| 1. |
- Behboudi, A, et al.
(författare)
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Functional significance of absence : The chromosomal segment harboring the Tp53 gene is missing in the T55 rat radiation hybrid mapping panel
- 2002
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Ingår i: Genomics. - : Academic Press. - 0888-7543 .- 1089-8646. ; 79:6, s. 844-848
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Tidskriftsartikel (refereegranskat)abstract
- The T55 rat radiation hybrid (RH) mapping panel has been reported to retain the entire rat genome at retention frequencies between 22% and 37%. However, we found that a small segment of rat chromosome 10 harboring at least four different genes, including Tp53, was completely absent from the panel (retention frequency = 0%). Two other markers located in the vicinity exhibited much reduced retention (2–6%). RH clones are generated by transferring highly fragmented DNA into a recipient cell. There might be a strong selection against the transfer and retention of chromosome segments harboring an intact Tp53, as the action of this gene might prevent proliferation and establishment of the RH clone. Our finding further suggests that unexpected low retention or absence of chromosome segments in an RH panel may represent indications that the segments harbor genes with important functions in cell proliferation control.
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| 2. |
- Helou, K, et al.
(författare)
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A dual-color FISH framework map for the characterization of the Sai1 tumor suppression region on rat chromosome 5
- 2000
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Ingår i: Genes, Chromosomes and Cancer. - : John Wiley & Sons, Inc.. - 1045-2257 .- 1098-2264. ; 27:4, s. 362-372
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Tidskriftsartikel (refereegranskat)abstract
- The analysis of cell hybrids between malignant mouse hepatoma cells and normal rat fibroblasts has previously demonstrated the critical role of a deletion in rat chromosome 5 (RNO5) that was related to an anchorage independent phenotype. Those hybrids that were anchorage independent displayed loss of the entire RNO5 or an interstitial deletion in RNO5. These findings suggested that a putative tumor suppressor gene, Sai1 (suppression of anchorage independence 1), was located within the deleted region. To explore the molecular basis of the tumor suppressor activity of the Sai1 region, we analyzed the RNO5q23-q36 region with several genes and microsatellite markers that could be assigned to the region, as well as with new markers derived by representational difference analysis (RDA) or by microdissection. Dual-color FISH was used to construct a detailed physical map of the entire RNO5. These new data can be used to connect the physical and linkage maps in the rat, as well as to identify the details of the comparative map with other mammalian species including humans and mice. Using as FISH reagents genomic YAC, P1, or phage lambda clones corresponding to RNO5 markers, the order and unique positions of 18 markers could be established. The map provided a framework for the detailed characterization of the deletion found in anchorage independent hybrids. All markers within the bands RNO5q31.3-q35 were shown to be lost, including known cancer-related genes such as Ifna (5q32), Cdkn2a, -b (5q32), Jun (5q34), and Cdkn2c (5q35). However, the aberration in the deletion chromosome turned out to be more complex than originally thought in that we detected the presence of a paracentric inversion in addition to a deletion. The inversion led to the juxtaposition of the gene markers Tal2 (5q24.1) and Cd30lg (5q24.3). The framework map will provide the basis for the detailed physical YAC clone contig mapping of this region, and facilitate the identification and characterization of the Sai1 locus.
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| 3. |
- Twigger, S, et al.
(författare)
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Rat Genome Database : A comparative genomics platform for rat mouse and human.
- 2001
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Ingår i: Journal of Molecular Medicine. - : Springer. - 0946-2716 .- 1432-1440. ; , s. B30-
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Konferensbidrag (refereegranskat)abstract
- The Rat Genome Database (RGD) is a NIH funded project who’s stated mission is “to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community.” In a collaboration between the Medical College of Wisconsin, the Jackson Lab, the National Center for Biotechnology and Information and the Genetics Lundberg Laboratory, Gothenburg, Sweden, RGD has been created to meet these stated aims. The primary focus of RGD is to aid Rat researchers in their work studying the rat as a model organism for human disease. To support these studies we have integrated a large amount of rat genetic and genomic resources in RGD and these are constantly being expanded through ongoing literature curation. One of the major features of RGD version 1.1, released in January of this year, is incorporation of QTL data to facilitate physiological genomics studies relating disease with the genome. In addition, a dynamic sequence-based homology tool is in final testing which will enable Rat, Mouse and Human researchers to view mapped genes and sequences and their locations in the other two organisms. We hope to release this tool in the second quarter of 2001. This will facilitate the application of results in one species to experiments in another species. In collaboration with the Mouse Genome Database and NCBI, close links are being created between RGD and MGD, LocusLink and UniGene to increase access to each set of data. To support its other general functions RGD has a variety of tools available for the rat researcher, plus ones that are equally useful to researchers working in other organisms and a sampling of these tools will be presented. Thus RGD is not only a valuable resource for those working with the rat but also for researchers in other model organisms wishing to harness the existing genetic and physiological data available in the rat to complement their own work.
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| 4. |
- Walentinsson, A, et al.
(författare)
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Genomewide assessment of genetic alterations in DMBA-induced rat sarcomas: cytogenetic, CGH, and allelotype analyses reveal recurrent DNA copy number changes in rat chromosomes 1, 2, 4, and 7.
- 2000
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Ingår i: Genes, chromosomes & cancer. - 1045-2257. ; 28:2, s. 184-95
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Tidskriftsartikel (refereegranskat)abstract
- Rat sarcomas, induced by subcutaneous injections of 7,12-dimethylbenz[a]anthracene (DMBA), were studied with the objective of identifying critical chromosome regions associated with tumorigenesis. We employed three genomewide screening techniques-cytogenetics, CGH, and allelotyping-in 19 DMBA-induced sarcomas in F1 (BN/Han x LE/Mol) rats. The most conspicuous finding in the cytogenetic analysis was a high incidence of trisomy for rat chromosome 2 (RNO2). Signs of gene amplification (hsr) were also seen in several tumors. The CGH analysis revealed that gains in copy number were much more common than losses. The gains mostly affected RNO2 (10/19), RNO12q (7/19), and RNO19q (5/19), as well as the proximal part of RNO4 (8/19) and the distal part of RNO7 (7/19). Reduction in copy number was seen in RNO17 (2/19). For the allelotyping, we used 318 polymorphic microsatellite marker loci covering the entire genome. We identified regions of allelic imbalance affecting most of the rat chromosomes. The highest incidences of recurrent allelic imbalance were observed at loci in certain regions in RNO1, 2, 4, and 7 and at lower incidences in parts of RNO12, 16, 18, and 19. The combined results suggested that genetic alterations detected in RNO2 and RNO12 usually corresponded to complete or partial trisomy, whereas those in RNO1 and RNO7 seemed to involve regional deletions and/or gains. Furthermore, we could confirm that copy number gains occur proximally in RNO4, where a previous study showed amplification of the Met oncogene in a subset of these tumors.
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| 5. |
- Helou, K, et al.
(författare)
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Between rat and mouse zoo-FISH reveals 49 chromosomal segments that have been conserved in evolution
- 2001
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Ingår i: Mammalian Genome. - : Springer New York LLC. - 0938-8990 .- 1432-1777. ; 10:12, s. 765-771
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Tidskriftsartikel (refereegranskat)abstract
- Mouse single chromosome paints were applied to rat prophase/prometaphase chromosomes to detect homologous chromosome regions. The analysis revealed 49 rat chromosomal regions ranging in size from whole chromosomes down to small bands near the limit of detection with this method, which was estimated to be 2-3 Mb. When all the painted regions were taken into account, the whole rat genome was covered with mouse-homologous regions, with the exception of small segments near the centromeres and the short arms of Chromosomes (Chrs) 3, 11, 12, and 13. These regions were shown to contain high levels of rat-specific repetitive DNA. The number of conserved segments between rat and mouse detected by our high-resolution zoo-FISH method was significantly higher than that reported in previous studies.
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| 6. |
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| 7. |
- Liska, F, et al.
(författare)
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Chromosome assignment of Cd36 transgenes in two rat SHR lines by FISH and linkage mapping of transgenic insert in the SHR-TG19 line.
- 2002
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Ingår i: Folia biologica. - 0015-5500. ; 48:4, s. 139-44
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Tidskriftsartikel (refereegranskat)abstract
- The chromosome position of the Cd36 insert was determined by FISH in two rat transgenic lines (SHR/Ola-TgN(EF1aCd36)10Ipcv (SHR-TG10) and SHR/Ola-TgN(EF1aCd36)19Ipcv (SHR-TG19). The Cd36 transgene construct labelled with digoxigenin-11-dNTP was used as a probe in the FISH analysis. In accord with the previous finding that the SHR-TG10 harbours 6-8 copies of the transgene, the signals from both metaphase and interphase nuclei of SHR-TG10 preparations were rather strong and the probe hybridized to both copies of chromosome 1 at band q55. The probe hybridization to SHR-TG19 metaphase preparations also showed homozygosity of the transgene with localization of both copies to chromosome 11 at band q11. The signals were distinct but much weaker compared to the SHR-TG10, which again is in accord with the fact that the SHR-TG19 line harbours only a single copy of the transgene. In order to look for a possible impact of the insertion site neighbourhood upon the transgene phenotypic effect, we performed linkage mapping of the transgene in the SHR-TG19 line. By linkage mapping, the placement of the transgene to the proximal part of RNO11 was confirmed, the critical interval being 4 cM between D11Rat20 and D11Rat21, in good agreement with the RH map. Within the close neighbourhood of the inserted Cd36 transgene, there are several genes known to be expressed in kidney, and so the influence of some regulatory sequences enhancing kidney expression of the Cd36 transgene can be envisaged.
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| 8. |
- Olson, Fredrik J., 1975, et al.
(författare)
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Blood group A glycosyltransferase occurring as alleles with high sequence difference is transiently induced during a Nippostrongylus brasiliensis parasite infection.
- 2002
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Ingår i: The Journal of biological chemistry. - 0021-9258. ; 277:17, s. 15044-52
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Tidskriftsartikel (refereegranskat)abstract
- Neutral mucin oligosaccharides from the small intestine of control rats and rats infected with the parasite Nippostrongylus brasiliensis were released and analyzed by gas chromatography-mass spectrometry. Infected animals expressed seven blood group A-like structures that were all absent in the control animals. The blood group A nature of these epitopes was confirmed by blood group A reactivity of the prepared mucins, of which Muc2 was one. Transferase assays and Northern blotting on small intestines from infected animals showed that an alpha-N-acetylgalactosaminyltransferase similar to the human blood group A glycosyltransferase had been induced. The expression was a transient event, with a maximum at day 6 of the 13-day-long infection. The rat blood group A glycosyltransferase was cloned, revealing two forms with an amino acid similarity of 95%. Both types had blood group A transferase activity and were probably allelic because none of 12 analyzed inbred strains carried both types. The second type was found in outbred rats and in one inbred strain. First generation offspring of inbred rats of each type were heterozygous, further supporting the allelic hypothesis. The transient induction and the large allelic variation could suggest that glycosyltransferases are part of a dynamic system altering mucins and other glycoconjugates as a protecting mechanism against microbial challenges.
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| 9. |
- Sjöling, Åsa, et al.
(författare)
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Analysis of chromosomal aberrations involving chromosome 1q31-->q53 in a DMBA-induced rat fibrosarcoma cell line : amplification and overexpression of Jak2
- 2001
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Ingår i: Cytogenetics and Cell Genetics. - : S. Karger. - 0301-0171 .- 1421-9816. ; 95:3-4, s. 202-209
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Tidskriftsartikel (refereegranskat)abstract
- In a study of DMBA-induced rat fibrosarcomas we repeatedly found deletions and/or amplifications in the long arm of rat chromosome 1 (RNO1). Comparative genome hybridization showed that there was amplification involving RNO1q31-->q53 in one of the DMBA-induced rat fibrosarcoma tumors (LB31) and a cell culture derived from it. To identify the amplified genes we physically mapped rat genes implicated in cancer and analyzed them for signs of amplification. The genes were selected based on their locations in comparative maps between rat and man. The rat proto-oncogenes Ccnd1, Fgf4, and Fgf3 (HSA11q13.3), were mapped to RNO1q43 by fluorescence in situ hybridization (FISH). The Ems1 gene was mapped by radiation hybrid (RH) mapping to the same rat chromosome region and shown to be situated centromeric to Ccnd1 and Fgf4. In addition, the proto-oncogenes Hras (HSA11p15.5) and Igf1r (HSA15q25-->q26) were mapped to RNO1q43 and RNO1q32 by FISH and Omp (HSA11q13.5) was assigned to RNO1q34. PCR probes for the above genes together with PCR probes for the previously mapped rat genes Bax (RNO1q31) and Jak2 (RNO1q51-->q53) were analyzed for signs of amplification by Southern blot hybridization. Low copy number increases of the Omp and Jak2 genes were detected in the LB31 cell culture. Dual color FISH analysis of tumor cells confirmed that chromosome regions containing Omp and Jak2 were amplified and were situated in long marker chromosomes showing an aberrant banding pattern. The configuration of the signals in the marker chromosomes suggested that they had arisen by a break-fusion-bridge (BFB) mechanism.
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| 10. |
- Walentinsson, A, et al.
(författare)
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Independent amplification of two gene clusters on chromosome 4 in rat endometrial cancer: identification and molecular characterization.
- 2001
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Ingår i: Cancer research. - 0008-5472. ; 61:22, s. 8263-73
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Tidskriftsartikel (refereegranskat)abstract
- The BDII rat is genetically predisposed to hormone-dependent endometrial adenocarcinoma and was used to model human cancer. Tumors arising spontaneously in strain crosses involving BDII rats were analyzed by means of comparative genome hybridization. The most common aberration was amplification of the proximal region of rat chromosome 4, centered around bands q12-q22. The copy numbers of 15 cancer-related genes from the region were examined in tissue cultures of 11 endometrial carcinomas (10 endometrial adenocarcinomas and 1 endometrial squamous cell carcinoma) and one peritoneal mesothelioma. Amplification in rat chromosome 4 was detected in six tumors (50%), five of which carried two separate amplified regions, situated at 4q12-q13 and 4q21-q22, interrupted by a nonamplified segment at 4q13-q21.1. The genes Cdk6 (cyclin-dependent kinase 6) and Met (hepatocyte growth factor receptor) were located in the core of each amplified region and were amplified most recurrently and at the highest levels among the genes tested. Using fluorescence in situ hybridization on tumor metaphases, it was observed that the amplified Cdk6 and Met sequences were situated on typical homogeneously staining regions (HSRs). In three tumors, both genes were amplified in the same HSRs, whereas in two tumors, the amplified sequences of each gene were situated in separate HSRs. In addition, Cdk6 and Met amplification was consistently associated with a corresponding increase in gene expression, suggesting that the two genes might represent the targets for the amplifications. In the sixth tumor, which carried amplified sequences of Met but not of Cdk6, coexpression of Met and the normally silent hepatocyte growth factor gene (Hgf; the ligand of Met) was observed. This finding suggests that an autocrine signaling circuit might be operating in this particular tumor. Taken together, our findings suggest that up-regulation of Cdk6 and/or Met may contribute to the development of endometrial cancers in the BDII rat.
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