during or after the ‘simulated’ battery operation conditions. These techniques can also be used to in situ characterize the electrochemical performances of other energy storage materials, especially in the form of the nanoparticles.

  3. Studies on In-situ Chelation/Supercritical Fluid Extraction of Lanthanides and Actinides Using a Radiotracer Technique

    International Nuclear Information System (INIS)

    Lin, Yuehe; Wu, Hong; Smart, Neil G.; Wai, Chien M.

    2001-01-01

    Radioisotope tracer techniques were used to study the process of in-situ chelation/supercritical fluid extraction(SFE) of La3+ and Lu3+ from solid matrix using mixed ligand hexafluoroacetylacetone (HFA) and tributylphosphate (TBP) as chelating agents. A lab-built SFE extactor was used in this study and the extractor design was optimized based on the experimental results. Quantitative recovery of La and Lu was achieved when the extrator design was optimized. Extraction of uranium from real world samples was also investigated to demonstrate the capability of this chelation/SFE technology for environmental remediation applications. A novel on-line back extraction technique for the recovery of metal ions and regeneration of ligands is also reported.

  4. A new in situ technique for studying deformation and fracture in thin film ductile/brittle laminates

    International Nuclear Information System (INIS)

    Hackney, S.A.; Milligan, W.W.

    1991-01-01

    A new technique for studying deformation and fracture of thin film ductile/brittle laminates is described. The laminates are prepared by sputtering a brittle coating on top of an electropolished TEM thin foil. The composites are then strained in situ in the TEM. In this preliminary investigation, the composites consisted of a ductile aluminum substrate and a brittle silicon coating. Cracks in the brittle film grew discontinuously in bursts several micrometers in length. The crack opening displacement initiated plastic deformation in the ductile film, thus dissipating energy and allowing crack arrest. The interface was well bonded, and delamination was not observed. Due to the good interfacial bond and the crack opening behind the crack tip, it was possible to study very large plastic deformations and ductile fracture in the aluminum in situ, without buckling of the foil. The possibility of micromechanical modeling of the fracture behavior is briefly discussed. (orig.)

  5. High luminescent fibers with hybrid SiO2-coated CdTe nanocrystals fabricated by electrospinning technique

    International Nuclear Information System (INIS)

    Cao, Yongqiang; Liu, Ning; Yang, Ping; Shi, Ruixia; Ma, Qian; Zhang, Aiyu; Zhu, Yuanna; Wang, Junpeng; Wang, Jianrong

    2015-01-01

    The polyvinylpyrrolidone (PVP) hybrid luminescent micro-/nanofibers doped with the novel hybrid SiO 2 -coated CdTe nanocrystals (HS-CdTe NCs) have been fabricated for the first time via the electrospinning technique. The morphologies and photoluminescence (PL) emissions of HS-CdTe/PVP micro-/nanofibers prepared by doping the HS-CdTe NCs with the different PL peak wavelength (571, 616, and 643 nm) in PVP fibers were investigated by optical and PL microscope. The results revealed that all the HS-CdTe/PVP hybrid fibers showed an ultralong length for several hundreds of micrometers and a relatively uniform diameter of 1000 ∼ 1200 nm. The hybrid fibers displayed a wavelength-tunable PL emission, determining by the PL of doped HS-CdTe NCs. Moreover, similar to the original PL properties of HS-CdTe NCs before the electrospinning, the HS-CdTe/PVP fibers also showed a series of superior PL properties, such as narrow and symmetry PL spectrum, high, and uniform brightness. For comparison purpose, we also prepared three CdTe/PVP hybrid fibers by doping the 553 nm, 600 nm, and 633 nm PL-emitting CdTe NCs respectively in PVP electrospinning fibers. The characterization results showed that, the obtained three CdTe/PVP hybrid fibers had a basically satisfactory micro-/nanofiber morphology with a long length and relatively uniform diameter, but all the fibers exhibited very weak PL emissions. The enormous contrast in PL properties between HS-CdTe/PVP and CdTe/PVP fibers should mainly be ascribed to the different connection modes of ligands with the NCs and the passivation effect of inert hybrid silica shell on HS-CdTe. It is hopeful that the high luminescent HS-CdTe/PVP micro-/nanofibers with the tunable PL peak wavelength would be a good candidate in the optical sensor, light-emitting devices (LEDs), nanometer-scale waveguides, and the other related photonic materials. - Highlights: • The HS-CdTe/PVP electrospun hybrid fibers were fabricated for the first time. • The

  6. Assessment of phytoremediation as an in-situ technique for cleaning oil-contaminated sites

    International Nuclear Information System (INIS)

    Frick, C. M.; Farrell, R. E.; Germida, J. J.

    1999-01-01

    Literature on examples of phytoremediation techniques used in the in-situ remediation of soils contaminated by petroleum hydrocarbons is reviewed. The review includes discussion of the key mechanisms involved in each case, benefits, limitations and costs compared to alternative approaches, including natural attenuation, engineering and bioremediation. Review of the literature led to the conclusion that phytoremediation is an effective method for degrading and containing petroleum hydrocarbons in soil, and confirmed the ability of plants to transfer volatile petroleum hydrocarbons, such as napthalene, from the soil to the atmosphere via transpiration. The primary loss mechanism for the degradation of petroleum hydrocarbons appears to be microorganisms in the rhizosphere of plants. The available information also suggests that plants may degrade petroleum hydrocarbons directly, although the indirect role played by plants is far more common. These roles include supplying root exudates for microbial use, releasing root-associated enzymes that degrade contaminants in the soil, and altering soil to promote phytoremediation. BTEX compounds are most easily amenable to phytoremediation; large and lipophilic compounds such as four or five-ring polyaromatic hydrocarbons are more difficult to remediate. The limited information available suggests that phytoremediation is slightly less expensive than bioremediation, and several order of magnitude less than engineering techniques. In general, phytoremediation is faster than natural attenuation, but typically slower than engineering and bioremediation. On the other hand, it is less disruptive to the site than ex-situ engineering and bioremediation that involve excavation efforts. Phytoremediation is most effective with shallow contamination. Preliminary screenings indicate that there are several plant species, native and introduced, that may be used with some success for phytoremediation in the Prairie and Boreal Plains ecozones

  7. Developing a western Siberia reference site for tropospheric water vapour isotopologue observations obtained by different techniques (in situ and remote sensing

    Directory of Open Access Journals (Sweden)

    K. Gribanov

    2014-06-01

    water cycle, affected by changes in air mass origin, non-convective and convective processes and continental recycling. Novel remote sensing and in situ measuring techniques have recently offered opportunities for monitoring atmospheric water vapour isotopic composition. Recently developed infrared laser spectrometers allow for continuous in situ measurements of surface water vapour δDv and δ18Ov. So far, very few intercomparisons of measurements conducted using different techniques have been achieved at a given location, due to difficulties intrinsic to the comparison of integrated with local measurements. Nudged simulations conducted with high-resolution isotopically enabled general circulation models (GCMs provide a consistent framework for comparison with the different types of observations. Here, we compare simulations conducted with the ECHAM5-wiso model with two types of water vapour isotopic data obtained during summer 2012 at the forest site of Kourovka, western Siberia: hourly ground-based FTIR total atmospheric columnar δDv amounts, and in situ hourly Picarro δDv measurements. There is an excellent correlation between observed and predicted δDv at surface while the comparison between water column values derived from the model compares well with FTIR estimates.

  8. Localization of pig Na[sup +], K[sup +]-ATPase [alpha] and [beta] subunit genes to chromosome 4 by radioactive in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Lahbib-Mansais, Y.; Yerle, M.; Dalens, M.; Chevalet, C.; Gellin, J. (Centre de Recherches de Toulouse (France))

    1993-01-01

    Two genes coding for Na[sup +],K[sup +] -ATPase [alpha] and [beta] subunits are localized on pig chromosome 4, to the q1.6[yields]q2.3 and 1.3[yields]q2.1 regions, respectively, by radioactive in situ hybridization. According to nucleotide and amino acid sequence comparisons with different human isoforms of Na[sup +] ,K[sup +]-ATPase, these pig [alpha] and [beta] ATPase genes show strong homologies with human [alpha]1 and [beta] subunit ATPase genes, respectively. These results are discussed with respect to comparative mapping data of conserved genes in mammalian species. We showed that the pig cDNA probes encoding ATPase [alpha] and, [beta] genes reveal DNA polymorphism in Meishan an Large White pigs. 35 refs., 4 figs., 2 tabs.

  9. Measurement of in-situ stress in salt and rock using NQR techniques

    International Nuclear Information System (INIS)

    Schempp, E.; Hirschfeld, T.; Klainer, S.

    1980-01-01

    A discussion of how stress and strain affect the quantities which can be measured in an NQR experiment shows that, for stresses of the magnitude to be expected at depths up to about 10,000 feet, quadrupole coupling constants will fall in the range of 1 to 10 kHz for both the sodium and chloride ions in NaCl. The most promising system involves pulsed nuclear double resonance detection; and alterative is to observe the quadrupolar splitting of the NMR signal. Choices to be made in the measurement and mapping techniques are discussed. The well-known perturbation of the homogenous stress field in the neighborhood of a borehole is shown to be advantageous from the point of view of obtaining directional information on the stress. Construction and operation of a borehole stress sensor are considered. The NQR technique seems feasible for measuring the magnitude and direction of underground stress with a resolution of about 25 psi, or 2.5% at 1000 psi. Downhole instrumentation suitable for in-situ determinations of stress appears within the state of the art. Additional tasks required on the project are identified

  10. One-step route to a hybrid TiO2/TixW1−xN nanocomposite by in situ selective carbothermal nitridation

    Directory of Open Access Journals (Sweden)

    Zoë Schnepp, Martin J Hollamby, Masahiko Tanaka, Yoshitaka Matsushita, Yoshio Katsuya and Yoshio Sakka

    2012-01-01

    Full Text Available Metal oxide/nitride nanocomposites have many existing and potential applications, e.g. in energy conversion or ammonia synthesis. Here, a hybrid oxide/nitride nanocomposite (anatase/TixW1−xN was synthesized by an ammonia-free sol–gel route. Synchrotron x-ray diffraction, complemented with electron microscopy and thermogravimetric analysis, was used to study the structure, composition and mechanism of formation of the nanocomposite. The nanocomposite contained nanoparticles (<5 nm diameter of two highly intermixed phases. This was found to arise from controlled nucleation and growth of a single oxide intermediate from the gel precursor, followed by phase separation and in situ selective carbothermal nitridation. Depending on the preparation conditions, the composition varied from anatase/TixW1−xN at low W content to an isostructural mixture of Ti-rich and W-rich TixW1−xN at high W content. In situ selective carbothermal nitridation offers a facile route to the synthesis of nitride-oxide nanocomposites. This conceptually new approach is a significant advance from previous methods, which generally require ammonolysis of a pre-synthesized oxide.

  11. Hybrid Clustering-GWO-NARX neural network technique in predicting stock price

    Science.gov (United States)

    Das, Debashish; Safa Sadiq, Ali; Mirjalili, Seyedali; Noraziah, A.

    2017-09-01

    Prediction of stock price is one of the most challenging tasks due to nonlinear nature of the stock data. Though numerous attempts have been made to predict the stock price by applying various techniques, yet the predicted price is not always accurate and even the error rate is high to some extent. Consequently, this paper endeavours to determine an efficient stock prediction strategy by implementing a combinatorial method of Grey Wolf Optimizer (GWO), Clustering and Non Linear Autoregressive Exogenous (NARX) Technique. The study uses stock data from prominent stock market i.e. New York Stock Exchange (NYSE), NASDAQ and emerging stock market i.e. Malaysian Stock Market (Bursa Malaysia), Dhaka Stock Exchange (DSE). It applies K-means clustering algorithm to determine the most promising cluster, then MGWO is used to determine the classification rate and finally the stock price is predicted by applying NARX neural network algorithm. The prediction performance gained through experimentation is compared and assessed to guide the investors in making investment decision. The result through this technique is indeed promising as it has shown almost precise prediction and improved error rate. We have applied the hybrid Clustering-GWO-NARX neural network technique in predicting stock price. We intend to work with the effect of various factors in stock price movement and selection of parameters. We will further investigate the influence of company news either positive or negative in stock price movement. We would be also interested to predict the Stock indices.

  12. Detection of {open_quotes}cryptic{close_quotes}karyotypic rearrangements in closely related primate species by fluorescence in situ hybridization (FISH) using human subtelomeric DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Youngblom, J.J. [California State University-Stanislaus, Turlock, CA (United States); Trask, B.J.; Friedman, C. [Univ. of Washington, Seattle, WA (United States)] [and others

    1994-09-01

    Specific human subtelomeric DNA probes were used to reveal cryptic chromosomal rearrangements that cannot be detected by conventional high resolution cytogenetic techniques, or by chromosomal in situ suppression hybridization using whole chromosome paint analysis. Two cosmids containing different subtelomeric DNA sequences were derived from human chromosome 19 and designated as 7501 and 16432. Cosmid 7501 was hybridized to chromosomes from humans, chimpanzee, gorilla and orangutan. In humans, 7501 consistently labeled chromosomes 3q, 15q, and 19p. Additional chromosomes were labeled in different individuals, indicating a polymorphic distribution of this sequence in the human genome. In contrast, 7501 consistently and strongly labeled only the q arm terminus of chromosome 3 in both chimp and gorilla. The identification of the chromosome was made by two-color FISH analysis using human chromosome 4-specific paint and homologous to human chromosome 4. None of the human subjects showed labeling of chromosome 4 with 7501. This finding suggests that in the course of human evolution, subsequent to the divergence of humans and African apes, a cryptic translocation occurred between the ancestral human chromosome 4 and one or more of the other human chromosomes that now contain this DNA segment. In orangutan, 7501 labeled a single acrocentric chromosome pair, a distinctly different chromosome than that labeled in chimp and gorilla. Comparison of chromosome sites labeled with cosmid 16432 showed the distribution of signals on chromosome 1q arm is the same for humans and chimp, but different in the gorilla. Humans and chimps show distinct labeling on sites 1q terminus and 1q41-42. In gorilla, there is instead a large cluster of intense signal near the terminus of 1q that clearly does not extend all the way to the terminus. A paracentric inversion or an unequal cross-over event may account for the observed difference between these species.

  13. Report of the first research co-ordination meeting under co-ordinated research project on 'In situ applications of XRF techniques'

    International Nuclear Information System (INIS)

    2001-03-01

    X-ray fluorescence is a well-established analytical technique widely used in industrial and research applications for materials characterisation. However, a relatively recent development has been the availability of portable instrumentation, which can be used for both the direct in situ non-destructive analysis of samples, and also is readily transportable to field sites for use in a 'mobile laboratory' style of operation. In situ analyses using the XRF technique can make an essential contribution to a wide range of projects, including: - Analysis of soils, particularly in the assessment of agricultural land and contaminated land - Sorting scrap metal alloys and plastics to increase the value of recyclable materials - Geochemical mapping and exploration to locate mineralisation deposits - Environmental monitoring related to air pollution studies and contamination of the work - The on-line control of industrial processes for the production of raw materials - Archaeological studies and the classification of artefacts, the restoration of sculptures, paintings and other objects of cultural heritage. - In situ geochemical studies on Mars, including the 1997 NASA Pathfinder mission and the forthcoming European Space Agency Mars Express mission, which includes the In these applications, the major advantages of field-portable X-ray fluorescence (FPXRF) spectrometry include: on-site immediate availability of analytical results, non-destructive analysis, a multielement capability, speed of operation and access to valuable/unique samples that otherwise would be unavailable for chemical analysis. The CRP on 'In situ applications of XRF techniques' is one element of the project on Nuclear Instruments for Specific Applications the major objective of which is to assist Member States in the development of nuclear instruments and software for special applications, such as the characterisation of materials. An overall objective of this CRP is to assist laboratories in Member States

  14. Sensitivity of Helicobacter pylori detection by Giemsa staining is poor in comparison with immunohistochemistry and fluorescent in situ hybridization and strongly depends on inflammatory activity.

    Science.gov (United States)

    Kocsmár, Éva; Szirtes, Ildikó; Kramer, Zsófia; Szijártó, Attila; Bene, László; Buzás, György Miklós; Kenessey, István; Bronsert, Peter; Csanadi, Agnes; Lutz, Lisa; Werner, Martin; Wellner, Ulrich Friedrich; Kiss, András; Schaff, Zsuzsa; Lotz, Gábor

    2017-08-01

    Conventional stainings (including H&E and special stains like Giemsa) are the most widely applied histopathologic detection methods of Helicobacter pylori (HP). We aimed to compare the diagnostic performance of Giemsa staining with immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) on a monocentric cohort of 2896 gastric biopsies and relate results to histologic alterations in order to find such histopathologic subgroups in which these methods underperform. All cases were categorized regarding presence or absence of chronic gastritis, inflammatory activity, and mucosal structural alterations. Giemsa revealed 687 cases (23.7%), IHC 795 cases (27.5%), and FISH 788 cases (27.2%) as being HP positive. Giemsa showed significantly lower overall sensitivity (83.3%) compared to IHC (98.8%) and FISH (98.0%). Moreover, the sensitivity of Giemsa dramatically dropped to 33.6% in the nonactive cases. We found that sensitivity of Giemsa strongly depends on HP density and, accordingly, on the presence of activity. Structural alterations (intestinal metaplasia, atrophy, etc.) had only no or weak effect on sensitivity of the three stainings. Both IHC and FISH proved to be equally reliable HP detecting techniques whose diagnostic performance is minimally influenced by mucosal inflammatory and structural alterations contrary to conventional stainings. We highly recommend immunohistochemistry for clinically susceptible, nonactive chronic gastritis cases, if the conventional stain-based HP detection is negative. Moreover, we recommend to use IHC more widely as basic HP stain. Helicobacter pylori FISH technique is primarily recommended to determine bacterial clarithromycin resistance. Furthermore, it is another accurate diagnostic tool for HP. © 2017 John Wiley & Sons Ltd.

  15. Detection of Group B Streptococci in Lim Broth by Use of Group B Streptococcus Peptide Nucleic Acid Fluorescent In Situ Hybridization and Selective and Nonselective Agars▿

    Science.gov (United States)

    Montague, Naomi S.; Cleary, Timothy J.; Martinez, Octavio V.; Procop, Gary W.

    2008-01-01

    The sensitivity, specificity, and positive and negative predictive values for the detection of group B streptococci from Lim enrichment broth with sheep blood agar (SBA), with selective Streptococcus agar (SSA), and by a peptide nucleic acid fluorescent in situ hybridization (PNA FISH) assay were as follows: for culture on SBA, 68.4%, 100%, 100%, and 87.9%, respectively; for culture on SSA, 85.5%, 100%, 100%, and 94.1%, respectively; and for the PNA FISH assay, 97.4%, 98.3%, 96.1%, and 98.9%, respectively. PMID:18667597

  16. WRHT: A Hybrid Technique for Detection of Wormhole Attack in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Rupinder Singh

    2016-01-01

    Full Text Available Wormhole attack is a challenging security threat to wireless sensor networks which results in disrupting most of the routing protocols as this attack can be triggered in different modes. In this paper, WRHT, a wormhole resistant hybrid technique, is proposed, which can detect the presence of wormhole attack in a more optimistic manner than earlier techniques. WRHT is based on the concept of watchdog and Delphi schemes and ensures that the wormhole will not be left untreated in the sensor network. WRHT makes use of the dual wormhole detection mechanism of calculating probability factor time delay probability and packet loss probability of the established path in order to find the value of wormhole presence probability. The nodes in the path are given different ranking and subsequently colors according to their behavior. The most striking feature of WRHT consists of its capacity to defend against almost all categories of wormhole attacks without depending on any required additional hardware such as global positioning system, timing information or synchronized clocks, and traditional cryptographic schemes demanding high computational needs. The experimental results clearly indicate that the proposed technique has significant improvement over the existing wormhole attack detection techniques.

  17. Fluorescent nanodiamond and lanthanide labelled in situ hybridization for the identification of RNA transcripts in fixed and CLARITY-cleared central nervous system tissues (Conference Presentation)

    Science.gov (United States)

    Parker, Lindsay M.; Staikopoulos, Vicky; Cordina, Nicole M.; Sayyadi, Nima; Hutchinson, Mark R.; Packer, Nicolle H.

    2016-03-01

    Despite significant advancement in the methodology used to conjugate, incorporate and visualize fluorescent molecules at the cellular and tissue levels, biomedical imaging predominantly relies on the limitations of established fluorescent molecules such as fluorescein, cyanine and AlexaFluor dyes or genetic incorporation of fluorescent proteins by viral or other means. These fluorescent dyes and conjugates are highly susceptible to photobleaching and compete with cellular autofluorescence, making biomedical imaging unreliable, difficult and time consuming in many cases. In addition, some proteins have low copy numbers and/or poor antibody recognition, further making detection and imaging difficult. We are developing better methods for imaging central nervous system neuroinflammatory markers using targeted mRNA transcripts labelled with fluorescent nanodiamonds or lanthanide chelates. These tags have increased signal and photostability and can also discriminate against tissue/cell autofluorescence. Brains and spinal cords from BALB/c mice with a chronic constriction model of neuropathic pain (neuroinflammation group) or that have undergone sham surgeries (control group) were collected. A subset of brains and spinal cords were perfused and fixed with paraformaldehyde (n=3 sham and n=3 pain groups) prior to sectioning and in situ hybridization using nanodiamond or lanthanide chelate conjugated complementary RNA probes. Another subset of brains and spinal cords from the same cohort of animals were perfused and processed for CLARITY hydrogel based clearing prior to in situ hybridization with the same probes. We will present our findings on the photostability, sensitivity and discrimination from background tissue autofluorescence of our novel RNA probes, compared to traditional fluorophore tags.

  18. Preparation of zeolite-A/chitosan hybrid composites and their bioactivities and antimicrobial activities

    International Nuclear Information System (INIS)

    Yu, Liang; Gong, Jie; Zeng, Changfeng; Zhang, Lixiong

    2013-01-01

    Zeolite-A/chitosan hybrid composites with zeolite contents of 20–55 wt.% were prepared by in situ transformation of silica/chitosan mixtures in a sodium aluminate alkaline solution through impregnation–gelation–hydrothermal synthesis. The products were characterized by X-ray diffraction, diffuse reflectance infrared Fourier transform spectroscopy, scanning electron microscopy, thermogravimetric analysis, and mercury penetration porosimetry. Their in vitro bioactivities were examined using as-synthesized and Ca 2+ -exchanged hybrid composites in simulated body fluid (SBF) for hydroxyapatite (HAP) growth. Their antimicrobial activities for Escherichia coli (E. coli) in trypticase soy broth (TSB) were evaluated using Ag + -exchanged hybrid composites. The zeolite-A/chitosan hybrid composites could be prepared as various shapes, including cylinders, plates and thin films. They possessed macropores with pore sizes ranging from 100 to 300 μm and showed compressive mechanical strength as high as 3.2 MPa when the zeolite content was 35 wt.%. Fast growth on the Ca 2+ -exchanged hybrid composites was observed with the highest weight gain of 51.4% in 30 days. The 35 wt.% Ag + -exchanged hybrid composite showed the highest antimicrobial activity, which could reduce the 9 × 10 6 CFU mL −1 E. coli concentration to zero within 4 h of incubation time with the Ag + -exchanged hybrid composite amount of 0.4 g L −1 . The bioactivity and antimicrobial activity could be combined by ion-exchanging the composites first with Ca 2+ and then with Ag + . These zeolite-A/chitosan hybrid composites have potential applications on tissue engineering and antimicrobial food packaging. - Graphical abstract: Zeolite A/chitosan hybrid composites were prepared by in situ transformation of precursors in the chitosan matrix, which possess macroporous structures and exhibit superior bioactivity and antimicrobial activity and potential biomedical application. Highlights: • Zeolite A

  19. Preparation of zeolite-A/chitosan hybrid composites and their bioactivities and antimicrobial activities

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Liang; Gong, Jie [State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009 (China); Zeng, Changfeng [College of Mechanic and Power Engineering, Nanjing University of Technology, Nanjing 210009 (China); Zhang, Lixiong, E-mail: lixiongzhang@yahoo.com [State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210009 (China)

    2013-10-15

    Zeolite-A/chitosan hybrid composites with zeolite contents of 20–55 wt.% were prepared by in situ transformation of silica/chitosan mixtures in a sodium aluminate alkaline solution through impregnation–gelation–hydrothermal synthesis. The products were characterized by X-ray diffraction, diffuse reflectance infrared Fourier transform spectroscopy, scanning electron microscopy, thermogravimetric analysis, and mercury penetration porosimetry. Their in vitro bioactivities were examined using as-synthesized and Ca{sup 2+}-exchanged hybrid composites in simulated body fluid (SBF) for hydroxyapatite (HAP) growth. Their antimicrobial activities for Escherichia coli (E. coli) in trypticase soy broth (TSB) were evaluated using Ag{sup +}-exchanged hybrid composites. The zeolite-A/chitosan hybrid composites could be prepared as various shapes, including cylinders, plates and thin films. They possessed macropores with pore sizes ranging from 100 to 300 μm and showed compressive mechanical strength as high as 3.2 MPa when the zeolite content was 35 wt.%. Fast growth on the Ca{sup 2+}-exchanged hybrid composites was observed with the highest weight gain of 51.4% in 30 days. The 35 wt.% Ag{sup +}-exchanged hybrid composite showed the highest antimicrobial activity, which could reduce the 9 × 10{sup 6} CFU mL{sup −1}E. coli concentration to zero within 4 h of incubation time with the Ag{sup +}-exchanged hybrid composite amount of 0.4 g L{sup −1}. The bioactivity and antimicrobial activity could be combined by ion-exchanging the composites first with Ca{sup 2+} and then with Ag{sup +}. These zeolite-A/chitosan hybrid composites have potential applications on tissue engineering and antimicrobial food packaging. - Graphical abstract: Zeolite A/chitosan hybrid composites were prepared by in situ transformation of precursors in the chitosan matrix, which possess macroporous structures and exhibit superior bioactivity and antimicrobial activity and potential biomedical

  20. Assignment of the human gene for pregnancy-associated plasma protein A (PAPPA) to 9q33.1 by fluorescence in situ hybridization to mitotic and meiotic chromosomes

    DEFF Research Database (Denmark)

    Silahtaroglu, A N; Tümer, Z; Kristensen, Torsten

    1993-01-01

    Low levels of pregnancy-associated plasma protein A (PAPPA) during the first trimester has been suggested as a biochemical indicator of pregnancies with aneuploid fetuses. Furthermore, the complete absence of PAPPA in pregnancies associated with Cornelia de Lange syndrome (CL) has suggested...... a causal connection between PAPPA and the development of CL. We have assigned the locus for PAPPA to chromosome region 9q33.1 on mitotic and meiotic chromosomes by fluorescence in situ hybridization, using a 3.7-kb partial PAPPA cDNA probe...