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At least 235 records · Page 13Linked to original sources
PubMed1993

Sublocalization of the synovial sarcoma-associated t(X;18) chromosomal breakpoint in Xp11.2 using cosmid cloning and fluorescence in situ hybridization.

In a previous study we localized the synovial sarcoma-associated t(X;18)(p11;q11) breakpoint within the ornithine aminotransferase-like 1 (OATL1) cluster on the X chromosome. This localization was delineated from both somatic cell hybrid and fluorescence in situ hybridization (FISH) analysis of patient material, using OAT-specific cDNA and YAC probes. Simultaneously, Knight et al. (1992, Mol. Hum. Genet, in press) mapped this same breakpoint in their patient material adjacent to the more proximal OATL2 region on the X chromosome. Here we report the analysis of two additional tumors and demonstrate that again in these cases the chromosomal break occurs within the OATL1 cluster. In order to further specify the breakpoint, we subcloned the OATL1 YAC (no. 2) into cosmids. At least one of these cosmids (0.38) hybridizes to sequences that bracket the translocation breakpoint, as demonstrated by both Southern blot and FISH analysis. These observations confirm and substantiate our previous findings. In addition, cosmid 0.38 should be a valuable instrument for the ultimate isolation and identification of the gene(s) involved in the development of synovial sarcoma.

Animals↗
PubMed1996

Construction of a 600-kilobase cosmid clone contig and generation of a transcriptional map surrounding the lung cancer tumor suppressor gene (TSG) locus on human chromosome 3p21.3: progress toward the isolation of a lung cancer TSG.

The critical region on human chromosome 3p21.3 harboring a putative lung cancer tumor suppressor gene (TSG) was previously defined by allelotyping and recently refined by overlapping homozygous deletions. We report the construction of a 700-kb (cosmid and one P1 phage) clone contig covering the deletion overlap and its flanks. The minimal set of 23 cosmids comprises 600 kb and is extended by one P1 phage to 700 kb to cover the distal breakpoint of the overlap. The clone contig was extensively characterized by restriction and expression mapping to produce high resolution physical and transcription maps of the cloned region. Potential transcribed fragments were detected by hybridization with PCR-amplified cDNA libraries, direct cDNA selection "zoo" blotting, cDNA screening, and identification of 24 CpG islands. Thus far, 15 new genes represented by partial or full-length cDNAs were isolated, characterized, and precisely positioned on the contig. Two previously cloned genes, namely GNAI-2 and GNAT-1, were also positioned. In addition, the telomeric breakpoint of the NCI H740 deletion and centromeric breakpoint of the overlapping GLC20 deletion were discovered and mapped to define precisely the candidate TSG region. This large cosmid clone contig and high resolution maps will prove crucial in the identification of the lung cancer TSG(s).

Chromosome Mapping↗
PubMed1998

Construction of a cosmid library and physical mapping of Bombyx mori nucleopolyhedrovirus genome.

Bombyx mori nucleopolyhedrovirus (BmNPV) DNA was partially digested with BamHI and BglII, or EcoRI, and cloned into the cosmid pWE15. Eight cosmid clones possessing viral DNA fragments with a size range from 34.9 kb to 45.1 kb were obtained, and they covered the entire viral DNA sequence. Using the cosmid library and plasmid libraries obtained previously, physical maps of BmNPV DNA were constructed for EcoRI, SmaI, PstI, SacI and SacII.

Baculoviridae↗
PubMed2002

Rapid screening of a novel arrayed medaka (Oryzias latipes) cosmid library.

Medaka (Oryzias latipes) has many advantages for genetic and developmental studies. With recent advances in the genome analyses of other species, rapid accumulation of resources for medaka genomics is expected. In this study, we generated an arrayed medaka cosmid library from the HNI inbred strain, carrying a 40-kb insert on average. The library consists of approximately 120,000 clones with a 6-fold genomic coverage. Cosmid clones can be screened within 2 days using standard polymerase chain reaction. Considering the advantage of the cosmid insert size and the compact genome size of the medaka, this library provides a powerful tool for future genome analyses.

Journal Article↗
PubMed1980

A small cosmid for efficient cloning of large DNA fragments.

The production and use of the 6 kb cosmid pHC79, a derivative of pBR322, is described. It can be used for cloning of fragments cleaved by EcoRI, ClaI, BamHI (also BglII, BclI, Sau3A and MboI), SalI (also XhoI and AvaI), EcaI and PstI. Hybrid cosmids containing inserts in the size range of 40 kb are packaged in vitro and transduced with an efficiency of 5 X 10(4) - 5 X 10(5) clones/microgram of insert DNA. Prefractionation of the DNA fragments to be cloned into 40 kb sized fragments ensures the cloning of contiguous stretches of DNA. Proteins produced in vitro by the cosmid pHC79 are identical to the ones produced by its pBR322 parent.

Bacteriophage lambda↗
PubMed1982

Cloning of the complete human cytomegalovirus genome in cosmids.

Purified virion DNA (155 X 10(6) Mr) of human cytomegalovirus (CMV) strain Ad169 was partially cleaved with restriction endonucleases HindIII and EcoRI and cloned in the respective cleavage sites of cosmid pHC79. A complete gene library was established in a set of clones containing the viral DNA in long overlapping segments. Restriction maps for HindIII (29 fragments) and EcoRI (36 fragments) were constructed from the linkage of cosmid-cloned fragments, from double digestions of cloned DNA, and from blot hybridization of labeled cloned viral DNA with restriction fragments of virion DNA and singly or doubly cleaved cosmid clones.

Cloning, Molecular↗
PubMed1984

New cosmid vectors developed for eukaryotic DNA cloning.

A series of ColE1 and pSC101 cosmid vectors have been constructed suitable for cloning large stretches of DNA. All contain a single BamHI site allowing cloning of Sau3A, MboI, BglII, BclI , and BamHI-generated fragments. These vectors have the following characteristics: (i) they are relatively small (1.7-3.4 kb); (ii) the BamHI cloning site is flanked by restriction enzyme sites enabling direct cloning of unfractionated insert DNA without generating multiple insert or vector ligation products [ Ish - Horowitz and Burke, Nucl . Acids Res. 9 (1981) 2989-2998]; (iii) two vectors ( pHSG272 and pHSG274 ) contain a hybrid Tn5 KmR/ G418R gene which is selectable in both prokaryotic and eukaryotic cells, making them suitable for transferring DNA into eukaryotic cells, and (iv) the different prokaryotic selectable markers available in the other vectors described facilitate cosmid rescue of the transferred DNA sequences from the eukaryotic cell: CmR, ApR, KmR, ( pHSG429 ), CmR, ( pHSG439 ), colicin E1 immunity ( pHSG250 ), (v) the cosmid pHSG272 was used successfully to construct a shuttle vector based on the BPVI replicon [ Matthias et al., EMBO J. 2 (1983) 1487-1492].

Animals↗
PubMed1985

A cosmid for selecting genes by complementation in Aspergillus nidulans: Selection of the developmentally regulated yA locus.

We constructed a 9.9-kilobase cloning vector, designated pKBY2, for isolating genes by complementation of mutations in Aspergillus nidulans. pKBY2 contains the bacteriophage lambda cos site, to permit in vitro assembly of phage particles; a bacterial origin of replication and genes for resistance to ampicillin and chloramphenicol, to permit propagation in Escherichia coli; the A. nidulans trpC(+) gene, to permit selection in Aspergillus; and a unique BamHI restriction site, to permit insertion of DNA fragments produced by digestion with restriction endonucleases BamHI, BglII, Mbo I, or Sau3A. We used this cosmid to form a quasirandom recombinant DNA library containing 35- to 40-kilobase DNA fragments from a wild-type strain of A. nidulans. DNA from this library transformed a yellow-spored (yA(-)) pabaA(-)trpC(-)Aspergillus strain (FGSC237) to trpC(+) at frequencies of approximately 10 transformants per mug of DNA. Three of approximately 1000 trpC(+)pabaA(-) colonies obtained were putative yA(+) transformants, because they produced wild-type (green) spores. DNA from each of the green-spored transformants contained pKBY2 sequences and DNA from two transformants transduced E. coli to ampicillin resistance following treatment in vitro with a lambda packaging extract. The cosmids recovered in E. coli had similar restriction patterns and both yielded trpC(+) transformants of A. nidulans FGSC237, 85% of which produced green spores. Several lines of evidence indicate that the recovered cosmids contain a wild-type copy of the yA gene.

Journal Article↗
PubMed1994

Island rescue PCR: a rapid and efficient method for isolating transcribed sequences from yeast artificial chromosomes and cosmids.

The identification of transcripts from large genomic regions cloned in yeast artificial chromosomes (YACs) or cosmids continues to be a critical and often rate-limiting step in positional cloning of human disease genes. We have developed a PCR-based method for rapid and efficient generation of probes from YACs or cosmids that can be used for cDNA library screening. The method, which we call island rescue PCR (IRP), is based upon the observation that the 5' ends of many genes are associated with (G+C)-rich regions called CpG islands. In IRP, the YAC of interest is digested with a restriction enzyme that recognizes sequences of high CpG content, and vectorette linkers are ligated to the cleaved ends. The PCR is used to amplify the region extending from the cleaved restriction enzyme site to the nearest SINE (Alu) repeat. In many cases this product contains sequences from the 5' end of the associated gene. cDNA clones isolated with these products are then verified by mapping them back to the original YAC. The method allows rapid screening of > 500 kb of human genomic insert in one experiment, is tolerant of contaminating yeast sequences, and can also be applied to cosmid pools. In a control experiment, the method was able to identify cDNA clones for the neurofibromatosis type 1 (NF1) gene using a probe generated from a YAC in the region. Application of IRP has yielded nine other genes from YACs isolated from chromosome locations 4p16.3 and 17q21.

Base Composition↗
PubMed1991

Identification of Mycobacterium leprae antigens from a cosmid library: characterization of a 15-kilodalton antigen that is recognized by both the humoral and cellular immune systems in leprosy patients.

Screening of the Mycobacterium leprae cosmid library with pooled sera from lepromatous leprosy (LL) patients by a colony immunoblot technique resulted in the identification of about 100 colonies that produced immunologically reactive proteins. Twenty-four of these clones were purified, analyzed, and found to comprise two groups according to the reactivity of the recombinant proteins with LL sera and to the DNA restriction patterns of the recombinant plasmids and cosmids. Proteins specified by clones from group I reacted strongly with LL patients' sera on a Western blot (immunoblot), demonstrating a 15-kDa protein band designated A15. The A15 antigen also reacted with pooled sera from patients with tuberculoid leprosy from the United States and Brazil. Clones from group II did not show any reactive protein band on a Western blot, when reacted with patients' sera. DNAs from cosmids of group II all contain a 10-kb PstI fragment that hybridized to the unique repetitive M. leprae DNA. Sequence analysis of a 1.2-kb fragment containing the entire coding sequence of A15 revealed three open reading frames (ORFs), only one of which (ORF II) contains sufficient genetic information to encode for A15. Part of the A15 gene was found to exist also in a group of lambda gt11:M. leprae clones previously isolated in our laboratory by immunological screening with LL patients' sera. One of the lambda gt11 clones (L8) expresses a beta-galactosidase fusion protein with 89 amino acids from the C terminus of A15. An important result was that the fusion protein was clearly recognized by T cells from leprosy patients. Interestingly, Mycobacterium tuberculosis-stimulated T cells from M. leprae nonresponder (LL as well as borderline tuberculoid) patients were able to respond to the isolated recombinant M. leprae antigen, indicating that nonresponsiveness to M. leprae antigens can be reversible. The sequence of the M. leprae DNA fused to the beta-galactosidase gene of lambda gt11 clone L8 was identical to that of a lambda gt11:M. leprae clone isolated recently that expresses an immunologically reactive fusion protein (S. Laal, Y. D. Sharma, H. K. Prasad, A. Murtaza, S. Singh, S. Tangri, R. Misra, and I. Nath, Proc. Natl. Acad. Sci. USA 88:1054-1058, 1991). Besides the complete sequence of the A15 gene, sequencing data of two flanking ORFs are presented. Downstream from ORF II (A15), ORF III has a high degree of similarity to the genes for tomato ATP-dependent proteases that are members of a larger class of highly conserved proteases ubiquitous among prokaryotes and eukaryotes.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1986

Nonrandom cosmid cloning and prophage SP beta homology near the replication terminus of the Bacillus subtilis chromosome.

From a library of Bacillus subtilis DNA cloned with the Escherichia coli cosmid vector pHC79, 85 recombinant cosmids containing DNA from near the replication terminus, terC, were identified. The DNA inserts of these cosmids were confined to three regions of a 350-kilobase segment of the chromosome extending from the left end of the SP beta prophage to approximately 75 kilobases on the right of terC. All B. subtilis genes known to reside in this segment, as well as the portion of the SP beta prophage that is expressed early in the lytic cycle of the phage, appeared to be absent from the library. A region of SP beta homology distinct from the prophage and just to the left of terC was identified.

Bacillus subtilis↗
PubMed1996

Expression of a cosmid containing the LCR, (A)gamma, delta, and beta globin genes in mouse erythroleukemia cells.

A novel method involving the packaging of phage particles was used to introduce cosmids containing components of the human beta-globin locus control region (LCR) and the human (A)gamma, delta, and beta globin genes into mouse erythroleukemia (MEL) cells. After stable transfection, MEL clones were selected and analyzed for expression of human genes. Both (A)gamma and beta globin mRNA were expressed in these clones, indicating that MEL cells do not suppress transcription of the human gamma globin gene. The variability of human (A)gamma vs. beta globin expression from clone to clone prevents a clear delineation of differences in the expression of these two genes with a cosmid in which a region potentially involved in gamma-to-beta switching has been deleted. The results suggest that MEL cells are capable of supporting human gamma expression, despite their predominantly adult phenotype.

Adult↗
PubMed1997

The DNA sequence of cosmid 14-13b from chromosome XIV of Saccharomyces cerevisiae reveals an unusually high number of overlapping open reading frames.

This work is part of the effort for sequencing chromosome XIV of Saccharomyces cerevisiae. Cosmid 14-13b contains a 37.8 kb insert derived from a partial Sau3A digestion of the genome, cloned into the BamHI site of the vector Pou6. The strategy used for sequencing is based on the fragmentation of the whole cosmid by sonication, followed by shotgun sequencing on an Applied Biosystem DNA sequencer. The clones with inserts corresponding to the vector were identified by dot-blot hybridization, without the need of sequencing. The analysis of the DNA sequence reveals 29 open reading frames (ORFs) longer than 300 bases. Nine ORFs are internal to some other ORFs. Similarity searches against DNA and protein data banks show that six ORFs correspond to already known yeast genes (OMP1, PSU1, MLS1, RPC19, DBP2, CYB5) and one ORF matches the sequence of a putative yeast gene (ESBP6).

Chromosome Mapping↗
PubMed1999

Arylamine N-acetyltransferase type 2 (NAT2), chromosome 8 aneuploidy, and identification of a novel NAT1 cosmid clone: an investigation in bladder cancer by interphase FISH.

Two genes (arylamine N-acetyltransferase types 1 and 2, NAT1 and NAT2), which are known to metabolize bladder carcinogens, are located on chromosome band 8p22. Alterations in chromosome 8, including deletions of 8p, occur frequently in many epithelium-derived tumors. In this study, fluorescence in situ hybridization (FISH) was used for study of the relationship between chromosome 8 deletions in the region of NAT1 and NAT2 and grade and stage of tumor in bladder cancer. Cells from 52 bladder tumors were examined by dual-labeling FISH with a centromere 8-specific probe and a cosmid probe for NAT2. A more limited number were examined for loss with both the NAT2 probe and a newly constructed NAT1-specific cosmid. Loss of NAT2 was found in 6/52 patients in more than 30% of cells, and in 10/52 in 10%-30% of cells examined. Six samples also showed loss of NAT1, indicating that the region of deletion spans at least the distance of the two genes. No obvious correlation between loss of NAT genes with grade and stage of tumor was evident. Interestingly, 17/52 (32%) tumors showed an increased copy number of chromosome 8, with tumors of low stage showing relatively smaller increases of chromosome 8. Loss of 8p22 and genetic instability involving chromosome 8 indicate that this chromosome is important in bladder cancer and that NAT genes will act as important genetic landmarks in defining deletions in this disease. Genes Chromosomes Cancer 25:376-383, 1999.

Acetyltransferases↗
PubMed2000

Sequence analysis of two cosmids from the right arm of the Schizosaccharomyces pombe chromosome II.

We report the complete sequence of two cosmids, SPBC19C7 (34815 bp insert, Accession No. AL023859) and SPBC15D4 (33203 bp insert, Accession No. AL031349), localized on chromosome II of the S. pombe genome. Twelve open reading frames (ORFs) were identified in SPBC19C7 and 16 in SPBC5D4. Two known genes were found on each cosmid: cyr1 and uve1 on SPBC19C7, encoding adenylate cyclase and a UV-endonuclease, respectively, and gpt and pho2 on SPBC15D4, encoding an N-acetylglucosamine-1-phosphate transferase and a4-nitrophenylphosphatase, respectively. Five ORFs similar to known proteins were found on SPBC19C7, and six on SPBC15D4. They include putative genes for a ubiquitin protein ligase, a prolyl-tRNA synthetase, a tRNA splicing endonuclease, a voltage-gated chloride channel, a mannosyl transferase, a kinesin-like protein, a histone transcriptional regulator, an N-acetyltransferase, a cystathionine gamma-synthase and a TFIID subunit. Two ORF products of SPBC15D4 do not have clear homologues: one encodes a putative transcriptional regulator with a binuclear zinc domain and the other a protein with six transmembrane domains. Two ORFs from SPBC15D4 are similar to unknown ORFs, one from Saccharomyces cerevisiae and the other from Caenorhabditis elegans. Finally, two ORFs of SPBC19C7 and six of SPBC15D4 correspond to orphan genes. The frequent occurrence of introns and the short and degenerated intron-exon boundaries consensus sequences significantly complicated ORF predictions. Two potential ORF-free regions spanning several kb were predicted, and a clustering of ORFs transcribed in the same orientation was observed.

Amino Acid Sequence↗
PubMed2000

Construction of a cosmid library of DNA replicated early in the S phase of normal human fibroblasts.

We constructed a subgenomic cosmid library of DNA replicated early in the S phase of normal human diploid fibroblasts. Cells were synchronized by release from confluence arrest and incubation in the presence of aphidicolin. Bromodeoxyuridine (BrdUrd) was added to aphidicolin-containing medium to label DNA replicated as cells entered S phase. Nuclear DNA was partially digested with Sau 3AI, and hybrid density DNA was separated in CsCl gradients. The purified early-replicating DNA was cloned into sCos1 cosmid vector. Clones were transferred individually into the wells of 96 microtiter plates (9,216 potential clones). Vigorous bacterial growth was detected in 8,742 of those wells. High-density colony hybridization filters (1, 536 clones/filter) were prepared from a set of replicas of the original plates. Bacteria remaining in the wells of replica plates were combined, mixed with freezing medium, and stored at -80 degrees C. These pooled stocks were analyzed by polymerase chain reaction to determine the presence of specific sequences in the library. Hybridization of high-density filters was used to identify the clones of interest, which were retrieved from the frozen cultures in the 96-well plates. In testing the library for the presence of 14 known early-replicating genes, we found sequences at or near 5 of them: APRT, beta-actin, beta-tubulin, c-myc, and HPRT. This library is a valuable resource for the isolation and analysis of certain DNA sequences replicated at the beginning of S phase, including potential origins of bidirectional replication.

Aphidicolin↗
PubMed1994

Screening of a mouse/human Y-chromosomal cosmid library for gene candidates and markers by using (short) oligonucleotide probes.

A comprehensive approach is described for the identification of sequences of interest from a human Y chromosomal cosmid library via (short) consensus oligonucleotide probes. It involves the ordering of cosmid clones grown in microtiter plates onto small filter membranes by a robot workstation. A high number of the clones are characterized by their repetitive sequence content, either by ubiquitously interspersed simple tandem blocks or by Y-specific elements. The Y chromosomal repeat (DYZ2) appears underrepresented in the library. In contrast many novel microsatellite marker systems can now be developed for the Y chromosome on the basis of the simple repeat blocks described here. Though novel genes were not yet delineated so far, a number of candidate sequences with high coding potential and other interesting characteristics are described.

Animals↗
PubMed1994

Hybridization of the variable number of tandem repeat core oligonucleotide GNNGTGGG to 350 cosmids from chromosome 7.

An efficient method using short oligonucleotides is described for the isolation of minisatellite markers of the type variable number of tandem repeats (VNTR). It is used to screen 350 cosmids from chromosome 7 for the presence of such potentially polymorphic DNA segments. From the number of hybridization signals to chromosome 7 cosmids, I estimate the human genome to have at least about 15000 VNTR loci containing minisatellite core sequences, which is well above previous estimates.

Chromosomes, Human, Pair 7↗