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Sample records for situ hybridization analyses

  1. Fluorescent in situ hybridization analyses of human oocytes in trisomy 18 and 21

    SciTech Connect

    Cheng, E.Y.; Chen, Y.J.; Gartler, S.M.

    1994-09-01

    The commonly accepted view of synapsis is that only 2 homologues can synapse at any one site and that this restriction applies to polyploids as well. However, triple synapsis has been observed is some triploid plants and in triploid chicken. In humans, triple synapsis of the long arm of chromosome 21 was detected in sperm of a trisomic 21 individual. More recently, studies of oocytes from trisomic 21 and 18 fetuses also indicated extensive triple synapsis along the entire length of the chromosomes. To further investigate this question, we undertook an evaluation of trivalent synapsis in fetal oocytes from 2 trisomic 21 and 2 trisomic 18 fetuses using fluorescent in situ hybridization (FISH) with whole chromosome probes. Oocytes were hybridized with whole chromosome probes obtained from ONCOR, Inc. after fixation with methanol and acetic acid. Slides were scored for the distribution of prophase stages, hybridization efficiency, and hybridization characteristics of chromosomes 18 and 21 in the trisomic 18 and 21 fetuses respectively. Fifty-eight per cent (379/650) of pachytenes analyzed for chromosome 18 contained a conspicous trivalent and 319 (48%) of these nuclei contained a single, thick, continuous fluorescent signal consistent with complete triple synapsis along the entire length of all 3 chromosomes. Sixteen per cent (104/650) of pachytene contained 2 signals consistent with a bivalent and a univalent, and 9 cells contained 3 thin signals consistent with asynapsis of all 3 chromosomes. The remaining 158 pachytenes had unusual pairing configurations that we could not classify, but they most likely represent trivalents with partial pairing between different homologues. In the 2 trisomic 21 fetuses, the majority (143/232) of pachytenes also contained one signal while only 52 cells contained a bivalent and univalent. Five cells contained 3 separate signals. These results confirm the existence of triple synapsis in human meiosis.

  2. Triplex in-situ hybridization

    DOEpatents

    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.

  3. Reutilization of previously hybridized slides for fluorescence in situ hybridization

    SciTech Connect

    Epstein, L.; DeVries, S.; Waldman, F.M.

    1995-12-01

    Application of fluorescence in situ hybridization (FISH) to clinical material is sometimes limited by sample size. In addition, heterogeneity among slides prepared from a single sample may lead to variation in FISH analyses. Reutilization of material for repeated FISH analyses would help to alleviate these problems. We have developed a simple procedure for repeated FISH analyses with directly conjugated probes. Previously hybridized probes are removed by incubation in denaturing solution, and slides can then be rehybridized without residual signals remaining. Several cycles of this procedure allow a full complement of chromosomal loci to be analyzed on the same population of cells. Advantages of this protocol include gaining more cytogenetic information from small samples and eliminating the problem of intratumorvariability. 5 refs., 4 figs.

  4. The effect of acute haloperidol treatment on brain proneurotensin mRNA: in situ hybridization analyses using a novel fluorescence detection procedure.

    PubMed

    Williams, F G; Murtaugh, M P; Beitz, A J

    1990-05-01

    These studies describe the normal anatomical distribution of neurons containing the mRNA coding for neurotensin (proneurotensin/neuromedin N) in the rat forebrain and midbrain and examine how that distribution is altered by acute administration of the dopamine antagonist haloperidol. A novel fluorescence detection method was developed and employed with biotinylated oligonucleotides to permit the rapid, sensitive visualization of in situ hybridization. The hybridization was temperature-sensitive, eliminated by ribonuclease, and co-localized in neurotensin-immunoreactive perikarya in the midbrain. In the forebrain of control rats, proneurotensin mRNA-containing neurons were found in the dorsomedial and ventrolateral caudate/putamen, in the nucleus accumbens, in the ventral striatum including the olfactory tubercles, and in the septal nuclei. Haloperidol induced significant increases in the frequencies and distributions of hybridization-positive neurons in the striatum and septal nuclei. In the midbrain, the highest frequency of hybridization-positive neurons occurred in the substantia nigra and the superior colliculus. Prominent populations were also present in the dorsal and ventral periaqueductal gray, the oculomotor region, and the medial longitudinal fasciculus. Less prominent were populations of neurons in the dorsomedial deep mesencephalic nuclei and the ventral tegmental area. Haloperidol induced only modest increases in the frequency of pro-neurotensin mRNA-containing neurons in the ventral tegmental area, and had no effects elsewhere in the midbrain. These results show that the fluorescent detection techniques used in this analysis provide a very rapid, reliable method for localizing hybridized mRNA in the rat brain. This study also suggests that a subpopulation of striatal neurons begin to express proneurotensin mRNA in response to haloperidol treatment. This effect of haloperidol on striatal neurons contrasts with results from additional studies of

  5. Effects of chronic low level lead exposure on the expression of GFAP and vimentin mRNA in the rat brain hippocampus analysed by in situ hybridization.

    PubMed

    Peters, B; Stoltenburg, G; Hummel, M; Herbst, H; Altmann, L; Wiegand, H

    1994-01-01

    In this study we used in situ hybridization to examine the effects of chronic low level lead toxicity during different periods of brain development. Low level lead is known to affect astroglia. GFAP and Vimentin were chosen as glialtypic markers for neurotoxicity. The effects of lead were investigated on male Wistar rats. Animals were divided into four groups: a control group, a permanent group exposed during gestation, lactation and post-weaning (E0-P100), a perinatal group exposed during gestation and postnatally until weaning (E0-P16), and a post-weaning exposed group (P16-P100). All experimental animals were fed a diet containing 750 ppm lead acetate. With respect to Vimentin mRNA no major differences could be detected among the treatment groups. Significant differences in GFAP mRNA levels were detected in the post-weaning group relative to controls. In this group we observed a strong increase of GFAP mRNA in the polymorphic zone of the dentate gyrus and in the CA1 region of the hippocampus. Permanent and perinatal groups showed no overt changes compared to controls. Our findings suggest that an irritation of the mature astrocyte results in a change from the quiescent to the reactive state. The majority of astrocytes that have been exposed during their development and differentiation fail to react even if the exposure is continued to adulthood. This suggests an irreversible insult by low level lead exposure during this period of time.

  6. In situ hybridization of termite microbes.

    PubMed

    Moriya, Shigeharu; Noda, Satoko; Ohkuma, Moriya; Kudo, Toshiaki

    2007-01-01

    In situ hybridization is one of the most direct and reliable ways to ascertain the origin of the gene from complex mixed cellular systems. This method is essential for studying communities of uncultured microorganism in their natural ecosystem. In this chapter, we introduce our protocols for the in situ hybridization of the messenger RNA of uncultured symbiotic protists of termite hindgut and the ribosomal RNA of the symbiotic bacteria of the protists using nonradioactive labeling protocols. We hope that you will find these protocols useful in your own work to unravel the complex functions and to discover new organisms in the ecosystem.

  7. DNA/DNA in situ hybridization with enzyme linked probes

    SciTech Connect

    Grillo, S.; Mosher, M.; Charles, P.; Henry, S.; Taub, F.

    1987-05-01

    A non-radioactive in situ nucleic acid hybridization method which requires no antibodies, haptens, avidin or biotin intermediateries is presented. Horseradish peroxidase (HRP) labeled nucleic acid probes are hybridized in situ for 2 hours or less, followed by brief washing of hybridized cells and the direct detection of in situ hybrids with diaminobenzidine (DAB). Application of this method to the detection of Human Papilloma Virus (HPV) in human cells is shown.

  8. Painting of parental chromatin in Beta hybrids by multi-colour fluorescent in situ hybridization.

    PubMed

    Desel, Christine; Jansen, Rita; Dedong, Gue; Schmidt, Thomas

    2002-02-01

    Sugar beet (Beta vulgaris L.) is a relatively young crop and has a narrow gene pool. In order to introduce genetic variability into the crop, interspecific hybrids, selected from crosses with wild beets of the sections Corollinae and Procumbentes, have been generated. The introgressed B. procumbens chromatin carries resistance genes to beet cyst nematode Heterodera schachtii Schm. These lines are important for breeding of nematode-resistant sugar beet, while Corollinae species are potential donors of tolerance to biotic and abiotic stresses such as drought or saline soils. We have used in situ hybridization of genomic DNA to discriminate the parental chromosomes in these interspecific hybrids. Suppression of cross-hybridization by blocking DNA was not necessary indicating that the investigated Beta genomes contain sufficient species-specific DNA enabling the unequivocal determination of the genomic composition of the hybrids. Interspecific hybrid lines with an additional chromosome (2n = 18 + 1), chromosome fragment (2n = 18 + fragment) or translocation of B. procumbens (2n = 18) were analysed by genomic in situ hybridization (GISH) at mitosis and meiosis. Species-specific satellites and ribosomal genes used in combination with genomic DNA or in rehybridization experiments served as landmark probes for chromosome identification in hybrid genomes. The detection of a B. procumbens translocation of approx. I Mbp demonstrated the sensitivity and resolution of GISH and showed that this approach is a powerful method in genome analysis projects of the genus Beta.

  9. Fluorescent in situ hybridization to ascidian chromosomes.

    PubMed

    Shoguchi, Eiichi; Ikuta, Tetsuro; Yoshizaki, Fumiko; Satou, Yutaka; Satoh, Nori; Asano, Katsutoshi; Saiga, Hidetoshi; Nishikata, Takahito

    2004-02-01

    The draft genome of the ascidian Ciona intestinalis has been sequenced. Mapping of the genome sequence to the Ciona 14 haploid chromosomes is essential for future studies of the genome-wide control of gene expression in this basal chordate. Here we describe an efficient protocol for fluorescent in situ hybridization for mapping genes to the Ciona chromosomes. We demonstrate how the locations of two BAC clones can be mapped relative to each other. We also show that this method is efficient for coupling two so-far independent scaffolds into one longer scaffold when two BAC clones represent sequences located at either end of the two scaffolds.

  10. Molecular cytogenetics using fluorescence in situ hybridization

    SciTech Connect

    Gray, J.W.; Kuo, Wen-Lin; Lucas, J.; Pinkel, D.; Weier, H-U.; Yu, Loh-Chung.

    1990-12-07

    Fluorescence in situ hybridization (FISH) with chromosome-specific probes enables several new areas of cytogenetic investigation by allowing visual determination of the presence and normality of specific genetic sequences in single metaphase or interphase cells. in this approach, termed molecular cytogenetics, the genetic loci to be analyzed are made microscopically visible in single cells using in situ hybridization with nucleic acid probes specific to these loci. To accomplish this, the DNA in the target cells is made single stranded by thermal denaturation and incubated with single-stranded, chemically modified probe under conditions where the probe will anneal only with DNA sequences to which it has high DNA sequence homology. The bound probe is then made visible by treatment with a fluorescent reagent such as fluorescein that binds to the chemical modification carried by the probe. The DNA to which the probe does not bind is made visible by staining with a dye such as propidium iodide that fluoresces at a wavelength different from that of the reagent used for probe visualization. We show in this report that probes are now available that make this technique useful for biological dosimetry, prenatal diagnosis and cancer biology. 31 refs., 3 figs.

  11. In situ DNA-hybridization chain reaction (HCR): a facilitated in situ HCR system for the detection of environmental microorganisms.

    PubMed

    Yamaguchi, Tsuyoshi; Kawakami, Shuji; Hatamoto, Masashi; Imachi, Hiroyuki; Takahashi, Masanobu; Araki, Nobuo; Yamaguchi, Takashi; Kubota, Kengo

    2015-07-01

    In situ detection of microorganisms by fluorescence in situ hybridization (FISH) is a powerful tool for environmental microbiology, but analyses can be hampered by low rRNA content in target organisms, especially in oligotrophic environments. Here, we present a non-enzymatic, hybridization chain reaction (HCR)-based signal amplified in situ whole-cell detection technique (in situ DNA-HCR). The components of the amplification buffer were optimized to polymerize DNA amplifier probes for in situ DNA-HCR. In situ hybridization of initiator probes followed by signal amplification via HCR produced bright signals with high specificity and probe permeation into cells. The detection rates for Bacteria in a seawater sample and Archaea in anaerobic sludge samples were comparable with or greater than those obtained by catalyzed reporter deposition (CARD)-FISH or standard FISH. Detection of multiple organisms (Bacteria, Archaea and Methanosaetaceae) in an anaerobic sludge sample was achieved by simultaneous in situ DNA-HCR. In summary, in situ DNA-HCR is a simple and easy technique for detecting single microbial cells and enhancing understanding of the ecology and behaviour of environmental microorganisms in situ.

  12. Establishment of the genomic in situ hybridization (GISH) technique for analysis in interspecific hybrids of Passiflora.

    PubMed

    Melo, C A F; Silva, G S; Souza, M M

    2015-01-01

    The genomic in situ hybridization (GISH) technique was applied to Passiflora interspecific F1 HD13-133 hybrids (Passiflora sublanceolata x Passiflora foetida) and HD15-101 (Passiflora gardineri x Passiflora gibertii), and the backcrossed hybrids (BC1) HD18-106 and HD18-113 (Passiflora sublanceolata x HD13-133). GISH was performed using genomic probes prepared with the DNA from the paternal genitor, whereas the maternal DNA was used as blocking DNA and employed at various concentrations (20X, 40X, 60X, and 100X) in relation to the probe concentration. At the same time, GISH was applied with the use of simultaneous probes from both genomes, paternal and maternal, that were detected with avidin-FITC and anti-digoxigenin-rhodamine, respectively. Both methodologies allowed the distinguishing of the maternal and paternal genomes, thus confirming the hybrid nature of all the analyzed genotypes. Furthermore, the presence of recombinant chromosomes in BC1 hybrids revealed the occurrence of meiotic recombination in HD13 hybrids. This application of the GISH technique is an important step towards genomic analyses of Passiflora hybrids: it can broaden the phylogenetic and evolutionary studies of the genus and, at the same time, contribute to breeding programs. PMID:25867365

  13. Chromogenic in situ hybridization: a multicenter study comparing silver in situ hybridization with FISH.

    PubMed

    Bartlett, J M S; Campbell, Fiona M; Ibrahim, Merdol; Wencyk, Peter; Ellis, Ian; Kay, Elaine; Connolly, Yvonne; O'Grady, Anthony; Di Palma, Silvana; Starczynski, Jane; Morgan, John M; Jasani, Bharat; Miller, Keith

    2009-10-01

    Our purposes were to perform a robust assessment of a new HER2 chromogenic in situ hybridization test and report on concordance of silver in situ hybridization (SISH) data with fluorescence in situ hybridization (FISH) data and on intraobserver and interlaboratory scoring consistency. HER2 results were scored from 45 breast cancers in 7 laboratories using the Ventana (Tucson, AZ) INFORM HER-2 SISH assay and in 1 central laboratory using a standard FISH assay. Overall, 94.8% of cases were successfully analyzed by SISH across the 6 participating laboratories that reported data. Concordance for diagnosis of HER2 amplification by SISH compared with FISH was high (96.0% overall). Intraobserver variability (8.0%) and intersite variability (12.66%) of absolute HER2/chromosome 17 ratios appear to be tightly controlled across all 6 participating laboratories. The Ventana INFORM HER-2 SISH assay is robust and reproducible, shows good concordance with a standard FISH assay, and complies with requirements in national guidelines for performance of diagnostic tests.

  14. Single Molecule Techniques for Advanced in situ Hybridization

    SciTech Connect

    Hollars, C W; Stubbs, L; Carlson, K; Lu, X; Wehri, E

    2003-02-03

    One of the most significant achievements of modern science is completion of the human genome sequence, completed in the year 2000. Despite this monumental accomplishment, researchers have only begun to understand the relationships between this three-billion-nucleotide genetic code and the regulation and control of gene and protein expression within each of the millions of different types of highly specialized cells. Several methodologies have been developed for the analysis of gene and protein expression in situ, yet despite these advancements, the pace of such analyses is extremely limited. Because information regarding the precise timing and location of gene expression is a crucial component in the discovery of new pharmacological agents for the treatment of disease, there is an enormous incentive to develop technologies that accelerate the analytical process. Here we report on the use of plasmon resonant particles as advanced probes for in situ hybridization. These probes are used for the detection of low levels of gene-probe response and demonstrate a detection method that enables precise, simultaneous localization within a cell of the points of expression of multiple genes or proteins in a single sample.

  15. Measuring in situ primary and competitive hybridization events on microspheres

    NASA Astrophysics Data System (ADS)

    Milam, Valeria; Hardin, James

    2012-02-01

    Understanding hybridization events at surfaces is crucial for optimizing nucleic acid detection platforms as well as DNA-mediated colloidal assembly. We used flow cytometry to measure time-dependent primary and competitive hybridization events of perfectly matched and mismatched targets on microsphere surfaces. In addition to more conventional sample preparation involving multiple wash and resuspension steps prior to measurement, we sampled the reaction volume directly for in situ measurements to minimize potential dissociation events between weaker partner strands during wash steps. Similar to prior reports for oligonucletide solutions, the nearly identical rates for primary hybridization events on microsphere surfaces were independent of target sequence and reached an equilibrium value within 30 min. The extent of in situ primary hybridization events for immobilized probes, however, deviated from solution model predictions. In situ competitive hybridization events were at least 100-fold slower than primary hybridization events and did not appear to reach equilibrium. The kinetics of competitive hybridization events on microspheres are consistent with predicted effects stemming from toehold effects or base length differences between primary and secondary targets.

  16. Strategies for In situ and Sample Return Analyses

    NASA Astrophysics Data System (ADS)

    Papanastassiou, D. A.

    2006-12-01

    There is general agreement that planetary exploration proceeds from orbital reconnaissance of a planet, to surface and near-surface in situ exploration, to sample return missions, which bring back samples for investigations in terrestrial laboratories, using the panoply of state-of-the-art analytical techniques. The applicable techniques may depend on the nature of the returned material and complementary and multi- disciplinary techniques can be used to best advantage. High precision techniques also serve to provide the "ground truth" and calibrate past and future orbital and in situ measurements on a planet. It is also recognized that returned samples may continue to be analyzed by novel techniques as the techniques become developed, in part to address specific characteristics of returned samples. There are geophysical measurements such as those of the moment of inertia of a planet, seismic activity, and surface morphology that depend on orbital and in-situ science. Other characteristics, such as isotopic ages and isotopic compositions (e.g., initial Sr and Nd) as indicators of planetary mantle or crust evolution and sample provenance require returned samples. In situ analyses may be useful for preliminary characterization and for optimization of sample selection for sample return. In situ analyses by Surveyor on the Moon helped identify the major element chemistry of lunar samples and the need for high precision mass spectrometry (e. g., for Rb-Sr ages, based on extremely low alkali contents). The discussion of in-situ investigations vs. investigations on returned samples must be directly related to available instrumentation and to instrumentation that can be developed in the foreseeable future. The discussion of choices is not a philosophical but instead a very practical issue: what precision is required for key investigations and what is the instrumentation that meets or exceeds the required precision. This must be applied to potential in situ instruments and

  17. FISH-ing for Genes: Modeling Fluorescence "in situ" Hybridization

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton Buck

    2006-01-01

    Teaching methods of genetic analysis such as fluorescence in situ hybridization (FISH) can be an important part of instructional units in biology, microbiology, and biotechnology. Experience, however, indicates that these topics are difficult for many students. The authors of this article describe how they created an activity that effectively…

  18. The detection of HIV by in situ hybridization.

    PubMed

    Shapshak, P; Sun, N C; Resnick, L; Hsu, M Y; Tourtellotte, W W; Schmid, P; Conrad, A; Fiala, M; Imagawa, D T

    1990-03-01

    A simplified method of in situ hybridization is described for the detection of HIV targets. This standardized method can be applied to sections of formalin-fixed paraffin-embedded tissues, cell blocks, and smears of cultured cells using 3H- or 35S-labeled DNA and 35S-labeled RNA probes. In order to use elevated stringencies in the hybridization and wash steps, tissue sections and cells are covalently bonded to silanated glass slides without their subsequent loss from the slides. Routine hematoxylin and eosin or Romanovsky's stains enable the identification of the cells detected by in situ hybridization. HIV-infected neuroblastoma and lymphoid cell lines, lymph nodes, bone marrow, kidney, as well as brain tissue from patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex are used to demonstrate the generality of the procedure. The standardized method described widens the ease and applicability of in situ hybridization in the investigation of pathologic tissues with the use of diverse specimens and probes.

  19. Nucleic acid in-situ hybridization detection of infectious agents

    NASA Astrophysics Data System (ADS)

    Thompson, Curtis T.

    2000-04-01

    Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

  20. Hybrid Propulsion In-Situ Resource Utilization Test Facility Development

    NASA Technical Reports Server (NTRS)

    Chandler, Ashley A.; Gatto, Corinne; Nakazono, Barry; Grayson, Kristian; Vaughan, David

    2014-01-01

    Hybrid propulsion could be a potential game changing technology for several Mars applications, such as Mars Sample Return (MSR) and human exploration. A flexible hybrid test facility has been built at the Jet Propulsion Laboratory to provide data relevant to the design of such systems. This paper presents the motivations for such a system and its design. The facility is capable of testing 5 cm diameter fuel grains with gaseous oxygen and Mars in situ propellant production simulating oxidizer (varying mixtures of GO2, CO2 and CO). All currently planned tests utilize paraffin based fuels; however, alternative hybrid fuels may be used in the future. Variable length to outer diameter (L/D) ratios may also be tested to give insight on potential packaging constraints. The goal of this research is to enable the inclusion of hybrid propulsion systems in future mission design studies by determining the empirical constants in the regression rate equation for paraffin-based fuels with space storable and/or in situ oxidizers and to investigate the effect of L/D on combustion efficiency. Test results will be reported separately.

  1. Fluorescent In Situ Hybridization in Suspension by Imaging Flow Cytometry.

    PubMed

    Maguire, Orla; Wallace, Paul K; Minderman, Hans

    2016-01-01

    The emergence of imaging flow cytometry (IFC) has brought novel applications exploiting its advantages over conventional flow cytometry and microscopy. One of the new applications is fluorescence in situ hybridization in suspension (FISH-IS). Conventional FISH is a slide-based approach in which the spotlike imagery resulting from hybridization with fluorescently tagged probes is evaluated by fluorescence microscopy. The FISH-IS approach evaluated by IFC enables the evaluation of tens to hundreds of thousands of cells in suspension and the analysis can be automated and standardized diminishing operator bias from the analysis. The high cell number throughput of FISH-IS improves the detection of rare events compared to conventional FISH. The applicability of FISH-IS is currently limited to detection of abnormal quantitative differences of hybridization targets such as occur in numerical chromosome abnormalities, deletions and amplifications.Here, we describe a protocol for FISH-IS using chromosome enumeration probes as an example. PMID:27460240

  2. Analysis of microRNA expression by in situ hybridization with RNA oligonucleotide probes

    PubMed Central

    Thompson, Robert C.; Deo, Monika; Turner, David L.

    2007-01-01

    In situ hybridization is an important tool for analyzing gene expression and developing hypotheses about gene functions. The discovery of hundreds of microRNA (miRNA) genes in animals has provided new challenges for analyzing gene expression and functions. The small size of the mature miRNAs (∼20-24 nucleotides in length) presents difficulties for conventional in situ hybridization methods. However, we have developed a modified in situ hybridization method for detection of mammalian miRNAs in tissue sections, based upon the use of RNA oligonucleotide probes in combination with highly specific wash conditions. Here we present detailed procedures for detection of miRNAs in tissue sections or cultured cells. The methods described can utilize either nonradioactive hapten-conjugated probes that are detected by enzyme-coupled antibodies, or radioactively labeled probes that are detected by autoradiography. The ability to visualize miRNA expression patterns in tissue sections provides an additional tool for the analyses of miRNA expression and function. In addition, the use of radioactively labeled probes should facilitate quantitative analyses of changes in miRNA gene expression. PMID:17889803

  3. Identification of mosaicism in Prader-Willi syndrome using fluorescent in situ hybridization

    SciTech Connect

    Mowery-Rushton, P.A.; Surti, U.; Hanchett, J.M.

    1996-12-30

    We report on our findings of 4 patients with mosaicism for a deletion of chromosome 15, most commonly associated with Prader-Willi syndrome (PWS). We examined a series of typical and atypical PWS patients in order to identify cytogenetically undetected deletions, using fluorescence in situ hybridization. In 4 of the patients analyzed we detected a deletion in 14-60% of peripheral blood leukocytes, using four commercially available probes. Our results indicate that mosaicism may play a role in the etiology of some PWS cases. These findings may be especially useful in patients who display discrepancies between clinical phenotype and established diagnostic criteria. Methylation and microsatellite polymorphism analyses of 2 patients with low-level mosaicism failed to identify the deletion. We propose that fluorescence in situ hybridization is the most effective method for detecting somatic mosaicism, since a large number of cells can be individually examined for the presence or absence of a specific deletion. 47 refs., 5 figs., 3 tabs.

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

    PubMed

    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

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

    PubMed

    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

  6. Genetic profiling of yeast industrial strains using in situ comparative genomic hybridization (CGH).

    PubMed

    Wnuk, Maciej; Panek, Anita; Golec, Ewelina; Magda, Michal; Deregowska, Anna; Adamczyk, Jagoda; Lewinska, Anna

    2015-09-20

    The genetic differences and changes in genomic stability may affect fermentation processes involving baker's, brewer's and wine yeast strains. Thus, it seems worthwhile to monitor the changes in genomic DNA copy number of industrial strains. In the present study, we developed an in situ comparative genomic hybridization (CGH) to investigate the ploidy and genetic differences between selected industrial yeast strains. The CGH-based system was validated using the laboratory Saccharomyces cerevisiae yeast strains (haploid BY4741 and diploid BY4743). DNA isolated from BY4743 cells was considered a reference DNA. The ploidy and DNA gains and losses of baker's, brewer's and wine strains were revealed. Taken together, the in situ CGH was shown a helpful molecular tool to identify genomic differences between yeast industrial strains. Moreover, the in situ CGH-based system may be used at the single-cell level of analysis to supplement array-based techniques and high-throughput analyses at the population scale. PMID:26116136

  7. Fluorescence in situ hybridization analysis of formalin fixed paraffin embedded tissues, including tissue microarrays.

    PubMed

    Summersgill, Brenda M; Shipley, Janet M

    2010-01-01

    Formalin fixed paraffin embedded (FFPE) material is frequently the most convenient readily available source of diseased tissue, including tumors. Multiple cores of FFPE material are being used increasingly to construct tissue microarrays (TMAs) that enable simultaneous analyses of many archival samples. Fluorescence in situ hybridization (FISH) is an important approach to analyze FFPE material for specific genetic aberrations that may be associated with tumor types or subtypes, cellular morphology, and disease prognosis. Annealing, or hybridization of labeled nucleic acid sequences, or probes, to detect and locate one or more complementary nucleic acid sequences within fixed tissue sections allows the detection of structural (translocation/inversion) and numerical (deletion/gain) aberrations and their localization within tissues. The robust protocols described include probe preparation, hybridization, and detection and take 2-3 days to complete. A protocol is also described for the stripping of probes for repeat FISH in order to maximize the use of scarce tissue resources.

  8. Detection of prokaryotic cells with fluorescence in situ hybridization.

    PubMed

    Zwirglmaier, Katrin

    2010-01-01

    Fluorescence in situ hybridization with rRNA targeted oligonucleotide probes is nowadays one of the core techniques in microbial ecology, allowing the identification and quantification of microbial cells in environmental samples in situ. Next to the classic FISH protocol, which uses fluorescently monolabelled probes, the more sensitive CARD-FISH (also known as TSA-FISH), which involves an enzyme catalyzed signal amplification step, is becoming increasingly popular. This chapter describes protocols for both methods. While classic FISH has the advantage of being relatively cheap and easy to do on morphologically diverse samples, CARD-FISH offers a significantly higher sensitivity, allowing the detection of slow growing or metabolically inactive cells, which are below the detection limit of classic FISH. The drawback here is the considerably higher price for the probes and advanced cell fixation and permeabilization requirements that have to be optimized for different target cells.

  9. 10p Duplication characterized by fluorescence in situ hybridization

    SciTech Connect

    Wiktor, A.; Feldman, G.L.; Van Dyke, D.L.; Kratkoczki, P.; Ditmars, D.M. Jr.

    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. Alkaline fixation drastically improves the signal of in situ hybridization

    PubMed Central

    Basyuk, Eugenia; Bertrand, Edouard; Journot, Laurent

    2000-01-01

    In situ hybridization (ISH) is widely used to detect DNA and RNA sequences within the cell and tissue sections. The important step in performing this technique is tissue fixation. We investigated the influence of the pH of the fixative on the outcome of ISH. Our studies indicate that alkaline formaldehyde dramatically increases the ISH signal with RNA probes. The increase in signal was observed for detection of low as well as for high abundance messages. The sensitivity of the method was increased 5- to 6-fold. PMID:10773094

  11. Hybrid-type temperature sensor for in situ measurement

    SciTech Connect

    Iuchi, Tohru; Hiraka, Kensuke

    2006-11-15

    A hybrid-type surface temperature sensor combines the contact and noncontact methods, which allows us to overcome the shortcomings of both methods. The hybrid-type surface thermometer is composed mainly of two components: a metal film sheet that makes contact with an object and a radiometer that is used to detect the radiance of the rear surface of the metal film, which is actually a modified radiation thermometer. Temperature measurement using the hybrid-type thermometer with a several tens micrometer thick Hastelloy sheet, a highly heat and corrosion resistant alloy, is possible with a systematic error of -0.5 K and random errors of {+-}0.5 K, in the temperature range from 900 to 1000 K. This thermometer provides a useful means for calibration of in situ temperature measurement in various processes, especially in the silicon semiconductor industry. This article introduces the basic idea of the hybrid-type surface sensor, presents experimental results and discussions, and finally describes some applications.

  12. Fluorescence in situ hybridization of bacterial cell suspensions.

    PubMed

    Parsley, Larissa C; Newman, Molli M; Liles, Mark R

    2010-09-01

    The use of fluorescence in situ hybridization (FISH) to identify and enumerate specific bacteria within a mixed culture or environmental sample has become a powerful tool in combining microscopy with molecular phylogenetic discrimination. However, processing a large number of samples in parallel can be difficult because the bacterial cells are typically fixed and hybridized on microscope slides rather than processed in solution. In addition, gram-positive cells and certain environmental samples present a unique challenge to achievement of adequate cell fixation and uniform hybridization for optimal FISH analysis. Here, we describe a protocol for FISH in solution that can be performed entirely in suspension, in a microcentrifuge tube format, prior to microscopy. This protocol can be applied to both gram-positive and -negative cells, as well as complex microbial assemblages. The method employs a rapid technique for performing multiple hybridizations simultaneously, which may be used to qualitatively assess the presence of specific phylogenetic groups in bacterial cultures or environmental samples, and/or directly quantify fluorescence by fluorometry or flow cytometry.

  13. Whole-mount in situ hybridization using DIG-labeled probes in planarian.

    PubMed

    Rybak-Wolf, Agnieszka; Solana, Jordi

    2014-01-01

    In recent years freshwater flatworms (planarian) have become a powerful model for studies of regeneration and stem cell biology. Whole-mount in situ hybridization (WISH) and fluorescent in situ hybridization (FISH) are key and most commonly used techniques to determine and visualize gene expression patterns in planaria. Here, we present the established version of whole-mount in situ hybridization (WISH) and whole-mount fluorescence in situ hybridization (WFISH) protocol optimized over the last years by several labs from the rapidly growing planaria field and give an overview of recently introduced modifications which can be critical in the study of low abundant transcripts.

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

    PubMed Central

    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

  15. In situ hybridization of IL-6 in rheumatoid arthritis.

    PubMed Central

    Wood, N C; Symons, J A; Dickens, E; Duff, G W

    1992-01-01

    IL-6, an important mediator of the acute phase response, has been implicated in the pathogenesis of rheumatoid arthritis (RA). Many cell types including macrophages, T cells, B cells, endothelial cells and fibroblasts can produce this cytokine and production is largely regulated at the level of gene transcription or mRNA stabilization. In this paper we have first measured the levels of IL-6 activity in synovial fluid (SF) and serum from patients with RA and then localized IL-6-producing cells in the synovium by in situ hybridization combined with immunophenotyping. Patients with RA had raised levels of IL-6 in both SF and serum compared with patients with osteoarthritis and age-matched healthy controls. In individual RA patients tested serially after admission to hospital, serum IL-6 was initially raised and, unexpectedly, increased with clinical improvement. In situ hybridization of IL-6 mRNA showed positive cells both in the lymphocyte-rich aggregates and adjacent to small blood vessels. With immunophenotyping it was found that cells containing IL-6 mRNA were often in contact with CD14+ tissue macrophages and double immunophenotyping revealed that immunoreactive IL-6 was often associated with synovial T cells. Images Fig. 3 Fig. 4 Fig. 5 PMID:1531188

  16. A novel fluorescence in situ hybridization test for rapid pathogen identification in positive blood cultures.

    PubMed

    Makristathis, A; Riss, S; Hirschl, A M

    2014-10-01

    A novel molecular beacon-based fluorescence in situ hybridization (FISH) test allowing for the identification of a wide range of bacterial pathogens directly in positive blood cultures (BCs) was evaluated with positive BCs of 152 patients. Depending on the Gram stain, either a Gram-negative or a Gram-positive panel was used. The time to result was 30 min, and the hands-on time was only 10 min. Seven per cent of the cultured microorganisms were not included in the FISH panels; the identification rate of those included was 95.2%. Overall, the FISH test enabled accurate pathogen identification in 88.2% of all cases analysed.

  17. Detection of in-situ hybridization to human metaphase chromosomes by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Okamoto, Naoaki; Ishikawa, Mitsuru

    2000-04-01

    Detection of in situ hybridization to human metaphase chromosomes provides important information about gene mappings and about analysis of chromosomal disorders. We applied atomic force microscopy (AFM) to the detection of in situ hybridization to get better resolution as compared to light microscopy. Chromosomes were spread over a glass substrate and hybridized with DNA probes labeled with biotin or digoxigenin. The hybridized probes were reacted with streptavidin or anti-digoxigenin antibody, both of which were conjugated with 5-nm gold colloidal particles. We missed direct detection of the conjugated gold colloidal particles by micro-meter scale AFM scanning , but obtained clear topographic difference between the site of hybridization and the chromosome arm with the help of silver enhancement. We thus clearly detected the in situ hybridization using chromosome painting probes, alpha satellite probes, and locus specific gene probes by AFM. The in situ hybridization to DNA fiber was also detected by AFM. The detection of in situ hybridization by AFM has advantages over fluorescence in situ hybridization: no reduction of signal intensity under light irradiation. Application of AFM to the detection of in situ hybridization will be a useful method to analyze chromosomes.

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

    ERIC Educational Resources Information Center

    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…

  19. Human cDNA mapping using fluorescence in situ hybridization

    SciTech Connect

    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.

  20. Fluorescent in situ hybridization on comets: FISH comet.

    PubMed

    Shaposhnikov, Sergey; El Yamani, Naouale; Collins, Andrew R

    2015-01-01

    The DNA in eukaryotic cells is organized into loop domains that represent basic structural and functional units of chromatin packaging. The comet assay, a sensitive method for monitoring DNA damage and repair, involves electrophoresis of nucleoids comprising supercoiled DNA attached to the nuclear matrix. Breaks in the DNA relax the supercoiling and allow DNA loops to expand, and on electrophoresis to move towards the anode, giving the appearance of a comet tail. We use fluorescent in situ hybridization (FISH) to investigate the structure of the chromatin within comet preparations and to study specific DNA sequences within comets. In this chapter we describe our FISH comets protocols, deal with some technical questions and outline the theory. FISH with comets should be useful to researchers interested in the structural organization of DNA and chromatin, the localization of DNA damage, and the kinetics of repair of damage. PMID:25827891

  1. Characterization of acute rat parvovirus infection by in situ hybridization.

    PubMed

    Gaertner, D J; Jacoby, R O; Johnson, E A; Paturzo, F X; Smith, A L; Brandsma, J L

    1993-04-01

    In situ hybridization and virus titration were used to characterize early stages of rat virus (RV) infection of rat pups after oronasal inoculation. Results suggest that virus enters through the lung and that early viremia leads rapidly to pantropic infection. Cells derived from all three germ layers were infected with RV, but those of endodermal and mesodermal origin were the predominant targets. Infection of vascular endothelium was widespread and was associated with hemorrhage and infarction in the brain. Convalescence from acute infection was accompanied by mononuclear cell infiltrates at sites containing RV DNA. Viral DNA was also detected in endothelium, fibroblasts and smooth muscle myofibers four weeks after inoculation. Further examination of these cells as potential sites of persistent infection is warranted.

  2. Detection of viral RNA by fluorescence in situ hybridization (FISH).

    PubMed

    Vyboh, Kishanda; Ajamian, Lara; Mouland, Andrew J

    2012-01-01

    localization using a method like this, abundant information has been gained on both viral and cellular RNA trafficking events. For instance, HIV-1 produces RNA in the nucleus of infected cells but the RNA is only translated in the cytoplasm. When one key viral protein is missing (Rev), FISH of the viral RNA has revealed that the block to viral replication is due to the retention of the HIV-1 genomic RNA in the nucleus. Here, we present the method for visual analysis of viral genomic RNA in situ. The method makes use of a labelled RNA probe. This probe is designed to be complementary to the viral genomic RNA. During the in vitro synthesis of the antisense RNA probe, the ribonucleotide that is modified with digoxigenin (DIG) is included in an in vitro transcription reaction. Once the probe has hybridized to the target mRNA in cells, subsequent antibody labelling steps (Figure 1) will reveal the localization of the mRNA as well as proteins of interest when performing FISH/IF. PMID:22588480

  3. Fluorescence in situ hybridization (FISH) in diagnostic and investigative neuropathology.

    PubMed

    Fuller, Christine E; Perry, Arie

    2002-01-01

    Over the last decade, fluorescence in situ hybridization (FISH) has emerged as a powerful clinical and research tool for the assessment of target DNA dosages within interphase nuclei. Detectable alterations include aneusomies, deletions, gene amplifications, and translocations, with primary advantages to the pathologist including its basis in morphology, its applicability to archival, formalin-fixed paraffin-embedded (FFPE) material, and its similarities to immunohistochemistry. Recent technical advances such as improved hybridization protocols, markedly expanded probe availability resulting from the human genome sequencing initiative, and the advent of high-throughput assays such as gene chip and tissue microarrays have greatly enhanced the applicability of FISH. In our lab, we currently utilize only a limited battery of DNA probes for routine diagnostic purposes, with determination of chromosome 1p and 19q dosage in oligodendroglial neoplasms representing the most common application. However, research applications are numerous and will likely translate into a growing list of clinically useful markers in the near future. In this review, we highlight the advantages and disadvantages of FISH and familiarize the reader with current applications in diagnostic and investigative neuropathology.

  4. Genomic in situ hybridization to sectioned nuclei shows chromosome domains in grass hybrids.

    PubMed

    Leitch, A R; Mosgöller, W; Schwarzacher, T; Bennett, M D; Heslop-Harrison, J S

    1990-03-01

    In situ hybridization using biotinylated total genomic DNA and avidin detection systems was adapted for examination of thin-sectioned plant material in the light and electron microscopes. Root tip material was preserved prior to sectioning, so that the in vivo disposition of the chromatin was maintained. Use of total genomic DNA from Secale africanum as a probe enabled the chromatin from the two parental genomes in the grass hybrid Hordeum chilense x S. africanum to be distinguished. The biotinylated probe preferentially labelled the chromosomes of S. africanum origin. DNA-DNA hybrids were visualized at the light-microscope level by Texas Red fluorescence and at the electron-microscope level by the enzymic precipitation of DAB (diaminobenzidine) or by colloidal gold particles. The use of thin sections allowed the location of probe hybridization to be established unequivocally in both metaphase and interphase nuclei. Analysis of interphase nuclei showed that chromatin originating from the two parental genomes did not intermix but occupied distinct domains. PMID:2384518

  5. In situ hybridization of carbon nanotubes with bacterial cellulose for three-dimensional hybrid bioscaffolds.

    PubMed

    Park, Subeom; Park, Jooyeon; Jo, Insu; Cho, Sung-Pyo; Sung, Dongchul; Ryu, Seungmi; Park, Minsung; Min, Kyung-Ah; Kim, Jangho; Hong, Suklyun; Hong, Byung Hee; Kim, Byung-Soo

    2015-07-01

    Carbon nanotubes (CNTs) have shown great potential in biomedical fields. However, in vivo applications of CNTs for regenerative medicine have been hampered by difficulties associated with the fabrication of three-dimensional (3D) scaffolds of CNTs due to CNTs' nano-scale nature. In this study, we devised a new method for biosynthesis of CNT-based 3D scaffold by in situ hybridizing CNTs with bacterial cellulose (BC), which has a structure ideal for tissue-engineering scaffolds. This was achieved simply by culturing Gluconacetobacter xylinus, BC-synthesizing bacteria, in medium containing CNTs. However, pristine CNTs aggregated in medium, which hampers homogeneous hybridization of CNTs with BC scaffolds, and the binding energy between hydrophobic pristine CNTs and hydrophilic BC was too small for the hybridization to occur. To overcome these problems, an amphiphilic comb-like polymer (APCLP) was adsorbed on CNTs. Unlike CNT-coated BC scaffolds (CNT-BC-Imm) formed by immersing 3D BC scaffolds in CNT solution, the APCLP-adsorbed CNT-BC hybrid scaffold (CNT-BC-Syn) showed homogeneously distributed CNTs throughout the 3D microporous structure of BC. Importantly, in contrast to CNT-BC-Imm scaffolds, CNT-BC-Syn scaffolds showed excellent osteoconductivity and osteoinductivity that led to high bone regeneration efficacy. This strategy may open a new avenue for development of 3D biofunctional scaffolds for regenerative medicine. PMID:25941786

  6. In situ hybridization of carbon nanotubes with bacterial cellulose for three-dimensional hybrid bioscaffolds.

    PubMed

    Park, Subeom; Park, Jooyeon; Jo, Insu; Cho, Sung-Pyo; Sung, Dongchul; Ryu, Seungmi; Park, Minsung; Min, Kyung-Ah; Kim, Jangho; Hong, Suklyun; Hong, Byung Hee; Kim, Byung-Soo

    2015-07-01

    Carbon nanotubes (CNTs) have shown great potential in biomedical fields. However, in vivo applications of CNTs for regenerative medicine have been hampered by difficulties associated with the fabrication of three-dimensional (3D) scaffolds of CNTs due to CNTs' nano-scale nature. In this study, we devised a new method for biosynthesis of CNT-based 3D scaffold by in situ hybridizing CNTs with bacterial cellulose (BC), which has a structure ideal for tissue-engineering scaffolds. This was achieved simply by culturing Gluconacetobacter xylinus, BC-synthesizing bacteria, in medium containing CNTs. However, pristine CNTs aggregated in medium, which hampers homogeneous hybridization of CNTs with BC scaffolds, and the binding energy between hydrophobic pristine CNTs and hydrophilic BC was too small for the hybridization to occur. To overcome these problems, an amphiphilic comb-like polymer (APCLP) was adsorbed on CNTs. Unlike CNT-coated BC scaffolds (CNT-BC-Imm) formed by immersing 3D BC scaffolds in CNT solution, the APCLP-adsorbed CNT-BC hybrid scaffold (CNT-BC-Syn) showed homogeneously distributed CNTs throughout the 3D microporous structure of BC. Importantly, in contrast to CNT-BC-Imm scaffolds, CNT-BC-Syn scaffolds showed excellent osteoconductivity and osteoinductivity that led to high bone regeneration efficacy. This strategy may open a new avenue for development of 3D biofunctional scaffolds for regenerative medicine.

  7. In Situ Carbon and Oxygen Isotope Analyses of Calcite in CM1 Chondrites

    NASA Astrophysics Data System (ADS)

    Telus, M.; Alexander, C. M. O.'D.; Wang, J.; Hauri, E. H.

    2016-08-01

    We present results from in situ C and O isotope analyses of calcite from CM1 chondrites. There are large isotope variations on small spatial scales. This provides some insight into the evolution of fluids in chondrite parent bodies.

  8. Pallister-Killian syndrome detected by fluorescence in situ hybridization

    SciTech Connect

    Butler, M.G.; Dev, V.G.

    1995-07-03

    The Pallister-Killian syndrome is a rare cytogenetic condition first described in 1977 by Pallister et al. in 3 adults; the first affected child was reported in 1981. This syndrome (also known as Pallister mosaic aneuploidy syndrome or isochromosome 12p mosaicism) is characterized by postnatal growth retardation, seizures, hypotonia, deafness, profound mental retardation, minimal speech development, and a distinctive facial appearance (high prominent forehead, ocular hypertelorism, sparse anterior scalp hair, prominent lower lip, large ears with thick protruding lobules, cupid-bow shaped upper lip, and a long philtrum). A chromosome 12 abnormality (tetrasomy 12p) has been reported in skin biopsies from these patients but this chromosome anomaly is usually not found (or in only a small proportion, e.g., <0.5%, of blood cells) in peripheral blood. We report on an additional patient with Pallister-Killian syndrome confirmed with fluorescence in situ hybridization (FISH) using an alpha satellite DNA probe for chromosome 12. This report further illustrates the application of FISH in identifying the source of chromosomal markers of unknown origin in infants with multiple congenital anomalies specifically before the natural history of a condition allows for definitive diagnosis based on clinical findings. 9 refs., 2 figs.

  9. Double-target in situ hybridization in brightfield microscopy.

    PubMed

    Kerstens, H M; Poddighe, P J; Hanselaar, A G

    1994-08-01

    For brightfield detection of two different DNA target sequences in one sample, we developed a double-target in situ hybridization (ISH) technique, using biotin- and digoxigenin-labeled chromosome-specific DNA probes. First, several immunochemical detection systems were optimized and compared for sensitivity and simultaneous applicability. Two non-interfering immunochemical systems were chosen for simultaneous detection of the DNA probe labels. This resulted in combination of an alkaline phosphatase (AP)-conjugated avidin-biotin system with a horseradish peroxidase (HRP)-conjugated antibody system for detection of biotin- and digoxigenin-labeled DNA probes, respectively. Development of AP with New Fuchsin-naphthol phosphate and HRP with diaminobenzidine-H2O2 resulted in stable, well-contrasting (red and black, respectively) color precipitates visible by conventional light microscopy. The double-target ISH technique was successfully applied on a wide variety of biological materials, such as metaphase spreads, cytospin, and Thin-prep samples of cytological specimens, frozen tissue sections, and formalin-fixed, paraffin-embedded tissue sections. In particular, on tissue sections, where quantitative interpretation of ISH data can be hampered by truncation of nuclei, the double-target ISH technique appeared to be a valuable tool for demonstration of chromosome aberrations and chromosome imbalances. PMID:8027526

  10. Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue

    PubMed Central

    Chen, Chun-Chun; Wada, Kazuhiro; Jarvis, Erich D.

    2012-01-01

    Knowing the timing, level, cellular localization, and cell type that a gene is expressed in contributes to our understanding of the function of the gene. Each of these features can be accomplished with in situ hybridization to mRNAs within cells. Here we present a radioactive in situ hybridization method modified from Clayton et al. (1988)1 that has been working successfully in our lab for many years, especially for adult vertebrate brains2-5. The long complementary RNA (cRNA) probes to the target sequence allows for detection of low abundance transcripts6,7. Incorporation of radioactive nucleotides into the cRNA probes allows for further detection sensitivity of low abundance transcripts and quantitative analyses, either by light sensitive x-ray film or emulsion coated over the tissue. These detection methods provide a long-term record of target gene expression. Compared with non-radioactive probe methods, such as DIG-labeling, the radioactive probe hybridization method does not require multiple amplification steps using HRP-antibodies and/or TSA kit to detect low abundance transcripts. Therefore, this method provides a linear relation between signal intensity and targeted mRNA amounts for quantitative analysis. It allows processing 100-200 slides simultaneously. It works well for different developmental stages of embryos. Most developmental studies of gene expression use whole embryos and non-radioactive approaches8,9, in part because embryonic tissue is more fragile than adult tissue, with less cohesion between cells, making it difficult to see boundaries between cell populations with tissue sections. In contrast, our radioactive approach, due to the larger range of sensitivity, is able to obtain higher contrast in resolution of gene expression between tissue regions, making it easier to see boundaries between populations. Using this method, researchers could reveal the possible significance of a newly identified gene, and further predict the function of the

  11. Rapid human chromosome aberration analysis using fluorescence in situ hybridization.

    PubMed

    Lucas, J N; Tenjin, T; Straume, T; Pinkel, D; Moore, D; Litt, M; Gray, J W

    1989-07-01

    We have used in situ hybridization of repeat-sequence DNA probes, specific to the paracentromric locus 1q12 and the telomeric locus 1p36, to fluorescently stain regions that flank human chromosome 1p. This procedure was used for fast detection of structural aberrations involving human chromosome 1p in two separate experiments. In one, human lymphocytes were irradiated with 0, 0.8, 1.6, 2.4 and 3.2 Gy of 137Cs gamma-rays. In the other, human lymphocytes were irradiated with 0, 0.09, 0.18, 2.0, 3.1 and 4.1 Gy of 60Co gamma-rays. The frequencies (per cell) of translocations and dicentrics with one breakpoint in 1p and one elsewhere in the genome were determined for cells irradiated at each dose point. These frequencies both increased with dose, D, in a linear-quadratic manner. The delta, alpha, and beta coefficients resulting from a fit of the equation f(D)=delta + alphaD + betaD2 to the translocation frequency dose-response data were 0.0025, 0.0027 and 0.0037 for 137Cs gamma-rays, and 0.0010, 0.0041, and 0.0057 for 60Co gamma-rays. The delta, alpha, and beta coefficients resulting from a fit to the dicentric frequency dose-response data were 0.0005, 0.0010 and 0.0028 for 137Cs gamma-rays and 0.0001, 0.0002 and 0.0035, for 60Co gamma-rays. Approximately 32,000 metaphase spreads were scored in this study. The average analysis rate was over two metaphase spreads per minute. However, an experienced analyst was able to find and score one metaphase spread every 10s. The importance of this new cytogenetic analysis technique for biological dosimetry and in vivo risk assessment is discussed.

  12. Fluorescent In Situ Hybridization of Nuclear Bodies in Drosophila melanogaster Ovaries.

    PubMed

    Nizami, Zehra F; Liu, Ji-Long; Gall, Joseph G

    2015-01-01

    Fluorescent in situ hybridization (FISH) is a technique for determining the cytological localization of RNA or DNA molecules. There are many approaches available for generating in situ hybridization probes and conducting the subsequent hybridization steps. Here, we describe a simple and reliable FISH method to label small RNAs (200-500 nucleotides in length) that are enriched in nuclear bodies in Drosophila melanogaster ovaries, such as Cajal bodies (CBs) and histone locus bodies (HLBs). This technique can also be applied to other Drosophila tissues, and to abundant mRNAs such as histone transcripts. PMID:26324435

  13. Stillwater Hybrid Geo-Solar Power Plant Optimization Analyses

    SciTech Connect

    Wendt, Daniel S.; Mines, Gregory L.; Turchi, Craig S.; Zhu, Guangdong; Cohan, Sander; Angelini, Lorenzo; Bizzarri, Fabrizio; Consoli, Daniele; De Marzo, Alessio

    2015-09-02

    The Stillwater Power Plant is the first hybrid plant in the world able to bring together a medium-enthalpy geothermal unit with solar thermal and solar photovoltaic systems. Solar field and power plant models have been developed to predict the performance of the Stillwater geothermal / solar-thermal hybrid power plant. The models have been validated using operational data from the Stillwater plant. A preliminary effort to optimize performance of the Stillwater hybrid plant using optical characterization of the solar field has been completed. The Stillwater solar field optical characterization involved measurement of mirror reflectance, mirror slope error, and receiver position error. The measurements indicate that the solar field may generate 9% less energy than the design value if an appropriate tracking offset is not employed. A perfect tracking offset algorithm may be able to boost the solar field performance by about 15%. The validated Stillwater hybrid plant models were used to evaluate hybrid plant operating strategies including turbine IGV position optimization, ACC fan speed and turbine IGV position optimization, turbine inlet entropy control using optimization of multiple process variables, and mixed working fluid substitution. The hybrid plant models predict that each of these operating strategies could increase net power generation relative to the baseline Stillwater hybrid plant operations.

  14. Synthesis of PCR-derived, single-stranded DNA probes suitable for in situ hybridization.

    PubMed

    Hannon, K; Johnstone, E; Craft, L S; Little, S P; Smith, C K; Heiman, M L; Santerre, R F

    1993-08-01

    We report the novel synthesis of polymerase chain reaction (PCR)-derived single-stranded DNA (ssDNA) probes and their subsequent application in in situ hybridizations. Serial transverse sections of an 11.5-day postcoitum mouse embryo were hybridized to a 33P-ssDNA, 33P-RNA, or 35S-RNA probe corresponding to the same 181-bp sequence in the myogenin cDNA. Signal obtained using 33P-ssDNA was more intense than that using 33P-RNA probe, while signal/noise ratios obtained with both 33P-probes were far superior to those obtained with 35S-probe. Digoxigenin-labeled chicken growth hormone (GH) ssDNA gave slightly more intense signal than did digoxigenin-labeled chicken GH RNA when hybridized to chicken pituitary sections. 32P-ssDNA probes were found to be suitable for Northern blot hybridization. Advantages of using ssDNA probes for in situ hybridization include: (1) The ssDNA technique is rapid and simple. There was no need to clone a DNA template into a special RNA vector or order special T7-containing PCR primers. ssDNA probes can be synthesized in less than 1 day using any primers which currently exist in a laboratory (optimal probe length for in situ hybridization is between 50 and 200 bp). (2) In three separate in situ experiments, ssDNA probes yielded more intense signal than RNA probes. (3) ssDNA probes are potentially more stable than RNA probes. (4) Since the RNAse rinse is eliminated, posthybridization rinses are shortened when hybridizing with ssDNA probes. The ssDNA probes produced by this protocol can be labeled with a variety of different isotopes (both radioactive and nonradioactive), and are excellent probes for use in in situ hybridizations.

  15. Simultaneous identification of A, B, D and R genomes by genomic in situ hybridization in wheat-rye derivatives.

    PubMed

    Sánchez-Morán, E; Benavente, E; Orellana, J

    1999-09-01

    Multicolour genomic in situ hybridization was carried out in wheat-rye hybrids and in a wheat-rye translocation line. Different hybridization conditions and mixture compositions were used, and A, B and D genomes of hexaploid wheat as well as the R genome of rye were distinguished simultaneously in somatic cells. Combination of genomic and rDNA probes in multicolour in situ hybridization was also performed to identify chromosomes within a specific genome.

  16. Fast and Non-Toxic In Situ Hybridization without Blocking of Repetitive Sequences

    PubMed Central

    Matthiesen, Steen H.; Hansen, Charles M.

    2012-01-01

    Formamide is the preferred solvent to lower the melting point and annealing temperature of nucleic acid strands in in situ hybridization (ISH). A key benefit of formamide is better preservation of morphology due to a lower incubation temperature. However, in fluorescence in situ hybridization (FISH), against unique DNA targets in tissue sections, an overnight hybridization is required to obtain sufficient signal intensity. Here, we identified alternative solvents and developed a new hybridization buffer that reduces the required hybridization time to one hour (IQFISH method). Remarkably, denaturation and blocking against repetitive DNA sequences to prevent non-specific binding is not required. Furthermore, the new hybridization buffer is less hazardous than formamide containing buffers. The results demonstrate a significant increased hybridization rate at a lowered denaturation and hybridization temperature for both DNA and PNA (peptide nucleic acid) probes. We anticipate that these formamide substituting solvents will become the foundation for changes in the understanding and performance of denaturation and hybridization of nucleic acids. For example, the process time for tissue-based ISH for gene aberration tests in cancer diagnostics can be reduced from days to a few hours. Furthermore, the understanding of the interactions and duplex formation of nucleic acid strands may benefit from the properties of these solvents. PMID:22911704

  17. A and C genome distinction and chromosome identification in brassica napus by sequential fluorescence in situ hybridization and genomic in situ hybridization.

    PubMed

    Howell, Elaine C; Kearsey, Michael J; Jones, Gareth H; King, Graham J; Armstrong, Susan J

    2008-12-01

    The two genomes (A and C) of the allopolyploid Brassica napus have been clearly distinguished using genomic in situ hybridization (GISH) despite the fact that the two extant diploids, B. rapa (A, n = 10) and B. oleracea (C, n = 9), representing the progenitor genomes, are closely related. Using DNA from B. oleracea as the probe, with B. rapa DNA and the intergenic spacer of the B. oleracea 45S rDNA as the block, hybridization occurred on 9 of the 19 chromosome pairs along the majority of their length. The pattern of hybridization confirms that the two genomes have remained distinct in B. napus line DH12075, with no significant genome homogenization and no large-scale translocations between the genomes. Fluorescence in situ hybridization (FISH)-with 45S rDNA and a BAC that hybridizes to the pericentromeric heterochromatin of several chromosomes-followed by GISH allowed identification of six chromosomes and also three chromosome groups. Our procedure was used on the B. napus cultivar Westar, which has an interstitial reciprocal translocation. Two translocated segments were detected in pollen mother cells at the pachytene stage of meiosis. Using B. oleracea chromosome-specific BACs as FISH probes followed by GISH, the chromosomes involved were confirmed to be A7 and C6.

  18. Chromosomal localization of several families of repetitive sequences by in situ hybridization.

    PubMed Central

    Devine, E A; Nolin, S L; Houck, G E; Jenkins, E C; Brown, W T

    1985-01-01

    Four recombinant DNA clones (H1, H7, H12, and H15) carrying low-repetitive human DNA were previously isolated from a human genomic library based on their specificity for chromosome 21 and were studied for their distribution as determined by in situ hybridization. Clone H7 hybridized to the satellite regions of chromosomes 13, 14, 15, 21, and 22 as well as to the centromere region of chromosome 1. Clone H12 hybridized strongly to chromosomes 11 and 17 and the centromere of the X. Clones H1 and H15 had a very widespread distribution throughout the genome. Clone H15 hybridized significantly more to the short arm of chromosome 18 than to any other chromosomal segment. Clone H1 hybridized strongly to the centromere of chromosome 19 and also showed random distribution on all the other human chromosomes. We conclude that these probes appear to represent four repetitive families that demonstrate in situ hybridization patterns that do not correspond with those of any other repetitive family. Further, the in situ hybridization patterns do not show the strong chromosome 21 specificity originally defined by Southern blot analysis. The nature and chromosomal localization of these repetitive families should be useful in regional mapping and evolutionary studies and give additional insight into chromosomal organization. Images Fig. 1 Fig. 3 PMID:3976654

  19. Combined analysis of cervical smears. Cytopathology, image cytometry and in situ hybridization.

    PubMed

    Multhaupt, H; Bruder, E; Elit, L; Rothblat, I; Warhol, M

    1993-01-01

    This study was an attempt to correlate the Bethesda System of Papanicolaou smear classification with DNA content by image analysis and the presence of human papillomavirus (HPV) as determined by in situ hybridization. DNA histograms were classified as normal diploid, diploid proliferative, polyploid and aneuploid. HPV in situ hybridization was performed with a cocktail of probes specific to HPV types 6, 11, 16 and 18. There was a good correlation between normal cytology and normal DNA histograms. Cytologically normal smears with bacterial or fungal infections showed a high proliferation index. HPV infection correlated with DNA polyploidy but was seen in 15 of 29 smears classified as cytologically normal. Morphologically abnormal Papanicolaou smears correlated with aneuploid DNA content. Smears classified as intraepithelial neoplasia correlated with aneuploid DNA content in all 12 cases. Four of five cases cytologically suspicious for HPV infection had HPV by in situ hybridization.

  20. Formamide-Free Genomic in situ Hybridization Allows Unambiguous Discrimination of Highly Similar Parental Genomes in Diploid Hybrids and Allopolyploids.

    PubMed

    Jang, Tae-Soo; Weiss-Schneeweiss, Hanna

    2015-01-01

    Polyploidy and hybridization play an important role in plant diversification and speciation. The application of genomic in situ hybridization (GISH) allows the identification of parental genomes in hybrids, thus elucidating their origins and allowing for analysis of their genomic evolution. The performance of GISH depends on the similarity of the parental genomes and on the age of hybrids. Here, we present the formamide-free GISH (ff-GISH) protocol applied to diploid and polyploid hybrids of monocots (Prospero, Hyacinthaceae) and dicots (Melampodium, Asteraceae) differing in similarity of the parental genomes and in chromosome and genome sizes. The efficiency of the new protocol is compared to the standard GISH protocol. As a result, ff-GISH allowed efficient labeling and discrimination of the parental chromosome sets in diploid and allopolyploid hybrids in Prospero autumnale species complex. In contrast, the standard GISH protocol failed to differentiate the parental genomes due to high levels of similar repetitive DNA. Likewise, an unambiguous identification of parental genomes in allotetraploid Melampodium nayaritense (Asteraceae) was possible after ff-GISH, whereas the standard GISH hybridization performance was suboptimal. The modified method is simple and non-toxic and allows the discrimination of very similar parental genomes in hybrids. This method lends itself to modifications and improvements and can also be used for FISH. PMID:26492445

  1. Evolution in situ: hybrid origin and establishment of willows (Salix L.) on alpine glacier forefields.

    PubMed

    Gramlich, S; Sagmeister, P; Dullinger, S; Hadacek, F; Hörandl, E

    2016-06-01

    Little attention has been paid to the evolutionary consequences of the colonizing dynamics and succession processes following glacier retreat. Here we studied hybrid populations that have recently formed and established on glacier forefields of the European Alps owing to secondary contact of a lowland colonizer with a subalpine species. We analyzed the composition of two hybrid populations between Salix purpurea and Salix helvetica with nine microsatellite markers by using Bayesian methods (structure and NewHybrids), and simulations. We also studied niche differentiation between the hybrids and the parental species based on indicator values, soil pH and water retention potential measurements. Allelic structure of hybrids confirms the assumed parentage and in situ origin of the crosses on two independent sites within the last decades. Both hybrid populations comprised F1 and later generation hybrids (F2 and backcrosses), confirming hybrid fertility. The parental species showed significant differences in niche characteristics for temperature, soil pH, nutrients and moisture. Remarkably, the hybrids exhibited a higher tolerance to cold temperatures, nutrient-poor and acidic soils than either parent. Our results show that willow hybrids originated after glacier retreat and have established persistent populations within a few decades. One factor contributing to hybrid establishment in sympatry with their parents is their ability to occupy more extreme niches than either parental species within a mosaic-like pattern of microhabitats on the forefield. Introgression and/or transgressive segregation may have resulted in novel genotypes that are able to expand the ecological spectrum of either parent.

  2. [Non-radioactive in situ hybridization of alpha-satellite sequences in cytogenetic diagnosis].

    PubMed

    Perfumo, C; Arslanian, A; Zara, F; Piombo, G; Pierluigi, M

    1992-01-01

    Non isotopic in situ hybridization with alpha-satellite DNA probes in the cytogenetic diagnosis. Standard banding cytogenetic techniques do not always allow to define the structure and the origin of chromosome rearrangements involving the centromere region. Non-isotopic in situ hybridization of alphoid sequences has allowed to determine the origin of the centromeres in the metaphases of 5 patients referred to us for: 2 structural rearrangements involving chromosome 21, 2 structural rearrangements involving chromosome Y and 1 reciprocal translocation involving on chromosome 20 and one chromosome 15.

  3. [Non-radioactive in situ hybridization of alpha-satellite sequences in cytogenetic diagnosis].

    PubMed

    Perfumo, C; Arslanian, A; Zara, F; Piombo, G; Pierluigi, M

    1992-01-01

    Non isotopic in situ hybridization with alpha-satellite DNA probes in the cytogenetic diagnosis. Standard banding cytogenetic techniques do not always allow to define the structure and the origin of chromosome rearrangements involving the centromere region. Non-isotopic in situ hybridization of alphoid sequences has allowed to determine the origin of the centromeres in the metaphases of 5 patients referred to us for: 2 structural rearrangements involving chromosome 21, 2 structural rearrangements involving chromosome Y and 1 reciprocal translocation involving on chromosome 20 and one chromosome 15. PMID:1465321

  4. Mapping pachytene chromosomes of coffee using a modified protocol for fluorescence in situ hybridization

    PubMed Central

    Iacia, Ana Amélia Sanchez; Pinto-Maglio, Cecília A. F.

    2013-01-01

    Fluorescence in situ hybridization (FISH) is the most direct method for physically mapping DNA sequences on chromosomes. Fluorescence in situ hybridization mapping of meiotic chromosomes during the pachytene stage is an important tool in plant cytogenetics, because it provides high-resolution measurements of physical distances. Fluorescence in situ hybridization mapping of coffee pachytene chromosomes offers significant advantages compared with FISH mapping of somatic chromosomes, because pachytene chromosomes are 30 times longer and provide additional cytological markers. However, the application of this technique to pachytene chromosomes has been complicated by problems in making preparations of meiotic chromosomes and by difficulties in the application of standard FISH protocols. We have been able to overcome most of these obstacles in applying the FISH technique to the pachytene chromosomes of coffee plants. Digesting the external callose layer surrounding the pollen mother cells (PMCs) in conjunction with other procedures permitted suitable pachytene chromosomes to be obtained by increasing cell permeability, which allowed the probe sequences to enter the cells. For the first time, hybridization signals were registered on coffee pachytene chromosomes using the FISH technique with a repetitive sequence as a probe. We obtained slides on which 80 % of the PMCs had hybridization signals, resulting in FISH labelling with high efficiency. The procedure does not seem to be dependent on the genotype, because hybridization signals were detected in genetically different coffee plants. These findings enhance the possibilities for high-resolution physical mapping of coffee chromosomes. PMID:24244840

  5. Distribution and evolution of repeated sequences in genomes of Triatominae (Hemiptera-Reduviidae) inferred from genomic in situ hybridization.

    PubMed

    Pita, Sebastian; Panzera, Francisco; Sánchez, Antonio; Panzera, Yanina; Palomeque, Teresa; Lorite, Pedro

    2014-01-01

    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.

  6. Distribution and Evolution of Repeated Sequences in Genomes of Triatominae (Hemiptera-Reduviidae) Inferred from Genomic In Situ Hybridization

    PubMed Central

    Pita, Sebastian; Panzera, Francisco; Sánchez, Antonio; Panzera, Yanina; Palomeque, Teresa; Lorite, Pedro

    2014-01-01

    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. PMID:25478792

  7. Quantitative analysis of in situ hybridization methods for the detection of actin gene expression.

    PubMed Central

    Lawrence, J B; Singer, R H

    1985-01-01

    We have implemented an efficient, quantitative approach for the optimization of in situ hybridization using double-stranded recombinant DNA probes. The model system studied was actin mRNA expression in chicken embryonic muscle cultures. Actin and control (pBR322) probes were nick-translated with p32 labeled nucleotides, hybridized to cells grown on coverslips, and quantitated in a scintillation counter. Cellular RNA retention was monitored via the incorporation of H3-Uridine into RNA prior to cell fixation. Over a thousand samples were analyzed, and among the technical variables examined were the fixation protocol, proteolytic cell pretreatment, the time course of hybridization, saturation kinetics, hybridization efficiency, and effect of probe size on hybridization and network formation. Results have allowed us to develop a reproducible in situ hybridization methodology which is simpler and less destructive to cellular RNA and morphology than other protocols. Moreover, this technique is highly sensitive and efficient in detection of cellular RNAs. Lastly, the rapid quantitative approach used for this analysis is valuable in itself as a potential alternative to filter or solution hybridizations. Images PMID:3889842

  8. Dissolved methane profiles in marine sediments observed in situ differ greatly from analyses of recovered cores

    NASA Astrophysics Data System (ADS)

    Zhang, X.; Brewer, P. G.; Hester, K.; Ussler, W.; Walz, P. M.; Peltzer, E. T.; Ripmeester, J.

    2009-12-01

    The flux of dissolved methane through continental margin sediments is of importance in marine geochemistry due to its role in massive hydrate formation with enigmatic climate consequences, and for the huge and complex microbial assemblage it supports. Yet the actual dissolved methane concentration driving this flux is poorly known since strong degassing during sample recovery from depth is commonplace. Thus, pore water analyses from high CH4 environments typically show values clustered around the one-atmosphere equilibrium value of 1-2 mM, erasing the original pore water profile and frustrating model calculations. We show that accurate measurement of pore water profiles of dissolved CH4, SO4, and H2S can be made rapidly in situ using a Raman-based probe. While Raman spectra were formerly believed to yield only qualitative data we show that by using a peak area ratio technique to known H2O bands and a form of Beer’s Law quantitative data may be readily obtained. Results from Hydrate Ridge, Oregon clearly show coherent profiles of all three species in this high flux environment, and while in situ Raman and conventional analyses of SO4 in recovered cores agree well, very large differences in CH4 are found. The in situ CH4 results show up to 35 mM in the upper 30cm of seafloor sediments and are inversely correlated with SO4. This is below the methane hydrate saturation value, yet disturbing the sediments clearly released hydrate fragments suggesting that true saturation values may exist only in the hydrate molecular boundary layer, and that lower values may typically characterize the bulk pore fluid of hydrate-hosting sediments. The in situ Raman measurement protocols developed take only a few minutes. Profiles obtained in situ showed minimal fluorescence while pore water samples from recovered cores quickly developed strong fluorescence making laboratory analyses using Raman spectroscopy challenging and raising questions over the reaction sequence responsible for

  9. De Novo nonreciprocal translocation 1;8 confirmed by fluorescent in situ hybridization

    SciTech Connect

    Wiley, J.E.; Stout, C.; Palmer, S.M.

    1995-07-17

    Constitutional nonreciprocal translocations are extremely rare, and even their existence is controversial. We report on a newborn infant with a de novo nonreciprocal translocation between chromosomes 1 and 8 resulting in 1q42.3 deletion syndrome. Fluorescent in situ hybridization with whole chromosome paints confirmed the conventional cytogenetic diagnosis. 3 refs., 2 figs., 1 tab.

  10. Fluorescence in situ hybridization for identification of microorganisms in acute chorioamnionitis.

    PubMed

    Schmiedel, D; Kikhney, J; Masseck, J; Rojas Mencias, P D; Schulze, J; Petrich, A; Thomas, A; Henrich, W; Moter, A

    2014-09-01

    The relevance of microorganisms in preterm birth is still under discussion. Using a diagnostic fluorescence in situ hybridization probe panel, we visualized Staphylococcus aureus and Streptococcus mitis group in two cases of acute chorioamnionitis. This technique provides spatial resolution and quantity of bacteria, clarifying the epidemiology and pathogenic pathways of acute chorioamnionitis.

  11. Evolution of Chromosome 6 of Solanum Species Revealed by Comparative Fluorescence in Situ Hybridization Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative genome mapping is an important tool in evolutionary research. Here we demonstrate a comparative fluorescent in situ hybridization (FISH) mapping strategy. A set of 13 bacterial artificial chromosome (BAC) clones derived from potato chromosome 6 was used for FISH mapping in seven differen...

  12. Investigation of varicella-zoster virus infection of lymphocytes by in situ hybridization

    SciTech Connect

    Koropchak, C.M.; Solem, S.M.; Diaz, P.S.; Arvin, A.M.

    1989-05-01

    Peripheral blood mononuclear cells harboring viral gene sequences were detected during primary varicella-zoster virus (VZV) infection of the human host and the strain 2 guinea pig by in situ hybridization with a /sup 3/H-labeled VZV DNA probe. Activated T lymphocytes were permissive for VZV infection at low frequency in vitro.

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

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  14. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  15. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  16. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  17. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Automated fluorescence in situ hybridization (FISH) enumeration systems. 866.4700 Section 866.4700 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES...

  18. Quantitative in situ hybridization for the study of gene expression at the regional and cellular levels.

    PubMed

    Le Moine, Catherine

    2003-08-01

    Quantitative in situ hybridization allows measurement of mRNA level modifications in a variety of experimental conditions. This analysis may be performed both at the regional anatomical and cellular levels by densitometry, neuronal counting and silver grain measurements. PMID:18428577

  19. Human growth hormone and prolactin secreting pituitary adenomas analyzed by in situ hybridization.

    PubMed

    Lloyd, R V; Cano, M; Chandler, W F; Barkan, A L; Horvath, E; Kovacs, K

    1989-03-01

    Acidophilic pituitary adenomas commonly produce growth hormone (GH) or prolactin (PRL), according to studies employing immunohistochemical and ultrastructural methods. To examine this question, in situ hybridization with oligonucleotide probes was done on routinely processed tissues received in the pathology laboratory to analyze for the presence of GH and PRL messenger RNA (mRNA) in 4 normal pituitaries, 10 prolactinomas, and 16 GH-secreting adenomas. Most acidophilic cells in normal pituitaries expressed either GH or PRL hormone and the respective mRNAs, but GH mRNA and PRL hormone were also detected in some of the same cells. Patients with a clinical diagnosis of prolactinoma had cells with only PRL mRNA in their tumors, while most (14 of 16) patients with a clinical diagnosis of acromegaly or gigantism had both GH and PRL mRNAs in their tumors. The GH adenomas varied in these studies. In situ hybridization was helpful in characterizing the adenoma from a patient with acromegaly who had immunoreactive PRL, but no immunoreactive GH in the resected tumor; in situ hybridization analysis revealed mRNAs for both GH and PRL in the same tumor cells. Our findings indicate that pituitary adenomas from patients with acromegaly commonly express PRL mRNA. It is concluded that in situ hybridization provides new information about the clinical biology and the histopathologic classification of pituitary adenomas. PMID:2466405

  20. Demonstration of tissue-specific gene expression by in situ hybridization

    SciTech Connect

    Angerer, L.M.; Cox, K.H.; Angerer, R.C.

    1987-01-01

    In situ hybridization has emerged as a valuable tool for the identification of individual cells expressing specific genes. Recently, methods have become sufficiently sensitive to detect mRNAs present at the level of only a few molecules per cell. When mRNAs are expressed in only a small fraction of the cells in a mixed population, in situ hybridization may be the most sensitive nucleic acid hybridization technique available. The authors' laboratory has shown that antisense RNA probes offer a unique combination of advantages for detection of individual mRNAs by in situ hybridization. Most importantly, antisense probes provide a large increase in sensitivity due to the absence of competing probe self-reassociation. The high stability of RNA-RNA duplexes allows use of higher post hybridization wash temperatures to achieve a given fidelity of base pairing (stringency), which also reduced backgrounds. RNA transcripts can be synthesized from truncated templates such that they are essentially devoid of vector sequences. This sequence purity maximizes the signal to noise ratio since lower probe concentrations are required to saturate target RNAs.

  1. Dual-color ultrasensitive bright-field RNA in situ hybridization with RNAscope.

    PubMed

    Wang, Hongwei; Su, Nan; Wang, Li-Chong; Wu, Xingyong; Bui, Son; Nielsen, Allissa; Vo, Hong-Thuy; Luo, Yuling; Ma, Xiao-Jun

    2014-01-01

    In situ hybridization (ISH) techniques have been important to the study of gene expression signatures in cells and tissues. The ability to detect multiple targets simultaneously is especially valuable, since it allows dissecting gene expression of distinct cell types with precise cellular and subcellular resolution within morphological context. Recently, we have reported using a novel dual-color ultrasensitive bright-field RNA in situ hybridization for detection of clonally restricted immunoglobulin light chain mRNA expression in B cell lymphomas. Here, we present detailed protocols of RNAscope 2-Plex assays for FFPE tissue sections. The protocols describe the tissue preparation, pretreatment, probe hybridization, signal amplification, visualization, and analysis, as well as emphasize the critical steps for ensuring successful staining.

  2. Coordinated In Situ Nanosims Analyses of H-C-O Isotopes in ALH 84001 Carbonates

    NASA Technical Reports Server (NTRS)

    Usui, T.; Alexander, C. M. O'D.; Wang, J.; Simon, J. I.; Jones, J. H.

    2016-01-01

    The surface geology and geomorphology of Mars indicate that it was once warm enough to maintain a large body of liquid water on its surface, though such a warm environment might have been transient. This study reports the hydrogen, carbon, and oxygen isotope compositions of the ancient atmosphere/hydrosphere of Mars based on in situ ion microprobe analyses of approximately 4 Ga-old carbonates in Allan Hills (ALH) 84001. The ALH 84001 carbonates are the most promising targets because they are thought to have formed from fluid that was closely associated with the Noachian atmosphere. While there are a number of carbon and oxygen isotope studies of the ALH 84001 carbonates, in situ hydrogen isotope analyses of these carbonates are limited and were reported more than a decade ago. Well-documented coordinated in situ analyses of carbon, oxygen and hydrogen isotopes provide an internally consistent dataset that can be used to constrain the nature of the Noachian atmosphere/hydrosphere and may eventually shed light on the hypothesis of ancient watery Mars.

  3. Fluorescence in situ hybridization to improve the diagnosis of endocarditis: a pilot study.

    PubMed

    Mallmann, C; Siemoneit, S; Schmiedel, D; Petrich, A; Gescher, D M; Halle, E; Musci, M; Hetzer, R; Göbel, U B; Moter, A

    2010-06-01

    Infective endocarditis is a rare but life-threatening disease associated with high mortality. Early diagnosis of the causative microorganism is critical to patient outcome. However, conventional diagnostic methods are often unsatisfactory in achieving this goal. As a proof of concept, we applied fluorescence in situ hybridization (FISH) for detection and identification of bacteria in histological sections of heart valves. Biopsy specimens from 54 suspected endocarditis patients were obtained during valve surgery and analysed via FISH. Specimens were screened with a probe panel that identifies the most common bacteria implicated in endocarditis. Results were compared with those of culture-based diagnostics and clinical data. Discrepant results were subjected to comparative sequence analysis of PCR-amplified 16S rRNA genes. FISH detected bacteria in 26 of the 54 heart valves. FISH allowed successful diagnosis of infective endocarditis in five of 13 blood culture-negative cases and in 11 of 37 valve culture-negative cases, showing the bacteria within their histological context. This technique allows the simultaneous detection and identification of microorganisms at the species or genus level directly from heart valves and might be a valuable tool for diagnosis of endocarditis.

  4. Fluorescence in situ hybridization rapidly detects three different pathogenic bacteria in urinary tract infection samples.

    PubMed

    Wu, Qing; Li, Yan; Wang, Ming; Pan, Xiao P; Tang, Yong F

    2010-11-01

    The detection of pathogenic bacteria in urine is an important criterion for diagnosing urinary tract infections (UTIs). By using fluorescence in situ hybridization (FISH) with rRNA-targeted, fluorescently labeled oligonucleotide probes, bacterial pathogens present in urine samples were identified within 3-4 h. In this study, three probes that are specific for Escherichia coli, Enterococcus faecalis and Staphylococcus aureus were designed based on the conserved 16S RNA sequences, whereas probe Eub338 broadly recognizes all bacteria. We collected a total of 1000 urine samples, and 325 of these samples tested positive for a UTI via traditional culturing techniques; additionally, all 325 of these samples tested positive with the Eub338 probe in FISH analysis. FISH analyses with species-specific probes were performed in parallel to the test the ability to differentiate among several pathogenic bacteria. The samples for these experiments included 76 E. coli infected samples, 32 E. faecalis infected samples and 9 S. aureus infected samples. Compared to conventional methods of bacterial identification, the FISH method produced positive results for >90% of the samples tested. FISH has the potential to become an extremely useful diagnostic tool for UTIs because it has a quick turnaround time and high accuracy.

  5. Nanogold In Situ Hybridization for Phylogenetic Identification in Geologic Samples Using Environmental Scanning Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Ehrhardt, C.; Haymon, R.; Sievert, S.; Holden, P.

    2006-12-01

    Collecting phylogenetic information simultaneously with mineral textures and associations for geomicrobiological studies has always been a challenge. Recently a new type of nucleotide reporter system has been developed that utilizes small particles of nanogold (1.4 nm) covalently attached to oligonucelotide probes. Due to the small size and electron density of these nanogold reporter molecules, this in situ hybridization technique allows for the phylogenetic identification of microbial targets with a scanning electron microscope. Here we present new applications of the nanogold hybridization technique for pure cultures and natural microbial communities in a range of geologic samples including sand grains, basalt chips incubated on deep sea hydrothermal vents, and gypsum crusts sampled from a saline lake. While we do observe nonspecific binding of nanogold probes to minerals and organic compounds in geologic matrices, this can be distinguished from positive hybridization events with a spatial variety analysis. To assess the potential of nanogold hybridizations for quantitative assessments of microbial communities, fluorescent in situ hybridizations (FISH) were performed on all samples and compared to cell counts generated from nanogold hybridizations.

  6. Genome discrimination by in situ hybridization in Icelandic species of Elymus and Elytrigia (Poaceae: Triticeae).

    PubMed

    Orgaard, M; Anamthawat-Jónsson, K

    2001-04-01

    The genome constitution of Icelandic Elymus caninus, E. alaskanus, and Elytrigia repens was examined by fluorescence in situ hybridization using genomic DNA and selected cloned sequences as probes. Genomic in situ hybridization (GISH) of Hordeum brachyantherum ssp. californicum (diploid, H genome) probe confirmed the presence of an H genome in the two tetraploid Elymus species and identified its presence in the hexaploid Elytrigia repens. The H chromosomes were painted uniformly except for some chromosomes of Elytrigia repens which showed extended unlabelled pericentromeric and subterminal regions. A mixture of genomic DNA from H. marinum ssp. marinum (diploid, Xa genome) and H. murinum ssp. leporinum (tetraploid, Xu genome) did not hybridize to chromosomes of the Elymus species or Elytrigia repens, confirming that these genomes were different from the H genome. The St genomic probe from Pseudoroegneria spicata (diploid) did not discriminate between the genomes of the Elymus species, whereas it produced dispersed and spotty hybridization signals most likely on the two St genomes of Elytrigia repens. Chromosomes of the two genera Elymus and Elytrigia showed different patterns of hybridization with clones pTa71 and pAes41, while clones pTa1 and pSc119.2 hybridized only to Elytrigia chromosomes. Based on FISH with these genomic and cloned probes, the two Elymus species are genomically similar, but they are evidently different from Elytrigia repens. Therefore the genomes of Icelandic Elymus caninus and E. alaskanus remain as StH, whereas the genomes of Elytrigia repens are proposed as XXH.

  7. Evolution in situ: hybrid origin and establishment of willows (Salix L.) on alpine glacier forefields

    PubMed Central

    Gramlich, S; Sagmeister, P; Dullinger, S; Hadacek, F; Hörandl, E

    2016-01-01

    Little attention has been paid to the evolutionary consequences of the colonizing dynamics and succession processes following glacier retreat. Here we studied hybrid populations that have recently formed and established on glacier forefields of the European Alps owing to secondary contact of a lowland colonizer with a subalpine species. We analyzed the composition of two hybrid populations between Salix purpurea and Salix helvetica with nine microsatellite markers by using Bayesian methods (structure and NewHybrids), and simulations. We also studied niche differentiation between the hybrids and the parental species based on indicator values, soil pH and water retention potential measurements. Allelic structure of hybrids confirms the assumed parentage and in situ origin of the crosses on two independent sites within the last decades. Both hybrid populations comprised F1 and later generation hybrids (F2 and backcrosses), confirming hybrid fertility. The parental species showed significant differences in niche characteristics for temperature, soil pH, nutrients and moisture. Remarkably, the hybrids exhibited a higher tolerance to cold temperatures, nutrient-poor and acidic soils than either parent. Our results show that willow hybrids originated after glacier retreat and have established persistent populations within a few decades. One factor contributing to hybrid establishment in sympatry with their parents is their ability to occupy more extreme niches than either parental species within a mosaic-like pattern of microhabitats on the forefield. Introgression and/or transgressive segregation may have resulted in novel genotypes that are able to expand the ecological spectrum of either parent. PMID:26980342

  8. Rapid prenatal diagnosis of chromosomal aneuploidies by fluorescence in situ hybridization: clinical experience with 4,500 specimens.

    PubMed Central

    Ward, B E; Gersen, S L; Carelli, M P; McGuire, N M; Dackowski, W R; Weinstein, M; Sandlin, C; Warren, R; Klinger, K W

    1993-01-01

    Detection of chromosome aneuploidies in uncultured amniocytes is possible using fluorescence in situ hybridization (FISH). We herein describe the results of the first clinical program which utilized FISH for the rapid detection of chromosome aneuploidies in uncultured amniocytes. FISH was performed on physician request, as an adjunct to cytogenetics in 4,500 patients. Region-specific DNA probes to chromosomes 13, 18, 21, X, and Y were used to determine ploidy by analysis of signal number in hybridized nuclei. A sample was considered to be euploid when all autosomal probes generated two hybridization signals and when a normal sex chromosome pattern was observed in greater than or equal to 80% of hybridized nuclei. A sample was considered to be aneuploid when greater than or equal to 70% of hybridized nuclei displayed the same abnormal hybridization pattern for a specific probe. Of the attempted analyses, 90.2% met these criteria and were reported as informative to referring physicians within 2 d of receipt. Based on these reporting parameters, the overall detection rate for aneuploidies was 73.3% (107/146), with an accuracy of informative results for aneuploidies of 93.9% (107/114). Compared to cytogenetics, the accuracy of all informative FISH results, euploid and aneuploid, was 99.8%, and the specificity was 99.9%. In those pregnancies where fetal abnormalities had been observed by ultrasound, referring physicians requested FISH plus cytogenetics at a significantly higher rate than they requested cytogenetics alone. The current prenatal FISH protocol is not designed to detect all chromosome abnormalities and should only be utilized as an adjunctive test to cytogenetics. This experience demonstrates that FISH can provide a rapid and accurate clinical method for prenatal identification of chromosome aneuploidies. PMID:8488836

  9. Rapid prenatal diagnosis of chromosomal aneuploidies by fluorescence in situ hybridization: Clinical experience with 4,500 specimens

    SciTech Connect

    Ward, B.E.; Gersen, S.L.; Carelli, M.P.; McGuire, N.M.; Dackowski, W.R.; Klinger, K.W. ); Weinstein, M. ); Sandlin, C. ); Klinger, K.W. )

    1993-05-01

    Detection of chromosome aneuploidies in uncultured amniocytes is possible using fluorescence in situ hybridization (FISH). The authors herein describe the results of the first clinical program which utilized FISH for the rapid detection of chromosome aneuploidies in uncultured amniocytes. FISH was performed on physician request, as an adjunct to cytogenetics in 4,500 patients. Region-specific DNA probes to chromosomes 13, 18, 21, X, and Y were used to determine ploidy by analysis of signal number in hybridized nuclei. A sample was considered to be euploid when all autosomal probes generated two hybridization signals and when a normal sex chromosome pattern was observed in greater than or equal to 80% of hybridized nuclei. A sample was considered to be aneuploid when greater than or equal to 70% of hybridized nuclei displayed the same abnormal hybridization pattern for a specific probe. Of the attempted analyses, 90.2% met these criteria and were reported as informative to referring physicians within 2 d of receipt. Based on these reporting parameters, the overall detection rate for aneuploidies was 73.3% (107/146), with an accuracy of informative results for aneuploidies of 93.9% (107/114). Compared to cytogenetics, the accuracy of all informative FISH results, euploid and aneuploid, was 99.8%, and the specificity was 99.9%. In those pregnancies where fetal abnormalities had been observed by ultrasound, referring physicians requested FISH plus cytogenetics at a significantly higher rate than they requested cytogenetics alone. The current prenatal FISH protocol is not designed to detect all chromosome abnormalities and should only be utilized as an adjunctive test to cytogenetics. This experience demonstrates that FISH can provide a rapid and accurate clinical method for prenatal identification of chromosome aneuploidies. 40 refs., 1 fig., 5 tabs.,

  10. In situ hybridization method for studies of cell wall deficient M. paratuberculosis in tissue samples.

    PubMed

    Hulten, K; Karttunen, T J; El-Zimaity, H M; Naser, S A; Almashhrawi, A; Graham, D Y; El-Zaatari, F A

    2000-12-20

    Cell wall deficient forms of mycobacteria may be important in the pathogenesis of Crohn's disease and sarcoidosis. However, no method has been available to localize this type of organisms in tissue sections. We developed an in situ hybridization method for the demonstration of Mycobacterium paratuberculosis spheroplasts (cell wall deficient forms) in paraffin embedded tissue sections.M. paratuberculosis spheroplasts were prepared by treatment with glycine and lysozyme. Pieces of beef were injected with the prepared spheroplasts. The samples were fixed in buffered formalin and paraffin embedded. A M. paratuberculosis-specific probe derived from the IS900 gene was used. Specificity was controlled by using an irrelevant probe and by hybridizing sections with spheroplasts from other bacteria. Beef samples injected with M. paratuberculosis spheroplasts were the only samples that hybridized with the probe. Beef samples containing acid-fast or spheroplast forms of M. smegmatis and M. tuberculosis as well as the acid-fast forms of M. paratuberculosis did not hybridize with the probe. Unrelated bacterial controls, i.e. Helicobacter pylori and Escherichia coli were also negative in the assay. In situ hybridization with the IS900 probe provides a specific way to localize M. paratuberculosis spheroplasts in tissue sections and may be useful for studies of the connection between M. paratuberculosis and Crohn's disease and sarcoidosis. The assay may also be valuable for studies on Johne's diseased animals. PMID:11118736

  11. [Three cases of vulvar bowenoid papulosis: the localization of HPV DNA by in situ hybridization].

    PubMed

    Kioka, H; Nagai, N; Tanioka, Y; Fujii, T; Katsube, Y; Egawa, K; Fujiwara, A

    1989-09-01

    Cytological, histological, and molecular biological studies were conducted in 3 cases of vulvar Bowenoid papulosis, using biotinylated HPV DNA probes by in situ hybridization. 1) Cytological findings showed dyskaryotic cells that revealed hyperchromatism with a coarse granular pattern, and a high N/C ratio was observed among the dyskeratotic cells. 2) In 2 cases of Bowenoid papulosis lesions, HPV 16 DNA was detected in the nucleus of the dysplastic cells. 3) In one case of Bowenoid papulosis, a complicated carcinoma in situ of the uterine cervix was observed, and the HPV 16 DNA was found to be positive in both the vulva and cervix. PMID:2550688

  12. Energization of Oxygen Ions at Mars: Comparison of a Global Hybrid Model to In Situ Observations

    NASA Astrophysics Data System (ADS)

    Jarvinen, R.; Brain, D. A.; Fedorov, A.; Holmstrom, M.; Modolo, R.

    2015-12-01

    We study the energization of planetary oxygen ions escaping from the atmosphere of Mars in a global hybrid model for the Mars-solar wind interaction. In the hybrid approach ions are modelled as particles moving under the Lorentz force and electrons are a charge-neutralizing fluid. Thus, electric and magnetic field are self-consistently coupled with ion dynamics. We identify ion energization regions in the induced magnetosphere of Mars in the model. Further, we study electric and magnetic fields associated with the ion acceleration processes. Finally, we compare our simulation results to in situ particle and magnetic field observations on the MAVEN and Mars Express missions.

  13. Resolution of sex chromosome constitution by genomic in situ hybridization and fluorescence in situ hybridization with (TTAGG)( n ) telomeric probe in some species of Lepidoptera.

    PubMed

    Yoshido, Atsuo; Marec, Frantisek; Sahara, Ken

    2005-08-01

    We have developed a simple method to resolve the sex chromosome constitution in females of Lepidoptera by using a combination of genomic in situ hybridization (GISH) and fluorescence in situ hybridization with (TTAGG)( n ) telomeric probe (telomere-FISH). In pachytene configurations of sex chromosomes, GISH differentiated W heterochromatin and telomere-FISH detected the chromosome ends. With this method we showed that Antheraea yamamai has a standard system with a fully differentiated W-Z sex chromosome pair. In Orgyia antiqua, we confirmed the presence of neo-W and neo-Z chromosomes, which most probably originated by fusion of the ancestral W and Z with an autosome pair. In contrast to earlier data, Orgyia thyellina females displayed a neo-ZW(1)W(2) sex chromosome constitution. A neo-WZ(1)Z(2) trivalent was found in females of Samia cynthia subsp. indet., originating from a population in Nagano, Japan. Whereas another subspecies collected in Sapporo, Japan, and determined as S. cynthia walkeri, showed a neo-W/neo-Z bivalent similar to O. antiqua, and the subspecies S. cynthia ricini showed a Z univalent (a Z/ZZ system). The combination of GISH and telomere-FISH enabled us to acquire not only reliable information about sex chromosome constitution but also an insight into sex chromosome evolution in Lepidoptera.

  14. Orbitrap mass analyser for in situ characterisation of planetary environments: Performance evaluation of a laboratory prototype

    NASA Astrophysics Data System (ADS)

    Briois, Christelle; Thissen, Roland; Thirkell, Laurent; Aradj, Kenzi; Bouabdellah, Abdel; Boukrara, Amirouche; Carrasco, Nathalie; Chalumeau, Gilles; Chapelon, Olivier; Colin, Fabrice; Coll, Patrice; Cottin, Hervé; Engrand, Cécile; Grand, Noel; Lebreton, Jean-Pierre; Orthous-Daunay, François-Régis; Pennanech, Cyril; Szopa, Cyril; Vuitton, Véronique; Zapf, Pascal; Makarov, Alexander

    2016-10-01

    For decades of space exploration, mass spectrometry has proven to be a reliable instrumentation for the characterisation of the nature and energy of ionic and neutral, atomic and molecular species in the interplanetary medium and upper planetary atmospheres. It has been used as well to analyse the chemical composition of planetary and small bodies environments. The chemical complexity of these environments calls for the need to develop a new generation of mass spectrometers with significantly increased mass resolving power. The recently developed OrbitrapTM mass analyser at ultra-high resolution shows promising adaptability to space instrumentation, offering improved performances for in situ measurements. In this article, we report on our project named "Cosmorbitrap" aiming at demonstrating the adaptability of the Orbitrap technology for in situ space exploration. We present the prototype that was developed in the laboratory for demonstration of both technical feasibility and analytical capabilities. A set of samples containing elements with masses ranging from 9 to 208 u has been used to evaluate the performance of the analyser, in terms of mass resolving power (reaching 474,000 at m/z 9) and ability to discriminate between isobaric interferences, accuracy of mass measurement (below 15 ppm) and determination of relative isotopic abundances (below 5%) of various samples. We observe a good agreement between the results obtained with the prototype and those of a commercial instrument. As the background pressure is a key parameter for in situ exploration of atmosphere planetary bodies, we study the effect of background gas on the performanceof the Cosmorbitrap prototype, showing an upper limit for N2 in our set-up at 10-8 mbar. The results demonstrate the strong potential to adapt this technology to space exploration.

  15. Identification of genome constitutions in Begonia×chungii and its putative parents, B. longifolia and B. palmata, by genomic in situ hybridization (GISH).

    PubMed

    Kono, Yoshiko; Chung, Mei-Chu; Peng, Ching-I

    2012-04-01

    Based mainly on morphological features and geographical distribution, Begonia×chungii (2n=22) was recently reported as a natural hybrid between B. longifolia and B. palmata in Taiwan. This study aims to confirm the hybridity of B.×chungii and to sort out the genome constitutions of its putative parents, using genomic in situ hybridization (GISH). Genomic DNAs of both parental species were used as probes for B.×chungii and the experimental F(1) hybrid, B. palmata×B. longifolia, in GISH analyses. Bicolor-GISH analyses in B.×chungii showed that the 22 chromosomes consisted of six chromosomes hybridized with a probe derived from the B. palmata genome, six with another probe from the B. longifolia genome and the remaining ten with both genomes overlapped. Meanwhile, bicolor-GISH in B. palmata×B. longifolia showed a remarkable similarity to that of B.×chungii. The reciprocal GISH results between B. longifolia and B. palmata were comparable. Our GISH analyses confirmed that B.×chungii is a natural F(1) hybrid between B. longifolia and B. palmata. Genomes of the parental species were shown to be partially homologous, suggesting a derived common ancestral genome in them.

  16. Coordinated in Situ Analyses of Organic Nanoglobules in the Sutter's Mill Meteorite

    NASA Technical Reports Server (NTRS)

    Nakamura-Messenger, K.; Messenger, S.; Keller, L. P.; Clemett, S. J.; Nguyen, A. N.; Gibson, E. K.

    2013-01-01

    The Sutter's Mill meteorite is a newly fallen carbonaceous chondrite that was collected and curated quickly after its fall. Preliminary petrographic and isotopic investigations suggest affinities to the CM2 carbonaceous chondrites. The primitive nature of this meteorite and its rapid recovery provide an opportunity to investigate primordial solar system organic matter in a unique new sample. Here we report in-situ analyses of organic nanoglobules in the Sutter's Mill meteorite using UV fluorescence imaging, Fourier-transform infrared spectroscopy (FTIR), scanning transmission electron microscopy (STEM), NanoSIMS, and ultrafast two-step laser mass spectrometry (ultra-L2MS).

  17. A portable X-ray diffraction apparatus for in situ analyses of masters' paintings

    NASA Astrophysics Data System (ADS)

    Eveno, Myriam; Duran, Adrian; Castaing, Jacques

    2010-09-01

    It is rare that the analyses of materials in paintings can be carried out by taking micro-samples. Valuable works of art are best studied in situ by non-invasive techniques. For that purpose, a portable X-ray diffraction and fluorescence apparatus has been designed and constructed at the C2RMF. This apparatus has been used for paintings of Rembrandt, Leonardo da Vinci, Van Gogh, Mantegna, etc. Results are given to illustrate the performance of X-ray diffraction, especially when X-ray fluorescence does not bring sufficient information to conclude.

  18. Localization of cytomegalovirus DNA in plastic-embedded sections by in situ hybridization. A methodologic study.

    PubMed Central

    Cao, M.; Beckstead, J. H.

    1989-01-01

    The use of in situ hybridization for the identification of specific nucleic acid sequences in tissue sections has the potential for broad application in pathology. Although this technique has been successfully applied to routine paraffin sections, there have been few studies of the application of in situ hybridization to plastic-embedded tissue sections. The authors adapted techniques developed for paraffin sections to take advantage of the potential for improved morphology and more precise localization inherent in the plastic sections. A commercially available biotinylated DNA probe specific for the cytomegalovirus to develop a practical method for detection of nucleic acid sequences in plastic-embedded tissues was used. Using plastic sections, cytomegalovirus DNA sequences could readily be identified with precise localization of the virus and superb histology. Images Figure 2 Figure 3 Figure 1 Figure 4 PMID:2537020

  19. Preparative in situ hybridization: Selection of chromosome region-specific libraries on mitotic chromosomes

    SciTech Connect

    Hozier, J.; Graham, R.; Westfall, T.; Davis, L. ); Siebert, P. )

    1994-02-01

    The authors have developed preparative in situ hybridization (Prep-ISH) of complex DNA populations to mitotic chromosomes as a means of generating chromosome region-specific DNA subpopulations. Prep-ISH is a combination of two cytogenetic techniques: in situ hybridization of DNA molecules to mitotic chromosomes and chromosome microdissection. Here, they present test cases demonstrating the feasibility of this approach on mouse and human genomes, using single nuclei, single chromosomes, or single chromosomal subregions to assess sensitivity, specificity, and representation of the Prep-ISH technique. Prep-ISH has a number of applications in studies of gene expression and genome organization, including efficient cytogenetic sorting of tissue-specific cDNAs and genomic DNA libraries. In addition, Prep-ISH is likely to dramatically reduce the number of candidate genes to aid in gene discovery efforts and to improve efficiency of developing transcription maps and YAC and cosmid contigs through defined cytogenetic regions. 34 refs., 4 figs.

  20. Cytodiagnosis of Extraskeletal Ewing's Sarcoma and its Confirmation by Fluorescence in situ Hybridization.

    PubMed

    Dey, Biswajit; Singh, Ashish Ranjan; Barwad, Adarsh; Dange, Prasad; Siddaraju, Neelaiah

    2016-08-01

    Extraskeletal Ewing's sarcoma is an aggressive malignant small round cell tumour usually occuring in children and adolescents. It needs to be differentiated from other malignant small round cell tumours and immunohistochemistry plays a pivotal role in establishing the diagnosis. Fluorescence in situ hybridization or real time-polymerase chain reaction helps in confirming the diagnosis by demonstration of EWS-FLI1 translocation, which is found in approximately 85% of the cases. We report a case of extraskeletal Ewing's sarcoma in a10-year-old male, who presented with a right gluteal region mass. Fine needle aspiration and cell block preparation followed by a panel of immunohistochemical markers were performed. Immunohistochemistry for CD99 and FLI1 was positive. EWS-FLI1 translocation was confirmed by fluorescence in situ hybridization. PMID:27656453

  1. Characterization of circulating tumor cells by fluorescence in situ hybridization.

    PubMed

    Swennenhuis, Joost F; Tibbe, Arjan G J; Levink, Rianne; Sipkema, Ronald C J; Terstappen, Leon W M M

    2009-06-01

    Tumor cells in blood of patients with metastatic carcinomas have been associated with poor survival prospects. Further characterization of these cells may provide further insights into the metastatic process. Circulating Tumor Cells (CTC) were enumerated in 7.5 mL of blood with the CellSearch system. After enumeration of Cytokeratin+, CD45-, nucleated cells, the cells are fixed in the cartridge while maintaining their original position. Cartridges were hybridized with FISH probes against the centromeric regions of chromosome 1, 7, 8, and 17. Next fluorescence images of the FISH probes of the previous identified CTC were acquired. Leukocytes surrounding the CTC were used as internal controls. The number of copies of chromosome 1, 7, 8, and 17 could be determined in 118 CTC containing blood samples from 59 metastatic prostate cancer patients. The samples contained a total of 21,751 CTC (mean 184, median 16, SD 650). Chromosome counts were obtained in 61% of the relocated CTC. On an average, these CTC contained 2.8 copies of chromosome 1, 2.7 copies of chromosome 7, 3.1 copies of chromosome 8, and 2.3 copies of chromosome 17. CTC in which no chromosome count was obtained most likely underwent apoptosis indicated by the expression of M30. In 6/59 patients only diploid CTC were detected these samples, however, only contained 1-5 CTC. Heterogeneity in the chromosomal abnormalities was observed between CTC of different patients as well as among CTC of the same patient. Cytogenetic composition of CTC can be reliably assessed after they have been identified by the CellSearch system. The majority of CTC in hormone refractory prostate cancer are aneuploid confirming that they indeed are cancer cells. An extensive heterogeneity in the copy number of each of the chromosomes was observed.

  2. Tyramide Signal Amplification: Fluorescence In Situ Hybridization for Identifying Homoeologous Chromosomes.

    PubMed

    Fominaya, Araceli; Loarce, Yolanda; González, Juan M; Ferrer, Esther

    2016-01-01

    Tyramide signal amplification (TSA) fluorescence in situ hybridization (FISH) has been shown as a valuable molecular tool for visualizing specific amplified DNA sequences in chromosome preparations. This chapter describes how to perform TSA-FISH, paying special interest to its two critical steps: probe generation and metaphase plate generation. The potential of physically mapping 12S-globulin sequences by TSA-FISH as a means of identifying homeology among chromosome regions of Avena species was tested and is discussed. PMID:27511165

  3. Rapid triple-labeling method combining in situ hybridization and double immunocytochemistry.

    PubMed

    Lopez-Sanchez, Carmen; Garcia-Martinez, Virginio; Lawson, Aaron; Chapman, Susan C; Schoenwolf, Gary C

    2004-06-01

    A new, rapid method is described for combining in situ hybridization and immunocytochemistry to define cell populations and to map three-dimensional movements of groups of labeled cells within developing chick embryos. The method allows fluorescently labeled cells to be followed in living embryos and subsequently detected as a permanent reaction product for detailed three-dimensional analysis by immunocytochemistry in histological serial sections. Cell identity can be ascertained using a specific riboprobe and in situ hybridization. With this approach, the movements of two groups of cells can be mapped simultaneously (using two different fluorescent trackers and, subsequently, two different chromogens for immunocytochemistry) to analyze relative movements within an embryo, and when combined with in situ hybridization with a specific riboprobe for cell identity, allows fate mapping studies to be conducted using molecular criteria, rather than solely at morphological/positional criteria. The improved method enables the investigator to extract substantially more information from individual embryos, maximizing the results obtained from labor-intensive fate mapping studies.

  4. Study of SGD along the French Mediterranean coastline using airborne TIR images and in situ analyses

    NASA Astrophysics Data System (ADS)

    van Beek, Pieter; Stieglitz, Thomas; Souhaut, Marc

    2015-04-01

    Although submarine groundwater discharge (SGD) has been investigated in many places of the world, very few studies were conducted along the French coastline of the Mediterranean Sea. Almost no information is available on the fluxes of water and chemical elements associated with these SGD and on their potential impact on the geochemical cycling and ecosystems of the coastal zones. In this work, we combined the use of airborne thermal infrared (TIR) images with in situ analyses of salinity, temperature, radon and radium isotopes to study SGD at various sites along the French Mediterranean coastline and in coastal lagoons. These analyses allowed us to detect SGD sites and to quantify SGD fluxes (that include both the fluxes of fresh groundwater and recirculated seawater). In particular, we will show how the Ra isotopes determined in the La Palme lagoon were used to estimate i) the residence time of waters in the lagoon and ii) SGD fluxes.

  5. Fluorescent in situ hybridization with arbitrarily amplified DNA fragments differentiates carrot (Daucus carota L.) chromosomes.

    PubMed

    Nowicka, Anna; Grzebelus, Ewa; Grzebelus, Dariusz

    2012-03-01

    Carrot (Daucus carota L.) chromosomes are small and poorly differentiated in size and morphology. Here we demonstrate that fluorescent in situ hybridization (FISH) signals derived from arbitrary PCR probes can be used for chromosome identification in carrot. To prepare probes, we searched for nonpolymorphic products abundantly amplified with arbitrary decamer primers in a group of accessions representing carrot genetic diversity. As a result, 13 fragments ranging in size from 517 to 1758 bp were selected, sequenced, and used as probes for fluorescent in situ hybridization. Four of these probes produced clear and reproducible hybridization signals. The sequences showed similarity to a number of carrot BAC-end sequences, indicating their repetitive character. Three of them were similar to internal portions of gypsy and copia LTR retrotransposons previously identified in plants. Hybridization signals for the four probes were observed as dotted tracks on chromosomes, differing in distribution and intensity. Generally, they were present in pericentromeric and (or) interstitial localizations on chromosome arms. The use of the four probes allowed discrimination of chromosome pairs and construction of more detailed karyotypes and idiograms of carrot.

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

    PubMed

    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. PMID:27157766

  7. Detection of Hepatitis B Virus DNA in Hepatocytes, Bile Duct Epithelium, and Vascular Elements by in situ Hybridization

    NASA Astrophysics Data System (ADS)

    Blum, Hubert E.; Stowring, Linda; Figus, Annalena; Montgomery, Carolyn K.; Haase, Ashley T.; Vyas, Girish N.

    1983-11-01

    A radiolabeled probe specific for hepatitis B virus (HBV) nucleotide sequences was hybridized in situ to liver tissue from three patients with chronic hepatitis B. The HBV genome was detected not only in infected hepatocytes but also in bile duct epithelial cells, endothelial cells, and smooth muscle cells. These findings extend the known host cell range for HBV, suggest new mechanisms of viral dissemination, and illustrate the usefulness of in situ hybridization in the study of pathogenesis of HBV infection.

  8. Advanced polymer-inorganic hybrid hard coatings utilizing in situ polymerization method.

    PubMed

    Takaki, Toshihiko; Nishiura, Katsunori; Mizuta, Yasushi; Itou, Yuichi

    2006-12-01

    Hard coatings are frequently used to give plastics high scratch resistance. Coating hardness and adhesion to the substrate are considered to be key factors influencing scratch resistance, but it is difficult to produce coatings that have both properties. Hybridization of polymers and inorganic materials is a promising approach for solving this problem. We prepared polymer-silica hybrid coatings by using in situ polymerization to carry out radical polymerization of vinyl monomers in a sol-gel solution of alkoxysilanes, and measured the abrasion resistance of the coatings. However, the expected properties were not obtained because the sol-gel reaction did not perfectly proceed on the surface of the coatings under the N2 conditions. We found that curing the hybrid coatings by UV irradiation in air promoted the sol-gel reaction on the surface, resulting in coatings having excellent abrasion resistance.

  9. In situ hybridization of oxytocin messenger RNA: macroscopic distribution and quantitation in rat hypothalamic cell groups

    SciTech Connect

    Burbach, J.P.; Voorhuis, T.A.; van Tol, H.H.; Ivell, R.

    1987-05-29

    Oxytocin mRNA was detected in the rat hypothalamus by in situ hybridization to a single stranded /sup 35/S-labelled DNA probe and the distribution of oxytocin mRNA-containing cell groups was studied at the macroscopic level. Specificity of hybridization was confirmed by comparison to vasopressin mRNA hybridization in parallel tissue sections. Cell groups containing oxytocin mRNA were confined to a set of hypothalamic cell groups, i.c. the supraoptic, paraventricular, anterior commissural nuclei, nucleus circularis and scattered hypothalamic islets. These cell groups displayed similar densities of autoradiographic signals indicating that the oxytocin gene is expressed at approximately the same average level at these various sites.

  10. In situ DNA hybridization analysis of human papillomavirus (HPV) sequences in benign oral mucosal lesions.

    PubMed

    Syrjänen, S M; Syrjänen, K J; Happonen, R P; Lamberg, M A

    1987-01-01

    A series of 144 surgically treated benign oral mucosal lesions were analysed using an in situ DNA hybridization technique with 35S-labeled human papillomavirus (HPV) DNA probes to demonstrate the DNA of HPV types 6, 11, 13, and 16, in routinely processed, paraffin-embedded biopsy specimens. These lesions and an additional 62 benign oral mucosal biopsy specimens (total, 206 specimens) were also assessed by the indirect immunoperoxidase (IP-PAP) technique to detect the expression of HPV structural proteins (viral antigens). A total of 54/206 (26.2%) lesions were observed to express HPV antigens, being found in 45/92 (48.9%) of the squamous cell papillomas/condylomas, in 1/54 fibrous hyperplasias, in 1/8 true fibromas, and in 7/8 (87.5%) of the focal epithelial hyperplasia (FEH) lesions. Of the HPV DNA-positive lesions, 15/45 (33.3%) expressed HPV antigens, the expression not being related to any particular HPV type. HPV DNA sequences were found in 45/144 (31.3%) of the lesions. HPV DNA was present with the highest frequency in FEH (83.3%), followed by the papilloma/condyloma group (33.8%), papillary hyperplasia (28.6%), fibrous hyperplasia (24.4%), and true fibromas (14.3%). The most frequent HPV type was HPV 11, representing 37.8% of the DNA-positive lesions. HPV 13 DNA, previously regarded as specific to FEH, was disclosed as a single HPV type in seven cases, and as a double infection by HPV 11 and 13 in an additional three cases, including all five morphologically distinct entities. Noteworthy is the discovery of the high-risk HPV type 16 DNA in 17.8% of the DNA-positive lesions, four papilloma/condyloma lesions, three fibrous hyperplasias, and one FEH.(ABSTRACT TRUNCATED AT 250 WORDS)

  11. Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility

    PubMed Central

    2013-01-01

    Background Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Helianthus annuus and H. petiolaris have a rich history of hybridization in natural populations. Although first-generation hybrids generally have low fertility, hybrid swarms that include later generation and fully fertile backcross plants have been identified, as well as at least three independently-originated stable hybrid taxa. We examine patterns of transcript accumulation in the earliest stages of hybridization of these species via analyses of transcriptome sequences from laboratory-derived F1 offspring of an inbred H. annuus cultivar and a wild H. petiolaris accession. Results While nearly 14% of the reference transcriptome showed significant accumulation differences between parental accessions, total F1 transcript levels showed little evidence of dominance, as midparent transcript levels were highly predictive of transcript accumulation in F1 plants. Allelic bias in F1 transcript accumulation was detected in 20% of transcripts containing sufficient polymorphism to distinguish parental alleles; however the magnitude of these biases were generally smaller than differences among parental accessions. Conclusions While analyses of allelic bias suggest that cis regulatory differences between H. annuus and H. petiolaris are common, their effect on transcript levels may be more subtle than trans-acting regulatory differences. Overall, these analyses found little evidence of regulatory incompatibility or dominance interactions between parental genomes within F1 hybrid individuals, although it is unclear whether this is a legacy or an enabler of introgression between species. PMID:23701699

  12. Specific Detection of Arcobacter and Campylobacter Strains in Water and Sewage by PCR and Fluorescent In Situ Hybridization

    PubMed Central

    Moreno, Yolanda; Botella, Salut; Alonso, José Luis; Ferrús, María A.; Hernández, Manuel; Hernández, Javier

    2003-01-01

    The aim of this study was to evaluate PCR and fluorescent in situ hybridization (FISH) techniques for detecting Arcobacter and Campylobacter strains in river water and wastewater samples. Both 16S and 23S rRNA sequence data were used to design specific primers and oligonucleotide probes for PCR and FISH analyses, respectively. In order to assess the suitability of the methods, the assays were performed on naturally and artificially contaminated samples and compared with the isolation of cells on selective media. The detection range of PCR and FISH assays varied between 1 cell/ml (after enrichment) to 103 cells/ml (without enrichment). According to our results, both rRNA-based techniques have the potential to be used as quick and sensitive methods for detection of campylobacters in environmental samples. PMID:12571045

  13. Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

    PubMed Central

    Stupar, Robert M; Gardiner, Jack M; Oldre, Aaron G; Haun, William J; Chandler, Vicki L; Springer, Nathan M

    2008-01-01

    Background Heterosis is the superior performance of F1 hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis. Results We observed that the distributions of better parent heterosis among a series of 25 maize hybrids generally do not exhibit significant correlations between different traits. Expression profiling analyses for six of these hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the six different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range. Conclusion We have found that maize inbred genetic diversity is correlated with transcriptional variation. However, sampling of seedling tissues indicated that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents. The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits. PMID:18402703

  14. Using in situ hybridization and PFGE Southern hybridization to detect translocation breakpoints in a BOR/TRPS patient cell line

    SciTech Connect

    Gu, J.Z.; Sapru, M.; Smith, D.

    1994-09-01

    Branchio-oto-renal syndrome (BOR) is an autosomal dominant disorder characterized by ear malformations, cervical fistulae, hearing loss and renal abnormalities. We have integrated the Genethon YAC contig maps with additional markers in the chromosome 8q region genetically linked by a unique patient cell line. This cell line is from a patient who has both the branchio-oto-renal syndrome and tricho-rhino-phalangeal syndrome (TRPS). High resolution cytogenetics demonstrated a direct insertion of materials from 8q13.3q21.13 to 8q24.11. TRPS has been previously linked to deletions involving 8q24.11-q24.13. The rearrangement in this patient suggests that TRPS results from loss of gene function due to insertion at the 8q24.11 breakpoint and the possible location for the BOR gene is at either of the two breakpoints of 8q13.3 and 8q21.13. We have constructed cosmid contigs in 8q24.11. In situ hybridization with cosmids mapped to these locations as probes has helped to narrow down the breakpoints. Combinations of cosmids on either side or overlapping the 8q24.11 breakpoint show split signals on one chromosome 8q arm due to insertion of the materials from the proximal region. Cosmids mapped to the TRPS deletion region have been used to hybridize to pulsed field gel genomic blots of DNA from the patient cell line and detected rearranged genomic fragments. Both in situ hybridization and genomic PFGE Southern blot will be used to precisely locate the breakpoints.

  15. In Situ Detection of Freshwater Fungi in an Alpine Stream by New Taxon-Specific Fluorescence In Situ Hybridization Probes▿

    PubMed Central

    Baschien, Christiane; Manz, Werner; Neu, Thomas R.; Marvanová, Ludmila; Szewzyk, Ulrich

    2008-01-01

    New rRNA-targeting oligonucleotide probes permitted the fluorescence in situ hybridization (FISH) identification of freshwater fungi in an Austrian second-order alpine stream. Based on computer-assisted comparative sequence analysis, nine taxon-specific probes were designed and evaluated by whole-fungus hybridizations. Oligonucleotide probe MY1574, specific for a wide range of Eumycota, and the genus (Tetracladium)-specific probe TCLAD1395, as well as the species-specific probes ALacumi1698 (Alatospora acuminata), TRIang322 (Tricladium angulatum), and Alongi340 (Anguillospora longissima), are targeted against 18S rRNA, whereas probes TmarchB10, TmarchC1_1, TmarchC1_2, and AlongiB16 are targeted against the 28S rRNA of Tetracladium marchalianum and Anguillospora longissima, respectively. After 2 weeks and 3 months of exposure of polyethylene slides in the stream, attached germinating conidia and growing hyphae of freshwater fungi were accessible for FISH. Growing hyphae and germinating conidia on leaves and in membrane cages were also visualized by the new FISH probes. PMID:18776035

  16. Chemical composition and in situ dry matter and fiber disappearance of sorghum x Sudangrass hybrids.

    PubMed

    Beck, P A; Hutchison, S; Gunter, S A; Losi, T C; Stewart, C B; Capps, P K; Phillips, J M

    2007-02-01

    Three sorghum x Sudangrass hybrids were planted in twelve 0.2-ha plots to test the effect of date of harvest and hybrid on plant maturity, DM yield, chemical composition, and in situ DM and fiber disappearance. Sweet Sunny Sue (a non-brown midrib (BMR) hybrid; nonBMR), NutriPlus BMR (a BMR hybrid; NP-BMR), and Dry Stalk BMR (a BMR hybrid; DS-BMR) were planted on 26 June 2003 at 22.4 kg of seed/ha. Beginning 34 d after planting, plant height and phenological growth stage were assessed weekly in 10 random, 0.5-m(2) quadrats per plot. Plants were clipped to 2.5 cm in height and analyzed for CP, NDF, and ADF using near-infrared spectroscopy. Composite samples harvested from each plot on d 34, 48, and 63 were incubated in the rumen of 3 steers to determine the in situ disappearance of DM and NDF in a 3 x 3 Latin square. Forage yield was greater (P < or =0.02) for nonBMR than NP-BMR on d 41 and 55 and tended (P = 0.08) to be greater on d 48. The DS-BMR hybrid produced more (P = 0.04) forage DM than the NP-BMR on d 48. When DM yield was regressed on growth stage at harvest, BMR hybrids were predicted to produce 265 kg/ha more DM (P < 0.01) than nonBMR, at the late-boot stage. At all harvest dates, NDF concentrations were less (P < or =0.02) for BMR than nonBMR. The DS-BMR had greater (P < or =0.02) NDF concentrations than NP-BMR on d 41, 48, 55, and 63. Detergent fiber concentrations were predicted to be greater (P < 0.01) in nonBMR than BMR when regressed on growth stage at harvest, but the magnitude of the differences in fiber concentration diminished with growth stage. The A fractions of DM and NDF were greater (P < 0.01) and the C fraction was less (P < 0.01) for BMR hybrids than nonBMR. The B fraction of DM was not affected (P = 0.15) by hybrid type. The B fraction of NDF was not different (P = 0.28) on d 34 but was greater (P < 0.01) on d 48 and 63 for BMR than nonBMR. Effective degradability of NDF and DM was greater (P < 0.02) for BMR than nonBMR on all harvest

  17. Rapid detection of chromosome aneuploidies in uncultured amniocytes by using fluorescence in situ hybridization (FISH)

    PubMed Central

    Klinger, Katherine; Landes, Greg; Shook, Donna; Harvey, Robert; Lopez, Linda; Locke, Pat; Lerner, Terry; Osathanondh, Rapin; Leverone, Benjamin; Houseal, Timothy; Pavelka, Karen; Dackowski, William

    1992-01-01

    Herein we report the results of the first major prospective study directly comparing aneuploidy detection by fluorescence in situ hybridization of interphase nuclei with the results obtained by cytogenetic analysis. We constructed probes derived from specific subregions of human chromosomes 21, 18, 13, X, and Y that give a single copy–like signal when used in conjunction with suppression hybridization. A total of 526 independent amniotic fluid samples were analyzed in a blind fashion. All five probes were analyzed on 117 samples, while subsets of these five probes were used on the remaining samples (because of insufficient sample size), for a total of over 900 autosomal hybridization reactions and over 400 sex chromosome hybridization reactions. In this blind series, 21 of 21 abnormal samples were correctly identified. The remaining samples were correctly classified as disomic for these five chromosomes. The combination of chromosome-specific probe sets composed primarily of cosmid contigs and optimized hybridization/detection allowed accurate chromosome enumeration in uncultured human amniotic fluid cells, consistent with the results obtained by traditional cytogenetic analysis. Imagesp[60]-aFigure 1 PMID:1609805

  18. Simultaneous in situ hybridization for DNA and RNA reveals the presence of HPV in the majority of cervical cancer cells.

    PubMed

    D'Amato, L; Pilotti, S; Longoni, A; Donghi, R; Rilke, F

    1992-02-01

    Thirteen cases of invasive squamous cell carcinoma of the uterine cervix containing HPV types 16 or 18 DNA sequences, as detected by Southern blot analysis, were investigated by in situ hybridization on routine paraffin sections, using 35S nick-translated DNA probes. Simultaneous in situ hybridization for DNA and RNA showed that in ten out of 13 cases (77%) the percentage of tumor cells containing HPV 16 or 18 varied from 75 to 100%. In one case, harboring both in situ and invasive carcinoma, the same type of HPV DNA was detected in both components. This finding suggests that neoplastic cells retained the viral genome during progression to invasiveness.

  19. Comparative analysis of crossover exchanges and chiasmata in Allium cepa x fistulosum after genomic in situ hybridization (GISH).

    PubMed

    Stevenson, M; Armstrong, S J; Ford-Lloyd, B V; Jones, G H

    1998-11-01

    Genomic in situ hybridization (GISH) successfully differentiated homoeologous genomes in the inter-specific hybrid Allium cepa x fistulosum, thus allowing the detection of reciprocal crossover events as label exchanges in separating anaphase I chromosomes. Three of the eight chromosome pairs were positively identified by fluorescence in situ hybridization (FISH) to rDNA sequences. There was a general similarity of the GISH-based label exchange frequencies and metaphase I chiasma frequencies, but with a 20% deficit of chiasmata. Reasons for this apparent deficit are discussed. The locations of chiasmata and label exchanges are in broad agreement. PMID:9886776

  20. Detection of sex chromosome aneuploidy in dog spermatozoa by triple color fluorescence in situ hybridization.

    PubMed

    Komaki, Haruna; Oi, Maya; Suzuki, Hiroshi

    2014-09-01

    With the development of a direct visualization of sex chromosome in a single sperm by fluorescence in situ hybridization (FISH) technique, the frequency of aberration (aneuploidy) in spermatozoa in several mammals has been investigated. However, there is no report in the incidence of X-Y aneuploidy in the sperm population of dogs. Therefore, in this study, the aneuploidy in dog spermatozoa was examined by multicolor FISH using specific molecular probes for canine sex chromosomes and autosome. Semen from eight male Labrador retrievers was used as specimen. For decondensation of sperm nuclei, the specimen was treated with 1 M NaOH for 4 minutes at room temperature. Probes for chromosomes X, Y, and 1, labeled with SpectrumGreen, Cy3 and Cy5, respectively, were hybridized with decondensed spermatozoa. Fluorescence in situ hybridization signals in sperm heads were clearly detected in each specimen, regardless of the sperm donor. The FISH signal of at least one of the three probes was detected in all sperm heads examined. There was no significant difference between the theoretical ratio (50:50) and the observed ratio of X and Y chromosomes in spermatozoa of all the eight dogs. Mean percentage of sex chromosome aneuploidy was 0.127% (ranged between 0% and 0.316%). This percentage of canine sex chromosome aneuploidy was lower than the one reported in cattle, horses, river buffalo, and goats sperm, but higher than that observed in mice and sheep.

  1. In situ analyses on negative ions in the indium-gallium-zinc oxide sputtering process

    SciTech Connect

    Jia, Junjun; Torigoshi, Yoshifumi; Shigesato, Yuzo

    2013-07-01

    The origin of negative ions in the dc magnetron sputtering process using a ceramic indium-gallium-zinc oxide target has been investigated by in situ analyses. The observed negative ions are mainly O{sup -} with energies corresponding to the target voltage, which originates from the target and barely from the reactive gas (O{sub 2}). Dissociation of ZnO{sup -}, GaO{sup -}, ZnO{sub 2}{sup -}, and GaO{sub 2}{sup -} radicals also contributes to the total negative ion flux. Furthermore, we find that some sputtering parameters, such as the type of sputtering gas (Ar or Kr), sputtering power, total gas pressure, and magnetic field strength at the target surface, can be used to control the energy distribution of the O{sup -} ion flux.

  2. Ga adsorption on si(111) analysed by in situ ellipsometry: 2D and 3D growth

    NASA Astrophysics Data System (ADS)

    Andrieu, S.; d'Avitaya, F. Arnaud; Pfister, J. C.

    1990-11-01

    In this paper, Ga adsorption on Si(111) is analysed by in situ ellipsometry. Three regimes of adsorption and two orders of desorption are distinguished. The results are interpreted as amorphous growth at room temperature, Stranski-Krastanov growth in the substrate temperature range 400-600°C, and Volmer-Weber growth at higher temperatures. The difference in ellipsometric response between both growth modes allows an estimation of the critical coverage at which three-dimensional nucleation takes place. A phase diagram is thus proposed, taking into account the 3 × 3 superstructures occurring between 0 and 1/3 ML on Si(111). These results are compared to those obtained on Si(100), and show marked similarities.

  3. QUANTITATIVE IMAGING AND STATISTICAL ANALYSIS OF FLUORESCENCE IN SITU HYBRIDIZATION (FISH) OF AUREOBASIDIUM PULLULANS. (R823845)

    EPA Science Inventory

    Abstract

    Image and multifactorial statistical analyses were used to evaluate the intensity of fluorescence signal from cells of three strains of A. pullulans and one strain of Rhodosporidium toruloides, as an outgroup, hybridized with either a universal o...

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

    PubMed Central

    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

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

    PubMed

    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

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

    PubMed Central

    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

  7. Making a Hybrid Microfluidic Platform Compatible for In Situ Imaging by Vacuum-Based Techniques

    SciTech Connect

    Yang, Li; Yu, Xiao-Ying; Zhu, Zihua; Thevuthasan, Suntharampillai; Cowin, James P.

    2011-10-26

    A self-contained microfluidic-based device was designed and fabricated for in situ imaging of aqueous surfaces using vacuum techniques. The device is a hybrid between a microfluidic PDMS block and external accessories, all portable on a small platform (10 cm-8 cm). The key feature is that a small aperture with a diameter of 2-3 micrometers is opened to the vacuum, which serves as a detection window for in situ imaging of aqueous surfaces. Vacuum compatibility and temperature drop due to water vaporization are the two most important challenges in this invention. Theoretical calculations and fabrication strategies are presented from multiple design aspects. In addition, results from the time-of-flight secondary ion mass spectrometry (ToF-SIMS) of aqueous surfaces are presented.

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

    SciTech Connect

    Rennert, P.D.; Heinrich, G.

    1986-07-31

    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.

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

    SciTech Connect

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

    1990-12-01

    Insulin receptor mRNA was demonstrated in rat brain slices by in situ hybridization with three {sup 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.

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

    PubMed

    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.

  11. PNA-based fluorescence in situ hybridization for identification of bacteria in clinical samples.

    PubMed

    Fazli, Mustafa; Bjarnsholt, Thomas; Høiby, Niels; Givskov, Michael; Tolker-Nielsen, Tim

    2014-01-01

    Fluorescence in situ hybridization with PNA probes (PNA-FISH) that target specific bacterial ribosomal RNA sequences is a powerful and rapid tool for identification of bacteria in clinical samples. PNA can diffuse readily through the bacterial cell wall due to its uncharged backbone, and PNA-FISH can be performed with high specificity due to the extraordinary thermal stability of RNA-PNA hybrid complexes. We describe a PNA-FISH procedure and provide examples of the application of PNA-FISH for the identification of bacteria in chronic wounds, cystic fibrosis lungs, and soft tissue fillers. In all these cases, bacteria can be identified in biofilm aggregates, which may explain their recalcitrance to antibiotic treatment.

  12. A Formaldehyde-based Whole-Mount In Situ Hybridization Method for Planarians

    PubMed Central

    Pearson, Bret J.; Eisenhoffer, George T.; Gurley, Kyle A.; Rink, Jochen C.; Miller, Diane E.; Alvarado, Alejandro Sánchez

    2009-01-01

    Whole-mount in situ hybridization (WISH) is a powerful tool for visualizing gene expression patterns in specific cell and tissue types. Each model organism presents its own unique set of challenges for achieving robust and reproducible staining with cellular resolution. Here we describe a formaldehyde-based WISH method for the freshwater planarian Schmidtea mediterranea developed by systematically comparing and optimizing techniques for fixation, permeabilization, hybridization and post-processing. The new method gives robust, high-resolution labeling in fine anatomical detail, allows co-labeling with fluorescent probes, and is sufficiently sensitive to resolve the expression pattern of a microRNA in planarians. Our WISH methodology not only provides significant advancements over current protocols that make it a valuable asset for the planarian community, but should also find wide applicability in WISH methods used in other systems. PMID:19161223

  13. Multiplexed miRNA Fluorescence In Situ Hybridization for Formalin-Fixed Paraffin-Embedded Tissues

    PubMed Central

    Renwick, Neil; Cekan, Pavol; Bognanni, Claudia; Tuschl, Thomas

    2015-01-01

    Multiplexed miRNA fluorescence in situ hybridization (miRNA FISH) is an advanced method for visualizing differentially expressed miRNAs, together with other reference RNAs, in archival tissues. Some miRNAs are excellent disease biomarkers due to their abundance and cell-type specificity. However, these short RNA molecules are difficult to visualize due to loss by diffusion, probe mishybridization, and signal detection and signal amplification issues. Here, we describe a reliable and adjustable method for visualizing and normalizing miRNA signals in formalin-fixed paraffin-embedded (FFPE) tissue sections. PMID:25218385

  14. Detection of white spot syndrome virus (WSSV) of Penaeus chinensis by in situ hybridization

    NASA Astrophysics Data System (ADS)

    Zhan, Wen-Bin; Wang, Yuan-Hong; Zhang, Zhi-Dong; Hideo, Fukuda

    2000-09-01

    White Spot Syndrome Virus (WSSV) was purified from hemolymph of infected shrimp. After nucleic acid extraction from the purified virus particles, EcoR I-digested fragments of the WSSV genome were cloned; three of these fragments were used as non-radioactive probes labeled with DIG-11-dUTP. The probes hybridized in situ, with sections located in the nuclei of all WSSV-infected tissues. The virus was detected in the gill, stomach, epidermis, and connective tissue and so on, but not detected in healthy shrimp tissues and epithelial cells of hepatopancreatic tubules of diseased shrimp.

  15. Catalyzed reported deposition-fluorescence in situ hybridization protocol to evaluate phagotrophy in mixotrophic protists.

    PubMed

    Medina-Sánchez, Juan M; Felip, Marisol; Casamayor, Emilio O

    2005-11-01

    We describe a catalyzed reported deposition-fluorescence in situ hybridization (CARD-FISH) protocol particularly suited to assess the phagotrophy of mixotrophic protists on prokaryotes, since it maintains cell and plastid integrity, avoids cell loss and egestion of prey, and allows visualization of labeled prey against plastid autofluorescence. This protocol, which includes steps such as Lugol's-formaldehyde-thiosulfate fixation, agarose cell attachment, cell wall permeabilization with lysozyme plus achromopeptidase, and signal amplification with Alexa-Fluor 488, allowed us to detect almost 100% of planktonic prokaryotes (Bacteria and Archaea) and, for the first time, to show archaeal cells ingested by mixotrophic protists.

  16. In situ pneumococcal vaccine production and delivery through a hybrid biological-biomaterial vector

    PubMed Central

    Li, Yi; Beitelshees, Marie; Fang, Lei; Hill, Andrew; Ahmadi, Mahmoud Kamal; Chen, Mingfu; Davidson, Bruce A.; Knight, Paul; Smith, Randall J.; Andreadis, Stelios T.; Hakansson, Anders P.; Jones, Charles H.; Pfeifer, Blaine A.

    2016-01-01

    The type and potency of an immune response provoked during vaccination will determine ultimate success in disease prevention. The basis for this response will be the design and implementation of antigen presentation to the immune system. Whereas direct antigen administration will elicit some form of immunological response, a more sophisticated approach would couple the antigen of interest to a vector capable of broad delivery formats and designed for heightened response. New antigens associated with pneumococcal disease virulence were used to test the delivery and adjuvant capabilities of a hybrid biological-biomaterial vector consisting of a bacterial core electrostatically coated with a cationic polymer. The hybrid design provides (i) passive and active targeting of antigen-presenting cells, (ii) natural and multicomponent adjuvant properties, (iii) dual intracellular delivery mechanisms, and (iv) a simple formulation mechanism. In addition, the hybrid format enables device-specific, or in situ, antigen production and consolidation via localization within the bacterial component of the vector. This capability eliminates the need for dedicated antigen production and purification before vaccination efforts while leveraging the aforementioned features of the overall delivery device. We present the first disease-specific utilization of the vector toward pneumococcal disease highlighted by improved immune responses and protective capabilities when tested against traditional vaccine formulations and a range of clinically relevant Streptococcus pneumoniae strains. More broadly, the results point to similar levels of success with other diseases that would benefit from the production, delivery, and efficacy capabilities offered by the hybrid vector. PMID:27419235

  17. In situ synthesis of C/Cu/ZnO porous hybrids as anode materials for lithium ion batteries.

    PubMed

    Wang, Yuyan; Jiang, Xiaojian; Yang, Lishan; Jia, Ning; Ding, Yi

    2014-02-12

    Porous structure and surface modification have been widely studied in applying metal oxide nanomaterials as Li-ion battery anodes for overcoming problems such as poor conductivity and large volume variation. Here, we demonstrate a direct triple-decomposition process for the in situ synthesis of C/Cu/ZnO porous hybrids. In a typical porous structure, 5-10 nm sized ZnO and Cu nanoparticles aggregate randomly and are modified with carbon layers in thickness of 1 nm. Moreover, the resulted hybrid nanostructures show a high and stable specific capacity of 818 mAh g(-1) at a current rate of 50 mA g(-1) with almost 100% capacity retention for up to 100 cycles when used an anode material for lithium ion batteries. By combination of the structural analyses and electrochemical behaviors, it could be speculated that the porous structure and the modifications of copper nanoparticles and carbon layers are mainly responsible for the dramatically improved electrochemical performance of ZnO anodes. PMID:24417493

  18. Confocal Raman microscopy and fluorescent in situ hybridization - A complementary approach for biofilm analysis.

    PubMed

    Kniggendorf, Ann-Kathrin; Nogueira, Regina; Kelb, Christian; Schadzek, Patrik; Meinhardt-Wollweber, Merve; Ngezahayo, Anaclet; Roth, Bernhard

    2016-10-01

    We combine confocal Raman microscopy (CRM) of wet samples with subsequent Fluorescent in situ hybridization (FISH) without significant limitations to either technique for analyzing the same sample of a microbial community on a cell-to-cell basis. This combination of techniques allows a much deeper, more complete understanding of complex environmental samples than provided by either technique alone. The minimalistic approach is based on laboratory glassware with micro-engravings for reproducible localization of the sample at cell scale combined with a fixation and de- and rehydration protocol for the respective techniques. As proof of concept, we analyzed a floc of nitrifying activated sludge, demonstrating that the sample can be tracked with cell-scale precision over different measurements and instruments. The collected information includes the microbial content, spatial shape, variant chemical compositions of the floc matrix and the mineral microparticles embedded within. In addition, the direct comparison of CRM and FISH revealed a difference in reported cell size due to the different cell components targeted by the respective technique. To the best of our knowledge, this is the first report of a direct cell-to-cell comparison of confocal Raman microscopy and Fluorescent in situ hybridization analysis performed on the same sample. An adaptation of the method to include native samples as a starting point is planned for the near future. The micro-engraving approach itself also opens up the possibility of combining other, functionally incompatible techniques as required for further in-depth investigations of low-volume samples. PMID:27423128

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

    PubMed

    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.

  20. Detection of a complex translocation using fluorescent in situ hybridization (FISH)

    SciTech Connect

    Rosen, B.A.; Abuelo, D.N.; Mark, H.F.

    1994-09-01

    The use of fluorescent in situ hybridization (FISH) allowed the detection of a complex 3-way translocation in a patient with multiple congenital malformations and mental retardation. The patient was a 10-year-old girl with mental retardation, seizures, repaired cleft palate, esotropia, epicanthal folds, broad nasal bridge, upward slanting palpebral fissures, single transverse palmar crease, brachydactyly, hypoplastic nails, ectrodactyly between the third and fourth right toes, and hypoplasia of the left third toe. Chromosome analysis performed at birth was reported as normal. We performed high resolution banding analysis which revealed an apparently balanced translocation between chromosomes 2 and 9. However, because of her multiple abnormalities, further studies were ordered. Fluorescent in situ hybridization (FISH) using chromosome painting probes revealed a karyotype of 46,XX,t(2;8;9) (2pter{yields}q31::8q21.2{yields}8qter; 8pter{yields}q21.2::2q31{yields}q34::9q34{yields}qter; 9pter{yields}q34::2q34{yields}qter). The 3-way translocation appears to be de novo, as neither parent is a translocation carrier. This case illustrates the importance of using FISH to further investigate cases of apparently balanced translocations in the presence of phenotypic abnormalities and/or mental retardation.

  1. Gene numerical imbalances in cytological specimens based on fluorescence/chromogenic in situ hybridization analysis.

    PubMed

    Tsiambas, E; Karameris, A; Lygeros, M; Athanasiou, A E; Salemis, N S; Gourgiotis, S; Ragkos, V; Metaxas, G E; Vilaras, G; Patsouris, E

    2012-01-01

    Design and development of novel targeted therapeutic strategies is an innovation in handling patients with solid malignancies including breast, colon, lung, head & neck or even pancreatic and hepatocellular carcinoma. For a long time, immunohistocytochemistry (IHC/ICC) has been performed as a routine method in almost all labs for evaluating protein expression. Modern molecular approaches show that identification of specific structural and numerical imbalances regarding genes involved in signal transduction pathways provide important data to the oncologists. Alterations in molecules such as epidermal growth factor receptor (EGFR), HER2/neu, PTEN or Topoisomerase IIa affect the response rates to specific chemotherapeutic agents modifying also patients' prognostic rates. In situ hybridization (ISH) techniques based on fluorescence and chromogenic variants (FISH/CISH) or silver in situ hybridization (SISH) are applicable in both tissue and cell substrates. Concerning cytological specimens, FISH/CISH analysis appears to be a fast and very accurate method in estimating gene/chromosome ratios. In this paper, we sought to evaluate the usefulness of FISH/ CISH analysis in cytological specimens, describing also the advantages and disadvantages of these methods from the technical point of view. PMID:23033306

  2. Ion cyclotron instability at Io: Hybrid simulation results compared to in situ observations

    NASA Astrophysics Data System (ADS)

    Šebek, Ondřej; Trávníček, Pavel M.; Walker, Raymond J.; Hellinger, Petr

    2016-08-01

    We present analysis of global three-dimensional hybrid simulations of Io's interaction with Jovian magnetospheric plasma. We apply a single-species model with simplified neutral-plasma chemistry and downscale Io in order to resolve the ion kinetic scales. We consider charge exchange, electron impact ionization, and photoionization by using variable rates of these processes to investigate their impact. Our results are in a good qualitative agreement with the in situ magnetic field measurements for five Galileo flybys around Io. The hybrid model describes ion kinetics self-consistently. This allows us to assess the distribution of temperature anisotropies around Io and thereby determine the possible triggering mechanism for waves observed near Io. We compare simulated dynamic spectra of magnetic fluctuations with in situ observations made by Galileo. Our results are consistent with both the spatial distribution and local amplitude of magnetic fluctuations found in the observations. Cyclotron waves, triggered probably by the growth of ion cyclotron instability, are observed mainly downstream of Io and on the flanks in regions farther from Io where the ion pickup rate is relatively low. Growth of the ion cyclotron instability is governed mainly by the charge exchange rate.

  3. Methods for simultaneous interphase in situ hybridization and nuclear antigen immunocytochemistry in T47-D cells.

    PubMed

    Mialhe, A; Cassanelli, S; Louis, J; Seigneurin, D

    1996-02-01

    Procedures that combine immunocytochemistry (ICC) and in situ hybridization (ISH) techniques are now used to investigate phenotype/genotype relationships in the same cells. In this report we describe three rapid procedures for simultaneous detection of a nuclear antigen, progesterone receptors (PR), and the centromeric region of chromosome 11 (to which the human PR gene has been assigned) in T47-D cells. Proteins were stained by precipitates of horseradish peroxidase-diaminobenzidine (PO-DAB, brown color), alkaline phosphatase-Fast Red (APase-Fast Red, red color) or alkaline phosphatase-nitroblue tetrazolium-X-phosphate (APase-NBT-X-Phosphate, blue color) respectively. To obtain a suitable contrast for the two labels, we detected DNA on PO-DAB and APase-NBT-X-phosphate-immunostained cells with interphasic fluorescent in situ hybridization (FISH). By contrast, we combined the APase-Fast Red ICC with an immunocytochemical ISH using alkaline phosphatase-NBT-X-phosphate detection. Only the procedure combining APase-NBT-X-phosphate ICC and FISH ensures optimal visualization of both the PR content and the number of chromosome 11. This method easily provides simultaneous localization of DNA and protein targets in the same cells and should be applicable to many other situations. PMID:8609377

  4. In situ hybridization analysis of human papillomavirus DNA in oral mucosal lesions.

    PubMed

    Zeuss, M S; Miller, C S; White, D K

    1991-06-01

    Commercial biotinylated DNA probes specific for human papillomavirus (HPV) types 6 and 11; 16 and 18; and 31, 33, and 35 were used for in situ hybridization analysis of 105 oral mucosal specimens from 5 cases of verruca vulgaris, 15 cases of condyloma acuminatum, 30 cases of squamous papilloma, 20 cases of hyperkeratosis/acanthosis, 15 cases of epithelial dysplasia, 5 cases of carcinoma in situ, and 15 cases of squamous cell carcinoma. Positive hybridization signals were found in 26 specimens (24.8%). Only HPV-6/11 was detected. HPV DNA occurred significantly more often (p less than 0.005, chi-square analysis) in condyloma acuminatum (100%) and verruca vulgaris (100%) than squamous papilloma (13.3%), hyperkeratotic/acanthotic lesions (10%), and malignant and premalignant lesions (0%). The tongue (19.1%) and labial epithelium (17.1%) were infected most frequently. Nuclear reaction products indicating HPV infection were associated primarily with koilocytes. These results demonstrate the usefulness of commercial biotinylated probes for HPV DNA analysis in routine paraffin-embedded lesion specimens. They confirm HPV involvement in benign lesions of the oral mucosa but fail to associate HPV infection with oral cancer and precancer.

  5. Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)

    SciTech Connect

    Deutsch, Eric W.; Ball, Catherine A.; Berman, Jules J.; Bova, G. Steven; Brazma, Alvis; Bumgarner, Roger E.; Campbell, David; Causton, Helen C.; Christiansen, Jeff; Daian, Fabrice; Dauga, Delphine; Davidson, Duncan; Gimenez, Gregory; Goo, Young Ah; Grimmond, Sean; Henrich, Thorsten; Herrmann, Bernhard G.; Johnson, Michael H.; Korb, Martin; Mills, Jason C.; Oudes, Asa; Parkinson, Helen E.; Pascal, Laura E.; Pollet, Nicolas; Quackenbush, John; Ramaialison, Mirana; Ringwald, Martin; Salgado, David; Sansone, Susanna A.; Sherlock, Gavin; Stoeckert, Christian Jr. J.; Swedlow, Jason; Taylor, Ronald C.; Walasheck, Laura; Warford, Anthony; Wilkinson, David G.; Zhou, Yi; Zon, Leonard I.; Liu, Alvin Y.; True, Lawrence D.

    2008-03-28

    Herein, we present for consideration such a specification, termed “Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)”. It is modelled after the MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments. The purpose of data standards like MIAME and MISFISHIE is to specify information content without specifying a format for encoding that information. The MISFISHIE standard specifies six sections of information that must be detailed for each experiment: Experimental Design, Specimens, Reporters, Staining, Imaging Data, and Image Characterizations. A general checklist is provided to quickly and efficiently establish adherence to the standard. Currently, we estimate that most articles describing gene expression localization studies, such as in situ hybridization assays, do not fully provide the minimum information needed for independent verification of results. In a small survey of 32 journal articles from the past five years, we found that nearly 90% did not meet all the requirements, although many met most of them. We propose that requiring authors to provide the minimum experimental detail about gene expression localization experiments would substantially facilitate reproducibility and interpretability of results by fellow investigators. Furthermore, inclusion of specific experimental details such as reagents and methods in publications would ultimately allow others to readily search the literature for these data items, especially given the ongoing trend towards open access full text journals.

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

    PubMed Central

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

    1996-01-01

    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

  7. In Situ Hybridization Methods for Mouse Whole Mounts and Tissue Sections with and Without Additional β-Galactosidase Staining

    PubMed Central

    Komatsu, Yoshihiro; Kishigami, Satoshi; Mishina, Yuji

    2014-01-01

    In situ hybridization is a powerful method for detecting endogenous mRNA sequences in morphologically preserved samples. We provide in situ hybridization methods, which are specifically optimized for mouse embryonic samples as whole mounts and section tissues. Additionally, β-Galactosidase (β-gal) is a popular reporter for detecting the expression of endogenous or exogenous genes. We reveal that 6-chloro-3-indoxyl-β-D-galactopyranoside (S-gal) is a more sensitive substrate for β-gal activity than 5-bromo-4-chloro-3-indolyl-β-D-galactoside (X-gal). S-gal is advantageous where β-gal activity is limited including early stage mouse embryos. As a result of the increased sensitivity as well as the color compatibility of S-gal, we successfully combined β-gal staining using S-gal with in situ hybridization using DIG-labeled probes in both whole mounts and sections. PMID:24318810

  8. 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.

    SciTech Connect

    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.

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

    PubMed

    Anthony, Giovanni; Lee, Ju-Ahng

    2016-01-01

    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. PMID:27489962

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

    PubMed Central

    Anthony, Giovanni; Lee, Ju-Ahng

    2016-01-01

    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. PMID:27489962

  11. Portable apparatus for in situ x-ray diffraction and fluorescence analyses of artworks.

    PubMed

    Eveno, Myriam; Moignard, Brice; Castaing, Jacques

    2011-10-01

    A portable X-ray fluorescence/X-ray diffraction (XRF/XRD) system for artwork studies has been designed constructed and tested. It is based on Debye Scherrer XRD in reflection that takes advantage of many recent improvements in the handling of X-rays (polycapillary optics; advanced two-dimensional detection). The apparatus is based on a copper anode air cooled X-ray source, and the XRD analysis is performed on a 5-20 μm thick layer from the object surface. Energy dispersive XRF elemental analysis can be performed at the same point as XRD, giving elemental compositions that support the interpretation of XRD diagrams. XRF and XRD analyses were tested to explore the quality and the limits of the analytical technique. The XRD diagrams are comparable in quality with diagrams obtained with conventional laboratory equipment. The mineral identification of materials in artwork is routinely performed with the portable XRF-XRD system. Examples are given for ceramic glazes containing crystals and for paintings where the determination of pigments is still a challenge for nondestructive analysis. For instance, lead compounds that provide a variety of color pigments can be easily identified as well as a pigment such as lapis lazuli that is difficult to identify by XRF alone. More than 70 works of art have been studied in situ in museums, monuments, etc. In addition to ceramics and paintings, these works include bronzes, manuscripts, etc., which permit improvement in the comprehension of ancient artistic techniques. PMID:21615981

  12. Portable apparatus for in situ x-ray diffraction and fluorescence analyses of artworks.

    PubMed

    Eveno, Myriam; Moignard, Brice; Castaing, Jacques

    2011-10-01

    A portable X-ray fluorescence/X-ray diffraction (XRF/XRD) system for artwork studies has been designed constructed and tested. It is based on Debye Scherrer XRD in reflection that takes advantage of many recent improvements in the handling of X-rays (polycapillary optics; advanced two-dimensional detection). The apparatus is based on a copper anode air cooled X-ray source, and the XRD analysis is performed on a 5-20 μm thick layer from the object surface. Energy dispersive XRF elemental analysis can be performed at the same point as XRD, giving elemental compositions that support the interpretation of XRD diagrams. XRF and XRD analyses were tested to explore the quality and the limits of the analytical technique. The XRD diagrams are comparable in quality with diagrams obtained with conventional laboratory equipment. The mineral identification of materials in artwork is routinely performed with the portable XRF-XRD system. Examples are given for ceramic glazes containing crystals and for paintings where the determination of pigments is still a challenge for nondestructive analysis. For instance, lead compounds that provide a variety of color pigments can be easily identified as well as a pigment such as lapis lazuli that is difficult to identify by XRF alone. More than 70 works of art have been studied in situ in museums, monuments, etc. In addition to ceramics and paintings, these works include bronzes, manuscripts, etc., which permit improvement in the comprehension of ancient artistic techniques.

  13. Coordinated In Situ Analyses of Organic Nanoglobules in the Sutter's Mill Meteorite

    NASA Technical Reports Server (NTRS)

    Nakamura--Messenger, K.; Messenger, S.; Keller, L. P.; Clemett, S. J.; Nguyen, A. N.; Gibson, E. K.

    2013-01-01

    The Sutter s Mill meteorite is a newly fallen carbonaceous chondrite that was collected and curated quickly after its fall [1]. Preliminary petrographic and isotopic investigations suggest affinities to the CM2 carbonaceous chondrites. The primitive nature of this meteorite and its rapid recovery provide an opportunity to investigate primordial solar system organic matter in a unique new sample. Organic matter in primitive meteorites and chondritic porous interplanetary dust particles (CP IDPs) is commonly enriched in D/H and N-15/N-14 relative to terrestrial values [2-4]. These anomalies are ascribed to the partial preservation of presolar cold molecular cloud material [2]. Some meteorites and IDPs contain gm-size inclusions with extreme H and N isotopic anomalies [3-5], possibly due to preserved primordial organic grains. The abundance and isotopic composition of C in Sutter's Mill were found to be similar to the Tagish Lake meteorite [6]. In the Tagish Lake meteorite, the principle carriers of large H and N isotopic anomalies are sub-micron hollow organic spherules known as organic nanoglobules [7]. Organic nanoglobules are commonly distributed among primitive meteorites [8, 9] and cometary samples [10]. Here we report in-situ analyses of organic nano-globules in the Sutter's Mill meteorite using UV fluorescence imaging, Fourier-transform infrared spectroscopy (FTIR), scanning transmission electron microscopy (STEM), NanoSIMS, and ultrafast two-step laser mass spectrometry (ultra-L2MS).

  14. Random amplified polymorphic DNA analysis, genome size, and genomic in situ hybridization of triploid viviparous onions

    PubMed

    Puizina; Javornik; Bohanec; Schweizer; Maluszynska; Papes

    1999-12-01

    Triploid viviparous onions (Allium cepa L. var. viviparum Metzg. (ALEF.), auct.), (2n = 3x = 24), are known in some countries only as a rare relic crop, while in other parts of the world they are still traditionally or even commercially cultivated. Results indicating an identical random amplified polymorphic DNA (RAPD) banding pattern and the same DNA content (2C = 43.4 pg) establish the high genetic similarity and the unique origin of the Croatian clone Ljutika and the Indian clone Pran. In order to determine the parental Allium species of these natural triploid hybrids, genomic fluorescent in situ hybridization (GISH) was applied. Biotinylated genomic DNAs from six diploid Allium species (A. cepa L., A. fistulosum L., A. roylei Stearn, A. vavilovii M. Pop. et Vved., A. galanthum Kar. et Kir., A. oschaninii O. Fedtsch.) were used as probes in this study. While probes obtained from genomic DNA of A. cepa, A. vavilovii, and A. roylei hybridized to somatic chromosomes of Ljutika probes from A. fistulosum, A. galanthum, and A. oschaninii did not. The DNA probes of A. cepa and A. roylei each completely or predominantly labelled one genome (eight chromosomes). A few chromosomes, the markers of the triploid karyotype, were not completely labelled by any probe applied. Our GISH results indicate that triploid viviparous onions might possess a complex triparental genome organization. PMID:10659789

  15. In situ composition and luminescence of terbium coordination polymers/PEMA hybrid thick films

    NASA Astrophysics Data System (ADS)

    Yan, Bing; Wang, Qian-Ming

    2004-12-01

    Some terbium coordination polymers with infinite chain polymeric structures were in situ composed with ethyl methacrylate (EMA). With the polymerization of EMA monomer and the formation of terbium coordination polymers of methylbenzoic acid and 2-chloro benzoic acid, the transparent hybrid thick films composed by [Tb(OMBA)3]n ([Tb(MMBA)3]n, [Tb(OCBA)3]n) and poly ethyl methacrylate (PEMA) have been achieved. The luminescence properties and energy transfer for these polymeric composite films were studied with absorption spectra, fluorescent excitation and emission spectra in detail. All the hybrid thick films composed with terbium coordination polymers show the characteristic strong green emission of terbium ions, which implies the same energy transfer mechanism as the pure complex and the hybrid composite film is a suitable substrate for the luminescence of terbium ions. In the range of composing concentration of luminescent species (0.005, 0.01, 0.025, 0.05, 0.1 and 0.2 mmol/7.5 ml EMA), emission intensities increases with the increasing of corresponding composing concentration and concentration quenching effect has not taken place.

  16. Identification of two Skeletonema costatum-like diatoms by fluorescence in situ hybridization

    NASA Astrophysics Data System (ADS)

    Zhang, Baoyu; Chen, Guofu; Wang, Guangce; Lu, Douding

    2010-03-01

    A harmful algae bloom (HAB) is a dense aggregation of algae in a marine or aquatic environment that can result in significant environmental problems. To forecast the occurrence of HAB, development of a rapid and precise detection method is urgently required. In this study, two Skeletonema costatum-like diatoms (SK-1 and SK-2), were identified morphologically under a light microscope, and detected using fluorescent in situ hybridization (FISH). Strain SK-1 was isolated from a frequently HAB affected area of the East China Sea, and strain SK-2 from an aquatic farm in Qingdao, China. Fluorescent DNA probes were designed that were complementary to the ITS sequence (including 5.8S rDNA) of strain SK-1. After hybridization, strong green fluorescence was observed in cells of strain SK-1 under an epifluorescence microscope; however, no such fluorescence was observed with strain SK-2, which indicates that probes hybridized only the DNA of the target strain, SK-1, in species-specific manner, and that the two strains do not belong to a same species. This finding was confirmed by ITS sequence analysis. The FISH technique used in this study was sensitive, simple, and rapid, and is a promising tool for detecting target HAB species in natural environments.

  17. [Quantitative use of fluorescence in situ hybridization to detect syntrophic acetogenic bacteria in anaerobic environmental samples].

    PubMed

    Li, Yan-Na; Xu, Ke-Wei; Du, Guo-Cheng; Chen, Jian; Liu, He

    2007-12-01

    Syntrophic acetogenic bacteria, an important functional one in anaerobic habitats, were detected and counted by fluorescence in situ hybridization (FISH) technology by using 16S rRNA-based oligonucleotide probes. For enumeration and quantification of the targeted bacteria, an attempt was made to optimize the hybridization conditions. The optimum conditions are as follows: a fixation time of 19h, a dehydrated time of 5 min, and a formamide concentration of 55% in hybridized solution. The abundance of syntrophic acetogenic bacteria of different environmental samples were quantified by FISH and the results showed that Upflow Anaerobic Sludge Reactor (UASB) treating STHZ high-concentration organic wastewater and the digestive tract of some animals were the main habitats of syntrophic acetogenic bacteria. The numbers of syntrophic acetogenic bacteria in UASB and cattle manure were 1.70 x 10(9) cells/mL sample and 6.50 x 10(8) cells/mL sample, respectively. Meanwhile, the sediments of rivers and lakes existed less of the bacteria and the contents of them were just about 1.20 x 10(8) cells/mL sample in Taihu lake.

  18. [Fluorescence in situ hybridization with DNA probes derived from individual chromosomes and chromosome regions].

    PubMed

    Bogomolov, A G; Karamysheva, T V; Rubtsov, N B

    2014-01-01

    A significant part of the eukaryotic genomes consists of repetitive DNA, which can form large clusters or distributed along euchromatic chromosome regions. Repeats located in chromosomal regions make a problem in analysis and identification of the chromosomal material with fluorescence in situ hybridization (FISH). In most cases, the identification of chromosome regions using FISH requires detection of the signal produced with unique sequences. The feasibility, advantages and disadvantages of traditional methods of suppression of repetitive DNA hybridization, methods of repeats-free probe construction and methods of chromosome-specific DNA sequences visualization using image processing of multicolor FISH results are considered in the paper. The efficiency of different techniques for DNA probe generation, different FISH protocols, and image processing of obtained microscopic images depends on the genomic size and structure of analyzing species. This problem was discussed and different approaches were considered for the analysis of the species with very large genome, rare species and species which specimens are too small in size to obtain the amount of genomic and Cot-1 DNA required for suppression of repetitive DNA hybridization.

  19. Detection of water buffalo sex chromosomes in spermatozoa by fluorescence in situ hybridization.

    PubMed

    Révay, T; Kovács, A; Presicce, G A; Rens, W; Gustavsson, I

    2003-10-01

    In order to identify X- and Y-bearing spermatozoa in water buffalo by fluorescence in situ hybridization (FISH), some available probes of closely related species were examined. An X- and Y-specific probe set, made from flow sorted yak chromosomes, labelled in somatic metaphases of water buffalo the whole X and Y, respectively, except their centromere regions. A cattle Y-chromosome repeat sequence (BC1.2) showed strong signal on the telomere region of the buffalo Y-chromosome, demonstrating the evolutionary conservation of this locus in water buffalo. In hybridization experiments with spermatozoa from five buffaloes, the yak X-Y paint set demonstrated clear signals in more than 92% (46.8% X and 45.8% Y) of the cells. Using the cattle Y-chromosome specific BC1.2 probe, clear hybridization signal was detected in more than 48% of the cells. Statistical analysis showed that there was no significant difference between bulls or from the expected 50 : 50 ratio of X- and Y-bearing cells. The probes presented here are reliable to assess separation of X- and Y-bearing spermatozoa.

  20. PCR-derived ssDNA probes for fluorescent in situ hybridization to HIV-1 RNA.

    PubMed

    Knuchel, M C; Graf, B; Schlaepfer, E; Kuster, H; Fischer, M; Weber, R; Cone, R W

    2000-02-01

    We developed a simple and rapid technique to synthesize single-stranded DNA (ssDNA) probes for fluorescent in situ hybridization (ISH) to human immunodeficiency virus 1 (HIV-1) RNA. The target HIV-1 regions were amplified by the polymerase chain reaction (PCR) and were simultaneously labeled with dUTP. This product served as template for an optimized asymmetric PCR (one-primer PCR) that incorporated digoxigenin (dig)-labeled dUTP. The input DNA was subsequently digested by uracil DNA glycosylase, leaving intact, single-stranded, digoxigenin-labeled DNA probe. A cocktail of ssDNA probes representing 55% of the HIV-1 genome was hybridized to HIV-1-infected 8E5 T-cells and uninfected H9 T-cells. For comparison, parallel hybridizations were done with a plasmid-derived RNA probe mix covering 85% of the genome and a PCR-derived RNA probe mix covering 63% of the genome. All three probe types produced bright signals, but the best signal-to-noise ratios and the highest sensitivities were obtained with the ssDNA probe. In addition, the ssDNA probe syntheses generated large amounts of probe (0.5 to 1 microg ssDNA probe per synthesis) and were easier to perform than the RNA probe syntheses. These results suggest that ssDNA probes may be preferable to RNA probes for fluorescent ISH. (J Histochem Cytochem 48:285-293, 2000)

  1. Characterization of honeybee (Apis mellifera L.) chromosomes using repetitive DNA probes and fluorescence in situ hybridization.

    PubMed

    Beye, M; Moritz, R F

    1995-01-01

    Two different repetitive DNA probes of Apis mellifera and ribosomal DNA from Drosophila melanogaster were used to characterize the chromosomal set of the honeybee (n = 16). The probes were hybridized to chromosome preparations of haploid testis tissue from drone larvae using fluorescence in situ hybridization (FISH). The honeybee probes hybridized to the telomeric (Alu I family) and centromeric region (Ava I family) of most chromosomes. The rDNA probe labeled two chromosomes only. Combination of the three probes yielded labeled patterns allowing us to identify each chromosome of the honeybee individually. This is the first report of an unambiguous identification of the chromosomal set of the honeybee, since classical banding techniques failed to yield clear patterns for identification. The consensus sequence of the centromeric reiterated probe (Ava I family) has a length of about 550 nucleotides and shows no homology to other known sequences. However, the structural organization of a 130-nucleotides long motif forming the unusually homogeneous 550 nucleotides repeat is similar to those found in mammals' repetitive DNAs.

  2. [Detection of numerical aberrations in chromosomes by fluorescence in situ hybridization in fine needle aspirates in the preoperative diagnosis of cancer].

    PubMed

    Noguchi, S; Tsukamoto, F; Miyoshi, Y; Inaji, H; Watatani, M; Sasa, M; Inazawa, J; Takami, S

    1999-12-01

    Fine needle aspiration (FNA) samples were obtained from 176 breast tumors suspected of malignancy, which were then subjected to conventional cytological and fluorescence in situ hybridization (FISH) analyses using the centromeric probes for chromosomes 1, 11, and 17. Histological examination revealed 157 breast cancers and 19 benign diseases (ten fibroadenomas, six intraductal papillomas, one intracystic papilloma, and two ADH). Sensitivity, specificity, and diagnostic accuracy were 85.4% 94.7%, and 86.4%, respectively, for cytology and 90.4%, 100%, and 91.5%, respectively, for FISH. These results demonstrate that FISH diagnosis of FNA samples has a diagnostic accuracy comparable to that of conventional cytology. PMID:10635294

  3. Fluorescent in situ hybridization assessment of chromosome 8 copy number in breast cancer.

    PubMed

    Afify, A; Bland, K I; Mark, H F

    1996-01-01

    Conventional cytogenetics of breast and other solid tumors has been hampered by a number of factors. An analysis of breast tumor tissues was therefore undertaken using fluorescent in situ hybridization (FISH). A total of 34 specimens were analyzed using a chromosome 8-specific alpha-satellite probe. Various approaches were tested and compared. Among 30 informative samples, 11 infiltrating ductal carcinomas, not otherwise specified (NOS), 5 ductal carcinomas in situ, 5 lobular carcinomas, 3 papillary carcinomas, and 6 benign lesions were studied. Of the 11 cases of infiltrating ductal carcinomas (NOS) analyzed, four cases showed 3 signals, one case showed 4 signals, and the rest showed 2 signals. Of the 5 cases of ductal carcinoma in situ samples, 1 showed 3 signals and the other 4 cases showed 2 signals. All cases of lobular carcinomas, papillary carcinomas, and benign lesions showed 2 signals. We inferred from these data that 36% of the infiltrating ductal carcinomas (NOS) were trisomic and 9% were tetrasomic, whereas 20% of the ductal carcinomas in situ were trisomic. All samples from lobular carcinomas, papillary carcinomas, and the benign lesions were disomic. From our preliminary data, it can further be concluded that a subset of breast cancer is characterized by chromosome 8 trisomy. These data are consistent with an ever-increasing database on the association of chromosomal 8 trisomy with other cancers such as leukemia, lymphoma, prostate cancer, ovarian carcinoma, salivary gland tumor, malignant melanoma, desmoid tumors, and recently gestational trophoblastic disease. It is also noted that the ability to analyze formalin-fixed, paraffin-embedded archival material will enable a more comprehensive cytogenetic study of breast cancer than is currently available.

  4. Simultaneous visualization of different genomes (J, JSt and St) in a Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid (Poaceae) and in its parental species by multicolour genomic in situ hybridization (mcGISH).

    PubMed

    Kruppa, Klaudia; Molnár-Láng, Márta

    2016-01-01

    Multicolour genomic in situ hybridization (mcGISH) using total genomic DNA probes from Thinopyrum bessarabicum (Săvulescu & Rayss, 1923) Á. Löve, 1984 (genome J(b) or E(b), 2n = 14), and Pseudoroegneria spicata (Pursh, 1814) Á. Löve, 1980 (genome St, 2n = 14) was used to characterize the mitotic metaphase chromosomes of a synthetic hybrid of Thinopyrum intermedium (Host, 1805) Barkworth & D.R. Dewey, 1985 and Thinopyrum ponticum (Podpěra, 1902) Z.-W. Liu et R.-C.Wang, 1993 named "Agropyron glael" and produced by N.V. Tsitsin in the former Soviet Union. The mcGISH pattern of this synthetic hybrid was compared to its parental wheatgrass species. Hexaploid Thinopyrum intermedium contained 19 J, 9 J(St) and 14 St chromosomes. The three analysed Thinopyrum ponticum accessions had different chromosome compositions: 43 J + 27 J(St) (PI531737), 40 J + 30 J(St) (VIR-44486) and 38 J + 32 J(St) (D-3494). The synthetic hybrid carried 18 J, 28 J(St) and 8 St chromosomes, including one pair of J-St translocation and/or decreased fluorescent intensity, resulting in unique hybridization patterns. Wheat line Mv9kr1 was crossed with the Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid in Hungary in order to transfer its advantageous agronomic traits (leaf rust and yellow rust resistance) into wheat. The chromosome composition of a wheat/A.glael F1 hybrid was 21 wheat + 28 wheatgrass (11 J + 14 J(St)+ 3 S). In the present study, mcGISH involving the simultaneous use of St and J genomic DNA as probes provided information about the type of Thinopyrum chromosomes in a Thinopyrum intermedium/Thinopyrum ponticum synthetic hybrid called A. glael. PMID:27551349

  5. Simultaneous visualization of different genomes (J, JSt and St) in a Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid (Poaceae) and in its parental species by multicolour genomic in situ hybridization (mcGISH).

    PubMed

    Kruppa, Klaudia; Molnár-Láng, Márta

    2016-01-01

    Multicolour genomic in situ hybridization (mcGISH) using total genomic DNA probes from Thinopyrum bessarabicum (Săvulescu & Rayss, 1923) Á. Löve, 1984 (genome J(b) or E(b), 2n = 14), and Pseudoroegneria spicata (Pursh, 1814) Á. Löve, 1980 (genome St, 2n = 14) was used to characterize the mitotic metaphase chromosomes of a synthetic hybrid of Thinopyrum intermedium (Host, 1805) Barkworth & D.R. Dewey, 1985 and Thinopyrum ponticum (Podpěra, 1902) Z.-W. Liu et R.-C.Wang, 1993 named "Agropyron glael" and produced by N.V. Tsitsin in the former Soviet Union. The mcGISH pattern of this synthetic hybrid was compared to its parental wheatgrass species. Hexaploid Thinopyrum intermedium contained 19 J, 9 J(St) and 14 St chromosomes. The three analysed Thinopyrum ponticum accessions had different chromosome compositions: 43 J + 27 J(St) (PI531737), 40 J + 30 J(St) (VIR-44486) and 38 J + 32 J(St) (D-3494). The synthetic hybrid carried 18 J, 28 J(St) and 8 St chromosomes, including one pair of J-St translocation and/or decreased fluorescent intensity, resulting in unique hybridization patterns. Wheat line Mv9kr1 was crossed with the Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid in Hungary in order to transfer its advantageous agronomic traits (leaf rust and yellow rust resistance) into wheat. The chromosome composition of a wheat/A.glael F1 hybrid was 21 wheat + 28 wheatgrass (11 J + 14 J(St)+ 3 S). In the present study, mcGISH involving the simultaneous use of St and J genomic DNA as probes provided information about the type of Thinopyrum chromosomes in a Thinopyrum intermedium/Thinopyrum ponticum synthetic hybrid called A. glael.

  6. Simultaneous visualization of different genomes (J, JSt and St) in a Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid (Poaceae) and in its parental species by multicolour genomic in situ hybridization (mcGISH)

    PubMed Central

    Kruppa, Klaudia; Molnár-Láng, Márta

    2016-01-01

    Abstract Multicolour genomic in situ hybridization (mcGISH) using total genomic DNA probes from Thinopyrum bessarabicum (Săvulescu & Rayss, 1923) Á. Löve, 1984 (genome Jb or Eb, 2n = 14), and Pseudoroegneria spicata (Pursh, 1814) Á. Löve, 1980 (genome St, 2n = 14) was used to characterize the mitotic metaphase chromosomes of a synthetic hybrid of Thinopyrum intermedium (Host, 1805) Barkworth & D.R. Dewey, 1985 and Thinopyrum ponticum (Podpěra, 1902) Z.-W. Liu et R.-C.Wang, 1993 named „Agropyron glael” and produced by N.V. Tsitsin in the former Soviet Union. The mcGISH pattern of this synthetic hybrid was compared to its parental wheatgrass species. Hexaploid Thinopyrum intermedium contained 19 J, 9 JSt and 14 St chromosomes. The three analysed Thinopyrum ponticum accessions had different chromosome compositions: 43 J + 27 JSt (PI531737), 40 J + 30 JSt (VIR-44486) and 38 J + 32 JSt (D-3494). The synthetic hybrid carried 18 J, 28 JSt and 8 St chromosomes, including one pair of J-St translocation and/or decreased fluorescent intensity, resulting in unique hybridization patterns. Wheat line Mv9kr1 was crossed with the Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid in Hungary in order to transfer its advantageous agronomic traits (leaf rust and yellow rust resistance) into wheat. The chromosome composition of a wheat/A.glael F1 hybrid was 21 wheat + 28 wheatgrass (11 J + 14 JSt+ 3 S). In the present study, mcGISH involving the simultaneous use of St and J genomic DNA as probes provided information about the type of Thinopyrum chromosomes in a Thinopyrum intermedium/Thinopyrum ponticum synthetic hybrid called A. glael. PMID:27551349

  7. WRF/Chem Analyses and Comparisons with In Situ, Aircraft and Satellite Data during MILAGRO

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Dubey, M. K.; Zavala, M. A.; Olsen, S.; Molina, L. T.; de Foy, B.

    2007-05-01

    During March 2006, the Megacity Initiative: Local and Global Research Observations (MILAGRO) field campaign was conducted over the Mexico City area in collaboration with several national and international institutions and agencies. Coordinated aircraft-based and ground-based measurements for gaseous pollutants (CO, O3, NOx, SO2 etc.) and aerosol particles (PM2.5, PM10) were made during MILAGRO supported by extensive satellite observations and modeling activities at various scales. The goal of this study is to examine and compare fully coupled WRF/Chem (Weather Research and Forecasting - Chemistry) model simulations at 3-km resolution with in situ, aircraft and satellite data during MILAGRO. Emissions input data compiled by the Molina Center for Energy and the Environment (MCE2) based on the official emissions inventory for Mexico City in 2004 are used for this study. The emissions rates in this inventory are regarded as representative for typical weekdays in Mexico City. For Saturday and Sunday, the emissions data are obtained by scaling the total emissions rates by 85% and 75%, respectively. For holidays, the emissions data are obtained by scaling the total emissions rates by 90%. Preliminary analyses suggest that the model simulations for gaseous species on weekdays agree reasonably well with observations in terms of pollutant concentrations and diurnal cycles. On weekends and holidays, appreciable discrepancies are noted between the model simulations and the observations, likely reflecting uncertainties in the emissions rates for weekends and holidays. Work is underway to employ the MCE2's newly constructed aerosols emissions data to validate the WRF/Chem simulated aerosol particles and to examine the transport and transformation of aerosols on local and regional scales. In this study, we will also discuss emissions control strategies for alleviating pollution problems in Mexico City based on model sensitivity results.

  8. WRF/Chem Analyses and Comparisons With In Situ, Aircraft and Satellite Data During MILAGRO

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Dubey, M. K.; Olsen, S.; Chylek, P.; Fast, J. D.; Tie, X.; de Foy, B.; Molina, L. T.; Boersma, K. F.; Millet, D. B.; Jacob, D. J.

    2006-12-01

    During March 2006, the Megacity Initiative: Local and Global Research Observations (MILAGRO) field campaign was conducted over the Mexico City area in collaboration with several national and international agencies. The main objective of MILAGRO was to conduct measurements of Mexico City gaseous pollutants (CO, O3, NOx, SO2, etc.) and aerosol particles (PM2.5, PM10), and to study the atmospheric processes leading to the formation of secondary aerosols from precursor gases, and the transport and transformation of these gases and aerosols on local, regional, and global scales. Coordinated aircraft-based and ground-based measurements were made during MILAGRO supported by extensive satellite observations and modeling activities at various scales. The goal of this study is to examine and compare fully coupled WRF/Chem (Weather Research and Forecasting Chemistry) model simulations at 3-km resolution with in situ, aircraft and satellite data during MILAGRO. Emissions inventories from NCAR and PNNL are used for this study. Preliminary analyses suggest that the model simulations during workdays agree reasonably well with observations in terms of pollutant concentrations and diurnal cycles when the PNNL emissions inventory is used; however, the model tends to overestimate the pollutant concentrations when using the NCAR emissions inventory. On weekends and holidays, appreciable discrepancies are noted between the model simulations and observations using either of the emissions inventories, pointing to the need for weekend and workday specific emissions inventories. Work is underway to constrain Mexico City emissions using formaldehyde (HCHO) and NO2 measurements from the Ozone Monitoring Instrument (OMI) on NASA's EOS-Aura satellite. In this study, we will also discuss emissions control strategies for alleviating pollution problems in Mexico City based on model sensitivity results.

  9. A laser GC-IRMS technique for in situ stable isotope analyses of carbonates and phosphates

    NASA Astrophysics Data System (ADS)

    Sharp, Z. D.; Cerling, T. E.

    1996-08-01

    A technique is described whereby in situ carbon and oxygen isotope analyses of carbonates and organic phosphates can be made with the use of a CO 2 laser. The CO 2 gas generated by thermal decarbonation from the laser is entrained in a helium carrier gas, passes through a chromatographic column (GC), and is admitted directly into the isotope ratio mass spectrometer (IRMS). No vacuum systems, pumps, or cryogenic traps are used. All carbonates and biogenic phosphates can be analyzed, no special sample preparation is required and analyses can be made every 3 minutes. The use of a helium carrier gas allows for extremely small samples to be analyzed and the GC column effectively separates CO 2 from any other potential contaminating gases (e.g., SO 2 which is a particular problem in organic apatite). The average reproducibility of calcite, dolomite, magnesite, rhodochrosite, siderite, and smithsonite (ZnCO 3) is 0.29‰ for oxygen and 0.1‰ for carbon (1σ); the most "homogeneous" samples are reproducible to better than 0.1‰ for carbon and 0.2‰ for oxygen. The difference between the laser and conventional values for carbon isotope ratios [Δ 13C (laser-conv)] is 0.05 ± 0.30‰ for all carbonates (excluding siderite). The Δ 18O(laser-conv) value varies from carbonate to carbonate and may be related to the electronegativities of the cations, grain size (or crystallinity), formation of CO and O 2, and reaction with included organic matter. For calcite and rhodochrosite, the Δ 18O(laser-conv) value is 0.3 ± 0.4‰; for siderite, magnesite, and dolomite, the Δ 18O(laser-conv) value is 1.7 ± 0.3‰. The δ 13C values of tooth enamel are the same as those obtained by conventional acid digestion. The laser δ 18O values are equal to the δ 18O values of the phosphate, and approx. 7‰ lighter than the "carbonate" oxygen. The carbonate group in the apatite (equiv. 7.6% oxygen) exchanges with the (PO 4=)-bound oxygen to produce CO 2 with a δ 18O equal to the phosphate

  10. Frequent TMPRSS2-ERG rearrangement in prostatic small cell carcinoma detected by fluorescence in situ hybridization: the superiority of fluorescence in situ hybridization over ERG immunohistochemistry.

    PubMed

    Schelling, Lindsay A; Williamson, Sean R; Zhang, Shaobo; Yao, Jorge L; Wang, Mingsheng; Huang, Jiaoti; Montironi, Rodolfo; Lopez-Beltran, Antonio; Emerson, Robert E; Idrees, Muhammad T; Osunkoya, Adeboye O; Man, Yan-Gao; Maclennan, Gregory T; Baldridge, Lee Ann; Compérat, Eva; Cheng, Liang

    2013-10-01

    Small cell carcinoma of the prostate is both morphologically and immunohistochemically similar to small cell carcinoma of other organs such as the urinary bladder or lung. TMPRSS2-ERG gene fusion appears to be a highly specific alteration in prostatic carcinoma that is frequently shared by small cell carcinoma. In adenocarcinoma, immunohistochemistry for the ERG protein product has been reported to correlate well with the presence of the gene fusion, although in prostatic small cell carcinoma, this relationship is not completely understood. We evaluated 54 cases of small cell carcinoma of the prostate and compared TMPRSS2-ERG gene fusion status by fluorescence in situ hybridization (FISH) to immunohistochemical staining with antibody to ERG. Of 54 cases of prostatic small cell carcinoma, 26 (48%) were positive for TMPRSS2-ERG gene fusion by FISH and 12 (22%) showed overexpression of ERG protein by immunohistochemistry. Of the 26 cases positive by FISH, 11 were also positive for ERG protein by immunohistochemistry. One tumor was positive by immunohistochemistry but negative by FISH. Urinary bladder small cell carcinoma (n = 25) showed negative results by both methods; however, 2 of 14 small cell carcinomas of other organs (lung, head, and neck) showed positive immunohistochemistry but negative FISH. Positive staining for ERG by immunohistochemistry is present in a subset of prostatic small cell carcinomas and correlates with the presence of TMPRSS2-ERG gene fusion. Therefore, it may be useful in confirming prostatic origin when molecular testing is not accessible. However, sensitivity and specificity of ERG immunohistochemistry in small cell carcinoma are decreased compared to FISH.

  11. Enumeration of methanogens with a focus on fluorescence in situ hybridization.

    PubMed

    Kumar, Sanjay; Dagar, Sumit Singh; Mohanty, Ashok Kumar; Sirohi, Sunil Kumar; Puniya, Monica; Kuhad, Ramesh C; Sangu, K P S; Griffith, Gareth Wyn; Puniya, Anil Kumar

    2011-06-01

    Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25034259

  13. Detection of Theiler's virus RNA in mouse central nervous system by in situ hybridization.

    PubMed

    Stroop, W G; Baringer, J R; Brahic, M

    1981-12-01

    The location and distribution of viral RNA were examined in the central nervous system tissues of weanling mice acutely infected with the GDVII strain of Theiler's murine encephalomyelitis virus. Viral RNA was detected by autoradiography following in situ hybridization of a 3H-labeled DNA synthesized in vitro complementary to purified viral RNA. Viral RNA was detected in pyramidal neurons of the hippocampus, cerebral cortex, brainstem nuclei, thalamus, basal ganglia, and spinal cord. Autoradiographic grains could be detected in the axonal and dendritic processes of many infected neurons. No viral RNA was detected in any cell of the cerebellum or white matter. In addition to demonstrating the location of viral RNA in infected central nervous system tissues, and hence the sites of viral replication during this acute polioencephalomyelitis, they indicate that necrosis of hippocampal neurons is due to lytic infection, rather than to hypoxia.

  14. Chromosomal loci of 50 human keratinocyte cDNAs assigned by fluorescence in situ hybridization

    SciTech Connect

    Morishima, Yohich; Ariyama, Takeshi; Yamanishi, Kiyofumi

    1995-07-20

    The chromosomal loci of expressed genes provide useful information for a candidate gene approach to the genes responsible for genetic diseases. A large set of randomly isolated cDNAs catalogued by partial sequencing can serve as a resource for accessing and isolating these disease genes. Using fluorescence in situ hybridization, we examined the chromosomal loci of 217 human keratinocyte-derived cDNAs, with independent novel sequence tags at the 3{prime} end region. Among them, we determined the loci of 50 cDNAs. Single-pass sequencing of these from the 5{prime} ends indicated that 39 cDNAs still can be produced for new genes. These cDNAs with identified chromosomal loci are powerful tools that can be used to help elucidate the genes responsible for hereditary skin disorders. 42 refs., 3 figs., 2 tabs.

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

    SciTech Connect

    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.

  16. Partial trisomy 13q identified by sequential fluorescence in situ hybridization

    SciTech Connect

    Gopal Rao, V.V.N.; Carpenter, N.J.; Gucsavas, M.

    1995-07-31

    We report on a 19-month-old boy with partial trisomy 13q resulting from a probable balanced translocation involving chromosomes 1 and 13. The infant presented with omphalocele, malrotation, microcephaly with overriding skull bones, micrognathia, apparently low-set ears, rocker-bottom feet, and congenital heart disease, findings suggestive of trisomy 13. Karyotypic studies from peripheral blood lymphocytes documented an unbalanced karyotype 46,XY,-1,+der. The mother`s chromosomes were normal, and the father was not available. Conventional cytogenetic techniques were unable to identify the extra material on the terminal 1q. Using fluorescence in situ hybridization (FISH) on the GTL-banded metaphases, the extra material on 1q was identified as the terminal long arm of 13, thus resulting in partial trisomy 13 (q32-qter). 8 refs., 2 figs., 1 tab.

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

    SciTech Connect

    Chen, H.; Tuck-Muller, C.M.; 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 of 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. 28 refs., 5 figs., 1 tab.

  18. DNA breakage detection-fluorescence in situ hybridization in buccal cells

    PubMed Central

    Cortés-Gutiérrez, E.I.; Dávila-Rodríguez, M.I.; Fernández, J.L.; López-Fernández, C.; Gosálvez, J.

    2012-01-01

    DNA breakage detection-fluorescence in situ hybridization (DBD-FISH) is a recently developed technique that allows cell-by-cell detection and quantification of DNA breakage in the whole genome or within specific DNA sequences. The present investigation was conducted to adapt the methodology of DBD-FISH to the visualization and evaluation of DNA damage in buccal epithelial cells. DBD-FISH revealed that DNA damage increased significantly according to H2O2 concentration (r2=0.91). In conclusion, the DBD-FISH technique is easy to apply in buccal cells and provides prompt results that are easy to interpret. Future studies are needed to investigate the potential applicability of a buccal cell DBD-FISH model to human biomonitoring and nutritional work. PMID:23361245

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

    PubMed

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

    2014-01-01

    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. PMID:25034259

  20. Enumeration of methanogens with a focus on fluorescence in situ hybridization

    NASA Astrophysics Data System (ADS)

    Kumar, Sanjay; Dagar, Sumit Singh; Mohanty, Ashok Kumar; Sirohi, Sunil Kumar; Puniya, Monica; Kuhad, Ramesh C.; Sangu, K. P. S.; Griffith, Gareth Wyn; Puniya, Anil Kumar

    2011-06-01

    Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.

  1. HIV detection by in-situ hybridization based on confocal reflected light microscopy

    NASA Astrophysics Data System (ADS)

    Smith, Louis C.; Jericevic, Zeljko; Cuellar, Roland; Paddock, Stephen W.; Lewis, Dorothy E.

    1991-05-01

    Elucidation of the pathogenesis of AIDS is confounded by the finding that few actively infected CD4+ cells (1 in 104-105) can be detected in the peripheral blood, even though there is dramatic depletion (often >90%) of CD4+ cells as the disease progresses. A sensitive, 35S-based human immunodeficiency virus (HIV) mRNA in situ hybridization technique was coupled with a new detection method, confocal laser scanning microscopy, to examine transcriptionally active HIV-infected cells from individuals at different disease stages. An algorithm for image segmentation and analysis has been developed to determine the proportion of HIV-positive cells. Data obtained using this improved detection method suggest that there are more HIV mRNA-producing cells in HIV-infected individuals than previously thought, based on other detection methods.

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

    PubMed

    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.

  3. FOXP1 status in splenic marginal zone lymphoma: a fluorescence in situ hybridization and immunohistochemistry approach.

    PubMed

    Baró, Cristina; Espinet, Blanca; Salido, Marta; Colomo, Lluís; Luño, Elisa; Florensa, Lourdes; Ferrer, Ana; Salar, Antonio; Campo, Elias; Serrano, Sergi; Solé, Francesc

    2009-11-01

    Splenic marginal zone lymphoma (SMZL) is a well-recognized entity in which chromosomal aberrations seem to be potential markers in diagnosis, prognosis and disease monitoring. FOXP1 is a transcriptional regulator of B lymphopoiesis that is deregulated in some types of NHL. Translocation t(3;14)(p14;q32) has been described in marginal zone lymphomas but few series have studied FOXP1 involvement in SMZL. We performed cytogenetic, fluorescence in situ hybridization (FISH) and immunohistochemical (IHC) studies in a series of 36 patients in order to study the status of FOXP1 in this entity. According to our results, FOXP1 is not rearranged in SMZL, although we were able to demonstrate gains of FOXP1 gene due to trisomy 3/3p by FISH. FOXP1 protein expression seemed to be not related to any aberration and IHC studies are not conclusive.

  4. Identification of Marteilia refringens infecting the razor clam Solen marginatus by PCR and in situ hybridization.

    PubMed

    López-Flores, Inmaculada; Garrido-Ramos, Manuel A; de la Herran, Roberto; Ruiz-Rejón, Carmelo; Ruiz-Rejón, Manuel; Navas, José I

    2008-06-01

    Marteilia refringens is a protozoan parasite recognized as a significant pathogen of the European flat oyster Ostrea edulis. It is believed to have a complex life-cycle involving several hosts. In this study, we applied molecular approaches to identify this parasite in samples of the razor clam Solen marginatus from the south west coast of Spain. We used a PCR assay to amplify a fragment of the IGS rDNA region. PCR products were sequenced and the phylogenetic affinity of the sequences was determined. In situ hybridization analysis showed tissue distribution and presence of different developmental stages of the parasite in the digestive diverticula epithelium, which suggested a true parasitism in these individuals. This is the first report of the occurrence of M. refringens in the razor clam S. marginatus in the south Atlantic. The methodology described herein may be useful for accurate identification of the parasite strain in different hosts and thus provide valuable information for marteiliosis control programmes.

  5. Proximal deletion of chromosome 21 confirmed by in situ hybridization and molecular studies

    SciTech Connect

    Courtens, W.; Peterson, M.B.; Noeel, J.C.; Flament-Durand, J.; Van Regemorter, N.; Delneste, D.; Cochaux, P.; Verschraegen-Spae, M.R.; Van Roy, N.; Speleman, F.

    1994-07-01

    Foetal blood sampling was performed at 35 weeks of gestation due to abnormal foetal ultrasound findings. There was apparent monosomy 21 (45,XX,-21) in all mitoses analyzed. The infant died at 37 weeks during delivery. Examination disclosed facial anomalies, clubfeet, hypoplasia of the left urogenital tract, agenesis of corpus callosum, ventricular dilatation, and heterotopias. Reevaluation of the karyotype showed an unbalanced translocation (1;21) (q44;q22.11) which resulted from a maternal balanced translocation. These findings were confirmed by fluorescence in situ hybridization and molecular studies with chromosome 21 specific markers. The latter showed a proximal deletion of the maternally derived chromosome 21 including all loci from centrometer down to the D21S210 locus. This case illustrates the need for complementary cytogenetic and molecular investigations in cases of apparent monosomy 21. 41 refs., 4 figs., 2 tabs.

  6. Chromosomal instability detected by fluorescence in situ hybridization in Japanese breast cancer patients.

    PubMed

    Takami, S; Kawasome, C; Kinoshita, M; Koyama, H; Noguchi, S

    2001-06-01

    The relationship between chromosomal instability (CIN) and prognostic factors was investigated in 31 breast cancers and 5 benign breast lesions (three fibroadenomas and two papillomas). Using fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes of chromosomes 1, 2, 6, 7, 10, 11, 17 and 18, CIN for each case was determined. CIN varied from 8.1% to 59.3% among the breast cancer patients tested, and was significantly higher than that observed in the benign breast lesions (p<0.01). Moreover, CIN showed a significant correlation with lymph node metastases (p<0.05) and estrogen receptor negativity (p<0.01). These findings suggest that CIN might be useful in the prediction of the biological aggressiveness of breast cancers. PMID:11412824

  7. Fluorescence in situ hybridization on 3D cultures of tumor cells.

    PubMed

    Meaburn, Karen J

    2010-01-01

    Genomes are spatially highly organized within interphase nuclei. Spatial genome organization is increasingly linked to genome function. Fluorescence in situ hybridization (FISH) allows the visualization of specific regions of the genome for spatial mapping. While most gene localization studies have been performed on cultured cells, genome organization is likely to be different in the context of tissues. Three-dimensional (3D) culture model systems provide a powerful tool to study the contribution of tissue organization to gene expression and organization. However, FISH on 3D cultures is technically more challenging than on monocultures. Here, we describe an optimized protocol for interphase DNA FISH on 3D cultures of the breast epithelial cell line MCF-10A.B2, which forms breast acini and can be used as a model for early breast cancer. PMID:20809324

  8. Fluorescence in situ hybridization (FISH) mapping of single copy genes on Trichomonas vaginalis chromosomes.

    PubMed

    Zubáčová, Zuzana; Krylov, Vladimír; Tachezy, Jan

    2011-04-01

    The highly repetitive nature of the Trichomonas vaginalis genome and massive expansion of various gene families has caused difficulties in genome assembly and has hampered genome mapping. Here, we adapted fluorescence in situ hybridization (FISH) for T. vaginalis, which is sensitive enough to detect single copy genes on metaphase chromosomes. Sensitivity of conventional FISH, which did not allow single copy gene detection in T. vaginalis, was increased by means of tyramide signal amplification. Two selected single copy genes, coding for serine palmitoyltransferase and tryptophanase, were mapped to chromosome I and II, respectively, and thus could be used as chromosome markers. This established protocol provides an amenable tool for the physical mapping of the T. vaginalis genome and other essential applications, such as development of genetic markers for T. vaginalis genotyping. PMID:21195113

  9. Simultaneous ultrasensitive subpopulation staining/hybridization in situ (SUSHI) in HIV-1 disease monitoring.

    PubMed

    Patterson, Bruce K

    2010-01-01

    The field of virology is undergoing a revolution as diagnostic tests and new therapies are allowing clinicians to treat, monitor, and predict outcomes of viral diseases. The majority of these techniques, however, destroy the factory of viral production and the information inherent in the reservoir - the cell. In this chapter, we describe a technique that combines cell surface immunophenotyping (to unequivocally identify cell types) and ultrasensitive fluorescence in situ hybridization (U-FISH) for HIV-1 to detect productively infected cells. Identification of virus and host (cells) allows earlier detection of changes in viral production and viral suppression but most importantly allows clinicians to monitor response to anti-viral therapy on a cell-by-cell and tissue-by-tissue basis taking into account the fact that the human body consists of very different, distinct compartments with unique selection pressures exerted on the viral life cycle.

  10. Development of single-cell array for large-scale DNA fluorescence in situ hybridization

    PubMed Central

    Liu, Yingru; Kirkland, Brett; Shirley, James; Wang, Zhibin; Zhang, Peipei; Stembridge, Jacquelyn; Wong, Wilson; Takebayashi, Shin-ichiro; Gilbert, David M.; Lenhert, Steven

    2013-01-01

    DNA fluorescence in situ hybridization (FISH) is a powerful cytogenetic assay, but conventional sample-preparation methods for FISH do not support large-scale high-throughput data acquisition and analysis, which are potentially useful for several biomedical applications. To address this limitation, we have developed a novel FISH sample-preparation method based on generating a centimetre-sized cell array, in which all cells are precisely positioned and separated from their neighbours. This method is simple and easy and capable of patterning nonadherent human cells. We have successfully performed DNA FISH on the single-cell arrays, which facilitate analysis of FISH results with the FISH-FINDER computer program. PMID:23370691

  11. Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)

    SciTech Connect

    Deutsch, Eric W.; Ball, Cathy; Berman, Jules J.; Bova, G. S.; Brazma, Alvis; Bumgarner, Roger E.; Campbell, David; Causton, Helen C.; Christiansen, Jeff; Daian, Fabrice; Dauga, Delphine; Davidson, Duncan; Gimenez, Gregory; Goo, Young Ah; Grimmond, Sean; Henrich, Thorsten; Herrmann, Bernhard G.; Johnson, Michael H.; Korb, Martin; Mills, Jason C.; Oudes, Asa; Parkinson, Helen E.; Pascal, Laura E.; Pollet, Nicolas; Quackenbush, John; Ramialison, Mirana; Ringwald, Martin; Salgado, David; Sansone, Susanna A.; Sherlock, Gavin; Stoeckert, Christian Jr. J.; Swedlow, Jason; Taylor, Ronald C.; Walashek, Laura; Warford, Anthony; Wilkinson, David G.; Zhou, Yi; Zon, Leonard I.; Liu, Alvin Y.; True, Lawrence D.

    2008-03-03

    We describe the creation process of the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Modeled after the existing minimum information specification for microarray data, we created a new specification for gene expression localization experiments, initially to facilitate data sharing within a consortium. After successful use within the consortium, the specification was circulated to members of the wider biomedical research community for comment and refinement. After a period of acquiring many new suggested requirements, it was necessary to enter a final phase of excluding those requirements that were deemed inappropriate as a minimum requirement for all experiments. The full specification will soon be published as a version 1.0 proposal to the community, upon which a more full discussion must take place so that the final specification may be achieved with the involvement of the whole community.

  12. Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization

    PubMed Central

    Hsu, Joanne H.; Zeng, Hui; Lemke, Kalistyn H.; Polyzos, Aris A.; Weier, Jingly F.; Wang, Mei; Lawin-O’Brien, Anna R.; Weier, Heinz-Ulrich G.; O’Brien, Benjamin

    2013-01-01

    Chromosome enumeration in interphase and metaphase cells using fluorescence in situ hybridization (FISH) is an established procedure for the rapid and accurate cytogenetic analysis of cell nuclei and polar bodies, the unambiguous gender determination, as well as the definition of tumor-specific signatures. Present bottlenecks in the procedure are a limited number of commercial, non-isotopically labeled probes that can be combined in multiplex FISH assays and the relatively high price and effort to develop additional probes. We describe a streamlined approach for rapid probe definition, synthesis and validation, which is based on the analysis of publicly available DNA sequence information, also known as “database mining”. Examples of probe preparation for the human gonosomes and chromosome 16 as a selected autosome outline the probe selection strategy, define a timeline for expedited probe production and compare this novel selection strategy to more conventional probe cloning protocols. PMID:23344021

  13. Fluorescent in situ hybridization (FISH) assessment of chromosome copy number in sperm

    SciTech Connect

    Sheu, M.; Sigman, M.; Mark, H.F.L.

    1994-09-01

    Approximately 15% of all recognized pregnancies end in spontaneous abortions. The overall frequency of chromosome abnormalities in spontaneous abortions is approximately 50%. Thus aneuploidy is a significant cause of fetal wastage. In addition, structural and numerical abnormalities of chromosomes can also lead to birth defects, developmental delay, mental retardation and infertility. Conventional cytogenetic analysis via GTG- and other banding techniques is a powerful tool in the elucidation of the nature of chromosomal abnormalities. Fluorescent in situ hybridization (FISH) enables detection of numerical chromosomal abnormalities, especially trisomies, in intact cells. Using FISH and commercially available biotin-labeled probes, we have initiated a prospective study to assess specific chromosome copy number of preparations of unstained smears from men referred for a male infertility evaluation as well as smears from normal control males chosen randomly from the sample of sperm donors. A total of approximately 19,000 sperm nuclei have been examined thus far. Of those suitable for analysis, 7382 (38.75%) were normal possessing one copy of chromosome 8, 155 (0.81%) were disomic, and 15 (0.079%) had more than two copies of chromosome 8. Comparisons with data available in the literature will be discussed. Work is ongoing to increase the efficiency of hybridization using both reported and previously untried pretreatment and fixation protocols. We have also initiated studies using multicolor FISH with various chromosome enumeration probes. The assay described here is a potentially powerful tool for detecting rare events such as spontaneous germ cell aneuploidy, aneuploidy detected in semen from men with carcinoma in situ of the testis and aneuploidy induced by potential environmental genotoxicants. It can also be utilized for segregation analysis and for correlating chromosome copy number with germ cell morphology.

  14. Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization.

    PubMed

    Caracciolo, Anna Barra; Grenni, Paola; Ciccoli, Roberto; Di Landa, Giuseppe; Cremisini, Carlo

    2005-09-01

    Pesticide and nitrate contamination of soil and groundwater from agriculture is an environmental and public health concern worldwide. Simazine, 6-chloro-N2,N4-diethyl-1,3,5-triazine-2,4-diamine, is a triazine herbicide used in agriculture for selective weed control with several types of crops and it is frequently applied to soils receiving N-fertilizers. Degradation experiments were performed in the laboratory to assess whether the biodegradation of simazine in soil may be influenced by the presence of urea. Simazine degradation rates under different experimental conditions (presence/absence of urea, microbiologically active/sterilized soil) were assessed together with the formation, degradation and transformation of its main metabolites in soil. Simazine degradation was affected by the presence of urea, in terms both of a smaller half-life (t(1/2)) and of a higher amount of desethyl-simazine formed. The soil bacterial community was also studied. Microbial abundances were determined by epifluorescence direct counting. Moreover in situ hybridization with rRNA-targeted fluorescent oligonucleotide probes was used to analyze the bacterial community structure. Fluorescent in situ hybridization (FISH) was used to detect specific groups of bacteria such as the alpha,beta,gamma-subdivisions of Proteobacteria, Gram-positive bacteria with a high G + C DNA content, Planctomycetes, Betaproteobacterial ammonia-oxidizing bacteria and nitrifying bacteria. The presence of the herbicide and/or urea affected the bacterial community structure, showing that FISH is a valuable tool for determining the response of bacterial populations to different environmental conditions.

  15. Genetic evidence of hybridization between the critically endangered Cuban crocodile and the American crocodile: implications for population history and in situ/ex situ conservation.

    PubMed

    Milián-García, Y; Ramos-Targarona, R; Pérez-Fleitas, E; Sosa-Rodríguez, G; Guerra-Manchena, L; Alonso-Tabet, M; Espinosa-López, G; Russello, M A

    2015-03-01

    Inter-specific hybridization may be especially detrimental when one species is extremely rare and the other is abundant owing to the potential for genetic swamping. The Cuban crocodile (Crocodylus rhombifer) is a critically endangered island endemic largely restricted to Zapata Swamp, where it is sympatric with the widespread American crocodile (C. acutus). An on-island, C. rhombifer captive breeding program is underway with the goals of maintaining taxonomic integrity and providing a source of individuals for reintroduction, but its conservation value is limited by lack of genetic information. Here we collected mtDNA haplotypic and nuclear genotypic data from wild and captive C. rhombifer and C. acutus in Cuba to: (1) investigate the degree of inter-specific hybridization in natural (in situ) and captive (ex situ) populations; (2) quantify the extent, distribution and in situ representation of genetic variation ex situ; and (3) reconstruct founder relatedness to inform management. We found high levels of hybridization in the wild (49.1%) and captivity (16.1%), and additional evidence for a cryptic lineage of C. acutus in the Antilles. We detected marginally higher observed heterozygosity and allelic diversity ex situ relative to the wild population, with captive C. rhombifer exhibiting over twice the frequency of private alleles. Although mean relatedness was high in captivity, we identified 37 genetically important individuals that possessed individual mean kinship (MK) values lower than the population MK. Overall, these results will guide long-term conservation management of Cuban crocodiles for maintaining the genetic integrity and viability of this species of high global conservation value.

  16. Analysis of chromosome band 1p36 alterations by chromosomal in situ suppression hybridization with a microclone DNA bank.

    PubMed

    Zink, D; Weith, A; Martinsson, T; Schwab, M

    1991-09-01

    Alterations of the distal portion of chromosome Ip are a recurrent abnormality of several types of human cancer. In this study we show that chromosomal in situ suppression hybridization with a regional 1p36 DNA bank generated by microdissection and microcloning can be employed to detect translocations involving 1p36.

  17. HER2 in situ hybridization in gastric and gastroesophageal adenocarcinoma: comparison of automated dual ISH to FISH.

    PubMed

    Grin, Andrea; Brezden-Masley, Christine; Bauer, Sharon; Streutker, Catherine J

    2013-12-01

    Patients with gastric and gastroesophageal junction (GEJ) adenocarcinomas that are HER2 positive by immunohistochemistry (IHC) or in situ hybridization show a significant survival benefit with trastuzumab therapy. In situ hybridization is traditionally done by fluorescence in situ hybridization (FISH), despite some limitations. An alternative is the dual in situ hybridization (Dual ISH) technique that is fully automated and uses differentially labeled CEP17 and HER2 probes that can be read by light microscopy on 1 slide. The aim of this study was to assess the utility of Dual ISH in gastric/GEJ cancer and to compare the results with those obtained by IHC and FISH. Cases of gastric/GEJ adenocarcinoma were analyzed by IHC, FISH, and Dual ISH and the correlation between methods calculated. Results for 50 patients were available. There was a 98% (49/50) concordance rate between Dual ISH and FISH. One discrepant case was nonamplified by FISH but showed focal amplification by Dual ISH. Discrepancy was attributed to tumor heterogeneity, which was a frequent finding (78% of HER2-positive cases). There was excellent correlation between Dual ISH and FISH for assessment of HER2 amplification. Dual ISH was rapid, easy to interpret, and maintained cell morphology, which was valuable in identifying tumor heterogeneity.

  18. Fluorescence in situ hybridization for the identification of Treponema pallidum in tissue sections.

    PubMed

    Petrich, Annett; Rojas, Pablo; Schulze, Julia; Loddenkemper, Christoph; Giacani, Lorenzo; Schneider, Thomas; Hertel, Moritz; Kikhney, Judith; Moter, Annette

    2015-10-01

    Syphilis is often called the great imitator because of its frequent atypical clinical manifestations that make the disease difficult to recognize. Because Treponema pallidum subsp. pallidum, the infectious agent of syphilis, is yet uncultivated in vitro, diagnosis is usually made using serology; however, in cases where serology is inconclusive or in patients with immunosuppression where these tests may be difficult to interpret, the availability of a molecular tool for direct diagnosis may be of pivotal importance. Here we present a fluorescence in situ hybridization (FISH) assay that simultaneously identifies and analyzes spatial distribution of T. pallidum in histological tissue sections. For this assay the species-specific FISH probe TPALL targeting the 16S rRNA of T. pallidum was designed in silico and evaluated using T. pallidum infected rabbit testicular tissue and a panel of non-syphilis spirochetes as positive and negative controls, respectively, before application to samples from four syphilis-patients. In a HIV positive patient, FISH showed the presence of T. pallidum in inguinal lymph node tissue. In a patient not suspected to suffer from syphilis but underwent surgery for phimosis, numerous T. pallidum cells were found in preputial tissue. In two cases with oral involvement, FISH was able to differentiate T. pallidum from oral treponemes and showed infection of the oral mucosa and tonsils, respectively. The TPALL FISH probe is now readily available for in situ identification of T. pallidum in selected clinical samples as well as T. pallidum research applications and animal models. PMID:26365167

  19. Development of a fluorescent in situ hybridization (FISH) technique for visualizing CGMMV in plant tissues.

    PubMed

    Shargil, D; Zemach, H; Belausov, E; Lachman, O; Kamenetsky, R; Dombrovsky, A

    2015-10-01

    Cucumber green mottle mosaic virus (CGMMV), which belongs to the genus Tobamovirus, is a major pathogen of cucurbit crops grown indoors and in open fields. Currently, immunology (e.g., ELISA) and molecular amplification techniques (e.g., RT-PCR) are employed extensively for virus detection in plant tissues and commercial seed lots diagnostics. In this study, a fluorescent in situ hybridization (FISH) technique, using oligonucleotides whose 5'-terminals were labeled with red cyanine 3 (Cy3) or green fluorescein isothiocyanate (FITC), was developed for the visualization of the pathogen in situ. This simple and reliable method allows detection and localization of CGMMV in the vegetative and reproductive tissues of cucumber and melon. When this technique was applied in male flowers, anther tissues were found to be infected; whereas the pollen grains were found to be virus-free. These results have meaningful epidemiological implications for the management of CGMMV, particularly with regard to virus transfer via seed and the role of insects as CGMMV vectors.

  20. Genomic in situ hybridization identifies parental chromosomes in hybrid scallop (Bivalvia, Pectinoida, Pectinidae) between female Chlamys farreri and male Argopecten irradians irradians

    PubMed Central

    Huang, Xiaoting; Bi, Ke; Lu, Wei; Wang, Shi; Zhang, Lingling; Bao, Zhenmin

    2015-01-01

    Abstract Interspecific crossing was artificially carried out between Chlamys farreri (Jones & Preston, 1904) ♀ and Argopecten irradians irradians (Lamarck, 1819) ♂, two of the dominant cultivated scallop species in China. Genomic in situ hybridization (GISH) was used to examine the chromosome constitution and variation in hybrids at early embryonic stage. The number of chromosomes in 66.38% of the metaphases was 2n = 35 and the karyotype was 2n = 3 m + 5 sm + 16 st + 11 t. After GISH, two parental genomes were clearly distinguished in hybrids, most of which comprised 19 chromosomes derived from their female parent (Chlamys farreri) and 16 chromosomes from their male parent (Argopecten irradians irradians). Some chromosome elimination and fragmentation was also observed in the hybrids. PMID:26140161

  1. Detection of Helicobacter pylori in raw bovine milk by fluorescence in situ hybridization (FISH).

    PubMed

    Angelidis, Apostolos S; Tirodimos, Ilias; Bobos, Mattheos; Kalamaki, Mary S; Papageorgiou, Demetrios K; Arvanitidou, Malamatenia

    2011-12-01

    The transmission pathways of Helicobacter pylori in humans have not been fully elucidated. Research in the last decade has proposed that foodborne transmission, among others, may be a plausible route of human infection. Owing to the organism's fastidious growth characteristics and its ability to convert to viable, yet unculturable states upon exposure to stress conditions, the detection of H. pylori in foods via culture-dependent methods has been proven to be laborious, difficult and in most cases unsuccessful. Hence, nucleic acid-based methods have been proposed as alternative methods but, to date, only PCR-based methods have been reported in the literature. In the current study, fluorescence in situ hybridization (FISH) was used for the detection of H. pylori in raw, bulk-tank bovine milk. After repeated milk centrifugation and washing steps, the bacterial flora of raw milk was subjected to fixation and permeabilization and H. pylori detection was conducted by FISH after hybridization with an H. pylori-specific 16S rRNA-directed fluorescent oligonucleotide probe. Using this protocol, H. pylori was detected in four out of the twenty (20%) raw milk samples examined. The data presented in this manuscript indicate that FISH can serve as an alternative molecular method for screening raw bovine milk for the presence of H. pylori.

  2. Calibration of interphase fluorescence in situ hybridization cutoff by mathematical models.

    PubMed

    Du, Qinghua; Li, Qingshan; Sun, Daochun; Chen, Xiaoyan; Yu, Bizhen; Ying, Yi

    2016-03-01

    Fluorescence in situ hybridization (FISH) continues to play an important role in clinical investigations. Laboratories may create their own cutoff, a percentage of positive nuclei to determine whether a specimen is positive or negative, to eliminate false positives that are created by signal overlap in most cases. In some cases, it is difficult to determine the cutoff value because of differences in both the area of nuclei and the number of signals. To address these problems, we established two mathematical models using probability theory. To verify these two models, normal disomy cells from healthy individuals were used to simulate cells with different numbers of signals by hybridization with different probes. We used an X/Y probe to obtain the average distance between two signals and the probability of signal overlap in different nuclei area. Frequencies of all signal patterns were scored and compared with theoretical frequencies, and models were assessed using a goodness of fit test. We used five BCR/ABL1-positive samples, 20 BCR/ABL1-negative samples and two samples with ambiguous results to verify the cutoff calibrated by these two models. The models were in agreement with experimental results. The dynamic cutoff can classify cases in routine analysis correctly, and it can also correct for influences from nuclei area and the number of signals in some ambiguous cases. The probability models can be used to assess the effect of signal overlap and calibrate the cutoff. PMID:26580488

  3. Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids.

    PubMed

    Fontenete, Silvia; Silvia, Fontenete; Barros, Joana; Joana, Barros; Madureira, Pedro; Pedro, Madureira; Figueiredo, Céu; Céu, Figueiredo; Wengel, Jesper; Jesper, Wengel; Azevedo, Nuno Filipe; Filipe, Azevedo Nuno

    2015-05-01

    In the past few years, several researchers have focused their attention on nucleic acid mimics due to the increasing necessity of developing a more robust recognition of DNA or RNA sequences. Fluorescence in situ hybridization (FISH) is an example of a method where the use of these novel nucleic acid monomers might be crucial to the success of the analysis. To achieve the expected accuracy in detection, FISH probes should have high binding affinity towards their complementary strands and discriminate effectively the noncomplementary strands. In this study, we investigate the effect of different chemical modifications in fluorescent probes on their ability to successfully detect the complementary target and discriminate the mismatched base pairs by FISH. To our knowledge, this paper presents the first study where this analysis is performed with different types of FISH probes directly in biological targets, Helicobacter pylori and Helicobacter acinonychis. This is also the first study where unlocked nucleic acids (UNA) were used as chemistry modification in oligonucleotides for FISH methodologies. The effectiveness in detecting the specific target and in mismatch discrimination appears to be improved using locked nucleic acids (LNA)/2'-O-methyl RNA (2'OMe) or peptide nucleic acid (PNA) in comparison to LNA/DNA, LNA/UNA, or DNA probes. Further, the use of LNA modifications together with 2'OMe monomers allowed the use of shorter fluorescent probes and increased the range of hybridization temperatures at which FISH would work.

  4. Single-mRNA counting using fluorescent in situ hybridization in budding yeast

    PubMed Central

    Trcek, Tatjana; Chao, Jeffrey A; Larson, Daniel R; Park, Hye Yoon; Zenklusen, Daniel; Shenoy, Shailesh M; Singer, Robert H

    2014-01-01

    Fluorescent in situ hybridization (FISH) allows the quantification of single mRNAs in budding yeast using fluorescently labeled single-stranded DNA probes, a wide-field epifluorescence microscope and a spot-detection algorithm. Fixed yeast cells are attached to coverslips and hybridized with a mixture of FISH probes, each conjugated to several fluorescent dyes. Images of cells are acquired in 3D and maximally projected for single-molecule analysis. Diffraction-limited labeled mRNAs are observed as bright fluorescent spots and can be quantified using a spot-detection algorithm. FISH preserves the spatial distribution of cellular RNA distribution within the cell and the stochastic fluctuations in individual cells that can lead to phenotypic differences within a clonal population. This information, however, is lost if the RNA content is measured on a population of cells by using reverse transcriptase PCR, microarrays or high-throughput sequencing. The FISH procedure and image acquisition described here can be completed in 3 d. PMID:22301778

  5. Localization of the expression of complement component 3 in the human endometrium by in situ hybridization

    SciTech Connect

    Sayegh, R.A.; Tao, Xiao Jing; Awwad, J.T.

    1996-04-01

    C3 production by the human endometrium has been previously described. The objective of the current study was to localize the site of expression and regulation of the third component of complement, C3, in the endometrium. Eight secretory and eight proliferative archival endometrial samples from hysterectomy and endometrial biopsy specimens were used for in situ hybridization analysis. This analysis was performed with a radiolabeled riboprobe synthesized from a 736-bp template representing sequence 1944-2680 of the human C3 complementary DNA. Duplicate sections were hybridized with sense and antisense riboprobes. Resultant autoradiograms were analyzed qualitatively by light- and darkfield microscopy. In proliferative endometrium, minimal expression of C3 was observed and was limited to a few stromal patches and glands throughout the section. In the secretory samples, prominent C3 expression was observed in both the glands and stroma of the basalis layer. Endometrial lymphocytes did not express C3. Endometrial stromal and glandular cells express the C3 gene. Endometrial lymphocytes did not express C3, but other nondistinct lymphoid elements scattered in the stroma may be expressing C3. There was a visibly more intense expression of C3 in the basalis layer of the secretory endometrium than in proliferative endometrium. The spatial and temporal pattern of C3 expression may have implications in normal menstrual physiology and in the immunological response of the endometrium to the invading trophoblast during placentation. 23 refs., 4 figs., 1 tab.

  6. X chromosome aneuploidy in infertile women: Analysis by interphase fluorescent in situ hybridization

    SciTech Connect

    Morris, M.A.; Moix, I.; Mermillod, B.

    1994-09-01

    Up to 1 in 3 couples have a problem of infertility at some time in their lives. Sex chromosome anomalies are found in 5-10% of couples, with mosaic aneuploidy being a common finding in primary infertility. Recurrent spontaneous abortion (RSA), in contrast, is frequently associated with autosomal structural anomalies. We hypothesized that low-level mosaic X chromosome aneuploidy was associated with primary infertility but not with RSA. Three groups were studied: women from couples with primary infertillity (n=26); women with three or more spontaneous abortions (n=22); and age-matched normally fertile women (at least two pregnancies; n=28). Interphase fluorescent in situ hybridization (FISH) was used to determine X chromosome ploidy in 100 nuclei per patient, using a contig of three cosmids from MAO locus (kindly donated by W. Berger, Nijmegen). A control probe (chr. 15 centromere) was simultaneously hybridized, and only nuclei containing two control signals were scored for the X chromosome. The mean numbers of nuclei with two X chromosome signals were the same in all groups (Welch equality of means test: p>0.97). However, there is a significant difference between the variances of the primary infertile and RSA groups (Levene`s test: p=0.025 after Bonferrone correction for multiple testing). This provides preliminary support for the hypothesis of an association between primary infertility and low-level mosaic X chromosome aneuploidy.

  7. An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells.

    PubMed

    Carter, Mark G; Stagg, Carole A; Falco, Geppino; Yoshikawa, Toshiyuki; Bassey, Uwem C; Aiba, Kazuhiro; Sharova, Lioudmila V; Shaik, Nabeebi; Ko, Minoru S H

    2008-02-01

    We previously reported that Zscan4 showed heterogeneous expression patterns in mouse embryonic stem (ES) cells. To identify genes that show similar expression patterns, we carried out high-throughput in situ hybridization assays on ES cell cultures for 244 genes. Most of the genes are involved in transcriptional regulation, and were selected using microarray-based comparisons of gene expression profiles in ES and embryonal carcinoma (EC) cells versus differentiated cell types. Pou5f1 (Oct4, Oct3/4) and Krt8 (EndoA) were used as controls. Hybridization signals were detected on ES cell colonies for 147 genes (60%). The majority (136 genes) of them showed relatively homogeneous expression in ES cell colonies. However, we found that two genes unequivocally showed Zscan4-like spotted expression pattern (spot-in-colony pattern; Whsc2 and Rhox9). We also found that nine genes showed relatively heterogeneous expression pattern (mosaic-in-colony pattern: Zfp42/Rex1, Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). Among these genes, Zfp42/Rex1 showed unequivocally heterogeneous expression in individual ES cells prepared by the CytoSpin. These results show the presence of different types or states of cells within ES cell cultures otherwise thought to be undifferentiated and homogeneous, suggesting a previously unappreciated complexity in ES cell cultures.

  8. Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization.

    PubMed

    Chan, PokMan; Yuen, Tony; Ruf, Frederique; Gonzalez-Maeso, Javier; Sealfon, Stuart C

    2005-10-13

    The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through streptavidin and biotin interactions, as well as protocols for their use in multiple-label FISH. We validated this technique in mouse brainstem sections. The subcellular localization of the vesicular monoamine transporter (Vmat2) mRNA corresponds when using probes labeled with two different QDs in the same hybridization. We developed protocols for combined direct QD FISH and QD immunohistochemical labeling within the same neurons as well as for simultaneous study of the subcellular distribution of multiple mRNA targets. We demonstrated increased sensitivity of FISH using QDs in comparison with organic fluorophores. These techniques gave excellent histological results both for multiplex FISH and combined FISH and immunohistochemistry. This approach can facilitate the ultrasensitive simultaneous study of multiple mRNA and protein markers in tissue culture and histological section.

  9. Differentiation of melanoma and benign nevi by fluorescence in-situ hybridization.

    PubMed

    Hossain, Deloar; Qian, Junqi; Adupe, Joy; Drewnowska, Krystyna; Bostwick, David G

    2011-10-01

    Malignant melanoma is sometimes difficult to distinguish from benign nevus, and ancillary confirmatory studies would be of value in selected cases. To accurately differentiate melanoma from benign nevus, we investigated the utility of chromosomal anomalies in skin biopsy specimens using multitargeted fluorescence in-situ hybridization (FISH). Skin biopsy specimens were retrospectively collected from 63 patients diagnosed with benign compound nevus (n=32) or malignant melanoma (n=31); each diagnosis was independently confirmed before study by a second dermatopathologist. Unstained tissue sections were hybridized for 30 min using fluorescence-labeled oligo-DNA probes for chromosomes 6, 7, 11, and 20. Fluorescent signals for each chromosome were enumerated in 30 cells per case. Numeric chromosomal anomalies were found in 0% (0 of 32) of normal epidermis, 6% (two of 32) of compound nevi, and 94% (29 of 31) of melanomas (nevus vs. melanoma, P<0.0001). The mean number of cells with chromosomal changes was 23 in melanoma specimens, significantly higher than that in compound nevi (P<0.0001). The most frequent chromosomal anomaly in melanoma was gain of chromosome 11, followed consecutively by gains of chromosomes 7, 20, and 6. Chromosomal anomalies detected by FISH had an overall sensitivity of 94% and specificity of 94% in the separation of nevus and melanoma. With the use of oligo-DNA probes, multitargeted FISH directed against chromosomes 6, 7, 11, and 20 is highly sensitive and specific for separation of nevus and melanoma. Unlike other traditional FISH probes, oligo-DNA probes required shorter hybridization time, allowing faster diagnostic evaluation. PMID:21900793

  10. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids.

    PubMed

    Denef, Vincent J; Banfield, Jillian F

    2012-04-27

    Few data are available on how quickly free-living microorganisms evolve. We analyzed biofilms collected from a well-defined acid mine drainage system over 9 years to investigate the processes and determine rates of bacterial evolution directly in the environment. Population metagenomic analyses of the dominant primary producer yielded the nucleotide substitution rate, which we used to show that proliferation of a series of recombinant bacterial strains occurred over the past few decades. The ecological success of hybrid bacterial types highlights the role of evolutionary processes in rapid adaptation within natural microbial communities. PMID:22539719

  11. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids.

    PubMed

    Denef, Vincent J; Banfield, Jillian F

    2012-04-27

    Few data are available on how quickly free-living microorganisms evolve. We analyzed biofilms collected from a well-defined acid mine drainage system over 9 years to investigate the processes and determine rates of bacterial evolution directly in the environment. Population metagenomic analyses of the dominant primary producer yielded the nucleotide substitution rate, which we used to show that proliferation of a series of recombinant bacterial strains occurred over the past few decades. The ecological success of hybrid bacterial types highlights the role of evolutionary processes in rapid adaptation within natural microbial communities.

  12. Technical Note: Determination of the metabolically active fraction of benthic foraminifera by means of Fluorescent In Situ Hybridization (FISH)

    NASA Astrophysics Data System (ADS)

    Borrelli, C.; Sabbatini, A.; Luna, G. M.; Nardelli, M. P.; Sbaffi, T.; Morigi, C.; Danovaro, R.; Negri, A.

    2011-08-01

    Benthic foraminifera are an important component of the marine biota, but protocols for investigating their viability and metabolism are still extremely limited. Classical studies on benthic foraminifera have been based on direct counting under light microscopy. Typically, these organisms are stained with Rose Bengal, which binds proteins and other macromolecules, but does not allow discrimination between viable and recently dead organisms. The fluorescent in situ hybridization technique (FISH) represents a new and useful approach to identify living cells possessing an active metabolism. Our work is the first test of the suitability of the FISH technique, based on fluorescent probes targeting the 18S rRNA, to detect live benthic foraminifera. The protocol was applied on Ammonia group and Miliolids, as well as on agglutinated polythalamous (i.e., Leptohalysis scottii and Eggerella scabra) and soft-shelled monothalamous (i.e., Psammophaga sp. and saccamminid morphotypes) taxa. The results from FISH analyses were compared with those obtained, on the same specimens assayed with FISH, from microscopic analysis of the cytoplasm colour, presence of pigments and pseudopodial activity. Our results indicate that FISH targets only metabolically active foraminifera, and allows discerning from low to high cellular activity, validating the hypothesis that the intensity of the fluorescent signal emitted by the probe is dependent upon the physiological status of cells. These findings support the usefulness of this molecular approach as a key tool for obtaining information on the physiology of living foraminifera, both in field and experimental settings.

  13. Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization.

    PubMed

    Li, Jinhong; Webster, Margaret A; Wright, Jonathan; Cocker, Jonathan M; Smith, Matthew C; Badakshi, Farah; Heslop-Harrison, Pat; Gilmartin, Philip M

    2015-10-01

    Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location. We have employed a combination of classical genetics and three-point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization. We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of sequence containing 82 S-linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair. These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus.

  14. Applicability of a Diffuse Reflectance Infrared Fourier Transform handheld spectrometer to perform in situ analyses on Cultural Heritage materials.

    PubMed

    Arrizabalaga, Iker; Gómez-Laserna, Olivia; Aramendia, Julene; Arana, Gorka; Madariaga, Juan Manuel

    2014-08-14

    This work studies the applicability of a Diffuse Reflectance Infrared Fourier Transform handheld device to perform in situ analyses on Cultural Heritage assets. This portable diffuse reflectance spectrometer has been used to characterise and diagnose the conservation state of (a) building materials of the Guevara Palace (15th century, Segura, Basque Country, Spain) and (b) different 19th century wallpapers manufactured by the Santa Isabel factory (Vitoria-Gasteiz, Basque Country, Spain) and by the well known Dufour and Leroy manufacturers (Paris, France), all of them belonging to the Torre de los Varona Castle (Villanañe, Basque Country, Spain). In all cases, in situ measurements were carried out and also a few samples were collected and measured in the laboratory by diffuse reflectance spectroscopy (DRIFT) in order to validate the information obtained by the handheld instrument. In the analyses performed in situ, distortions in the diffuse reflectance spectra can be observed due to the presence of specular reflection, showing the inverted bands caused by the Reststrahlen effect, in particular on those IR bands with the highest absorption coefficients. This paper concludes that the results obtained in situ by a diffuse reflectance handheld device are comparable to those obtained with laboratory diffuse reflectance spectroscopy equipment and proposes a few guidelines to acquire good spectra in the field, minimising the influence caused by the specular reflection.

  15. Branched chain in situ hybridization for albumin as a marker of hepatocellular differentiation: evaluation of manual and automated in situ hybridization platforms

    PubMed Central

    Shahid, Mohammad; Mubeen, Aysha; Tse, Julie; Kakar, Sanjay; Bateman, Adrian; Borger, Darrell; Rivera, Miguel; Ting, David T.; Deshpande, Vikram

    2015-01-01

    Introduction Albumin, widely recognized as a highly sensitive and specific marker of hepatocellular carcinoma (HCC) is currently unavailable in the diagnostic laboratory because of the lack of a robust platform. In a prior study we detected albumin mRNA in the majority of intrahepatic cholangiocarcinomas using a novel branched chain RNA in situ hybridization (ISH) platform. We now explore the utility of albumin ISH as a marker of hepatocellular differentiation in hepatocellular carcinomas, and compare its sensitivity with Hep Par 1 and Arginase-1. Methods We evaluated 93 HCCs and its mimics including neuroendocrine tumors of the gastrointestinal tract (n= 31), neuroendocrine tumors of the pancreas (n= 163), melanoma (n= 15), and gallbladder carcinoma (n=34). We performed ISH for albumin and immunohistochemistry for Hep Par 1 and Arginase-1. Five previously uncharacterized hepatic neoplasms from our files were also evaluated. Immunohistochemistry for Arginase-1 was performed on 59 intrahepatic cholangiocarcinomas. In addition, 43 HCCs evaluated on the manual platform, were also examined on the automated instrument. Results 55% of HCCs were moderately differentiated and 39% poorly differentiated. The sensitivity of ISH for Albumin was 99% with 92 of 93 of HCCs staining positive for albumin. In contrast to ISH, the sensitivity of immunohistochemistry for Hep Par1 and Arginase-1 was 84 % and 83 %, respectively. The sensitivity of albumin for poorly differentiated HCCs was 99%, while that for Arginase-1 and Hep Par 1 was 71% and 64%, respectively. 97% of the HCCs showed albumin positivity in >50% of tumor cells using the ISH platform, as compared to 76% and 70% for Hep Par 1 and Arginase-1 immunohistochemistry, respectively. 3 of the 5 previously uncharacterized neoplasms were positive for albumin ISH. Automated albumin ISH platform performed equivalently to the manual format, with albumin reactivity in >50% of tumor cells in all 43 cases that were tested on both

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

    SciTech Connect

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

    1987-11-01

    Twenty-three conjunctival papillomas and 28 conjunctival dysplasias were examined for human papillomavirus (HPV)-DNA sequences by in situ hybridization with nick-translated /sup 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.

  17. Comparison of 35S and biotin as labels for in situ hybridization: Use of an HPV model system

    SciTech Connect

    Unger, E.R.; Hammer, M.L.; Chenggis, M.L. )

    1990-01-01

    Colorimetric in situ hybridization is a method of potential importance in diagnosis and research. The largest criticism of the method has been a perceived loss of sensitivity compared with autoradiographic techniques. Our more positive experience with automation of colorimetric in situ hybridization led us to undertake a direct comparison of the sensitivity of 35S- and biotin-labeled probes. Serial sections of formalin-fixed, paraffin-embedded cell pellets from four human cervical carcinoma cell lines with known copies of HPV (CaSki, 400-600 copies HPV 16; HeLa, 10-50 copies HPV 18; SiHa, 1-2 copies HPV 16; HTB31, no known copies HPV) were hybridized with protocols optimized for autoradiographic or colorimetric detection. Both methods gave comparable results, with differences in each technique seen at the limits of sensitivity. The 1-2 copies of HPV 16 per SiHa cell can be detected with both methods; however, grain counting is required for interpretation of the autoradiographic result. This degree of sensitivity for colorimetric in situ hybridization in formalin-fixed, paraffin-embedded material is achieved through careful optimization of probe size and labeling, adequate tissue digestion, and removal of background. Autoradiography may be preferred in situations where quantitation is required, but colorimetric detection retains the advantages of speed, potential for automation, and improved localization of signal with comparable sensitivity.

  18. Luminescent hybrid lanthanide sulfates and lanthanide sulfonate-carboxylates with 1,10-phenanthroline involving in-situ oxidation of 2-mercaptonbenzoic acid

    SciTech Connect

    Zhong, Jie-Cen; Wan, Fang; Sun, Yan-Qiong; Chen, Yi-Ping

    2015-01-15

    A series of lanthanide sulfates and lanthanide sulfonate-carboxylates, [Ln{sub 2}(phen){sub 2}(SO{sub 4}){sub 3}(H{sub 2}O){sub 2}]{sub n} (I:Ln=Nd(1a), Sm(1b), Eu(1c), phen=1,10-phenanthroline) and [Ln(phen)(2-SBA)(BZA)]{sub 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{sub 4}{sup 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 {sup 5}D{sub 0}→{sup 7}F{sub J} (J=0–4) of the Eu(III)

  19. Identification of tissue contamination by polymorphic deletion probe fluorescence in situ hybridization.

    PubMed

    Chiang, Sarah; Yip, Stephen; Betensky, Rebecca A; Batten, Julie M; Misdraji, Joseph; John Iafrate, A

    2012-10-01

    Potential sources of error in surgical pathology include specimen misidentification, unidentified tissue, and tissue contamination of paraffin blocks and slides. Current molecular approaches to characterize unidentified or misidentified tissue include fluorescence in situ hybridization identification of sex chromosomes (XY FISH) and microsatellite analysis. Polymorphic deletion probe (PDP) FISH, a novel FISH assay based on copy number variants, can distinguish between cells and tissues from 2 individuals in situ, independent of gender. Using a panel of 3 PDPs, we compared the genotypes of potential tissue contaminants (n=19) and unidentified tissues (n=6) with patient tissues to determine the utility of PDP FISH in resolving specimen identity. XY FISH was added to increase the informative potential of the assay, and microsatellite analysis was used as a gold standard to confirm PDP FISH results. PDP FISH distinguished between putative contaminants and patient tissues in 13 of 14 cases and indicated a high likelihood of 2 tissues originating from the same source in 11 of 11 cases. The assay has a sensitivity and specificity of 86% [6/7, exact 95% confidence interval (CI): 42%, 97%] and 100% (9/9, exact 1-sided 97.5% CI: 68%, 100%), respectively, and a positive predictive value and negative predictive value of 100% (6/6, exact 1-sided 97.5% CI: 54%, 100%) and 90% (9/10, exact 95% CI: 55%, 98%), respectively. PDP FISH is an accurate and practical molecular assay for the genetic characterization of potential tissue contaminants and unidentified tissues, especially in the setting of small sample size, and permits concomitant assessment of morphology.

  20. Rapid and sensitive identification of marine bacteria by an improved in situ DNA hybridization chain reaction (quickHCR-FISH).

    PubMed

    Yamaguchi, Tsuyoshi; Fuchs, Bernhard Maximilian; Amann, Rudolf; Kawakami, Shuji; Kubota, Kengo; Hatamoto, Masashi; Yamaguchi, Takashi

    2015-09-01

    Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with rRNA-targeted oligonucleotide probes has significantly improved the identification of microorganisms in various environmental samples. However, one of the major constraints of CARD-FISH is the low probe penetration due to the high molecular weight of the horseradish peroxidase (HRP) label. Recently, this limitation has been overcome by a novel signal amplification approach termed in situ DNA-hybridization chain reaction (in situ DNA-HCR). In this study, we present an improved and accelerated in situ DNA-HCR protocol (quickHCR-FISH) with increased signal intensity, which was approximately 2 times higher than that of standard in situ DNA-HCR. In addition, the amplification time was only 15 min for the extension of amplifier probes from the initiator probe compared to 2h in the original protocol. The quickHCR-FISH was successfully tested for the quantification of marine bacteria with low rRNA contents in both seawater and sediment samples. It was possible to detect the same number of marine bacteria with quickHCR-FISH compared to CARD-FISH within only 3h. Thus, this newly developed protocol could be an attractive alternative to CARD-FISH for the detection and visualization of microorganisms in their environmental context.

  1. [Chromosomal structure of the hybrids between Allium cepa L. and Allium fistulosum L. with relative resistance to downy mildew based on in situ hybridization].

    PubMed

    Budylin, M V; Kan, L Iu; Romanov, V S; Khrustaleva, L I

    2014-04-01

    Genomic in situ hybridization (GISH) was used for a chromosomal composition study of the later generations of interspecific hybrids between A. cepa L. and A. fistulosum L., which are relatively resistant to downy mildew (peronosporosis). GISH revealed that F2 hybrids, which did not produce seeds, were triploids (2n = 3x = 24) with 24 chromosomes and possessed in their compliments 16 chromosomes of A. fistulosum L. and eight chromosomes of A. cepa L. or eight chromosomes of A. fistulosum L. and 16 chromosomes of A. cepa L. The advanced F5 hybrid, which produced few seeds, was amphidiploid with 32 chromosomes. BC1F5 hybrid was triploid with eight chromosomes of A. fistulosum L. and 16 chromosomes of A. cepa L., which did not produce seeds. BC2 (BC1F5) plant was amphidiploid that possessed 4 recombinant chromosomes and produced few seeds. GISH results point to 2n-gametes formation in macro- and microsporogenesis of the hybrids. The mechanism of 2n-gametes formation and the possibility of apomixes events in the backcrossing progeny are discussed.

  2. [Chromosomal structure of the hybrids between Allium cepa L. and Allium fistulosum L. with relative resistance to downy mildew based on in situ hybridization].

    PubMed

    Budylin, M V; Kan, L Iu; Romanov, V S; Khrustaleva, L I

    2014-04-01

    Genomic in situ hybridization (GISH) was used for a chromosomal composition study of the later generations of interspecific hybrids between A. cepa L. and A. fistulosum L., which are relatively resistant to downy mildew (peronosporosis). GISH revealed that F2 hybrids, which did not produce seeds, were triploids (2n = 3x = 24) with 24 chromosomes and possessed in their compliments 16 chromosomes of A. fistulosum L. and eight chromosomes of A. cepa L. or eight chromosomes of A. fistulosum L. and 16 chromosomes of A. cepa L. The advanced F5 hybrid, which produced few seeds, was amphidiploid with 32 chromosomes. BC1F5 hybrid was triploid with eight chromosomes of A. fistulosum L. and 16 chromosomes of A. cepa L., which did not produce seeds. BC2 (BC1F5) plant was amphidiploid that possessed 4 recombinant chromosomes and produced few seeds. GISH results point to 2n-gametes formation in macro- and microsporogenesis of the hybrids. The mechanism of 2n-gametes formation and the possibility of apomixes events in the backcrossing progeny are discussed. PMID:25715446

  3. Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization.

    PubMed

    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. PMID:25511566

  4. Porous titania/carbon hybrid microspheres templated by in situ formed polystyrene colloids.

    PubMed

    Cheng, Ting; Zhang, Guoqiang; Xia, Yonggao; Sun, Zaicheng; Yang, Zhaohui; Liu, Rui; Xiao, Ying; Wang, Xiaoyan; Wang, Meimei; Ban, Jianzhen; Yang, Liangtao; Ji, Qing; Qiu, Bao; Chen, Guoxin; Chen, Huifeng; Lin, Yichao; Pei, Xiaoying; Wu, Qiang; Meng, Jian-Qiang; Liu, Zhaoping; Chen, Liang; Xiao, Tonghu; Sun, Ling-Dong; Yan, Chun-Hua; Butt, Hans Jürgen; Cheng, Ya-Jun

    2016-05-01

    A new strategy to synthesize hierarchical, porous titania/carbon (TiO2/C) hybrid microspheres via solvothermal reaction in N,N'-dimethyl formamide (DMF) has been developed. In situ formed polystyrene (PS) colloids have been used as templating agent and carbon source, through which TiO2/PS microspheres with a diameter of ca. 1 μm are built by packed TiO2 nanoparticles of tens of nanometers. The TiO2/PS microspheres are converted to TiO2/C microspheres with different amounts of carbon under controlled calcination condition. The mechanism investigation unveils that the introduction of concentrated HCl creates surface tension between PS and DMF, leading to the formation of PS colloids in solution. The solvothermal treatment further promotes the formation of PS colloids and integration of the titania nanoparticles within the PS colloids. The morphology, crystallinity, nature and content of carbon, UV-Vis absorption, carbon doping, pore size distribution, pore volume, and BET surface area of the TiO2 microspheres with different amounts of carbon have been measured. The applications of the TiO2/C hybrid microspheres as photo catalyst for water splitting and lithium-ion battery anode have been demonstrated. Superior photo catalytic activity for hydrogen conversion under both full spectrum and visible light illumination compared to commercial P25 has been observed for the TiO2/C microspheres with 2 wt% of carbon. Besides, the TiO2/C microspheres with 8 wt% of carbon as lithium-ion battery anode showed a much higher capacity than the bare TiO2 microsphere anode. The origin for the enhanced performance as photo catalyst and lithium-ion battery anode is discussed.

  5. A novel triple-color detection procedure for brightfield microscopy, combining in situ hybridization with immunocytochemistry.

    PubMed

    Speel, E J; Jansen, M P; Ramaekers, F C; Hopman, A H

    1994-10-01

    We describe a fast light microscopic procedure for the simultaneous enzyme cytochemical detection of three different DNA target sequences in contrasting colors in both interphase and metaphase cell preparations. Chromosome-specific DNA probes labeled with either biotin, digoxygenin, or fluorescein were hybridized as a mixture and detected clearly and accurately by precipitates of the horseradish peroxidase-diaminobenzidine (PO-DAB, brown color), alkaline phosphatase-Fast Red (APase-Fast Red, red color), or horseradish peroxidase-tetramethylbenzidine (PO-TMB, green color) reaction, respectively. The PO-TMB reaction product was stabilized effectively by the addition of sodium tungstate to the reaction mixture, thus making the PO-TMB reaction now generally applicable to in situ hybridization (ISH). To avoid mixing of the precipitates of the two PO reactions used in the triple-color ISH method, the first detected PO activity was always completely inactivated by a mild acid treatment before the second one was applied. Finally, the cell preparations were embedded in a thin protein layer cross-linked by formaldehyde to ensure permanent stabilization of the enzyme reaction products and optimal visualization of color contrast. The triple-color ISH detection procedure could be combined with beta-galactosidase-5-bromo-4-chloro-3-indolyl-beta- D-galactoside (beta-Gal-BCIG) immunocytochemistry (ICC), leading to the simultaneous localization of multiple DNA targets and a protein target in the same cell. The described procedure may therefore be a valuable tool in the areas of cytogenetics, cell biology, and molecular pathology. PMID:7930513

  6. Microfluidic fluorescence in situ hybridization and flow cytometry (µFlowFISH)

    PubMed Central

    Liu, Peng; Meagher, Robert J.; Light, Yooli Kim; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P.; Hazen, Terry C.; Singh, Anup K.

    2011-01-01

    We describe an integrated microfluidic device (µFlowFISH) capable of performing 16S rRNA fluorescence in situ hybridization (FISH) followed by flow cytometric detection for identifying bacteria in natural microbial communities. The device was used for detection of species involved in bioremediation of Cr(VI) and other metals in groundwater samples from a highly-contaminated environmental site (Hanford, WA, USA). The µFlowFISH seamlessly integrates two components: a hybridization chamber formed between two photopolymerized membranes, where cells and probes are electrophoretically loaded, incubated and washed; and a downstream cross structure for electrokinetically focusing cells into a single-file flow for flow cytometry analysis. The device is capable of analyzing a wide variety of bacteria including aerobic, facultative and anaerobic bacteria and was initially tested and validated using cultured microbes, including Escherichia coli, as well as two strains isolated from Hanford site: Desulfovibrio vulgaris strain RCH1, and Pseudomonas sp. strain RCH2 that are involved in Cr(VI) reduction and immobilization. Combined labeling and detection efficiencies of 74–97% were observed in experiments with simple mixtures of cultured cells confirmed specific labeling. Results obtained were in excellent agreement with those obtained by conventional flow cytometry confirming the accuracy of µFlowFISH. Finally, the device was used for analyzing water samples collected on different dates from the Hanford Site. We were able to monitor the numbers of Pseudomonas sp. with only 100–200 cells loaded into the microchip. The µFlowFISH approach provides an automated platform for quantitative detection of microbial cells from complex samples, and is ideally suited for analysis of precious samples with low cell numbers such as those found at extreme environmental niches, bioremediation sites, and the human microbiome. PMID:21755095

  7. Porous titania/carbon hybrid microspheres templated by in situ formed polystyrene colloids.

    PubMed

    Cheng, Ting; Zhang, Guoqiang; Xia, Yonggao; Sun, Zaicheng; Yang, Zhaohui; Liu, Rui; Xiao, Ying; Wang, Xiaoyan; Wang, Meimei; Ban, Jianzhen; Yang, Liangtao; Ji, Qing; Qiu, Bao; Chen, Guoxin; Chen, Huifeng; Lin, Yichao; Pei, Xiaoying; Wu, Qiang; Meng, Jian-Qiang; Liu, Zhaoping; Chen, Liang; Xiao, Tonghu; Sun, Ling-Dong; Yan, Chun-Hua; Butt, Hans Jürgen; Cheng, Ya-Jun

    2016-05-01

    A new strategy to synthesize hierarchical, porous titania/carbon (TiO2/C) hybrid microspheres via solvothermal reaction in N,N'-dimethyl formamide (DMF) has been developed. In situ formed polystyrene (PS) colloids have been used as templating agent and carbon source, through which TiO2/PS microspheres with a diameter of ca. 1 μm are built by packed TiO2 nanoparticles of tens of nanometers. The TiO2/PS microspheres are converted to TiO2/C microspheres with different amounts of carbon under controlled calcination condition. The mechanism investigation unveils that the introduction of concentrated HCl creates surface tension between PS and DMF, leading to the formation of PS colloids in solution. The solvothermal treatment further promotes the formation of PS colloids and integration of the titania nanoparticles within the PS colloids. The morphology, crystallinity, nature and content of carbon, UV-Vis absorption, carbon doping, pore size distribution, pore volume, and BET surface area of the TiO2 microspheres with different amounts of carbon have been measured. The applications of the TiO2/C hybrid microspheres as photo catalyst for water splitting and lithium-ion battery anode have been demonstrated. Superior photo catalytic activity for hydrogen conversion under both full spectrum and visible light illumination compared to commercial P25 has been observed for the TiO2/C microspheres with 2 wt% of carbon. Besides, the TiO2/C microspheres with 8 wt% of carbon as lithium-ion battery anode showed a much higher capacity than the bare TiO2 microsphere anode. The origin for the enhanced performance as photo catalyst and lithium-ion battery anode is discussed. PMID:26896772

  8. Multiplex fluorescence in situ hybridization (M-FISH) and confocal laser scanning microscopy (CLSM) to analyze multispecies oral biofilms.

    PubMed

    Karygianni, Lamprini; Hellwig, Elmar; Al-Ahmad, Ali

    2014-01-01

    Multiplex fluorescence in situ hybridization (M-FISH) constitutes a favorable microbiological method for the analysis of spatial distribution of highly variable phenotypes found in multispecies oral biofilms. The combined use of confocal laser scanning microscopy (CLSM) produces high-resolution three-dimensional (3D) images of individual bacteria in their natural environment. Here, we describe the application of M-FISH on early (Streptococcus spp., Actinomyces naeslundii) and late colonizers (Fusobacterium nucleatum, Veillonella spp.) of in situ-formed oral biofilms, the acquisition of CLSM images, as well as the qualitative and quantitative analysis of these digitally obtained and processed images.

  9. Development of a PNA Probe for Fluorescence In Situ Hybridization Detection of Prorocentrum donghaiense

    PubMed Central

    Chen, Guofu; Zhang, Chunyu; Zhang, Baoyu; Wang, Guangce; Lu, Douding; Xu, Zhong; Yan, Peishen

    2011-01-01

    Prorocentrum donghaiense is a common but dominant harmful algal bloom (HAB) species, which is widely distributed along the China Sea coast. Development of methods for rapid and precise identification and quantification is prerequisite for early-stage warning and monitoring of blooms due to P. donghaiense. In this study, sequences representing the partial large subunit rDNA (D1–D2), small subunit rDNA and internal transcribed spacer region (ITS-1, 5.8S rDNA and ITS-2) of P. donghaiense were firstly obtained, and then seven candidate DNA probes were designed for performing fluorescence in situ hybridization (FISH) tests on P. donghaiense. Based on the fluorescent intensity of P. donghaiense cells labeled by the DNA probes, the probe DP0443A displayed the best hybridization performance. Therefore, a PNA probe (PP0443A) analogous to DP0443A was used in the further study. The cells labeled with the PNA probe displayed more intensive green fluorescence than that labeled with its DNA analog. The PNA probe was used to hybridize with thirteen microalgae belonging to five families, i.e., Dinophyceae, Prymnesiophyceae, Raphidophyceae, Chlorophyceae and Bacillariophyceae, and showed no visible cross-reaction. Finally, FISH with the probes PP0443A and DP0443A and light microscopy (LM) analysis aiming at enumerating P. donghaiense cells were performed on the field samples. Statistical comparisons of the cell densities (cells/L) of P. donghaiense in the natural samples determined by FISH and LM were performed using one-way ANOVA and Duncan's multiple comparisons of the means. The P. donghaiense cell densities determined by LM and the PNA probe are remarkably higher than (p<0.05) that determined by the DNA probe, while no significant difference is observed between LM and the PNA probe. All results suggest that the PNA probe is more sensitive that its DNA analog, and therefore is promising for the monitoring of harmful algal blooms of P. donghaiense in the future. PMID:22022408

  10. Miniaturised 'lab-on-a-chip' nitrate analyser applied to high resolution in situ analysis of glacial meltwater

    NASA Astrophysics Data System (ADS)

    Beaton, A.; Mowlem, M.; Wadham, J. L.

    2013-12-01

    In situ chemical measurements of glacial meltwater can provide high temporal and spatial resolution data that allow us to infer biogeochemical processes and calculate export from glacial systems. Despite this, in situ measurements of single chemical parameters in glacial meltwater have so far largely been restricted to pH and dissolved oxygen. The lack of high performance ruggedized in situ sensors for other analytes means that the laboratory-based analysis of manually collected samples is still routine. Microfluidics (through lab-on-a-chip technology) permits the miniaturisation of established chemical analysis techniques so that they can be performed in situ. The advantages of decreased size and low power and reagent consumption make these systems suitable for deployment in extreme and inaccessible environments where regular manual sample collection is logistically difficult. We present data from a novel stand-alone microfluidic wet chemical nitrate analyser that has been deployed to monitor a proglacial meltwater river draining from the Greenland ice sheet. By performing a measurement every 20 minutes, the analyser was able to reveal diurnal fluctuations and short term trends in nitrate concentrations that would not discernible using standard daily sampling. High resolution in situ measurements such as these can allow a more accurate determination of nutrient export fluxes from glacial systems into the polar oceans, and allow enhanced interpretation of water quality datasets. Steps have been taken to ruggedize the system so that it can survive the freeze-thaw conditions, dilute concentrations and high sediment loads that can be associated with cryospheric environments. The system is small, has low power consumption and detects nitrate and nitrite with a limit of detection (LOD) of 0.025 μM, which is sufficient for low nutrient glacial environments. On-going work looks to deploy similar nutrient analysers more widely, not only in glacial systems, but also in

  11. Assessment of retrospective dose estimation, with fluorescence in situ hybridization (FISH), of six victims previously exposed to accidental ionizing radiation.

    PubMed

    Liu, Qing-Jie; Lu, Xue; Zhao, Xiao-Tao; Feng, Jiang-Bin; Lü, Yu-Min; Jiang, En-Hai; Zhang, Shu-Lan; Chen, De-Qing; Jia, Ting-Zhen; Liang, Li

    2014-01-01

    The present study aims to evaluate the use of the fluorescence in situ hybridization (FISH) translocation assay for retrospective dose estimation of acute accidental exposure to radiation in the past. Reciprocal translocation analysis by FISH with three whole-chromosome probes was performed on normal peripheral blood samples. Samples were irradiated with 0-5Gy (60)Co γ-rays in vitro, and dose-effect curves were established. FISH-based translocation analyses for six accident victims were then performed, and biological doses were estimated retrospectively by comparison with the dose-effect curves. Reconstructed doses by FISH were compared with estimated doses obtained by analysis of di-centrics performed soon after exposure, or with dose estimates from tooth-enamel electron paramagnetic resonance (EPR) data obtained at the same time as the FISH analysis. Follow-up FISH analyses for an adolescent victim were performed. Results showed that dose-effect curves established in the present study follow a linear-quadratic model, regardless of the background translocation frequency. Estimated doses according to two dose-effect curves for all six victims were similar. FISH dose estimations of three adult victims exposed to accidental radiation less than a decade prior to analysis (3, 6, or 7 years ago) were consistent with those estimated with tooth-enamel EPR measurements or analyses of di-centrics. Estimated doses of two other adult victims exposed to radiation over a decade prior to analysis (16 or 33 years ago) were underestimated and two to three times lower than the values obtained from analysis of di-centrics or tooth-enamel EPR. Follow-up analyses of the adolescent victim showed that doses estimated by FISH analysis decrease rapidly over time. Therefore, the accuracy of dose estimates by FISH is acceptable only when analysis is performed less than 7 years after exposure. Measurements carried out more than a decade after exposure through FISH analysis resulted in

  12. Automated evaluation of Her-2/neu status in breast tissue from fluorescent in situ hybridization images.

    PubMed

    Raimondo, Francesco; Gavrielides, Marios A; Karayannopoulou, Georgia; Lyroudia, Kleoniki; Pitas, Ioannis; Kostopoulos, Ioannis

    2005-09-01

    The evaluation of fluorescent in situ hybridization (FISH) images is one of the most widely used methods to determine Her-2/neu status of breast samples, a valuable prognostic indicator. Conventional evaluation is a difficult task since it involves manual counting of dots in multiple images. In this paper, we present a multistage algorithm for the automated classification of FISH images from breast carcinomas. The algorithm focuses not only on the detection of FISH dots per image, but also on combining results from multiple images taken from a slice for overall case classification. The algorithm includes mainly two stages for nuclei and dot detection respectively. The dot segmentation consists of a top-hat filtering stage followed by template matching to separate real signals from noise. Nuclei segmentation includes a nonlinearity correction step, global thresholding to identify candidate regions, and a geometric rule to distinguish between holes within a nucleus and holes between nuclei. Finally, the marked watershed transform is used to segment cell nuclei with markers detected as regional maxima of the distance transform. Combining the two stages allows the measurement of FISH signals ratio per cell nucleus and the collective classification of cases as positive or negative. The system was evaluated with receiver operating characteristic analysis and the results were encouraging for the further development of this method. PMID:16190465

  13. Specific Detection of Two Divergent Simian Arteriviruses Using RNAscope In Situ Hybridization

    PubMed Central

    Yú, Shuǐqìng; Caì, Yíngyún; Lyons, Cassandra; Johnson, Reed F.; Postnikova, Elena; Mazur, Steven; Johnson, Joshua C.; Radoshitzky, Sheli R.; Bailey, Adam L.; Lauck, Michael; Goldberg, Tony L.; O’Connor, David H.; Jahrling, Peter B.; Friedrich, Thomas C.; Kuhn, Jens H.

    2016-01-01

    Simian hemorrhagic fever (SHF) is an often lethal disease of Asian macaques. Simian hemorrhagic fever virus (SHFV) is one of at least three distinct simian arteriviruses that can cause SHF, but pathogenesis studies using modern methods have been scarce. Even seemingly straightforward studies, such as examining viral tissue and cell tropism in vivo, have been difficult to conduct due to the absence of standardized SHFV-specific reagents. Here we report the establishment of an in situ hybridization assay for the detection of SHFV and distantly related Kibale red colobus virus 1 (KRCV-1) RNA in cell culture. In addition, we detected SHFV RNA in formalin-fixed, paraffin-embedded tissues from an infected rhesus monkey (Macaca mulatta). The assay is easily performed and can clearly distinguish between SHFV and KRCV-1. Thus, if further developed, this assay may be useful during future studies evaluating the mechanisms by which a simian arterivirus with a restricted cell tropism can cause a lethal nonhuman primate disease similar in clinical presentation to human viral hemorrhagic fevers. PMID:26963736

  14. miRNA in situ hybridization in circulating tumor cells - MishCTC

    PubMed Central

    Ortega, Francisco G.; Lorente, Jose A.; Garcia Puche, Jose L.; Ruiz, Maria P.; Sanchez-Martin, Rosario M.; de Miguel-Pérez, Diego; Diaz-Mochon, Juan J.; Serrano, Maria J.

    2015-01-01

    Circulating tumor cells (CTCs) must be phenotypically and genetically characterized before they can be utilized in clinical applications. Here, we present the first protocol for the detection of miRNAs in CTCs using in situ hybridization (ISH) combined with immunomagnetic selection based on cytokeratin (CK) expression and immunocytochemistry. Locked-Nucleic Acid (LNA) probes associated with an enzyme-labeled fluorescence (ELF) signal amplification approach were used to detect miRNA-21 in CTCs. This protocol was optimized using both epithelial tumor (MDA-MB468) and epithelial non-tumor (MCF-10A) cell lines, and miRNA-21 was selected as the target miRNA because of its known role as an onco-miRNA. Hematopoietic cells do not express miRNA-21; thus, miRNA-21 is an ideal marker for detecting CTCs. Peripheral blood samples were taken from 25 cancer patients and these samples were analyzed using our developed protocol. Of the 25 samples, 11 contained CTCs. For all 11 CTC-positive samples, the isolated CTCs expressed both CK and miRNA-21. Finally, the protocol was applied to monitor miRNA-21 expression in epithelial to mesenchymal transition (EMT)-induced MCF-7 cells, an epithelial tumor cell line. CK expression was lost in these cells, whereas miRNA-21 was still expressed, suggesting that miRNA-21 might be a good marker for detecting CTCs with an EMT phenotype. PMID:25777797

  15. In situ synthesis of TiO2/polyethylene terephthalate hybrid nanocomposites at low temperature

    NASA Astrophysics Data System (ADS)

    Peng, Xinyan; Ding, Enyong; Xue, Feng

    2012-06-01

    TiO2 nanoflowers were in situ grown on polyethylene terephthalate (PET) non-woven fabric by hydrolysis of TiCl4 in aqueous solution in the presence of nanocrystal cellulose grafted PET fabric (NCC-g-PET) at a low temperature of 70 °C. Nanocrystal cellulose (NCC) pre-grafted on PET fabric acted as hydrophilic substrate and morphology inducing agent to promote the nucleation and crystal growth of TiO2. Detailed information on the synthetic process was presented. The resulting samples were characterized using FE-SEM, EDS, ATR-IR, Raman microscopy, XRD and TG analysis. The photocatalytic activity of the samples was evaluated by the degradation of orange methyl under solar light. Characteristic results indicate that rutile TiO2 nanoflowers have grown abundantly on PET non-woven fabric, and the established hydrogen bonding strengthens the interfacial interaction between the inorganic particles and the polymeric substrates. The methyl orange decoloration test under natural solar light demonstrates that this TiO2/PET hybrid nanocomposites exhibit excellent self-cleaning performance which is expected to have a good potential for commercialization.

  16. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization.

    PubMed

    Sekar, Raju; Pernthaler, Annelie; Pernthaler, Jakob; Warnecke, Falk; Posch, Thomas; Amann, Rudolf

    2003-05-01

    We tested a previously described protocol for fluorescence in situ hybridization of marine bacterioplankton with horseradish peroxidase-labeled rRNA-targeted oligonucleotide probes and catalyzed reporter deposition (CARD-FISH) in plankton samples from different lakes. The fraction of Bacteria detected by CARD-FISH was significantly lower than after FISH with fluorescently monolabeled probes. In particular, the abundances of aquatic Actinobacteria were significantly underestimated. We thus developed a combined fixation and permeabilization protocol for CARD-FISH of freshwater samples. Enzymatic pretreatment of fixed cells was optimized for the controlled digestion of gram-positive cell walls without causing overall cell loss. Incubations with high concentrations of lysozyme (10 mg ml(-1)) followed by achromopeptidase (60 U ml(-1)) successfully permeabilized cell walls of Actinobacteria for subsequent CARD-FISH both in enrichment cultures and environmental samples. Between 72 and >99% (mean, 86%) of all Bacteria could be visualized with the improved assay in surface waters of four lakes. For freshwater samples, our method is thus superior to the CARD-FISH protocol for marine Bacteria (mean, 55%) and to FISH with directly fluorochrome labeled probes (mean, 67%). Actinobacterial abundances in the studied systems, as detected by the optimized protocol, ranged from 32 to >55% (mean, 45%). Our findings confirm that members of this lineage are among the numerically most important Bacteria of freshwater picoplankton.

  17. Fifty probands with extra structurally abnormal chromosomes characterized by fluorescence in situ hybridization

    SciTech Connect

    Blennow, E.; Telenius, H.; Nordenskjoeld, M.

    1995-01-02

    Extra structurally abnormal chromosomes (ESACs) are small supernumerary chromosomes often associated with developmental abnormalities and malformations. We present 50 probands with ESACs characterized by fluorescence in situ hybridization using centromere-specific probes and chromosome-specific libraries. ESAC-specific libraries were constructed by flow sorting and subsequent amplification by DOP-PCR. Using such ESAC-specific libraries we were able to outline the chromosome regions involved. Twenty-three of the 50 ESACs were inverted duplications of chromosome 15 (inv dup(15)), including patients with normal phenotypes and others with similar clinical symptoms. These 2 groups differed in size and shape of the inv dup(15). Patients with a large inv dup(15), which included the Prader-Willi region, had a high risk of abnormality, whereas patients with a small inv dup(15), not including the Prader-Willi region, were normal. ESACs derived from chromosomes 13 or 21 appeared to have a low risk of abnormality, while one out of 3 patients with an ESAC derived from chromosome 14 had discrete symptoms. One out of 3 patients with an ESAC derived from chromosome 22 had severe anomalies, corresponding to some of the manifestations of the cat eye syndrome. Small extra ring chromosomes of autosomal origin and ESACs identified as i(12p) or i(18p) were all associated with a high risk of abnormality. 42 refs., 2 figs., 2 tabs.

  18. Potential clinical impact of three-dimensional visualization for fluorescent in situ hybridization image analysis

    NASA Astrophysics Data System (ADS)

    Li, Zheng; Li, Shibo; Bin, Zheng; Zhang, Roy; Li, Yuhua; Tian, Huimin; Chen, Wei; Liu, Hong

    2012-05-01

    Chromosomal translocation is strong indication of cancers. Fluorescent in situ hybridization (FISH) can effectively detect this translocation and achieve high accuracy in disease diagnosis and prognosis assessment. For this purpose, whole chromosome paint probes are utilized to image the configuration of DNA fragments. Although two-dimensional (2-D) microscopic images are typically used in FISH signal analysis, we present a case where the translocation occurs in the depth direction where two probed FISH signals are overlapped in the projected image plane. Thus, the translocation cannot be identified. However, when imaging the whole specimen with a confocal microscope at 27 focal planes with 0.5-μm step interval, the translocation can be clearly identified due to the free rotation capability by the three-dimensional (3-D) visualization. Such a translocation detection error of using 2-D images might be critical in detecting and diagnosing early or subtle disease cases where detecting a small number of abnormal cells can make diagnostic difference. Hence, the underlying implication of this report suggests that utilizing 3-D visualization may improve the overall accuracy of FISH analysis for some clinical cases. However, the clinical efficiency and cost of using 3-D versus 2-D imaging methods are also to be assessed carefully.

  19. Analysis of human invasive cytotrophoblasts using multicolor fluorescence in situ hybridization.

    PubMed

    Weier, Jingly F; Hartshorne, Christy; Nguyen, Ha Nam; Baumgartner, Adolf; Polyzos, Aris A; Lemke, Kalistyn H; Zeng, Hui; Weier, Heinz-Ulrich G

    2013-12-01

    Multicolor fluorescence in situ hybridization, or FISH, is a widely used method to assess fixed tissues or isolated cells for numerical and structural chromosome aberrations. Unlike other screening procedures which provide average chromosome numbers for heterogeneous samples, FISH is a sensitive cell-by-cell method to analyze the distribution of abnormal cells in complex tissues. Here, we applied FISH to characterize chromosomal composition of a rare, but very important class of human cells that stabilize the fetal-maternal interface connecting the placenta to the uterine wall during early pregnancy, called invasive cytotrophoblasts (iCTBs). Combining differently-labeled, chromosome-specific DNA probes, we were able to unambiguously determine the number of up to six different autosomes and gonosomes in individual cell nuclei from iCTBs selected on the basis of their invasive behavior. In this manuscript, we describe a method for generation of iCTBs from placental villi, and provide the complete workflow of our FISH experiments including a detailed description of reagents and a trouble-shooting guide. We also include an in-depth discussion of the various types and sources of DNA probes which have evolved considerably in the last two decades. Thus, this communication represents both a complete guide as well as a valuable resource, intended to allow an average laboratory to reproduce the experiments and minimize the amount of specialized, and often costly, equipment.

  20. Quantitative analysis of microRNAs in tissue microarrays by in situ hybridization

    PubMed Central

    Hanna, Jason A.; Wimberly, Hallie; Kumar, Salil; Slack, Frank; Agarwal, Seema; Rimm, David L.

    2013-01-01

    MicroRNAs (miRNAs) have emerged as key regulators in the pathogenesis of cancers where they can act as either oncogenes or tumor suppressors. Most miRNA measurement methods require total RNA extracts which lack critical spatial information and present challenges for standardization. We have developed and validated a method for the quantitative analysis of miRNA expression by in situ hybridization (ISH) allowing for the direct assessment of tumor epithelial expression of miRNAs. This co-localization based approach (called qISH) utilizes DAPI and cytokeratin immunofluorescence to establish subcellular compartments in the tumor epithelia, then multiplexed with the miRNA ISH, allows for quantitative measurement of miRNA expression within these compartments. We use this approach to assess miR-21, miR-92a, miR-34a, and miR-221 expression in 473 breast cancer specimens on tissue microarrays. We found that miR-221 levels are prognostic in breast cancer illustrating the high-throughput method and confirming that miRNAs can be valuable biomarkers in cancer. Furthermore, in applying this method we found that the inverse relationship between miRNAs and proposed target proteins is difficult to discern in large population cohorts. Our method demonstrates an approach for large cohort, tissue microarray-based assessment of miRNA expression. PMID:22482439

  1. Morphing hybrid honeycomb (MOHYCOMB) with in situ Poisson’s ratio modulation

    NASA Astrophysics Data System (ADS)

    Heath, Callum J. C.; Neville, Robin M.; Scarpa, Fabrizio; Bond, Ian P.; Potter, Kevin D.

    2016-08-01

    Electrostatic adhesion can be used as a means of reversible attachment. Through application of high voltage (~2 kV) across closely spaced parallel plate electrodes, significant shear stresses (11 kPa) can be generated. The highest levels of electrostatic holding force can be achieved through close contact of connection surfaces; this is facilitated by flexible electrodes which can conform to reduce air gaps. Cellular structures are comprised of thin walled elements, making them ideal host structures for electrostatic adhesive elements. The reversible adhesion provides control of the internal connectivity of the cellular structure, and determines the effective cell geometry. This would offer variable stiffness and control of the effective Poisson’s ratio of the global cellular array. Using copper-polyimide thin film laminates and PVDF thin film dielectrics, double lap shear electrostatic adhesive elements have been introduced to a cellular geometry. By activating different groups of reversible adhesive interfaces, the cellular array can assume four different cell configurations. A maximum stiffness modulation of 450% between the ‘All off’ and ‘All on’ cell morphologies has been demonstrated. This structure is also capable of in situ effective Poisson’s ratio variations, with the ability to switch between values of ‑0.45 and 0.54. Such a structure offers the potential for tuneable vibration absorption (due to its variable stiffness properties), or as a smart honeycomb with controllable curvature and is termed morphing hybrid honeycomb.

  2. Specific Detection of Two Divergent Simian Arteriviruses Using RNAscope In Situ Hybridization.

    PubMed

    Yú, Shu Qìng; Caì, Yíngyún; Lyons, Cassandra; Johnson, Reed F; Postnikova, Elena; Mazur, Steven; Johnson, Joshua C; Radoshitzky, Sheli R; Bailey, Adam L; Lauck, Michael; Goldberg, Tony L; O'Connor, David H; Jahrling, Peter B; Friedrich, Thomas C; Kuhn, Jens H

    2016-01-01

    Simian hemorrhagic fever (SHF) is an often lethal disease of Asian macaques. Simian hemorrhagic fever virus (SHFV) is one of at least three distinct simian arteriviruses that can cause SHF, but pathogenesis studies using modern methods have been scarce. Even seemingly straightforward studies, such as examining viral tissue and cell tropism in vivo, have been difficult to conduct due to the absence of standardized SHFV-specific reagents. Here we report the establishment of an in situ hybridization assay for the detection of SHFV and distantly related Kibale red colobus virus 1 (KRCV-1) RNA in cell culture. In addition, we detected SHFV RNA in formalin-fixed, paraffin-embedded tissues from an infected rhesus monkey (Macaca mulatta). The assay is easily performed and can clearly distinguish between SHFV and KRCV-1. Thus, if further developed, this assay may be useful during future studies evaluating the mechanisms by which a simian arterivirus with a restricted cell tropism can cause a lethal nonhuman primate disease similar in clinical presentation to human viral hemorrhagic fevers. PMID:26963736

  3. Fluorescent In situ hybridization allows rapid identification of microorganisms in blood cultures.

    PubMed

    Kempf, V A; Trebesius, K; Autenrieth, I B

    2000-02-01

    Using fluorescent in situ hybridization (FISH) with rRNA-targeted fluorescently labelled oligonucleotide probes, pathogens were rapidly detected and identified in positive blood culture bottles without cultivation and biotyping. In this study, 115 blood cultures with a positive growth index as determined by a continuous-reading automated blood culture system were examined by both conventional laboratory methods and FISH. For this purpose, oligonucleotide probes that allowed identification of approximately 95% of those pathogens typically associated with bacteremia were produced. The sensitivity and specificity of these probes were 100%. From all 115 blood cultures, microorganisms were grown after 1 day and identification to the family, genus, or species level was achieved after 1 to 3 days while 111 samples (96.5%) were similarly identified by FISH within 2.5 h. Staphylococci were identified in 62 of 62 samples, streptococci and enterococci were identified in 19 of 20 samples, gram-negative rods were identified in 28 of 30 samples, and fungi were identified in two of two samples. Thus, FISH is an appropriate method for identification of pathogens grown in blood cultures from septicemic patients.

  4. A novel three-color, clone-specific fluorescence in situ hybridization procedure for monoclonal gammopathies.

    PubMed

    Ahmann, G J; Jalal, S M; Juneau, A L; Christensen, E R; Hanson, C A; Dewald, G W; Greipp, P R

    1998-02-01

    We have developed a three-color cytoplasmic immunoglobulin (cIg) and fluorescence in situ hybridization (FISH) technique to detect plasma cell chromosomal aneuploidy in patients with multiple myeloma (MM), monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), and amyloidosis (AL). Immunofluorescent-labeled antibodies to detect light chain expression and six directly labeled alpha-satellite chromosome specific enumeration probes (CEP) were used simultaneously to detect aneuploidy of the plasma cells. The six probes were specific for chromosomes 7, 9, 11, 15, 18, and X. The technique was tested in 12 consecutive patient samples (5 MM, 2 MGUS, 3 SMM, and 2 AL). Based on the alpha-satellite signals, we found trisomic clones for CEP 7 (4 of 12), CEP 11 (4 of 12), CEP X (1 of 12), CEP 9 (8 of 12), CEP 15 (7 of 12), and CEP 18 (5 of 12). Trisomic clones of at least one of the six chromosomes were present in 9 of 12 patients. We believe that this technique efficiently identifies monotypic plasma cells and permits simultaneous analysis of numeric chromosome anomalies by FISH in emerging neoplastic cells. We are in the process of applying this technique to a series of about 100 newly diagnosed monoclonal gammopathy patients. PMID:9460493

  5. Does polyomavirus infection interfere with bladder cancer fluorescence in situ hybridization?

    PubMed

    Hossain, Deloar; Hull, David; Kalantarpour, Fatemeh; Maitlen, Rebecca; Qian, Junqi; Bostwick, David G

    2014-03-01

    Urine cytology is a proven and widely used screening tool for the detection of urothelial carcinoma. However, morphologic features of polyomavirus infected cells, characterized by nuclear inclusions (decoy cells) are a known source of diagnostic confusion with malignancy. Fluorescence in situ hybridization (FISH) is now routinely used to support the cytological diagnosis of urothelial carcinoma and monitor for recurrence. We sought to determine whether polyomavirus infection could result in positive FISH results (aneuploidy). This study deals with retrospective study of 100 polyomavirus-infected urine samples from patients with no history of urothelial carcinoma or organ transplantation. All cases were stained with Papanicolaou and acid hematoxylin stain. One slide from each sample was de-stained and FISH was performed using chromosome enumeration probes 3, 7, 17, and locus-specific probe 9p21. Adequate cells for FISH analysis (25 cells) were present in 81 cases; 19 cases were insufficient due to loss of cells during de-staining and FISH preparation process. All polyomavirus-infected cells (decoy cells) exhibited a normal chromosome pattern. Four cases were FISH positive, but there were no positive decoy cells. Decoy cells did not exhibit aneuploidy by FISH. The presence of decoy cells does not exclude the possibility of concurrent urothelial carcinoma. Acid hematoxylin stain appeared to supplement the Papanicolou stain in identifying and confirming the presence of polyomavirus infection. PMID:24006232

  6. Fluorescence In Situ Hybridization (FISH) Assays for Diagnosing Malaria in Endemic Areas

    PubMed Central

    Shah, Jyotsna; Mark, Olivia; Weltman, Helena; Barcelo, Nicolas; Lo, Wai; Wronska, Danuta; Kakkilaya, Srinivas; Rao, Aravinda; Bhat, Shalia T.; Sinha, Ruchi; Omar, Sabah; Moro, Manuel; Gilman, Robert H.; Harris, Nick

    2015-01-01

    Malaria is a responsible for approximately 600 thousand deaths worldwide every year. Appropriate and timely treatment of malaria can prevent deaths but is dependent on accurate and rapid diagnosis of the infection. Currently, microscopic examination of the Giemsa stained blood smears is the method of choice for diagnosing malaria. Although it has limited sensitivity and specificity in field conditions, it still remains the gold standard for the diagnosis of malaria. Here, we report the development of a fluorescence in situ hybridization (FISH) based method for detecting malaria infection in blood smears and describe the use of an LED light source that makes the method suitable for use in resource-limited malaria endemic countries. The Plasmodium Genus (P-Genus) FISH assay has a Plasmodium genus specific probe that detects all five species of Plasmodium known to cause the disease in humans. The P. falciparum (PF) FISH assay and P. vivax (PV) FISH assay detect and differentiate between P. falciparum and P. vivax respectively from other Plasmodium species. The FISH assays are more sensitive than Giemsa. The sensitivities of P-Genus, PF and PV FISH assays were found to be 98.2%, 94.5% and 98.3%, respectively compared to 89.9%, 83.3% and 87.9% for the detection of Plasmodium, P. falciparum and P. vivax by Giemsa staining respectively. PMID:26333092

  7. Visualization of episomal and integrated Epstein-Barr virus DNA by fiber fluorescence in situ hybridization.

    PubMed

    Reisinger, Jürgen; Rumpler, Silvia; Lion, Thomas; Ambros, Peter F

    2006-04-01

    For many Epstein-Barr virus (EBV)-associated malignancies, it is still a matter of controversy whether infected cells harbor episomal or chromosomally integrated EBV genomes or both. It is well established that the expression of EBV genes per se carries oncogenic potential, but the discrimination between episomal and integrated forms is of great relevance because integration events can contribute to the oncogenic properties of EBV, whereas host cells that exclusively harbor viral episomes may not carry the risks mediated by chromosomal integration. This notion prompted us to establish a reliable technique that not only allows to unequivocally discriminate episomal from integrated EBV DNA, but also provides detailed insights into the genomic organization of the virus. Here, we show that dynamic molecular combing of host cell DNA combined with fluorescence in situ hybridization (FISH) using EBV-specific DNA probes facilitate unambiguous discrimination of episomal from integrated viral DNA. Furthermore, the detection of highly elongated internal repeat 1 (IR1) sequences provides evidence that this method permits detection of major genomic alterations within the EBV genome. Thus, fiber FISH may also provide valuable insights into the genomic organization of viral genomes other than EBV. PMID:16217752

  8. Human papillomavirus (HPV) DNA in focal epithelial hyperplasia by in situ hybridization.

    PubMed

    Padayachee, A; van Wyk, C W

    1991-05-01

    Eighteen cases of focal epithelial hyperplasia (FEH) were investigated for the presence of human papillomavirus (HPV) group specific antigen by immunocytochemistry and HPV types 1, 6, 11, 13, 16, 18 and 32 by DNA in situ hybridization employing biotinylated probes. Seven (39%) specimens demonstrated the presence of HPV group specific antigen. Fifteen (83%) specimens were positive for HPV DNA: 9 (60%) showed HPV 32, of which 6 were on non-keratinized mucosa and 3 on border of keratinized and non-keratinized mucosa; 5 (33%) showed HPV 13, 4 lesions on keratinized mucosa and 1 on non-keratinized mucosa; 1 (7%) specimen on non-keratinized mucosa showed HPV-11 related. Two specimens on different sites from one patient showed the same HPV type and one patient had, in addition to FEH, a squamous papilloma also demonstrating the same HPV type. Results show a specific HPV distribution pattern in the epithelium indicating areas of high viral concentration adjacent to areas of low or no viral concentration. This study also indicates the possibility of tissue-site specificity or a latent infection and the possibility of a yet unidentified HPV type associated with FEH. It is suggested that future monitoring of patients be carried out with special reference to HPV type and anatomical distribution pattern for FEH lesions.

  9. Improved quantification of Dehalococcoides species by fluorescence in situ hybridization and catalyzed reporter deposition.

    PubMed

    Fazi, Stefano; Aulenta, Federico; Majone, Mauro; Rossetti, Simona

    2008-03-01

    Chlorinated ethenes contamination of soil and groundwater is a widespread problem in most industrialized countries. To date, there is a general consensus in the literature that members of the genus Dehalococcoides are required for complete dechlorination of these compounds. The availability of specific identification tools to track their distribution in the field is therefore a topic of particular relevance in environmental studies. These microorganisms have been successfully visualized by fluorescence in situ hybridization (FISH) in highly active dechlorinating cultures. However, FISH detection of Dehalococcoides under low activity conditions can be strongly hampered by their small cell size and low ribosome content. In this study, catalyzed reporter deposition (CARD)-FISH was employed as an alternative detection method. In a trichloroethene (TCE) dechlorinating enrichment culture, CARD-FISH, using proteinase K as a permeabilization pre-treatment, was found to be significantly superior to conventional FISH in terms of both microscopic visualization and quantification efficiency (about 30%). An application of this method on contaminated aquifer samples is also presented and discussed.

  10. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH).

    PubMed

    Vilas Boas, Diana; Almeida, Carina; Sillankorva, Sanna; Nicolau, Ana; Azeredo, Joana; Azevedo, Nuno F

    2016-01-01

    Bacteriophage-host interaction studies in biofilm structures are still challenging due to the technical limitations of traditional methods. The aim of this study was to provide a direct fluorescence in situ hybridization (FISH) method based on locked nucleic acid (LNA) probes, which targets the phage replication phase, allowing the study of population dynamics during infection. Bacteriophages specific for two biofilm-forming bacteria, Pseudomonas aeruginosa and Acinetobacter, were selected. Four LNA probes were designed and optimized for phage-specific detection and for bacterial counterstaining. To validate the method, LNA-FISH counts were compared with the traditional plaque forming unit (PFU) technique. To visualize the progression of phage infection within a biofilm, colony-biofilms were formed and infected with bacteriophages. A good correlation (r = 0.707) was observed between LNA-FISH and PFU techniques. In biofilm structures, LNA-FISH provided a good discrimination of the infected cells and also allowed the assessment of the spatial distribution of infected and non-infected populations. PMID:26813295

  11. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method.

    PubMed

    Machado, António; Castro, Joana; Cereija, Tatiana; Almeida, Carina; Cerca, Nuno

    2015-01-01

    Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6-99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis. PMID:25737820

  12. Fluorescent In Situ Hybridization Allows Rapid Identification of Microorganisms in Blood Cultures

    PubMed Central

    Kempf, Volkhard A. J.; Trebesius, Karlheinz; Autenrieth, Ingo B.

    2000-01-01

    Using fluorescent in situ hybridization (FISH) with rRNA-targeted fluorescently labelled oligonucleotide probes, pathogens were rapidly detected and identified in positive blood culture bottles without cultivation and biotyping. In this study, 115 blood cultures with a positive growth index as determined by a continuous-reading automated blood culture system were examined by both conventional laboratory methods and FISH. For this purpose, oligonucleotide probes that allowed identification of approximately 95% of those pathogens typically associated with bacteremia were produced. The sensitivity and specificity of these probes were 100%. From all 115 blood cultures, microorganisms were grown after 1 day and identification to the family, genus, or species level was achieved after 1 to 3 days while 111 samples (96.5%) were similarly identified by FISH within 2.5 h. Staphylococci were identified in 62 of 62 samples, streptococci and enterococci were identified in 19 of 20 samples, gram-negative rods were identified in 28 of 30 samples, and fungi were identified in two of two samples. Thus, FISH is an appropriate method for identification of pathogens grown in blood cultures from septicemic patients. PMID:10655393

  13. Multicolour preparations for in situ hybridization using precipitating enzyme cytochemistry in combination with reflection contrast microscopy.

    PubMed

    Speel, E J; Kamps, M; Bonnet, J; Ramaekers, F C; Hopman, A H

    1993-11-01

    We have further developed a method for the detection of different enzyme cytochemical reaction products by means of reflection contrast microscopy (RCM). By embedding these enzyme precipitates in a protein matrix, we were able to prevent the reaction products from dissolving in immersion oil, which is required for RCM analysis. The applicability of the RCM procedure is, therefore, extended to a range of cytochemical enzyme precipitation methods, which normally result in oil soluble reaction products. To test their usefulness, these enzyme precipitates have been used in single- and well as double-label in situ hybridization (ISH) procedures to visualize a number of DNA target sequences by several different reflection colours, i.e. white, yellow and red. Three repetitive DNA probes for the (sub)centromeric regions of chromosomes 1, 7 and 17, as well as a repetitive DNA probe for the telomeric region of chromosome 1, and two cosmid DNA probes (40 kb each) for both arms of chromosome 11 could be detected with high efficiency in both interphase and metaphase preparations. Moreover the enzyme precipitates were shown to be stable upon exposure to excitation light or upon storage. It may be concluded that these findings render RCM a sensitive method for the visualization of multiple targets in biological specimens. PMID:8307777

  14. Does polyomavirus infection interfere with bladder cancer fluorescence in situ hybridization?

    PubMed

    Hossain, Deloar; Hull, David; Kalantarpour, Fatemeh; Maitlen, Rebecca; Qian, Junqi; Bostwick, David G

    2014-03-01

    Urine cytology is a proven and widely used screening tool for the detection of urothelial carcinoma. However, morphologic features of polyomavirus infected cells, characterized by nuclear inclusions (decoy cells) are a known source of diagnostic confusion with malignancy. Fluorescence in situ hybridization (FISH) is now routinely used to support the cytological diagnosis of urothelial carcinoma and monitor for recurrence. We sought to determine whether polyomavirus infection could result in positive FISH results (aneuploidy). This study deals with retrospective study of 100 polyomavirus-infected urine samples from patients with no history of urothelial carcinoma or organ transplantation. All cases were stained with Papanicolaou and acid hematoxylin stain. One slide from each sample was de-stained and FISH was performed using chromosome enumeration probes 3, 7, 17, and locus-specific probe 9p21. Adequate cells for FISH analysis (25 cells) were present in 81 cases; 19 cases were insufficient due to loss of cells during de-staining and FISH preparation process. All polyomavirus-infected cells (decoy cells) exhibited a normal chromosome pattern. Four cases were FISH positive, but there were no positive decoy cells. Decoy cells did not exhibit aneuploidy by FISH. The presence of decoy cells does not exclude the possibility of concurrent urothelial carcinoma. Acid hematoxylin stain appeared to supplement the Papanicolou stain in identifying and confirming the presence of polyomavirus infection.

  15. Ectopic adrenal tissue in the thorax: a case report with in situ hybridization and immunohistochemical studies.

    PubMed

    Shigematsu, Kazuto; Toriyama, Kan; Kawai, Kioko; Takahara, Osamu

    2007-01-01

    Ectopic or accessory adrenal tissues are usually found in the upper abdomen or along the path of descent of the gonads. The occurrence of supradiaphragmatic adrenal tissue is extremely rare. We report a case of ectopic adrenal tissue composed of both cortical and medullary cells in a 99-year-old woman. The lesion was found incidentally in the paratracheal region at autopsy. We performed in situ hybridization and immunohistochemistry to confirm that the ectopic adrenal tissue possessed the same steroidogenesis as a normal adrenal gland. The ectopic adrenal tissue was encapsulated by fibrous tissue and composed of cells expressing all steroidogenic enzyme mRNAs. The centrally located cells showed immunoreactivities for tyrosine hydroxylase (TH), dopamine beta hydroxylase (DBH), and phenylethanolamine-N-methyltransferase (PNMT). Expression of ACTH receptor (ACTHR) was also evident. These findings indicated that this ectopic adrenal tissue had the capability for steroid and catecholamine biosynthesis under the control of ACTH, and that it might function adequately even under a condition of bilateral adrenal insufficiency.

  16. In Situ Growth of In2S3 Nanorods in Poly(3-Hexylthiophene) Hybrid Films

    NASA Astrophysics Data System (ADS)

    Cota-Leal, M.; Sotelo-Lerma, M.; Corona-Corona, I.; Quevedo-Lopez, M. A.

    2016-04-01

    A novel and efficient gas-liquid method for the in situ synthesis of In2S3 nanorods in a poly(3-hexylthiophene) (P3HT) matrix is demonstrated. The method involves a self-contained reaction between Na2S and HCl that produces H2S, which reacts with a P3HT/InCl3 solution resulting in hybrid P3HT/In2S3 films. The Na2S solution is regenerated for further use. The method yielded results in In2S3 nanoparticles and nanorods in a P3HT matrix, as observed by transmission electron microscopy. The In2S3 nanorods are 3 nm wide and ~30 nm long. The size of the nanorods is dependent on the P3HT concentration. The band gap (E g) of the resulting In2S3/P3HT is in the range of 2.97-3.71 eV, as measured by UV-visible spectroscopy (UV-Vis) Charge transfer in the In2S3/P3HT was demonstrated by the presence of quenching in the fluorescence spectra of the composite. Chemical composition was investigated by energy dispersive x-ray spectroscopy analysis, as well as x-ray photoelectron spectroscopy. Both techniques demonstrated the formation of In2S3.

  17. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method

    PubMed Central

    Machado, António; Castro, Joana; Cereija, Tatiana; Almeida, Carina

    2015-01-01

    Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6–99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis. PMID:25737820

  18. The design of a microscopic system for typical fluorescent in-situ hybridization applications

    NASA Astrophysics Data System (ADS)

    Yi, Dingrong; Xie, Shaochuan

    2013-12-01

    Fluorescence in situ hybridization (FISH) is a modern molecular biology technique used for the detection of genetic abnormalities in terms of the number and structure of chromosomes and genes. The FISH technique is typically employed for prenatal diagnosis of congenital dementia in the Obstetrics and Genecology department. It is also routinely used to pick up qualifying breast cancer patients that are known to be highly curable by the prescription of Her2 targeted therapy. During the microscopic observation phase, the technician needs to count typically green probe dots and red probe dots contained in a single nucleus and calculate their ratio. This procedure need to be done to over hundreds of nuclei. Successful implementation of FISH tests critically depends on a suitable fluorescent microscope which is primarily imported from overseas due to the complexity of such a system beyond the maturity of the domestic optoelectrical industry. In this paper, the typical requirements of a fluorescent microscope that is suitable for FISH applications are first reviewed. The focus of this paper is on the system design and computational methods of an automatic florescent microscopy with high magnification APO objectives, a fast spinning automatic filter wheel, an automatic shutter, a cooled CCD camera used as a photo-detector, and a software platform for image acquisition, registration, pseudo-color generation, multi-channel fusing and multi-focus fusion. Preliminary results from FISH experiments indicate that this system satisfies routine FISH microscopic observation tasks.

  19. Morphing hybrid honeycomb (MOHYCOMB) with in situ Poisson’s ratio modulation

    NASA Astrophysics Data System (ADS)

    Heath, Callum J. C.; Neville, Robin M.; Scarpa, Fabrizio; Bond, Ian P.; Potter, Kevin D.

    2016-08-01

    Electrostatic adhesion can be used as a means of reversible attachment. Through application of high voltage (~2 kV) across closely spaced parallel plate electrodes, significant shear stresses (11 kPa) can be generated. The highest levels of electrostatic holding force can be achieved through close contact of connection surfaces; this is facilitated by flexible electrodes which can conform to reduce air gaps. Cellular structures are comprised of thin walled elements, making them ideal host structures for electrostatic adhesive elements. The reversible adhesion provides control of the internal connectivity of the cellular structure, and determines the effective cell geometry. This would offer variable stiffness and control of the effective Poisson’s ratio of the global cellular array. Using copper-polyimide thin film laminates and PVDF thin film dielectrics, double lap shear electrostatic adhesive elements have been introduced to a cellular geometry. By activating different groups of reversible adhesive interfaces, the cellular array can assume four different cell configurations. A maximum stiffness modulation of 450% between the ‘All off’ and ‘All on’ cell morphologies has been demonstrated. This structure is also capable of in situ effective Poisson’s ratio variations, with the ability to switch between values of -0.45 and 0.54. Such a structure offers the potential for tuneable vibration absorption (due to its variable stiffness properties), or as a smart honeycomb with controllable curvature and is termed morphing hybrid honeycomb.

  20. Visualizing the Spatial Relationship of the Genome with the Nuclear Envelope Using Fluorescence In Situ Hybridization.

    PubMed

    Clements, Craig S; Bikkul, Ural; Ahmed, Mai Hassan; Foster, Helen A; Godwin, Lauren S; Bridger, Joanna M

    2016-01-01

    The genome has a special relationship with the nuclear envelope in cells. Much of the genome is anchored at the nuclear periphery, tethered by chromatin binding proteins such nuclear lamins and other integral membrane proteins. Even though there are global assays such as DAM-ID or ChIP to assess what parts of the genome are associated with the nuclear envelope, it is also essential to be able to visualize regions of the genome in order to reveal their individual relationships with nuclear structures in single cells. This is executed by fluorescence in situ hybridization (FISH) in 2-dimensional flattened nuclei (2D-FISH) or 3-dimensionally preserved cells (3D-FISH) in combination with indirect immunofluorescence to reveal structural proteins. This chapter explains the protocols for 2D- and 3D-FISH in combination with indirect immunofluorescence and discusses options for image capture and analysis. Due to the nuclear envelope proteins being part of the non-extractable nucleoskeleton, we also describe how to prepare DNA halos through salt extraction and how they can be used to study genome behavior and association when combined with 2D-FISH. PMID:27147055

  1. Hybrid Al + Al3Ni metallic foams synthesized in situ via laser engineered net shaping

    NASA Astrophysics Data System (ADS)

    Zheng, Baolong; Li, Ying; Smugeresky, John E.; Zhou, Yizhang; Baker, Dean; Lavernia, Enrique J.

    2011-09-01

    A hybrid, Al + Al3Ni metallic foam was synthesized in situ via laser engineered net shaping (LENS®) of Ni-coated 6061 Al powder in the absence of a foaming agent. During LENS® processing, the Ni coating reacted with the Al matrix, resulting in the simultaneous formation of a fine dispersion of Al3Ni, and a high volume fraction of porosity. As a reinforcement phase, the intermetallic compound formed particles with a size range of 1-5 µm and a volume fraction of 63%, with accompanying 35-300 µm pores with a 60% volume fraction. The microstructure of the as-deposited Al + Al3Ni composite foams was characterized using SEM, EDS, XRD and TEM/HRTEM techniques. The evolution of the microstructure was analyzed on the basis of the thermal field present during deposition, paying particular attention to the thermodynamics of the Al3Ni intermetallic compound formation as well as discussing the mechanisms that may be responsible for the observed porosity. The mechanical behavior of the as-deposited material was characterized using compression and microhardness testing, indicating that the yield strength and hardness are 190 MPa and 320 HV, respectively, which represents an increase of over three times higher than that of annealed Al6061, or similar to heat-treated Al6061 fully dense matrix, and much higher than those of traditional Al alloy foams, and with a low density of 1.64 g/m3.

  2. Visualizing the Spatial Relationship of the Genome with the Nuclear Envelope Using Fluorescence In Situ Hybridization.

    PubMed

    Clements, Craig S; Bikkul, Ural; Ahmed, Mai Hassan; Foster, Helen A; Godwin, Lauren S; Bridger, Joanna M

    2016-01-01

    The genome has a special relationship with the nuclear envelope in cells. Much of the genome is anchored at the nuclear periphery, tethered by chromatin binding proteins such nuclear lamins and other integral membrane proteins. Even though there are global assays such as DAM-ID or ChIP to assess what parts of the genome are associated with the nuclear envelope, it is also essential to be able to visualize regions of the genome in order to reveal their individual relationships with nuclear structures in single cells. This is executed by fluorescence in situ hybridization (FISH) in 2-dimensional flattened nuclei (2D-FISH) or 3-dimensionally preserved cells (3D-FISH) in combination with indirect immunofluorescence to reveal structural proteins. This chapter explains the protocols for 2D- and 3D-FISH in combination with indirect immunofluorescence and discusses options for image capture and analysis. Due to the nuclear envelope proteins being part of the non-extractable nucleoskeleton, we also describe how to prepare DNA halos through salt extraction and how they can be used to study genome behavior and association when combined with 2D-FISH.

  3. A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans.

    PubMed

    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. PMID:27154969

  4. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH).

    PubMed

    Vilas Boas, Diana; Almeida, Carina; Sillankorva, Sanna; Nicolau, Ana; Azeredo, Joana; Azevedo, Nuno F

    2016-01-01

    Bacteriophage-host interaction studies in biofilm structures are still challenging due to the technical limitations of traditional methods. The aim of this study was to provide a direct fluorescence in situ hybridization (FISH) method based on locked nucleic acid (LNA) probes, which targets the phage replication phase, allowing the study of population dynamics during infection. Bacteriophages specific for two biofilm-forming bacteria, Pseudomonas aeruginosa and Acinetobacter, were selected. Four LNA probes were designed and optimized for phage-specific detection and for bacterial counterstaining. To validate the method, LNA-FISH counts were compared with the traditional plaque forming unit (PFU) technique. To visualize the progression of phage infection within a biofilm, colony-biofilms were formed and infected with bacteriophages. A good correlation (r = 0.707) was observed between LNA-FISH and PFU techniques. In biofilm structures, LNA-FISH provided a good discrimination of the infected cells and also allowed the assessment of the spatial distribution of infected and non-infected populations.

  5. Profiling T cell activation using single-molecule fluorescence in situ hybridization and flow cytometry.

    PubMed

    Bushkin, Yuri; Radford, Felix; Pine, Richard; Lardizabal, Alfred; Mangura, Bonita T; Gennaro, Maria Laura; Tyagi, Sanjay

    2015-01-15

    Flow cytometric characterization of Ag-specific T cells typically relies on detection of protein analytes. Shifting the analysis to detection of RNA would provide several significant advantages, which we illustrate by developing a new host immunity-based platform for detection of infections. Cytokine mRNAs synthesized in response to ex vivo stimulation with pathogen-specific Ags are detected in T cells with single-molecule fluorescence in situ hybridization followed by flow cytometry. Background from pre-existing in vivo analytes is lower for RNAs than for proteins, allowing greater sensitivity for detection of low-frequency cells. Moreover, mRNA analysis reveals kinetic differences in cytokine expression that are not apparent at the protein level but provide novel insights into gene expression programs expected to define different T cell subsets. The utility of probing immunological memory of infections is demonstrated by detecting T cells that recognize mycobacterial and viral Ags in donors exposed to the respective pathogens. PMID:25505292

  6. Salmonellae in fish feces analyzed by in situ hybridization and quantitative polymerase chain reaction.

    PubMed

    Sha, Qiong; Forstner, Michael R J; Bonner, Timothy H; Hahn, Dittmar

    2013-09-01

    The potential of fish to transfer salmonellae from heterogeneous aquatic biofilms into feces was assessed in controlled aquarium studies with Suckermouth Catfish Hypostomus plecostomus and with biofilms inoculated with salmonellae. Neither the presence of catfish nor inoculation with salmonellae had detectable effects on the abundance of the microbial community. Densities of the microbial community were about 10(5) cells/mL in the water during a 1-week period, whereas densities of the microbial community increased 10-fold (10(6) to 10(7) cells/mg) in catfish feces during the same period. Salmonellae were detected by both quantitative polymerase chain reaction (qPCR) and situ hybridization in water samples immediately after inoculation, in numbers of about 10(4) cells/mL, representing up to 20% of the cells of the microbial community. Numbers decreased by three orders of magnitude within the first 3 d of the study, which represented only 0.01% of the community, and became undetectable after day 5. In catfish feces, numbers of Salmonella initially increased to up to 6% of the cells of the community but then declined. These results suggest that Salmonella are not biomagnified during gut passage, and thus, fish only provide a means for the translocation of this pathogen.

  7. Identification of pathogens in mastitis milk samples with fluorescent in situ hybridization.

    PubMed

    Gey, Annerose; Werckenthin, Christiane; Poppert, Sven; Straubinger, Reinhard K

    2013-05-01

    Traditionally, the bacteriological examination of mastitis milk samples is performed by culture followed by biochemical tests on the cultured bacteria to allow identification of the causative pathogen. Depending on the species involved, this classic identification is time-consuming compared to other techniques such as fluorescent in situ hybridization (FISH), a culture-independent method that utilizes oligonucleotides (labeled with a fluorophore) that are specific to a string of target DNA/RNA. In the current study, the applicability of FISH was evaluated for the detection of mastitis pathogens directly in milk samples. To remove interfering lipids and proteins from mastitis milk samples prior to FISH, a previously published enzymatic treatment with savinase was evaluated. FISH was performed using oligonucleotides specific for Staphylococcus aureus, Streptococcus agalactiae, Streptococcus uberis, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, and Trueperella (Arcanobacterium) pyogenes. The enzymatic pretreatment and the sensitivity of FISH were evaluated using spiked whole milk samples and mastitis milk samples with bacterial loads of less than 10(3) up to 10(8) colony-forming units (CFU)/ml. Bacteria were reliably detected in milk samples with bacterial numbers of 10(6) CFU/ml or higher. However, bacteria present in numbers below 10(6) CFU/ml were not detectable in all cases. The ability of FISH to identify mastitis-causing pathogens directly in milk samples, and therefore earlier than classical culture methods, can supplement the classic diagnostic procedures for mastitis milk samples. PMID:23632662

  8. The detection of Alcelaphine herpesvirus-1 DNA by in situ hybridization of tissues from rabbits affected with malignant catarrhal fever.

    PubMed

    Bridgen, A; Munro, R; Reid, H W

    1992-05-01

    Tissue sections and cultured lymphocytes from rabbits clinically affected following experimental infection with Alcelaphine herpesvirus-1 (AHV-1) were assessed for the presence of viral DNA by in situ hybridization with the cloned major HindII repeat sequence of this virus. Small numbers of virus-infected cells were consistently detected only in submandibular lymph nodes, while other tissues showed no evidence of viral DNA. Virus titration in culture suggested that there were higher titres of virus in the lymph nodes, spleen and lung of infected animals than in the kidney or peripheral blood lymphocytes and confirmed the low level of virus in these animals. Substantially more viral DNA was detected by in situ hybridization in lymphocytes following at least 24 h of culture, suggesting that viral replication is normally repressed by the host.

  9. Imaging of multiple mRNA targets using quantum dot based in situ hybridization and spectral deconvolution in clinical biopsies

    SciTech Connect

    Tholouli, Eleni; Hoyland, Judith A.; Di Vizio, Dolores; O'Connell, Fionnuala; MacDermott, Sarah A.; Twomey, David; Levenson, Richard; Yin, John A. Liu; Golub, Todd R.; Loda, Massimo; Byers, Richard . E-mail: r.byers@manchester.ac.uk

    2006-09-22

    Gene expression mapping using microarray analysis has identified useful gene signatures for predicting outcome. However, little of this has been translated into clinically effective diagnostic tools as microarrays require high quality fresh-frozen tissue samples. We describe a methodology of multiplexed in situ hybridization (ISH) using a novel combination of quantum dot (QD)-labeled oligonucleotide probes and spectral imaging analysis in routinely processed, formalin-fixed paraffin embedded human biopsies. The conditions for QD-ISH were optimized using a poly d(T) oligonucleotide in decalcified bone marrow samples. Single and multiplex QD-ISH was performed in samples with acute leukemia and follicular lymphoma using oligonucleotide probes for myeloperoxidase, bcl-2, survivin, and XIAP. Spectral imaging was used for post hybridization tissue analysis, enabling separation of spatially colocalized signals. The method allows quantitative characterization of multiple gene expression using non-bleaching fluorochromes. This is expected to facilitate multiplex in situ transcript detection in routinely processed human clinical tissue.

  10. Analyses of in-situ airborne volcanic ash from the February 2000 eruption of Hekla Volcano, Iceland

    NASA Astrophysics Data System (ADS)

    Pieri, D.; Ma, C.; Simpson, J. J.; Hufford, G.; Grindle, T.; Grove, C.

    2002-08-01

    A McDonnell-Douglas DC-8 NASA research aircraft inadvertently flew into an airborne volcanic ash plume from the 26 February 2000 eruption of Hekla Volcano. Filter samples from the aircraft were compared with ``normal use'' and ``pristine clean'' filters using SEM, energy-dispersive x-ray spectrometer, and Nicolet FTIR spectrophotometer analyses. These analyses confirm that the DC-8 encountered airborne volcanic ash from Hekla Volcano. This result is supported by independent onboard heated aerosol observations at the time of the encounter. The analyses further demonstrate the ambiguous nature of the dual band thermal IR (``split window'') method for detecting volcanic ash from the point of view of aviation safety. They also highlight the utility of in situ aircraft filter-based observations of volcanic aerosols for scientific purposes.

  11. Localization of the human OB gene (OBS) to chromosome 7q32 by fluorescence in situ hybridization

    SciTech Connect

    Geffroy, S.; Duban, B.; Martinville, B. de

    1995-08-10

    An important gene involved in the pathogenesis of obesity is the product of the human homologue of the murine obese gene (gene symbol OBS). Using fluorescence in situ hybridization (FISH), we have localized the human OB gene to human chromosome 7, specifically to region 7q32.1. The FISH data of human OBS provide a gene-associated marker for genetic mapping. 8 refs., 1 fig.

  12. Fetal t(5p;21q) misdiagnosed as monosomy 21: A plea for in situ hybridization studies

    SciTech Connect

    Gill, P.; Uhrich, S.; Cheng, E.; Disteche, C.

    1994-10-01

    We report a case of 45,XY,-5,-21,+der (5)t(5;21) (p13 or p14;q11.2 or q21) that was prenatally misdiagnosed as complete monosomy 21 and terminated at 24 weeks of gestation. Subsequent fluorescence in situ hybridization studies with a chromosome 21 painting probe documented the cryptic unbalanced translocation. 17 refs., 2 figs., 1 tab.

  13. Combining in situ isotopic, trace element and textural analyses of quartz from four magmatic-hydrothermal ore deposits

    NASA Astrophysics Data System (ADS)

    Tanner, Dominique; Henley, Richard W.; Mavrogenes, John A.; Holden, Peter

    2013-10-01

    This study couples in situ 16O, 17O and 18O isotope and in situ trace element analyses to investigate and characterize the geochemical and textural complexity of magmatic-hydrothermal quartz crystals. Euhedral quartz crystals contemporaneous with mineralization were obtained from four magmatic-hydrothermal ore deposits: El Indio Au-Ag-Cu deposit; Summitville Au-Ag-Cu deposit; North Parkes Cu-Au deposit and Kingsgate quartz-Mo-Bi-W deposit. The internal features of the crystals were imaged using cathodoluminescence and qualitative electron microprobe maps. Quantitative isotopic data were collected in situ using 157 nm laser ablation inductively coupled plasma mass spectrometry (for 40 trace elements in quartz) and sensitive high-resolution ion microprobe (for 3 isotopes in quartz). Imaging revealed fine oscillatory zoning, sector zoning, complex "macromosaic" textures and hidden xenocrystic cores. In situ oxygen isotope analyses revealed a δ18O range of up to 12.4 ± 0.3 ‰ in a single crystal—the largest isotopic range ever ascribed to oscillatory zonation in quartz. Some of these crystals contain a heavier δ18O signature than expected by existing models. While sector-zoned crystals exhibited strong trace element variations between faces, no evidence for anisotropic isotope fractionation was found. We found: (1) isotopic heterogeneity in hydrothermal quartz crystals is common and precludes provenance analysis (e.g., δD-δ18O) using bulk analytical techniques, (2) the trace element signature of quartz is not an effective pathfinder toward noble metal mineralization and (3) in three of the four samples, both textural and isotopic data indicate non-equilibrium deposition of quartz.

  14. Vaginal micropapillary lesions are not related to human papillomavirus infection: in situ hybridization and polymerase chain reaction detection techniques.

    PubMed

    Garzetti, G G; Ciavattini, A; Goteri, G; Menzo, S; De Nictolis, M; Clementi, M; Brugia, M; Romanini, C

    1994-01-01

    The objective of this study was to assess the human papillomavirus DNA presence in vaginal papillary lesions, with particular regard to micropapillomatosis to better define their clinical significance. Prospective study: the study population was composed of 62 women who were recruited consecutively from the Colposcopy Centre of the Ancona University, Department of Obstetrics and Gynecology, on the grounds of vaginal papillomatosis or/and typical acuminata warts. Biopsies for routine histology, and for human papillomavirus (HPV) DNA detection by means of in situ hybridization and polymerase chain reaction (PCR) were taken from the papillary lesions and from 24 healthy women, who were selected as controls. Macroscopically, vaginal micropapillomatosis was ascertained in 51 cases (82.3%), while in 11 cases (17.7%) the colposcopic diagnosis was condyloma acuminatum. During in situ hybridization, HPV DNA positivity was observed in 8 (9.4%) out of 85 samples of squamous papillae and in 11 (64.7%) out of 17 samples of condylomata; in control specimens, HPV DNA was detected in 2 (8.3%) out of 24 bioptic samples. The correspondence between in situ hybridization and PCR was 96.1%, with 17.4% more diagnosis obtained by PCR. Vaginal micropapillomatosis may be regarded as a variation in the normal anatomy of the lower genital tract without any significant relationship with HPV infection, and as a lesion easily distinguishable from condylomata acuminata by clinical examination alone. PMID:7959342

  15. Silver-enhanced in situ hybridization for detection of polyomavirus DNA in patients with BK virus nephropathy.

    PubMed

    Fritzsche, Florian R; Pianca, Silvio; Gaspert, Ariana; Varga, Zsuzsanna; Wang, Lin; Farrell, Michael P; Chen, Xiao-Bo; Hirsch, Hans H; Springer, Erik; Fehr, Thomas; Myles, Jonathan; Tubbs, Raymond; Moch, Holger

    2011-06-01

    BK virus nephropathy is not an infrequent complication of renal transplantation associated with high rates of graft loss. Although antibodies against SV40 antigen detect different viruses of the polyomavirus family, immunohistochemistry is widely used to confirm the diagnosis of BK virus nephropathy in renal biopsies. Here we aimed to validate the novel silver-enhanced in situ hybridization (SISH) technique for the automated detection of BK virus in renal transplant biopsies. Two different patient cohorts were included. Twenty-nine consecutive patients suspicious for BK virus infection were investigated by SISH and chromogenic in situ hybridization. An additional 26 renal biopsies positive by SV40 immunohistochemistry from 19 patients were analyzed by SISH. Polyomavirus DNA serum levels, as determined by nested PCR analysis, were available for all of these patients. The presence of BK virus DNA in renal tubular cells was identified in 5 of the suspicious cases by both, SISH and chromogenic in situ hybridization . One additional patient was only positive in the SISH. In the second cohort, SISH was positive in all SV40 positive biopsies, but SISH signals were less extensive than SV40 immunohistochemistry. Our results show that the BK virus SISH is an ancillary tool for the detection of polyomavirus DNA in renal biopsies using bright-field microscopy. However, its diagnostic value in comparison with standard immunohistochemistry seems to be limited.

  16. HSV hepatitis in the mouse: a light and electron microscopic study with immunohistology and in situ hybridization.

    PubMed

    Schirmacher, P; Wörsdörfer, M; Lübbe, K; Falke, D; Thoenes, W; Dienes, H P

    1989-01-01

    In order to characterize better the morphology and immune response in acute necrotizing HSV infection, murine HSV hepatitis was examined. BALB/c mice were inoculated intraperitoneally with 10(6) plaque-forming units (PFU) of HSV-1 (Lenette) and HSV-2 (D316). In both groups half the animals were pretreated with silica particles to block macrophage function. Up to 6 days after infection four mice from each group were sacrificed at daily intervals and the livers were examined by light and electron microscopy, immunohistology, in situ hybridization, combined immunohistology/in situ hybridization and titration of viral PFU. HSV-2 infected mice developed severe necrotizing hepatitis with persistence of HSV in the liver tissue until the end of the study. HSV-1 infected mice rapidly eliminated the virus and revealed only small necrotic foci. Early phase alterations and necrotic phase lesions were distinguished and characterized and morphologic evidence of a direct cytopathic effect of HSV was detected. A specific immune reaction in late stages appeared to be mediated by T4-positive T-lymphocytes. In situ hybridization and immunohistochemistry showed a close correlation with virus titration and were valuable in characterizing early phases and in the assessment of prognosis and differential diagnosis.

  17. Quantification of Uncultured Ruminococcus obeum-Like Bacteria in Human Fecal Samples by Fluorescent In Situ Hybridization and Flow Cytometry Using 16S rRNA-Targeted Probes

    PubMed Central

    Zoetendal, Erwin G.; Ben-Amor, Kaouther; Harmsen, Hermie J. M.; Schut, Frits; Akkermans, Antoon D. L.; de Vos, Willem M.

    2002-01-01

    A 16S rRNA-targeted probe was designed and validated in order to quantify the number of uncultured Ruminococcus obeum-like bacteria by fluorescent in situ hybridization (FISH). These bacteria have frequently been found in 16S ribosomal DNA clone libraries prepared from bacterial communities in the human intestine. Thirty-two reference strains from the human intestine, including a phylogenetically related strain and strains of some other Ruminococcus species, were used as negative controls and did not hybridize with the new probe. Microscopic and flow cytometric analyses revealed that a group of morphologically similar bacteria in feces did hybridize with this probe. Moreover, it was found that all hybridizing cells also hybridized with a probe specific for the Clostridium coccoides-Eubacterium rectale group, a group that includes the uncultured R. obeum-like bacteria. Quantification of the uncultured R. obeum-like bacteria and the C. coccoides-E. rectale group by flow cytometry and microscopy revealed that these groups comprised approximately 2.5 and 16% of the total community in fecal samples, respectively. The uncultured R. obeum-like bacteria comprise about 16% of the C. coccoides-E. rectale group. These results indicate that the uncultured R. obeum-like bacteria are numerically important in human feces. Statistical analysis revealed no significant difference between the microscopic and flow cytometric counts and the different feces sampling times, while a significant host-specific effect on the counts was observed. Our data demonstrate that the combination of FISH and flow cytometry is a useful approach for studying the ecology of uncultured bacteria in the human gastrointestinal tract. PMID:12200269

  18. Detection and quantification of Epstein-Barr virus EBER1 in EBV-infected cells by fluorescent in situ hybridization and flow cytometry

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed

    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.

  20. Fungal-Induced Deterioration of Mural Paintings: In Situ and Mock-Model Microscopy Analyses.

    PubMed

    Unković, Nikola; Grbić, Milica Ljaljević; Stupar, Miloš; Savković, Željko; Jelikić, Aleksa; Stanojević, Dragan; Vukojević, Jelena

    2016-04-01

    Fungal deterioration of frescoes was studied in situ on a selected Serbian church, and on a laboratory model, utilizing standard and newly implemented microscopy techniques. Scanning electron microscopy (SEM) with energy-dispersive X-ray confirmed the limestone components of the plaster. Pigments used were identified as carbon black, green earth, iron oxide, ocher, and an ocher/cinnabar mixture. In situ microscopy, applied via a portable microscope ShuttlePix P-400R, proved very useful for detection of invisible micro-impairments and hidden, symptomless, microbial growth. SEM and optical microscopy established that observed deterioration symptoms, predominantly discoloration and pulverization of painted layers, were due to bacterial filaments and fungal hyphal penetration, and formation of a wide range of fungal structures (i.e., melanized hyphae, chlamydospores, microcolonial clusters, Cladosporium-like conidia, and Chaetomium perithecia and ascospores). The all year-round monitoring of spontaneous and induced fungal colonization of a "mock painting" in controlled laboratory conditions confirmed the decisive role of humidity level (70.18±6.91% RH) in efficient colonization of painted surfaces, as well as demonstrated increased bioreceptivity of painted surfaces to fungal colonization when plant-based adhesives (ilinocopie, murdent), compared with organic adhesives of animal origin (bone glue, egg white), are used for pigment sizing.

  1. Polarization-extinction-based detection of DNA hybridization in situ using a nanoparticle wire-grid polarizer.

    PubMed

    Yu, Hojeong; Oh, Youngjin; Kim, Soowon; Song, Seok Ho; Kim, Donghyun

    2012-09-15

    Metallic wires can discriminate light polarization due to strong absorption of electric fields oscillating in parallel to wires. Here, we explore polarization-based biosensing of DNA hybridization in situ by employing metal target-conjugated nanoparticles to form a wire-grid polarizer (WGP) as complementary DNA strands hybridize. Experimental results using gold nanoparticles of 15 nm diameter to form a WGP of 400 nm period suggest that polarization extinction can detect DNA hybridization with a limit of detection in the range of 1 nM concentration. The sensitivity may be improved by more than an order of magnitude if larger nanoparticles are employed to define WGPs at a period between 400 and 500 nm.

  2. Small RNA in situ hybridization in Caenorhabditis elegans, combined with RNA-seq, identifies germline-enriched microRNAs.

    PubMed

    McEwen, Tamara J; Yao, Qiuming; Yun, Sijung; Lee, Chin-Yung; Bennett, Karen L

    2016-10-15

    Over four hundred different microRNAs (miRNAs) have been identified in the genome of the model organism the nematode Caenorhabditis elegans. As the germline is dedicated to the preservation of each species, and almost half of all the cells in an adult nematode are germline, it is likely that regulatory miRNAs are important for germline development and maintenance. In C. elegans the miR35 family has strong maternal effects, contributing to normal embryogenesis and to adult fecundity. To determine whether any particular miRNAs are greatly enriched in the C. elegans germline we used RNA-seq to compare the miRNA populations in several germline-defective strains of adult C. elegans worms, including glp-4(germline proliferation-4), glh-1(germline helicase-1) and dcr-1(dicer-1). Statistical analyses of RNA-seq comparisons identified 13 miRNAs that are germline-enriched, including seven members of the well-studied miR35 family that were reduced as much as 1000-fold in TaqMan qRT PCR miRNA assays. Along with the miR35s, six others: miR-56 (a member of the miR51 family),-70, -244, -260 , -788 and -4813, none of which previously considered as such, were also identified by RNA-seq as germline-enriched candidates. We went on to develop a successful miRNA in situ hybridization protocol for C. elegans, revealing miR35s specifically concentrate during oogenesis in the pachytene region of the gonad, and persist throughout early embryogenesis, while in adult animals neither let-7 nor miR-228 has a germline-bias.

  3. Correlation of modified Shimada classification with MYCN and 1p36 status detected by fluorescence in situ hybridization in neuroblastoma.

    PubMed

    Altungoz, Oguz; Aygun, Nevim; Tumer, Sait; Ozer, Erdener; Olgun, Nur; Sakizli, Meral

    2007-01-15

    Neuroblastoma (NB) is a childhood cancer derived from neural crest cells, with a highly variable clinical course and biologic behavior. NB cells harbor complex genetic changes. Also, MYCN amplification is a well-known molecular marker for aggressive progression, and deletion of the short arm of chromosome 1 is frequently observed in NB. The aim of this study was to investigate the correlation between genetic markers and prognostic morphological parameters to address the biology and underlying the clinical complexity of NB. Therefore, we performed fluorescence in situ hybridization analyses of chromosome band 1p36 and MYCN in a series of tumors from 43 cases classified according to the recommendation of International Neuroblastoma Pathology Committee (modification of Shimada classification). The correlations of MYCN amplification status and two distinct types of 1p36 alterations (deletion and imbalance) with Shimada classification and histologic prognostic factors were statistically analyzed. Amplification of MYCN and 1p36 deletion was present in 14 (32.6%) and 18 (41.9%) cases, respectively. Sixteen cases (37.2%) displayed a favorable histology, while 27 (62.8%) had an unfavorable histology. The 1p36 deletion was found to be an independent predictor of unfavorable histology by multivariate analysis (logistic regression test, P = 0.03), but the 1p36 imbalance did not show any significance. Both 1p36 deletion and MYCN amplification showed significant correlation with undifferentiated tumors (chi-square test, P = 0.002 and 0.03, respectively). Highly significant correlation was found between the higher mitotic karyorrhectic index (MKI) and MYCN amplification (chi-square test, P < 0.001), whereas neither 1p36 deletion nor 1p36 imbalance significantly correlated with a higher MKI (chi-square test, P > 0.05). We conclude that 1p36 deletion may be a reliable parameter in determining unfavorable histology and predicting prognosis in NB. Further studies with prognostic data

  4. A compact μ-XRF spectrometer for (in situ) analyses of cultural heritage and forensic materials

    NASA Astrophysics Data System (ADS)

    Vittiglio, G.; Bichlmeier, S.; Klinger, P.; Heckel, J.; Fuzhong, W.; Vincze, L.; Janssens, K.; Engström, P.; Rindby, A.; Dietrich, K.; Jembrih-Simbürger, D.; Schreiner, M.; Denis, D.; Lakdar, A.; Lamotte, A.

    2004-01-01

    A compact, light weight and relatively inexpensive μ-XRF instrument that allows for non-destructive and local analysis of sub-mm samples with minor/trace level sensitivity was developed. Two versions of this prototype instrument exist: a table-top version that can be used in a laboratory environment while for in situ measurements a readily transportable version was constructed. Polycapillary lenses are used to focus the primary X-ray beam down to the level of 70-100 μm in diameter. Relative detection limits of transition elements in biological and glass matrices are situated at the 10-100 ppm level. These instruments are useful for characterization of various materials from the cultural heritage and forensic sector.

  5. Development of the Minimum Information Specification for in situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)

    SciTech Connect

    Deutsch, Eric W.; Ball, Catherine A.; Bova, G. Steven; Brazma, Alvis; Bumgarner, Roger E.; Campbell, David; Causton, Helen C.; Christiansen, Jeff; Davidson, Duncan; Eichner, Lillian J.; Goo, Young Ah; Grimmond, Sean; Henrich, Thorsten; Johnson, Michael H.; Korb, Martin; Mills, Jason C.; Oudes, Asa; Parkinson, Helen E.; Pascal, Laura E.; Quackenbush, John; Ramialison, Mirana; Ringwald, Martin; Sansone, Susanna A.; Sherlock, Gavin; Stoeckert, Christian Jr. J.; Swedlow, Jason; Taylor, Ronald C.; Walashek, Laura; Zhou, Yi; Liu, Alvin Y.; True, Lawrence D.

    2006-06-06

    Background One purpose of the biomedical literature is to report results in sufficient detail so that the methods of data collection and analysis can be independently replicated and verified. In order to ensure that this level of detail is provided in published works, a minimum information specification is needed for each experimental data type and for this specification to be a requirement for publication in peer-reviewed journals. This is especially beneficial for researchers working with complex data types and experiments. A data content specification has already been widely accepted by, and directly benefited, the microarray community, and efforts are well underway to develop a comparable specification for proteomics data types. However, no similar specification exists for visual interpretation-based tissue protein and transcript abundance/localization experiments (hereafter referred to as ‘gene expression localization experiments’), such as in situ hybridization and experiments involving immunohistochemistry. Results Here we present for consideration a specification, called the “Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)”. It is modelled after the MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments. Data specifications like MIAME and MISFISHIE specify the information content without specifying a format for encoding that information. The MISFISHIE specification describes six types of information that should be provided for each gene expression localization experiment: Experimental Design, Biomaterials and Treatments, Reporters, Staining, Imaging Data, and Image Characterizations. A general checklist is provided for quick and easy reference and to promote adherence to the specification. We consider that most articles describing gene expression localization studies do not fully provide the minimum information needed for independent verification

  6. Novel Hybrid Monte Carlo/Deterministic Technique for Shutdown Dose Rate Analyses of Fusion Energy Systems

    SciTech Connect

    Ibrahim, Ahmad M; Peplow, Douglas E.; Peterson, Joshua L; Grove, Robert E

    2013-01-01

    The rigorous 2-step (R2S) method uses three-dimensional Monte Carlo transport simulations to calculate the shutdown dose rate (SDDR) in fusion reactors. Accurate full-scale R2S calculations are impractical in fusion reactors because they require calculating space- and energy-dependent neutron fluxes everywhere inside the reactor. The use of global Monte Carlo variance reduction techniques was suggested for accelerating the neutron transport calculation of the R2S method. The prohibitive computational costs of these approaches, which increase with the problem size and amount of shielding materials, inhibit their use in the accurate full-scale neutronics analyses of fusion reactors. This paper describes a novel hybrid Monte Carlo/deterministic technique that uses the Consistent Adjoint Driven Importance Sampling (CADIS) methodology but focuses on multi-step shielding calculations. The Multi-Step CADIS (MS-CADIS) method speeds up the Monte Carlo neutron calculation of the R2S method using an importance function that represents the importance of the neutrons to the final SDDR. Using a simplified example, preliminarily results showed that the use of MS-CADIS enhanced the efficiency of the neutron Monte Carlo simulation of an SDDR calculation by a factor of 550 compared to standard global variance reduction techniques, and that the increase over analog Monte Carlo is higher than 10,000.

  7. In situ hybridization for the differentiation of Actinomyces and Nocardia in tissue sections.

    PubMed

    Isotalo, Phillip A; Qian, Xiang; Hayden, Randall T; Roberts, Glenn D; Lloyd, Ricardo V

    2009-09-01

    The specific identification of filamentous bacteria in tissue sections can be difficult. The filamentous bacteria Actinomyces and Nocardia often produce similar host responses and single bacterial organisms seem morphologically similar; however, their differentiation may be clinically significant. In situ hybridization (ISH) may assist in the rapid and accurate identification of these microorganisms. In this study, DNA probes were directed against the variable regions of 16S ribosomal RNA genes of multiple Actinomyces and Nocardia spp. Probes were tested on 26 formalin-fixed, paraffin-embedded tissue specimens, each of which contained diagnostic foci of filamentous bacteria confirmed by both Gram and Grocott methenamine silver stains. On the basis of histology and clinical features, cases were classified as Actinomyces-related, n = 13 with 6 culture-proven cases and Nocardia-related, n = 13 with 11 culture-proven cases. Using this classification, all cases were assessed for cross-reactivity using other species-specific probes and probe specificity was determined. Overall, Gram and Grocott methenamine silver histochemical stains (100% sensitivity) were more sensitive than ISH (77% sensitivity for both Actinomyces and Nocardia probes). The slender caliber of filamentous bacteria was a limitation for ISH interpretation and necessitated careful examination of some slides. Probes demonstrated 100% specificity for identifying both species, 100% positive predictive value and 81% negative predictive value. No mixed infections were observed. This study demonstrates that ISH is highly specific for distinguishing between Actinomyces and Nocardia spp. in tissue sections. Although histochemical stains demonstrate greater sensitivity for organism detection, ISH is a rapid and specific technique that is especially useful for evaluating culture-negative or clinically unsuspected cases of filamentous bacterial infection.

  8. Optimizing Ventana chromogenic dual in-situ hybridization for mucinous epithelial ovarian cancer

    PubMed Central

    2013-01-01

    Background Dual in-situ hybridization (DISH) assay is a relatively new assay for evaluating Human Epidermal Growth Factor Receptor 2 (HER2) genomic amplification. Optimization protocol for the assay is not yet well established, especially for archival tissues. Although there is a recommended nominal protocol, it is not suited for formalin-fixed and paraffin-embedded (FFPE) samples that were archived for long periods. Findings In a study on local population of mucinous epithelial ovarian cancer, we developed a series of optimization protocols based on the age of samples to improve success of the DISH assay. A decision workflow was generated to facilitate individualization of further optimization protocols. The optimizations were evaluated on 92 whole tissue sections of FFPE mucinous ovarian tumors dating from 1990 to 2011. Overall, 79 samples were successfully assayed for DISH using the series of optimization protocols. We found samples older than 1 year required further optimization beyond the nominal protocol recommended. Thirteen samples were not further assayed after first DISH assay due to inadequately preserved nuclear morphology with no ISH signals throughout the tissue section. Conclusion The study revealed age of samples and storage conditions were major factors in successful DISH assays. Samples that were ten years or less in age, and archived in-house were successfully optimized, whereas older samples, which were also archived off-site, have a higher frequency of unsuccessful optimizations. The study provides practical and important guidelines for the new DISH assay which can facilitate successful HER2 evaluation in ovarian cancers and possibly other cancers as well. PMID:24373486

  9. Fluorescence In Situ Hybridization and Optical Mapping to Correct Scaffold Arrangement in the Tomato Genome

    PubMed Central

    Shearer, Lindsay A.; Anderson, Lorinda K.; de Jong, Hans; Smit, Sandra; Goicoechea, José Luis; Roe, Bruce A.; Hua, Axin; Giovannoni, James J.; Stack, Stephen M.

    2014-01-01

    The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules of the recently published tomato (Solanum lycopersicum, 2n = 2x = 24) genome sequence were positioned based on marker order in a high-density linkage map. Here, we report the arrangement of these scaffolds determined by two independent physical methods, bacterial artificial chromosome–fluorescence in situ hybridization (BAC-FISH) and optical mapping. By localizing BACs at the ends of scaffolds to spreads of tomato synaptonemal complexes (pachytene chromosomes), we showed that 45 scaffolds, representing one-third of the tomato genome, were arranged differently than predicted by the linkage map. These scaffolds occur mostly in pericentric heterochromatin where 77% of the tomato genome is located and where linkage mapping is less accurate due to reduced crossing over. Although useful for only part of the genome, optical mapping results were in complete agreement with scaffold arrangement by FISH but often disagreed with scaffold arrangement based on the linkage map. The scaffold arrangement based on FISH and optical mapping changes the positions of hundreds of markers in the linkage map, especially in heterochromatin. These results suggest that similar errors exist in pseudomolecules from other large genomes that have been assembled using only linkage maps to predict scaffold arrangement, and these errors can be corrected using FISH and/or optical mapping. Of note, BAC-FISH also permits estimates of the sizes of gaps between scaffolds, and unanchored BACs are often visualized by FISH in gaps between scaffolds and thus represent starting points for filling these gaps. PMID:24879607

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

    PubMed

    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. PMID:22425347

  11. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome.

    PubMed

    Shearer, Lindsay A; Anderson, Lorinda K; de Jong, Hans; Smit, Sandra; Goicoechea, José Luis; Roe, Bruce A; Hua, Axin; Giovannoni, James J; Stack, Stephen M

    2014-08-01

    The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules of the recently published tomato (Solanum lycopersicum, 2n = 2x = 24) genome sequence were positioned based on marker order in a high-density linkage map. Here, we report the arrangement of these scaffolds determined by two independent physical methods, bacterial artificial chromosome-fluorescence in situ hybridization (BAC-FISH) and optical mapping. By localizing BACs at the ends of scaffolds to spreads of tomato synaptonemal complexes (pachytene chromosomes), we showed that 45 scaffolds, representing one-third of the tomato genome, were arranged differently than predicted by the linkage map. These scaffolds occur mostly in pericentric heterochromatin where 77% of the tomato genome is located and where linkage mapping is less accurate due to reduced crossing over. Although useful for only part of the genome, optical mapping results were in complete agreement with scaffold arrangement by FISH but often disagreed with scaffold arrangement based on the linkage map. The scaffold arrangement based on FISH and optical mapping changes the positions of hundreds of markers in the linkage map, especially in heterochromatin. These results suggest that similar errors exist in pseudomolecules from other large genomes that have been assembled using only linkage maps to predict scaffold arrangement, and these errors can be corrected using FISH and/or optical mapping. Of note, BAC-FISH also permits estimates of the sizes of gaps between scaffolds, and unanchored BACs are often visualized by FISH in gaps between scaffolds and thus represent starting points for filling these gaps.

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

    PubMed

    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.

  13. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome.

    PubMed

    Shearer, Lindsay A; Anderson, Lorinda K; de Jong, Hans; Smit, Sandra; Goicoechea, José Luis; Roe, Bruce A; Hua, Axin; Giovannoni, James J; Stack, Stephen M

    2014-08-01

    The order and orientation (arrangement) of all 91 sequenced scaffolds in the 12 pseudomolecules of the recently published tomato (Solanum lycopersicum, 2n = 2x = 24) genome sequence were positioned based on marker order in a high-density linkage map. Here, we report the arrangement of these scaffolds determined by two independent physical methods, bacterial artificial chromosome-fluorescence in situ hybridization (BAC-FISH) and optical mapping. By localizing BACs at the ends of scaffolds to spreads of tomato synaptonemal complexes (pachytene chromosomes), we showed that 45 scaffolds, representing one-third of the tomato genome, were arranged differently than predicted by the linkage map. These scaffolds occur mostly in pericentric heterochromatin where 77% of the tomato genome is located and where linkage mapping is less accurate due to reduced crossing over. Although useful for only part of the genome, optical mapping results were in complete agreement with scaffold arrangement by FISH but often disagreed with scaffold arrangement based on the linkage map. The scaffold arrangement based on FISH and optical mapping changes the positions of hundreds of markers in the linkage map, especially in heterochromatin. These results suggest that similar errors exist in pseudomolecules from other large genomes that have been assembled using only linkage maps to predict scaffold arrangement, and these errors can be corrected using FISH and/or optical mapping. Of note, BAC-FISH also permits estimates of the sizes of gaps between scaffolds, and unanchored BACs are often visualized by FISH in gaps between scaffolds and thus represent starting points for filling these gaps. PMID:24879607

  14. ERBB2 amplification in breast cancer analyzed by fluorescence in situ hybridization.

    PubMed Central

    Kallioniemi, O P; Kallioniemi, A; Kurisu, W; Thor, A; Chen, L C; Smith, H S; Waldman, F M; Pinkel, D; Gray, J W

    1992-01-01

    We illustrate the use of fluorescence in situ hybridization (FISH) for analysis of ERBB2 oncogene copy number, the level of amplification (here defined as the ratio of ERBB2 copy number to copy number of chromosome 17 centromeres), and the distribution of amplified genes in breast cancer cell lines and uncultured primary breast carcinomas. The relative ERBB2 copy number determined by FISH in 10 breast cancer cell lines correlated strongly with Southern blot results (r = 0.98) when probes for an identical reference locus were used in the two methods. Metaphase analysis of cell lines showed that amplified ERBB2 copies always occurred in intrachromosomal clusters but that the number and chromosomal location of these clusters varied among the cell lines. In interphase nuclei of primary tumors showing ERBB2 amplification (10/44), ERBB2 copies were seen as one to four clusters, also suggesting intrachromosomal localization. Regardless of the average level of amplification, all these tumors contained highly amplified cell subpopulations with at least 25, and sometimes more than 100, ERBB2 copies per cell. Tumors that did not show amplification by FISH (34/44) had an average of one to five ERBB2 copies scattered randomly in the nuclei and completely lacked cells with high copy levels. FISH results on primary tumors were concordant with slot blot results on amplification and with immunohistochemical detection of overexpression. Quantitative analysis of ERBB2 amplification by FISH may improve prognostic assessments based on the pattern of amplification and detection of heavily amplified tumor cell subpopulations. Images PMID:1351679

  15. Sex chromosome loss and aging: In situ hybridization studies on human interphase nuclei

    SciTech Connect

    Guttenbach, M.; Koschorz, B.; Bernthaler, U.

    1995-11-01

    A total of 1,000 lymphocyte interphase nuclei per proband from 90 females and 138 males age 1 wk to 93 years were analyzed by in situ hybridization for loss of the X and Y chromosomes, respectively. Both sex chromosomes showed an age-dependent loss. In males, Y hypoploidy was very low up to age 15 years (0.05%) but continuously increased to a frequency of 1.34% in men age 76-80 years. In females, the baseline level for X chromosome loss is much higher than that seen for the Y chromosome in males. Even prepubertal females show a rate of X chromosome loss on the order of 1.5%-2.5%, rising to {approximately}4.5%-5% in women older than 75 years. Dividing the female probands into three biological age groups on the basis of sex hormone function (<13 years, 13-51 years, and >51 years), a significant correlation of X chromosome loss versus age could clearly be demonstrated in women beyond age 51 years. Females age 51-91 years showed monosomy X at a rate from 3.2% to 5.1%. In contrast to sex chromosomal loss, the frequency of autosomal monosomies does not change during the course of aging: chromosome 1 and chromosome 17 monosomic cells were found with a constant incidence of 1.2% and 1%, respectively. These data also indicate that autosome loss in interphase nuclei is not a function of chromosome size. 34 refs., 5 figs., 6 tabs.

  16. Fluorescence In Situ Hybridization for Melanoma Diagnosis: A Review and a Reappraisal.

    PubMed

    Ferrara, Gerardo; De Vanna, Anna Chiara

    2016-04-01

    Although conventional histopathological examination is the undisputable mainstay for the diagnosis of melanocytic skin neoplasms, fluorescence in situ hybridization (FISH) has the potential to provide important information to morphologically challenging cases. The standard melanoma FISH test targeting RREB1 (6p25), MYB (6q23), CCND1 (11q13), and centromere 6 is an effective compromise between cost, technical complexity, and sensitivity. The authors use the standard FISH-positivity as a tie-breaker for challenging melanocytic neoplasms mainly in a non-Spitzoid morphologic context because the currently available test leaves several unresolved issues: namely, a relatively low diagnostic accuracy in morphologically ambiguous melanocytic neoplasms; a relatively low sensitivity and specificity in Spitzoid neoplasms; and the occurrence of false positives due to tetraploidy in Spitz nevi and in nevi with an atypical epithelioid component. Under investigation is currently a new melanoma probe cocktail targeting RREB1 (6p25), C-MYC (8q24), CDKN2A (9p21), and CCND1 (11q13). However, CDKN2A is a significant parameter only if lost in homozygosis, and this complicates the interpretation of the results. Furthermore, the new melanoma probe cocktail has been tested on cases of atypical Spitzoid proliferations with fatal outcomes which at present are too few to allow definite conclusions. The authors propose the implementation of a FISH algorithm (standard 4-probe test followed by either C-MYC or CDKN2A/centromere 9) to assist the histopathological diagnosis and minimize the technical problems. Nevertheless, because the diagnostic accuracy of the FISH technique is far from being absolute, the overall clinicopathological context must always guide the decision-making process about the management of morphobiologically ambiguous melanocytic proliferations. PMID:26999337

  17. Identification of triclosan-degrading bacteria using stable isotope probing, fluorescence in situ hybridization and microautoradiography.

    PubMed

    Lolas, Ihab Bishara; Chen, Xijuan; Bester, Kai; Nielsen, Jeppe Lund

    2012-11-01

    Triclosan is considered a ubiquitous pollutant and can be detected in a wide range of environmental samples. Triclosan removal by wastewater treatment plants has been largely attributed to biodegradation processes; however, very little is known about the micro-organisms involved. In this study, DNA-based stable isotope probing (DNA-SIP) combined with microautoradiography-fluorescence in situ hybridization (MAR-FISH) was applied to identify active triclosan degraders in an enrichment culture inoculated with activated sludge. Clone library sequences of 16S rRNA genes derived from the heavy DNA fractions of enrichment culture incubated with (13)C-labelled triclosan showed a predominant enrichment of a single bacterial clade most closely related to the betaproteobacterial genus Methylobacillus. To verify that members of the genus Methylobacillus were actively utilizing triclosan, a specific probe targeting the Methylobacillus group was designed and applied to the enrichment culture incubated with (14)C-labelled triclosan for MAR-FISH. The MAR-FISH results confirmed a positive uptake of carbon from (14)C-labelled triclosan by the Methylobacillus. The high representation of Methylobacillus in the (13)C-labelled DNA clone library and its observed utilization of (14)C-labelled triclosan by MAR-FISH reveal that these micro-organisms are the primary consumers of triclosan in the enrichment culture. The results from this study show that the combination of SIP and MAR-FISH can shed light on the networks of uncultured micro-organisms involved in degradation of organic micro-pollutants.

  18. The role of fluorescence in situ hybridization and gene expression profiling in myeloma risk stratification.

    PubMed

    Hose, Dirk; Seckinger, Anja; Jauch, Anna; Rème, Thierry; Moreaux, Jérôme; Bertsch, Uta; Neben, Kai; Klein, Bernard; Goldschmidt, Hartmut

    2011-12-01

    Multiple myeloma patients' survival under treatment varies from a few months to more than 15 years. Clinical prognostic factors, especially beta2-microglobulin (B2M) and the international staging system (ISS), allow risk assessment to a certain extent, but do not identify patients at very high risk. As malignant plasma cells are characterized by a variety of chromosomal aberrations and changes in gene expression, a molecular characterization ofCD138-purified myeloma cells by interphase fluorescence in situ hybridization (iFISH) and gene expression profiling (GEP) can be used for improved risk assessment, iFISH allows a risk stratification with presence of a translocation t(4;14) and/or deletion of 17p13 being the best documented adverse prognostic factors. A deletion of 13q14 is no longer considered to define adverse risk. Patients harbouring a t(4;14) seems to benefit from a bortezomib- or lenalidomide containing regimen, whereas patients with deletion 17p13 seem only to benefit from a high dose therapy approach using long term bortezomib (in induction and maintenance) and autologous tandem-transplantation as used in the GMMG-HD4 trial, or the total therapy 3 concept. Gene expression profiling allows the assessment of high risk scores (IFM, UAMS), remaining prognostic despite treatment with novel agents, and prognostic surrogates of biological factors (e.g. proliferation) and (prognostic) target gene expression (e.g. Aurora-kinase A). Thus, assessment of B2M and ISS-stage, iFISH, and GEP is considered extended routine diagnostics in therapy requiring multiple myeloma patients for risk assessment and, even now, to a certain extent selection of treatment.

  19. Evaluation of fluorescence in situ hybridization for the detection of bacteria in feline inflammatory liver disease.

    PubMed

    Twedt, David C; Cullen, John; McCord, Kelly; Janeczko, Stephanie; Dudak, Julie; Simpson, Kenny

    2014-02-01

    The etiopathogenesis of feline inflammatory liver disease (ILD) is unclear. Therefore, we sought to determine the presence and distribution of bacteria within the livers of cats with ILD using eubacterial fluorescence in situ hybridization (FISH). Histopathology from 39 cats with ILD and 19 with histologically normal livers (C) were classified using World Small Animal Veterinary Association guidelines. Hepatic sections were examined by 16 and 23S ribosomal RNA FISH. Antibodies against cytokeratins and factor VIIIa were used to distinguish bile ducts and vascular structures. Histopathologic findings included non-specific reactive hepatitis (12), neutrophilic cholangitis (NC; 12), lymphocytic cholangitis (seven), cholestasis/obstruction (three), probable lymphoma (three) and acute hepatitis (two). Bacteria were observed in 21/39 ILD and 3/19 C (P = 0.0054). In 8/39 ILD and 2/19 C bacteria were restricted to the outer liver capsule (P = 0.29) and may represent contaminants. The prevalence of intrahepatic bacteria was higher (P = 0.008) in ILD (13/31) than C (1/17). Bacteria in ILD were more frequently (P <0.0001) localized to portal vessels, venous sinusoids and parenchyma (12/13) than bile duct (1/13). Bacterial colonization was highest in Escherichia coli-positive NC cats. Concurrent non-hepatic disease, predominantly pancreatic and intestinal (8/10 cats biopsied), was present in all 13 cats with intrahepatic bacteria. Bacterial culture was positive (predominantly E coli and Enterococcus species) in 11/23 (48%) samples, and concurred with FISH in 15/23 cases. The presence of intrahepatic bacteria in 13/31 (41%) cats with ILD suggests a role in etiopathogenesis. The distribution of bacteria within the liver supports the possibility of colonization via either enteric translocation or hematogenous seeding.

  20. Fluorescence In Situ Hybridization Analysis of Atypical Melanocytic Proliferations and Melanoma in Young Patients

    PubMed Central

    DeMarchis, Emilia H; Swetter, Susan M; Jennings, Charay D; Kim, Jinah

    2014-01-01

    Morphologic heterogeneity among melanocytic proliferations is a common challenge in the diagnosis of melanoma. In particular, atypical melanocytic lesions in children, adolescents, and young adults may be difficult to classify because of significant morphologic overlap with melanoma. Recently a four-probe fluorescence in situ hybridization (FISH) protocol to detect chromosomal abnormalities in chromosomes 6 and 11 has shown promise for improving the classification of melanocytic lesions. We sought to determine the correlation between FISH results, morphology, and clinical outcomes in a series of challenging melanocytic proliferations in young patients. We retrospectively performed the standard four-probe FISH analysis on 21 melanocytic neoplasms from 21 patients younger than 25 years of age (range 5–25 years, mean 14.6 years) from Stanford University Medical Center who were prospectively followed for a median of 51 months (range 1–136 months). The study cohort included patients with 5 confirmed melanomas, 2 melanocytic tumors of uncertain malignant potential (MelTUMPs), 10 morphologically challenging atypical Spitz tumors (ASTs), and 4 typical Spitz nevi. FISH detected chromosomal aberrations in all five melanomas and in one MelTUMP, in which the patient developed subsequent lymph node and distant metastasis. All 10 ASTs, 4 Spitz nevi, and 1 of 2 MelTUMPs were negative for significant gains or losses in chromosomes 6 and 11q. Our findings demonstrated a strong correlation between positive FISH results and the histomorphologic impression of melanoma. This finding was also true for the MelTUMP with poor clinical outcome. Therefore FISH may serve as a helpful adjunct in the classification of controversial melanocytic tumors in young patients. PMID:24924836

  1. MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells

    PubMed Central

    Kleiner, Manuel; Wetzel, Silke; Liebeke, Manuel; Dubilier, Nicole

    2015-01-01

    Fluorescence in situ hybridization (FISH) has become a vital tool for environmental and medical microbiology and is commonly used for the identification, localization, and isolation of defined microbial taxa. However, fluorescence signal strength is often a limiting factor for targeting all members in a microbial community. Here, we present the application of a multilabeled FISH approach (MiL-FISH) that (i) enables the simultaneous targeting of up to seven microbial groups using combinatorial labeling of a single oligonucleotide probe, (ii) is applicable for the isolation of unfixed environmental microorganisms via fluorescence-activated cell sorting (FACS), and (iii) improves signal and imaging quality of tissue sections in acrylic resin for precise localization of individual microbial cells. We show the ability of MiL-FISH to distinguish between seven microbial groups using a mock community of marine organisms and its applicability for the localization of bacteria associated with animal tissue and their isolation from host tissues using FACS. To further increase the number of potential target organisms, a streamlined combinatorial labeling and spectral imaging-FISH (CLASI-FISH) concept with MiL-FISH probes is presented here. Through the combination of increased probe signal, the possibility of targeting hard-to-detect taxa and isolating these from an environmental sample, the identification and precise localization of microbiota in host tissues, and the simultaneous multilabeling of up to seven microbial groups, we show here that MiL-FISH is a multifaceted alternative to standard monolabeled FISH that can be used for a wide range of biological and medical applications. PMID:26475101

  2. A pre-breeding screening program for transgenic boars based on fluorescence in situ hybridization assay.

    PubMed

    Bou, Gerelchimeg; Sun, Mingju; Lv, Ming; Zhu, Jiang; Li, Hui; Wang, Juan; Li, Lu; Liu, Zhongfeng; Zheng, Zhong; He, Wenteng; Kong, Qingran; Liu, Zhonghua

    2014-08-01

    For efficient transgenic herd expansion, only the transgenic animals that possess the ability to transmit transgene into next generation are considered for breeding. However, for transgenic pig, practically lacking a pre-breeding screening program, time, labor and money is always wasted to maintain non-transgenic pigs, low or null transgenic transmission pigs and the related fruitless gestations. Developing a pre-breeding screening program would make the transgenic herd expansion more economical and efficient. In this technical report, we proposed a three-step pre-breeding screening program for transgenic boars simply through combining the fluorescence in situ hybridization (FISH) assay with the common pre-breeding screening workflow. In the first step of screening, combined with general transgenic phenotype analysis, FISH is used to identify transgenic boars. In the second step of screening, combined with conventional semen test, FISH is used to detect transgenic sperm, thus to identify the individuals producing high quality semen and transgenic sperm. In the third step of screening, FISH is used to assess the in vitro fertilization embryos, thus finally to identify the individuals with the ability to produce transgenic embryos. By this three-step screening, the non-transgenic boars and boars with no ability to produce transgenic sperm or transgenic embryos would be eliminated; therefore only those boars could produce transgenic offspring are maintained and used for breeding and herd expansion. It is the first time a systematic pre-breeding screening program is proposed for transgenic pigs. This program might also be applied in other transgenic large animals, and provide an economical and efficient strategy for herd expansion.

  3. Fixation conditions for DNA and RNA in situ hybridization: a reassessment of molecular morphology dogma.

    PubMed Central

    Tbakhi, A.; Totos, G.; Hauser-Kronberger, C.; Pettay, J.; Baunoch, D.; Hacker, G. W.; Tubbs, R. R.

    1998-01-01

    Neutral buffered formalin (NBF) (4% neutral buffered formaldehyde) has been advocated by most investigators as the primary fixative of choice for in situ hybridization (ISH), and specific anecdotal cautions interdicting the use of precipitating fixatives, which otherwise may offer certain advantages such as superior nuclear detail, are common. Few systematic studies addressing ISH fixation conditions have been published. We reasoned that heavy metals present in some precipitating fixatives may compromise duplex formation during ISH. Cell lines containing known viral gene content (CaSki, 200 to 600 human papilloma virus 16 copies/cell, and SiHa, 1 to 2 human papilloma virus 16 copies/cell) and two negative cell lines (K562 and MOLT 4) were expanded to >10(10) and pellets fixed in NBF, zinc formalin, B5, and Bouin's and Hollande's solutions, and subjected to DNA ISH using biotinylated genomic probes. Ten tissue biopsies fixed in both Hollande's and NBF solutions were also evaluated for human papilloma virus content using DNA ISH. Additionally, 17 cases of Hodgkin's disease fixed in B5 and formalin were compared for Epstein-Barr encoded RNA detection using RNA ISH with fluorescein isothiocyanate-labeled oligonucleotides. Catalyzed reporter deposition combined with Streptavidin-Nanogold staining and silver acetate autometallography (Catalyzed reporter deposition-Ng-autometallography ISH) and a conventional indirect alkaline phosphatase method were used for detection for both DNA and RNA. Contaminating heavy metals entrapped in fixed tissues were removed by two exposures to Lugol's iodine. Results for both DNA and RNA ISH comparing B5 and NBF fixatives were virtually identical. Hollande's, Bouin's, B5, and zinc formalin fixed tissue showed results indistinguishable from NBF fixed tissue in DNA ISH. Precipitating fixatives such as B5 and Hollande's solution may be used for DNA and RNA ISH under appropriate conditions. Images Figure 1 Figure 2 Figure 3 PMID:9422521

  4. Miniature flow injection analyser for laboratory, shipboard and in situ monitoring of nitrate in estuarine and coastal waters.

    PubMed

    Gardolinski, Paulo C F C; David, Anthony R J; Worsfold, Paul J

    2002-12-01

    A miniature, submersible flow injection analyser, with solid-state spectrophotometric detection, for the in situ determination of nitrate is described. It utilises the standard laboratory chemistry of cadmium reduction followed by diazotisation. The detection limit was 2.8 mug l(-1) N and the linear range could be varied from 2.8 to 100 mug l(-1) N up to 100-2000 mug l(-1) N to suit local environmental conditions. The versatility of the instrument is demonstrated by results from laboratory, shipboard (North Sea IMPACT Cruise) and in situ (Tamar Estuary, UK) deployments. They show the excellent temporal and spatial resolution that can be achieved for studying dynamic processes in estuarine and coastal waters. The results acquired during the IMPACT Cruise map the transport of nitrate from the Humber Estuary into the North Sea and show that nitrate uptake was more pronounced in areas of shallow and clear waters (Dogger Bank) than in the coastal mixing zone with higher suspended solids. A key feature of the analyser is its portability and ease of deployment due to the small size and weight and low buoyancy. Accuracy was assessed by participation in an international intercomparison exercise and the results were within the assigned tolerance interval of the consensus mean (Z<2). PMID:18968836

  5. Establishment of a human malignant fibrous histiocytoma cell line, COMA. Characterization By conventional cytogenetics, comparative genomic hybridization, and multiplex fluorescence In situ hybridization.

    PubMed

    Mairal, A; Chibon, F; Rousselet, A; Couturier, J; Terrier, P; Aurias, A

    2000-09-01

    The human COMA cell line has been established from a storiform pleomorphic malignant fibrous histiocytoma (MFH). As expected for this tumor type, a very complex karyotype was observed after R-banding analysis. An extensive analysis by 24-color painting, comparative genomic hybridization (CGH), and fluorescence in situ hybridization (FISH) was performed. Twelve complex marker chromosomes recurrently observed were clearly identified; among them, three were systematically present in all analyzed metaphases. Amplifications detected by CGH were refined by FISH with probes specific for various candidate loci. A significant aneuploidy and numerous micronuclei were observed, which could be related to the anomalies of centriole numbers detected in a proportion of cells. Such an analysis, performed on a series of MFH cell lines, would allow the delineation of the genomic alterations specific for the oncogenesis or progression of this complex tumor type or both. PMID:11063793

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

    PubMed Central

    Nikolakakis, K.; Lehnert, E.

    2015-01-01

    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. PMID:25956763

  7. In-situ U Pb geochronology and Hf isotope analyses of the Rayner Complex, east Antarctica

    NASA Astrophysics Data System (ADS)

    Halpin, J. A.; Gerakiteys, C. L.; Clarke, G. L.; Belousova, E. A.; Griffin, W. L.

    2005-02-01

    In-situ zircon U Pb and Hf isotopic analysis via laser ablation microprobe-inductively coupled plasma mass spectrometer (LAM-ICPMS) of samples from Kemp and MacRobertson Lands, east Antarctica suggests that the Kemp Land terrane evolved separately from the rest of the Rayner Complex prior to the ca. 940 Ma Rayner Structural Episode. Several Archaean metamorphic events in rocks from western Kemp Land can be correlated with events previously reported for the adjacent Napier Complex. Recently reported ca. 1,600 Ma isotopic disturbance in rocks from the Oygarden Group may be correlated with a charnockitic intrusion in the Stillwell Hills before ca. 1,550 Ma. Despite being separated by some 200 km, THfDM ages indicate felsic orthogneiss from Rippon Point, the Oygarden Group, Havstein Island and the Stillwell Hills share a ca. 3,660 3,560 Ma source that is indistinguishable from that previously reported for parts of the Napier Complex. More recent additions to this crust include Proterozoic charnockite in the Stillwell Hills and the vicinity of Mawson Station. These plutons have distinct 176Hf/177Hf ratios and formed via the melting of crust generated at ca. 2,150 2,550 Ma and ca. 1,790 1,870 Ma respectively.

  8. Analysing the Floral Elements of the Lost Tree of Easter Island: A Morphometric Comparison between the Remaining Ex-Situ Lines of the Endemic Extinct Species Sophora toromiro

    PubMed Central

    Püschel, Thomas A.; Espejo, Jaime; Sanzana, María-José; Benítez, Hugo A.

    2014-01-01

    Sophora toromiro (Phil) Skottsb. is a species that has been extinct in its natural habitat Easter Island (Rapa Nui) for over 50 years. However, seed collections carried out before its extinction have allowed its persistence ex-situ in different botanical gardens and private collections around the world. The progenies of these diverse collections have been classified in different lines, most of them exhibiting high similarity as corroborated by molecular markers. In spite of this resemblance observed between the different lines, one of them (Titze) has dissimilar floral elements, thus generating doubts regarding its species classification. The floral elements (wing, standard and keel) belonging to three different S. toromiro lines and two related species were analyzed using geometric morphometrics. This method was applied in order to quantify the floral shape variation of the standard, wing, and keel between the different lines and control species. Geometric morphometrics analyses were able to distinguish the floral elements at both intra (lines) and inter-specific levels. The present results are on line with the cumulative evidence that supports the Titze line as not being a proper member of the S. toromiro species, but probably a hybridization product or even another species of the Edwardsia section. The reintroduction programs of S. toromiro should consider this information when assessing the authenticity and origin of the lines that will be used to repopulate the island. PMID:25526512

  9. Analysing the floral elements of the lost tree of Easter Island: a morphometric comparison between the remaining ex-situ lines of the endemic extinct species Sophora toromiro.

    PubMed

    Püschel, Thomas A; Espejo, Jaime; Sanzana, María-José; Benítez, Hugo A

    2014-01-01

    Sophora toromiro (Phil) Skottsb. is a species that has been extinct in its natural habitat Easter Island (Rapa Nui) for over 50 years. However, seed collections carried out before its extinction have allowed its persistence ex-situ in different botanical gardens and private collections around the world. The progenies of these diverse collections have been classified in different lines, most of them exhibiting high similarity as corroborated by molecular markers. In spite of this resemblance observed between the different lines, one of them (Titze) has dissimilar floral elements, thus generating doubts regarding its species classification. The floral elements (wing, standard and keel) belonging to three different S. toromiro lines and two related species were analyzed using geometric morphometrics. This method was applied in order to quantify the floral shape variation of the standard, wing, and keel between the different lines and control species. Geometric morphometrics analyses were able to distinguish the floral elements at both intra (lines) and inter-specific levels. The present results are on line with the cumulative evidence that supports the Titze line as not being a proper member of the S. toromiro species, but probably a hybridization product or even another species of the Edwardsia section. The reintroduction programs of S. toromiro should consider this information when assessing the authenticity and origin of the lines that will be used to repopulate the island.

  10. Analysing the floral elements of the lost tree of Easter Island: a morphometric comparison between the remaining ex-situ lines of the endemic extinct species Sophora toromiro.

    PubMed

    Püschel, Thomas A; Espejo, Jaime; Sanzana, María-José; Benítez, Hugo A

    2014-01-01

    Sophora toromiro (Phil) Skottsb. is a species that has been extinct in its natural habitat Easter Island (Rapa Nui) for over 50 years. However, seed collections carried out before its extinction have allowed its persistence ex-situ in different botanical gardens and private collections around the world. The progenies of these diverse collections have been classified in different lines, most of them exhibiting high similarity as corroborated by molecular markers. In spite of this resemblance observed between the different lines, one of them (Titze) has dissimilar floral elements, thus generating doubts regarding its species classification. The floral elements (wing, standard and keel) belonging to three different S. toromiro lines and two related species were analyzed using geometric morphometrics. This method was applied in order to quantify the floral shape variation of the standard, wing, and keel between the different lines and control species. Geometric morphometrics analyses were able to distinguish the floral elements at both intra (lines) and inter-specific levels. The present results are on line with the cumulative evidence that supports the Titze line as not being a proper member of the S. toromiro species, but probably a hybridization product or even another species of the Edwardsia section. The reintroduction programs of S. toromiro should consider this information when assessing the authenticity and origin of the lines that will be used to repopulate the island. PMID:25526512

  11. A study of myc-related gene expression in small cell lung cancer by in situ hybridization.

    PubMed Central

    Gu, J.; Linnoila, R. I.; Seibel, N. L.; Gazdar, A. F.; Minna, J. D.; Brooks, B. J.; Hollis, G. F.; Kirsch, I. R.

    1988-01-01

    The expression of myc-related genes (c-myc, N-myc, and L-myc) in small cell lung cancer (SCLC) was studied by RNA-RNA tissue in situ hybridization. The tissues investigated included cytospins of ten cell lines derived from patients with SCLC, four corresponding nude mouse xenografts from cell lines, and metastatic tumor tissue obtained by surgical biopsy and at autopsy. The probes were prepared as 35S labeled complementary RNA. The expression of each gene was demonstrated specifically by autoradiography in the cytoplasm of the neoplastic cell samples. The average levels of oncogene expression in each specimen corroborated previous data obtained by Northern blot assays. In addition, heterogeneity in gene expression from cell to cell in each sample was noted. This study represents the first attempt to demonstrate oncogene expression in lung cancer cell lines and tissues in situ, and confirms that the expression of these myc related genes can be seen in the primary tumor. The technique of RNA-RNA tissue in situ hybridization has great potential in answering fundamental questions of tumor cell heterogeneity and progression in SCLC. It should be useful in both prospective and retrospective studies. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:2456019

  12. Observation and Quantification of Telomere and Repetitive Sequences Using Fluorescence In Situ Hybridization (FISH) with PNA Probes in Caenorhabditis elegans.

    PubMed

    Seo, Beomseok; Lee, Junho

    2016-01-01

    Telomere is a ribonucleoprotein structure that protects chromosomal ends from aberrant fusion and degradation. Telomere length is maintained by telomerase or an alternative pathway, known as alternative lengthening of telomeres (ALT)(1). Recently, C. elegans has emerged as a multicellular model organism for the study of telomere and ALT(2). Visualization of repetitive sequences in the genome is critical in understanding the biology of telomeres. While telomere length can be measured by telomere restriction fragment assay or quantitative PCR, these methods only provide the averaged telomere length. On the contrary, fluorescence in situ hybridization (FISH) can provide the information of the individual telomeres in cells. Here, we provide protocols and representative results of the method to determine telomere length of C. elegans by fluorescent in situ hybridization. This method provides a simple, but powerful, in situ procedure that does not cause noticeable damage to morphology. By using fluorescently labeled peptide nucleic acid (PNA) and digoxigenin-dUTP-labeled probe, we were able to visualize two different repetitive sequences: telomere repeats and template of ALT (TALT) in C. elegans embryos and gonads. PMID:27583462

  13. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

    PubMed Central

    Moffitt, Jeffrey R.; Hao, Junjie; Wang, Guiping; Chen, Kok Hao

    2016-01-01

    Image-based approaches to single-cell transcriptomics, in which RNA species are identified and counted in situ via imaging, have emerged as a powerful complement to single-cell methods based on RNA sequencing of dissociated cells. These image-based approaches naturally preserve the native spatial context of RNAs within a cell and the organization of cells within tissue, which are important for addressing many biological questions. However, the throughput of these image-based approaches is relatively low. Here we report advances that lead to a drastic increase in the measurement throughput of multiplexed error-robust fluorescence in situ hybridization (MERFISH), an image-based approach to single-cell transcriptomics. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule fluorescence in situ hybridization (smFISH) to read out these barcodes. Here we increase the throughput of MERFISH by two orders of magnitude through a combination of improvements, including using chemical cleavage instead of photobleaching to remove fluorescent signals between consecutive rounds of smFISH imaging, increasing the imaging field of view, and using multicolor imaging. With these improvements, we performed RNA profiling in more than 100,000 human cells, with as many as 40,000 cells measured in a single 18-h measurement. This throughput should substantially extend the range of biological questions that can be addressed by MERFISH. PMID:27625426

  14. Improved in situ hybridization and G-banding by pretreatment with Denhardt's solution and gelatin-chrome alum.

    PubMed

    Lee, G M; Rasch, E M; Musich, P R

    1985-11-01

    Various pretreatments of metaphase spreads were examined to obtain optimal DNA labelling patterns while maintaining chromosome integrity during in situ hybridization procedures. Preparations of African green monkey (AGM) chromosomes fixed in methanol-acetic acid (CV-1 cell line) were treated by coating with Denhardt's solution, dilute gelatin-chrome alum, nonfat instant dry milk dissolved in saline-citrate solution (SSC) and/or acetylation prior to denaturation of chromosomal DNA in 70% formamide-2 X SSC for 2 min at 70 degrees C. A 3H-labelled, cloned DNA fragment of the highly repetitive AGM component alpha DNA was hybridized to the chromosomes by incubation at 45 degrees C for 16 h. Treatment with gelatin-chrome alum prior to denaturation greatly improved chromosome morphology and decreased background, but reduced pericentromeric labelling. Sequential treatment with 5 X Denhardt's solution followed by gelatin-chrome alum resulted in enhanced specificity of labelling and excellent chromosome morphology, as well as reduced levels of background. Acetylation had little effect after pretreatment with gelatin-chrome alum, but reduced background levels after pretreatment with Denhardt's solution. Chromosomes treated with Denhardt's solution plus gelatin-chrome alum can be routinely G-banded using trypsin after in situ hybridization.

  15. Detection of genomic and intermediate replicative strands of hepatitis C virus in liver tissue by in situ hybridization.

    PubMed Central

    Nouri Aria, K T; Sallie, R; Sangar, D; Alexander, G J; Smith, H; Byrne, J; Portmann, B; Eddleston, A L; Williams, R

    1993-01-01

    Nonisotopic in situ hybridization using a digoxigenin-labeled cDNA probe to the 3' nonstructural region (NS5) of hepatitis C virus (HCV) was performed on liver tissue from 33 patients. The results were compared with PCR detection of HCV RNA performed on 24 of the biopsies. Nonisotopic in situ hybridization correlated well with PCR findings. Hybridization signals were detected, within the cytoplasm and nuclei/nucleoli of hepatocytes, mononuclear, and biliary epithelial cells. In patients with clinically and histologically defined chronic active hepatitis related to active HCV infection, HCV genome was frequently detected in biliary epithelium and correlated well with biliary damage, an otherwise uncommon finding in chronic active hepatitis due to other hepatotropic viruses. Further studies using sense and antisense probes synthesized from the 5' non-coding region of the HCV genome confirmed the localization of positive strand of HCV in the above cell populations. The replicative intermediate strand was also present in all cells, although less frequently observed, apart from biliary epithelium, where negative strand of HCV was undetectable. The findings of HCV genome in liver biopsies of two patients with no significant histological abnormalities may suggest that the damage seen in chronic HCV infection is immune mediated, although the cytopathic effect of the virus may also be important. Images PMID:8387544

  16. Rapid In Situ Hybridization using Oligonucleotide Probes on Paraformaldehyde-prefixed Brain of Rats with Serotonin Syndrome.

    PubMed

    Shokry, Ibrahim M; Callanan, John J; Sousa, John; Tao, Rui

    2015-01-01

    3,4-Methylenedioxymethamphetamine (MDMA; ecstasy) toxicity may cause region-specific changes in serotonergic mRNA expression due to acute serotonin (5-hydroxytryptamine; 5-HT) syndrome. This hypothesis can be tested using in situ hybridization to detect the serotonin 5-HT2A receptor gene htr2a. In the past, such procedures, utilizing radioactive riboprobe, were difficult because of the complicated workflow that needs several days to perform and the added difficulty that the technique required the use of fresh frozen tissues maintained in an RNase-free environment. Recently, the development of short oligonucleotide probes has simplified in situ hybridization procedures and allowed the use of paraformaldehyde-prefixed brain sections, which are more widely available in laboratories. Here, we describe a detailed protocol using non-radioactive oligonucleotide probes on the prefixed brain tissues. Hybridization probes used for this study include dapB (a bacterial gene coding for dihydrodipicolinate reductase), ppiB (a housekeeping gene coding for peptidylprolyl isomerase B), and htr2a (a serotonin gene coding for 5-HT2A receptors). This method is relatively simply, cheap, reproducible and requires less than two days to complete. PMID:26437182

  17. Hybrids between olive flounder Paralichthys olivaceus and stone flounder Kareius bicoloratus: karyotype, allozyme and RAPD analyses

    NASA Astrophysics Data System (ADS)

    You, Feng; Wang, Wei; Xu, Dongdong; Zhu, Xiangping; Ni, Jing; Wu, Zhihao; Xu, Yongli; Wang, Xincheng; Zhang, Peijun

    2009-05-01

    The hybrid between olive flounder Paralichthys olivaceus and stone flounder Kareius bicoloratus was produced by artificial insemination of olive flounder eggs with stone flounder sperm. Sinistral and dextral are two types of hybrid progeny after metamorphosis. Karyotypes of both hybrid flounders are the same as those of the two parental species. Of the 22 loci examined from 12 allozymes, 12 confirmed hybridization of the paternal and maternal loci in hybrids and no difference was found in allozyme patterns of sinistral and dextral hybrid fishes. RAPD patterns of these specimens were also studied with 38 primers selected from 104 tested. Among them, the PCR products of 30 primers showed hybridization of the paternal and maternal bands. Genetic variation between hybrids and their parental stocks was analyzed by RAPD using 10 of the above 38 primers. The average heterozygosity and genetic distance were calculated. The results suggested that the filial generation could inherit a little more genetic materials from paternal fish than that from maternal fish.

  18. Analysis of unfertilized oocytes subjected to intracytoplasmic sperm injection using two rounds of fluorescence in-situ hybridization and probes to five chromosomes.

    PubMed

    Martini, E; Flaherty, S P; Swann, N J; Payne, D; Matthews, C D

    1997-09-01

    Chromosomal aberrations are the major cause of pre- and post-implantation embryo wastage and some studies suggest that half of all human conception have a chromosomal abnormality. Analysis of gametes provides information on the origin of these chromosomal aberrations. The purpose of this study was to develop a reliable multi-probe fluorescence in-situ hybridization (FISH) procedure that would enable us to investigate aneuploidy in unfertilized oocytes subjected to intracytoplasmic sperm injection (ICSI). Oocytes were spread with HCl and Tween 20 solution, and then two rounds of triple-probe FISH were performed on each oocyte using directly-labelled centromeric probes: chromosomes 1, 7, 15 (overnight hybridization); chromosomes 1, X, Y (2 h hybridization). After the first round, the slides were counterstained and evaluated, and the positions of FISH signals were recorded. For the second round, the counterstain was removed and the second probe cocktail was applied. The chromosome 1 probe was an internal control for the two hybridization procedures, while the Y chromosome probe was used to detect sperm DNA. To evaluate the method, a total of 79 oocytes from 27 patients were studied. Of these, 67 (84.8%) were successfully spread and 97% of these oocytes exhibited discernible FISH signals. Upon lysis, oocytes exhibited one or more DNA fragments (mean 1.9, range 1-3). Of the 65 analysable oocytes, 17 (26.2%) displayed a normal haploid chromosome constitution with paired spots for the two chromatids. A further 23 oocytes (35.4%) showed an ambiguous chromosome complement due to an abnormal number of DNA fragments which may have resulted from loss of DNA during spreading or to an abnormal oocyte, while 25 oocytes (38.4%) displayed aneuploidy for one or more of the chromosomes studied. In conclusion, this new approach is a quick and efficient method with which numerical chromosomal abnormalities in human oocytes can be studied; interpretation of the patterns of DNA fragments

  19. Rapid in situ hybridization technique using 16S rRNA segments for detecting and differentiating the closely related gram-positive organisms Bacillus polymyxa and Bacillus macerans

    NASA Technical Reports Server (NTRS)

    Jurtshuk, R. J.; Blick, M.; Bresser, J.; Fox, G. E.; Jurtshuk, P. Jr

    1992-01-01

    A rapid, sensitive, inexpensive in situ hybridization technique, using 30-mer 16S rRNA probes, can specifically differentiate two closely related Bacillus spp., B. polymyxa and B. macerans. The 16S rRNA probes were labeled with a rhodamine derivative (Texas Red), and quantitative fluorescence measurements were made on individual bacterial cells. The microscopic fields analyzed were selected by phase-contrast microscopy, and the fluorescence imaging analyses were performed on 16 to 67 individual cells. The labeled 16S rRNA probe, POL, whose sequence was a 100% match with B. polymyxa 16S rRNA but only a 60% match with B. macerans 16S rRNA, gave quantitative fluorescence ratio measurements that were 34.8-fold higher for B. polymyxa cells than for B. macerans cells. Conversely, the labeled probe, MAC, which matched B. polymyxa 16S rRNA in 86.6% of its positions and B. macerans 16S rRNA in 100% of its positions, gave quantitative fluorescence measurements that were 59.3-fold higher in B. macerans cells than in B. polymyxa cells. Control probes, whose 16S rRNA sequence segment (P-M) was present in both B. polymyxa and B. macerans as well as a panprokaryotic probe (16S), having a 100% match with all known bacteria, hybridized equally well with both organisms. These latter hybridizations generated very high fluorescence signals, but their comparative fluorescence ratios (the differences between two organisms) were low. The control paneukaryotic probe (28S), which had less than 30% identity for both B. macerans and B. polymyxa, did not hybridize with either organism.

  20. Compound hybrid geothermal-fossil power plants - Thermodynamic analyses and site-specific applications

    NASA Astrophysics Data System (ADS)

    Dipippo, R.; Kestin, J.; Avelar, E. M.; Khalifa, H. E.

    1980-02-01

    In this paper, we extend the analysis of hybrid fossil-geothermal power plants to compound systems which combine the features of the two previously analyzed hybrid plants, the geothermal preheat and the fossil superheat systems. Compound systems of the one- and two-stage type are considered. A complete summary of formulae to assess the performance of the plants is included for completeness. From the viewpoint of thermodynamics, compound hybrid plants are superior to individual all-geothermal and all-fossil plants, and have certain advantages over basic geothermal-preheat and fossil-superheat hybrid plants. The flexibility of compound hybrid systems is illustrated by showing how such plants might be used at several geothermal sites in the western United States.

  1. PM Motor Parametric Design Analyses for a Hybrid Electric Vehicle Traction Drive Application

    SciTech Connect

    Staunton, R.H.

    2004-10-11

    The Department of Energy's (DOE) Office of FreedomCAR (Cooperative Automotive Research) and Vehicle Technologies office has a strong interest in making rapid progress in permanent magnet (PM) machine development. The DOE FreedomCAR program is directing various technology development projects that will advance the technology and hopefully lead to a near-term request for proposals (RFP) for a to-be-determined level of initial production. This aggressive approach is possible because the technology is clearly within reach and the approach is deemed essential, based on strong market demand, escalating fuel prices, and competitive considerations. In response, this study began parallel development paths that included a literature search/review, development and utilization of multiple parametric models, verification of the modeling methodology, development of an interior PM (IPM) machine baseline design, development of alternative machine baseline designs, and cost analyses for several candidate machines. This report summarizes the results of these activities as of September 2004. This report provides background and summary information for recent machine parametric studies and testing programs that demonstrate both the potential capabilities and technical limitations of brushless PM machines (axial gap and radial gap), the IPM machine, the surface-mount PM machines (interior or exterior rotor), induction machines, and switched-reluctance machines. The FreedomCAR program, while acknowledging the progress made by Oak Ridge National Laboratory (ORNL), Delphi, Delco-Remy International, and others in these programs, has redirected efforts toward a ''short path'' to a marketable and competitive PM motor for hybrid electric vehicle (HEV) traction applications. The program has developed a set of performance targets for the type of traction machine desired. The short-path approach entails a comprehensive design effort focusing on the IPM machine and meeting the performance targets

  2. Electrophoretic and immunological analyses of almond (Prunusdulcis l.) genotypes and hybrids.

    PubMed

    Sathe, S K; Teuber, S S; Gradziel, T M; Roux, K H

    2001-04-01

    Aqueous extracts from sixty almond samples representing various genotypes and interspecies hybrids of almond, including almond-peach, were analyzed for protein and peptide content using electrophoresis, Western immunoblotting, and enzyme-linked immunosorbent assay (ELISA). Nondenaturing nondissociating polyacrylamide gel electrophoresis (NDND-PAGE) of the aqueous extracts indicated that a single major storage protein (almond major protein -- AMP or amandin) dominated the total soluble protein composition. Denaturing SDS--PAGE analyses of the aqueous extracts revealed that the AMP was mainly composed of two sets of polypeptides with estimated molecular masses in the ranges of 38--41 kDa and 20--22 kDa, regardless of the source; however, distinct variations in the intensity and electrophoretic mobility of some bands were noted between samples. In addition to AMP, several minor polypeptides were also present in all the genotypes, and variations were seen in these as well. Regardless of the genotype, AMP was recognized in Western blots by rabbit polyclonal anti-AMP antibodies, mouse monoclonal anti-AMP antibodies (mAbs), and serum IgE from patients displaying strong serum anti-almond IgE reactivity. As with protein staining results, antibody reactivity also revealed common patterns but displayed some variation between samples. An anti-AMP inhibition ELISA was used to quantify and compare aqueous extracts for various samples. All samples (n = 60) reacted in this assay with a mean +/- standard deviation (sigma n) = 0.82 +/- 0.18 when compared to reference aqueous extract from Nonpareil designated as 1.0. PMID:11308365

  3. PM Motor Parametric Design Analyses for Hybrid Electric Vehicle Traction Drive Application: Interim Report

    SciTech Connect

    Staunton, R.H.

    2004-08-11

    The Department of Energy's (DOE) Office of FreedomCAR (Cooperative Automotive Research) and Vehicle Technologies has a strong interest in making rapid progress in permanent magnet (PM) machine development. The program is directing various technology development projects that will advance the technology and lead to request for proposals (RFP) for manufacturer prototypes. This aggressive approach is possible because the technology is clearly within reach and the approach is deemed essential, based on strong market demand, escalating fuel prices, and competitive considerations. In response, this study began parallel development paths that included a literature search/review, development and utilization of multiple parametric models to determine the effects of design parameters, verification of the modeling methodology, development of an interior PM (IPM) machine baseline design, development of alternative machine baseline designs, and cost analyses for several candidate machines. This interim progress report summarizes the results of these activities as of June 2004. This report provides background and summary information for recent machine parametric studies and testing programs that demonstrate both the potential capabilities and technical limitations of brushless PM machines (axial gap and radial gap), the IPM machine, the surface-mount PM machines (interior or exterior rotor), induction machines, and switched reluctance machines. The FreedomCAR program, while acknowledging the progress made by Oak Ridge National Laboratory, Delphi, Delco-Remy International, and others in these programs, has redirected efforts toward a ''short path'' to a marketable and competitive PM motor for hybrid electric vehicle traction applications. The program has developed a set of performance targets for the type of traction machine desired. The short-path approach entails a comprehensive design effort focusing on the IPM machine and meeting the performance targets. The selection of the

  4. Depth Profile Of Radiolytic Fluence On Europa: Implications for Remote Sensing and In-Situ Analyses

    NASA Astrophysics Data System (ADS)

    Carlson, R. W.

    2003-05-01

    exposed material at meter depths, i.e. fresh craters with diameters > about 10 m. The time required to attain a fluence of 1000 eV per 16-amu molecule in a mm thick optical layer is about 1400 years on Europa's trailing side. An in-situ astrobiological mission should obtain samples from depths > 1 m. This work was supported by NASA's Planetaty Geology and Geophysics Program.

  5. Innovative tribometer for in situ spectroscopic analyses of wear mechanisms and phase transformation in ceramic femoral heads.

    PubMed

    Puppulin, Leonardo; Leto, Andrea; Wenliang, Zhu; Sugano, Nobuhiko; Pezzotti, Giuseppe

    2014-03-01

    The literature on tribological assessments of artificial hip joints usually focuses on correlations between joint composition, size, and specific wear rates, but conspicuously ignores the physical aspects behind the occurrence of degradation mechanisms of friction and wear. Surface degradation in artificial joints occurs because of increases in temperature and local exacerbation of contact stresses inside the moving contact as a consequence of physical and chemical modifications of the sliding surfaces. This article reports about the development of a new pin-on-ball spectroscopy-assisted tribometer device that enables investigating also physical rather than merely engineering aspects of wear processes using in situ Raman and fluorescence techniques. This innovative tribometer is designed to bring about, in addition to conventional tribological parameters, also information of temperature, stress and phase transformations in the femoral heads as received from the manufacturer. Raman and fluorescence spectra at the point of sliding contact are recorded durilng reciprocating hard-on-hard dry-sliding tests. Preliminary results were collected on two different commercially available ceramic-on-ceramic hip joint bearing couples, made of monolithic alumina and alumina-zirconia composites. Although the composite couple showed direct evidence of tetragonal-to-monoclinic phase transformation, which enhanced the coefficient of friction, the specific wear rate was significantly lower than that of the monolithic one (i.e., by a factor 2.63 and 4.48 on the pin and head side, respectively). In situ collected data compared to ex situ analyses elucidated the surface degradation processes and clarified the origin for the higher wear resistance of the composite as compared to the monolithic couple.

  6. Cytogenetic abnormality in patients with multiple myeloma analyzed by fluorescent in situ hybridization

    PubMed Central

    Hu, Ying; Chen, Wenming; Chen, Shilun; Huang, Zhongxia

    2016-01-01

    Objective To analyze the fluorescent in situ hybridization (FISH) data and the association with clinical characteristics, therapy response, and survival time in patients with multiple myeloma. Method We performed a retrospective review of patients with multiple myeloma from November 2010 to April 2014. Results Cytogenetic abnormalities by FISH were detectable in 66% of patients. One cytogenetic abnormality, two cytogenetic abnormalities, and complex abnormalities were detectable in 21.2%, 51.5%, and 27.3% of cases, respectively. 1q21 amplification, t(4p16.3/14q32), and 17p deletion were observed in 69.7%, 30.3%, and 21.2% of cases, respectively. Total response rates (complete response [CR] + near CR + partial response) were 93.8% and 82.1%, respectively, in cytogenetic normality group and abnormality group. CR rates were 50% and 32.1%, respectively. Median overall survival (OS) time was 51 months and 24 months, respectively, in cytogenetic normality group and abnormality group (P<0.05). Median OS time was not significantly different between 1q21 amplification group and no 1q21 amplification group in patients with FISH abnormalities (P>0.05). Median OS time was not significantly different between t(4;14) group and no t(4;14) group in patients with FISH abnormalities (P>0.05). Seven patients of 17p deletion died in 2 years. Conclusion Multiple myeloma is characterized by a high occurrence of chromosomal aberrations. 1q21 amplification and t(4;14) are the most common abnormalities. Multiple cytogenetic abnormalities are frequently observed in the same one patient. The total response rate, CR rate, and OS time are worse in cytogenetic abnormal patients compared with cytogenetic normal patients. Patients with 17p deletion have a very poor prognosis. Future goals of therapy will be to achieve minimal residual disease, biomarkers, and genomic data, which might provide a better estimate of the depth of response to therapy and OS. PMID:27042105

  7. Fluorescence in situ hybridization investigation of potentially pathogenic bacteria involved in neonatal porcine diarrhea

    PubMed Central

    2014-01-01

    Background Neonatal diarrhea is a multifactorial condition commonly present on pig farms and leads to economic losses due to increased morbidity and mortality of piglets. Immature immune system and lack of fully established microbiota at birth predispose neonatal piglets to infection with enteric pathogens. The microorganisms that for decades have been associated with enteritis and diarrhea in suckling piglets are: rotavirus A, coronavirus, enterotoxigenic Escherichia coli (ETEC), Clostridium perfringens type C, Cryptosporidium spp., Giardia spp., Cystoisospora suis and Strongyloides ransomi. However, in recent years, the pig industry has experienced an increased number of neonatal diarrhea cases in which the above mentioned pathogens are no longer detected. Potentially pathogenic bacteria have recently received focus in the research on the possible etiology of neonatal diarrhea not caused by common pathogens. The primary aim of this study was to investigate the role of E. coli, Enterococcus spp., C. perfringens and C. difficile in the pathogenesis of neonatal porcine diarrhea with no established casual agents. Fluorescence in situ hybridization with oligonucleotide probes was applied on the fixed intestinal tissue samples from 51 diarrheic and 50 non-diarrheic piglets collected from four Danish farms during outbreaks of neonatal diarrhea not caused by well-known enteric pathogens. Furthermore, an association between the presence of these bacteria and histological lesions was evaluated. Results The prevalence of fluorescence signals specific for E. coli, C. perfringens and C. difficile was similar in both groups of piglets. However, Enterococcus spp. was primarily detected in the diarrheic piglets. Furthermore, adherent bacteria were detected in 37 % diarrheic and 14 % non-diarrheic piglets. These bacteria were identified as E. coli and Enterococcus spp. and their presence in the intestinal mucosa was associated with histopathological changes. Conclusions The

  8. Oncogene amplification detected by in situ hybridization in radiation induced rat skin tumors. [C-myc:a3

    SciTech Connect

    Yi Jin.

    1991-02-01

    Oncogene activation may play an important role in radiation induced carcinogenesis. C-myc oncogene amplification was detected by in situ hybridization in radiation-induced rat skin tumors, including squamous and basal cell carcinomas. In situ hybridization was performed with a biotinylated human c-myc third exon probe, visualized with an avidin-biotinylated alkaline phosphate detection system. No c-myc oncogene amplification was detected in normal rat skin at very early times after exposure to ionizing radiation, which is consistent with the view that c-myc amplification is more likely to be related to carcinogenesis than to normal cell proliferation. The incorporation of tritiated thymidine into the DNA of rat skin cells showed that the proliferation of epidermal cells reached a peak on the seventh day after exposure to ionizing radiation and then decreased. No connection between the proliferation of epidermal cell and c-myc oncogene amplification in normal or irradiated rat skin was found. The results indicated that c-myc amplification as measured by in situ hybridization was correlated with the Southern bolt results, but only some of the cancer cells were amplified. The c-myc positive cells were distributed randomly within regions of the tumor and exhibited a more uniform nuclear structure in comparison to the more vacuolated c-myc negative cells. No c-myc signal was detected in unirradiated normal skin or in irradiated skin cells near the tumors. C-myc amplification appears to be cell or cell cycle specific within radiation-induced carcinomas. 28 refs., 3 figs., 3 tabs.

  9. Quantitative determination of the oxidation state of iron in biotite using x-ray photoelectron spectroscopy: II. In situ analyses

    SciTech Connect

    Raeburn, S.P. |; Ilton, E.S.; Veblen, D.R.

    1997-11-01

    X-ray photoelectron spectroscopy (XPS) was used to determine Fe(III)/{Sigma}Fe in individual biotite crystals in thin sections of ten metapelites and one syenite. The in situ XPS analyses of Fe(III)/{Sigma}Fe in biotite crystals in the metapelites were compared with published Fe(III)/{Sigma}Fe values determined by Moessbauer spectroscopy (MS) for mineral separates from the same hand samples. The difference between Fe(III)/{Sigma}Fe by the two techniques was greatest for samples with the lowest Fe(III)/{Sigma}Fe (by MS). For eight metamorphic biotites with Fe(III)/{Sigma}Fe = 9-27% comparison of the two techniques yielded a linear correlation of r = 0.94 and a statistically acceptable fit of [Fe(III)/{Sigma}Fe]{sub xps} = [Fe(III)/{Sigma}Fe]{sub ms}. The difference between Fe(III)/{Sigma}Fe by the two techniques was greater for two samples with Fe(III)/{Sigma}Fe {le} 6% (by MS). For biotite in the syenite sample, Fe(III)/{Sigma}Fe determined by both in situ XPS and bulk wet chemistry/electron probe microanalysis were similar. This contribution demonstrates that XPS can be used to analyze bulk Fe(III)/{Sigma}Fe in minerals in thin sections when appropriate precautions taken to avoid oxidation of the near-surface during preparation of samples. 25 refs., 3 figs., 4 tabs.

  10. Covalent binding of formalin fixed paraffin embedded brain tissue sections to glass slides suitable for in situ hybridization.

    PubMed

    Tourtellotte, W W; Verity, A N; Schmid, P; Martinez, S; Shapshak, P

    1987-02-01

    A novel method for covalently binding formalin fixed paraffin embedded (FFPE) tissue sections to glass microscope slides is validated suitable for in situ hybridization (ISH). Using the organosilane methodology of Maples (1985), 100% tissue adhesion is reported with no nonspecific probe binding, staining, or autoradiographic artefacts. JC viral nucleic acid sequences are successfully detected in FFPE progressive multifocal leukoencephalopathy brain tissue and the Tm of the hybridized product is estimated. From the Tm the most stringent washing condition resulting in an optimal signal to noise ratio is determined. A comparison is made between currently used methods of tissue adhesion and the proposed organosilane methodology. This methodology greatly facilitates studies of conditions for ISH and elucidation of mechanisms of viral infections requiring consecutive FFPE sections. It is also applicable to studies using cryosections and cultured cells.

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

    SciTech Connect

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

    1988-02-01

    To determine which cells within the brain produce ..beta..-amyloid mRNA and to assess expression of the ..beta..-amyloid gene in Alzheimer disease, the authors analyzed brain tissue from Alzheimer and control patients by in situ hybridization. The results demonstrate that ..beta..-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 ..beta..-amyloid probe than those from controls. These observations support the hypothesis that increased expression of the ..beta..-amyloid gene plays an important role in the deposition of amyloid in the brains of patients with Alzheimer disease.

  12. Sudan Black B treatment reduces autofluorescence and improves resolution of in situ hybridization specific fluorescent signals of brain sections.

    PubMed

    Oliveira, V C; Carrara, R C V; Simoes, D L C; Saggioro, F P; Carlotti, C G; Covas, D T; Neder, L

    2010-08-01

    Interference by autofluorescence is one of the major concerns of immunofluorescence analysis of in situ hybridization-based diagnostic assays. We present a useful technique that reduces autofluorescent background without affecting the tissue integrity or direct immunofluorescence signals in brain sections. Using six different protocols, such as ammonia/ethanol, Sudan Black B (SBB) in 70% ethanol, photobleaching with UV light and different combinations of them in both formalin-fixed paraffin-embedded and frozen human brain tissue sections, we have found that tissue treatment of SBB in a concentration of 0.1% in 70% ethanol is the best approach to reduce/eliminate tissue autofluorescence and background, while preserving the specific fluorescence hybridization signals. This strategy is a feasible, non-time consuming method that provides a reasonable compromise between total reduction of the tissue autofluorescence and maintenance of specific fluorescent labels.

  13. Chromosomal localization of genes by scanning electron microscopy using in situ hybridization with biotinylated probes: Y chromosome repetitive sequences.

    PubMed

    Ferguson, D J; Burns, J; Harrison, D; Jonasson, J A; McGee, J O

    1986-05-01

    The feasibility of using scanning electron microscopy (SEM) to identify the position of specific DNA sequences was examined using a Y chromosome 'specific' probe (pHY2.1). Tests were carried out on chromosome spreads hybridized in situ with biotinylated pHY2.1. Chromosomal sites of hybridization of the probe were localized by an indirect immunohistochemical procedure which resulted in a gold product which could be amplified by silver precipitation. In the SEM, the specific location of the probe was easily identified due to the enhanced signal produced by the gold-silver complex. The probe was localized both on the long arm of the Y chromosome and within interphase nuclei. It was found that SEM was more sensitive than light microscopy since the probe could be identified without silver amplification. With refinements to the technique, SEM could provide a useful method for high resolution localizing of unique DNA sequences (i.e. single copy genes). PMID:3528066

  14. Localization by high resolution in situ hybridization of the ribosomal minichromosomes during the nucleolar cycle of Physarum polycephalum.

    PubMed

    Puvion-Dutilleul, F; Pierron, G

    1992-12-01

    We have used biotinylated rDNA probes to localize by in situ hybridization the extrachromosomal genes for ribosomal RNA in the slime mold Physarum polycephalum. We established conditions that allow for highly specific hybridization at the ultrastructural level and determined that the 60-kb palindromic rDNA molecules are confined to the nucleolus in interphase. Our study definitively locates these extrachromosomal genes in mitosis in the form of thin DNA fibers contained within nucleolar remnants. We further show that these rDNA minichromosomes do not condense and that they segregate as entities independent of the condensed chromosomal DNA. In telophase, these minichromosomes migrate from the poles toward the equatorial region of the nucleus in a direction opposite that of the chromosomes. Our results illustrate the discontinuous nature of the nucleolar organizing region in Physarum. PMID:1459200

  15. [A Case of Xp.11.2 Traslocational Renal Cell Carcinoma Diagnosed by Fluorescence in Situ Hybridization (FISH)].

    PubMed

    Iinuma, Koji; Kojima, Keitaro; Okamoto, Kiyohisa; Yuhara, Kazuya

    2016-08-01

    A 72-year-old woman was referred to our hospital with complaints of macro-hematuria. The radiographic evaluation including computed tomography (CT) and magnetic resonance imaging (MRI) suggested it to be renal cell carcinoma (RCC) in her right kidney. She underwent laparoscopic nephrectomy. We diagnosed her with renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion, based on pathological findings and break apart of transcription factor E3 (TFE3)by fluorescence in situ hybridization. She was free of recurrence at 8 months postoperatively. PMID:27624107

  16. Spreading and fluorescence in situ hybridization of male and female meiocyte chromosomes from Arabidopsis thaliana for cytogenetical analysis.

    PubMed

    Armstrong, Susan

    2013-01-01

    Advances in molecular biology and in the genetics of Arabidopsis thaliana have led to it becoming an important model for the analysis of meiosis in plants. Cytogenetic investigations are pivotal to meiotic studies and a number of technological improvements for Arabidopsis cytology have provided a range of tools to investigate chromosome behavior during meiosis. This chapter contains a detailed description of cytological techniques currently used in our laboratory for the basic preparation of meiotic chromosomes for investigation of the female and male meiotic pathway and fluorescence in situ hybridization (FISH) analysis for the frequency and distribution of crossovers (chiasmata) at metaphase I.

  17. Initial stages of TiO 2 thin films MOCVD growth studied by in situ surface analyses

    NASA Astrophysics Data System (ADS)

    Brevet, A.; Peterlé, P. M.; Imhoff, L.; Marco de Lucas, M. C.; Bourgeois, S.

    2005-02-01

    In situ chemical surface analyses using X-ray photoelectron spectroscopy (XPS) were performed to understand the initial stages of TiO 2 thin-film MOCVD growth. Deposits on Si (1 0 0), a few nanometres thick, were obtained at a fixed temperature of 650 °C and for two different pressures, 2.9 and 0.05 mbar, using titanium tetraisopropoxide (TTIP) as precursor. Pressure lowering led to a higher deposit growth rate. Reduction of titanium with respect to stoichiometric titanium dioxide and oxidation of the wet-cleaned silicon substrate are observed from decomposition of the Ti 2p and Si 2p peaks. The formation of a TiSi xO y mixed oxide is also pointed out and confirmed by the presence of a characteristic component in the O 1 s peak.

  18. Non-radioactive in situ Hybridization Protocol Applicable for Norway Spruce and a Range of Plant Species

    PubMed Central

    Karlgren, Anna; Carlsson, Jenny; Gyllenstrand, Niclas; Lagercrantz, Ulf; Sundström, Jens F.

    2009-01-01

    The high-throughput expression analysis technologies available today give scientists an overflow of expression profiles but their resolution in terms of tissue specific expression is limited because of problems in dissecting individual tissues. Expression data needs to be confirmed and complemented with expression patterns using e.g. in situ hybridization, a technique used to localize cell specific mRNA expression. The in situ hybridization method is laborious, time-consuming and often requires extensive optimization depending on species and tissue. In situ experiments are relatively more difficult to perform in woody species such as the conifer Norway spruce (Picea abies). Here we present a modified DIG in situ hybridization protocol, which is fast and applicable on a wide range of plant species including P. abies. With just a few adjustments, including altered RNase treatment and proteinase K concentration, we could use the protocol to study tissue specific expression of homologous genes in male reproductive organs of one gymnosperm and two angiosperm species; P. abies, Arabidopsis thaliana and Brassica napus. The protocol worked equally well for the species and genes studied. AtAP3 and BnAP3 were observed in second and third whorl floral organs in A. thaliana and B. napus and DAL13 in microsporophylls of male cones from P. abies. For P. abies the proteinase K concentration, used to permeablize the tissues, had to be increased to 3 g/ml instead of 1 g/ml, possibly due to more compact tissues and higher levels of phenolics and polysaccharides. For all species the RNase treatment was removed due to reduced signal strength without a corresponding increase in specificity. By comparing tissue specific expression patterns of homologous genes from both flowering plants and a coniferous tree we demonstrate that the DIG in situ protocol presented here, with only minute adjustments, can be applied to a wide range of plant species. Hence, the protocol avoids both extensive

  19. Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci

    PubMed Central

    2011-01-01

    Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species. PMID:21794180

  20. Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation.

    PubMed

    Zhang, Laining; Yang, Xiaoyu; Tian, Li; Chen, Lei; Yu, Weichang

    2016-09-01

    The cultivated peanut Arachis hypogaea (AABB) is thought to have originated from the hybridization of Arachis duranensis (AA) and Arachis ipaënsis (BB) followed by spontaneous chromosome doubling. In this study, we cloned and analyzed chromosome markers from cultivated peanut and its wild relatives. A fluorescence in situ hybridization (FISH)-based karyotyping cocktail was developed with which to study the karyotypes and chromosome evolution of peanut and its wild relatives. Karyotypes were constructed in cultivated peanut and its two putative progenitors using our FISH-based karyotyping system. Comparative karyotyping analysis revealed that chromosome organization was highly conserved in cultivated peanut and its two putative progenitors, especially in the B genome chromosomes. However, variations existed between A. duranensis and the A genome chromosomes in cultivated peanut, especially for the distribution of the interstitial telomere repeats (ITRs). A search of additional A. duranensis varieties from different geographic regions revealed both numeric and positional variations of ITRs, which were similar to the variations in tetraploid peanut varieties. The results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and also suggest that multiple hybridization events of A. ipaënsis with different varieties of A. duranensis may have occurred during the origination of peanut.

  1. Chromosome analysis of nuclear power plant workers using fluorescence in situ hybridization and Giemsa assay.

    PubMed

    Hristova, Rositsa; Hadjidekova, Valeria; Grigorova, Mira; Nikolova, Teodora; Bulanova, Minka; Popova, Ljubomira; Staynova, Albena; Benova, Donka

    2013-09-01

    The aim of this study was to evaluate the genotoxic effects of ionizing radiation in vivo in exposed Bulgarian nuclear power plant workers by using classical cytogenetic and molecular cytogenetic analyses of peripheral lymphocytes. Chromosome analysis using fluorescence in situ hybrydization (FISH) and Giemsa techniques was undertaken on 63 workers and 45 administrative staff controls from the Bulgarian Nuclear Power Plant. Using the Giemsa method, the frequencies of cells studied with chromosome aberrations, dicentrics plus rings and chromosome fragments in the radiation workers were significantly higher compared with the control group (P = 0.044, P = 0.014, and P = 0.033, respectively). A significant association between frequencies of dicentrics plus rings and accumulated doses was registered (P < 0.01). In the present study, a FISH cocktail of whole chromosome paints for chromosomes 1, 4 and 11 was used. A significant association between frequency of translocations and accumulated doses was also observed (P < 0.001). Within the control group, a correlation was found between age and the spontaneous frequency of translocations. No correlation was found between smoking status and frequency of translocations. When compared with the control group, workers with accumulated doses up to 100 mSv showed no increase in genome translocation frequency, whereas workers with accumulated doses from 101 to 200 mSv showed a statistically significant doubling of genome translocation frequency (P = 0.009). Thus, in cases of chronic exposure and for purposes of retrospective dosimetry, the genome frequency of translocations is a more useful marker for evaluation of genotoxic effects than dicentric frequency.

  2. Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers.

    PubMed

    Parham, James F; Papenfuss, Theodore J; Dijk, Peter Paul van; Wilson, Byron S; Marte, Cristian; Schettino, Lourdes Rodriguez; Brian Simison, W

    2013-04-01

    Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using (*)BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the "coestimated" gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated

  3. Duplex PCR assay and in situ hybridization for detection of Francisella spp. and Francisella noatunensis subsp. orientalis in red tilapia.

    PubMed

    Dong, Ha T; Gangnonngiw, Warachin; Phiwsaiya, Kornsunee; Charoensapsri, Walaiporn; Nguyen, Vuong V; Nilsen, Pål; Pradeep, Padmaja J; Withyachumnarnkul, Boonsirm; Senapin, Saengchan; Rodkhum, Channarong

    2016-06-15

    Conventional isolation and identification based on phenotypic characteristics is challenging with the highly fastidious, intracellular bacterium Francisella noatunensis subsp. orientalis (Fno). Here, we developed a duplex PCR method for simultaneous detection of the Francisella genus and Fno in one PCR reaction and an in situ hybridization method for paraffin section based diagnosis of Fno. The PCR results showed genus- and species-specific bands (1140 and 203 bp) from Fno but only one genus-specific band (1140 bp) from F. noatunensis subsp. noatunensis. Sensitivity of the duplex PCR assay revealed a detection limit of 20 to 200 fg genomic DNA (~10 to 100 genome equivalents) depending on DNA template extraction methods. The newly developed duplex PCR assay could be used to detect Fno from clinically sick fish exhibiting signs of visceral granulomas and would also be able to detect Fno infection in naturally diseased fish without symptoms of francisellosis, indicating potential application for diagnosis of field samples. The in situ hybridization assay using Fno species-specific probe revealed positive signals in multiple organs including the spleen, liver, kidney, gills and intestine of infected fish. PMID:27304869

  4. Complete Spinal Cord Injury and Brain Dissection Protocol for Subsequent Wholemount In Situ Hybridization in Larval Sea Lamprey

    PubMed Central

    Barreiro-Iglesias, Antón; Zhang, Guixin; Selzer, Michael E.; Shifman, Michael I.

    2014-01-01

    After a complete spinal cord injury, sea lampreys at first are paralyzed below the level of transection. However, they recover locomotion after several weeks, and this is accompanied by short distance regeneration (a few mm) of propriospinal axons and spinal-projecting axons from the brainstem. Among the 36 large identifiable spinal-projecting neurons, some are good regenerators and others are bad regenerators. These neurons can most easily be identified in wholemount CNS preparations. In order to understand the neuron-intrinsic mechanisms that favor or inhibit axon regeneration after injury in the vertebrates CNS, we determine differences in gene expression between the good and bad regenerators, and how expression is influenced by spinal cord transection. This paper illustrates the techniques for housing larval and recently transformed adult sea lampreys in fresh water tanks, producing complete spinal cord transections under microscopic vision, and preparing brain and spinal cord wholemounts for in situ hybridization. Briefly, animals are kept at 16 °C and anesthetized in 1% Benzocaine in lamprey Ringer. The spinal cord is transected with iridectomy scissors via a dorsal approach and the animal is allowed to recover in fresh water tanks at 23 °C. For in situ hybridization, animals are reanesthetized and the brain and cord removed via a dorsal approach. PMID:25350040

  5. Lysozyme is an inducible marker of macrophage activation in murine tissues as demonstrated by in situ hybridization

    PubMed Central

    1991-01-01

    This study demonstrates the induction of lysozyme mRNA expression in situ in tissue macrophages (M phi) of mice following in vivo stimulation. The resting resident tissue M phi of most tissues do not contain enough lysozyme mRNA to be detected by in situ hybridization using 35S-labeled RNA probes. Following Bacille Calmette Guerin or Plasmodium yoelli infection, however, M phi recruited to liver and spleen hybridize strongly to the lysozyme probe. Within 24 h of infection, cells found in the marginal zone of the spleen begin to produce lysozyme mRNA. This response is also evoked by a noninfectious agent (intravenously injected sheep erythrocytes), and is possibly the result of an early phagocytic interaction. Later in the infection, other cells in the red and white pulp of the spleen, and cells in granulomas in the liver, become lysozyme-positive. Kupffer cells are rarely lysozyme-positive. Lysozyme mRNA levels in liver granulomas remain relatively constant during the infection, and lysozyme is produced by most granuloma cells. This contrasts with tumor necrosis factor alpha (TNF alpha) mRNA, which is produced by fewer cells in the granuloma, and which can be massively induced by lipopolysaccharide administration. The production of lysozyme, previously considered a constitutive function of M phi, is therefore an indicator of M phi activation in vivo, where immunologically specific and nonspecific stimuli both stimulate lysozyme production at high levels in subpopulations of cells occupying discrete anatomical locations. PMID:1940787

  6. Improvements in histological quality and signal retention following in situ hybridization in early chick embryos using plastic resin and recolorization.

    PubMed

    Sawitzke, A L; Chapman, S C; Bleyl, S B; Schoenwolf, G C

    2005-01-01

    We describe a novel method that allows reliable detection of in situ hybridization signals in thin sections of plastic embedded embryos. Sections from plastic embedded embryos are thinner and have superior histological quality compared to paraffin, gelatin, agarose embedded sections or cryosections; however, plastic resin traditionally has not been used as an embedding medium following in situ hybridization because of loss of signal. When signal is detected with alkaline phosphatase and NBT/BCIP, the resulting colored precipitate is subject to fading when samples are exposed to organic compounds. The colored precipitate can be redeposited by repeating the NBT/BCIP reaction following plastic sectioning. This recolorization shows no loss of specificity, because signal is detected only where the anti-digoxigenin/alkaline phosphatase conjugated antibody is bound to the riboprobe. Strong signals can be detected without recolorization; however, weaker signals require the recolorization step. This novel method of re-depositing colored precipitate after processing and sectioning allows accurate determination of the location of gene expression and study of this expression in high quality histological sections of early chick embryos.

  7. Multi-target Chromogenic Whole-mount In Situ Hybridization for Comparing Gene Expression Domains in Drosophila Embryos

    PubMed Central

    Hauptmann, Giselbert; Söll, Iris; Krautz, Robert; Theopold, Ulrich

    2016-01-01

    To analyze gene regulatory networks active during embryonic development and organogenesis it is essential to precisely define how the different genes are expressed in spatial relation to each other in situ. Multi-target chromogenic whole-mount in situ hybridization (MC-WISH) greatly facilitates the instant comparison of gene expression patterns, as it allows distinctive visualization of different mRNA species in contrasting colors in the same sample specimen. This provides the possibility to relate gene expression domains topographically to each other with high accuracy and to define unique and overlapping expression sites. In the presented protocol, we describe a MC-WISH procedure for comparing mRNA expression patterns of different genes in Drosophila embryos. Up to three RNA probes, each specific for another gene and labeled by a different hapten, are simultaneously hybridized to the embryo samples and subsequently detected by alkaline phosphatase-based colorimetric immunohistochemistry. The described procedure is detailed here for Drosophila, but works equally well with zebrafish embryos. PMID:26862978

  8. Towards a cellular multi-parameter analysis platform: fluorescence in situ hybridization (FISH) on microhole-array chips.

    PubMed

    Kurz, Christian M; Moosdijk, Stefan V D; Thielecke, Hagen; Velten, Thomas

    2011-01-01

    Highly-sensitive analysis systems based on cellular multi-parameter are needed in the diagnostics. Therefore we improved our previously developed chip platform for another additional analysis method, the fluorescence in situ hybridization. Fluorescence in situ hybridization (FISH) is a technique used in the diagnostics to determine the localization and the presence or absence of specific DNA sequence. To improve this labor- and cost-intensive method, we reduced the assay consumption by a factor of 5 compared to the standard protocol. Microhole chips were used for making the cells well addressable. The chips were fabricated by semiconductor technology on the basis of a Silicon wafer with a thin deposited silicon nitride layer (Si(3)N(4)). Human retina pigment epithelia (ARPE-19) cells were arrayed on 5-μm holes of a 35 × 35 microhole-array by a gently negative differential pressure of around 5 mbar. After 3 hours of incubation the cells were attached to the chip and the FISH protocol was applied to the positioned cells. A LabView software was developed to simplify the analysis. The software automatically counts the number of dots (positive labeled chromosome regions) as well as the distance between adjacent dots. Our developed platform reduces the assay consumption and the labor time. Furthermore, during the 3 hours of incubation non-invasive or minimal-invasive methods like Raman- and impedance-spectroscopy can be applied. PMID:22256298

  9. Using whole mount in situ hybridization to link molecular and organismal biology.

    PubMed

    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

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

    SciTech Connect

    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

    2008-10-15

    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 {mu}g/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.

  11. Expression of simple epithelial type cytokeratins in stratified epithelia as detected by immunolocalization and hybridization in situ

    PubMed Central

    1988-01-01

    Multi-layered ("stratified") epithelia differ from one-layered ("simple") polar epithelia by various architectural and functional properties as well as by their cytoskeletal complements, notably a set of cytokeratins characteristic of stratified tissue. The simple epithelial cytokeratins 8 and 18 have so far not been detected in any stratified epithelium. Using specific monoclonal antibodies we have noted, in several but not all samples of stratified epithelia, including esophagus, tongue, exocervix, and vagina, positive immunocytochemical reactions for cytokeratins 8, 18, and 19 which in some regions were selective for the basal cell layer(s) but extended into suprabasal layers in others. In situ hybridization with different probes (riboprobes, synthetic oligonucleotides) for mRNAs of cytokeratin 8 on esophageal epithelium has shown, in extended regions, relatively strong reactivity for cytokeratin 8 mRNA in the basal cell layer. In contrast, probes to cytokeratin 18 have shown much weaker hybridization which, however, was rather evenly spread over basal and suprabasal strata. These results, which emphasize the importance of in situ hybridization in studies of gene expression in complex tissues, show that the genes encoding simple epithelial cytokeratins can be expressed in stratified epithelia. This suggests that continual expression of genes coding for simple epithelial cytokeratins is compatible with the formation of squamous stratified tissues and can occur, at least in basal cell layers, simultaneously with the synthesis of certain stratification-related cytokeratins. We also emphasize differences of expression and immunoreactivity of these cytokeratins between different samples and in different regions of the same stratified epithelium and discuss the results in relation to changes of cytokeratin expression during fetal development of stratified epithelia, in response to environmental factors and during the formation of squamous cell carcinomas. PMID:2453518

  12. Microstructures of Metallic NiCrBSi Coatings Manufactured via Hybrid Plasma Spray and In Situ Laser Remelting Process

    NASA Astrophysics Data System (ADS)

    Serres, Nicolas; Hlawka, Françoise; Costil, Sophie; Langlade, Cécile; Machi, Frédérique

    2011-01-01

    This paper deals with coating alternatives to hard chromium plating. Thermal spraying is already used in industry, but results are not always satisfactory for reasons of porosity and microstructures. In this study, atmospheric plasma spraying (APS) and in situ laser irradiation by diode laser processes were combined to modify the structural characteristics of thick NiCrBSi alloy layers. The microstructure evolution was studied, and results show that in situ laser remelting induced the growth of a dendritic structure, which strongly decreased the porosity of as-sprayed coatings and increased the adhesion on the substrate. Moreover, no phase transition after laser treatment was observed. Lastly, a mechanical investigation demonstrated that the combination between plasma spray and in situ melting with a diode laser could result in very good mechanical properties. The increase of the laser incident power involved an increase of the mean contact pressure, along with coating hardness. The hybrid process appears to be a possible alternative to hard chromium plating, in order to protect mechanical parts, because of the improved mechanical properties of the NiCrBSi layer.

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

    PubMed

    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.

  14. Identification and characterization of marker chromosomes, de novo rearrangements and microdeletions in 100 cases with fluorescence in situ hybridization (FISH)

    SciTech Connect

    Anderson, S.M.; Liu, Y.; Papenhausen, P.R.

    1994-09-01

    Results of molecular cytogenetic analysis are presented for 100 cases in which fluorescence in situ hybridization (FISH) was used as an adjunct to standard cytogenetics. Commercially available centromeric, telomeric, chromosome painting and unique sequence probes were used. Cases were from a 12-month period (June 1993-May 1994) and included examples of sex chromosome abnormalities (8), duplications (5), de novo translocations (6), satellited (12) and non-satellited (7) markers, and microdeletion syndromes (62). Satellited marker chromosomes were evaluated using a combination of DAPI/Distamycin A staining, hybridization with a classical satellite probe for chromosome 15 and hybridization with alpha-satellite probes for chromosomes 13, 14, 21 and 22. Markers positive for the chromosome 15 probe were further evaluated using unique sequence probes for the Prader-Willi/Angelman region. Microdeletion analysis was performed for Prader-Willi/Angelman (49) and DiGeorge/VCF (13) syndromes. Seven cases evaluated for Prader-Willi/Angelman syndrome demonstrated evidence of a deletion within this region. Uniparental disomy analysis was available in cases where a deletion was not detected by FISH, yet follow-up was clinically indicated. Two cases evaluated for DiGeorge/VCF syndrome demonstrated molecular evidence of a deletion. Included in our analysis is an example of familial DiGeorge syndrome.

  15. One-step in situ synthesis of graphene–TiO{sub 2} nanorod hybrid composites with enhanced photocatalytic activity

    SciTech Connect

    Sun, Mingxuan Li, Weibin; Sun, Shanfu; He, Jia; Zhang, Qiang; Shi, Yuying

    2015-01-15

    Chemically bonded graphene/TiO{sub 2} nanorod hybrid composites with superior dispersity were synthesized by a one-step in situ hydrothermal method using graphene oxide (GO) and TiO{sub 2} (P25) as the starting materials. The as-prepared samples were characterized by XRD, XPS, TEM, FE-SEM, EDX, Raman, N{sub 2} adsorption, and UV–vis DRS techniques. Enhanced light absorption and a red shift of absorption edge were observed for the composites in the ultraviolet–visible diffuse reflectance spectroscopy (UV–vis DRS). Their effective photocatalytic activity was evaluated by the photodegradation of methylene blue under visible light irradiation. An enhancement of photocatalytic performance was observed over graphene/TiO{sub 2} nanorod hybrid composite photocatalysts, as 3.7 times larger than that of pristine TiO{sub 2} nanorods. This work demonstrated that the synthesis of TiO{sub 2} nanorods and simultaneous conversion of GO to graphene “without using reducing agents” had shown to be a rapid, direct and clean approach to fabricate chemically bonded graphene/TiO{sub 2} nanorod hybrid composites with enhanced photocatalytic performance.

  16. Localization of avian bornavirus RNA by in situ hybridization in tissues of psittacine birds with proventricular dilatation disease.

    PubMed

    Weissenböck, H; Fragner, K; Nedorost, N; Mostegl, M M; Sekulin, K; Maderner, A; Bakonyi, T; Nowotny, N

    2010-09-28

    Proventricular dilatation disease (PDD) of psittacine birds is caused by a number of different genotypes of a novel viral species, avian bornavirus (ABV). Here we present an in situ hybridization (ISH) procedure using digoxigenin-labeled RNA probes for localizing viral genomic and mRNA of ABV-2 and ABV-4 in tissues of affected birds. Out of eleven immunohistochemically positive birds ISH signals were only found in seven. Partial sequencing of the viral genome had shown that four of them were infected with ABV-2, two with ABV-4 and one had a mixed infection with ABV-2 and ABV-4. ISH signals were present in the brain, in the vegetative nerve system, glandular epithelia and smooth muscle cells of the intestinal tract and in cardiomyocytes. Hybridization signals for viral genome were more abundant than signals for mRNA. As the probes were not strictly genotype-specific, four of the birds had hybridization signals with both, the ABV-2 and ABV-4 probes. The signals achieved with the homologous probes were more intense and more abundant than those resulting from heterologous probes. Taken together, the results of this study show that ISH can be used as a tool for localizing ABV sequences in tissues of birds with PDD and confirm the causative role of ABVs by showing viral replication in affected tissues.

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

    SciTech Connect

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

    1990-07-01

    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.

  18. Signal intensities of radiolabeled cRNA probes used alone or in combination with non-isotopic in situ hybridization histochemistry

    PubMed Central

    Son, Jong-Hyun; Winzer-Serhan, Ursula H.

    2009-01-01

    This study addressed the question of whether radioactive hybridization signal intensities are reduced in combined isotopic and non-isotopic double in situ hybridization (DISH) compared with those in single in situ hybridization (ISH). Non-isotopic Digoxigenin (Dig)-labeled hybrids were detected using an alkaline phosphatase (AP) enzymatic reaction which results in NBT/BCIP-salt precipitation that could shield S35-radiation from penetrating to the surface. Sections were plastic coated of with 2% parlodion to prevent a chemical reaction between AP and developer during processing of the photosensitive emulsion, which could further reduce radioactive hybridization signal detection by autoradiography. We used DISH with a hybridization cocktail of radioactive S35- and Dig-labeled GAD67 cRNA probes. In order to avoid competition for the same complementary sequence, the probes were directed towards different sequences of the glutamic acid decarboxylase (GAD67) mRNA, resulting in co-detection of isotopic and non-isotopic hybrids in close to 100% of GAD67 positive cells. Quantitation of autoradiograms showed that there was no reduction of autoradiographic signal intensity from S35-labeled hybrids in the presence of Dig-labeled hybrids. Plastic coating of single or dual hybridized sections did not reduce the radioactive signal intensity. When mRNAs for nicotinic acetylcholine receptor (nAChR) subunits were detected with subunit specific S35-labeled cRNA probes in GAD67 hippocampal interneurons the total numbers of nAChR subunit expressing cells remained the same in single or double hybridized sections even for low abundant mRNAs. Together, these results indicate that combined radioactive and non-radioactive DISH does not interfere with the detection of the radiation signal from the S35-labeled hybrids, and neither specificity nor sensitivity is compromised. PMID:19428522

  19. Combining fluorescent in situ hybridization data with ISS staging improves risk assessment in myeloma: an International Myeloma Working Group collaborative project

    PubMed Central

    Avet-Loiseau, H; Durie, BGM; Cavo, M; Attal, M; Gutierrez, N; Haessler, J; Goldschmidt, H; Hajek, R; Lee, JH; Sezer, O; Barlogie, B; Crowley, J; Fonseca, R; Testoni, N; Ross, F; Rajkumar, SV; Sonneveld, P; Lahuerta, J; Moreau, P; Morgan, G

    2014-01-01

    The combination of serum β2-microglobulin and albumin levels has been shown to be highly prognostic in myeloma as the International Staging System (ISS). The aim of this study was to assess the independent contributions of ISS stage and cytogenetic abnormalities in predicting outcomes. A retrospective analysis of international studies looking at both ISS and cytogenetic abnormalities was performed in order to assess the potential role of combining ISS stage and cytogenetics to predict survival. This international effort used the International Myeloma Working Group database of 12 137 patients treated worldwide for myeloma at diagnosis, of whom 2309 had cytogenetic studies and 5387 had analyses by fluorescent in situ hybridization (iFISH). Comprehensive analyses used 2642 patients with sufficient iFISH data available. Using the comprehensive iFISH data, combining both t(4;14) and deletion (17p), along with ISS stage, significantly improved the prognostic assessment in terms of progression-free survival and overall survival. The additional impact of patient age and use of high-dose therapy was also demonstrated. In conclusion, the combination of iFISH data with ISS staging significantly improves risk assessment in myeloma. PMID:23032723

  20. Assignment of the human RT6 gene to 11q13 by PCR screening of somatic cell hybrids and in situ hybridization

    SciTech Connect

    Koch-Nolte, F.; Haag, F.; Kuehl, M.; Thiele, H.G.; Singh, S. ); Van Heyningen, V. ); Hoovers, J. ); Grzeschik, K.H. )

    1993-11-01

    RT6 is a T cell membrane protein that has attracted interest because a defect in RT6 expression is associated with susceptibility to autoimmune type I diabetes in DP-BB rats and NOD mice. Using PCR screening of human/rodent somatic cell hybrids and fluorescence in situ hybridization, the authors have determined that the gene for the human RT6 homologue is located at 11q13, centromeric to the gene for tyrosinase (TYR, albino locus) and telomeric to that for fibroblast growth factor 4 (FGF4). The data suggest that the human RT6 gene constitutes a new linkage group with TYR and the gene for olfactory marker protein (OMP) on 11q, which has a counterpart in mouse chromosome 7. Thus, in the human, the RT6 locus is dissociated from the hemoglobin [beta] chain locus (HBB) and its neighboring conserved linkage group at 11q15, in contrast to the mouse, in which RT6 shows a tighter linkage to Hbb than to Tyr. The results support the conclusion that there has been considerable intrachromosomal reshuffling of linked genes since the divergence of primates and rodents. 9 refs., 1 fig.

  1. Characterization of chromosome 14 abnormalities by interphase in situ hybridization and comparative genomic hybridization in 124 meningiomas: correlation with clinical, histopathologic, and prognostic features.

    PubMed

    Tabernero, María Dolores; Espinosa, Ana Belén; Maíllo, Angel; Sayagués, José María; Alguero, María del Carmen; Lumbreras, Eva; Díaz, Pedro; Gonçalves, Jesús María; Onzain, Ignacio; Merino, Marta; Morales, Francisco; Orfao, Alberto

    2005-05-01

    We analyzed quantitative chromosome 14 abnormalities in 124 meningiomas by interphase fluorescence in situ hybridization (iFISH) and confirmed the nature of abnormalities by comparative genomic hybridization (CGH). We correlated the abnormalities with clinical, histopathologic, and prognostic factors. Of 124 cases, 50 (40.3%) showed loss (14.5%) or gain (25.8%) of the 14q32 chromosome region by iFISH. Most corresponded to numeric abnormalities: monosomy (12.9%), trisomy (1.6%), or tetrasomy (24.2%); in only 2 cases (1.6%), chromosome 14 loss did not involve the whole chromosome and was restricted to the 14q31-q32 region (confirmed by CGH). Cases with gain or monosomy corresponded more frequently to histologically malignant tumors (P = .009). Patients with monosomy 14/14q-, but not those with gain, more often were male (P = .04) and had a greater incidence of recurrence (P = .003) and shorter relapse-free survival (P = .03). The 2 patients with loss limited to 14q31-q32 had histologically benign tumors and no relapse after more than 5 years' follow-up. Most meningiomas with chromosome 14 abnormalities have numeric changes, with interstitial deletions of 14q31-q32 present in few cases. Of the abnormalities detected, only monosomy 14 showed an adverse prognostic impact. PMID:15981814

  2. A hybrid approach to analyse a beam-soil structure under a moving random load

    NASA Astrophysics Data System (ADS)

    Si, L. T.; Zhao, Y.; Zhang, Y. H.; Kennedy, D.

    2016-11-01

    To study the stochastic response of a beam-soil structure under a moving random load, a hybrid approach based on the pseudo-excitation method and the wavelet method is proposed. Using the pseudo-excitation method, the non-stationary random vibration analysis is transformed into a conventional moving harmonic load problem. Analytical solutions of the power spectral density and standard deviation of vertical displacement are derived in an integral form. However, the integrand is singular and highly oscillatory, and the computational time is an important consideration because a large number of frequency points must be computed. To calculate the response accurately and efficiently, a wavelet approach is introduced. Numerical results show that the frequency band which brings the most significant response is dependent on the load velocity. The hybrid method provides a useful tool to estimate the ground vibration caused by traffic loads.

  3. Fluorescence in situ hybridizations (FISH) for the localization of viruses and endosymbiotic bacteria in plant and insect tissues.

    PubMed

    Kliot, Adi; Kontsedalov, Svetlana; Lebedev, Galina; Brumin, Marina; Cathrin, Pakkianathan Britto; Marubayashi, Julio Massaharu; Skaljac, Marisa; Belausov, Eduard; Czosnek, Henryk; Ghanim, Murad

    2014-02-24

    Fluorescence in situ hybridization (FISH) is a name given to a variety of techniques commonly used for visualizing gene transcripts in eukaryotic cells and can be further modified to visualize other components in the cell such as infection with viruses and bacteria. Spatial localization and visualization of viruses and bacteria during the infection process is an essential step that complements expression profiling experiments such as microarrays and RNAseq in response to different stimuli. Understanding the spatiotemporal infections with these agents complements biological experiments aimed at understanding their interaction with cellular components. Several techniques for visualizing viruses and bacteria such as reporter gene systems or immunohistochemical methods are time-consuming, and some are limited to work with model organisms and involve complex methodologies. FISH that targets RNA or DNA species in the cell is a relatively easy and fast method for studying spatiotemporal localization of genes and for diagnostic purposes. This method can be robust and relatively easy to implement when the protocols employ short hybridizing, commercially-purchased probes, which are not expensive. This is particularly robust when sample preparation, fixation, hybridization, and microscopic visualization do not involve complex steps. Here we describe a protocol for localization of bacteria and viruses in insect and plant tissues. The method is based on simple preparation, fixation, and hybridization of insect whole mounts and dissected organs or hand-made plant sections, with 20 base pairs short DNA probes conjugated to fluorescent dyes on their 5' or 3' ends. This protocol has been successfully applied to a number of insect and plant tissues, and can be used to analyze expression of mRNAs or other RNA or DNA species in the cell.

  4. Visualization and quantification of archaeal and bacterial metabolically active cells in soil using fluorescence in situ hybridization method

    NASA Astrophysics Data System (ADS)

    Semenov, Mikhail; Manucharova, Natalia; Stepanov, Alexey

    2015-04-01

    The method of in situ hybridization using fluorescent labeled 16S rRNA-targeted oligonucleotide probes (FISH - fluorescence in situ hybridization) combines identification and quantification of groups of microorganisms at different phylogenetic levels, from domain to species. The FISH method enables to study the soil microbial community in situ, avoiding plating on nutrient media, and allows to identify and quantify living, metabolically active cells of Bacteria and Archaea. The full procedure consists of the following steps: desorption of the cells from the soil particles, fixation of cells, coating a fixed sample on the glass slide, hybridization with the specific probes and, finally, microscopic observation and cell counting. For the FISH analysis of Bacteria and Archaea, the paraformaldehyde-fixed samples were hybridized with Cy3-labeled Archaea-specific probe(Arc915) and 6-carboxyfluorescein (FAM)-labeled Bacteria-specific probe(EUB338). When a molecular probe is incorporated into a cell, it can hybridize solely with a complementary rRNA sequence. The hybridization can be visualized under the fluorescent microscope and counted. The application of FISH will be demonstrated by the abundance of metabolically active cells of Archaea and Bacteria depending on soil properties, depth and land use. The research was carried out at field and natural ecosystems of European part of Russia. Samples were collected within the soil profiles (3-6 horizons) of Chernozem and Kastanozem with distinct land use. Quantification of metabolically active cells in virgin and arable Chernozem revealed that the abundance of Archaea in topsoil of virgin Chernozem was doubled as compared with arable soil, but it leveled off in the deeper horizons. Plowing of Chernozem decreased an amount of archaeal and bacterial active cells simultaneously, however, Bacteria were more resistant to agrogenic impact than Archaea. In Kastanozem, a significant change in the abundance of metabolically active

  5. Surface-enhanced in-situ Raman-sensor applied in the arctic area for analyses of water and sediment

    NASA Astrophysics Data System (ADS)

    Kolomijeca, Anna; Kwon, Yong-Hyok; Kronfeldt, Heinz-Detlef

    2012-06-01

    Investigations on the seafloor in the arctic area are of great scientific interest as well as of progressive economic importance. Therefore, measurements in the water column and of sediments were carried out by applying different analytical methods. In JCR 253 arctic cruise a microsystem diode laser with reflection Bragg grating emitting at 671 nm was introduced and integrated into an optode housing which was laboratory pressure tested up to 200 bar. The connection to the mobile spectrometer is realized through an optical fiber. All performed measurements were carried out on the James-Clark-Ross research vessel during a three week experiment in August 2011. Conventional Raman spectra and SERS spectra of arctic surface water and sediment acquired from locations around 78° N and 9° E will be presented. Selected SERS substrates developed for SERS measurements in sea-water were tested for their capability to detect different substances in the water down to very small (pmol/l) concentrations. Additionally, the applicability of shifted excitation Raman difference spectroscopy (SERDS) and a combination of SERS with SERDS for analytical applications during sea-trials for in-situ analyses of sea-water and sediments will be discussed.

  6. Effects of central nervous system lesions on the expression of galanin: a comparative in situ hybridization and immunohistochemical study.

    PubMed Central

    Cortés, R; Villar, M J; Verhofstad, A; Hökfelt, T

    1990-01-01

    We have used in situ hybridization and immunohistochemistry to study the expression of galanin mRNA and galanin-like immunoreactivity after decortication and lesions of the ventral hippocampus. After decortication the levels of both galanin mRNA and galanin-like immunoreactivity were increased in the dorsal raphe nucleus. In addition, in decorticated rats, but not in controls, galanin mRNA could be seen in dorsal and ventral nuclei of the thalamus and in the remaining parts of the cortex. Increases in galanin mRNA and galanin-like immunoreactivity were also observed in the septum-vertical diagonal band after electrocoagulation lesions of the ventral hippocampus. In contrast, no changes were found after ibotenic acid lesions of the same hippocampal area. These results suggest that increases in the expression of galanin occur in certain neuron populations after direct lesion of their axons and/or terminal fields. Images PMID:1699231

  7. Distribution characteristics of ammonia-oxidizing bacteria in the Typha latifolia constructed wetlands using fluorescent in situ hybridization (FISH).

    PubMed

    Yan, Li; Inamori, Ryuhei; Gui, Ping; Xu, Kai-qin; Kong, Hai-nan; Matsumura, Masatoshi; Inamori, Yuhei

    2005-01-01

    A molecular biology method, fluorescent in situ hybridization (FISH), in which the pre-treatment was improved in allusion to the media of the constructed wetlands (CW), e.g. the soil and the grit, was used to investigate the vertical distribution characteristics of ammonia-oxidizing bacteria (AOB) quantity and the relation with oxidation-reduction potential (ORP) in the Typha latifolia constructed wetlands under three different loadings in summer from May to September. Results showed that the quantity of the AOB decreased in the Typha latifolia CW with the increase of vertical depth. However, the AOB quantity was 2-4 times the quantity of the control in the root area. Additionally, ORP in the rhizosphere was found to be higher than other areas, which showed that Typha latifolia CW was in an aerobic state in summer when using simulated non-point sewage at the rural area of Taihu Lake in China and small town combined sewage.

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

    SciTech Connect

    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.

  9. Microfluidic extraction and stretching of chromosomal DNA from single cell nuclei for DNA fluorescence in situ hybridization

    PubMed Central

    Wang, Xiaozhu; Takebayashi, Shin-ichiro; Bernardin, Evans; Gilbert, David M.; Chella, Ravindran

    2012-01-01

    We have developed a novel method for genetic characterization of single cells by integrating microfluidic stretching of chromosomal DNA and fiber fluorescence in situ hybridization (FISH). In this method, individually isolated cell nuclei were immobilized in a microchannel. Chromosomal DNA was released from the nuclei and stretched by a pressure-driven flow. We analyzed and optimized flow conditions to generate a millimeter-long band of stretched DNA from each nucleus. Telomere fiber FISH was successfully performed on the stretched chromosomal DNA. Individual telomere fiber FISH signals from single cells could be resolved and their lengths measured, demonstrating the ability of the method to quantify genetic features at the level of single cells. PMID:22231286

  10. In Situ Response of Nanostructured Hybrid Fluoridated Restorative Composites on Enamel Demineralization, Surface Roughness and Ion Release.

    PubMed

    Melo, Mary A S; Codes, Bruna M; Passos, Vanara F; Lima, Juliana P M; Rodrigues, Lidiany K A

    2014-12-01

    Recurrent caries at the tooth-restoration margins is the main reason for composite failure. Fluoride-releasing nanohybrid composite resin may reduce the recurrent caries rates. A fluoride-releasing resin (FCR) and non-fluoride-releasing resin (CR) were tested using an in situ model. Demineralization (ΔS), ion release and surface roughness of composite specimens were determined. The F concentration in the group FCR was higher than the CR group. ΔS (Mean ± SD) was 2579 ± 1582 and 1705 ± 1292, respectively, for FCR and CR. Surfaces roughness was altered by biofilm accumulation. The hybrid fluorated restorative composites containing nanoparticles have a slight anticaries action without alteration of surface smoothness of the material. PMID:26466443

  11. Bovine adenovirus type 10 identified in fatal cases of adenovirus-associated enteric disease in cattle by in situ hybridization.

    PubMed Central

    Smyth, J A; Benkö, M; Moffett, D A; Harrach, B

    1996-01-01

    A severe, naturally occurring enteric disease of cattle in which adenovirus inclusions are present in the intestinal vascular endothelium has been recognized in several countries; three different adenovirus serotypes have been isolated from affected animals. An in situ hybridization technique for the detection of bovine adenoviral DNA was developed and applied to tissue from 13 cattle in Northern Ireland diagnosed to have the disease. Bovine adenovirus serotype 10 (BAV-10) was identified in the vascular inclusions of all cattle, providing strong evidence that adenoviral enteric vascular disease in cattle is associated with this serotype. The existence of BAV-10 has only recently been recognized. The first molecular biology-based technique for the diagnosis of BAV-10 infection is described. The animals in the present study are the first in which BAV-10 has had a confirmed role in a pathologic process. PMID:8727916

  12. Diagnostics of common microdeletion syndromes using fluorescence in situ hybridization: Single center experience in a developing country

    PubMed Central

    Kurtovic-Kozaric, Amina; Mehinovic, Lejla; Stomornjak-Vukadin, Meliha; Kurtovic-Basic, Ilvana; Catibusic, Feriha; Kozaric, Mirza; Dinarevic, Senka Mesihovic; Hasanhodzic, Mensuda; Sumanovic-Glamuzina, Darinka

    2016-01-01

    Microdeletion syndromes are caused by chromosomal deletions of less than 5 megabases which can be detected by fluorescence in situ hybridization (FISH). We evaluated the most commonly detected microdeletions for the period from June 01, 2008 to June 01, 2015 in the Federation of Bosnia and Herzegovina, including DiGeorge, Prader-Willi/Angelman, Wolf-Hirschhorn, and Williams syndromes. We report 4 patients with DiGeorge syndromes, 4 patients with Prader-Willi/Angelman, 4 patients with Wolf-Hirschhorn syndrome, and 3 patients with Williams syndrome in the analyzed 7 year period. Based on the positive FISH results for each syndrome, the incidence was calculated for the Federation of Bosnia and Herzegovina. These are the first reported frequencies of the microdeletion syndromes in the Federation of Bosnia and Herzegovina. PMID:26937776

  13. Diagnostics of common microdeletion syndromes using fluorescence in situ hybridization: single center experience in a developing country.

    PubMed

    Kurtovic-Kozaric, Amina; Mehinovic, Lejla; Stomornjak-Vukadin, Meliha; Kurtovic-Basic, Ilvana; Catibusic, Feriha; Kozaric, Mirza; Mesihovic-Dinarevic, Senka; Hasanhodzic, Mensuda; Glamuzina, Darinka

    2016-01-01

    Microdeletion syndromes are caused by chromosomal deletions of less than 5 megabases which can be detected by fluorescence in situ hybridization (FISH). We evaluated the most commonly detected microdeletions for the period from June 01, 2008 to June 01, 2015 in the Federation of Bosnia and Herzegovina, including DiGeorge, Prader-Willi/Angelman, Wolf-Hirschhorn, and Williams syndromes. We report 4 patients with DiGeorge syndromes, 4 patients with Prader-Willi/Angelman, 4 patients with Wolf-Hirschhorn syndrome, and 3 patients with Williams syndrome in the analyzed 7 year period. Based on the positive FISH results for each syndrome, the incidence was calculated for the Federation of Bosnia and Herzegovina. These are the first reported frequencies of the microdeletion syndromes in the Federation of Bosnia and Herzegovina. PMID:26937776

  14. Detection of viral genomes in the liver by in situ hybridization using 35S-, bromodeoxyuridine-, and biotin-labeled probes

    SciTech Connect

    Niedobitek, G.; Finn, T.; Herbst, H.; Stein, H.

    1989-03-01

    Methods employing /sup 35/S-, biotin-, and bromodeoxyuridine (BrdUrd)-labeled DNA probes were compared for the detection of hepatitis B virus (HBV) and cytomegalovirus (CMV) in the liver. The results demonstrate that: 1) HBV can be detected reliably only by the use of radiolabeled probes, whereas methods employing nonradioactive probes obviously are not sensitive enough for this virus. The use of /sup 35/S-labeled probes shortens the exposure times considerably in comparison to tritiated probes. 2) Biotin-labeled probes are of limited value for in situ hybridization on liver tissues because the presence of endogenous avidin-binding activity often leads to false positive results. 3) Brd-Urd-labeled probes are a useful alternative to biotinylated probes for the detection of CMV. In comparison with biotinylated probes, BrdUrd-labeled probes produce a specific signal of similar staining intensity in the absence of background staining in the liver.

  15. High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization

    PubMed Central

    Yoshikawa, Toshiyuki; Piao, Yulan; Zhong, Jinhui; Matoba, Ryo; Carter, Mark G.; Wang, Yuxia; Goldberg, Ilya; Ko, Minoru S.H.

    2006-01-01

    Mammalian preimplantation embryos provide an excellent opportunity to study temporal and spatial gene expression in whole mount in situ hybridization (WISH). However, large-scale studies are made difficult by the size of the embryos (∼60 μm diameter) and their fragility. We have developed a chamber system that allows parallel processing of embryos without the aid of a microscope. We first selected 91 candidate genes that were transcription factors highly expressed in blastocysts, and more highly expressed in embryonic (ES) than in trophoblast (TS) stem cells. We then used the WISH to identify 48 genes expressed predominantly in the ICM and to follow several of these genes in all seven preimplantation stages. The ICM-predominant expressions of these genes suggest their involvement in the pluripotency of embryonic cells. This system provides a useful tool to a systematic genome-scale analysis of preimplantation embryos. PMID:16325481

  16. Undifferentiated carcinoma of the parotid gland in a white patient: detection of Epstein-Barr virus by in situ hybridization.

    PubMed

    Kotsianti, A; Costopoulos, J; Morgello, S; Papadimitriou, C

    1996-01-01

    Paraffin sections of an undifferentiated salivary gland carcinoma of lymphoepithelioma type, arising in a white (Greek) patient and confirmed by immunohistochemistry, were examined for the presence of Epstein-Barr virus (EBV), using in situ hybridization to detect EBV-specific EBER1 message. Epstein-Barr virus was detected in malignant epithelial cells, but was not found in lymphoid stroma or in residual benign salivary epithelium. These results confirm the existence of an association between EBV and tumor cells of undifferentiated carcinoma of parotid gland. This is the first demonstration of EBV in a salivary gland lymphoepithelioma arising in a non-Eskimo, white patient. This finding suggests that the association of EBV with undifferentiated salivary gland carcinoma may exist in geographic regions remote from Greenland.

  17. Detection of numerical alterations of chromosome 1 in cytopathological specimens of breast tumors by chromogen in situ hybridization.

    PubMed

    Takarabe, T; Tsuda, H; Okada, S; Fukutomi, T; Hirohashi, S

    2001-10-01

    To investigate the effectiveness of chromogen in situ hybridization (CISH) in the diagnosis of breast tumors, numerical alterations of chromosome 1 were examined by CISH and fluorescence in situ hybridization (FISH) methods, and the presence of der(16)t(1;16) was also examined by FISH in imprinted cytology specimens from resected tissues of 14 carcinomas and five non-malignant lesions. The modal signal counts of chromosome 1 were compared between the specimens processed by CISH and FISH for each case. Aneusomies of the long arm of chromosome 1 were detected in 10 (71%) carcinomas as the major clones by both methods. In addition, one atypical papilloma demonstrated tetrasomy of 1q12 as a major clone by CISH, but such a clone was at first overlooked by FISH. Four other benign lesions showed disomic 1q12 signals as a major clone by both CISH and FISH. As additional information from FISH, eight cancers showed structural or numerical alterations of chromosome 16, and four showed der(16)t(1;16). In total, 10 carcinomas showed chromosome 16 alterations, and all of these overlapped with the carcinomas with 1q12 aneusomies. The CISH method provided almost the same results as the FISH method, and both methods were considered applicable in supportive diagnosis of cytological specimens of breast tumors. In addition, the CISH method was superior in the detection of numerical alterations in carcinoma cells by referring to the morphology of cells and in the detection of significant clones which might be missed under dark-field microscopy. PMID:11881731

  18. Assignment of the human tear lipocalin gene (LCN1) to 9q34 by in situ hybridization

    SciTech Connect

    Lassagne, H.; Ressot, C.; Gachon, A.M.F. ); Mattei, M.G. )

    1993-10-01

    Lipocalins are a group of extracellular proteins, first described by Pervaiz and Brew, that are able to bind lipophiles by enclosure within their structures, minimizing solvent contact. A cDNA library was constructed from human lacrimal glands obtained post-mortem, after extraction of total RNA by phenol chloroform and purification of poly(A)[sup +] RNA by an oligo(dT) column. The library was screened using an oligonucleotide probe whose sequence was deduced from the already mentioned N-terminal sequence. Sequencing one of the positive clones (clone 16) allowed us to determine the main characteristics of the protein and to confirm that it belongs to the lipocalin family. This results was assessed, at the same time, by another independent team that demonstrated that this protein is also present in saliva. We report the use of clone 16 cDNA to map the tear lipocalin gene by in situ hybridization. The results from the best experiment are as follows: In the 100 metaphase cells examined after in situ hybridization, there were 148 silver grains associated with chromosomes, and 56 (37.8%) were located on chromosome 9. The distribution of the grains on this chromosome was not random: 46/56 (82.1%) of them mapped to the q34.1-q34.3 region of chromosome 9 with a maximum in the q34.3 band. No other chromosomal region was observed to have signal above background. These results allow us to map the tear lipocalin probe to human chromosome 9q34.

  19. Midkine gene (MDK), a gene for prenatal differentiation and neuroregulation, maps to band 11p11. 2 by fluorescence in situ hybridization

    SciTech Connect

    Kaname, Tadashi; Uehara, Kazuyoshi; Muramatsu, Taskashi ); Kuwano, Akira; Murano, Ichiro; Kajii, Tadashi )

    1993-08-01

    Midkine (MDK) is a retinoic acid-responsive gene concerned with prenatal development and neurite growth. The authors mapped the gene to band p11.2 of chromosome 11 through fluorescence in situ hybridization analysis and using a 4.5-kb fragment of its human genomic DNA. 11 refs., 1 fig.

  20. Assignment of the human FKBP12-rapamycin-associated protein (FRAP) gene to chromosome 1p36 by fluorescence in situ hybridization

    SciTech Connect

    Moore, P.A.; Rosen, C.A.; Carter, K.C.

    1996-04-15

    This report describes the localization of the human FKBP12-rapamycin-associated protein (FRAP) gene to human chromosome 1p36 using fluorescence in situ hybridization. This protein is the binding site for rapamycin and FK506, two potent immunosuppressive drugs. 12 refs., 1 fig.

  1. Cytogenetic follow-up by karyotyping and fluorescence in situ hybridization: implications for monitoring patients with myelodysplastic syndrome and deletion 5q treated with lenalidomide

    PubMed Central

    Göhring, Gudrun; Giagounidis, Aristoteles; Büsche, Guntram; Hofmann, Winfried; Kreipe, Hans Heinrich; Fenaux, Pierre; Hellström-Lindberg, Eva; Schlegelberger, Brigitte

    2011-01-01

    In patients with low and intermediate risk myelodysplastic syndrome and deletion 5q (del(5q)) treated with lenalidomide, monitoring of cytogenetic response is mandatory, since patients without cytogenetic response have a significantly increased risk of progression. Therefore, we have reviewed cytogenetic data of 302 patients. Patients were analyzed by karyotyping and fluorescence in situ hybridization. In 85 patients, del(5q) was only detected by karyotyping. In 8 patients undergoing karyotypic evolution, the del(5q) and additional chromosomal aberrations were only detected by karyotyping. In 3 patients, del(5q) was only detected by fluorescence in situ hybridization, but not by karyotyping due to a low number of metaphases. Karyotyping was significantly more sensitive than fluorescence in situ hybridization in detecting the del(5q) clone. In conclusion, to optimize therapy control of myelodysplastic syndrome patients with del(5q) treated with lenalidomide and to identify cytogenetic non-response or progression as early as possible, fluorescence in situ hybridization alone is inadequate for evaluation. Karyotyping must be performed to optimally evaluate response. (clinicaltrials.gov identifier: NCT01099267 and NCT00179621) PMID:21109690

  2. Assignment of the gastric inhibitory polypeptide receptor gene (GIPR) to chromosome bands 19q13.2-q13.3 by fluorescence in situ hybridization

    SciTech Connect

    Stoffel, M.; Fernald, A.A.; Bell, G.I.; Le Beau, M.M.

    1995-08-10

    The gastric inhibitory polypeptide receptor gene (GIPR) was localized, using fluorescence in situ hybridization (FISH), to human chromosome bands 19q13.2-q13.3. Gastric inhibitory polypeptide (GIP) is a potent stimulator of insulin secretion and mutations in the GIPR gene may be related to non-insulin-dependent diabetes mellitus (NIDDM). 13 refs., 1 fig.

  3. Chromosomal localization of the human natural killer cell class I receptor family genes to 19q13.4 by fluorescence in situ hybridization

    SciTech Connect

    Suto, Yumiko; Maenaka, Katsumi; yabe, Toshio

    1996-07-01

    This report describes the localization of the human natural killer cell I receptor family genes to human chromosome 19q13.4 using fluorescence in situ hybridization. These genes mediate the inhibition of the cytotoxicity of subsets of natural killer cells. 8 refs., 1 fig.

  4. Localization of the DCTN1 gene encoding p150{sup Glued} to human chromosome 2p13 by fluorescence in situ hybridization

    SciTech Connect

    Holzbaur, E.L.F.; Tokito, M.K.

    1996-02-01

    This report discusses the genetic mapping of the DCTN1 gene to human chromosome 2p13 using fluorescence in situ hybridization. This gene encodes the largest polypeptide of the dynactin complex, which is one of two microtubule-based biological motor protein complexes. 12 refs., 1 fig.

  5. Detection of Newcastle disease virus RNA by reverse transcription polymerase chain reaction using formalin-fixed, paraffin-embedded tissue and comparison with immunohistochemistry and in situ hybridization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The usefulness of reverse transcription polymerase chain reaction (RT-PCR) from formalin-fixed, paraffin-embedded (FFPE) tissues was examined and compared to the immunohistochemistry (IHC) and in situ hybridization (ISH) assays for detection of Newcastle disease virus (NDV). Spleen and lung tissues...

  6. Assessment of impact of peptide nucleic acid fluorescence in situ hybridization for rapid identification of coagulase-negative staphylococci in the absence of antimicrobial stewardship intervention.

    PubMed

    Holtzman, Carol; Whitney, Dana; Barlam, Tamar; Miller, Nancy S

    2011-04-01

    Peptide nucleic acid fluorescence in situ hybridization (PNA FISH) was instituted at Boston Medical Center for the rapid identification of coagulase-negative staphylococci (CoNS). Without active notification or antimicrobial stewardship intervention, a pre- and postimpact analysis showed no benefit of this assay with respect to the length of hospital stay or vancomycin use.

  7. HYBRID BRIDGMAN ANVIL DESIGN: AN OPTICAL WINDOW FOR IN-SITU SPECTROSCOPY IN LARGE VOLUME PRESSES

    SciTech Connect

    Lipp, M J; Evans, W J; Yoo, C S

    2005-07-29

    The absence of in-situ optical probes for large volume presses often limits their application to high-pressure materials research. In this paper, we present a unique anvil/optical window-design for use in large volume presses, which consists of an inverted diamond anvil seated in a Bridgman type anvil. A small cylindrical aperture through the Bridgman anvil ending at the back of diamond anvil allows optical access to the sample chamber and permits direct optical spectroscopy measurements, such as ruby fluorescence (in-situ pressure) or Raman spectroscopy. This performance of this anvil-design has been demonstrated by loading KBr to a pressure of 14.5 GPa.

  8. A rapid procedure to detect in situ DNA/RNA hybrids

    SciTech Connect

    Reddy, A.R.; Sofer, W.

    1981-12-15

    A new method was developed for detecting DNA/RNA hydrids formed in situ using anti-DNA/RNA antibodies and the Peroxidase-antiperoxidase immunohistochemical procedure. Using RNA synthesized in vitro from cloned Drosophila histone genes (pDm 500H), we localized by this procedure, the histone genes to the 39 D-E region of the left arm of the second chromosome. This method has several advantages compared to conventional procedures.

  9. Epizootic hemorrhagic disease: analysis of tissues by amplification and in situ hybridization reveals widespread orbivirus infection at low copy numbers.

    PubMed

    Brodie, S J; Bardsley, K D; Diem, K; Mecham, J O; Norelius, S E; Wilson, W C

    1998-05-01

    A recent outbreak of hemorrhagic fever in wild ruminants in the northwest United States was characterized by rapid onset of fever, followed shortly thereafter by hemorrhage and death. As a result, a confirmed 1,000 white-tailed deer and pronghorn antelope died over the course of 3 months. Lesions were multisystemic and included severe edema, congestion, acute vascular necrosis, and hemorrhage. Animals that died with clinical signs and/or lesions consistent with hemorrhagic fever had antibody to epizootic hemorrhagic disease virus serotype 2 (EHDV-2) by radioimmune precipitation but the antibody was limited exclusively to class immunoglobulin M. These findings, indicative of acute infection, were corroborated by the observation that numerous deer were found dead; however, clinically affected deer were rarely seen during the outbreak. Furthermore, only in animals with hemorrhagic lesions was EHDV-2 isolated and/or erythrocyte-associated EHDV-2 RNA detected by serotype-specific reverse transcription (RT)-PCR. By using a novel RT in situ PCR assay, viral nucleic acid was localized to the cytoplasm of large numbers of tissue leukocytes and vascular endothelium in tissues with hemorrhage and to vessels, demonstrating acute intimal and medial necrosis. Because PCR amplification prior to in situ hybridization was essential for detecting EHDV, the virus copy number within individual cells was low, <20 virus copies. These findings suggest that massive covert infection characterized by rapid dissemination of virus facilitates the severe and lethal nature of this disease. PMID:9557671

  10. Flexible microfabricated film sensors for the in situ quantum dot-based voltammetric detection of DNA hybridization in microwells.

    PubMed

    Kokkinos, Christos; Economou, Anastasios; Speliotis, Thanasis; Petrou, Panagiota; Kakabakos, Sotirios

    2015-01-20

    A new flexible miniaturized integrated device was microfabricated for the in situ ultrasensitive voltammetric determination of DNA mutation in a microwell format, using quantum dots (QDs) labels. The integrated device consisted of thin Bi, Ag, and Pt films (serving as the working, reference, and counter electrode, respectively) deposited by sputtering on a flexible polyimide substrate. A DNA assay was employed in microwell format, where an immobilized complementary oligonucleotide probe hybridized with the biotinylated target oligonucleotide followed by reaction with streptavidin-conjugated PbS QDs. After the acidic dissolution of the QDs, the flexible sensor was rolled and inserted into the microwell and the Pb(II) released was determined in situ by anodic stripping voltammetry. Since the analysis took place directly in the microwell, the volume of the working solution was only 100 μL and the target DNA could be detected at a concentration down to 1.1 fmol L(-1). The proposed flexible microdevice addresses the restrictions of conventional rigid electrodes while it provides a low cost integrated transducer for the ultrasensitive detection of important biomolecules. PMID:25514352

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

    PubMed

    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.

  12. Detection of alien chromatin conferring resistance to the beet cyst nematode (Heterodera schachtii Schm.) in cultivated beet (Beta vulgaris L.) using in situ hybridization.

    PubMed

    Schmidt, T; Jung, C; Heslop-Harrison, J S; Kleine, M

    1997-05-01

    Chromatin originating from wild beets of the genus Beta, section Procumbentes, has been investigated in nematode-resistant hybrid-derived lines of sugar beet (Beta vulgaris L.) by in situ hybridization using satellite, telomeric and ribosomal DNA repeats, a yeast artificial chromosome (YAC) and total genomic DNA as probes. The allen chromosome was detected in three monosomic addition lines (2n = 18 + 1) by genomic in situ hybridization. Fluorescence in situ hybridization with a genome-specific satellite repeat and YAC DNA enabled the visualization of Procumbentes chromosomes, and in double-target hybridization it was shown that they do not carry 18S-5.8S-25S rRNA and 5S rRNA genes. The wild beet-specific satellite repeat and the telomere sequence from Arabidopsis thaliana were used to perform a structural analysis of the wild beet chromosome fragments of two resistant fragment addition lines. It was shown that one physical end of the chromosome fragments consists of telomeric repeats. Comparison of fragment sizes indicated that the small chromosome fragments harbouring the resistance gene most likely resulted from the loss of one wild beet chromosome arm and an internal deletion of the remaining arm.

  13. Detection of numerical chromosome aberrations using in situ hybridization in paraffin sections of routinely processed bladder cancers.

    PubMed

    Hopman, A H; van Hooren, E; van de Kaa, C A; Vooijs, P G; Ramaekers, F C

    1991-07-01

    An improved protocol for in situ hybridization (ISH) to routinely processed, paraffin-imbedded tissue sections from transitional bladder carcinoma (TCC) is presented. The protocol to detect numerical chromosome aberrations involved treatment of sections with thiocyanate prior to proteolytic digestion, resulting in reproducible ISH reactions. It was used to explore the influence of nuclear truncation in the detection of numerical chromosome aberrations and the detection of tumor cells among stromal and inflammatory cells, to compare the flow cytometric DNA index with chromosome copy number, and to study chromosome heterogeneity within tumors. For this study, a DNA probe for the chromosome region 1q12 was used. Hybridization of model systems with known chromosome numbers, such as sections of paraffin-embedded lymph nodes, paraffin-embedded human peripheral lymphocytes, T24 and Molt-4 cells with two, three, and four chromosomes 1, respectively, showed in at least 50% of the cells the proper number of chromosome hybridization signals in standard 6-microns-thick sections. Depending on the size of the nucleus, a certain percentage of the cells showed lower copy numbers as a result of truncation. In four cases of normal urothelium in paraffin sections, the percentage of nuclei with more than two chromosome spots did not exceed 5%. Comparison of the number of ISH signals, as detected in ethanol-fixed single cell suspensions of 11 TCCs [five flow cytometric (FCM) diploid, three FCM aneuploid, and three FCM tetraploid], with ISH results obtained in paraffin sections of the same tumors showed that typical numerical chromosome aberrations, such as trisomy and tetrasomy up to nonasomy, could be detected. However, the real chromosome copy number is underestimated, especially in tumors with high copy numbers, as detected in the single cell suspensions of the same tumors. Hybridization of a TCC with extremely large nuclei (DNA index = 3.2) containing six to nine ISH signals as

  14. General principles and methods for routine automated microRNA in situ hybridization and double labeling with immunohistochemistry.

    PubMed

    Singh, U; Keirstead, N; Wolujczyk, A; Odin, M; Albassam, M; Garrido, R

    2014-05-01

    MicroRNAs (miRNAs) are small non-coding RNAs that modulate gene expression by binding to complementary sequences on target messenger RNA transcripts. Changes in the expression levels of specific miRNAs have been associated with a variety of disease conditions. We developed a reliable and high throughput in situ hybridization (ISH) method and optimized tissue fixation conditions for formalin fixed, paraffin embedded (FFPE) tissues. ISH methods were automated to visualize four miRNAs: miRNA-145 (smooth muscle cells), miRNA-126 (endothelial cells), miRNA-21 (neoplastic cells) and U6 small nuclear RNA (nuclear marker) using locked nucleic acid (LNA) probes and the Discovery Ultra Ventana(™) platform. The FFPE tissue sections were pretreated with protease 3, hybridized with probe concentrations of ≤ 25 nM; signal was detected using an enhanced, polymer-based detection method. The ISH signal was stronger and more uniform for tissue samples fixed for ≥ 48 h. To investigate the specificity of the method, we developed an automated dual ISH for miRNA-145 coupled with immunohistochemistry for smooth muscle actin, which confirmed the specific distribution of miRNA-145 to smooth muscle cells. These methods may be used routinely for exploratory studies of biomarker development, sample screening and understanding the role of miRNA in the pathophysiology of specific diseases. PMID:24106971

  15. Facile fabrication of ultrathin hybrid membrane for highly flexible supercapacitors via in-situ phase separation of polyethersulfone

    NASA Astrophysics Data System (ADS)

    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.

  16. Peptide nucleic acid fluorescence in situ hybridization for identification of Listeria genus, Listeria monocytogenes and Listeria ivanovii.

    PubMed

    Zhang, Xiaofeng; Wu, Shan; Li, Ke; Shuai, Jiangbing; Dong, Qiang; Fang, Weihuan

    2012-07-01

    A fluorescent in situ hybridization (FISH) method in conjunction with fluorescin-labeled peptide nucleic acid (PNA) probes (PNA-FISH) for detection of Listeria species was developed. In silico analysis showed that three PNA probes Lis-16S-1, Lm-16S-2 and Liv-16S-5 were suitable for specific identification of Listeria genus, Listeria monocytogenes and Listeria ivanovii, respectively. These probes were experimentally verified by their reactivity against 19 strains of six Listeria species (excluding newly described species Listeria marthii and Listeria rocourtiae) and eight other bacterial species. The PNA-FISH method was optimized as 30 min of hybridization with 0.2% Triton X-100 in the solution and used to identify 85 Listeria strains from individual putative Listeria colonies on PALCAM agar plates streaked from selectively enriched cultures of 780 food or food-related samples. Of the 85 Listeria strains, thirty-seven were identified as L. monocytogenes with the probe Lm-16S-2 and two as L. ivanovii with the probe Liv-16S-5 which was in agreement with the results obtained by the API LISTERIA method. Thus, the PNA-FISH protocol has the potential for identification of pathogenic Listeria spp. from food or food-related samples.

  17. Detection of aneuploidy in sperm of an ataxia telangiectasia patient using three-chromosome fluorescence in situ hybridization

    SciTech Connect

    Lowe, X.R.; Baulch, J.E.; Arnheim, N.

    1994-09-01

    Ataxia telangiectasia (A-T) is an inherited, recessive, cancer-prone disorder. Fluorescence in situ hybridization (FISH) with DNA probes specific for three chromosomes was applied to sperm of an A-T patient to determine if there may be an increased germinal risk for aneuploidy. Air-dried sperm smears were treated with proteinase K and were decondensed with DTT and LIS. The slides were then hybridized with fluorescently labeled repetitive DNA probes specific for chromosomes X, Y and 8, and a total of 11,825 sperm cells were scored. The ratio of sperm bearing X-8 and Y-8 was 1:1, as predicted. The frequencies of hyperhaploidy were 3.9, 1.0, 17.6 and 7.8 per 10,000 cells for categories X-X-8, Y-Y-8, X-Y-8 and 8-8-(X or Y), respectively, In addition, the frequency of diploidy (X-Y-8-8) was 18.6 and auto-diploidies (X-X-8-8 and Y-Y-8-8) were 1.0 and 2.0, respectively. These frequencies were not significantly different when compared with levels in healthy men (p > 0.1). Our finding suggests that chromosome X, Y and 8 aneuploidies are not elevated in the sperm of A-T patients, but studies with additional patients and chromosomes are needed.

  18. Chromosomal mapping of tandem repeats in the Yesso Scallop, Patinopecten yessoensis (Jay, 1857), utilizing fluorescence in situ hybridization

    PubMed Central

    Li, Xuan; Yang, Zujing; Liao, Huan; Zhang, Zhengrui; Huang, Xiaoting; Bao, Zhenmin

    2016-01-01

    Abstract Construction of cytogenetic maps can provide important information for chromosome identification, chromosome evolution and genomic research. However, it hasn’t been conducted in many scallop species yet. In the present study, we attempted to map 12 fosmid clones containing tandem repeats by fluorescence in situ hybridization (FISH) in the Yesso scallop Patinopecten yessoensis (Jay, 1857). The results showed 6 fosmid clones were successfully mapped and distributed in 6 different pairs of chromosomes. Three clones were respectively assigned to a pair of metacentric chromosomes, a pair of submetacentric chromosomes and a pair of telocentric chromosomes and the remaining 3 clones showed their loci on three different pairs of subtelocentric chromosomes by co-hybridization. In summary, totally 8 pairs of chromosomes of the Yesso scallop were identified by 6 fosmid clones and two rDNA probes. Furthermore, 6 tandem repeats of 5 clones were sequenced and could be developed as chromosome specific markers for the Yesso scallop. The successful localization of fosmid clones will undoubtedly facilitate the integration of linkage groups with cytogenetic map and genomic research for the Yesso scallop. PMID:27186345

  19. Direct fluorescence in situ hybridization (FISH) in Escherichia coli with a target-specific quantum dot-based molecular beacon.

    PubMed

    Wu, Sheng-Mei; Tian, Zhi-Quan; Zhang, Zhi-Ling; Huang, Bi-Hai; Jiang, Peng; Xie, Zhi-Xiong; Pang, Dai-Wen

    2010-10-15

    Quantum dots (QDs) are inorganic fluorescent nanocrystals with excellent properties such as tunable emission spectra and photo-bleaching resistance compared with organic dyes, which make them appropriate for applications in molecular beacons. In this work, quantum dot-based molecular beacons (QD-based MBs) were fabricated to specifically detect β-lactamase genes located in pUC18 which were responsible for antibiotic resistance in bacteria Escherichia coli (E. coli) DH5α. QD-based MBs were constructed by conjugating mercaptoacetic acid-quantum dots (MAA-QDs) with black hole quencher 2 (BHQ2) labeled thiol DNA vial metal-thiol bonds. Two types of molecular beacons, double-strands beacons and hairpin beacons, were observed in product characterization by gel electrophoresis. Using QD-based MBs, one-step FISH in tiny bacteria DH5α was realized for the first time. QD-based MBs retained their bioactivity when hybridizing with complementary target DNA, which showed excellent advantages of eliminating background noise caused by adsorption of non-specific bioprobes and achieving clearer focus of genes in plasmids pUC18, and capability of bacterial cell penetration and signal specificity in one-step in situ hybridization.

  20. Comparison of Southern blot analysis with isotopic and nonisotopic in situ hybridization for the detection of human papillomavirus sequences in invasive carcinoma of the uterine cervix.

    PubMed

    D'Amato, L; Pilotti, S; Rotola, A; Di Luca, D; Cassai, E; Rilke, F

    1992-03-01

    To compare the efficiency of hybridization methods for the detection of HPV genome, 22 cases of invasive squamous cell carcinoma of the uterine cervix were analyzed by Southern blot analysis and in situ hybridization carried out with 35S- and biotin-labeled probes. These cases contained from less than one to as many as 50 copies per cell of HPV 16 and 18 types. To increase the sensitivity of biotinylated probes, a silver enhancement procedure of the peroxidase reaction product was applied. Results showed that in situ hybridization performed with isotopic probes is as sensitive as Southern blot analysis and is more sensitive than that performed with biotin-labeled probe. However, the application of the silver enhancement procedure increases the percentage of HPV-positive cases from 27 to 50%.

  1. One-Pot Synthesis of Organic-Sulfur-Zinc Hybrid Materials via Polycondensation of a Zinc Salt and Thiols Generated in Situ from Cyclic Dithiocarbonates.

    PubMed

    Ochiai, Bungo; Konta, Hirohisa

    2015-08-17

    Soluble organic-sulfur-zinc hybrid polymers were prepared via a one-pot reaction consisting of ring-opening addition and subsequent polycondensation. The first reaction is the nucleophilic ring-opening addition of 2-ethylhexylamine to multifunctional cyclic dithiocarbonates giving multiple thiols in situ. The sequential polycondensation of the in situ generated thiols with Zn(OAc)2 gave the target hybrid polymers. This one-pot method enabled the use of a shorter amine than the previous polycondensation of Zn(OAc)2 and purified thiols, which required octadecylamine to obtain a soluble product. The obtained hybrid polymers may be cast as composite films with polystyrene and poly(methyl methacrylate). Owing to the shorter alkyl chain, the calculated nD values of the products (1.60 or 1.61) are higher than that of the previous product bearing octadecyl chains (1.53).

  2. Detection of intrahepatic replication of hepatitis C virus RNA by in situ hybridization and comparison with histopathology.

    PubMed Central

    Negro, F; Pacchioni, D; Shimizu, Y; Miller, R H; Bussolati, G; Purcell, R H; Bonino, F

    1992-01-01

    A nonisotopic in situ hybridization (NISH) assay was used to detect hepatitis C virus (HCV) RNA. A synthetic oligonucleotide complementary to bases 252-301 of the highly conserved 5' noncoding region of the HCV genome was end-labeled by terminal deoxynucleotidyltransferase using digoxigenin-conjugated dUTP. The hybridized oligomer was revealed by an immunohistochemical reaction after incubation with an alkaline phosphatase-conjugated anti-digoxigenin antibody and subsequent amplification with a complex of alkaline phosphatase and anti-alkaline phosphatase antibodies. The intracellular distribution of HCV RNA was monitored in the livers of two chimpanzees experimentally infected with the H strain of HCV and compared with the serum alanine aminotransferase activity, serum HCV RNA, and liver histopathology. Most cells were stained in the cytoplasm as early as 2 days after inoculation, 1 and 2 days, respectively, before the appearance of viral RNA in the serum. The time course of HCV RNA replication was correlated with increases in serum alanine aminotransferase. However, neither one paralleled the appearance of liver cell necrosis nor showed any correlation with the inflammatory response. The NISH signal was not found in liver biopsy specimens taken from these two animals before inoculation with HCV, from chimpanzees with acute hepatitis type A, B, or delta, or from two animals never experimentally infected with any hepatitis agent; moreover, it disappeared when the positive specimens were predigested with RNase and it was not observed after hybridization of positive controls with a labeled oligomer unrelated to HCV RNA. Thus, detection of liver HCV RNA by NISH is a sensitive and specific method for studying HCV replication at the cellular level. Intracellular replication of HCV did not appear to be associated with histopathologic changes in the liver, although the correlation with increases of liver enzyme activity in the serum suggested possible damage to the liver

  3. Development of a flow-fluorescence in situ hybridization protocol for the analysis of microbial communities in anaerobic fermentation liquor

    PubMed Central

    2013-01-01

    Background The production of bio-methane from renewable raw material is of high interest because of the increasing scarcity of fossil fuels. The process of biomethanation is based on the inter- and intraspecific metabolic activity of a highly diverse and dynamic microbial community. The community structure of the microbial biocenosis varies between different biogas reactors and the knowledge about these microbial communities is still fragmentary. However, up to now no approaches are available allowing a fast and reliable access to the microbial community structure. Hence, the aim of this study was to originate a Flow-FISH protocol, namely a combination of flow cytometry and fluorescence in situ hybridization, for the analysis of the metabolically active microorganisms in biogas reactor samples. With respect to the heterogenic texture of biogas reactor samples and to collect all cells including those of cell aggregates and biofilms the development of a preceding purification procedure was indispensable. Results Six different purification procedures with in total 29 modifications were tested. The optimized purification procedure combines the use of the detergent sodium hexametaphosphate with ultrasonic treatment and a final filtration step. By this treatment, the detachment of microbial cells from particles as well as the disbandment of cell aggregates was obtained at minimized cell loss. A Flow-FISH protocol was developed avoiding dehydration and minimizing centrifugation steps. In the exemplary application of this protocol on pure cultures as well as biogas reactor samples high hybridization rates were achieved for commonly established domain specific oligonucleotide probes enabling the specific detection of metabolically active bacteria and archaea. Cross hybridization and autofluorescence effects could be excluded by the use of a nonsense probe and negative controls, respectively. Conclusions The approach described in this study enables for the first time the

  4. The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits.

    PubMed

    Lusis, Aldons J; Seldin, Marcus M; Allayee, Hooman; Bennett, Brian J; Civelek, Mete; Davis, Richard C; Eskin, Eleazar; Farber, Charles R; Hui, Simon; Mehrabian, Margarete; Norheim, Frode; Pan, Calvin; Parks, Brian; Rau, Christoph D; Smith, Desmond J; Vallim, Thomas; Wang, Yibin; Wang, Jessica

    2016-06-01

    The Hybrid Mouse Diversity Panel (HMDP) is a collection of approximately 100 well-characterized inbred strains of mice that can be used to analyze the genetic and environmental factors underlying complex traits. While not nearly as powerful for mapping genetic loci contributing to the traits as human genome-wide association studies, it has some important advantages. First, environmental factors can be controlled. Second, relevant tissues are accessible for global molecular phenotyping. Finally, because inbred strains are renewable, results from separate studies can be integrated. Thus far, the HMDP has been studied for traits relevant to obesity, diabetes, atherosclerosis, osteoporosis, heart failure, immune regulation, fatty liver disease, and host-gut microbiota interactions. High-throughput technologies have been used to examine the genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes of the mice under various environmental conditions. All of the published data are available and can be readily used to formulate hypotheses about genes, pathways and interactions. PMID:27099397

  5. The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits.

    PubMed

    Lusis, Aldons J; Seldin, Marcus M; Allayee, Hooman; Bennett, Brian J; Civelek, Mete; Davis, Richard C; Eskin, Eleazar; Farber, Charles R; Hui, Simon; Mehrabian, Margarete; Norheim, Frode; Pan, Calvin; Parks, Brian; Rau, Christoph D; Smith, Desmond J; Vallim, Thomas; Wang, Yibin; Wang, Jessica

    2016-06-01

    The Hybrid Mouse Diversity Panel (HMDP) is a collection of approximately 100 well-characterized inbred strains of mice that can be used to analyze the genetic and environmental factors underlying complex traits. While not nearly as powerful for mapping genetic loci contributing to the traits as human genome-wide association studies, it has some important advantages. First, environmental factors can be controlled. Second, relevant tissues are accessible for global molecular phenotyping. Finally, because inbred strains are renewable, results from separate studies can be integrated. Thus far, the HMDP has been studied for traits relevant to obesity, diabetes, atherosclerosis, osteoporosis, heart failure, immune regulation, fatty liver disease, and host-gut microbiota interactions. High-throughput technologies have been used to examine the genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes of the mice under various environmental conditions. All of the published data are available and can be readily used to formulate hypotheses about genes, pathways and interactions.

  6. Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

    PubMed Central

    Bisha, Bledar; Brehm-Stecher, Byron F.

    2010-01-01

    This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in situ hybridization (FISH) for rapid culture-independent detection of Salmonella spp. Cell-charged tapes can also be placed face-down on selective agar for solid-phase enrichment prior to detection. Alternatively, low-volume liquid enrichments (liquid surface miniculture) can be performed on the surface of the tape in non-selective broth, followed by FISH and analysis via flow cytometry. To begin, sterile adhesive tape is brought into contact with fresh produce, gentle pressure is applied, and the tape is removed, physically extracting microbes present on these surfaces. Tapes are mounted sticky-side up onto glass microscope slides and the sampled cells are fixed with 10% formalin (30 min) and dehydrated using a graded ethanol series (50, 80, and 95%; 3 min each concentration). Next, cell-charged tapes are spotted with buffer containing a Salmonella-targeted DNA probe cocktail and hybridized for 15 - 30 min at 55°C, followed by a brief rinse in a washing buffer to remove unbound probe. Adherent, FISH-labeled cells are then counterstained with the DNA dye 4',6-diamidino-2-phenylindole (DAPI) and results are viewed using fluorescence microscopy. For solid-phase enrichment, cell-charged tapes are placed face-down on a suitable selective agar surface and incubated to allow in situ growth of Salmonella microcolonies, followed by FISH and microscopy as described above. For liquid surface miniculture, cell-charged tapes are placed sticky side up and a silicone perfusion chamber is applied so that the tape and microscope slide form the bottom of a water-tight chamber into which a small volume (≤ 500 μL) of Trypticase Soy Broth (TSB) is introduced. The inlet ports are sealed and the chambers are incubated at 35 - 37°C, allowing growth-based amplification of tape-extracted microbes. Following incubation, inlet ports

  7. Identification of PML/RARalpha fusion gene transcripts that showed no t(15;17) with conventional karyotyping and fluorescent in situ hybridization.

    PubMed

    Choughule, A; Polampalli, S; Amre, P; Shinde, S; Banavali, S; Prabhash, K; Nair, R; Subramanian, P G; Gujral, S; Parikh, P M

    2009-01-01

    Acute promyelocytic leukemia (APL) is characterized by a reciprocal translocation, t(15;17)(q22;q11-21), resulting in the fusion of the promyelocytic leukemia (PML) and retinoic acid receptor alpha (RARalpha) genes. Using conventional cytogenetic methods, these translocations are normally detected in about 70-90% of patients; most negative results are due to technical problems or cryptic variants. These masked PML/RARalpha fusions can be identified by molecular analyses, such as reverse transcriptase-polymerase chain reaction (RT-PCR) or fluorescence in situ hybridization (FISH). Approximately 5 to 10% of all APL cases reported do not show PML/RARalpha fusion transcripts, even with dual-colored FISH. We report three of 40 diagnosed APL cases that showed morphological, cytochemical, and immunophenotypic features of hypergranular APL, but did not show a PML/RARalpha fusion signal or any of its variants, on FISH. All cases were identified by RT-PCR, which was further confirmed by cDNA sequencing. Conventional karyotyping showed other clonal aberrations in these cases, but failed to show t(15;17) or any other variants or complex translocations. PMID:19224461

  8. Detection of numerical and structural alterations and fusion of chromosomes 16 and 1 in low-grade papillary breast carcinoma by fluorescence in situ hybridization.

    PubMed

    Tsuda, H; Takarabe, T; Susumu, N; Inazawa, J; Okada, S; Hirohashi, S

    1997-10-01

    Intracystic papillary breast tumors, including intraductal papilloma and low-grade intracystic papillary carcinoma, constitute a group for which differential diagnosis is frequently difficult. We examined the status of chromosomes 16 and 1 by multicolor fluorescence in situ hybridization (FISH) analyses and the DNA ploidy patterns by flow cytometry in 26 intracystic papillary tumors. Alterations of chromosomes 16 and 1 were detected by FISH in 93 and 85%, respectively, of 14 low-grade papillary carcinomas, and the latter alterations always concurred with the former. Two-color FISH using probes for the D1Z1 (1q12) and D16Z2 (16cen) loci or the D1Z1 and D16Z3 (16q11) loci showed that fusion of chromosomes 16 and 1, mostly with breakpoints distal to 16q11.2 and proximal to 1q12, occurred in 77% of the papillary carcinomas. DNA aneuploidy was detected in 6% of these carcinomas. No papilloma showed these chromosome alterations or DNA aneuploidy. Chromosome 16 and 1 fusions appeared to occur frequently in diploid breast carcinomas and to be involved in the acquisition of a malignant phenotype by duct epithelial cells. We suggest that two-color FISH methods for detecting 1;16 fusions might be applicable as supportive methods for the differential diagnosis of intracystic papillary breast tumors. PMID:9327736

  9. Rapid sex determination on buccal smears using DNA probes and fluorescence in situ hybridization

    SciTech Connect

    Giraldez, R.A.; Harris, C.

    1994-09-01

    Hybridization of dual-labeled DNA probes for the repetitive sequences on the X and Y chromosomes allows a fast, non-invasive, more reliable method for sex determination that current cytogenetic Barr body and Y chromatin assays. Scrapes of squamous epithelial cells were collected from the oral cavity of 14 subjects (5{male}, 9{female}) and smeared onto silanized slides. The smears were allowed to air dry. Samples were blinded and then fixed in 50% methanol/50% glacial acetic acid for 10 minutes, and allowed to dry. The slides were incubated in a pretreatment solution containing 30% sodium bisulfite at 45{degrees}C for 10 minutes. They were rinsed in 2XSSC pH 7.0 and then dehydrated through a series of 70%, 85%, and 100% ethanols at room temperature and allowed to air dry. A probe mixture (30 {mu}L containing 10 ng/{mu}L biotin-labeled DXZ1 and digoxigenin-labeled DYZ1/DYZ3 in 70% Formamide/2XSSC) was aliquoted onto each slide, coverslipped, and sealed with rubber cement. Probe and target DNA were simultaneously denatured at 72{degrees}C on a slide warmer for 6 minutes. Probe was allowed to hybridize overnight in a humidified chamber at 37{degrees}C. Slides were postwashed at 72{degrees}C in 0.5xSSC pH 7.0 for 5 minutes, then soaked at room temperature 1XPBD for 2 minutes, and detected with rhodamine/anti-digoxigenin-FITC/avidin for 15 minutes at 37{degrees}C. Slides were soaked 3X in 1XPBD and then counterstained with 15 {mu}L 0.05 {mu}g/mL DAP1/Antifade. 200 nuclei were scored for the presence of one green (X), two green (XX), one green and one red (XY), or a single red (Y) signal, using a fluorescent microscope equipped with a triple band pass filter. Greater than 90% of the hybridized nuclei from each of the 14 cases studied conformed to the sex chromosome pattern. The modal number in 9 cases showed two green signals (XX), and a green and a red signal (XY) in the other 5 cases; this was in complete agreement with the cytogenetic results.

  10. The human tissue transglutaminase gene maps on chromosome 20q12 by in situ fluorescence hybridization

    SciTech Connect

    Gentile, V.; Davies, P.J.A. ); Baldini, A. )

    1994-03-15

    A cDNA encoding for the human tissue transglutaminase gene has been used to identify the chromosomal localization of the corresponding structural gene. The precise chromosomal and subregional localizations have been established by using in situ fluorescence mapping with a recombinant [lambda]-Zap phage containing the full cDNA coding sequence. The study showed that the human tissue transglutaminase gene is localized on chromosome 20 and, more precisely, within the band 20q12. To date, this is the third member of the transglutaminase gene family to be mapped. Human factor XIIIa (plasma transglutaminase), human keratinocyte transglutaminase (type I), and human tissue transglutaminase (type II) genes, although codifying for homologous enzymes, are localized on three different chromosomes. 16 refs., 1 fig.

  11. Detection of human papillomavirus DNA by in situ hybridization and polymerase chain reaction in human papillomavirus equivocal and dysplastic cervical biopsies.

    PubMed

    Shroyer, K R; Lovelace, G S; Abarca, M L; Fennell, R H; Corkill, M E; Woodard, W D; Davilla, G H

    1993-09-01

    One hundred twenty-one paraffin-embedded cervical biopsy specimens were tested for the presence of human papillomavirus (HPV) DNA by in situ hybridization and polymerase chain reaction. By in situ hybridization using probes for HPV types 6/11, 16/18, 31/33/35, 42/43/44, 51/52, and 45/56, HPV DNA was found in none of 20 normal/squamous metaplasia biopsy specimens, in one of 76 HPV equivocal biopsy specimens, in seven of 12 condyloma/mild dysplasia biopsy specimens, and in 12 of 13 moderate/severe dysplasia biopsy specimens. Polymerase chain reaction using HPV L1 consensus sequence primers followed by filter hybridization of the amplification products was positive for HPV DNA in two of 20 normal/squamous metaplasia biopsy specimens, in 23 of 76 HPV equivocal biopsy specimens, in eight of 12 condyloma/mild dysplasia biopsy specimens, and in 12 of 13 moderate/severe dysplasia biopsy specimens. Among biopsies that tested positive by polymerase chain reaction but that were negative by in situ hybridization, the most commonly identified HPV was type 16. We conclude that although HPV equivocal biopsy specimens contain HPV DNA more frequently than histologically normal tissue, the majority of biopsy specimens in this category test negative for HPV DNA. The clinical significance of a positive test for HPV, in the absence of unequivocal histologic changes, remains to be determined.

  12. Fluid-structure-interaction analyses of reactor vessel using improved hybrid Lagrangian Eulerian code ALICE-II

    SciTech Connect

    Wang, C.Y.

    1993-06-01

    This paper describes fluid-structure-interaction and structure response analyses of a reactor vessel subjected to loadings associated with postulated accidents, using the hybrid Lagrangian-Eulerian code ALICE-II. This code has been improved recently to accommodate many features associated with innovative designs of reactor vessels. Calculational capabilities have been developed to treat water in the reactor cavity outside the vessel, internal shield structures and internal thin shells. The objective of the present analyses is to study the cover response and potential for missile generation in response to a fuel-coolant interaction in the core region. Three calculations were performed using the cover weight as a parameter. To study the effect of the cavity water, vessel response calculations for both wet- and dry-cavity designs are compared. Results indicate that for all cases studied and for the design parameters assumed, the calculated cover displacements are all smaller than the bolts` ultimate displacement and no missile generation of the closure head is predicted. Also, solutions reveal that the cavity water of the wet-cavity design plays an important role of restraining the downward displacement of the bottom head. Based on these studies, the analyses predict that the structure integrity is maintained throughout the postulated accident for the wet-cavity design.

  13. Fluid-structure-interaction analyses of reactor vessel using improved hybrid Lagrangian Eulerian code ALICE-II

    SciTech Connect

    Wang, C.Y.

    1993-01-01

    This paper describes fluid-structure-interaction and structure response analyses of a reactor vessel subjected to loadings associated with postulated accidents, using the hybrid Lagrangian-Eulerian code ALICE-II. This code has been improved recently to accommodate many features associated with innovative designs of reactor vessels. Calculational capabilities have been developed to treat water in the reactor cavity outside the vessel, internal shield structures and internal thin shells. The objective of the present analyses is to study the cover response and potential for missile generation in response to a fuel-coolant interaction in the core region. Three calculations were performed using the cover weight as a parameter. To study the effect of the cavity water, vessel response calculations for both wet- and dry-cavity designs are compared. Results indicate that for all cases studied and for the design parameters assumed, the calculated cover displacements are all smaller than the bolts' ultimate displacement and no missile generation of the closure head is predicted. Also, solutions reveal that the cavity water of the wet-cavity design plays an important role of restraining the downward displacement of the bottom head. Based on these studies, the analyses predict that the structure integrity is maintained throughout the postulated accident for the wet-cavity design.

  14. Chemical and mineralogical analyses of planetary rocks using a laser ablation mass spectrometer for in situ space research

    NASA Astrophysics Data System (ADS)

    Brigitte Neuland, Maike; Mezger, Klaus; Riedo, Andreas; Tulej, Marek; Wurz, Peter

    2015-04-01

    The context chemical analysis is of considerable importance in space research. High resolution in situ studies of planetary materials can yield important information on surface heterogeneity, basic grain mineralogy and chemical composition of surface and subsurface. In turn, these data are the basis for our understanding of the physical and chemical processes which led to the formation and alteration of planetary material [1] [2]. A highly heterogeneous sample of Allende meteorite, representative for extraterrestrial material, is investigated by LMS, a miniature laser ablation mass spectrometer designed for space research [3]. In the current setup a fs-laser ablation ion source is applied, allowing chemical analysis with lateral resolution of about 10-15 μm and sub-micrometre depth resolution [4]. The reflectron TOF mass analyser is used to measure elemental and isotopic composition of the sampled surface. The LMS instrument supports mass resolution 400 and dynamic range of 108 [5]. In the current studies with the fs-ablation ion source significant improvements in the detection efficiency of several metals e.g., Ni, Co, and non-metals e.g., Si, P, S and O, was achieved comparing to our previous setup [6]. Also the values of sensitivity coefficients for these elements are determined to be close to one, which resulted in the substantial improvements of the quantitative element analysis of the sample. Since the ablation crater depth is expected to be about 1 nm/laser shot also the possible changes of the main element or isotope distribution in depth can be analysed to assess their influence on the mineralogical analysis [7]. Several areas on an Allende sample were investigated and the chemical composition across the surface was determined from the mass spectrometric analysis. Also accurate isotope analysis could be conducted for most of main elements with sufficiently high signal to noise ratio. Correlation of elements was conducted and yielded mineralogical maps

  15. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Modern biological analyses are often assisted by recent technologies making the sequencing of complex genomes both technically possible and feasible. We recently sequenced the tomato genome that, like many eukaryotic genomes, is large and complex. Current sequencing technologies allow the developmen...

  16. Improved assumed-stress hybrid shell element with drilling degrees of freedom for linear stress, buckling, and free vibration analyses

    NASA Technical Reports Server (NTRS)

    Rengarajan, Govind; Aminpour, Mohammad A.; Knight, Norman F., Jr.

    1992-01-01

    An improved four-node quadrilateral assumed-stress hybrid shell element with drilling degrees of freedom is presented. The formulation is based on Hellinger-Reissner variational principle and the shape functions are formulated directly for the four-node element. The element has 12 membrane degrees of freedom and 12 bending degrees of freedom. It has nine independent stress parameters to describe the membrane stress resultant field and 13 independent stress parameters to describe the moment and transverse shear stress resultant field. The formulation encompasses linear stress, linear buckling, and linear free vibration problems. The element is validated with standard tests cases and is shown to be robust. Numerical results are presented for linear stress, buckling, and free vibration analyses.

  17. A facile approach for in situ synthesis of graphene-branched-Pt hybrid nanostructures with excellent electrochemical performance

    NASA Astrophysics Data System (ADS)

    Sahu, Subash Chandra; Samantara, Aneeya K.; Satpati, Biswarup; Bhattacharjee, Sarama; Jena, Bikash Kumar

    2013-10-01

    A facile and green approach for the synthesis of highly electroactive branched Pt nanostructures well dispersed on graphene has been developed by in situ reduction of graphene oxides and Pt(iv) ions in an aqueous medium. The as-synthesized branched Pt and graphene hybrid nanomaterials (GR-BPtNs) were thoroughly characterized using Transmission Electron Microscope (TEM), UV-Visible spectroscopy, Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA) and Raman spectroscopy. This report clearly exploits the decisive role of the graphene support, the pH of the solution and the stabiliser on shaping the branched morphology of the Pt nanostructures well dispersed on graphene. Cyclic voltammetry, chronoamperometry and electrochemical impedance spectroscopy (EIS) measurements were employed to investigate the electrocatalytic performance and durability of GR-BPtNs towards methanol oxidation and oxygen reduction. The results reveal that the synergetic effect of the graphene support and the branched morphology triggers electrocatalytic performance and robust tolerance to surface poisoning of GR-BPtNs.A facile and green approach for the synthesis of highly electroactive branched Pt nanostructures well dispersed on graphene has been developed by in situ reduction of graphene oxides and Pt(iv) ions in an aqueous medium. The as-synthesized branched Pt and graphene hybrid nanomaterials (GR-BPtNs) were thoroughly characterized using Transmission Electron Microscope (TEM), UV-Visible spectroscopy, Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA) and Raman spectroscopy. This report clearly exploits the decisive role of the graphene support, the pH of the solution and the stabiliser on shaping the branched morphology of the Pt nanostructures well dispersed on graphene. Cyclic voltammetry, chronoamperometry and electrochemical impedance spectroscopy (EIS) measurements were employed to investigate the electrocatalytic

  18. Fluorescent in situ hybridization with specific DNA probes offers adequate detection of Enterococcus faecalis and Enterococcus faecium in clinical samples.

    PubMed

    Waar, Karola; Degener, John E; van Luyn, Marja J; Harmsen, Hermie J M

    2005-10-01

    Enterococcus faecalis and Enterococcus faecium are among the leading causes of hospital-acquired infections. Reliable and quick identification of E. faecalis and E. faecium is important for accurate treatment and understanding their role in the pathogenesis of infections. Fluorescent in situ hybridization (FISH) of whole bacterial cells with oligonucleotides targeted at the 16S rRNA molecule leads to a reduced time to identification. In clinical practice, FISH therefore can be used in situations in which quick identification is necessary for optimal treatment of the patient. Furthermore, the abundance, spatial distribution and bacterial cell morphology can be observed in situ. This report describes the design of two fluorescent-labelled oligonucleotides that, respectively, detect the 16S rRNA of E. faecalis and the 16S rRNA of E. faecium, Enterococcus hirae, Enterococcus mundtii, Enterococcus villorum and Enterococcus saccharolyticus. Different protocols for the application of these oligonucleotides with FISH in different clinical samples such as faeces or blood cultures are given. Enterococci in a biofilm attached to a biomaterial were also visualized. Embedding of the biomaterial preserved the morphology and therefore the architecture of the biofilm could be observed. The usefulness of other studies describing FISH for detection of enterococci is generally hampered by the fact that they have only focused on one material and one protocol to detect the enterococci. However, the results of this study show that the probes can be used both in the routine laboratory to detect and determine the enterococcal species in different clinical samples and in a research setting to enumerate and detect the enterococci in their physical environment.

  19. Development of rRNA-Targeted PCR and In Situ Hybridization with Fluorescently Labelled Oligonucleotides for Detection of Yersinia Species

    PubMed Central

    Trebesius, Karlheinz; Harmsen, Dag; Rakin, Alexander; Schmelz, Jochen; Heesemann, Jürgen

    1998-01-01

    In this report, we present details of two rapid molecular detection techniques based on 16S and 23S rRNA sequence data to identify and differentiate Yersinia species from clinical and environmental sources. Near-full-length 16S rRNA gene (rDNA) sequences for three different Yersinia species and partial 23S rDNA sequences for three Y. pestis and three Y. pseudotuberculosis strains were determined. While 16S rDNA sequences of Y. pestis and Y. pseudotuberculosis were found to be identical, one base difference was identified within a highly variable region of 23S rDNA. The rDNA sequences were used to develop primers and fluorescently tagged oligonucleotide probes suitable for differential detection of Yersinia species by PCR and in situ hybridization, respectively. As few as 102 Yersinia cells per ml could be detected by PCR with a seminested approach. Amplification with a subgenus-specific primer pair followed by a second PCR allowed differentiation of Y. enterocolitica biogroup 1B from biogroups 2 to 5 or from other pathogenic Yersinia species. Moreover, a set of oligonucleotide probes suitable for rapid (3-h) in situ detection and differentiation of the three pathogenic Yersinia species (in particular Y. pestis and Y. pseudotuberculosis) was developed. The applicability of this technique was demonstrated by detection of Y. pestis and Y. pseudotuberculosis in spiked throat and stool samples, respectively. These probes were also capable of identifying Y. enterocolitica within cryosections of experimentally infected mouse tissue by the use of confocal laser scanning microscopy. PMID:9705392

  20. DNA damage and repair measured in different genomic regions using the comet assay with fluorescent in situ hybridization.

    PubMed

    Horváthová, Eva; Dusinská, Mária; Shaposhnikov, Sergey; Collins, Andrew R

    2004-07-01

    The comet assay is a sensitive method for measuring DNA strand breaks in eukaryotic cells. After embedding in agarose, cells are lysed and electrophoresed at high pH. DNA loops containing breaks (in which supercoiling is relaxed) escape from the nucleoid comet head to form a tail. Oligonucleotide probes were designed for 5' and 3' regions of the genes for dihydrofolate reductase (DHFR) and O6-methylguanine DNA methyltransferase (MGMT), both from the Chinese hamster, and the human tumour suppressor p53 gene. Alternate ends were labelled with either biotin or fluorescein. These probes were hybridized to the DNA of comets from Chinese hamster ovary (CHO) cells or human lymphocytes treated with H2O2 or photosensitizer plus light to induce oxidative damage. Amplification with Texas red- and fluorescein-tagged antibodies led, in the case of p53 in human cells, to red and green signals located in the comet tail (as well as in the head), indicating the presence of breaks in the vicinity of the gene. However, only one end of the MGMT gene appeared in the tail and almost no signals from the DHFR gene, either red or green, were in the tail of comets from CHO cells. Restriction on movement from the head to tail may result from the presence of a 'matrix-associated region' in the gene. The kinetics of repair of oxidative damage were followed; strand breaks in the p53 gene were repaired more rapidly than total DNA. Thus, fluorescent in situ hybridization in combination with the comet assay provides a powerful method for studying repair of specific genes in relation to chromatin structure. PMID:15215325

  1. Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization.

    PubMed

    DeLong, E F; Taylor, L T; Marsh, T L; Preston, C M

    1999-12-01

    Fluorescent in situ hybridization (FISH) using rRNA-specific oligonucleotide probes has emerged as a popular technique for identifying individual microbial cells. In natural samples, however, the signal derived from fluor-labeled oligonucleotide probes often is undetectable above background fluorescence in many cells. To circumvent this difficulty, we applied fluorochrome-labeled polyribonucleotide probes to identify and enumerate marine planktonic archaea and bacteria. The approach greatly enhanced the sensitivity and applicability of FISH with seawater samples, allowing confident identification and enumeration of planktonic cells to ocean depths of 3,400 m. Quantitative whole-cell hybridization experiments using these probes accounted for 90 to 100% of the total 4',6-diamidino-2-phenylindole (DAPI)-stained cells in most samples. As predicted in a previous study (R. Massana, A. E. Murray, C. M. Preston, and E. F. DeLong, Appl. Environ. Microbiol. 63:50-56, 1997), group I and II marine archaea predominate in different zones in the water column, with maximal cell densities of 10(5)/ml. The high cell densities of archaea, extending from surface waters to abyssal depths, suggest that they represent a large and significant fraction of the total picoplankton biomass in coastal ocean waters. The data also show that the vast majority of planktonic prokaryotes contain significant numbers of ribosomes, rendering them easily detectable with polyribonucleotide probes. These results imply that the majority of planktonic cells visualized by DAPI do not represent lysed cells or "ghosts," as was suggested in a previous report. PMID:10584017

  2. Reliability of aneuploidy estimates in human sperm: Results of fluorescence in situ hybridization studies using two different scoring criteria

    SciTech Connect

    Martin, R.H. |; Rademaker, A.

    1994-09-01

    Aneuploidy estimates for individual chromosomes in human sperm have varied more than 10-fold in different laboratories using fluorescence in situ hybridization (FISH). These laboratories use different scoring criteria in the assessment of a disomic sperm. In order to determine reliable estimates of aneuploidy, we have investigated whether scoring criteria affect the aneuploidy frequency in human sperm. Aneuploidy estimates for chromosomes 1(pUC1.77), 12(pBR12), X(XC) and Y(DYZ3Z) were obtained in human sperm from five donors using multicolor FISH analysis to provide an internal control to differentiate between nullisomy and lack of hybridization and between disomy and diploidy. Disomy frequencies were obtained by scoring a minimum of 10,000 sperm for each chromosome probe per donor. This analysis was replicated for two scoring criteria: one scoring criterion used one-half a signal domain as the minimum distance between two signals to be counted as two and thus disomic; the other scoring criterion set one signal domain as the minimum distance between two signals. A total of 120,870 sperm were assessed using one half domain as the scoring criterion and 113,478 were scored using one domain as the criterion. The mean percent disomy for chromosomes 1, 12, X, Y and XY was .18, .16, .15, .19, .25 respectively using the one-half domain criterion and .08, .17, .07, .12, .16 respectively using the one domain criterion. The percent disomy decreased significantly with use of one domain as the minimum distance for signal separation for all chromosomes except chromosome number 12. These lower disomy frequencies correlated well with frequencies derived from human sperm karyotypes analyzed in our laboratory. This suggests that the fluorescent signals for chromosomes 1, X and Y split into more than one domain in decondensed interphase sperm and use of the one-half domain criterion leads to an overestimate of aneuploidy frequencies.

  3. Sensitivity and Specificity of In Situ Hybridization for Diagnosis of Cutaneous Infection by Leishmania infantum in Dogs

    PubMed Central

    Figueiredo, Fabiano B.; Wise, Annabel G.; Madeira, Maria F.; Oliveira, Raquel V. C.; Schubach, Tânia M. P.; Kiupel, Matti; Langohr, Ingeborg M.

    2013-01-01

    An accurate diagnosis of infection by Leishmania infantum in dogs is fundamental for the control of zoonotic visceral leishmaniasis (VL). Histopathology (HP) and immunohistochemistry (IHC) are frequently used for the histological diagnosis of L. infantum in dogs but have shown limited accuracy. To improve the sensitivity and specificity of the histological diagnosis of VL, we evaluated automated in situ hybridization (ISH) using a generic probe for Leishmania and a specific probe for L. infantum in surgical skin biopsy specimens of dogs. The ISH results were compared with those of HP and IHC, using parasitological culture as the reference standard. Skin samples from 51 dogs with cutaneous L. infantum infection and 51 noninfected dogs were randomly selected from samples of dogs from various cities in Brazil where canine VL is endemic. These samples were processed for parasitological culture, HP, IHC, and ISH using both probes. The sensitivities of ISH using the specific probe, ISH using the generic probe, IHC, and HP were, respectively, 74.5%, 70.6%, 69.5%, and 57.6%. The specificity of both ISH probes tested was 100%, and there was no cross-hybridization of the generic and specific probes with selected pathogenic fungi and protozoa. The specific probe discriminated L. infantum from the other species of Leishmania that infect dogs in the New World. ISH is highly sensitive and specific for the diagnosis of L. infantum in histologic samples of skin from infected dogs and can be used on routine biopsy material to make a diagnosis of leishmaniasis. PMID:23135932

  4. Detection of sex chromosomal aneuploidies X-X, Y-Y, and X-Y in human sperm using two-chromosome fluorescence in situ hybridization

    SciTech Connect

    Wyrobek, A.J.; Robbins, W.A. |; Pinkel, D.; Weier, H.U.; Mehraein, Y. |

    1994-10-15

    Sex chromosome aneuploidy is the most common numerical chromosomal abnormality in humans at birth and a substantial portion of these abnormalities involve paternal chromosomes. An efficient method is presented for using air-dried smears of human semen to detect the number of X and Y chromosomes in sperm chromatin using two-chromosome fluorescence in situ hybridization. Air-dried semen smears were pre-treated with dithiothreitol and 3,4-diiodosalicylate salt to decondense the sperm chromatin and then were hybridized with repetitive sequence DNA probes that had been generated by PCR and differentially labeled. Hybridizations with X and Y specific probes showed the expected ratio of 50%X:50%Y bearing sperm. Sperm carrying extra fluorescence domains representing disomy for the X or Y chromosomes occurred at frequencies of {approximately} 4 per 10,000 sperm each. Cells carrying both X and Y fluorescence domains occurred at a frequency of {approximately} 6/10,000. Thus, the overall frequency of sperm that carried an extra sex chromosome was 1.4/1,000. The frequencies of sperm carrying sex chromosome aneuploidies determined by hybridization did not differ statistically from those reported from the same laboratory using the human-sperm/hamster-egg cytogenetic technique. Multi-chromosome fluorescence in situ hybridization to sperm is a promising method for assessing sex-ratio alterations in human semen and for determining the fraction of sperm carrying sex or other chromosome aneuploidies which may be transmissible to offspring. 44 refs., 1 fig., 3 tabs.

  5. Detection of virus-specific RNA in simian sarcoma-leukemia virus-infected cells in in situ hybridization to viral complementary DNA.

    PubMed Central

    Kaufman, S L; Gallo, R C; Miller, N R

    1979-01-01

    An in situ molecular hybridization system which will detect retrovirus RNA in the cytoplasm of individual virus-infected cells has been developed. The technique was applied to cells infected with simian sarcoma-leukemia virus, where the virus-specific RNA was detected by hybridization to simian sarcoma-leukemia virus 3H-labeled complementary DNA. The system is useful for detecting viral RNA-containing cells in the presence of an excess of virus-negative cells and for determining which type of cell in a heterogenous population is expressing viral RNA. Images PMID:224220

  6. Hybrid Photopatterned Enzymatic Reaction (HyPER) for In situ Cell Manipulation

    PubMed Central

    Griffin, Donald R; Borrajo, Jacob; Soon, Allyson; Acosta-Vélez, Giovanny F.; Oshita, Victor; Darling, Nicole; Mack, Julia; Barker, Thomas; Iruela-Arispe, M. Luisa; Segura, Tatiana

    2014-01-01

    The ability to design artificial extracellular matrices as cell instructive scaffolds has opened the door to technologies capable of studying cell fate in vitro and to guide tissue repair in vivo. One main component of the design of artificial extracellular matrices is the incorporation of biochemical cues to guide cell phenotype and multicellular organization. The extracellular matrix is composed of a heterogeneous mixture of proteins that present a variety of spatially discrete signals to residing cell populations. In contrast, most engineered ECMs do not mimic this heterogeneity. In recent years the use of photodeprotection has been used to achieve spatial immobilization of signals. However, these approaches have been limited mostly to small peptides. Here we combine photodeprotection with enzymatic reaction to achieve spatially controlled immobilization of active bioactive signals that range from small molecules to large proteins. A peptide substrate for transglutaminase factor XIII (FXIIIa) is caged with a photodeprotectable group, which is then immobilized to the bulk of a cell compatible hydrogel. With the use of focused light the substrate can be deprotected and used to immobilize patterned bioactive signals. This approach offers an innovative strategy to immobilize delicate bioactive signals, such as growth factors, without loss of activity and enables In situ cell manipulation of encapsulated cells. PMID:24399784

  7. Aneuploidy detection for chromosomes 1, X and Y by fluorescence in situ hybridization in human sperm from oligoasthenoteratozoospermic patients

    SciTech Connect

    Pang, M.G.; Zackowski, J.L.; Acosta, A.A.

    1994-09-01

    Oligoasthenoteratozoospermic males (n=15) were investigated for infertility as compared with proven fertile donors. The oligoasthenoteratozoospermic population showed a mean sperm concentration of 9.7 x 10{sup 6}/ml (Range 4.2-19.7), mean motility of 38.5% (Range 10.6-76.8) and morphology (measured by the percentage of normal forms evaluated by strict criteria) with a mean of 3.49% (Range 1.5-5.0). Fluorescence in situ hybridization (FISH) using satellite DNA probes specific for chromosomes 1 (puc 1.77), X (alpha satellite), and Y (satellite-III at Yqh) was performed on human interphase sperm nuclei. DNA probes were either directly labelled with rhodamine-dUTP, FITC-dUTP, or biotinylated by nick translation. Hybridization and signal detection were done by routine laboratory protocols. Microscopic analysis was performed using a cooled CCD camera attached to an epi-fluorescent microscope. After hybridization, fertile donors yielded a frequency of 0.96% (n=12) nullisomic, 98.5% (n=1231) monosomic and 0.96% (n=12) disomic for chromosome 1, whereas oligoasthenoteratozoospermic males yielded a frequency of 16% (n=600) nullisomic, 74.5% (n=2792) monosomic and 9.9% (n=370) disomic. In addition, fertile donors yielded a frequency of 45.7% (n=633) monosomic and 0.7% (n=11) disomic for chromosome X, whereas oligoasthenoteratozoospermic males yielded a frequency of 38.7% (n=760) monosomic and 0.8% (n=13) disomic. Chromosome Y frequencies for fertile donors showed 44.6% (n=614) monosomic and 0.6% (n=2) disomic, whereas oligoasthenoteratozoospermic males yielded a frequency of 33.2% (n=701) monosomic and 0.8% (n=15) disomic. This suggests that the frequency of nullisomy for chromosome 1 is significantly higher (p<0.001) in sperm from oligoasthenoteratozoospermic makes versus sperm from our fertile donors. We conclude that FISH is a powerful tool to determine the frequency of aneuploidy in sperm from oligoasthenoteratozoospermic patients.

  8. Directly incorporating fluorochromes into DNA probes by PCR increases the efficience of fluorescence in situ hybridization

    SciTech Connect

    Dittmer, Joy

    1996-05-01

    The object of this study was to produce a directly labeled whole chromosome probe in a Degenerative Oligonucleotide Primed-Polymerase Chain Reaction (DOP-PCR) that will identify chromosome breaks, deletions, inversions and translocations caused by radiation damage. In this study we amplified flow sorted chromosome 19 using DOP-PCR. The product was then subjected to a secondary DOP PCR amplification, After the secondary amplification the DOP-PCR product was directly labeled in a tertiary PCR reaction with rhodamine conjugated with dUTP (FluoroRed) to produce a DNA fluorescent probe. The probe was then hybridized to human metaphase lymphocytes on slides, washed and counterstained with 4{prime},6-diamino-2-phenylindole (DAPI). The signal of the FluoroRed probe was then compared to a signal of a probe labeled with biotin and stained with avidin fluorescein isothio cynate (FITC) and anti-avidin FITC. The results show that the probe labeled with FluoroRed gave signals as bright as the probe with biotin labeling. The FluoroRed probe had less noise than the biotin labeled probe. Therefore, a directly labeled probe has been successfully produced in a DOP-PCR reaction. In future a probe labeled with FluoroRed will be produced instead of a probe labeled with biotin to increase efficiency.

  9. Microbial populations identified by fluorescence in situ hybridization in a constructed wetland treating acid coal mine drainage

    SciTech Connect

    Nicomrat, D.; Dick, W.A.; Tuovinen, O.H.

    2006-07-15

    Microorganisms are an integral part of the biogeochemical processes in wetlands, yet microbial communities in sediments within constructed wetlands receiving acid mine drainage (AMD) are only poorly understood. The purpose of this study was to characterize the microbial diversity and abundance in a wetland receiving AMD using fluorescence in situ hybridization (FISH) analysis. Seasonal samples of oxic surface sediments, comprised of Fe(III) precipitates, were collected from two treatment cells of the constructed wetland system. The pH of the bulk samples ranged between pH 2.1 and 3.9. Viable counts of acidophilic Fe and S oxidizers and heterotrophs were determined with a most probable number (MPN) method. The MPN counts were only a fraction of the corresponding FISH counts. The sediment samples contained microorganisms in the Bacteria (including the subgroups of acidophilic Fe- and S-oxidizing bacteria and Acidiphilium spp.) and Eukarya domains. Archaea were present in the sediment surface samples at < 0.01% of the total microbial community. The most numerous bacterial species in this wetland system was Acidithiobacillus ferrooxidans, comprising up to 37% of the bacterial population. Acidithiobacillus thiooxidans was also abundant.

  10. [Rapid enrichment and cultivation of denitrifying phosphate-removal bacteria and its identification by fluorescence in situ hybridization technology].

    PubMed

    Liu, Li; Tang, Bing; Huang, Shao-Song; Fu, Feng-Lian; Zhang, Qi-Qin; Li, Jian-Bin; Luo, Jian-Zhong

    2013-07-01

    The present work focused on a rapid enrichment and cultivation of denitrifying phosphate-removal bacteria (DPB) in a membrane bio-reactor(MBR) by using A2/O anaerobic sludge from a wastewater treatment plant as seed, as well as providing an identification method. In the experiments, sodium acetate was used as the carbon source and a certain amount of nitrate was added to the MBR in the anoxic stage. Results showed that, with the efficient trap of the hollow-fiber membrane module, the proportion of DPB in all the phosphate-accumulating organisms (PAOs) increased from 24% to 93% within 35 days after two-stage's cultivation including anaerobic/aerobic and anaerobic/anoxic, during which the removal efficiency of nitrogen and phosphorus reached more than 90%. The activated sludge was identified by combining a regular method and the fluorescence in situ hybridization (FISH) technique, which demonstrated that Pseudomonas sp. and Rhodocyclus sp. were the dominant bacteria in the used bioreactor.

  11. Comparative cytogenetics of six Indo-Pacific moray eels (Anguilliformes: Muraenidae) by chromosomal banding and fluorescence in situ hybridization.

    PubMed

    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.

  12. Validation of break-apart and fusion MYC probes using a digital fluorescence in situ hybridization capture and imaging system

    PubMed Central

    Liew, Michael; Rowe, Leslie; Clement, Parker W.; Miles, Rodney R.; Salama, Mohamed E.

    2016-01-01

    Introduction: Detection of MYC translocations using fluorescence in situ hybridization (FISH) is important in the evaluation of lymphomas, in particular, Burkitt lymphoma and diffuse large B-cell lymphoma. Our aim was to validate a digital FISH capture and imaging system for the detection of MYC 8q24 translocations using LSI-MYC (a break-apart probe) and MYC 8;14 translocation using IGH-MYC (a fusion probe). Materials and Methods: LSI-MYC probe was evaluated using tissue sections from 35 patients. IGH-MYC probe was evaluated using tissue sections from forty patients. Sections were processed for FISH and analyzed using traditional methods. FISH slides were then analyzed using the GenASIs capture and analysis system. Results: Results for LSI-MYC had a high degree of correlation between traditional method of FISH analysis and digital FISH analysis. Results for IGH-MYC had a 100% concordance between traditional method of FISH analysis and digital FISH analysis. Conclusion: Annotated whole slide images of H and E and FISH sections can be digitally aligned, so that areas of tumor within a section can be matched and evaluated with a greater degree of accuracy. Images can be archived permanently, providing a means for examining the results retrospectively. Digital FISH imaging of the MYC translocations provides a better diagnostic tool compared to traditional methods for evaluating lymphomas. PMID:27217970

  13. Pituitary adenylate cyclase-activating peptide in the rat central nervous system: an immunohistochemical and in situ hybridization study.

    PubMed

    Hannibal, Jens

    2002-11-25

    In the present study the localization of pituitary adenylate cyclase-activating peptide (PACAP)-expressing cell bodies and PACAP projections were mapped in the adult rat brain and spinal cord by using immunohistochemistry and in situ hybridization histochemistry. A widespread occurrence of PACAP-containing cell bodies was found, with the greatest accumulation in several hypothalamic nuclei and in several brainstem nuclei, especially the habenular nuclei, the pontine nucleus, the lateral parabrachial nucleus (LPB), and the vagal complex. PACAP was also present in cell bodies in the olfactory areas, in neocortical areas, in the hippocampus, in the vestibulo- and cochlear nuclei, in cell bodies of the intermediolateral cell column of the spinal cord and in Purkinje cells of the cerebellum, in the subfornical organ, and in the organum vasculosum of the lamina terminalis. An intense accumulation of PACAP-immunoreactive (-IR) nerve fibers was observed throughout the hypothalamus, in the amydaloid and extended amygdaloid complex, in the anterior and paraventricular thalamic nuclei, in the intergeniculate leaflet, in the pretectum, and in several brainstem nuclei, such as the parabrachial nucleus, the sensory trigeminal nucleus, and the nucleus of the solitary tract. PACAP-IR nerve fibers were also found in the area postrema, the posterior pituitary and the choroid plexus, and the dorsal and ventral horn of the spinal cord. The widespread distribution of PACAP in the brain and spinal cord suggests that PACAP is involved in the control of many autonomic and sensory functions as well as higher cortical processes.

  14. Fully Automated RNAscope In Situ Hybridization Assays for Formalin-Fixed Paraffin-Embedded Cells and Tissues.

    PubMed

    Anderson, Courtney M; Zhang, Bingqing; Miller, Melanie; Butko, Emerald; Wu, Xingyong; Laver, Thomas; Kernag, Casey; Kim, Jeffrey; Luo, Yuling; Lamparski, Henry; Park, Emily; Su, Nan; Ma, Xiao-Jun

    2016-10-01

    Biomarkers such as DNA, RNA, and protein are powerful tools in clinical diagnostics and therapeutic development for many diseases. Identifying RNA expression at the single cell level within the morphological context by RNA in situ hybridization provides a great deal of information on gene expression changes over conventional techniques that analyze bulk tissue, yet widespread use of this technique in the clinical setting has been hampered by the dearth of automated RNA ISH assays. Here we present an automated version of the RNA ISH technology RNAscope that is adaptable to multiple automation platforms. The automated RNAscope assay yields a high signal-to-noise ratio with little to no background staining and results comparable to the manual assay. In addition, the automated duplex RNAscope assay was able to detect two biomarkers simultaneously. Lastly, assay consistency and reproducibility were confirmed by quantification of TATA-box binding protein (TBP) mRNA signals across multiple lots and multiple experiments. Taken together, the data presented in this study demonstrate that the automated RNAscope technology is a high performance RNA ISH assay with broad applicability in biomarker research and diagnostic assay development. J. Cell. Biochem. 117: 2201-2208, 2016. © 2016 Wiley Periodicals, Inc.

  15. Cryptic Subtelomeric Rearrangements and X Chromosome Mosaicism: A Study of 565 Apparently Normal Individuals with Fluorescent In Situ Hybridization

    PubMed Central

    Wise, Jasen L.; Crout, Richard J.; McNeil, Daniel W.; Weyant, Robert J.; Marazita, Mary L.; Wenger, Sharon L.

    2009-01-01

    Five percent of patients with unexplained mental retardation have been attributed to cryptic unbalanced subtelomeric rearrangements. Half of these affected individuals have inherited the rearrangement from a parent who is a carrier for a balanced translocation. However, the frequency of carriers for cryptic balanced translocations is unknown. To determine this frequency, 565 phenotypically normal unrelated individuals were examined for balanced subtelomeric rearrangements using Fluorescent In Situ hybridization (FISH) probes for all subtelomere regions. While no balanced subtelomeric rearrangements were identified, three females in this study were determined to be mosaic for the X chromosome. Mosaicism for XXX cell lines were observed in the lymphocyte cultures of 3 in 379 women (0.8%), which is a higher frequency than the 1 in 1000 (0.1%) reported for sex chromosome aneuploidies. Our findings suggest that numerical abnormalities of the X chromosome are more common in females than previously reported. Based on a review of the literature, the incidence of cryptic translocation carriers is estimated to be approximately 1/8,000, more than ten-fold higher than the frequency of visible reciprocal translocations. PMID:19516895

  16. Interphase fluorescence in situ hybridization and reverse transcription polymerase chain reaction as a diagnostic aid for synovial sarcoma.

    PubMed Central

    Shipley, J.; Crew, J.; Birdsall, S.; Gill, S.; Clark, J.; Fisher, C.; Kelsey, A.; Nojima, T.; Sonobe, H.; Cooper, C.; Gusterson, B.

    1996-01-01

    Identification of the t(X;18)(p11.2;q11.2) that is associated with a high proportion of synovial sarcoma can be a useful diagnostic aid. The translocation results in fusion of the SYT gene on chromosome 18 to either the SSX1 or the SSX2 gene, two homologous genes within Xp11.2. Two-color interphase fluorescence in situ hybridization and reverse transcription polymerase chain reaction were assessed as approaches to identify the rearrangement in well characterized cases. The presence of the translocation, and the specific chromosome X gene disrupted, were inferred from the configuration of signals from chromosome-specific centromere probes, paints, and markers flanking each gene in preparations of interphase nuclei. Rearrangement was found in two cell lines and eight of nine tumor samples, including analysis of five touch imprints. This was consistent with cytogenetic data in four cases and reverse transcription polymerase chain reaction analysis using primers known to amplify both SYT-SSX1 and SYT-SSX2 transcripts. The transcripts were distinguished by restriction with LspI and SmaI. Contrary to previous suggestions, there was no obvious correlation between histological subtype and involvement of the SSX1 or SSX2 gene. These approaches could also be applied to the identification of tumor-free margins and metastatic disease. Images Figure 1 Figure 3 PMID:8579118

  17. Rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH) from colony and blood culture material

    PubMed Central

    Essig, A.; Hagen, R. M.; Riecker, M.; Jerke, K.; Ellison, D.; Poppert, S.

    2011-01-01

    Multi-drug-resistant strains of the Acinetobacter baumannii complex cause nosocomial infections. Rapid identification of Acinetobacter spp. is desirable in order to facilitate therapeutic or hygiene decisions. We evaluated a newly designed DNA probe that can be used under standard conditions in both a microwave oven and a slide chamber for the rapid identification of Acinetobacter spp. by fluorescence in situ hybridization (FISH). Using FISH, the new probe correctly identified 81/81 Acinetobacter spp. isolates and excluded 109/109 tested non-target organisms from agar culture. Furthermore, the new probe correctly identified 7/7 Acinetobacter spp. in 214 blood cultures determined to contain Gram-negative bacteria by Gram staining. Using either the microwave oven or slide chamber technique, the new probe was able to identify Acinetobacter spp. in 100% of the samples tested. FISH used in conjunction with our newly designed probe provides an easy, cheap, precise, and rapid method for the preliminary identification of Acinetobacter spp., especially in laboratories where more sophisticated methods like matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) are not available. PMID:24516735

  18. Fluorescent in situ hybridization (FISH) and high resolution karyotype analysis reveal a novel inversion duplication of 10q

    SciTech Connect

    Czarnecki, P.; Dyke, D.L. Van; Dowling, P.K.

    1994-09-01

    A white male born with dysmorphic features, including upslanting palpebral fissures, bilateral simian creases, posteriorly rotated ears, bitemporal narrowing, frontal bossing, camptodactyly and head circumference and weight less than the 5th percentile was found to have a de novo add(10)(q26.1). High resolution karyotype analysis revealed a novel chromosomal abnormality: 46,XY,inv dup(10)(q26.3-q25.1). Fluorescent in situ hybridization using a chromosome 10-specific painting probe (Oncor, Inc.) confirmed that the extra material was derived from chromosome 10. Duplication of 10q24 or 10q25 is associated with characteristic craniofacial malformations, minor malformations of the hands and feet, major malformations of the heart, skeleton, and kidneys and severe mental retardation. Our patient, currently 7 months old, has many of the skeletal and craniofacial manifestations of other patients, but is developmentally normal at this early age. This is the first FISH confirmation of a 10q duplication and demonstrates the utility of this technology in addition to karyotype analysis. Molecular studies to determine the parental origin and extent of the duplication are in progress, since the apparent lack of developmental delay was unexpected. Identification of the origin of duplicated material will help assist in genetic counseling by further delineating new genetic syndromes.

  19. Gene expression analysis in sections and tissue microarrays of archival tissues by mRNA in situ hybridization.

    PubMed

    Henke, R T; Maitra, A; Paik, S; Wellstein, A

    2005-01-01

    Altered expression of genes in diseased tissues can prognosticate a distinct natural progression of the disease as well as predict sensitivity or resistance to particular therapies. Archival tissues from patients with a known medical history and treatments are an invaluable resource to validate the utility of candidate genes for prognosis and prediction of therapy outcomes. However, stored tissues with associated long-term follow-up information typically are formalin-fixed, paraffin-embedded specimen and this can severely restrict the methods applicable for gene expression analysis. We report here on the utility of tissue microarrays (TMAs) that use valuable tissues sparingly and provide a platform for simultaneous analysis of gene expression in several hundred samples. In particular, we describe a stable method applicable to mRNA expression screening in such archival tissues. TMAs are constructed from sections of small drill cores, taken from tissue blocks of archival tissues and multiple samples can thus be arranged on a single microscope slide. We used mRNA in situ hybridization (ISH) on >500 full sections and >100 TMAs for >10 different cDNAs that yielded >10,000 data points. We provide detailed experimental protocols that can be implemented without major hurdles in a molecular pathology laboratory and discuss quantitative analysis and the advantages and limitations of ISH. We conclude that gene expression analysis in archival tissues by ISH is reliable and particularly useful when no protein detection methods are available for a candidate gene.

  20. Monitoring of chimerism using fluorescence in situ hybridization in a child with severe combined immune deficiency following bone marrow transplant

    SciTech Connect

    Wenger, S.L.; Chen, X.O.; Katz, A.J. |

    1994-09-01

    A boy with severe combined immunodeficiency received a bone marrow transplant from his sister when he was approximately 3 years of age. His peripheral blood karyotype at age 3 and 4 years was 46,XX (20 cells analyzed). Because of a decline in antibody production at 19 years of age, the patient`s peripheral blood was analyzed again for suspected chimerism. His karyotype in phytohemagglutinin (PHA)-stimulated culture was 46,XX in 49 cells and 46,XY in one cell. Both metaphase and interphase cells were examined for sex chromosome constitution using X and Y dual-color alpha-satellite probes for fluorescence in situ hybridization (FISH). FISH results for metaphase cells showed 1/50 XY cells, but 38% of interphase cells showed the presence of both X and Y centromere. Pokeweed mitogen (PWM)-stimulated cultures grew poorly and were therefore analyzed using FISH only: 81% of interphase cells were 46,XX. The discrepancy between metaphase and interphase in the PHA-stimulated cultures most likely represents a failure of this boy`s own XY T-cells to be stimulated.

  1. The Dohner fluorescence in situ hybridization prognostic classification of chronic lymphocytic leukaemia (CLL): the CLL Research Consortium experience.

    PubMed

    Van Dyke, Daniel L; Werner, Lillian; Rassenti, Laura Z; Neuberg, Donna; Ghia, Emanuella; Heerema, Nyla A; Dal Cin, Paola; Dell Aquila, Marie; Sreekantaiah, Chandrika; Greaves, Andrew W; Kipps, Thomas J; Kay, Neil E

    2016-04-01

    This study revisited the Dohner prognostic hierarchy in a cohort of 1585 well-documented patients with chronic lymphocytic leukaemia. The duration of both time to first treatment (TTFT) and overall survival (OS) were significantly longer than observed previously, and this is at least partly due to improved therapeutic options. Deletion 13q remains the most favourable prognostic group with median TTFT and OS from fluorescence in situ hybridization (FISH) testing of 72 months and >12 years, respectively. Deletion 11q had the poorest median TTFT (22 months) and 17p deletion the poorest median OS (5 years). The percentages of abnormal nuclei were significantly associated with differential TTFT for the trisomy 12, 13q and 17p deletion cohorts but not for the 11q deletion cohort. From the date of the first FISH study, patients with >85% 13q deletion nuclei had a notably shorter TTFT (24 months). Patients with ≤20% 17p deletion nuclei had longer median TTFT and OS from the date of the first FISH study (44 months and 11 years), and were more likely to be IGHV mutated.

  2. Targeting topoisomerase IIa in endometrial adenocarcinoma: a combined chromogenic in situ hybridization and immunohistochemistry study based on tissue microarrays.

    PubMed

    Tsiambas, E; Alexopoulou, D; Lambropoulou, S; Gerontopoulos, K; Karakitsos, P; Karameris, A

    2006-01-01

    Topoisomerase IIa is a nucleic enzyme that affects the topological structure of DNA and also is a target for chemotherapy (ie, anthracyclines). In this study, we coevaluated its protein expression with chromosome 17 and gene status. Using tissue microarrays, 40 cases of sporadic, primary endometrial adenocarcinomas, 5 cases of atypical hyperplasia, and 5 cases of benign hyperplasia were obtained and reembedded into two paraffin blocks with a core diameter of 1 mm. Immunohistochemistry combined with chromogenic in situ hybridization was performed in 2 and 5 microm sections, respectively. Finally using a semiautomated Image Analysis System, we evaluated the levels of Nuclear labeling index of topoisomerase IIa expression. Statistical analysis was performed by SPSS version 11.0 software. The results indicate that chromosome 17 instability (aneuploidy in 7/40 cases) and Topo IIa gene deregulation (amplification in 3/40 and deletion in 1/40 cases) are significant genetic events correlated with biologic behavior in endometrial adenocarcinoma. Because protein overexpression was observed in a significant proportion of the tumors (18/40), detection of the specific gene deregulation mechanism is a crucial process for application of targeted chemotherapies, which are characterized by different levels of cardiotoxicity and other serious effects.

  3. Feasibility of using fluorescence in situ hybridization (FISH) to detect early gene changes in sputum cells from uranium miners

    SciTech Connect

    Neft, R.E.; Rogers, J.L.; Belinsky, S.A.

    1995-12-01

    Epidemiological studies have shown that combined exposure to radon progeny and tobacco smoke produce a greater than additive or synergistic increase in lung cancer risk. Lung cancer results from multiple genetic changes over a long period of time. An early change that occurs in lung cancer is trisomy 7 which is found in 50% of non-small cell lung cancer and in the far margins of resected lung tumors. The 80% mortality associated with lung cancer is in part related to the high proportion of patients who present with an advanced, unresectable tumor. Therefore, early detection of patients at risk for tumor development is critical to improve treatment of this disease. Currently, it is difficult to detect lung cancer early while it is still amendable by surgery. Saccomanno, G. has shown that premalignant cytologic changes in sputum cells collected from uranium miners can be detected by a skilled, highly trained cytopathologist. A more objective alternative for identifying premalignant cells in sputum may be to determine whether an early genetic change such as trisomy 7 is present in these cells. Fluorescence in situ hybridization (FISH) can be used to identify cells with trisomy 7. The results of this investigation indicate that FISH may prove to be an accurate, efficient method to test at-risk individuals for genetic alterations in bronchial epithelial cells from sputum.

  4. Regulation of tumor necrosis factor gene expression in colorectal adenocarcinoma: In vivo analysis by in situ hybridization

    SciTech Connect

    Beissert, S.; Bergholz, M.; Waase, I.; Lepsien, G.; Schauer, A.; Pfizenmaier, K.; Kroenke, M. )

    1989-07-01

    Tumor necrosis factor (TNF) produced by macrophages is though to contribute to the host defense against development of cancer. However, since tumor cells themselves are able to produce TNF, it is conceivable that TNF may also play an adverse pathological role in carcinogenesis. To better understand the functional significance of TNF in neoplastic disease, they authors have determined the cellular source of TNF activity produced in 10 patients with colorectal cancer. Northern blot analysis of RNAs extracted from fresh biopsy specimens revealed detectable TNF mRNA levels in all instances. By using in situ hybridization of frozen sections, scattered cells expressing TNF mRNA could be discerned. Based on morphological criteria, these TNF-positive cells most likely belong to the macrophage lineage. Macrophages in normal tissue surrounding the tumor did not express TNF mRNA, suggesting that macrophage activation occurs locally at the site of neoplastic transformation. Immunohistochemistry using anti-TNF monoclonal antibodies revealed that less than 1% of tumor-infiltrating macrophages synthesize TNF protein. Thus they present evidence that in colorectal cancer only a small proportion of tumor-infiltrating macrophages produces TNF, indicating that the microenvironment of the tumor provides adequate, yet suboptimal, conditions for macrophage activation.

  5. Detection by fluorescence in situ hybridization of microdeletions at 1p36 in lymphomas, unidentified on cytogenetic analysis.

    PubMed

    Rajgopal, Achuthan; Carr, Ian M; Leek, Jack P; Hodge, Donald; Bell, Sandra M; Roberts, Paul; Horgan, Kieran; Bonthron, David T; Selby, Peter J; Markham, Alexander F; MacLennan, Kenneth A

    2003-04-01

    The chromosomal band 1p36 exhibits frequent loss of heterozygosity in a variety of human malignancies, suggesting the presence of an as yet unidentified tumor suppressor gene. The faint terminal subbands often make cytogenetic analysis of 1p36 particularly difficult. Small deletions at this locus may therefore escape detection on analysis by conventional cytogenetics, a hypothesis that we have explored using fluorescence in situ hybridization (FISH) in malignant lymphoma. The study cohort consisted of 20 cases of lymphoma of various subtypes without any 1p abnormality on G-banded karyotyping. FISH was performed using a human chromosome 1 paint and a bacterial artificial chromosome probe RP4-755G5 localizing to 1p36.33, the most telomeric subband of 1p36. Tumors demonstrating 1p36.33 deletions were additionally analyzed by FISH using a second probe from the proximal 1p36.1 subband, to further define the breakpoint. Eight cases of follicular lymphoma (FL), 5 diffuse large B-cell lymphomas (DLBCL), 2 Hodgkin disease, 2 B-cell small lymphocytic lymphomas, 2 T-cell lymphomas, and 1 marginal zone lymphoma were analyzed. FISH identified deletions at 1p36.33 in 5 of the 20 cases: 3 DLBCL and 2 FL. FISH is considerably more sensitive for identifying lymphoma genetic alterations than conventional cytogenetics. Deletion of the distal part of the 1p36 may be a much more common aberration than previously recognized in lymphoma.

  6. Subcellular distribution of small interfering RNA: directed delivery through RNA polymerase III expression cassettes and localization by in situ hybridization.

    PubMed

    Paul, Cynthia P

    2005-01-01

    Reduction in the expression of specific genes through small interfering RNAs (siRNAs) is dependent on the colocalization of siRNAs with other components of the RNA interference (RNAi) pathways within the cell. The expression of siRNAs within cells from cassettes that are derived from genes transcribed by RNA polymerase III (pol III) and provide for selective subcellular distribution of their products can be used to direct siRNAs to the cellular pathways. Expression from the human U6 promoter, resulting in siRNA accumulation in the nucleus, is effective in reducing gene expression, whereas cytoplasmic and nucleolar localization of the siRNA when expressed from the 5S or 7 SL promoters is not effective. The distribution of siRNA within the cell is determined by fluorescence in situ hybridization. Although the long uninterrupted duplex of siRNA makes it difficult to detect with DNA oligonucleotide probes, labeled oligonucleotide probes with 2'-O-methyl RNA backbones provide the stability needed for a strong signal. These methods contribute to studies of the interconnected cellular RNAi pathways and are useful in adapting RNAi as a tool to determine gene function and develop RNA-based therapeutics. PMID:15644179

  7. Localization of cystic fibrosis transmembrane conductance regulator mRNA in the human gastrointestinal tract by in situ hybridization.

    PubMed Central

    Strong, T V; Boehm, K; Collins, F S

    1994-01-01

    We have used in situ hybridization to localize expression of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in the human gastrointestinal tract and associated organs. The stomach exhibits a low level of CFTR expression throughout gastric mucosa. In the small intestine, expression is relatively high in the mucosal epithelium, with a decreasing gradient of expression along the crypt to tip axis. The cells of the Brunner's glands express high levels of CFTR mRNA. In addition, there is a small subpopulation of highly positive cells scattered along the epithelium in the duodenum and jejunum, but not in the ileum. These cells do not represent endocrine cells, as determined by lack of colocalization with an endocrine-specific marker. The distribution of CFTR mRNA in the colon is similar to the small intestine, with highest level of expression in the epithelial cells at the base of the crypts. In the pancreas, CFTR is expressed at high levels in the small, intercalated ducts and at lower levels in the interlobular ducts. CFTR transcripts are expressed at uniformly high levels in the epithelium of the gallbladder. Throughout the gastrointestinal tract, CFTR expression is increased in mucosal epithelial cells that are near lymph nodules. Images PMID:7506713

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

    SciTech Connect

    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.

  9. Hybrid Electrodes by In-Situ Integration of Graphene and Carbon-Nanotubes in Polypyrrole for Supercapacitors

    NASA Astrophysics Data System (ADS)

    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.

  10. Design and validation of an oligonucleotide probe for detection of protozoa from the order Trichomonadida using chromogenic in situ hybridization

    PubMed Central

    Mostegl, Meike Marissa; Richter, Barbara; Nedorost, Nora; Maderner, Anton; Dinhopl, Nora; Kulda, Jaroslav; Liebhart, Dieter; Hess, Michael; Weissenböck, Herbert

    2010-01-01

    Infections with protozoal parasites of the order Trichomonadida are often observed in veterinary medicine. Based on the trichomonad species involved these infections are either asymptomatic or can lead to sometimes serious disease. To further study protozoal agents of the order Trichomonadida the establishment of a method to detect trichomonads directly in the tissue, allowing parasite-lesion correlation, is necessary. Here we describe the design and evaluation of an oligonucleotide probe for chromogenic in situ hybridization, theoretically allowing detection of all hitherto known members of the order Trichomonadida. The probe was designed on a region of the 18S ribosomal RNA gene homologue for all representatives of the order Trichomonadida available in the GenBank. Functionality of the probe was proven using protozoal cultures containing different trichomonads (Monocercomonas colubrorum, Hypotrichomonas acosta, Pentatrichomonas hominis, Trichomitus batrachorum, Trichomonas gallinae, Tetratrichomonas gallinarum, Tritrichomonas foetus, and Tritrichomonas augusta). Furthermore, three different tissue sections containing either Trichomonas gallinae, Tritrichomonas foetus or Histomonas meleagridis were tested positive. Additionally, to rule out cross reactivity of the probe a large number of different pathogenic protozoal agents, fungi, bacteria and viruses were tested and gave negative results. The probe presented here can be considered an important tool for diagnosis of all to date described relevant protozoal parasites of the order Trichomonadida in tissue samples. PMID:20395049

  11. Paternal-age effects on sperm aneuploidy investigated in mice and humans by three-chromosome fluorescence in situ hybridization

    SciTech Connect

    Wyrobek, A.J.; Lowe, X.; Holland, N.T.

    1994-09-01

    We conducted a cross-species comparison of the effects of paternal age on sperm aneuploidy in mice and humans. A new murine assay was developed to detect sperm hyperhaploidy and polyploidy for chromosomes X, Y, and 8 using fluorescence in situ hybridization with chromosome-specific DNA probes, to serve as a direct corollate to the three-chromosome method developed early for human sperm. Sperm aneuploidy was evaluated in eight male B6C3F1 male mice (aged 22.5-30.5 mo) and compared to young controls (2.4 mo). The aged group showed significant ({approximately}2.0-fold) increases in hyperhaploidies involving chromosomes X, Y and 8, with the greatest effects seen in the oldest animals. Sperm aneuploidy was also evaluated in two groups of healthy men who differed in mean age [46.8{plus_minus}3.1 (n=4) vs. 28.5{plus_minus}5.0 (n=10) yrs], using the three-chromosome method. The older group showed a statistically significant increase in hyperhaploid sperm for both sex chromosomes. Additional controlled human studies are planned. Taken together, the murine and human data are consistent with a positive effect of paternal age on sperm aneuploidy. In both species, the strongest age effect was observed for hyperhaploidies of chromosome Y. Future studies are needed to investigate the shape of the age-effect curve and to evaluate chromosomal differences, especially for humans in their late reproductive years.

  12. Hybrid Electrodes by In-Situ Integration of Graphene and Carbon-Nanotubes in Polypyrrole for Supercapacitors

    PubMed Central

    Aphale, Ashish; Maisuria, Krushangi; Mahapatra, Manoj K.; Santiago, Angela; Singh, Prabhakar; Patra, Prabir

    2015-01-01

    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. PMID:26395922

  13. Detection of Epstein-Barr virus in children and adolescents with Burkitt's lymphoma by in situ hybridization using tissue microarrays.

    PubMed

    Pizza, Maria; Bruniera, Paula; Luporini, Silvia Maria; Marcelino da Silva, Helena Reis; Borsato, Maria Luisa; de Castro, Helaine Cristina; Soares, Fernando Augusto; Paes, Roberto Antoônio Pinto

    2008-04-01

    In this retrospective study, we evaluated 53 patients diagnosed with Burkitt's lymphoma (BL). Patients were admitted to the Pediatric Department of Santa Casa de São Paulo, Brazil from August 1988 to September 2006. The male gender was found more frequently in the proportion of three males to one female. At the time of the diagnosis, the mean age was 6 years. The most frequent clinical presentation was abdominal (extra nodal) in 42 (79.2%) cases. The patients were treated with chemotherapy using two different treatment methods, 30 cases until September 1994 with BGLTI -87 and the other 23 until September of 2006 with BGLTI -96. According to Murphy's classification, 90.2% of the patients were diagnosed as stages III and VI showing an advanced disease at time of diagnosis. Using Tissue Microarrays (TMA); we searched for the expression of the Epstein-Barr virus (EBV) RNA in 50 patients. The presence of EBV using in situ hybridization was found in 33/50 (66%) and there was no association between the presence of the virus in the tumor cells or patient age, as well as the survival rate. There was 74.5% global survival rate until September, 2005 of 12 years and 8 months. The disease free survival rate was 86.5%. The frequency of the EBV association with this neoplasia in Brazil is intermediate between the endemic and sporadic forms of disease.

  14. A novel fluorescence detection method for in situ hybridization, based on the alkaline phosphatase-fast red reaction.

    PubMed

    Speel, E J; Schutte, B; Wiegant, J; Ramaekers, F C; Hopman, A H

    1992-09-01

    We have used naphthol-ASMX-phosphate and Fast Red TR in combination with alkaline phosphatase (APase) to produce fluorescent precipitated reaction products in a non-radioactive in situ hybridization (ISH) method. To obtain optimal and discrete localization of the strongly red fluorescent ISH signals, the enzyme precipitation procedure was optimized. The optimal reaction time and the concentrations of substrate and capture agent were determined. Furthermore, polyvinyl alcohol (PVA) was used to increase the viscosity of the reaction mixture and thus to reduce diffusion of the reaction product. Our results show that the APase-Fast Red detection method has at least the same sensitivity as currently observed in other immunofluorescent detection systems. A single copy DNA sequence of 15.8 KB could be localized with high efficiency in metaphase spreads and in interphase nuclei. Double labeling procedures, in which the FITC- and azo-dye fluorescence are combined, are also feasible. The red fluorescent ISH signals showed hardly any fading as compared with FITC fluorescence on exposure to either light from the mercury-arc lamp or laser light. Therefore, these red fluorescent signals with a virtually permanent character allow a better analysis and three-dimensional localization of such cytochemically detected genomic fractions by means of confocal scanning laser microscopy as compared with the use of FITC, TRITC, or Texas Red as label. PMID:1506667

  15. C-Banding/DAPI and in situ hybridization reflect karyotype structure and sex chromosome differentiation in Humulus japonicus Siebold & Zucc.

    PubMed

    Grabowska-Joachimiak, A; Mosiolek, M; Lech, A; Góralski, G

    2011-01-01

    Japanese hop (Humulus japonicus Siebold & Zucc.) was karyotyped by chromosome measurements, fluorescence in situ hybridization with rDNA and telomeric probes, and C-banding/DAPI. The karyotype of this species consists of sex chromosomes (XX in female and XY1Y2 in male plants) and 14 autosomes difficult to distinguish by morphology. The chromosome complement also shows a rather monotonous terminal distribution of telomeric repeats, with the exception of a pair of autosomes possessing an additional cluster of telomeric sequences located within the shorter arm. Using C-banding/DAPI staining and 5S and 45S rDNA probes we constructed a fluorescent karyotype that can be used to distinguish all autosome pairs of this species except for the 2 largest autosome pairs, lacking rDNA signals and having similar size and DAPI-banding patterns. Sex chromosomes of H. japonicus display a unique banding pattern and different DAPI fluorescence intensity. The X chromosome possesses only one brightly stained AT-rich terminal segment, the Y1 has 2 such segments, and the Y2 is completely devoid of DAPI signal. After C-banding/DAPI, both Y chromosomes can be easily distinguished from the rest of the chromosome complement by the increased fluorescence of their arms. We discuss the utility of these methods for studying karyotype and sex chromosome evolution in hops. PMID:21079383

  16. Comparative cytogenetics of six Indo-Pacific moray eels (Anguilliformes: Muraenidae) by chromosomal banding and fluorescence in situ hybridization.

    PubMed

    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. PMID:26242690

  17. Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH).

    PubMed

    Malic, Sladjana; Hill, Katja E; Hayes, Anthony; Percival, Steven L; Thomas, David W; Williams, David W

    2009-08-01

    Biofilms provide a reservoir of potentially infectious micro-organisms that are resistant to antimicrobial agents, and their importance in the failure of medical devices and chronic inflammatory conditions is increasingly being recognized. Particular research interest exists in the association of biofilms with wound infection and non-healing, i.e. chronic wounds. In this study, fluorescent in situ hybridization (FISH) was used in combination with confocal laser scanning microscopy (CLSM) to detect and characterize the spatial distribution of biofilm-forming bacteria which predominate within human chronic skin wounds (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sp. and Micrococcus sp.). In vitro biofilms were prepared using a constant-depth film fermenter and a reconstituted human epidermis model. In vivo biofilms were also studied using biopsy samples from non-infected chronic venous leg ulcers. The specificity of peptide nucleic acid (PNA) probes for the target organisms was confirmed using mixed preparations of planktonic bacteria and multiplex PNA probing. Identification and location of individual bacterial species within multi-species biofilms demonstrated that P. aeruginosa was predominant. CLSM revealed clustering of individual species within mixed-species biofilms. FISH analysis of archive chronic wound biopsy sections showed bacterial presence and allowed bacterial load to be determined. The application of this standardized procedure makes available an assay for identification of single- or multi-species bacterial populations in tissue biopsies. The technique provides a reliable tool to study bacterial biofilm formation and offers an approach to assess targeted biofilm disruption strategies in vivo. PMID:19477903

  18. Use of in situ hybridization for HPV in head and neck tumors: experience from a national reference laboratory.

    PubMed

    Witt, Benjamin L; Albertson, Daniel J; Coppin, Margaret G; Horrocks, Christian F; Post, Melissa; Gulbahce, H Evin

    2015-03-01

    The human papillomavirus (HPV) status of head and neck squamous cell carcinomas (SCCs) is a frequent request for Anatomic Pathology labs. However, prognostic value of HPV status is limited to identification of high risk HPV in oropharyngeal SCCs. The purpose of this study is to investigate the ordering practices of in situ hybridization (ISH) for HPV in head and neck tissues at our national reference laboratory. All testing orders for low risk, high risk, and combined low and high risk HPV-ISH tests requested at ARUP Laboratories between January 2010 and November 2013 had their results reviewed and were grouped by anatomic location of the tested tissue. The H&E and HPV-ISH slides from a sample of the most recent 123 tests were reviewed by two pathologists. A total of 1,128 HPV-ISH tests were ordered during the study period. Testing for combined low and high risk HPV was the most commonly ordered test. The positivity rate for high risk HPV was highest in oropharyngeal tissues. 49 of 123 reviewed cases had testing requested on non-malignant tissue, 11 of which were non-neoplastic. Unnecessary HPV-ISH ordering is prevalent in head and neck tissues. Dual testing for low and high risk HPV, frequent testing outside of the oropharynx, and testing non-neoplastic tissues appear to be common practices. PMID:24935815

  19. Complex structural rearrangement of chromosomes 13, 19 and 20 detected cytogenetically and by fluorescence in situ hybridization (FISH)

    SciTech Connect

    Al-Nassar, K.E.; Murthy, S.K.; Verghese, L.

    1994-09-01

    Complex chromosomal rearrangements (CCRs) are rare. To date, 72 CCRs have been reported. We report here a case of CCR in a 10 year old boy and his mother involving chromosomes 13, 19 and 20, detected by G-,C- and Ag-NOR banding and by fluorescence in situ hybridization (FISH) technique. Father and other sibs were found to be chromosomally normal. The patient presented with clinical features having obesity, micropenis, slow learning and IQ=70. Mother was clinically normal. Karyotype of the patient and mother showed apparently balanced chromosomal rearrangements involving chromosomes 13, 19 and 20. The karyotypes were interpreted as: 45,XY,-19,der(13),der(20),t(13;19)(13p11.2)::(19q13.2{r_arrow}19pter),t(19;20)(19q13.3{r_arrow}19qter::20qter) in the patient and 45,XX,-19,t(13;19),t(19;20) involving the same breakpoints in the mother. C-banding showed dicentric der(13). FISH using alpha-satellite DNA probes for 13/21 showed the presence of centromeric region of 13 in the der(13). Deletion of 13p11.2{r_arrow}pter was confirmed by negative Ag-NOR staining in der(13).

  20. Fluorescence "in situ" hybridization for the detection of biofilm in the middle ear and upper respiratory tract mucosa.

    PubMed

    Nistico, Laura; Gieseke, Armin; Stoodley, Paul; Hall-Stoodley, Luanne; Kerschner, Joseph E; Ehrlich, Garth D

    2009-01-01

    Most chronic bacterial infections are associated with biofilm formation wherein the bacteria attach to mucosal surfaces, wound tissue, or medical device surfaces in the human body via the formation of an extracellular matrix. Biofilms assume complex three-dimensional structures dependent on the species, the strain, and the prevailing environmental conditions and are composed of both the bacteria and the extracellular slime-like matrices, which surround the bacteria. Bacteria deep in the biofilm live under anaerobic conditions and must use alternatives to O(2) as a terminal electron acceptor. Thus, the metabolic rates of these deep bacteria are greatly reduced, which renders them extremely resistant to antibiotic treatment, and for reasons not clearly understood, it is often very difficult to culture biofilm bacteria using traditional microbiologic techniques. To directly identify and visualize biofilm bacteria in a species-specific manner, we developed a confocal laser scanning microscopy (CLSM)-based 16S rRNA fluorescence in situ hybridization (FISH) protocol, to find biofilm bacteria in middle ear and upper respiratory tract mucosa, which preserves the three-dimensional structure of the biofilm and avoids the use of traditional culture techniques.

  1. Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH).

    PubMed

    Malic, Sladjana; Hill, Katja E; Hayes, Anthony; Percival, Steven L; Thomas, David W; Williams, David W

    2009-08-01

    Biofilms provide a reservoir of potentially infectious micro-organisms that are resistant to antimicrobial agents, and their importance in the failure of medical devices and chronic inflammatory conditions is increasingly being recognized. Particular research interest exists in the association of biofilms with wound infection and non-healing, i.e. chronic wounds. In this study, fluorescent in situ hybridization (FISH) was used in combination with confocal laser scanning microscopy (CLSM) to detect and characterize the spatial distribution of biofilm-forming bacteria which predominate within human chronic skin wounds (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sp. and Micrococcus sp.). In vitro biofilms were prepared using a constant-depth film fermenter and a reconstituted human epidermis model. In vivo biofilms were also studied using biopsy samples from non-infected chronic venous leg ulcers. The specificity of peptide nucleic acid (PNA) probes for the target organisms was confirmed using mixed preparations of planktonic bacteria and multiplex PNA probing. Identification and location of individual bacterial species within multi-species biofilms demonstrated that P. aeruginosa was predominant. CLSM revealed clustering of individual species within mixed-species biofilms. FISH analysis of archive chronic wound biopsy sections showed bacterial presence and allowed bacterial load to be determined. The application of this standardized procedure makes available an assay for identification of single- or multi-species bacterial populations in tissue biopsies. The technique provides a reliable tool to study bacterial biofilm formation and offers an approach to assess targeted biofilm disruption strategies in vivo.

  2. Comprehensive measurement of chromosomal instability in cancer cells: combination of fluorescence in situ hybridization and cytokinesis-block micronucleus assay.

    PubMed

    Camps, Jordi; Ponsa, Immaculada; Ribas, Maria; Prat, Esther; Egozcue, Josep; Peinado, Miguel A; Miró, Rosa

    2005-05-01

    Most tumors show abnormal karyotypes involving either chromosome rearrangements and/or aneuploidies. The aim of our study is to measure the rate of both structural and numerical chromosome instability in two colorectal cancer cell lines: HCT116, and SW480 and its single subclones. To determine structural instability, we measured the nonclonal chromosome alterations of the last cell division by means of multicolor-fluorescence in situ hybridization (FISH). To quantify numerical instability, we used centromere-specific DNA probes to simultaneously detect chromosome loss and nondisjunctional events in binucleated cells obtained by cytokinesis-block micronucleus assay (CBMN). After clonal episodes, the structural chromosome instability rate increased significantly, confirming the large contribution of structural rearrangements to the heterogeneity of cancer cells. On the other hand, the aneuploidy rate was high and conserved in both the parental SW480 cell line and its subclones. The ability to differentiate chromosome loss and nondisjunction by the CBMN assay allowed us to conclude that no significant differences were detected among these events. Analysis of nucleoplasmic bridges, micronuclei, and nuclear blebs also demonstrated the differences among the structural instability rates of the parental cell line and its subclones. Overall, our results demonstrate the prevalence of structural over numerical chromosome instability in the subclones when comparing them with their parental cell line, confirming the contribution of ongoing chromosomal reorganizations in the generation of tumor cell heterogeneity.

  3. Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: Fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency

    SciTech Connect

    Worley, K.C.; Lindsay, E.A.; McCabe, E.R.B.

    1995-07-17

    Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosome deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available. 17 refs., 2 figs.

  4. Middle ear squamous papilloma: A report of four cases analyzed by HPV and EBV in situ hybridization

    PubMed Central

    ZHOU, HAN; CHEN, ZHIBIN; ZHANG, WEIMING; XING, GUANGQIAN

    2014-01-01

    Squamous papilloma involving the middle ear as a primary lesion is an extremely rare occurrence. The aims of the present study were to investigate the presence of human papilloma virus (HPV) and Epstein-Barr virus (EBV) infections in primary middle ear squamous papilloma and to describe the clinical and pathological features of the disease along with therapeutic strategies. A retrospective review was conducted of four patients with clinical and pathological diagnoses of middle ear squamous papilloma. In situ hybridization (ISH) for a wide range of HPV DNA subtypes and EBV-encoded RNA was performed in the tissue samples obtained from these patients. Only two cases of primary squamous papilloma in the middle ear have been previously reported in the English literature. These papillomas developed in males of ~60-years of age and otorrhea was the most frequent complaint. Premalignant changes were observed in two of the present cases and ISH of HPV and EBV was negative in all four cases. The results of the present study indicated that chronic inflammatory stimulation, not HPV and EBV infection, is involved in the occurrence of middle ear squamous papilloma and its malignant transformation. Radical surgery and long-term postoperative follow-up are recommended due to its malignant and recurrent potential. Further genetic investigations with additional new cases are required to clarify the pathogenesis of squamous papilloma involving the middle ear. PMID:24348817

  5. TERT and AURKA gene copy number gains enhance the detection of acral lentiginous melanomas by fluorescence in situ hybridization.

    PubMed

    Diaz, Alba; Puig-Butillé, Joan Anton; Valera, Alexandra; Muñoz, Concha; Costa, Dolors; Garcia-Herrera, Adriana; Carrera, Cristina; Sole, Francesc; Malvehy, Josep; Puig, Susana; Alos, Llucia

    2014-03-01

    The study of specific chromosomal loci through fluorescence in situ hybridization (FISH) is useful in differential diagnosis of melanocytic tumors. However, sensitivity rates vary, probably because of molecular heterogeneity. Acral lentiginous melanomas are characterized by copy number gains of small genomic regions, including CCND1, TERT, and AURKA. In a series of 58 acral melanocytic lesions, we explored the value of a four-color FISH probe, used in addition to determining MYC gene status, and assessed the potential diagnostic usefulness of newly developed probes targeting TERT and AURKA. Moreover, we tested CCND1, TERT, and AURKA protein expression by immunohistochemistry. The four-color FISH probe detected 85.3% of melanomas and 29.4% of TERT and AURKA copy number gains. Sensitivity was 97% (confidence interval 95%, 82.9% to 99.8%) for the combined results of all probes. No MYC copy number gains were detected. No nevi showed aberrations. Immunohistochemistry revealed a higher percentage of cells positive for CCND1, TERT, and AURKA protein in melanomas than in nevi (P ≤ 0.001). A significant correlation between gene copy number gain and protein expression was found for CCND1 (P = 0.015). Our results indicate that addition of specific FISH probes to the current probe could improve sensitivity for the diagnosis of acral melanomas. Further studies in larger numbers of cases are needed to validate these results.

  6. Fluorescence in situ hybridization of TP53 for the detection of chromosome 17 abnormalities in myelodysplastic syndromes.

    PubMed

    Sánchez-Castro, Judit; Marco-Betés, Víctor; Gómez-Arbonés, Xavier; García-Cerecedo, Tomás; López, Ricard; Talavera, Elisabeth; Fernández-Ruiz, Sara; Ademà, Vera; Marugan, Isabel; Luño, Elisa; Sanzo, Carmen; Vallespí, Teresa; Arenillas, Leonor; Marco Buades, Josefa; Batlle, Ana; Buño, Ismael; Martín Ramos, María Luisa; Blázquez Rios, Beatriz; Collado Nieto, Rosa; Vargas, Ma Teresa; González Martínez, Teresa; Sanz, Guillermo; Solé, Francesc

    2015-01-01

    Conventional G-banding cytogenetics (CC) detects chromosome 17 (chr17) abnormalities in 2% of patients with de novo myelodysplastic syndromes (MDS). We used CC and fluorescence in situ hybridization (FISH) (LSI p53/17p13.1) to assess deletion of 17p in 531 patients with de novo MDS from the Spanish Group of Hematological Cytogenetics. FISH detected - 17 or 17p abnormalities in 13 cases (2.6%) in whom no 17p abnormalities were revealed by CC: 0.9% of patients with a normal karyotype, 0% in non-informative cytogenetics, 50% of patients with a chr17 abnormality without loss of 17p and 4.7% of cases with an abnormal karyotype not involving chr17. Our results suggest that applying FISH of 17p13 to identify the number of copies of the TP53 gene could be beneficial in patients with a complex karyotype. We recommend using FISH of 17p13 in young patients with a normal karyotype or non-informative cytogenetics, and always in isolated del(17p). PMID:25754580

  7. Regulation of Tumor Necrosis Factor Gene Expression in Colorectal Adenocarcinoma: In vivo Analysis by in situ Hybridization

    NASA Astrophysics Data System (ADS)

    Beissert, Stefan; Bergholz, Michael; Waase, Inge; Lepsien, Gerd; Schauer, Alfred; Pfizenmaier, Klaus; Kronke, Martin

    1989-07-01

    Tumor necrosis factor (TNF) produced by macrophages is thought to contribute to the host defense against development of cancer. However, since tumor cells themselves are able to produce TNF, it is conceivable that TNF may also play an adverse pathological role in carcinogenesis. To better understand the functional significance of TNF in neoplastic disease, we have determined the cellular source of TNF activity produced in 10 patients with colorectal cancer. Northern blot analysis of RNAs extracted from fresh biopsy specimens revealed detectable TNF mRNA levels in all instances. By using in situ hybridization of frozen sections, scattered cells expressing TNF mRNA could be discerned. Based on morphological criteria, these TNF-positive cells most likely belong to the macrophage lineage. Macrophages in normal tissue surrounding the tumor did not express TNF mRNA, suggesting that macrophage activation occurs locally at the site of neoplastic transformation. Immunohistochemistry using anti-TNF monoclonal antibodies revealed that less than 1% of tumor-infiltrating macrophages synthesize TNF protein. Thus we present evidence that in colorectal cancer only a small proportion of tumor-infiltrating macrophages produces TNF, indicating that the microenvironment of the tumor provides adequate, yet suboptimal, conditions for macrophage activation.

  8. 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.

    PubMed

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

    2010-06-01

    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.

  9. Detection of human papillomavirus DNA in genital lesions by enzymatic in situ hybridization with Fast Red and laser scanning confocal microscopy.

    PubMed

    Lizard, G; Chignol, M C; Roignot, P; Souchier, C; Chardonnet, Y; Schmitt, D

    1997-07-01

    Human papillomavirus (HPV) infection with potentially oncogenic types 16 or 18 is common in genital lesions especially in uterine carcinomas. In such lesions, in situ hybridization with non-radioactive probes is a powerful tool for the histopathologist to detect and type HPV DNA either on cell deposits or on tissue sections. The use of an immunohistochemical method involving alkaline phosphatase and Fast Red TR salt/naphthol AS-MX phosphate is proposed for use with conventional bright-field or fluorescence microscopy as well as by laser scanning confocal microscopy. The alkaline phosphatase-Fast Red reaction has the advantage of producing a red precipitate that permits the detection of in situ hybridization signals by bright-field microscopy, and of obtaining a strong red fluorescence characterized by a lack of bleaching when excited by a green light. Therefore, the alkaline phosphatase-Fast Red reaction is well adapted for observations by fluorescence and confocal microscopy, the latter method allowing the detection, in tissue sections of cervical intraepithelial lesions, of small punctate and large diffuse hybridization signals, considered as integrated and episomal states of HPV DNA respectively. The combination of in situ hybridization with the alkaline phosphatase-Fast Red reaction and confocal microscopy is particularly convincing when hybridization signals are of small size and/or of low fluorescence intensity, especially if they are present in various focal planes; in such conditions, infected cells are easily detected by three-dimensional reconstruction. Therefore, this combination is a suitable method for identifying and characterizing HPV DNA in cells and tissue sections.

  10. In situ investigation of energy transfer in hybrid organic/colloidal quantum dot light-emitting diodes via magneto-electroluminescence.

    PubMed

    Chen, Lixiang; Chen, Qiusong; Lei, Yanlian; Jia, Weiyao; Yuan, De; Xiong, Zuhong

    2016-08-10

    Energy transfer (ET) and charge injection (CI) in the hybrid organic/colloidal quantum dot light-emitting diodes (QD-LEDs) have been investigated by using magneto-electroluminescence (MEL) as an in situ tool. The feasibility and availability of MEL as an in situ tool were systematically demonstrated in the typical QD-LEDs based on CdSe-ZnS core-shell QDs. Our results suggest that the ET and CI processes can be well discerned by MEL measurements since these two processes exhibit distinct responses to the applied magnetic field. Through measurement of the MEL and current efficiency, we indicated that ET would be the main mechanism for light emission in the present hybrid QD-LEDs. This study strongly suggests that MEL could be a highly sensitive fingerprint for ET, which provides a facile and efficient method for the in situ investigation of fundamental processes in hybrid organic/colloidal QD-LEDs and other organic/inorganic composites. PMID:27461412

  11. Rapid Detection of Starved Escherichia coli with Respiratory Activity in Potable Water by Signal-Amplified in situ Hybridization Following Formazan Reduction.

    PubMed

    Yamaguchi, Nobuyasu; Sasada, Makoto; Nasu, Masao

    2009-01-01

    The aim of this study was to develop a rapid method for the specific detection of respiring Escherichia coli (an indicator of fecal contamination) in potable water. Fluorescence in situ hybridization (FISH) with a rRNA-targeted oligonucleotide probe was used to detect E. coli cells and bacterial respiratory activity was estimated using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC). Fluorescent signals from hybridized cells were increased by optimized tyramide signal amplification (TSA). Respiring E. coli in potable ground water with low rRNA content were enumerated within 8 hours using signal-amplified in situ hybridization following formazan reduction (TSA-CTC-FISH), whereas these starved E. coli cells could not be detected by conventional FISH (FISH without signal amplification) which generated weak fluorescence. TSA-CTC-FISH can be used for simultaneous identification in situ based on phylogenetic information and the activity of individual bacterial cells in potable water. This method would be useful in the rapid monitoring of harmful or fecal indicator bacteria in potable water.

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

    SciTech Connect

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

    2008-03-15

    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.

  13. The importance of fixation procedures on DNA template and its suitability for solution-phase polymerase chain reaction and PCR in situ hybridization.

    PubMed

    O'Leary, J J; Browne, G; Landers, R J; Crowley, M; Healy, I B; Street, J T; Pollock, A M; Murphy, J; Johnson, M I; Lewis, F A

    1994-04-01

    Conventional solution-phase polymerase chain reaction (PCR) and in situ PCR/PCR in situ hybridization are powerful tools for retrospective analysis of fixed paraffin wax-embedded material. Amplification failure using these techniques is now encountered in some centres using archival fixed tissues. Such 'failures' may not only be due to absent target DNA sequences in the tissues, but may be a direct effect of the type of fixative, fixation time and/or fixation temperature used. The type of nucleic acid extraction procedure applied will also influence amplification results. This is particularly true with in situ PCR/PCR in situ hybridization. To examine these effects in solution-phase PCR, beta-globin gene was amplified in 100 mg pieces of tonsillar tissue fixed in Formal saline, 10% formalin, neutral buffered formaldehyde, Carnoy's Bouin's, buffered formaldehyde sublimate, Zenker's, Helly's and glutaraldehyde at 0 to 4 degrees C, room temperature and 37 degrees C fixation temperatures and for fixation periods of 6, 24, 48 and 72 hours and 1 week. DNA extraction procedures used were simple boiling and 5 days' proteinase K digestion at 37 degrees C. Amplified product was visible primarily yet variably from tissue fixed in neutral buffered formaldehyde and Carnoy's, whereas fixation in mercuric chloride-based fixatives produced consistently negative results. Room temperature and 37 degrees C fixation temperature appeared most conducive to yielding amplifiable DNA template. Fixation times of 24 and 48 hours in neutral buffered formaldehyde and Carnoy's again favoured amplification.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Optimization of a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the detection of bacteria and disclosure of a formamide effect.

    PubMed

    Santos, Rita S; Guimarães, Nuno; Madureira, Pedro; Azevedo, Nuno F

    2014-10-10

    Despite the fact that fluorescence in situ hybridization (FISH) is a well-established technique to identify microorganisms, there is a lack of understanding concerning the interaction of the different factors affecting the obtained fluorescence. In here, we used flow cytometry to study the influence of three essential factors in hybridization - temperature, time and formamide concentration - in an effort to optimize the performance of a Peptide Nucleic Acid (PNA) probe targeting bacteria (EUB338). The PNA-FISH optimization was performed with bacteria representing different families employing response surface methodology. Surprisingly, the optimum concentration of formamide varied according to the bacterium tested. While hybridization on the bacteria possessing the thickest peptidoglycan was more successful at nearly 50% (v/v) formamide, hybridization on all other microorganisms appeared to improve with much lower formamide concentrations. Gram staining and transmission electron microscopy allowed us to confirm that the overall effect of formamide concentration on the fluorescence intensity is a balance between a harmful effect on the bacterial cell envelope, affecting cellular integrity, and the beneficial denaturant effect in the hybridization process. We also conclude that microorganisms belonging to different families will require different hybridization parameters for the same FISH probe, meaning that an optimum universal PNA-FISH procedure is non-existent for these situations.

  15. Detection of aneuploid human sperm by fluorescence in situ hybridization: Evidence for a donor difference in frequency of sperm disomic for chromosomes 1 and Y

    SciTech Connect

    Robbins, W.A. Lawrence Livermore National Lab., CA ); Segraves, R.; Pinkel, D. ); Wyrobek, A.J. )

    1993-04-01

    Fluorescence in situ hybridization with repetitive-sequence DNA probes was used to detect human sperm disomic for chromosomes 1 and Y in three healthy men. Data on these same men had been obtained previously, using the human-sperm/hamster-egg cytogenetic technique, providing a cytogenetic reference for validating sperm hybridization measurements. Air-dried smears were prepared from semen samples and treated with DTT and lithium diiodosalicylate to expand sperm chromatin. Hybridization with fluorescently tagged DNA probes for chromosomes 1 (pUC177) or Y (pY3.4) yielded average frequencies of sperm with two fluorescent domains of 14.2[+-]2.4/10,000 and 5.6[+-]1.6/10,000 sperm, respectively. These frequencies did not differ statistically from frequencies of hyperploidy observed for these chromosomes with the hamster technique. In addition, frequencies of disomic sperm from one donor were elevated [approximately]2.5-fold above those of other donors, for both chromosomes 1 (P = .045) and Y (P = .01), consistent with a trend found with the hamster technique. The authors conclude that fluorescence in situ hybridization to sperm chromosomes provides a valid and promising measure of the frequency of disomic human sperm. 43 refs., 1 fig., 4 tabs.

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

    SciTech Connect

    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 TVS-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 TVS-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.

  17. Vasopressin mRNA in situ hybridization: localization and regulation studied with oligonucleotide cDNA probes in normal and Brattleboro rat hypothalamus

    SciTech Connect

    Uhl, G.R.; Zingg, H.H.; Habener, J.F.

    1985-08-01

    Hybridizable vasopressin mRNA may be quantitatively localized in situ in sections from rat hypothalamus. Radiolabeled oligonucleotide cDNA probes, synthesized by chemical and enzymatic means, provide strong hybridization in zones known to contain vasopressin cell bodies. Multiple single-stranded /sup 32/P-, /sup 35/S-, or /sup 3/H-labeled oligonucleotides demonstrate localized hybridization that increases as probes are lengthened from 8 to 75 bases. Competition studies, RNase experiments, anatomic localization, and use of multiple probes all support hybridization specificity. An approximate doubling of hybridizable mRNA in both supraoptic and paraventricular nuclei can be detected with dehydration of the animals. Hybridizable mRNA densities are virtually normal in hypothalamic nuclei of Brattleboro rats given free access to water. These methods can provide insight into regional mRNA dynamics and may reflect functional activity of peptidergic neurons.

  18. Evaluation of whole-mount in situ hybridization as a tool for pathway-based toxicological research with early-life stage fathead minnows.

    PubMed

    Cavallin, J E; Schroeder, A L; Jensen, K M; Villeneuve, D L; Blackwell, B R; Carlson, K; Kahl, M D; LaLone, C A; Randolph, E C; Ankley, G T

    2015-12-01

    Early-life stage fish can be more sensitive to toxicants than adults, so delineating mechanisms of perturbation of biological pathways by chemicals during this life stage is crucial. Whole-mount in situ hybridization (WISH) paired with quantitative real-time polymerase chain reaction (QPCR) assays can enhance pathway-based analyses through determination of specific tissues where changes in gene expression are occurring. While WISH has frequently been used in zebrafish (Danio rerio), this technology has not previously been applied to fathead minnows (Pimephales promelas), another well-established small fish model species. The objective of the present study was to adapt WISH to fathead minnow embryos and larvae, and use the approach to evaluate the effects of estrone, an environmentally-relevant estrogen receptor (ER) agonist. Embryos were exposed via the water to 0, 18 or 1800 ng estrone/L (0, 0.067 and 6.7nM) for 3 or 6 days in a solvent-free, flow-through test system. Relative transcript abundance of three estrogen-responsive genes, estrogen receptor-α (esr1), cytochrome P450-aromatase B (cyp19b), and vitellogenin (vtg) was examined in pooled whole embryos using QPCR, and the spatial distribution of up-regulated gene transcripts was examined in individual fish using WISH. After 3 days of exposure to 1800 ng estrone/L, esr1 and cyp19b were significantly up-regulated, while vtg mRNA expression was not affected. After 6 days of exposure to 1800 ng estrone/L, transcripts for all three genes were significantly up-regulated. Corresponding WISH assays revealed spatial distribution of esr1 and vtg in the liver region, an observation consistent with activation of the hepatic ER. This study clearly demonstrates the potential utility of WISH, in conjunction with QPCR, to examine the mechanistic basis of the effects of toxicants on early-life stage fathead minnows. PMID:26485527

  19. Integrated Annotation and Analysis of In Situ Hybridization Images Using the ImAnno System: Application to the Ear and Sensory Organs of the Fetal Mouse

    PubMed Central

    Romand, Raymond; Ripp, Raymond; Poidevin, Laetitia; Boeglin, Marcel; Geffers, Lars; Dollé, Pascal; Poch, Olivier

    2015-01-01

    An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium. This study was carried out in 25 tissues of late gestation embryos (E14.5), with a special emphasis on the developing ear and on five distinct developing sensory organs, including the cochlea, the vestibular receptors, the sensory retina, the olfactory organ, and the vibrissae follicles. The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno. In addition to managing the multilevel micrograph annotations performed by human experts, ImAnno provides public access to various integrated databases and tools. Thus, it facilitates the analysis of complex ISH gene expression patterns, as well as functional annotation and interaction of gene sets. It also provides direct links to human pathways and diseases. Hierarchical clustering of expression patterns in the 25 tissues revealed three main branches corresponding to tissues with common functions and/or embryonic origins. To illustrate the integrative power of ImAnno, we explored the expression, function and disease traits of the sensory epithelia of the five presumptive sensory organs. The study identified 623 genes (out of 2000) concomitantly expressed in the five embryonic epithelia, among which many (∼12%) were involved in human disorders. Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes. These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth. PMID:25706271

  20. Visualization of 'Candidatus Liberibacter asiaticus' cells in the vascular bundle of citrus seed coats with fluorescence in situ hybridization and transmission electron microscopy.

    PubMed

    Hilf, Mark E; Sims, Kenneth R; Folimonova, Svetlana Y; Achor, Diann S

    2013-06-01

    'Candidatus Liberibacter asiaticus' is the bacterium implicated as a causal agent of the economically damaging disease of citrus called huanglongbing (HLB). Vertical transmission of the organism through seed to the seedling has not been demonstrated. Previous studies using real-time polymerase chain reaction assays indicated abundant bacterial 16S rRNA sequences in seed coats of citrus seed but the presence of intact bacterial cells was not demonstrated. We used microscopy to verify that intact bacterial cells were present in citrus seed coats. Bacterial cells with the morphology and physical dimensions appropriate for 'Ca. L. asiaticus' were seen in phloem sieve elements in the vascular bundle of grapefruit seed coats using transmission electron microscopy (TEM). Fluorescence in situ hybridization (FISH) analyses utilizing probes complementary to the 'Ca. L. asiaticus' 16S rRNA gene revealed bacterial cells in the vascular tissue of intact seed coats of grapefruit and pummelo and in fragmented vascular bundles excised from grapefruit seed coats. The physical measurements and the morphology of individual bacterial cells were consistent with those ascribed in the literature to 'Ca. L. asiaticus'. No bacterial cells were observed in preparations of seed from fruit from noninfected trees. A small library of clones amplified from seed coats from a noninfected tree using degenerate primers targeting prokaryote 16S rRNA gene sequences contained no 'Ca. L. asiaticus' sequences, whereas 95% of the sequences in a similar library from DNA from seed coats from an infected tree were identified as 'Ca. L. asiaticus', providing molecular genetic corroboration that the bacterial cells observed by TEM and FISH in seed coats from infected trees were 'Ca. L. asiaticus'. PMID:23676087

  1. Quantitative Use of Fluorescent In Situ Hybridization To Examine Relationships between Mycolic Acid-Containing Actinomycetes and Foaming in Activated Sludge Plants

    PubMed Central

    Davenport, Russell J.; Curtis, Thomas P.; Goodfellow, Michael; Stainsby, Fiona M.; Bingley, Marc

    2000-01-01

    The formation of viscous foams on aeration basins and secondary clarifiers of activated sludge plants is a common and widespread problem. Foam formation is often attributed to the presence of mycolic acid-containing actinomycetes (mycolata). In order to examine the relationship between the number of mycolata and foam, we developed a group-specific probe targeting the 16S rRNA of the mycolata, a protocol to permeabilize mycolata, and a statistically robust quantification method. Statistical analyses showed that a lipase-based permeabilization method was quantitatively superior to previously described methods (P << 0.05). When mixed liquor and foam samples were examined, most of the mycolata present were rods or cocci, although filamentous mycolata were also observed. A nested analysis of variance showed that virtually all of the measured variance occurred between fields of view and not between samples. On this basis we determined that as few as five fields of view could be used to give a statistically meaningful sample. Quantitative fluorescent in situ hybridization (FISH) was used to examine the relationship between foaming and the concentration of mycolata in a 20-m3 completely mixed activated sludge plant. Foaming occurred when the number of mycolata exceeded a certain threshold value. Baffling of the plant affected foaming without affecting the number of mycolata. We tentatively estimated that the threshold foaming concentration of mycolata was about 2 × 106 cells ml−1 or 4 × 1012 cells m−2. We concluded that quantitative use of FISH is feasible and that quantification is a prerequisite for rational investigation of foaming in activated sludge. PMID:10698786

  2. High prognostic value of minimal residual disease detected by flow-cytometry-enhanced fluorescence in situ hybridization in core-binding factor acute myeloid leukemia (CBF-AML).

    PubMed

    Wang, Libing; Gao, Lei; Xu, Sheng; Gong, Shenglan; Liu, Min; Qiu, Huiying; Xu, Xiaoqian; Ni, Xiong; Chen, Li; Lu, Shuqing; Chen, Jie; Song, Xianmin; Zhang, Weiping; Yang, Jianmin; Hu, Xiaoxia; Wang, Jianmin

    2014-10-01

    Acute myeloid leukemia (AML) is generally regarded as a disorder of stem cells, known as leukemic initiating cells (LICs), which initiate the disease and contribute to relapses. Although the phenotype of these cells remains unclear in most patients, they are enriched within the CD34(+)CD38(-) population. In core-binding factor (CBF) AML, the cytogenetic abnormalities also exist in LIC. The aim of this study was to determine the prognostic power of minimal residual disease (MRD) measured by fluorescence in situ hybridization (FISH) in CD34(+)CD38(-) cells sorted by flow cytometry at different periods during therapy. Thirty-six patients under 65 years of age with de novo CBF-AML treated with intensive chemotherapy were retrospectively included in this study. Correlations with relapse-free survival (RFS) and overall survival were evaluated with univariate and multivariate analyses. FISH efficiently identified LICs in the CD34(+)CD38(-) population. The presence of FISH(+)CD34(+)CD38(-) cells before consolidation was negatively associated with cumulative incidence of relapse (64 vs 18 %, P = .012), which showed prognostic value for RFS (12 vs 68 %, P = .008) and OS (11 vs 75 %, P = .0005), and retained prognostic significance for RFS in multivariate analysis. The detection of FISH(+)CD34(+)CD38(-) cells before consolidation therapy significantly correlated with long-term survival. Fluorescence-activated cell sorting (FACS)-FISH could be potentially adopted as a MRD monitor approach in clinical practice to identify CBF-AML patients at risk of treatment failure during therapy.

  3. A novel four-color fluorescence in situ hybridization assay for the detection of TMPRSS2 and ERG rearrangements in prostate cancer.

    PubMed

    Qu, Xiaoyu; Randhawa, Grace; Friedman, Cynthia; O'Hara-Larrivee, Siobhan; Kroeger, Kathleen; Dumpit, Ruth; True, Larry; Vakar-Lopez, Funda; Porter, Christopher; Vessella, Robert; Nelson, Peter; Fang, Min

    2013-01-01

    Since the identification of the TMPRSS2-ERG rearrangement as the most common fusion event in prostate cancer, various methods have been developed to detect this rearrangement and to study its prognostic significance. We report a novel four-color fluorescence in situ hybridization (FISH) assay that detects not only the typical TMPRSS2-ERG fusion but also alternative rearrangements of the TMPRSS2 or ERG gene. We validated this assay on fresh, frozen, or formalin-fixed paraffin-embedded prostate cancer specimens, including cell lines, primary prostate cancer tissues, xenograft tissues derived from metastatic prostate cancer, and metastatic tissues from castration-resistant prostate cancer (CRPC) patients. When compared with either reverse transcription-polymerase chain reaction or the Gen-Probe method as the technical reference, analysis using the four-color FISH assay demonstrated an analytical sensitivity of 94.5% (95% confidence interval [CI] 0.80-0.99) and specificity of 100% (95% CI 0.89-1.00) for detecting the TMPRSS2-ERG fusion. The TMPRSS2-ERG fusion was detected in 41% and 43% of primary prostate cancer (n = 59) and CRPC tumors (n = 82), respectively. Rearrangements other than the typical TMPRSS2-ERG fusion were confirmed by karyotype analysis and found in 7% of primary cancer and 13% of CRPC tumors. Successful karyotype analyses are reported for the first time on four of the xenograft samples, complementing the FISH results. Analysis using the four-color FISH assay provides sensitive detection of TMPRSS2 and ERG gene rearrangements in prostate cancer.

  4. Male infertility and copy number variants (CNVs) in the dog: a two-pronged approach using Computer Assisted Sperm Analysis (CASA) and Fluorescent In Situ Hybridization (FISH)

    PubMed Central

    2013-01-01

    Background Infertility affects ~10-15% of couples trying to have children, in which the rate of male fertility problems is approximately at 30-50%. Copy number variations (CNVs) are DNA sequences greater than or equal to 1 kb in length sharing a high level of similarity, and present at a variable number of copies in the genome; in our study, we used the canine species as an animal model to detect CNVs responsible for male infertility. We aim to identify CNVs associated with male infertility in the dog genome with a two-pronged approach: we performed a sperm analysis using the CASA system and a cytogenetic-targeted analysis on genes involved in male gonad development and spermatogenesis with fluorescence in situ hybridization (FISH), using dog-specific clones. This analysis was carried out to evaluate possible correlations between CNVs on targeted genes and spermatogenesis impairments or infertility factors. Results We identified two genomic regions hybridized by BACs CH82-321J09 and CH82-509B23 showing duplication patterns in all samples except for an azoospermic dog. These two regions harbor two important genes for spermatogenesis: DNM2 and TEKT1. The genomic region encompassed by the BAC clone CH82-324I01 showed a single-copy pattern in all samples except for one dog, assessed with low-quality sperm, displaying a marked duplication pattern. This genomic region harbors SOX8, a key gene for testis development. Conclusion We present the first study involving functional and genetic analyses in male infertility. We set up an extremely reliable analysis on dog sperm cells with a highly consistent statistical significance, and we succeeded in conducting FISH experiments on sperm cells using BAC clones as probes. We found copy number differences in infertile compared with fertile dogs for genomic regions encompassing TEKT1, DNM2, and SOX8, suggesting those genes could have a role if deleted or duplicated with respect to the reference copy number in fertility biology

  5. Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp.

    PubMed Central

    2013-01-01

    Background Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. Results Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI), from 87.8 to 99.9%) and 100% (95% CI, from 88.0 to 100.0%), for Lactobacillus spp.; and 100% (95% CI, from 92.8 to 100%) and 100% (95% CI, from 81.5 to 100.0%) for G. vaginalis. Moreover, the probes were evaluated in mixed samples mimicking women with BV or normal vaginal microflora, demonstrating efficiency and applicability of our PNA FISH. Conclusions This quick method accurately detects Lactobacillus spp. and G. vaginalis species in mixed samples, thus enabling efficient evaluation of the two bacterial groups, most frequently encountered in the vagina. PMID:23586331

  6. A high-resolution karyotype of Brassica rapa ssp. pekinensis revealed by pachytene analysis and multicolor fluorescence in situ hybridization.

    PubMed

    Koo, Dal-Hoe; Plaha, Prikshit; Lim, Yong Pyo; Hur, Yoonkang; Bang, Jae-Wook

    2004-11-01

    A molecular cytogenetic map of Chinese cabbage (Brassica rapa ssp. pekinensis, 2 n=20) was constructed based on the 4'-6-diamino-2-phenylindole dihydrochloride-stained mitotic metaphase and pachytene chromosomes and multicolor fluorescence in situ hybridization (McFISH), using three repetitive DNA sequences, 5S rDNA, 45S rDNA, and C11-350H. The lengths of mitotic metaphase chromosomes ranged from 1.46 microm to 3.30 microm. Five 45S and three 5S rDNA loci identified were assigned to different chromosomes. The C11-350H loci were located on all the mitotic metaphase chromosomes, except chromosomes 2 and 4. The pachytene karyotype consisted of two metacentric (chromosomes 1 and 6), five submetacentric (chromosomes 3, 4, 5, 9 and 10), two subtelocentric (chromosomes 7 and 8), and one acrocentric (chromosome 2) chromosome(s). The mean lengths of ten pachytene chromosomes ranged from 23.7 microm to 51.3 microm, with a total of 385.3 microm, which is 17.5-fold longer than that of the mitotic metaphase chromosomes. In the proposed pachytene karyotype, all the chromosomes of B. rapa ssp. pekinensis can be identified on the basis of chromosome length, centromere position, heterochromatin pattern, and the location of the three repetitive sequences. Moreover, the precise locations of the earlier reported loci of 5S rDNA, 45S rDNA, and Chinese cabbage tandem DNA repeat C11-350H were established using McFISH analysis. We also identified a 5S rDNA locus on the long arm of pachytene bivalent 7, which could not be detected in the mitotic metaphase chromosomes in the present and earlier studies. The deduced karyotype will be useful for structural and functional genomic studies in B. rapa.

  7. Assessment of chromosomal abnormalities in sperm of infertile men using sperm karyotyping and multicolour fluorescence in situ hybridization (FISH)

    SciTech Connect

    Moosani, N.; Martin, R.H.

    1994-09-01

    Individuals with male factor infertility resulting from idiopathic oligo-, astheno- or teratozoospermia are frequently offered IVF in an attempt to increase their chances of having a child. A concern remains whether these infertile males have an elevated risk of transmitting chromosomal abnormalities to their offspring. Sperm chromosomal complements from these men were assayed using the human sperm/hamster oocyte fusion system and fluorescence in situ hybridization (FISH) on sperm nuclei. For each of 5 infertile patients, 100 sperm karyotypes were analyzed and multicolour FISH analysis was performed on a minimum of 10,000 sperm nuclei for each chromosome-specific DNA probe for chromosomes 1 (pUC1.77), 12 (D12Z3), X (XC) and Y (DYZ3). As a group, the infertile patients showed increased frequencies of both numerical ({chi}{sup 2}=17.26, {proportional_to} <0.001) and total abnormalities ({chi}{sup 2}=7.78, {proportional_to} <0.01) relative to control donors when assessed by sperm karyotypes. Analysis of sperm nuclei by FISH indicated a significant increase in the frequency of disomy for chromosome 1 in three of the five patients as compared to control donors ({chi}{sup 2}>8.35, {proportional_to} <0.005). In addition, the frequency of XY disomy was significantly higher in four of the five patients studied by FISH ({chi}{sup 2}>10.58, {proportional_to}<0.005), suggesting that mis-segregation caused by the failure of the XY bivalent to pair may play a role in idiopathic male infertility.

  8. Application of rRNA probes and fluorescence in situ hybridization for rapid detection of the toxic dinoflagellate Alexandrium minutum

    NASA Astrophysics Data System (ADS)

    Tang, Xianghai; Yu, Rencheng; Zhou, Mingjiang; Yu, Zhigang

    2012-03-01

    The dinoflagellate Alexandrium minutum is often associated with harmful algal blooms (HABs). This species consists of many strains that differ in their ability to produce toxins but have similar morphology, making identification difficult. In this study, species-specific rRNA probes were designed for whole-cell fluorescence in situ hybridization (FISH) to distinguish A. minutum from two phylogenetic clades. We acquired the complete SSU to LSU rDNA sequences (GenBank accession numbers JF906989-JF906999) of 11 Alexandrium strains and used these to design rRNA targeted oligonucleotide probes. Three ribotype-specific probes, M-GC-1, M-PC-2, and M-PC-3, were designed. The former is specific for the GC clade ("Global clade") of A. minutum, the majority of which have been found non-toxic, and the latter two are specific for the PSP (paralytic shellfish poisoning)-producing PC clade ("Pacific clade"). The specificity of these three probes was confirmed by FISH. All cells in observed fields of view were fluorescently labeled when probes and target species were incubated under optimized FISH conditions. However, the accessibility of rRNA molecules in ribosomes varied among the probe binding positions. Thus, there was variation in the distribution of positive signals in labeled cells within nucleolus and cytosol (M-GC-1, M-PC-3), or just nucleolus (M-PC-2). Our results provide a methodological basis for studying the biogeography and population dynamics of A. minutum, and providing an early warning of toxic HABs.

  9. Brain in situ hybridization maps as a source for reverse-engineering transcriptional regulatory networks: Alzheimer's disease insights.

    PubMed

    Acquaah-Mensah, George K; Taylor, Ronald C

    2016-07-15

    Microarray data have been a valuable resource for identifying transcriptional regulatory relationships among genes. As an example, brain region-specific transcriptional regulatory events have the potential of providing etiological insights into Alzheimer Disease (AD). However, there is often a paucity of suitable brain-region specific expression data obtained via microarrays or other high throughput means. The Allen Brain Atlas in situ hybridization (ISH) data sets (Jones et al., 2009) represent a potentially valuable alternative source of high-throughput brain region-specific gene expression data for such purposes. In this study, Allen Brain Atlas mouse ISH data in the hippocampal fields were extracted, focusing on 508 genes relevant to neurodegeneration. Transcriptional regulatory networks were learned using three high-performing network inference algorithms. Only 17% of regulatory edges from a network reverse-engineered based on brain region-specific ISH data were also found in a network constructed upon gene expression correlations in mouse whole brain microarrays, thus showing the specificity of gene expression within brain sub-regions. Furthermore, the ISH data-based networks were used to identify instructive transcriptional regulatory relationships. Ncor2, Sp3 and Usf2 form a unique three-party regulatory motif, potentially affecting memory formation pathways. Nfe2l1, Egr1 and Usf2 emerge among regulators of genes involved in AD (e.g. Dhcr24, Aplp2, Tia1, Pdrx1, Vdac1, and Syn2). Further, Nfe2l1, Egr1 and Usf2 are sensitive to dietary factors and could be among links between dietary influences and genes in the AD etiology. Thus, this approach of harnessing brain region-specific ISH data represents a rare opportunity for gleaning unique etiological insights for diseases such as AD.

  10. Rapid differentiation of Francisella species and subspecies by fluorescent in situ hybridization targeting the 23S rRNA

    PubMed Central

    2010-01-01

    Background Francisella (F.) tularensis is the causative agent of tularemia. Due to its low infectious dose, ease of dissemination and high case fatality rate, F. tularensis was the subject in diverse biological weapons programs and is among the top six agents with high potential if misused in bioterrorism. Microbiological diagnosis is cumbersome and time-consuming. Methods for the direct detection of the pathogen (immunofluorescence, PCR) have been developed but are restricted to reference laboratories. Results The complete 23S rRNA genes of representative strains of F. philomiragia and all subspecies of F. tularensis were sequenced. Single nucleotide polymorphisms on species and subspecies level were confirmed by partial amplification and sequencing of 24 additional strains. Fluorescent In Situ Hybridization (FISH) assays were established using species- and subspecies-specific probes. Different FISH protocols allowed the positive identification of all 4 F. philomiragia strains, and more than 40 F. tularensis strains tested. By combination of different probes, it was possible to differentiate the F. tularensis subspecies holarctica, tularensis, mediasiatica and novicida. No cross reactivity with strains of 71 clinically relevant bacterial species was observed. FISH was also successfully applied to detect different F. tularensis strains in infected cells or tissue samples. In blood culture systems spiked with F. tularensis, bacterial cells of different subspecies could be separated within single samples. Conclusion We could show that FISH targeting the 23S rRNA gene is a rapid and versatile method for the identification and differentiation of F. tularensis isolates from both laboratory cultures and clinical samples. PMID:20205957

  11. Aberrations of chromosomes 9 and 22 in acute lymphoblastic leukemia cases detected by ES-fluorescence in situ hybridization.