The Experts below are selected from a list of 252 Experts worldwide ranked by ideXlab platform
Robert Haselkorn - One of the best experts on this subject based on the ideXlab platform.
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suppression of heterocyst differentiation in anabaena pcc 7120 by a Cosmid carrying wild type genes encoding enzymes for fatty acid synthesis
Fems Microbiology Letters, 1997Co-Authors: C C Bauer, K S Ramaswamy, S Endley, L A Scappino, James W Golden, Robert HaselkornAbstract:A Cosmid containing a wild-type Anabaena PCC 7120 DNA fragment was found to suppress heterocyst differentiation, creating a Het phenotype in an otherwise wild-type strain. Curing of the Cosmid restored the full wild-type Het+ Nif+ phenotype. The Cosmid contains at least four genes encoding proteins with significant sequence similarity to enzymes involved in the synthesis of fatty acids. Selection for Nif+ revertants of the suppressed strain yielded modified Cosmids, one of which contained a 10.2-kb transposon, Tas1, inserted into the promoter region of a gene encoding a protein with acyl carrier and β-keto reductase domains. This gene, called hetN, was shown previously by Black and Wolk (J. Bacteriol. (1994) 176, 2282–2292) to inhibit heterocyst differentiation when present alone on a plasmid. Oddly, hetN gene transcription is detected later than 6 h into heterocyst differentiation.
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Physical Mapping of Rhodobacter capsulatus: Cosmid Encyclopedia and High Resolution Genetic Map
Advances in Photosynthesis and Respiration, 1995Co-Authors: Michael Fonstein, Robert HaselkornAbstract:A combination of Cosmid genome walking and pulse field gel electrophoresis was used to construct a high resolution physical and genetic map of the 3.8 Mb genome of Rhodobacter capsulatus SB1003. The mapping was done by grouping and further mapping of Cosmids and bacteriophages from genomic libraries using PFGE-generated DNA fragments and SP6 and T7 specific transcripts corresponding to the ends of the Cosmid inserts. Cosmid and phage clones formed two uninterrupted and ordered groups, one corresponding to the chromosome of Rb. capsulatus, the other to its 134 kb plasmid. Cos site end-labeling and partial EcoRV digestion of Cosmids were used to construct a high resolution restriction map of the genome. Overlapping of the Cosmids was confirmed by the resemblance of the Cosmid restriction maps and by direct end-to-end hybridization. 34 genes or gene clusters were located in the ordered gene library and mapped with an accuracy of 1–10 kb. Three Rb. capsulatus strains; KB-1, St. Louis and 2.3.1., were chosen out of 14 others for a detailed comparison of their physical maps, which were partially constructed using the minimal Cosmid set of Rb. capsulatus SB1003 as a source of ordering probes. Blots of the minimal set of 192 Cosmids, covering the chromosome and the plasmid, with known map position of each Cosmid, gives to Rb. capsulatus the same advantages that the Kohara phage panel gives to E. coli. Blots of this minimal Cosmid set digested with EcoRV represent the entire genome split into gene-size pieces, and provide an opportunity for direct high resolution mapping of genes and transcripts.
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chromosomal structure of rhodobacter capsulatus strain sb1003 Cosmid encyclopedia and high resolution physical and genetic map
Proceedings of the National Academy of Sciences of the United States of America, 1993Co-Authors: Michael Fonstein, Robert HaselkornAbstract:Abstract A combination of Cosmid genome walking and pulsed-field gel electrophoresis was used to construct a high-resolution physical and genetic map of the 3.8-megabase (Mb) genome of Rhodobacter capsulatus SB1003. The mapping was done by hybridization of pulsed-field gel blots and by grouping and further mapping of the Cosmids and bacteriophages from genomic libraries. Cosmid clones formed two uninterrupted and ordered groups, one corresponding to the chromosome of R. capsulatus, the other to its 134-kb plasmid. Cos site end-labeling and partial EcoRV digestion of Cosmids were used to construct a high-resolution EcoRV map of the genome. Overlapping of the Cosmids was confirmed by the resemblance of the Cosmid restriction maps and by direct end-to-end hybridization with SP6- and T7-specific transcripts. Twenty-three previously cloned genes and eight groups of repeated sequences, revealed in this work, were located in the ordered gene library and mapped with an accuracy of 1-10 kb. Blots of a minimal set of 192 Cosmids, covering the chromosome and the plasmid with the known map position of each Cosmid, give to R. capsulatus the same advantages that the Kohara phage panel gives to E. coli.
Pieter J. De Jong - One of the best experts on this subject based on the ideXlab platform.
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isolation of a Cosmid sublibrary for a region of chromosome 12 frequently amplified in human cancers using a complex chromosome microdissection probe
Genomics, 1996Co-Authors: Abdel G Elkahloun, Pieter J. De Jong, Jennifer S Mcninch, Paul S Meltzer, Xin Yuan Guan, Jeffrey M TrentAbstract:Chromosome-specific Cosmid libraries are an extremely useful resource for positional cloning projects. Once a particular region of interest has been identified, it would be of value to have an approach for isolating chromosome band-specific Cosmids that could be assembled into a sublibrary for rapid screening. We constructed a region-specific sublibrary of 700 Cosmids by screening a chromosome 12-specific Cosmid library with a complex probe generated by degenerate oligonucleotide-primed PCR of a microdissected homogeneously staining region containing sequences amplified from chromosome 12q13-q15. Based on fluorescence in situ hybridization, approximately 60% of the Cosmids in the sublibrary were derived from the microdissected region. To demonstrate further the utility of this sublibrary, a 150-kb contig containing the SAS and CDK4 genes was constructed, as well as several additional contigs between CDK4 and MDM2. This study demonstrates the possibility of utilizing probes generated by microdissection for assembling band-specific sublibraries that are amenable to rapid screening with multiple markers.
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characterization of two chromosome 12 Cosmid libraries and development of stss from Cosmids mapped by fish
Genomics, 1993Co-Authors: Kate Montgomery, Pieter J. De Jong, David C. Ward, Janine M Leblanc, Peter Tsai, Jennifer S Mcninch, Raju Kucherlapati, Kenneth S KrauterAbstract:The authors have constructed and characterized two related human chromosome 12-specific Cosmid libraries. DNA from flow-sorted chromosomes from a somatic cell hybrid was cloned into a Cosmid vector. Approximately 61% of the Cosmids in the nearly 26,200 member arrayed libraries (LL12NC01 and LL12NC02) contain human DNA inserts, and 31% of the Cosmids derived from human DNA contain CA repeats. One hundred and fifty-two Cosmids isolated from the libraries have been mapped by fluorescence in situ hybridization (FISH). Cosmids containing human DNA inserts were localized by FISH exclusively to chromosome 12, confirming the chromosomal specificity of the libraries. The Cosmids have been localized to all parts of this chromosome, although some regions are more highly represented than others. Partial sequence information was obtained from 44 mapped Cosmids, and oligonucleotide primer pairs were synthesized that define unique sequence tagged sites (STSs). These mapped Cosmids, and unique STSs derived from them, provide a set of useful clones and primer pairs for screening YAC libraries and developing contigs centered on regions of interest within chromosome 12. In addition, 120 of the mapped Cosmids contain CA repeats, and thus they also provide a useful resource for defining highly polymorphic simple tandem repeat elements that servemore » as genetic markers for linkage analysis and disease gene localization. 56 refs., 4 figs., 2 tabs.« less
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A Cosmid and Yeast Artificial Chromosome Contig Containing the Complete Ryanodine Receptor (RYR1) Gene
Genomics, 1993Co-Authors: Sylvie Rouquier, Dominique Giorgi, Barbara J. Trask, Anne Bergmann, Michael S. Phillips, David H. Maclennan, Pieter J. De JongAbstract:The ryanodine receptor (RYR1) gene is responsible for some forms of malignant hyperthermia and has been localized to 19q13.1. Central core disease is a genetic myopathy that is genetically linked to RYR1. The authors have identified an overlapping set of Cosmid and YAC clones that spans more than 800 kb and includes the RYR1 gene ([approximately]205 kb). Cosmids from this region were identified by screening three chromosome 19 Cosmid libraries (11-fold coverage) with six subclones representing the entire RYR1 cDNA. Genomic sequences from positive Cosmids were then used as probes to identify additional Cosmids. A minimally overlapping set of 23 Cosmids was assembled into two contigs on the basis of restriction fragment analysis and hybridization data. Three YAC clones were isolated by screening a human YAC library with selected Cosmid inserts. Overlaps among these YACs and the Cosmid contigs were determined by hybridizing YAC Alu-PCR products to Cosmid DNAs. The YACs bridged the gap between the Cosmid contigs and extended the contig on both sides. Fluorescence in situ hybridization experiments positioned the RYR1 contig between GPI, MAG, and D19S191 on the proximal side and D19S190, CYP2A, CYP2F, SNRPA, BCKDHA, and other markers on the distal side. The 800-kb contig ofmore » cloned reagents will facilitate the detailed characterization of the RYR1 gene and other loci that may be closely related to central core disease. 62 refs., 3 figs., 3 tabs.« less
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stable propagation of Cosmid sized human dna inserts in an f factor based vector
Nucleic Acids Research, 1992Co-Authors: Hiroaki Shizuya, Pieter J. De Jong, Bruce W Birren, Melvin I SimonAbstract:Instability of complex mammalian genomic DNA inserts is commonplace in Cosmid libraries constructed in conventional multicopy vectors. To develop a means to construct stable libraries, we have developed a low copy number Cosmid vector based on the E.coli F factor replicon (Fosmid). We have tested relative stability of human DNA inserts in Fosmlds and in two conventional multicopy vectors (Lawrist 16 and Supercos) by comparing the frequency of changes In restriction patterns of the inserts after propagating randomly picked human genomic clones based on these vectors. We found that the clones based on Fosmid vector undergo detectable changes at a greatly reduced frequency. We also observed that sequences that undergo drastic rearrangements and deletions during propagation In a conventional vector were stably propagated when recloned as Fosmids. The results indicate that Fosmid system may be useful for constructing stable libraries from complex genomes.
Mitsuo Oshimura - One of the best experts on this subject based on the ideXlab platform.
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Cosmids and transcribed sequences from chromosome 11q23
Japanese journal of human genetics, 1995Co-Authors: Motonobu Katoh, Yuzuki Nakagawa, Toshio Yawata, Satoshi Kumano, Eisuke Kobayashi, Akihiro Kurimasa, Hiroyuki Kugoh, Mitsuo OshimuraAbstract:To obtain Cosmid markers and transcribed sequences from a specific chromosome region, a series of radiation-reduced hybrids (RHs) containing various regions of human chromosome 11 was prepared from microcell hybrid A9 ( neo 11) cells containing a normal human chromosome 11 tagged with pSV2 neo at 11p11.2. Among 15 radiation hybrid clones isolated, RH(11)-9 which contains a q23 fragment in addition to the neo integration site, was used for the construction of a Cosmid library. Cosmid clones having human DNA sequences were screened, and localized by Southern hybridization with the radiation hybrid panel. Fifty-nine Cosmids were assigned to 11q23 and 6 Cosmids to 11p11.2. Exon amplification proceeded with 23 of the 59 Cosmids and 16 putative exons were cloned. Three of them were identical to those constituting a known gene which locates on q23 (ATDC), and the others were unknown. Thus, the RHs containing various subchromosomal fragments of chromosome 11 were useful for constructing region-specific DNA markers. The RH-(11)-9 cells and putative exons also facilitate the positional cloning of genes in the 11q23 region.
Eiichi Soeda - One of the best experts on this subject based on the ideXlab platform.
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Cosmid assembly and anchoring to human chromosome 21
Genomics, 1995Co-Authors: Eiichi Soeda, Kazutoyo Osoegawa, Yasuo Atsuchi, Tetsushi Yamagata, Takanori Shimokawa, Haruo Kishida, Saishi Okano, Ilya Chumakov, Daniel CohenAbstract:A human chromosome 21-specific Cosmid library from the Lawrence Livermore National Laboratory has been analyzed by two complementary methods, finger printing and hybridization; 40% coverage of the entire chromosome 21 has been achieved. To prepare a contig pool, approximately 9300 Cosmid clones randomly selected from the library were fingerprinted and automatically assembled into 467 overlapping sets by the fluorescence-tagged restriction fragment method. The average size of the overlapping sets was 9.5 Cosmids with minimal tiling paths consisting of 5.4 Cosmids with a 10-kb extension each. However, as many as 10% of overlaps within members were estimated to be false. For regional localization, we hybridized gridded arrays of Cosmids with inter-Alu-PCR probes obtained from YAC clones and somatic cell hybrids and assigned 592 Cosmids to 26 subregions of 21q. Of these, 371 clones were incorporated into 139 contigs, anchoring the total 1864 Cosmids to the subregion. The remaining 221 clones were mapped as orphans. To correlate the cytogenetic, YAC, and Cosmid maps on 21q, the translocation breakpoints of the chromosomes contained in the somatic cell hybrids were mapped with respect to the STS content of the YACs. From the gene cluster regions, 176 ribosomal and 25 alphoid clones were isolated bymore » hybridization. Together, these sets of anchored contigs and Cosmids will provide a valuable resource for construction of a high-resolution map and for isolation of genes of interest from chromosome 21. 34 refs., 4 figs., 1 tab.« less
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ISOLATION OF HUMAN CHROMOSOME 21-SPECIFIC CosmidS AND THEIR USES IN MAPPING OF Cosmid CONTIGS ON CHROMOSOMAL SUBREGIONS
Journal of Human Genetics, 1994Co-Authors: Haruo Kishida, Takanori Shimokawa, Eiichi SoedaAbstract:A Cosmid library of 3×105 clones has been constructed from a human x hamster hybrid cell line, 153E9a3, which contains human chromosome 21 (HC21) as the only human chromosome. From 56,500 clones of this library, 229 HC21-specific Cosmids have been isolated by their hybridization to total human DNA and by their failure to hybridize to total Chinese hamster DNA. The Cosmids isolated were then characterized, of these, 28 Cosmids (12.2% of those tested) containedNot1 site(s), and 41 Cosmids were localized on the eight subregions of HC21 by differential hybridization withAlu-PCR products obtained from a hybrid mapping panel. The Cosmids localized were further integrated into the existing contigs using the end-specific probes of the clone insert. Therefore, they provided useful anchor points for contig mapping and walking.
Isamu Nishisho - One of the best experts on this subject based on the ideXlab platform.
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Refined mapping of eight Cosmid markers on human chromosome 22
Journal of Human Genetics, 1994Co-Authors: Hiroki Kurahashi, Gilles Thomas, Olivier Delattre, Kenzo Akagi, Shintaro Okada, Shin Ichiro Takai, Ikuo Yana, Thomas Melot, Isamu NishishoAbstract:Eight Cosmid clones were regionally assigned to small subregions of chromosome 22 by hybridization with a total of 22 somatic cell hybrids. One Cosmid was localized to the proximal part of 22q which contained the region commonly deleted in the DiGeorge syndrome. Seven Cosmids showing restriction fragment length polymorphisms were localized to the telomeric region distal to the MB locus, which was reported to be frequently deleted in sporadic meningioma. These Cosmids, when finely mapped and ordered, are considered useful for the identification of genetic alterations on this chromosome arm.
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isolation and mapping of Cosmid markers on human chromosome 22 including one within the submicroscopically deleted region of digeorge syndrome
Human Genetics, 1994Co-Authors: Hiroki Kurahashi, Kenzo Akagi, Katsu Karakawa, Tsutomu Nakamura, Jan P Dumanski, Tetsuya Sano, Shintaro Okada, Shin Ichiro Takai, Isamu NishishoAbstract:A genomic Cosmid library was constructed from a Chinese hamster/human hybrid cell containing human intact chromosome 22 as its only human component. Of 1000 Cosmids with inserts derived from human chromosome 22, 191 were tested for restriction fragment length polymorphisms (RFLPs). As a result, 64 clones detected RFLPs, including five variable number of tandem repeats systems. Of the remaining 127 Cosmids, 111 detected a single copy sequence on human chromosome 22. Five somatic cell hybrids allowed us to assign all of the 64 polymorphic Cosmids and 44 non-polymorphic Cosmids to four different regions of human chromosome 22. In two patients with DiGeorge syndrome, one of the Cosmids that had been sublocalized to 22pter-q11 detected hemizygosity. These 108 Cosmid markers regionally assigned to human chromosome 22 should be useful for the construction of long-range physical maps and the identification of genetic alterations on the chromosome.
