http://publicationslist.org/data/a.k.raap/atom.xml Anton Raaphttp://publicationslist.org/a.k.raap$basepathfavicon.icoRecent additions to Anton Raap's PublicationsList.org pagehttp://publicationslist.org/publications.png2009-04-15T10:24:59Z http://publicationslist.org/a.k.raap/refid186 2009-04-15T10:24:06Z

Cytoplasmic translation is under sophisticated control but how cells adapt its rate to constitutive loss of mitochondrial oxidative phosphorylation is unknown. Here we show that translation is repressed in cells with the pathogenic A3243G mtDNA mutation or in mtDNA-less rho(0) cells by at least two distinct pathways, one transiently targeting elongation factor eEF-2 and the other initiation factor...<br/><br/>G M C Janssen, P Schwertman, T A T Wanga, R S Jahangir Tafrechi, P J A van den Broek, A K Raap (2009) <i>Cell Mol Life Sci</i> <i></i> <i></i> 66: 4 721-730<br/>

http://publicationslist.org/a.k.raap/refid1 2008-08-19T18:50:29Z

Segregation of mitochondrial DNA (mtDNA) is an important underlying pathogenic factor in mtDNA mutation accumulation in mitochondrial diseases and aging, but the molecular mechanisms of mtDNA segregation are elusive. Lack of high-throughput single-cell mutation load assays lies at the root of the paucity of studies in which, at the single-cell level, mitotic mtDNA segregation patterns have been an...<br/><br/>Roshan S Jahangir Tafrechi, Frans M van de Rijke, Amin Allallou, Chatarina Larsson, Willem C R Sloos, Marchien van de Sande, Carolina Wählby, George M C Janssen, Anton K Raap (2007) <i>J Histochem Cytochem</i> <i></i> <i></i> 55: 11 1159-1166<br/>

http://publicationslist.org/a.k.raap/refid2 2008-08-19T18:50:29Z

Mutations in the mitochondrial tRNA(Leu(UUR)) gene are associated with a large variety of human diseases through a largely undisclosed mechanism. The A3243G tRNA(Leu(UUR)) mutation leads to reduction of mitochondrial DNA (mtDNA)-encoded proteins and oxidative phosphorylation activity even when the cells are competent in mitochondrial translation. These two aspects led to the suggestion that a domi...<br/><br/>George M C Janssen, Paul J Hensbergen, Frans J van Bussel, Crina I A Balog, J Antonie Maassen, André M Deelder, Anton K Raap (2007) <i>Hum Mol Genet</i> <i></i> <i></i> 16: 20 2472-2481<br/>

http://publicationslist.org/a.k.raap/refid5 2008-08-19T18:50:29Z

PURPOSE: To evaluate the clinical relevance of genomic aberrations in primary cutaneous large B-cell lymphoma (PCLBCL). PATIENTS AND METHODS: Skin biopsy samples of 31 patients with a PCLBCL classified as either primary cutaneous follicle center lymphoma (PCFCL; n = 19) or PCLBCL, leg type (n = 12), according to the WHO-European Organisation for Research and Treatment of Cancer (EORTC) classificat...<br/><br/>Remco Dijkman, Cornelis P Tensen, Ekaterina S Jordanova, Jeroen Knijnenburg, Juliette J Hoefnagel, Aat A Mulder, Carla Rosenberg, Anton K Raap, Rein Willemze, Károly Szuhai, Maarten H Vermeer (2006) <i>J Clin Oncol</i> <i></i> <i></i> 24: 2 296-305<br/>

http://publicationslist.org/a.k.raap/refid3 2008-08-19T18:50:29Z

The ability to probe for the location of DNA sequences in morphologically preserved chromosomes and nuclei by fluorescence in situ hybridization (FISH) provided for cytogenetics a quantum leap forward in resolution and ease of detection of chromosomal aberrations. COBRA-FISH, an acronym for COmbined Binary RAtio-FISH is a multicolor FISH methodology, which enables recognition of all human chromoso...<br/><br/>A K Raap, H J Tanke (2006) <i>Cytogenet Genome Res</i> <i></i> <i></i> 114: 3-4 222-226<br/>

http://publicationslist.org/a.k.raap/refid4 2008-08-19T18:50:29Z

The 3243A>G mutation in mitochondrial DNA (mtDNA) is a genetic variant that is associated with a high risk of developing diabetes during life. Enhanced aging of pancreatic beta-cells, a reduced capacity of these cells to synthesize large amounts of insulin,and a resetting of the ATP/ADP-regulated K-channel seem to be the pathogenic factors involved.<br/><br/>Johannes A Maassen, Roshan S Jahangir Tafrechi, George M C Janssen, Anton K Raap, Herman H Lemkes, Leen M 't Hart (2006) <i>Endocrinol Metab Clin North Am</i> <i></i> <i></i> 35: 2 385-96, x-xi<br/>

http://publicationslist.org/a.k.raap/refid7 2008-08-19T18:50:29Z

We have developed a multiplexed and miniaturized TB serological assay with the aim of identifying (combinations of) antigens that maximally discriminate between TB and non-TB patients. It features a microarray accommodating 54 TB antigens, less than 1 microl serum consumption and an indirect immunofluorescence detection protocol. With a panel of 20 TB and 80 non-TB sera we ranked combinations of T...<br/><br/>Miao Tong, Catharina E Jacobi, Frans M van de Rijke, Sjoukje Kuijper, Sjaak van de Werken, Todd L Lowary, Cornelis H Hokke, Ben J Appelmelk, Nico J D Nagelkerke, Hans J Tanke, Rob P M van Gijlswijk, Jacques Veuskens, Arend H J Kolk, Anton K Raap (2005) <i>J Immunol Methods</i> <i></i> <i></i> 301: 1-2 154-163<br/>

http://publicationslist.org/a.k.raap/refid9 2008-08-19T18:50:29Z

The hSNF5 subunit of human SWI/SNF ATP-dependent chromatin remodeling complexes is a tumor suppressor that is inactivated in malignant rhabdoid tumors (MRTs). Here, we report that loss of hSNF5 function in MRT-derived cells leads to polyploidization and chromosomal instability. Re-expression of hSNF5 restored the coupling between cell cycle progression and ploidy checkpoints. In contrast, cancer-a...<br/><br/>Robert G J Vries, Vladimir Bezrookove, Lobke M P Zuijderduijn, Sima Kheradmand Kia, Ada Houweling, Igor Oruetxebarria, Anton K Raap, C Peter Verrijzer (2005) <i>Genes Dev</i> <i></i> <i></i> 19: 6 665-670<br/>

http://publicationslist.org/a.k.raap/refid10 2008-08-19T18:50:29Z

Chromosomal translocations involving the immunoglobulin (Ig) receptor loci usually disrupt and silence these loci. On the basis of observations in follicular lymphoma (FL) with downstream Ig heavy chain (IGH) class switch recombination (CSR), we hypothesized that downstream CSR-mediated chromosomal translocations would leave the V(D)J-Cmu transcription unit intact, thereby still allowing IgM expre...<br/><br/>Jeroen E J Guikema, James A L Fenton, Conny de Boer, Karin Kleiverda, Antoinette A T P Brink, Anton K Raap, Zeev Estrov, Ed Schuuring, Philip M Kluin (2005) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 42: 2 164-169<br/>

http://publicationslist.org/a.k.raap/refid6 2008-08-19T18:50:29Z

The pathobiochemical pathways determining the wide variability in phenotypic expression of mitochondrial DNA (mtDNA) mutations are not well understood. Most pathogenic mtDNA mutations induce a general defect in mitochondrial respiration and thereby ATP synthesis. Yet phenotypic expression of the different mtDNA mutations shows large variations that are difficult to reconcile with ATP depletion as ...<br/><br/>Roshan S Jahangir Tafrechi, Peter J Svensson, George M C Janssen, Karoly Szuhai, J Antonie Maassen, Anton K Raap (2005) <i>Mutat Res</i> <i></i> <i></i> 578: 1-2 43-52<br/>

http://publicationslist.org/a.k.raap/refid185 2008-08-19T18:52:20Z

Knowledge of how molecules interact in space and time is crucial for understanding cellular processes. A host of novel techniques have been developed for the visualisation of single target molecules in living cells, many based on fluorescence in situ hybridisation (FISH) or immunocytochemistry (IC). To extend the applicability of FISH to living cells, special backbone-modified probes and specific ...<br/><br/>Hans J Tanke, Roeland W Dirks, Ton Raap (2005) <i>Curr Opin Biotechnol</i> <i></i> <i></i> 16: 1 49-54<br/>

http://publicationslist.org/a.k.raap/refid16 2008-08-19T18:50:29Z

Mutations in mitochondrial DNA (mtDNA) associate with various disease states. A few mtDNA mutations strongly associate with diabetes, with the most common mutation being the A3243G mutation in the mitochondrial DNA-encoded tRNA(Leu,UUR) gene. This article describes clinical characteristics of mitochondrial diabetes and its molecular diagnosis. Furthermore, it outlines recent developments in the pa...<br/><br/>J Antonie Maassen, Leen M 'T Hart, Einar Van Essen, Rob J Heine, Giel Nijpels, Roshan S Jahangir Tafrechi, Anton K Raap, George M C Janssen, Herman H P J Lemkes (2004) <i>Diabetes</i> <i></i> <i></i> 53 Suppl 1: S103-S109<br/>

http://publicationslist.org/a.k.raap/refid11 2008-08-19T18:50:29Z

Molecular cytogenetic analysis frequently shows human papillomavirus (HPV) integration near translocation breakpoints in cervical cancer cells. We have recently described a cluster of HPV18 integrations in the distal end of the common fragile site FRA8C at 8q24 in primary cervical carcinoma samples. Chromosome band 8q24 contains the MYC gene (alias c-MYC), FRA8C, and FRA8D. The MYC gene is frequen...<br/><br/>Matthew J Ferber, Paul Eilers, Ed Schuuring, James A L Fenton, Gert Jan Fleuren, Gemma Kenter, Károly Szuhai, David I Smith, Anton K Raap, Antoinette A T P Brink (2004) <i>Cancer Genet Cytogenet</i> <i></i> <i></i> 154: 1 1-9<br/>

http://publicationslist.org/a.k.raap/refid12 2008-08-19T18:50:29Z

Joop Wiegant, Kirsten Brouwer, Vladimir Bezrookove, Shirley Smits, Anton K Raap, Abraham Bout, Hans J Tanke (2004) <i>Biotechniques</i> <i></i> <i></i> 37: 2 <br/>

http://publicationslist.org/a.k.raap/refid13 2008-08-19T18:50:29Z

A novel microarray system that utilizes a porous aluminum-oxide substrate and flow-through incubation has been developed for rapid molecular biological testing. To assess its utility in gene expression analysis, we determined hybridization kinetics, variability, sensitivity and dynamic range of the system using amplified RNA. To show the feasibility with complex biological RNA, we subjected Jurkat...<br/><br/>Ying Wu, Peggy de Kievit, Lars Vahlkamp, Dirk Pijnenburg, Maarten Smit, Martijn Dankers, Diana Melchers, Martijn Stax, Piet J Boender, Colin Ingham, Niek Bastiaensen, Rik de Wijn, Dirk van Alewijk, Henk van Damme, Anton K Raap, Alan B Chan, Rinie van Beuningen (2004) <i>Nucleic Acids Res</i> <i></i> <i></i> 32: 15 <br/>

http://publicationslist.org/a.k.raap/refid15 2008-08-19T18:50:29Z

Cytogenetic studies in a patient with acute myelocytic leukemia (AML) revealed as the sole karyotypic alteration a half-cryptic rearrangement, identified with 48-color combined binary ratio-labeled fluorescence in situ hybridization (pq-COBRA-FISH) as a reciprocal t(6;14)(q?;q?). The breakpoints were later assigned on the basis of G-banding to t(6;14)(q25-q26;q32). FISH experiments using genomic p...<br/><br/>Vladimir Bezrookove, Shama L van Zelderen-Bhola, Antoinette Brink, Károly Szuhai, Anton K Raap, Renee Barge, Geoffrey C Beverstock, Carla Rosenberg (2004) <i>Cancer Genet Cytogenet</i> <i></i> <i></i> 149: 1 72-76<br/>

http://publicationslist.org/a.k.raap/refid8 2008-08-19T18:50:29Z

Methods are needed to study single molecules to reveal variability, interactions and mechanisms that may go undetected at the level of populations of molecules. We describe here an integrated series of reaction steps that allow individual nucleic acid molecules to be detected with excellent specificity. Oligonucleotide probes are circularized after hybridization to target sequences that have been ...<br/><br/>Chatarina Larsson, Jørn Koch, Anders Nygren, George Janssen, Anton K Raap, Ulf Landegren, Mats Nilsson (2004) <i>Nat Methods</i> <i></i> <i></i> 1: 3 227-232<br/>

http://publicationslist.org/a.k.raap/refid14 2008-08-19T18:50:29Z

Fluorescent cis-platinum compounds that react with the N7 atom of guanine are useful for labeling nucleic acids influorescence hybridization applications. Here we report that cyanin (CyN) cis-platinum labeling of DNA samples for array comparative genomic hybridizations (arrayCGH) can be achieved reproducibly and reliably. We demonstrate that degrees of labeling of approximately 1% of all nucleotid...<br/><br/>Anton K Raap, Marja J M van der Burg, Jeroen Knijnenburg, Eric Meershoek, Carla Rosenberg, Joe W Gray, Joop Wiegant, J Graeme Hodgson, Hans J Tanke (2004) <i>Biotechniques</i> <i></i> <i></i> 37: 1 130-134<br/>

http://publicationslist.org/a.k.raap/refid20 2008-08-19T18:50:29Z

The synthesis, characterization, and molecular interactions of platinum(II) coordination compounds, which contain a distal nonradioactive reporter molecule, with mono- and polynucleotides are described. A [Pt(II)(en)(NH(2)(CH(2))(6)NH-tBoc)Cl](NO(3)) (en=ethylenediamine) entity has been coupled, after removal of the tBoc group, to a number of hapten and fluorophore molecules through succinimide de...<br/><br/>R J Heetebrij, E G Talman, M A v Velzen, R P M van Gijlswijk, S S Snoeijers, M Schalk, J Wiegant, F v d Rijke, R M Kerkhoven, A K Raap, H J Tanke, J Reedijk, H-J Houthoff (2003) <i>Chembiochem</i> <i></i> <i></i> 4: 7 573-583<br/>

http://publicationslist.org/a.k.raap/refid18 2008-08-19T18:50:29Z

Chemical induction of premature chromosome condensation (PCC) was investigated and optimized to be able to analyze the chromosomal constitution of cancer cells independent of mitosis and with minimal culture artifacts. A potent protein phosphatase inhibitor, calyculin A, was used to induce PCC in normal diploid cells, in several established human tumor cell lines, and in cells isolated from freshl...<br/><br/>Vladimir Bezrookove, Ron Smits, Gabriela Moeslein, Riccardo Fodde, Hans Johannes Tanke, Anton Klaas Raap, Firouz Darroudi (2003) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 38: 2 177-186<br/>

http://publicationslist.org/a.k.raap/refid19 2008-08-19T18:50:29Z

Cryptic subtelomeric chromosome rearrangements play an important role in the aetiology of mental retardation, congenital anomalies, miscarriages and neoplasia. To facilitate a comprehensive molecular-cytogenetic analysis of these extremely gene-rich and mutation-prone chromosome regions, novel multicolour fluorescence in situ hybridisation (FISH) techniques are being developed. As yet, subtelomeri...<br/><br/>Hartmut Engels, Antje Ehrbrecht, Susanne Zahn, Kristin Bosse, Hans Vrolijk, Stefan White, Vera Kalscheuer, Jan M N Hoovers, Gesa Schwanitz, Peter Propping, Hans J Tanke, Joop Wiegant, Anton K Raap (2003) <i>Eur J Hum Genet</i> <i></i> <i></i> 11: 9 643-651<br/>

http://publicationslist.org/a.k.raap/refid21 2008-08-19T18:50:29Z

Recently, fluorescent, monofunctional cis-platin derivatives have been developed to chemically label nucleic acids for use in fluorescent hybridization assays. Here we show by hybridizations to microarrays containing oligonucleotide probes for the 3' ends, middle parts, and 5' ends of mRNAs, that this labeling methodology bypasses the problem of the 3' end bias that is characteristic of the conven...<br/><br/>R Hagedoorn, R Joseph, S Kasanmoentalib, P Eilers, J Killian, A K Raap (2003) <i>Biotechniques</i> <i></i> <i></i> 34: 5 974-6, 978, 980<br/>

http://publicationslist.org/a.k.raap/refid17 2008-08-19T18:50:29Z

Fluorescent and haptenized, monofunctionally binding platinum compounds are increasingly used for chemically labeling nucleic acids for hybridization detection purposes. Here we analyze in detail the effect of labeling density of the cyanin-3 and -5 platinum DNA adducts on fluorescence and thermal stability. We also analyzed the kinetics of the reaction of the cyanin platinum compounds with DNA. T...<br/><br/>Frans M van de Rijke, Robert J Heetebrij, Eduard G Talman, Hans J Tanke, Anton K Raap (2003) <i>Anal Biochem</i> <i></i> <i></i> 321: 1 71-78<br/>

http://publicationslist.org/a.k.raap/refid25 2008-08-19T18:50:29Z

We describe a method to monitor rolling-circle replication of circular oligonucleotides in dual-color and in real-time using molecular beacons. The method can be used to study the kinetics of the polymerization reaction and to amplify and quantify circularized oligonucleotide probes in a rolling-circle amplification (RCA) reaction. Modified molecular beacons were made of 2'-O-Me-RNA to prevent 3' ...<br/><br/>Mats Nilsson, Mats Gullberg, Fredrik Dahl, Karoly Szuhai, Anton K Raap (2002) <i>Nucleic Acids Res</i> <i></i> <i></i> 30: 14 <br/>

http://publicationslist.org/a.k.raap/refid24 2008-08-19T18:50:29Z

Growth hormone (GH) has direct effects on the growth plate to stimulate longitudinal growth, but it is not clear which chondrocyte populations GH acts on. The dual effector theory suggests that GH would act primarily on the "stem cells." However, staining with a GH receptor (GHR) antibody is found in all layers of the growth plate in rabbits and humans. We now have investigated the localization an...<br/><br/>Evelien F Gevers, Bram C J van der Eerden, Marcel Karperien, Anton K Raap, Iain C A F Robinson, Jan-Maarten Wit (2002) <i>J Bone Miner Res</i> <i></i> <i></i> 17: 8 1408-1419<br/>

http://publicationslist.org/a.k.raap/refid22 2008-08-19T18:50:29Z

Jaennelle Kraan, Anne R M von Bergh, Karin Kleiverda, Jan-Willem Vaandrager, Ekaterina S Jordanova, Anton K Raap, Philip M Kluin, Ed Schuuring (2002) <i>Methods Mol Biol</i> <i></i> <i></i> 204: 143-153<br/>

http://publicationslist.org/a.k.raap/refid26 2008-08-19T18:50:29Z

Mutations in the connexin 26 (Cx26) gene (GJB2) are associated with autosomal nonsyndromic sensorineural hearing loss. This study describes mutations in the Cx26 gene in cases of familial and sporadic hearing loss (HL) by gene sequencing and identifies the allelic frequency of the most common mutation leading to HL (35delG) in the population of eastern Austria. For this purpose we have developed a...<br/><br/>Klemens Frei, Károly Szuhai, Trevor Lucas, Klara Weipoltshammer, Christian Schöfer, Reinhard Ramsebner, Wolf-Dieter Baumgartner, Anton K Raap, Reginald Bittner, Franz J Wachtler, Karin Kirschhofer (2002) <i>Eur J Hum Genet</i> <i></i> <i></i> 10: 7 427-432<br/>

http://publicationslist.org/a.k.raap/refid27 2008-08-19T18:50:29Z

Infection with high-risk type human papillomavirus (HPV) is a necessary causal factor in the pathogenesis of cervical carcinoma. In most invasive cervical cancers, HPV is integrated in the host cell genome, and additional genetic aberrations are observed among which are chromosomal aberrations. To analyze in detail such often complex chromosomal changes and simultaneously map HPV integration sites...<br/><br/>Antoinette A T P Brink, Joop C A G Wiegant, Károly Szuhai, Hans J Tanke, Gemma G Kenter, Gert-Jan Fleuren, Ed Schuuring, Anton K Raap (2002) <i>Cancer Genet Cytogenet</i> <i></i> <i></i> 134: 2 145-150<br/>

http://publicationslist.org/a.k.raap/refid23 2008-08-19T18:50:29Z

A multi-colour fluorescence in situ hybridisation (MFISH) assay has been developed, for simultaneous visualisation of all human chromosomes in 24 different colours. This assay is based on the simultaneous use of combinatorial labelling and ratio labelling, the so called combined binary ratio labelling (COBRA). This technique is used to study the spectra of chromosomal exchanges induced by X ray an...<br/><br/>F Darroudi, V Bezrookove, J Fomina, W E Mesker, J C A G Wiegant, A K Raap, H J Tanke (2002) <i>Radiat Prot Dosimetry</i> <i></i> <i></i> 99: 1-4 189-192<br/>

http://publicationslist.org/a.k.raap/refid30 2008-08-19T18:50:29Z

An important application of robotically spotted DNA microarrays is the monitoring of RNA expression levels. A clear limitation of this technology is the relatively large amount of RNA that is required per hybridization as a result of low hybridization efficiency and limiting detection sensitivity provided by conventional fluorescent reporters. We have used a recently introduced luminescent reporte...<br/><br/>F van De Rijke, H Zijlmans, S Li, T Vail, A K Raap, R S Niedbala, H J Tanke (2001) <i>Nat Biotechnol</i> <i></i> <i></i> 19: 3 273-276<br/>

http://publicationslist.org/a.k.raap/refid28 2008-08-19T18:50:29Z

Human papillomaviruses (HPVs) play an important role in the pathogenesis of cervical cancer. For identification of the large number of different HPV types found in (pre)malignant lesions, a robust methodology is needed that combines general HPV detection with HPV genotyping. We have developed for formaldehyde-fixed samples a strategy that, in a homogeneous, real-time fluorescence polymerase chain ...<br/><br/>K Szuhai, E Sandhaus, S M Kolkman-Uljee, M Lemaître, J C Truffert, R W Dirks, H J Tanke, G J Fleuren, E Schuuring, A K Raap (2001) <i>Am J Pathol</i> <i></i> <i></i> 159: 5 1651-1660<br/>

http://publicationslist.org/a.k.raap/refid29 2008-08-19T18:50:29Z

U1snRNA, U3snRNA, 28 S ribosomal RNA, poly(A) RNA and a specific messenger RNA were visualized in living cells with microinjected fluorochrome-labeled 2' O-Methyl oligoribonucleotides (2' OMe RNA). Antisense 2' OMe RNA probes showed fast hybridization kinetics, whereas conventional oligodeoxyribonucleotide (DNA) probes did not. The nuclear distributions of the signals in living cells were similar ...<br/><br/>C Molenaar, S A Marras, J C Slats, J C Truffert, M Lemaître, A K Raap, R W Dirks, H J Tanke (2001) <i>Nucleic Acids Res</i> <i></i> <i></i> 29: 17 E89-E89<br/>

http://publicationslist.org/a.k.raap/refid188 2009-04-15T10:24:07Z

This unit presents protocols for preparing human metaphase chromosome slides from peripheral blood lymphocytes, isolating interphase nuclei from lymphocytes and paraffin-embedded tissues, and preparing DNA fibers. The protocols are designed so that the resulting preparations are amenable to FISH. The methods correspond to a selection of the specimens that can be analyzed with FISH techniques, and ...<br/><br/>J Wiegant, A K Raap (2001) <i>Curr Protoc Cytom</i> <i></i> <i></i> Chapter 8: <br/>

http://publicationslist.org/a.k.raap/refid189 2009-04-15T10:24:07Z

This unit presents an overview of the FISH methodology. It covers such topics as direct versus indirect methods, sensitivity, multiplicity, resolution, and applications.<br/><br/>A K Raap (2001) <i>Curr Protoc Cytom</i> <i></i> <i></i> Chapter 8: <br/>

http://publicationslist.org/a.k.raap/refid187 2009-04-15T10:24:07Z

This unit describes in detail basic protocols for probe labeling, denaturing of in situ target DNA, in situ hybridization, and post-hybridization washes. Support protocols for probe labeling cover probe purification and quality control.<br/><br/>J Wiegant, A K Raap (2001) <i>Curr Protoc Cytom</i> <i></i> <i></i> Chapter 8: <br/>

http://publicationslist.org/a.k.raap/refid34 2008-08-19T18:50:29Z

A method is presented to conjugate horseradish peroxidase (HRP) to oligodeoxynucleotides for fluorescence in situ hybridization assays employing tyramide signal amplification (TSA). HRP is covalently bound to the oligonucleotide by thiol ether linkage and purified by high-performance liquid chromatography. With TSA detection, a single HRP-labeled oligonucleotide probe is sufficient for in situ det...<br/><br/>R P van Gijlswijk, M P van de Corput, V Bezrookove, J Wiegant, H J Tanke, A K Raap (2000) <i>Histochem Cell Biol</i> <i></i> <i></i> 113: 3 175-180<br/>

http://publicationslist.org/a.k.raap/refid35 2008-08-19T18:50:29Z

We have recently diagnosed a patient with anaemia, severe tubulopathy, and diabetes mellitus. As the clinical characteristics resembled Pearson marrow-pancreas syndrome, despite the absence of malfunctioning of the exocrine pancreas in this patient, we have performed DNA analysis to seek for deletions in mtDNA. DNA analysis showed a novel heteroplasmic deletion in mtDNA of 8034bp in length, with h...<br/><br/>J M van den Ouweland, J B de Klerk, M P van de Corput, R W Dirks, A K Raap, H R Scholte, J G Huijmans, L M Hart, G J Bruining, J A Maassen (2000) <i>Eur J Hum Genet</i> <i></i> <i></i> 8: 3 195-203<br/>

http://publicationslist.org/a.k.raap/refid32 2008-08-19T18:50:29Z

The simultaneous identification, by fluorescence in situ hybridisation (FISH), of each chromosome in a distinct colour became feasible a few years ago. The key question in the application of this and many other developments in molecular cytogenetics to clinical situations is whether the results add significant further information that is relevant to the diagnosis. So far, limited data exist regard...<br/><br/>V Bezrookove, K Hansson, M van der Burg, J J van der Smagt, Y Hilhorst-Hofstee, J Wiegant, G C Beverstock, A K Raap, H Tanke, M H Breuning, C Rosenberg (2000) <i>Hum Genet</i> <i></i> <i></i> 106: 4 392-398<br/>

http://publicationslist.org/a.k.raap/refid36 2008-08-19T18:50:29Z

Combined binary ratio labeling (COBRA) fluorescence in situ hybridization (FISH) allows 24-color FISH karyotyping of human metaphase chromosomes utilizing only four fluorochromes, instead of the five required for combinatorial labeling procedures. Here we show that by introduction of a fifth fluorochrome, COBRA-FISH permits molecular cytogenetic mapping of viral integration sites in complex karyot...<br/><br/>K Szuhai, V Bezrookove, J Wiegant, J Vrolijk, R W Dirks, C Rosenberg, A K Raap, H J Tanke (2000) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 28: 1 92-97<br/>

http://publicationslist.org/a.k.raap/refid33 2008-08-19T18:50:29Z

Fluorescence in situ hybridization to DNA fibers (Fiber-FISH) is a high-resolution, wide-ranging physical DNA mapping method that finds increasing application in the study of pathological gene rearrangements. Here we present experiments designed to understand the nature of the discontinuous FISH signal patterns seen after Fiber-FISH. Use of a novel cisplatin-based chemical labeling method enabled ...<br/><br/>F M van de Rijke, R J Florijn, H J Tanke, A K Raap (2000) <i>J Histochem Cytochem</i> <i></i> <i></i> 48: 6 743-745<br/>

http://publicationslist.org/a.k.raap/refid31 2008-08-19T18:50:29Z

Recently we developed a novel strategy for differentially painting all 24 human chromosomes. It is termed COBRA-FISH, short for combined binary ratio labeling-fluorescence in situ hybridization. COBRA-FISH is distinct from the pure combinatorial approach in that only 4 instead of 5 fluorophores are needed to achieve color discrimination of 24 targets. Furthermore, multiplicity can be increased to ...<br/><br/>J Wiegant, V Bezrookove, C Rosenberg, H J Tanke, A K Raap, H Zhang, M Bittner, J M Trent, P Meltzer (2000) <i>Genome Res</i> <i></i> <i></i> 10: 6 861-865<br/>

http://publicationslist.org/a.k.raap/refid184 2008-08-19T18:52:20Z

Rearrangement of the BCL2 gene is an important parameter for the differential diagnosis of non-Hodgkin lymphomas. Although a relatively large proportion of breakpoints is clustered, many are missed by standard PCR. A FISH assay is therefore desired. Up to now, a lack of probes flanking the BCL2 gene has limited the possibilities for a FISH assay to an approach based on colocalization of probes for...<br/><br/>J W Vaandrager, E Schuuring, T Raap, K Philippo, K Kleiverda, P Kluin (2000) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 27: 1 85-94<br/>

http://publicationslist.org/a.k.raap/refid38 2008-08-19T18:50:29Z

To date, despite the increasing number of genomic tools, there is no repository of ordered human BAC clones that covers entire chromosomes. This project presents a resource of mapped large DNA fragments that span eight human chromosomes at approximately 1-Mb resolution. These DNA fragments are bacterial artificial chromosome (BAC) clones anchored to sequence tagged site (STS) markers. This clone c...<br/><br/>V G Cheung, H L Dalrymple, S Narasimhan, J Watts, G Schuler, A K Raap, M Morley, A Bruzel (1999) <i>Genome Res</i> <i></i> <i></i> 9: 10 989-993<br/>

http://publicationslist.org/a.k.raap/refid39 2008-08-19T18:50:29Z

Comparative genomic hybridization (CGH) has become a powerful technique for studying gains and losses of DNA sequences in solid tumors. Importantly, DNA derived from archival tumor tissue is also applicable in CGH analysis. However, DNA isolated from routinely processed, formalin-fixed, paraffin-embedded tissue is often degraded, with the bulk of DNA showing fragment sizes of only 400-750 bp. Enzy...<br/><br/>J C Alers, J Rochat, P J Krijtenburg, H van Dekken, A K Raap, C Rosenberg (1999) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 25: 3 301-305<br/>

http://publicationslist.org/a.k.raap/refid40 2008-08-19T18:50:29Z

Multicolour in situ hybridisation (MFISH) is increasingly applied to karyotyping and detection of chromosomal abnormalities. So far 27 colour analyses have been described using fluorescently labelled chromosome painting probes in a so-called combinatorial approach. In this paper a new strategy is presented to use efficiently the currently available number of spectrally separated fluorophores in or...<br/><br/>H J Tanke, J Wiegant, R P van Gijlswijk, V Bezrookove, H Pattenier, R J Heetebrij, E G Talman, A K Raap, J Vrolijk (1999) <i>Eur J Hum Genet</i> <i></i> <i></i> 7: 1 2-11<br/>

http://publicationslist.org/a.k.raap/refid37 2008-08-19T18:50:29Z

The broad extension of an existing chemical DNA labeling technique for molecular cytogenetics is described. Called the Universal Linkage System (ULS(TM)), it is based on the capability of monoreactive cisplatin derivatives to react at the N7 position of guanine moieties in DNA. Simple repetitive probes, cosmids, PACs, and chromosome-specific painting probes were labeled by ULS and used in a series...<br/><br/>J C Wiegant, R P van Gijlswijk, R J Heetebrij, V Bezrookove, A K Raap, H J Tanke (1999) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 87: 1-2 47-52<br/>

http://publicationslist.org/a.k.raap/refid47 2008-08-19T18:50:29Z

Biotin deoxyuridine 5'-triphosphate (dUTP) and digoxigenin dUTP are the labels most commonly used in comparative genomic hybridization (CGH). The relative infrequent use of direct fluorochrome-labeled nucleotides in CGH is related to the lower sensitivity they provide. Here we report the evaluation of two fluorochrome-conjugated nucleotides that have not been previously used in CGH (lissamine-5-dU...<br/><br/>C Rosenberg, R P van Gijlswijk, C B Vos, J Wiegant, C J Cornelisse, H J Tanke, A K Raap (1998) <i>Cytometry</i> <i></i> <i></i> 32: 4 337-341<br/>

http://publicationslist.org/a.k.raap/refid46 2008-08-19T18:50:29Z

Immunoglobulin class switching usually involves deletion of part of the immunoglobulin CH region. By DNA fiber fluorescence in situ hybridization (FISH) with a barcode of probes covering the DH, JH, and CH genes, the configuration of the entire CH region can be visualized on single DNA molecules. Using this technique, we have studied class switching in three types of B-cell neoplasia, mantle-cell ...<br/><br/>J W Vaandrager, E Schuuring, H C Kluin-Nelemans, M J Dyer, A K Raap, P M Kluin (1998) <i>Blood</i> <i></i> <i></i> 92: 8 2871-2878<br/>

http://publicationslist.org/a.k.raap/refid48 2008-08-19T18:50:29Z

The techniques of in situ hybridization (ISH) are widely applied for analyzing the genetic make-up and RNA expression patterns of individual cells. This review focusses on a number of advances made over the last 5 years in the fluorescence ISH (FISH) field, i.e., Fiber-FISH, Multi-colour chromosome painting, Comparative Genomic Hybridization, Tyramide Signal Amplification and FISH with Polypeptide...<br/><br/>A K Raap (1998) <i>Mutat Res</i> <i></i> <i></i> 400: 1-2 287-298<br/>

http://publicationslist.org/a.k.raap/refid50 2008-08-19T18:50:29Z

Using RNA in situ hybridization to reveal cytoplasmic localization patterns of mRNAs in cultured cells, we noted unexpected staining of a cytoplasmic component in telophase cells. Control experiments revealed that the anti-digoxin-specific antibody was responsible for this staining. Because the staining was observed only at a position where both daughter cells are still connected, we identified th...<br/><br/>R W Dirks, A K Raap (1998) <i>J Histochem Cytochem</i> <i></i> <i></i> 46: 6 779-782<br/>

http://publicationslist.org/a.k.raap/refid49 2008-08-19T18:50:29Z

Telomeres are G/C-rich repetitive DNA sequences at the end of all eukaryotic chromosomes. The loss of telomeric repeat sequences during cell divisions has been proposed as a possible mechanism for cell senescence. The standard procedure for measurement of telomere length is Southern blot (SB) hybridization with a telomere-specific probe. However, in using this technique no information can be obtai...<br/><br/>E S de Pauw, N P Verwoerd, N Duinkerken, R Willemze, A K Raap, W E Fibbe, H J Tanke (1998) <i>Cytometry</i> <i></i> <i></i> 32: 3 163-169<br/>

http://publicationslist.org/a.k.raap/refid45 2008-08-19T18:50:29Z

In Trypanosoma brucei, transcription by RNA polymerase II and 5' capping of messenger RNA are uncoupled: a capped spliced leader is trans spliced to every RNA. This decoupling makes it possible to have protein-coding gene transcription driven by RNA polymerase I. Indeed, indirect evidence suggests that the genes for the major surface glycoproteins, variant surface glycoproteins (VSGs) in bloodstre...<br/><br/>I Chaves, J Zomerdijk, A Dirks-Mulder, R W Dirks, A K Raap, P Borst (1998) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 95: 21 12328-12333<br/>

http://publicationslist.org/a.k.raap/refid43 2008-08-19T18:50:29Z

We have used horseradish peroxidase-labeled 40 mer oligodeoxynucleotides (HRP-ODNs) specific for the human cytomegalovirus immediate early gene (HCMV-IE) and a novel dinitrophenol-tyramide signal amplification reagent (DNP-TSA plus) to evaluate their utility in fluorescence in situ hybridization (FISH). For DNA FISH, single or cocktails of HRP-ODNs were hybridized to metaphase chromosomes of rat 9...<br/><br/>M P van de Corput, R W Dirks, R P van Gijlswijk, F M van de Rijke, A K Raap (1998) <i>Histochem Cell Biol</i> <i></i> <i></i> 110: 4 431-437<br/>

http://publicationslist.org/a.k.raap/refid42 2008-08-19T18:50:29Z

No data on the chromosomal constitution of spermatocytic seminomas are available thus far because of their rarity. Ploidy analysis performed on paraffin-embedded cases showed varying results from (near-) diploid to aneuploid. We applied comparative genomic hybridization on four snap-frozen primary spermatocytic seminomas of three different patients. Conventional cytogenetic analysis was successful...<br/><br/>C Rosenberg, M C Mostert, T B Schut, M van de Pol, J van Echten, B de Jong, A K Raap, H Tanke, J W Oosterhuis, L H Looijenga (1998) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 23: 4 286-291<br/>

http://publicationslist.org/a.k.raap/refid41 2008-08-19T18:50:29Z

To further define the structure of the pericentromeric region of human chromosome 7, we have identified and characterized a YAC clone (YAC 311.H5) containing the D7S1480 locus, which maps to the short arm near the centromere of this chromosome, by linkage in CEPH families and radiation hybrid analysis. This YAC contains two new blocks of alphoid DNA (named Z5 and Z6). Both Z5 and Z6 show monomeric...<br/><br/>A de la Puente, E Velasco, L A Pérez Jurado, C Hernández-Chico, F M van de Rijke, S W Scherer, A K Raap, J Cruces (1998) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 83: 3-4 176-181<br/>

http://publicationslist.org/a.k.raap/refid44 2008-08-19T18:50:29Z

With the ongoing progress in human genome projects, many genes are discovered whose function and/or expression pattern are not known. Most of these genes are expressed in relatively low abundance compared to housekeeping genes such as elongation factor-1alpha and beta-actin. Gene expression is studied by Northern blot assays or by semiquantitative PCR methods. Another method is the visualization o...<br/><br/>M P van de Corput, R W Dirks, R P van Gijlswijk, E van Binnendijk, C M Hattinger, R A de Paus, J E Landegent, A K Raap (1998) <i>J Histochem Cytochem</i> <i></i> <i></i> 46: 11 1249-1259<br/>

http://publicationslist.org/a.k.raap/refid55 2008-08-19T18:50:29Z

The peroxidase-mediated deposition of hapten- and fluorochrome-labeled tyramides has recently been shown to increase the sensitivity of immunofluorescence and fluorescence in situ hybridization techniques. We have evaluated a number of red, green, and blue fluorescent tyramides for detection of antigens in tissue sections and cytospin preparations and for the detection of hapten- and horseradish p...<br/><br/>R P van Gijlswijk, H J Zijlmans, J Wiegant, M N Bobrow, T J Erickson, K E Adler, H J Tanke, A K Raap (1997) <i>J Histochem Cytochem</i> <i></i> <i></i> 45: 3 375-382<br/>

http://publicationslist.org/a.k.raap/refid57 2008-08-19T18:50:29Z

DNA fibers can be released from cell suspensions and frozen tissue and can be used as a template for hybridization with multiple differently labeled probes. Simultaneous hybridization with 5-10 adjacent or partly overlapping probes generates a highly specific "color barcode" for individual DNA segments. Rearrangements in this barcode can be easily detected and mapped. The resolution of DNA fiber F...<br/><br/>J W Vaandrager, J K Kleiverda, E Schuuring, J C Kluin-Nelemans, A K Raap, P M Kluin (1997) <i>Verh Dtsch Ges Pathol</i> <i></i> <i></i> 81: 306-311<br/>

http://publicationslist.org/a.k.raap/refid59 2008-08-19T18:50:29Z

Pearson's marrow/pancreas syndrome is a disease associated with a large mitochondrial DNA (mtDNA) deletion. The various tissues of a patient contain heteroplasmic populations of wild-type (WT) and deleted mtDNA molecules. The clinical phenotype of Pearson's syndrome is variable and is not correlated with the size and position of the deletion. The histo- and cytological distribution of WT and delet...<br/><br/>M P van de Corput, J M van den Ouweland, R W Dirks, L M Hart, G J Bruining, J A Maassen, A K Raap (1997) <i>J Histochem Cytochem</i> <i></i> <i></i> 45: 1 55-61<br/>

http://publicationslist.org/a.k.raap/refid54 2008-08-19T18:50:29Z

Marginal zone B cell lymphoma (MZBCL) represents a distinct subtype of B cell non-Hodgkin's lymphoma, which has been recently recognized and defined as a disease entity. We investigated 25 cases (18 at primary diagnosis and seven during the course of disease) of MZBCL by comparative genomic hybridization (CGH) and compared these results with cytogenetic, fluorescence in situ hybridization (FISH), ...<br/><br/>J Dierlamm, C Rosenberg, M Stul, S Pittaluga, I Wlodarska, L Michaux, M Dehaen, G Verhoef, J Thomas, W de Kelver, T Bakker-Schut, J J Cassiman, A K Raap, C De Wolf-Peeters, H Van den Berghe, A Hagemeijer (1997) <i>Leukemia</i> <i></i> <i></i> 11: 5 747-758<br/>

http://publicationslist.org/a.k.raap/refid58 2008-08-19T18:50:29Z

A K Raap, F M van de Rijke, R W Dirks (1997) <i>Methods Mol Biol</i> <i></i> <i></i> 75: 367-375<br/>

http://publicationslist.org/a.k.raap/refid56 2008-08-19T18:50:29Z

Before being transported to the cytoplasm, intron-containing pre-mRNAs have to be spliced somewhere in the cell nucleus. Efficient splicing requires an ordered assembly of splicing factors onto the pre-mRNAs. To accomplish this, intron containing genes may be preferentially localized at nuclear sites enriched for splicing factors or alternatively, splicing factors may circulate throughout the nucl...<br/><br/>R W Dirks, E S de Pauw, A K Raap (1997) <i>J Cell Sci</i> <i></i> <i></i> 110 ( Pt 4): 515-522<br/>

http://publicationslist.org/a.k.raap/refid53 2008-08-19T18:50:29Z

The ultra-long telomeres that have been observed in mice are not in accordance with the concept that critical telomere shortening is related to aging and immortalization. Here, we have used quantitative fluorescence in situ hybridization to estimate (T2AG3)n lengths of individual telomeres in various mouse strains. Telomere lengths were very heterogeneous, but specific chromosomes of bone marrow c...<br/><br/>J M Zijlmans, U M Martens, S S Poon, A K Raap, H J Tanke, R K Ward, P M Lansdorp (1997) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 94: 14 7423-7428<br/>

http://publicationslist.org/a.k.raap/refid51 2008-08-19T18:50:29Z

Oestradiol has been conjugated to allylamine-dUTP with an 11-atom spacer to allow enzymatic incorporation of the label into DNA sequences. In a comparative DNA and mRNA FISH study we have used DNA probes that were either labelled with digoxigenin, biotin or oestradiol. Results show that oestradiol-labelled probes can detect DNA and RNA sequences in FISH equally well as digoxigenin- and biotin-labe...<br/><br/>M P van de Corput, R W Dirks, W W Wiegant, J Wiegant, K Mühlegger, A K Raap (1997) <i>Histochem Cell Biol</i> <i></i> <i></i> 108: 4-5 359-364<br/>

http://publicationslist.org/a.k.raap/refid52 2008-08-19T18:50:29Z

Hypotriploidy/hyperdiploidy ("intermediate ploidy") often occurs in testicular germ cell tumors of adolescents and adults. Disomic and trisomic chromosomes represent significant parts of the tumor genome and a few chromosomes fall outside the two- to three-copy number range. We performed comparative genomic hybridization (CGH) with DNA isolated from a cell line from a case of testicular germ cell ...<br/><br/>C Rosenberg, T B Schut, M C Mostert, H J Tanke, A K Raap, J W Oosterhuis, L H Looijenga (1997) <i>Cytometry</i> <i></i> <i></i> 29: 2 113-121<br/>

http://publicationslist.org/a.k.raap/refid72 2008-08-19T18:50:29Z

Recently, a peroxidase-mediated amplification system has been described for immunofluorescence and fluorescence in situ hybridization studies. It is based on the deposition of hapten- or fluorochrome-labeled tyramide molecules. Although providing a significantly increased detection sensitivity compared to conventional procedures, its localization properties are inferior because of free diffusion o...<br/><br/>R P van Gijlswijk, J Wiegant, A K Raap, H J Tanke (1996) <i>J Histochem Cytochem</i> <i></i> <i></i> 44: 4 389-392<br/>

http://publicationslist.org/a.k.raap/refid71 2008-08-19T18:50:29Z

Fluorescence in situ hybridization on human metaphase chromosomes is detected by near-field scanning optical microscopy. This combination of cytochemical and scanning probe techniques enables the localization and identification of several fluorescently labelled genomic DNA fragments on a single chromosome with an unprecedented resolution. Three nucleic acid probes are used: pUC1.77, p1-79 and the ...<br/><br/>M H Moers, W H Kalle, A G Ruiter, J C Wiegant, A K Raap, J Greve, B G de Grooth, N F van Hulst (1996) <i>J Microsc</i> <i></i> <i></i> 182: Pt 1 40-45<br/>

http://publicationslist.org/a.k.raap/refid70 2008-08-19T18:50:29Z

Synthesis of fluorochrome-modified deoxyribonucleotides has been carried out mostly by linking the fluorochrome molecule to the C-5 position of dUTP via an allylamine spacer, similar to the modification of allylamine-dUTP with the haptens biotin and digoxigenin. Recently, a new series of fluorescent nucleotides has been prepared by using an alkynyl bridge between the uracil moiety and the fluoroch...<br/><br/>J Wiegant, N Verwoerd, S Mascheretti, M Bolk, H J Tanke, A K Raap (1996) <i>J Histochem Cytochem</i> <i></i> <i></i> 44: 5 525-529<br/>

http://publicationslist.org/a.k.raap/refid73 2008-08-19T18:50:29Z

Fluorescence in situ hybridization (FISH) applied to metaphase chromosomes provides a mapping resolution of 1 to 3 Mb. FISH applied to interphase nuclei has a resolution of 50 kb and ranges 1-2 Mb. This better resolution is attributed to the higher degree of chromatin decondensation. Here, we describe FISH applied to naked DNA fibers (fiber FISH) and show that with such fully decondensed chromatin...<br/><br/> Raap, Florijn, Blonden, Wiegant, Vaandrager, Vrolijk, den Dunnen J, Tanke, van Ommen GJ (1996) <i>Methods</i> <i></i> <i></i> 9: 1 67-73<br/>

http://publicationslist.org/a.k.raap/refid183 2008-08-19T18:52:20Z

Rearrangements within the chromosome 11q13 region are frequent in hematologic malignancies. 50% of 75% of mantle cell lymphomas (MCLs) carry a translocation t(11;14) (q13;q32). Using Southern blot analysis, a BCL1 breakpoint can be detected in approximately 50% of MCLs. It is not known whether other MCLs harbor also breakpoints at 11q13. Breakpoints in this region not involved in t(11;14), are det...<br/><br/>L J Coignet, E Schuuring, R E Kibbelaar, T K Raap, K K Kleiverda, M F Bertheas, J Wiegant, G Beverstock, P M Kluin (1996) <i>Blood</i> <i></i> <i></i> 87: 4 1512-1519<br/>

http://publicationslist.org/a.k.raap/refid76 2008-08-19T18:50:29Z

The relevant microscopical conditions for the optimal visualization of ratio-color FISH stained cells were investigated. Special attention was given to the influence of the type of illumination, (semi)-critical vs. Köhler type illumination, in combination with the use of multi-band excitation and emission filters, on the registration of the colors of ratio labelled probes. Due to chromatic errors...<br/><br/>R J Florijn, J Bonnet, H Vrolijk, A K Raap, H J Tanke (1996) <i>Cytometry</i> <i></i> <i></i> 23: 1 8-14<br/>

http://publicationslist.org/a.k.raap/refid68 2008-08-19T18:50:29Z

Twenty-seven samples (cell cultures prepared for routine cytogenetics) of leukemia patients with known cytogenetic abnormalities were stained by in situ hybridization for interphase cytogenetics with centromere specific probes for chromosome Nos 4, 6, 7, 8, 9, 12, 17, 18, X and Y. The number of hybridization domains per nucleus was quantified using a semi-automated system developed in our laborato...<br/><br/>L J Coignet, F M Van de Rijke, J Vrolijk, M F Bertheas, A K Raap, H J Tanke (1996) <i>Leukemia</i> <i></i> <i></i> 10: 6 1065-1071<br/>

http://publicationslist.org/a.k.raap/refid77 2008-08-19T18:50:29Z

We present a sensitive and rapid fluorescence in situ hybridization (FISH) strategy for detecting chromosome-specific repeat sequences. It uses horseradish peroxidase (HRP)-labeled oligonucleotide sequences in combination with fluorescent tyramide-based detection. After in situ hybridization, the HRP conjugated to the oligonucleotide probe is used to deposit fluorescently labeled tyramide molecule...<br/><br/>R P van Gijlswijk, J Wiegant, R Vervenne, R Lasan, H J Tanke, A K Raap (1996) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 75: 4 258-262<br/>

http://publicationslist.org/a.k.raap/refid78 2008-08-19T18:50:29Z

Rat liver sinusoidal endothelial cells (LEC) contain fenestrae, which are clustered in sieve plates. Fenestrae control the exchange of fluids, solutes and particles between the sinusoidal blood and the space of Disse, which at its back side is flanked by the microvillous surface of the parenchymal cells. The surface of LEC can optimally be imaged by by scanning electron microscopy (SEM), and SEM i...<br/><br/>F Braet, W H Kalle, R B De Zanger, B G De Grooth, A K Raap, H J Tanke, E Wisse (1996) <i>J Microsc</i> <i></i> <i></i> 181: Pt 1 10-17<br/>

http://publicationslist.org/a.k.raap/refid75 2008-08-19T18:50:29Z

We have prepared avidin-labelled antibodies ('shuttles') with the aim of increasing the sensitivity of detecting mouse IgG and human complement factors in ELISA tests and of detecting monoclonal antibodies and digoxigenin haptens (DIG) in hybridization and immunoblot procedures. Avidin-D was conjugated to goat IgG anti-mouse IgG or to anti-digoxigenin antibodies by thiol/maleimide chemistry. Conju...<br/><br/>R P van Gijlswijk, D J van Gijlswijk-Janssen, A K Raap, M R Daha, H J Tanke (1996) <i>J Immunol Methods</i> <i></i> <i></i> 189: 1 117-127<br/>

http://publicationslist.org/a.k.raap/refid74 2008-08-19T18:50:29Z

The in situ hybridization (ISH) technique, as applied to electron microscopic detection of RNAs, was evaluated for ultra-thin cryosections of cultured rat fibroblasts (rat 9G). Experimental variables to balance penetration of detection reagents and preservation of ultrastructural morphology included various strengths of aldehyde fixation and pepsin treatment. We performed ISH for 28S ribosomal RNA...<br/><br/>M V Macville, A G Van Dorp, R W Dirks, J A Fransen, A K Raap (1996) <i>Histochem Cell Biol</i> <i></i> <i></i> 105: 2 139-145<br/>

http://publicationslist.org/a.k.raap/refid69 2008-08-19T18:50:29Z

Vertebrate chromosomes terminate in variable numbers of T2AG3 nucleotide repeats. In order to study telomere repeats at individual chromosomes, we developed novel, quantitative fluorescence in situ hybridization procedures using labeled (C3TA2)3 peptide nucleic acid and digital imaging microscopy. Telomere fluorescence intensity values from metaphase chromosomes of cultured human hematopoietic cel...<br/><br/>P M Lansdorp, N P Verwoerd, F M van de Rijke, V Dragowska, M T Little, R W Dirks, A K Raap, H J Tanke (1996) <i>Hum Mol Genet</i> <i></i> <i></i> 5: 5 685-691<br/>

http://publicationslist.org/a.k.raap/refid62 2008-08-19T18:50:29Z

The cellular origin of the sarcomatous component of gliosarcomas is controversial. It is not clear if the sarcoma arises in transition from the glial cells that comprise the gliomatous component or independently arises from non-neoplastic mesenchymal cells of the tumor stroma. Using comparative genomic hybridization (CGH) along with cytogenetic analysis, fluorescence in situ hybridization (FISH) a...<br/><br/>R H Boerman, K Anderl, J Herath, T Borell, N Johnson, J Schaeffer-Klein, A Kirchhof, A K Raap, B W Scheithauer, R B Jenkins (1996) <i>J Neuropathol Exp Neurol</i> <i></i> <i></i> 55: 9 973-981<br/>

http://publicationslist.org/a.k.raap/refid60 2008-08-19T18:50:29Z

We investigated the feasibility of automated counting of in situ hybridization signals (ISH) in interphase cells isolated from paraffin embedded prostate tissue. In total, 34 specimens from 7 patients with prostate cancer were stained with probes specific for the centromeric regions of chromosomes Y, 1, 7, 8, 10, and 15, using an immunoperoxidase based technique suitable for bright-field microscop...<br/><br/>W E Mesker, J C Alers, W C Sloos, H Vrolijk, A K Raap, H V Dekken, H J Tanke (1996) <i>Cytometry</i> <i></i> <i></i> 26: 4 298-304<br/>

http://publicationslist.org/a.k.raap/refid67 2008-08-19T18:50:29Z

With the advent of in situ hybridization techniques for the analysis of chromosome copy number or structure in interphase cells, the diagnostic and prognostic potential of cytogenetics has been augmented considerably. In theory, the strategies for detection of cytogenetically aberrant cells by in situ hybridization are simple and straightforward. In practice, however, they are fallible, because fa...<br/><br/>F M van de Rijke, H Vrolijk, W Sloos, H J Tanke, A K Raap (1996) <i>Cytometry</i> <i></i> <i></i> 24: 2 151-157<br/>

http://publicationslist.org/a.k.raap/refid63 2008-08-19T18:50:29Z

Several hematologic malignancies are associated with specific chromosomal translocations. Because of the dispersed distribution, chromosomal breakpoints may be difficult to detect using molecular techniques. We present a new application of a recently developed method, DNA fiber fluorescence in situ hybridization (fiber FISH), which allows direct visualization and mapping of chromosomal breakpoints...<br/><br/>J W Vaandrager, E Schuuring, E Zwikstra, C J de Boer, K K Kleiverda, J H van Krieken, H C Kluin-Nelemans, G J van Ommen, A K Raap, P M Kluin (1996) <i>Blood</i> <i></i> <i></i> 88: 4 1177-1182<br/>

http://publicationslist.org/a.k.raap/refid61 2008-08-19T18:50:29Z

In this study we systematically assessed the sensitivity limits of fiber-FISH in model experiments. Exonic fragments and cDNAs with exon sizes of >/=200 bp could be mapped on their cognate cosmid. This positional fiber-FISH mapping was validated by long-range PCR. It is expected that these two independent mapping approaches will help to refine current available gene maps and show their applicabili...<br/><br/>R J Florijn, F M van de Rijke, H Vrolijk, L A Blonden, M H Hofker, J T den Dunnen, H J Tanke, G J van Ommen, A K Raap (1996) <i>Genomics</i> <i></i> <i></i> 38: 3 277-282<br/>

http://publicationslist.org/a.k.raap/refid64 2008-08-19T18:50:29Z

The presence of complex karotypes with frequent numerical and structural abnormalities has been reported in 20 to 50% of multiple myeloma (MM) patients. This variability is mainly due to the difficulty of conventional cytogenetics to obtain tumor metaphases representative of all possible neoplastic clones in MM. To gain insight into the real incidence of numerical chromosome changes in MM we have ...<br/><br/>D Tabernero, J F San Miguel, M Garcia-Sanz, L Nájera, M García-Isidoro, J A Peréz-Simon, M Gonzalez, J Wiegant, A K Raap, A Orfão (1996) <i>Am J Pathol</i> <i></i> <i></i> 149: 1 153-161<br/>

http://publicationslist.org/a.k.raap/refid66 2008-08-19T18:50:29Z

In situ hybridization techniques allow the enumeration of chromosomal abnormalities and form a great potential for many clinical applications. Although the use of fluorescent labels is preferable regarding sensitivity and colormultiplicity, chromogenic labels can provide an excellent alternative in relatively simple situations, e.g., where it is sufficient to use a centromere specific probe to det...<br/><br/>H Vrolijk, W C Sloos, F M van de Rijke, W E Mesker, H Netten, I T Young, A K Raap, H J Tanke (1996) <i>Cytometry</i> <i></i> <i></i> 24: 2 158-166<br/>

http://publicationslist.org/a.k.raap/refid65 2008-08-19T18:50:29Z

In this study we investigated the possibility of imaging internal cellular molecules after cytochemical detection with atomic force microscopy (AFM). To this end, rat 9G and HeLa cells were hybridized with haptenized probes for 28S ribosomal RNA, human elongation factor mRNA and cytomegalovirus immediate early antigen mRNA. The haptenized hybrids were subsequently detected with a peroxidase-labell...<br/><br/>W H Kalle, M V Macville, M P van de Corput, B G de Grooth, H J Tanke, A K Raap (1996) <i>J Microsc</i> <i></i> <i></i> 182: Pt 3 192-199<br/>

http://publicationslist.org/a.k.raap/refid85 2008-08-19T18:50:29Z

We have applied two-colour fluorescence in situ hybridization (FISH) to DNA fibers and combined it with digital imaging microscopy for the mapping of large cosmid contigs. The technique was validated using a set of unique plasmids and a cosmid contig both originating from the thyroglobulin (Tg) gene and previously mapped by restriction analysis. The resolution proved to be close to the theoretical...<br/><br/>R J Florijn, L A Bonden, H Vrolijk, J Wiegant, J W Vaandrager, F Baas, J T den Dunnen, H J Tanke, G J van Ommen, A K Raap (1995) <i>Hum Mol Genet</i> <i></i> <i></i> 4: 5 831-836<br/>

http://publicationslist.org/a.k.raap/refid86 2008-08-19T18:50:29Z

We describe a detection principle for indirect fluorescence in situ hybridization (FISH) methods that with only one or two antibody layers dramatically improves FISH signal intensities. The method uses as a first layer an anti-hapten immunoglobulin [or (strept)avidin] conjugated to peroxidase. The quintessence of the method is the use of fluorochrome- or biotin labelled tyramides as peroxidase sub...<br/><br/>A K Raap, M P van de Corput, R A Vervenne, R P van Gijlswijk, H J Tanke, J Wiegant (1995) <i>Hum Mol Genet</i> <i></i> <i></i> 4: 4 529-534<br/>

http://publicationslist.org/a.k.raap/refid88 2008-08-19T18:50:29Z

This paper reviews methods and applications of CCD microscopy for analysing cells and chromosomes subjected to fluorescence in situ hybridization (FISH). The current status of indirect and direct FISH staining methods with respect to probe labelling, detection sensitivity, multiplicity and DNA resolution is summarized. Microscope hardware, including special multi-band pass filters and CCD cameras ...<br/><br/>H J Tanke, R J Florijn, J Wiegant, A K Raap, J Vrolijk (1995) <i>Histochem J</i> <i></i> <i></i> 27: 1 4-14<br/>

http://publicationslist.org/a.k.raap/refid84 2008-08-19T18:50:29Z

Fluorescence in situ hybridization (FISH) has profoundly altered the aspect of genome research and molecular diagnostics. Deletions of only a few kilobases can be detected by hybridizing probes to naked DNA fibers. Loss or gain of chromosomal material in tumor cells can be visualized using comparative genome hybridization. Further diversification of FISH application will result from new ultrasensi...<br/><br/>G J van Ommen, M H Breuning, A K Raap (1995) <i>Curr Opin Genet Dev</i> <i></i> <i></i> 5: 3 304-308<br/>

http://publicationslist.org/a.k.raap/refid87 2008-08-19T18:50:29Z

The utility of p-phenylenediamine, 1,4-di-azobicyclo-(2.2.2.)-octane, and the commercial products Citifluor, Slowfade, and Vectashield, antifading agents frequently used as mounting media for fluorescence in situ hybridization, was investigated. Fading curves for bound fluorochromes were recorded with digital microscopy, and relative fluorescence intensities of fluorochromes in solution were measu...<br/><br/>R J Florijn, J Slats, H J Tanke, A K Raap (1995) <i>Cytometry</i> <i></i> <i></i> 19: 2 177-182<br/>

http://publicationslist.org/a.k.raap/refid89 2008-08-19T18:50:29Z

Molecular biology techniques allow the unraveling of the genetic alterations that cause or accompany malignant disease. Since tumors are often heterogeneous, biochemical analysis of tissue homogenates is of limited diagnostic value. This paper gives examples of methods that are presently operational to analyze the genetic composition of individual cells. They are based on fluorescence in situ hybr...<br/><br/>H J Tanke, R J Florijn, J Vrolijk, A K Raap (1995) <i>World J Urol</i> <i></i> <i></i> 13: 3 138-142<br/>

http://publicationslist.org/a.k.raap/refid81 2008-08-19T18:50:29Z

We describe a method for detection of specific RNA targets in cultured cells at the electron microscopic (EM) level using pre-embedding in situ hybridization (ISH). The specimens were monitored by reflection-contrast microscopy (RCM) before processing for EM. A good balance between preservation of ultrastructure and intensity of hybridization signals was obtained by using mild aldehyde fixation fo...<br/><br/>M V Macville, K C Wiesmeijer, R W Dirks, J A Fransen, A K Raap (1995) <i>J Histochem Cytochem</i> <i></i> <i></i> 43: 10 1005-1018<br/>

http://publicationslist.org/a.k.raap/refid83 2008-08-19T18:50:29Z

We analyzed the effects of steps in RNA in situ hybridization (ISH) procedures on morphology and hybridization signal with reflection-contrast microscopy (RCM) and transmission electron microscopy (TEM). In chessboard experiments, a range of fixatives containing formaldehyde, glutaraldehyde, or both, and various permeabilization protocols, including ethanol and pepsin treatment, were investigated....<br/><br/>M V Macville, A G Van Dorp, K C Wiesmeijer, R W Dirks, J A Fransen, A K Raap (1995) <i>J Histochem Cytochem</i> <i></i> <i></i> 43: 7 665-674<br/>

http://publicationslist.org/a.k.raap/refid79 2008-08-19T18:50:29Z

M V Macville, K C Wiesmeijer, J A Fransen, R W Dirks, A K Raap (1995) <i>Eur J Cell Biol</i> <i></i> <i></i> 68: 4 470-474<br/>

http://publicationslist.org/a.k.raap/refid181 2008-08-19T18:52:20Z

T Raap (1995) <i>Cytometry</i> <i></i> <i></i> 19: 1 1-3<br/>

http://publicationslist.org/a.k.raap/refid182 2008-08-19T18:52:20Z

Fluorescent in situ hybridization (FISH) is a powerful, direct and sensitive technique with a wide resolution range that enables the simultaneous study of multiple targets, labelled in different colours. Spreading techniques, denoted here as 'Fiber-FISH', increase FISH-resolution to the DNA fiber, using decondensed nuclear DNA as hybridization target. FISH could be a powerful analytical tool for t...<br/><br/>C Rosenberg, R J Florijn, F M Van de Rijke, L A Blonden, T K Raap, G J Van Ommen, J T Den Dunnen (1995) <i>Nat Genet</i> <i></i> <i></i> 10: 4 477-479<br/>

http://publicationslist.org/a.k.raap/refid82 2008-08-19T18:50:29Z

Genes for Epstein-Barr virus, human cytomegalovirus immediate early antigen and luciferase are abundantly transcribed in Namalwa, rat 9G and X1 cells, respectively. The EBV transcripts and HCMV-IE transcripts are extensively spliced, while in the luciferase transcript only a small intron sequence has to be spliced out. EBV transcripts are hardly localized in the cytoplasm while the luciferase and ...<br/><br/>R W Dirks, K C Daniël, A K Raap (1995) <i>J Cell Sci</i> <i></i> <i></i> 108 ( Pt 7): 2565-2572<br/>

http://publicationslist.org/a.k.raap/refid80 2008-08-19T18:50:29Z

We investigated whether a probe specific for histone H3 mRNA could be used as a marker to study cell-cycle dependency of gene expression by double-fluorescent RNA in situ hybridization (FISH). First, we showed that all S-phase cells in cell cultures having incorporated BrdU revealed histone H3 mRNA expression by RNA FISH, indicating that histone H3 expression is a reliable marker for S-phase cells...<br/><br/>R W Dirks, A K Raap (1995) <i>Histochem Cell Biol</i> <i></i> <i></i> 104: 5 391-395<br/>

http://publicationslist.org/a.k.raap/refid90 2008-08-19T18:50:29Z

Human cytomegalovirus (HCMV) infections cause considerable morbidity and mortality in immunocompromised patients. During HCMV infection, leukocytes appear in the circulation in low frequencies that express the HCMV pp65 protein antigen. Since there is evidence that changes in the frequency of antigen-positive cells in the early phase of the infection have prognostic value, we applied automated ima...<br/><br/>N M Jiwa, W E Mesker, J J Ploem-Zaaijer, W van Dorp, T H The, A K Raap (1994) <i>Cytometry</i> <i></i> <i></i> 16: 1 69-73<br/>

http://publicationslist.org/a.k.raap/refid92 2008-08-19T18:50:29Z

We have used a fluorescent in situ hybridization procedure to detect human satellite 1 DNA, the simple sequence family that constitutes the non-male-specific fraction of classical satellite 1 DNA. Satellite 1 appears to be located on pericentromeric regions of chromosomes 3, 4 and 13, and on satellites of each acrocentric chromosome. These results suggest a possible relationship between quinacrine...<br/><br/>I Tagarro, J Wiegant, A K Raap, J J González-Aguilera, A M Fernández-Peralta (1994) <i>Hum Genet</i> <i></i> <i></i> 93: 2 125-128<br/>

http://publicationslist.org/a.k.raap/refid94 2008-08-19T18:50:29Z

A K Raap, J Wiegant (1994) <i>Methods Mol Biol</i> <i></i> <i></i> 33: 123-130<br/>

http://publicationslist.org/a.k.raap/refid93 2008-08-19T18:50:29Z

A K Raap, F M van de Rijke, R W Dirks (1994) <i>Methods Mol Biol</i> <i></i> <i></i> 33: 293-300<br/>

http://publicationslist.org/a.k.raap/refid91 2008-08-19T18:50:29Z

A cell detection method based upon automated screening is described for recognition of low frequencies (1 in 100,000) of immuno-enzymatically labelled white blood cells in human peripheral blood. The used image cytometry instrumentation (LEYTAS) includes a wide-field, fully automated microscope (Autoplan) and a modular image analysis computer (MIAC), both from Leica, Wetzlar, Germany. The MIAC con...<br/><br/>J J Ploem-Zaaijer, W E Mesker, G J Boland, W C Sloos, F M van de Rijke, M Jiwa, A K Raap (1994) <i>Cytometry</i> <i></i> <i></i> 15: 3 199-206<br/>

http://publicationslist.org/a.k.raap/refid95 2008-08-19T18:50:29Z

The human genome is made up of long DNA segments, the isochores, which are compositionally homogeneous and can be subdivided into a small number of families characterized by different G+C levels. Chromosome in situ suppression hybridization (in which excess unlabeled human DNA is added to suppress hybridization of repeated sequences present in the probe, enabling enhanced observation of single-cop...<br/><br/>S Saccone, A De Sario, J Wiegant, A K Raap, G Della Valle, G Bernardi (1993) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 90: 24 11929-11933<br/>

http://publicationslist.org/a.k.raap/refid103 2008-08-19T18:50:30Z

Atomic force microscopy (AFM) permits one to generate a topographic representation of the sample under investigation with high spatial resolution. We assumed that cytochemical staining techniques, which yield reaction products which can be discriminated from the surrounding material on basis of their topographic properties, would be applicable in AFM. Here we show the validity of this assumption b...<br/><br/>C A Putman, B G De Grooth, J Wiegant, A K Raap, K O Van der Werf, N F Van Hulst, J Greve (1993) <i>Cytometry</i> <i></i> <i></i> 14: 4 356-361<br/>

http://publicationslist.org/a.k.raap/refid105 2008-08-19T18:50:30Z

A large number of human hematopoietic growth factor and growth factor receptor genes are localized at the long arm of chromosome 5. In this study we have determined the order of the human interleukin-3 (IL3), IL4, IL5, IL9, granulocyte macrophage-colony stimulating factor (GMCSF), and the MCSF receptor (MCSFR) genes by fluorescence in situ hybridization. Genomic lambda-clones were isolated using p...<br/><br/>P M Kluck, J Wiegant, A K Raap, H Vrolijk, H J Tanke, R Willemze, J E Landegent (1993) <i>Ann Hematol</i> <i></i> <i></i> 66: 1 15-20<br/>

http://publicationslist.org/a.k.raap/refid106 2008-08-19T18:50:30Z

The human interleukin-6 receptor alpha chain (IL6R alpha) gene was regionally mapped to chromosome 1 band q21 by fluorescence in situ hybridization. As hybridization probes, partially overlapping lambda clones encompassing 28 kb of the genomic region of the gene were used. These clones were isolated using a polymerase chain reaction (PCR)-generated fragment of the 3' non-coding region of the gene....<br/><br/>P M Kluck, J Wiegant, R P Jansen, M W Bolk, A K Raap, R Willemze, J E Landegent (1993) <i>Hum Genet</i> <i></i> <i></i> 90: 5 542-544<br/>

http://publicationslist.org/a.k.raap/refid96 2008-08-19T18:50:29Z

Normal human bone marrow and peripheral blood leukocytes as well as malignant cells from a variety of leukemias and lymphomas, demonstrate somatic pairing of centromeres and p arms of chromosome 15 during interphase. This phenomenon, effected by sequences on the p arm and requiring the intranuclear transport of spatial domains for at least one of the homologs, was not seen in amniotic fluid cells,...<br/><br/>J P Lewis, H J Tanke, A K Raap, G C Beverstock, H C Kluin-Nelemans (1993) <i>Hum Genet</i> <i></i> <i></i> 92: 6 577-582<br/>

http://publicationslist.org/a.k.raap/refid102 2008-08-19T18:50:30Z

We have determined optimal conditions for the detection of mRNA sequences in cultured cells by nonradioactive in situ hybridization. For this purpose a number of different cell lines have been used: rat 9G cells for the detection of human cytomegalovirus immediate early mRNA, and HeLa as well as 5637 carcinoma cells for the detection of housekeeping gene mRNAs. Extensive optimization of fixation a...<br/><br/>R W Dirks, F M van de Rijke, S Fujishita, M van der Ploeg, A K Raap (1993) <i>J Cell Sci</i> <i></i> <i></i> 104 ( Pt 4): 1187-1197<br/>

http://publicationslist.org/a.k.raap/refid104 2008-08-19T18:50:30Z

We have tested the use of several newly developed red, green, and blue fluorescent dUTPs in direct, multiple, and sensitive fluorescence in situ hybridization procedures. Among the ones tested, the tetramethylrhodamine-dUTP proved to give the best sensitivity; using conventional epifluorescence microscopy, cosmids could be visualized with a hybridization efficiency of 90%. Fluorescein-dUTP permitt...<br/><br/>J Wiegant, C C Wiesmeijer, J M Hoovers, E Schuuring, A d'Azzo, J Vrolijk, H J Tanke, A K Raap (1993) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 63: 1 73-76<br/>

http://publicationslist.org/a.k.raap/refid101 2008-08-19T18:50:30Z

The technique of in situ hybridization has been used to evaluate the expression of an ovulation hormone mRNA (caudodorsal cell hormone; CDCH) in the central nervous system (CNS) of the mollusc Lymnaea stagnalis. Hybridization with radioactive as well as with nonradioactive labeled oligonucleotide and plasmid probes revealed a specific labeling on cell bodies of caudodorsal cells (CDCs), which are ...<br/><br/>R W Dirks, A G van Dorp, J van Minnen, J A Fransen, M van der Ploeg, A K Raap (1993) <i>Microsc Res Tech</i> <i></i> <i></i> 25: 1 12-18<br/>

http://publicationslist.org/a.k.raap/refid97 2008-08-19T18:50:29Z

The proto-oncogene bmi-1 is frequently activated by Moloney murine leukemia proviral insertions in E mu-myc transgenic mice1,2. Using a mouse bmi-1 cDNA probe a transcript of 3.3 kb was detected on Northern blots of human Burkitt's lymphoma cell lines. We have isolated and sequenced cDNA clones from a human erythroleukemia cell line (K562) derived cDNA library, using different mouse bmi-1 cDNA fra...<br/><br/>M J Alkema, J Wiegant, A K Raap, A Berns, M van Lohuizen (1993) <i>Hum Mol Genet</i> <i></i> <i></i> 2: 10 1597-1603<br/>

http://publicationslist.org/a.k.raap/refid98 2008-08-19T18:50:29Z

The pericentric inversion of chromosome 16 and the t(16;16) are two recurrent aberrations in bone marrow of patients with acute nonlymphocytic leukemia subtype M4 Eo, characterized by abnormal eosinophilic granulation. We describe here the precise localization of the breakpoints using fluorescence in situ hybridization (FISH) with cosmids spread over the short arm of chromosome 16 and the detectio...<br/><br/>J G Dauwerse, J W Wessels, R H Giles, J Wiegant, B A van der Reijden, G Fugazza, E A Jumelet, E Smit, F Baas, A K Raap (1993) <i>Hum Mol Genet</i> <i></i> <i></i> 2: 10 1527-1534<br/>

http://publicationslist.org/a.k.raap/refid99 2008-08-19T18:50:30Z

In situ hybridization (ISH) techniques on interphase cells, or interphase cytogenetics, have powerful potential clinical and biological applications, such as detection of minimal residual disease, early relapse, and the study of clonal evolution and expansion in neoplasia. Much attention has been paid to issues related to ISH data acquisition, i.e., the numbers, colors, intensities, and spatial re...<br/><br/>R E Kibbelaar, F Kok, E J Dreef, J K Kleiverda, C J Cornelisse, A K Raap, P M Kluin (1993) <i>Cytometry</i> <i></i> <i></i> 14: 7 716-724<br/>

http://publicationslist.org/a.k.raap/refid100 2008-08-19T18:50:30Z

Malignant cells from 24 cases of hairy cell leukemia were studied by in situ hybridization for evidence of selective aneuploidy using alphoid and satellite probes specific for 16 human chromosomes. Based on these data, hairy cell leukemia appears to be diploid for the chromosomes studied and is a malignancy which displays the phenomenon of pairing of the centromere and p arm of chromosome 15 durin...<br/><br/>J P Lewis, H J Tanke, A K Raap, R E Kibbelaar, P M Kluin, H C Kluin-Nelemans (1993) <i>Leukemia</i> <i></i> <i></i> 7: 9 1334-1338<br/>

http://publicationslist.org/a.k.raap/refid117 2008-08-19T18:50:30Z

Triple fluorescence in situ hybridization with a plasmid DNA library from sorted human chromosomes 8 in combination with bacteriophage clones flanking the breakpoint in 8q24 of the Burkitt lymphoma cell line J1 was used for the specific delineation of this breakpoint in individual tumor cells. With this approach, tumor-specific breakpoints in translocation chromosomes can be detected at all stages...<br/><br/>T Ried, C Lengauer, T Cremer, J Wiegant, A K Raap, M van der Ploeg, P Groitl, M Lipp (1992) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 4: 1 69-74<br/>

http://publicationslist.org/a.k.raap/refid115 2008-08-19T18:50:30Z

To expand the multiplicity of the in situ hybridization (ISH) procedure, which is presently limited by the number of fluorochromes spectrally separable in the microscope, a digital fluorescence ratio method is proposed. For this purpose, chromosome-specific repetitive probes were double-labeled with two haptens and hybridized to interphase nuclei of human peripheral blood lymphocytes. The haptens ...<br/><br/>P M Nederlof, S van der Flier, J Vrolijk, H J Tanke, A K Raap (1992) <i>Cytometry</i> <i></i> <i></i> 13: 8 839-845<br/>

http://publicationslist.org/a.k.raap/refid118 2008-08-19T18:50:30Z

H J Tanke, A K Raap (1992) <i>Eur J Histochem</i> <i></i> <i></i> 36: 1 27-28<br/>

http://publicationslist.org/a.k.raap/refid121 2008-08-19T18:50:30Z

The development of the inflammatory response within the brain, meninges and cerebrospinal fluid (CSF) compartment has been studied for the first time simultaneously in experimental herpes simplex virus (HSV) encephalitis after inoculation via the cornea. Two major viral pathways were found from the eye to the brain: one through the trigeminal nerve to the brain stem and one through the nasolacrima...<br/><br/>R H Boerman, A C Peters, B R Bloem, A K Raap, M van der Ploeg (1992) <i>Acta Neuropathol</i> <i></i> <i></i> 83: 3 300-307<br/>

http://publicationslist.org/a.k.raap/refid114 2008-08-19T18:50:30Z

In this study we aimed at the development of a cytometric system for quantification of specific DNA sequences using fluorescence in situ hybridization (ISH) and digital imaging microscopy. The cytochemical and cytometric aspects of a quantitative ISH procedure were investigated, using human peripheral blood lymphocyte interphase nuclei and probes detecting high copy number target sequences as a mo...<br/><br/>P M Nederlof, S van der Flier, N P Verwoerd, J Vrolijk, A K Raap, H J Tanke (1992) <i>Cytometry</i> <i></i> <i></i> 13: 8 846-852<br/>

http://publicationslist.org/a.k.raap/refid120 2008-08-19T18:50:30Z

Interphase cytogenetics is the application of nonradioactive in situ hybridization with chromosome-specific DNA probes to interphase nuclei. The possibilities and limitations of this new technique for the study of chromosomal aberrations in gliomas are discussed.<br/><br/>E P Arnoldus, A K Raap, A C Peters, M van der Ploeg (1992) <i>Clin Neurol Neurosurg</i> <i></i> <i></i> 94 Suppl: S34-S35<br/>

http://publicationslist.org/a.k.raap/refid119 2008-08-19T18:50:30Z

R H Boerman, A K Raap (1992) <i>Clin Neurol Neurosurg</i> <i></i> <i></i> 94 Suppl: S46-S48<br/>

http://publicationslist.org/a.k.raap/refid116 2008-08-19T18:50:30Z

This study aims at the quantification of specific DNA sequences by using fluorescence in situ hybridization (ISH) and digital imaging microscopy. The cytochemical and cytometric aspects of a quantitative ISH procedure were investigated, using human peripheral blood lymphocyte interphase nuclei and probes detecting high copy number target sequences as a model system. These chromosome-specific probe...<br/><br/>P M Nederlof, S van der Flier, A K Raap, H J Tanke (1992) <i>Cytometry</i> <i></i> <i></i> 13: 8 831-838<br/>

http://publicationslist.org/a.k.raap/refid108 2008-08-19T18:50:30Z

Fluorescence in situ hybridization (FISH) is now widely used for the localization of genomic DNA fragments, and the identification of chromosomes by painting. We now show that half of the chromosomal complement can be painted in twelve different colors by using human chromosome specific libraries carrying three distinct labels mixed in multiple ratios. The photographs are in 'real' color rather th...<br/><br/>J G Dauwerse, J Wiegant, A K Raap, M H Breuning, G J van Ommen (1992) <i>Hum Mol Genet</i> <i></i> <i></i> 1: 8 593-598<br/>

http://publicationslist.org/a.k.raap/refid113 2008-08-19T18:50:30Z

Bone marrow cells of four patients with t(1;7) and myelodysplasia or acute myeloid leukemia were analyzed using nonradioactive in situ hydridisation. As probes, centromeric alphoid DNA sequences of chromosomes 1 and 7, a satellite DNA probe for 1q12, and chromosome-specific libraries of chromosomes 1 and 7 were used. The breakpoints of the t(1;7)(p11;p11) as determined by banding analysis could be...<br/><br/>R E Kibbelaar, J W Mulder, H van Kamp, E J Dreef, H W Wessels, G C Beverstock, H L Haak, A K Raap, P M Kluin (1992) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 4: 2 128-134<br/>

http://publicationslist.org/a.k.raap/refid109 2008-08-19T18:50:30Z

To improve DNA resolution of fluorescence in situ hybridization we have adapted a nuclear extraction technique, resulting in highly extended DNA loops arranged around the nuclear matrix in a halo-like structure. In situ hybridization signals from alphoid and cosmid DNAs appear as beads-on-a-string, which, according to preliminary experiments, results from the association of individual probe fragme...<br/><br/>J Wiegant, W Kalle, L Mullenders, S Brookes, J M Hoovers, J G Dauwerse, G J van Ommen, A K Raap (1992) <i>Hum Mol Genet</i> <i></i> <i></i> 1: 8 587-591<br/>

http://publicationslist.org/a.k.raap/refid107 2008-08-19T18:50:30Z

The subcellular localization of mRNA sequences encoding neuropeptides in neuropeptidergic cells of the pond snail Lymnaea stagnalis was investigated at the electron microscopic (EM) level by non-radioactive in situ hybridization. Various classes of probes specific for 28S rRNA and for the ovulation hormone (caudodorsal cell hormone; CDCH) mRNA were labeled with biotin or digoxigenin and were detec...<br/><br/>R W Dirks, A G Van Dorp, J Van Minnen, J A Fransen, M Van der Ploeg, A K Raap (1992) <i>J Histochem Cytochem</i> <i></i> <i></i> 40: 11 1647-1657<br/>

http://publicationslist.org/a.k.raap/refid112 2008-08-19T18:50:30Z

The development of a sensitive, non-isotopic filter hybridization method based on the peroxidase catalyzed luminol reaction is described. High sensitivity was achieved by optimizing the conditions of the hybridization procedure, the immunochemical detection and the peroxidase/luminol reaction. This resulted in the reproducible detection of 10-30 femtogram of target DNA on blots within minutes when...<br/><br/>R P van Gijlswijk, A K Raap, H J Tanke (1992) <i>Mol Cell Probes</i> <i></i> <i></i> 6: 3 223-230<br/>

http://publicationslist.org/a.k.raap/refid111 2008-08-19T18:50:30Z

Interphase cytogenetics is the application of nonradioactive in situ hybridization with chromosome-specific DNA probes to interphase nuclei. In this study, interphase cytogenetics was used to investigate 66 primary brain tumors (33 gliomas, 30 meningiomas, and three medulloblastomas) for numerical chromosomal aberrations of chromosomes 1, 6, 7, 10, 11, 17, 18, X, and Y. Of the 33 gliomas (17 astro...<br/><br/>E P Arnoldus, L B Wolters, J H Voormolen, S G van Duinen, A K Raap, M van der Ploeg, A C Peters (1992) <i>J Neurosurg</i> <i></i> <i></i> 76: 6 997-1003<br/>

http://publicationslist.org/a.k.raap/refid110 2008-08-19T18:50:30Z

In this report two nonradioactive assays for quantitative analysis of polymerase chain reaction (PCR) products are presented. In the first assay, magnetic beads coated with streptavidin were used to capture biotinylated PCR fragments. After hybridization with a hapten-labeled probe, these beads were analyzed either by flow cytometry (method A) or by immunoenzymatic reactions (method B). Using a di...<br/><br/>A M Vlieger, A M Medenblik, R P van Gijlswijk, H J Tanke, M van der Ploeg, J W Gratama, A K Raap (1992) <i>Anal Biochem</i> <i></i> <i></i> 205: 1 1-7<br/>

http://publicationslist.org/a.k.raap/refid129 2008-08-19T18:50:30Z

We have used fluorescein-, digoxigenin- and biotin-(di)deoxyXTPs and terminal deoxynucleotidyl transferase for small scale labeling of synthetic oligonucleotide probes and here we show the applicability of such probes for the in situ detection of multiple RNA sequences. The enzymatic 3'-end-labeling methods proved to be good alternatives for the chemical fluorochrome and hapten labeling of 5'-end ...<br/><br/>R W Dirks, R P Van Gijlswijk, M A Vooijs, A B Smit, J Bogerd, J van Minnen, A K Raap, M Van der Ploeg (1991) <i>Exp Cell Res</i> <i></i> <i></i> 194: 2 310-315<br/>

http://publicationslist.org/a.k.raap/refid130 2008-08-19T18:50:30Z

The development and application of a procedure for interphase cytogenetics on brain tumor material is described. Nuclei isolated from freshly removed brain tumor tissue were investigated for chromosomal aberrations by nonradioactive in situ hybridization with a panel of chromosome-specific probes. The panel consisted of nine satellite DNA probes specific for the centromeric regions of chromosomes ...<br/><br/>E P Arnoldus, I A Noordermeer, A C Peters, J H Voormolen, G T Bots, A K Raap, M van der Ploeg (1991) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 3: 2 101-107<br/>

http://publicationslist.org/a.k.raap/refid132 2008-08-19T18:50:30Z

Nuclei isolated from normal human brain tissue, collected from six autopsies, were hybridized with a panel of nine satellite DNA probes specific for the centromeric regions of chromosomes 1, 6, 7, 10, 11, 17, 18, and the X and Y chromosomes. The results did not confirm the recently reported trisomy 7 and loss of sex chromosomes observed in metaphases obtained from normal brain tissue after short-t...<br/><br/>E P Arnoldus, I A Noordermeer, A C Peters, A K Raap, M Van der Ploeg (1991) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 56: 3-4 214-216<br/>

http://publicationslist.org/a.k.raap/refid128 2008-08-19T18:50:30Z

Normal lymphocyte prometaphase chromosome spreads were hybridized in situ using single- and double-color fluorescence techniques. The results obtained with either the 1.8-kb protective protein cDNA or a 12-kb genomic fragment of the human protective protein gene as probe demonstrate that the PPGB gene is localized on the long arm of chromosome 20. This assignment was confirmed by hybridization wit...<br/><br/>J Wiegant, N J Galjart, A K Raap, A d'Azzo (1991) <i>Genomics</i> <i></i> <i></i> 10: 2 345-349<br/>

http://publicationslist.org/a.k.raap/refid133 2008-08-19T18:50:30Z

An alphoid repetitive DNA (D8Z2) probe specific for the pericentromeric region of chromosome 8 was used to detect extra copies of chromosome 8 in bone marrow cells obtained from 10 patients with hematological disorders and five controls. Numerical aberrations of chromosome 8 were established by conventional banding techniques. Trisomy 8 was found in four patients with myelodysplastic syndrome (MDS...<br/><br/>R E Kibbelaar, H van Kamp, E J Dreef, J W Wessels, G C Beverstock, A K Raap, W E Fibbe, G J den Ottolander, P M Kluin (1991) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 56: 3-4 132-136<br/>

http://publicationslist.org/a.k.raap/refid131 2008-08-19T18:50:30Z

A series of experiments was carried out using a mouse HSV-1 encephalitis model for detecting HSV-DNA in CSF by the polymerase chain reaction (PCR). The results were correlated with the time period after corneal inoculation, clinical signs and symptoms, and progression of infection in brain tissue (antigen detection and histopathology), and were compared with virus isolation by spin-amplified cultu...<br/><br/>R H Boerman, E P Arnoldus, A C Peters, B R Bloem, A K Raap, M van der Ploeg (1991) <i>J Med Virol</i> <i></i> <i></i> 33: 2 83-88<br/>

http://publicationslist.org/a.k.raap/refid125 2008-08-19T18:50:30Z

Forty-five Swiss albino mice were inoculated with HSV-1 (strain McKrae) by the corneal route. The spread of HSV to the brain stem and the ventricular ependyma was investigated. The polymerase chain reaction (PCR) was used to detect HSV-DNA in the CSF during the course of infection. The ependyma of the third and fourth ventricle and the central canal contained viral antigen at a late stage of infec...<br/><br/>R H Boerman, A Mitro, B R Bloem, E P Arnoldus, A K Raap, A C Peters, M van der Ploeg (1991) <i>Acta Virol</i> <i></i> <i></i> 35: 5 450-457<br/>

http://publicationslist.org/a.k.raap/refid122 2008-08-19T18:50:30Z

The technique of nonradioactive in situ hybridization has been used to visualize the DNA and mRNA expression of human cytomegalovirus (HCMV) immediate early antigen (IEA) in a transfected rat fibroblast cell line. Expression of the transfected HCMV immediate early DNA can be induced by a cycloheximide treatment and is S-phase-dependent. In addition to cytoplasmic mRNA localization, a nuclear RNA h...<br/><br/>A K Raap, F M van de Rijke, R W Dirks, C J Sol, R Boom, M van der Ploeg (1991) <i>Exp Cell Res</i> <i></i> <i></i> 197: 2 319-322<br/>

http://publicationslist.org/a.k.raap/refid127 2008-08-19T18:50:30Z

We have used fluorescein-11-dUTP in a nick-translation format to produce fluoresceinated human nucleic acid probes. After in situ hybridization of fluoresceinated DNAs to human metaphase chromosomes, the detection sensitivity was found to be 50-100 kb. The feasibility and the increase in detection sensitivity of microscopic imaging of in situ hybridized, fluoresceinated DNA with an integrating sol...<br/><br/>J Wiegant, T Ried, P M Nederlof, M van der Ploeg, H J Tanke, A K Raap (1991) <i>Nucleic Acids Res</i> <i></i> <i></i> 19: 12 3237-3241<br/>

http://publicationslist.org/a.k.raap/refid123 2008-08-19T18:50:30Z

C J Janse, M van Dijk, A K Raap, B Mons (1991) <i>Trans R Soc Trop Med Hyg</i> <i></i> <i></i> 85: 6 727-728<br/>

http://publicationslist.org/a.k.raap/refid124 2008-08-19T18:50:30Z

The feasibility was studied of in situ hybridisation using chromosome specific DNA probes on paraffin wax embedded normal and malignant tissues from different organs. Both isolated nuclei and 5 microns sections were used in in situ hybridisation experiments with biotinylated repetitive DNA probes specific for the centromeric regions of chromosomes 1 and 17. The hybridisation results were visualise...<br/><br/>E P Arnoldus, E J Dreef, I A Noordermeer, M M Verheggen, R F Thierry, A C Peters, C J Cornelisse, M Van der Ploeg, A K Raap (1991) <i>J Clin Pathol</i> <i></i> <i></i> 44: 11 900-904<br/>

http://publicationslist.org/a.k.raap/refid126 2008-08-19T18:50:30Z

Chromosome aberrations of a hypodiploid ovarian carcinoma cell line (modal chromosome number 38) having a complex karyotype were analyzed using biotinylated DNA library probes that specifically hybridize to chromosomes 3, 6, 7, 8, 11, 13, and 16 from telomere (pter) to telomere (qter). A series of cosmid probes localized to the short arm of chromosome 16 were used to further investigate one of the...<br/><br/>V T Smit, J W Wessels, P Mollevanger, J G Dauwerse, M van Vliet, G C Beverstock, M H Breuning, P Devilee, A K Raap, C J Cornelisse (1991) <i>Genes Chromosomes Cancer</i> <i></i> <i></i> 3: 4 239-248<br/>

http://publicationslist.org/a.k.raap/refid139 2008-08-19T18:50:30Z

Nonradioactive in situ hybridization (ISH) using biotinylated centromere probes for chromosomes 1, 6, 7, 10, 16, 17, 18, and the X, respectively, was combined with GTG-banding to study cytogenetic changes in two different ovarian cancer cell lines. ISH was performed after GTG-banding on the same metaphase. The use of a low trypsin concentration (0.01%) in the banding procedure was essential for su...<br/><br/>V T Smit, J W Wessels, P Mollevanger, P I Schrier, A K Raap, G C Beverstock, C J Cornelisse (1990) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 54: 1-2 20-23<br/>

http://publicationslist.org/a.k.raap/refid180 2008-08-19T18:52:20Z

In two female patients with a 45,X/46,X, +mar karyotype the marker chromosomes were identified as normal length nonfluorescent Y chromosomes (nlYnf) using non-isotopic in situ hybridization (NISH) complementary to routine cytogenetic analysis and Southern hybridization. The recognition of the nlYnf as isodicentric in both patients illustrates and confirms the usefulness and importance of NISH in t...<br/><br/>F Speleman, B Van der Auwera, K Mangelschots, M Vercruyssen, T Raap, J Wiegant, M Craen, J Leroy (1990) <i>Hum Genet</i> <i></i> <i></i> 85: 6 569-575<br/>

http://publicationslist.org/a.k.raap/refid140 2008-08-19T18:50:30Z

DNA replication sites generally known as replicon domains were resolved as individual replication signals in interphase nuclei of permeabilized Chinese hamster ovary cells by immunofluorescent microscopy. Biotin-11-dUTP was utilized as a tool to label newly replicated DNA in permeable cells and to study the distribution of nascent DNA in pulselabel and in pulsechase experiments. Active sites of DN...<br/><br/>G Banfalvi, H Tanke, A K Raap, J Slats, M van der Ploeg (1990) <i>Histochemistry</i> <i></i> <i></i> 94: 4 435-440<br/>

http://publicationslist.org/a.k.raap/refid138 2008-08-19T18:50:30Z

Double fluorescence in situ hybridization was used to detect Philadelphia (Ph) chromosomes in interphase nuclei and metaphases of patients with chronic myeloid leukemia. Application of cosmid probes for 3' ABL and 5' BCR sequences gave better results than libraries for chromosomes 9 and 22. The present approach may provide an alternative method for monitoring minimal residual disease in Ph+ CML pa...<br/><br/>E P Arnoldus, J Wiegant, I A Noordermeer, J W Wessels, G C Beverstock, G C Grosveld, M van der Ploeg, A K Raap (1990) <i>Cytogenet Cell Genet</i> <i></i> <i></i> 54: 3-4 108-111<br/>

http://publicationslist.org/a.k.raap/refid134 2008-08-19T18:50:30Z

M van der Ploeg, A K Raap, P van Duijn (1990) <i>Ned Tijdschr Geneeskd</i> <i></i> <i></i> 134: 22 1084-1089<br/>

http://publicationslist.org/a.k.raap/refid135 2008-08-19T18:50:30Z

Interstitial pneumonia after allogeneic bone marrow transplantation is frequently associated with human cytomegalovirus (HCMV) infection. However, in a considerable proportion of the cases, no infectious agent can be determined and the interstitial pneumonia is then classified as idiopathic. Hypothetically, idiopathic interstitial pneumonia could be caused by HCMV present in such small amounts or ...<br/><br/>M Jiwa, R D Steenbergen, F E Zwaan, P M Kluin, A K Raap, M van der Ploeg (1990) <i>Am J Clin Pathol</i> <i></i> <i></i> 93: 4 491-494<br/>

http://publicationslist.org/a.k.raap/refid137 2008-08-19T18:50:30Z

A method for multiple fluorescence in situ hybridization is described allowing the simultaneous detection of more than three target sequences with only three fluorescent dyes (FITC, TRITC, AMCA), respectively emitting in the green, red, and blue. This procedure is based on the labeling of (DNA) probes with more than one hapten and visualisation in multiple colors. The possibility to detect multipl...<br/><br/>P M Nederlof, S van der Flier, J Wiegant, A K Raap, H J Tanke, J S Ploem, M van der Ploeg (1990) <i>Cytometry</i> <i></i> <i></i> 11: 1 126-131<br/>

http://publicationslist.org/a.k.raap/refid136 2008-08-19T18:50:30Z

Oligonucleotides labeled with FITC or biotin were applied for detection of specific mRNAs in microscopic preparations by in situ hybridization. The oligonucleotides were labeled with one FITC or biotin molecule at the 5' end or with a tail of biotin molecules at the 3' end. The target sequences were mRNAs coding for an ovulation hormone (CDCH) in the caudodorsal cells (CDC) of the pond snail Lymna...<br/><br/>R W Dirks, R P van Gijlswijk, R H Tullis, A B Smit, J van Minnen, M van der Ploeg, A K Raap (1990) <i>J Histochem Cytochem</i> <i></i> <i></i> 38: 4 467-473<br/>

http://publicationslist.org/a.k.raap/refid150 2008-08-19T18:50:30Z

A recently described immunoperoxidase method for the detection of nuclear human cytomegalovirus (HCMV) immediate early antigen (IEA) directly on peripheral blood leucocytes suffers from the drawback that the antigen is vulnerable to endogenous peroxidase inactivation procedures. To solve this problem a procedure is developed in which endogenous peroxidase is inactivated after binding and immobiliz...<br/><br/>N M Jiwa, F M van de Rijke, A Mulder, W van der Bij, T H The, P H Rothbarth, J Velzing, M van der Ploeg, A K Raap (1989) <i>Histochemistry</i> <i></i> <i></i> 91: 4 345-349<br/>

http://publicationslist.org/a.k.raap/refid151 2008-08-19T18:50:30Z

Methods for the simultaneous detection of two virus types in cytological preparations or tissue sections by non-radioactive in situ hybridization were investigated. As a model system, CaSki cells, which have human papilloma virus type 16 (HPV16) DNA integrated in their cellular genome, were in vitro infected with Herpes simplex virus 2 (HSV2). DNA probes for both viruses were labeled with biotin, ...<br/><br/>H Mullink, J M Walboomers, A K Raap, C J Meyer (1989) <i>Histochemistry</i> <i></i> <i></i> 91: 3 195-198<br/>

http://publicationslist.org/a.k.raap/refid153 2008-08-19T18:50:30Z

A method is described for visualizing three nucleic acid sequences simultaneously by in situ hybridization using a new blue immunofluorescent label, amino methyl coumarin acetic acid (AMCA), in combination with green and red fluorescing FITC and TRITC. Three chromosome-specific repetitive probes labeled with either amino acetyl fluorene (AAF), mercury, or biotin were hybridized simultaneously to m...<br/><br/>P M Nederlof, D Robinson, R Abuknesha, J Wiegant, A H Hopman, H J Tanke, A K Raap (1989) <i>Cytometry</i> <i></i> <i></i> 10: 1 20-27<br/>

http://publicationslist.org/a.k.raap/refid148 2008-08-19T18:50:30Z

In situ hybridisation with acetyl-aminofluorene (AAF) and 35S-labelled DNA probes for polyomaviruses, was used to detect JC virus DNA in brain necropsy material in a patient with progressive multifocal leucoencephalopathy (PML). In a second patient PML was diagnosed from a brain necropsy specimen using the same technique. The main infected cell type were oligodendrocytes; dot hybridisation was use...<br/><br/>R H Boerman, E P Arnoldus, A K Raap, A C Peters, J ter Schegget, M van der Ploeg (1989) <i>J Clin Pathol</i> <i></i> <i></i> 42: 2 153-161<br/>

http://publicationslist.org/a.k.raap/refid152 2008-08-19T18:50:30Z

The results of a comparison of three DNA-detection methods for human parvovirus B19 DNA are described. The sensitivity of detection of virus from hybridization assays using 32P-radiolabeled DNA and RNA probes was compared with a method for enzymatically amplifying specific target DNA sequences (polymerase chain reaction). B19 virus DNA was detected using a radiolabeled DNA probe at serum dilutions...<br/><br/>M M Salimans, S Holsappel, F M van de Rijke, N M Jiwa, A K Raap, H T Weiland (1989) <i>J Virol Methods</i> <i></i> <i></i> 23: 1 19-28<br/>

http://publicationslist.org/a.k.raap/refid149 2008-08-19T18:50:30Z

To develop and optimize non-radioactive in situ hybridization techniques for mRNA detection, we used the neuropeptidergic system of the pond snail Lymnaea stagnalis as a biological model system. First, we investigated the in situ hybridization procedure using radioactive-labeled cDNA and synthetic oligonucleotide probes specific for egg-laying hormone (ELH) mRNA and molluscan insulin-like peptide ...<br/><br/>R W Dirks, A K Raap, J Van Minnen, E Vreugdenhil, A B Smit, M Van der Ploeg (1989) <i>J Histochem Cytochem</i> <i></i> <i></i> 37: 1 7-14<br/>

http://publicationslist.org/a.k.raap/refid147 2008-08-19T18:50:30Z

Attempts were made to detect human parvovirus B19-DNA by in situ hybridisation and the polymerase chain reaction in placental and fetal tissues from a case of intrauterine fetal death. In the in situ hybridisation experiments radioactive and non-radioactive (labelled with 2-acetyl-aminofluorene, AAF) DNA probes were used. B19-DNA was detectable in paraffin wax embedded fetal tissue from the liver,...<br/><br/>M M Salimans, F M van de Rijke, A K Raap, A M van Elsacker-Niele (1989) <i>J Clin Pathol</i> <i></i> <i></i> 42: 5 525-530<br/>

http://publicationslist.org/a.k.raap/refid142 2008-08-19T18:50:30Z

In a blind study, chromosome aberrations in tumor cells were analyzed by conventional cytogenetic techniques (G banding) and nonradioactive in situ hybridization with chromosome-specific probes. The material was obtained directly from patients with hematologic diseases and from colon tumor derived cell lines. The cytogenetic data obtained with G banding were in accord with those obtained by in sit...<br/><br/>P M Nederlof, S van der Flier, A K Raap, H J Tanke, M van der Ploeg, F Kornips, J P Geraedts (1989) <i>Cancer Genet Cytogenet</i> <i></i> <i></i> 42: 1 87-98<br/>

http://publicationslist.org/a.k.raap/refid143 2008-08-19T18:50:30Z

E P Arnoldus, N M Jiwa, A C Peters, A K Raap (1989) <i>Ned Tijdschr Geneeskd</i> <i></i> <i></i> 133: 37 1825-1829<br/>

http://publicationslist.org/a.k.raap/refid144 2008-08-19T18:50:30Z

A technique is described for the detection of HSV-DNA in very small volumes (5-10 microliters) of cerebrospinal fluid (CSF). The method was evaluated in CSF samples of 4-6-week-old mice inoculated with HSV-1 via the corneal route. The sensitivity of the PCR assay was compared with results of spin-amplified viral culture with immunofluorescent visualization (SAC/IF), routine viral culture (RVC) and...<br/><br/>R H Boerman, E P Arnoldus, A K Raap, B R Bloem, M Verhey, G van Gemert, A C Peters, M van der Ploeg (1989) <i>J Virol Methods</i> <i></i> <i></i> 25: 2 189-197<br/>

http://publicationslist.org/a.k.raap/refid141 2008-08-19T18:50:30Z

Interphase nuclei isolated from paraffin-embedded tissue of four normal brains were hybridized with biotinated repetitive DNA probes specific for the (peri)centromeric regions of chromosomes 1 and 7. Hybridization results were visualized with a peroxidase-DAB system after which the number of specific signals per nucleus was counted using bright field microscopy. Using the probe specific for chromo...<br/><br/>E P Arnoldus, A C Peters, G T Bots, A K Raap, M van der Ploeg (1989) <i>Hum Genet</i> <i></i> <i></i> 83: 3 231-234<br/>

http://publicationslist.org/a.k.raap/refid146 2008-08-19T18:50:30Z

Peripheral blood leukocyte samples (n = 458) of 24 bone marrow transplant and 52 kidney transplant patients were examined weekly for the presence of human cytomegalovirus (HCMV) using an improved culture technique (DEAFF; detection of early antigen fluorescent foci). In total 5 (21%) bone marrow transplant and 11 (21%) kidney transplant patients developed a viremia. Patients' samples were investig...<br/><br/>N M Jiwa, G W Van Gemert, A K Raap, F M Van de Rijke, A Mulder, P F Lens, M M Salimans, F E Zwaan, W Van Dorp, M Van der Ploeg (1989) <i>Transplantation</i> <i></i> <i></i> 48: 1 72-76<br/>

http://publicationslist.org/a.k.raap/refid145 2008-08-19T18:50:30Z

Immunohistochemical techniques with monoclonal antibodies against cytomegalovirus (CMV) immediate early (IEA) and early antigens (EA), and in situ hybridisation, were used to detect CMV infection in routinely obtained, formaldehyde fixed and paraffin wax embedded tissues taken from bone marrow transplant patients, who had died form interstitial pneumonia. To improve the rates of detection of CMV-I...<br/><br/>N M Jiwa, A K Raap, F M van de Rijke, A Mulder, J J Weening, F E Zwaan, T H The, M van der Ploeg (1989) <i>J Clin Pathol</i> <i></i> <i></i> 42: 7 749-754<br/>

http://publicationslist.org/a.k.raap/refid158 2008-08-19T18:50:30Z

Acetylaminofluorene (AAF) modified cytomegalovirus (CMV) DNA probes have been applied for the rapid detection of CMV genomes by non-radioactive in situ hybridization in routinely obtained pathological material. To establish proper protocols, AAF modified mouse satellite DNA and mouse liver were used to investigate the procedural variables. Among these were type and time of fixation, glass slide co...<br/><br/>A K Raap, J L Geelen, J W van der Meer, F M van de Rijke, P van den Boogaart, M van der Ploeg (1988) <i>Histochemistry</i> <i></i> <i></i> 88: 3-6 367-373<br/>

http://publicationslist.org/a.k.raap/refid157 2008-08-19T18:50:30Z

Methods for single- and double-target in situ hybridization (ISH) to, cells isolated from solid transitional cell carcinomas (TCC's) of the urinary bladder are described. Single cell suspensions were prepared from solid tumors of the urinary bladder by mechanical disaggregation and fixed in 70% ethanol. Using two DNA probes specific for the centromeres of chromosomes #1 and #18, ISH procedures wer...<br/><br/>A H Hopman, F C Ramaekers, A K Raap, J L Beck, P Devilee, M van der Ploeg, G P Vooijs (1988) <i>Histochemistry</i> <i></i> <i></i> 89: 4 307-316<br/>

http://publicationslist.org/a.k.raap/refid154 2008-08-19T18:50:30Z

Experimentally infected mice were used to assess the value of immunofluorescence (IF) procedures in cerebrospinal fluid (CSF) cells in comparison with routine viral culture of CSF for diagnosis of herpes simplex type-1 (HSV-1) encephalitis. Virus specific antigen was detected by immunofluorescence in the majority of CSF cells in 75% of infected animals. In contrast, only 20% of infected mice had p...<br/><br/>R H Boerman, A C Peters, M Verheij, A K Raap, L T van Ekdom, A van Eer, M van der Ploeg (1988) <i>J Neurol Sci</i> <i></i> <i></i> 87: 2-3 245-254<br/>

http://publicationslist.org/a.k.raap/refid156 2008-08-19T18:50:30Z

The caudo-dorsal cells (CDC) in the cerebral ganglia of the pond snail Lymnaea stagnalis synthesize the 36-amino acid ovulation hormone (CDCH). We have used immuno-cytochemistry and in situ hybridization to reveal the localization of neurons and axons containing CDCH-like material. A monoclonal antibody to a fragment of CDCH and a cDNA probe encoding CDCH reacted with the CDC-system, with specific...<br/><br/>J van Minnen, C vd Haar, A K Raap, E Vreugdenhil (1988) <i>Cell Tissue Res</i> <i></i> <i></i> 251: 2 477-484<br/>

http://publicationslist.org/a.k.raap/refid155 2008-08-19T18:50:30Z

In this paper we describe stably transfected rat cell lines which harbour either the human cytomegalovirus (HCMV) immediate early (IE) gene encoding the 72K IE nuclear antigen (IEA) or the bacterial chloramphenicol acetyltransferase (CAT) gene both under transcriptional control of the HCMV IE enhancer-promoter (-484 to -19 relative to the IE cap site, +1). In these cell lines IE gene or CAT gene e...<br/><br/>R Boom, C J Sol, R P Minnaar, J L Geelen, A K Raap, J van der Noordaa (1988) <i>J Gen Virol</i> <i></i> <i></i> 69 ( Pt 6): 1179-1193<br/>

http://publicationslist.org/a.k.raap/refid179 2008-08-19T18:52:20Z

Exposure of L929 murine fibroblasts to ozone resulted in K+ leakage and inhibition of several enzymes. Most sensitive to ozone exposure were glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase. The activities of another cytosolic enzyme, lactate dehydrogenase, the mitochondrial enzymes glutamate dehydrogenase, succinate dehydrogenase, cytochrome c oxidase and the activity of the lysosomal...<br/><br/>J Van der Zee, T M Dubbelman, T K Raap, J Van Steveninck (1987) <i>Biochem J</i> <i></i> <i></i> 242: 3 707-712<br/>

http://publicationslist.org/a.k.raap/refid159 2008-08-19T18:50:30Z

Photodynamic treatment of murine L929 fibroblasts with hematoporphyrin-derivative resulted in the inactivation of cytosolic, mitochondrial and lysosomal enzymes and in a decrease in cellular adenosine triphosphate and reduced glutathione concentrations. Comparison of these results with those of previous studies revealed that transmembrane transport systems and DNA repair enzymes are inactivated af...<br/><br/>J P Boegheim, H Scholte, T M Dubbelman, E Beems, A K Raap, J van Steveninck (1987) <i>J Photochem Photobiol B</i> <i></i> <i></i> 1: 1 61-73<br/>

http://publicationslist.org/a.k.raap/refid160 2008-08-19T18:50:30Z

R H Boerman, A K Raap, M vd Ploeg, A C Peters, P H Rothbarth (1987) <i>Lancet</i> <i></i> <i></i> 2: 8550 <br/>

http://publicationslist.org/a.k.raap/refid161 2008-08-19T18:50:30Z

Upon transfection of Rat-2-TK- cells with plasmid pES, containing the cloned 7.0-kilobase (kb) EcoRI-SalI fragment (0.063 to 0.089 map units) of the human cytomegalovirus genome, major immediate-early antigen expression was obtained in 1 to 2% of the nuclei of the transfected cells, as determined by immunofluorescence with the E3 monoclonal antibody. Cotransfection of pES with the cloned herpes si...<br/><br/>R Boom, J L Geelen, C J Sol, A K Raap, R P Minnaar, B P Klaver, J van der Noordaa (1986) <i>J Virol</i> <i></i> <i></i> 58: 3 851-859<br/>

http://publicationslist.org/a.k.raap/refid165 2008-08-19T18:50:30Z

The nitrocellulose binding assay was used for quantitative studies on the cytochemical reactions for the three enzymes most frequently used in immunocytochemistry. The results show a linear relationship between the amount of enzyme immobilized on nitrocellulose and the amount of the enzyme reaction product. The similar course of the formation of the reaction product after DAB/H2O2 staining for per...<br/><br/>P H Nibbering, J G Marijnen, A K Raap, P C Leijh, R van Furth (1986) <i>Histochemistry</i> <i></i> <i></i> 84: 4-6 538-543<br/>

http://publicationslist.org/a.k.raap/refid164 2008-08-19T18:50:30Z

Fluorescence enzyme cytochemical procedures will contribute significantly to biomedical problems where knowledge of the enzymic composition of individual cells is important. Compared with the number of absorbance enzyme cytochemical methods, relatively few fluorescence procedures have been reported. In this paper, the merits of the described methods are discussed. A distinction is made between met...<br/><br/>A K Raap (1986) <i>Histochemistry</i> <i></i> <i></i> 84: 4-6 317-321<br/>

http://publicationslist.org/a.k.raap/refid163 2008-08-19T18:50:30Z

A non-radioactive in situ hybridization technique is described which allows the simultaneous detection of different DNA sequences. To demonstrate the feasibility of the procedure, metaphases and interphase nuclei of a human-mouse somatic cell hybrid were simultaneously hybridized with mercurated total human DNA and a biotinylated mouse satellite DNA probe. After the hybridization, the probes were ...<br/><br/>A H Hopman, J Wiegant, A K Raap, J E Landegent, M van der Ploeg, P van Duijn (1986) <i>Histochemistry</i> <i></i> <i></i> 85: 1 1-4<br/>

http://publicationslist.org/a.k.raap/refid162 2008-08-19T18:50:30Z

With the aim of optimizing in situ hybridization methods, alkaline, acid, and thermal denaturation procedures have been studied for their ability to separate the DNA strands of nuclear DNA and for the DNA losses they induce. Isolated methanol/acetic acid-fixed mouse liver nuclei have been used as a biological object. The results, obtained with acridine orange staining and microfluorometry, show th...<br/><br/>A K Raap, J G Marijnen, J Vrolijk, M van der Ploeg (1986) <i>Cytometry</i> <i></i> <i></i> 7: 3 235-242<br/>

http://publicationslist.org/a.k.raap/refid167 2008-08-19T18:50:30Z

The study of nuclear components in cells and tissues has resulted in a wealth of information with regard to the role of chromatin in cellular processes. Here, a survey is given of procedures which allow the cytochemical investigation of nucleic acid present in microscopic preparations of cells, nuclei or metaphase chromosomes. Special attention is given to recent developments in hybridocytochemist...<br/><br/>M van der Ploeg, P van Duijn, J G Bauman, J E Landegent, A K Raap (1985) <i>Basic Appl Histochem</i> <i></i> <i></i> 29: 3 181-189<br/>

http://publicationslist.org/a.k.raap/refid166 2008-08-19T18:50:30Z

Various chromogen protocols for visualizing peroxidase and alkaline phosphatase activity in immunoenzyme histochemistry were compared with respect to their sensitivity. They were tested on tissue sections of human skeletal muscle and in an antigen spot test using antibodies against slow skeletal muscle myosin. The chromogens included 3-amino-9-ethylcarbazole (AEC), 3, 3'-diaminobenzidine (DAB), p-...<br/><br/>A S De Jong, M Van Kessel-van Vark, A K Raap (1985) <i>Histochem J</i> <i></i> <i></i> 17: 10 1119-1130<br/>

http://publicationslist.org/a.k.raap/refid168 2008-08-19T18:50:30Z

Erythrocyte ghosts containing varying amounts of alkaline phosphatase were used to study the localization mechanisms of three metal salt and one azo method for this enzyme. For the azo method, the minimal amount of alkaline phosphatase that can be visualized within the ghosts proved only to be limited by the optical properties of the azo compound. In contrast, for the metal salt methods, a certain...<br/><br/>A K Raap, P Van Duijn (1984) <i>J Histochem Cytochem</i> <i></i> <i></i> 32: 8 815-820<br/>

http://publicationslist.org/a.k.raap/refid170 2008-08-19T18:50:30Z

The specificity of anti-nucleic acid antisera can immunocytochemically be evaluated with test systems which apply various nucleic acids immobilized to inert matrices. When using polyrA.polyrU as a model compound for dsRNA, it is important to prevent the formation of the triple stranded form polyrA.(polyrU)2. Anti-dsRNA antibodies which, when tested with the correct test system, proved to be presen...<br/><br/>A K Raap, J G Marijnen, M van der Ploeg (1984) <i>Histochemistry</i> <i></i> <i></i> 81: 6 517-520<br/>

http://publicationslist.org/a.k.raap/refid169 2008-08-19T18:50:30Z

J E Landegent, R A Baan, J H Hoeijmakers, A K Raap, M Van der Ploeg (1984) <i>Cell Biol Int Rep</i> <i></i> <i></i> 8: 3 <br/>

http://publicationslist.org/a.k.raap/refid171 2008-08-19T18:50:30Z

A study was made of the involvement of superoxide anions in the aerobic reduction of tetrazolium salts by NAD(P)H and phenazine methosulphate (PMS). On the basis of experiments with superoxide dismutase two mechanisms of tetrazolium reduction could be distinguished--one in which fully reduced PMS (PMSH) is the reducer and one in which superoxide anion is the reducer of tetrazolium salts. It is pro...<br/><br/>A K Raap (1983) <i>Histochem J</i> <i></i> <i></i> 15: 10 977-986<br/>

http://publicationslist.org/a.k.raap/refid173 2008-08-19T18:50:30Z

The correct localization of oxidative enzymes using cytochemical tetrazolium methods, in which low molecular weight electron carriers such as NAD(P)H and reduced phenazine methosulphate (PMSH) are used, can be endangered by the escape of the reduced intermediates before they react to form the insoluble formazan at the true enzyme-containing sites. To investigate this phenomenon, the glucose-6-phos...<br/><br/>A K Raap, G R Van Hoof, P Van Duijn (1983) <i>Histochem J</i> <i></i> <i></i> 15: 9 861-879<br/>

http://publicationslist.org/a.k.raap/refid172 2008-08-19T18:50:30Z

The results in the preceding paper have shown that the PMS-tetrazolium capture reaction as such is not sufficient to guarantee a correct localization of formazan in microscopically small dehydrogenase sites. For cytochemical reactions where the application of PMS leads to increased formazan formation, it is proposed that PMS functions not on its own, but as an efficient acceptor of NAD(P)H-oxidizi...<br/><br/>A K Raap, P Van Duijn (1983) <i>Histochem J</i> <i></i> <i></i> 15: 9 881-893<br/>

http://publicationslist.org/a.k.raap/refid174 2008-08-19T18:50:30Z

E Prosperi, A K Raap (1982) <i>Histochem J</i> <i></i> <i></i> 14: 4 689-692<br/>

http://publicationslist.org/a.k.raap/refid176 2008-08-19T18:50:30Z

The reliability of histochemical determinations of the enzyme activity after thermal damage has been studied with the aid of two model systems. Polyacrylamide films and erythrocyte ghosts containing either beta-glucuronidase or alkaline phosphatase, were submitted to heating and the activities retained were assessed both biochemically and histochemically. For the enzymes studied, the results show ...<br/><br/>E Prosperi, A K Raap, M van der Ploeg (1982) <i>Histochemistry</i> <i></i> <i></i> 75: 3 387-397<br/>

http://publicationslist.org/a.k.raap/refid175 2008-08-19T18:50:30Z

The properties of aminoalkylsilane-treated glass slides for the preparation of metaphase spreads and their staining quality have been studied and compared with those of slides which had only been cleaned in ethanol/ether. The parameters investigated were: (1) the average area of metaphases from cultures of blood from both healthy donors and haematology patients; (2) the influence of the positively...<br/><br/>A C van Prooijen-Knegt, A K Raap, M J van der Burg, J Vrolijk, M van der Ploeg (1982) <i>Histochem J</i> <i></i> <i></i> 14: 2 333-344<br/>

http://publicationslist.org/a.k.raap/refid177 2008-08-19T18:50:30Z

The preparation and properties of a new microscopic model system for quantitative enzyme cytochemistry are described. The enzyme to be studied is entrapped in human erythrocyte ghosts by a simple hypotonic procedure. After fixation in suspension the ghosts can be analyzed both biochemically and cytochemically. The system has been tested with alkaline phosphatase. It is demonstrated that an azo met...<br/><br/>A K Raap, P Van Duijn (1981) <i>J Histochem Cytochem</i> <i></i> <i></i> 29: 12 1418-1424<br/>

http://publicationslist.org/a.k.raap/refid178 2008-08-19T18:50:30Z

(1) In agreement with Eisenbach and Gutman (Eisenbach, M. and Gutman, M. (1975) Eur. J. Biochem. 52, 107--116) the reduction of cytochrome b in beef-heart submitochondrial particles by succinate in the presence of antimycin was found to be biphasic, the relative amounts of fast and slow phases being dependent on the redox state of a compound located on the oxygen side of the antimycin block. (2) H...<br/><br/>G Van Ark, A K Raap, J A Berden, E C Slater (1981) <i>Biochim Biophys Acta</i> <i></i> <i></i> 637: 1 34-42<br/>