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At least 199 records · Page 11Linked to original sources
PubMed1992

A high-resolution cytogenetic map of 168 cosmid DNA markers for human chromosome 11.

We have constructed a high-resolution cytogenetic map with 168 DNA markers, including 90 RFLP markers for human chromosome 11. The cosmid clones were mapped by fluorescence in situ suppression hybridization, in which discrete fluorescent signals can be detected directly on prometaphase R-banded chromosomes. Although these cosmid clones were distributed throughout the chromosome, they had some tendency to localize in the regions of R-positive band, such as 11p15, 11p11.2, 11q13, 11q23, and 11q25. Since these regions of chromosome 11 are considered to contain genes responsible for certain genetic diseases, cancer breakpoints involved in chromosome rearrangements, and tumor-suppressor genes, this high-resolution cytogenetic map will contribute to the molecular characterization of such genes. This map will also provide many landmarks essential for construction of the complete physical map with contigs of cosmid and YAC clones.

Chromosomes, Human, Pair 11↗
PubMed1992

Rapid isolation of cosmids from defined subregions by differential Alu-PCR hybridization on chromosome 22-specific library.

A method based on the differential screening of a chromosome-specific cosmid library with amplified inter-Alu sequences obtained from a set of somatic cell hybrids has been developed to target the isolation of probes from predefined subchromosomal regions. As a model system, we have used a chromosome 22-specific cosmid library and four cell hybrids containing different parts of this chromosome. The procedure has identified cosmids that demonstrate differential hybridization signals with Alu-PCR products from these cell hybrids. We show, by in situ hybridization or individual mapping, that their hybridization pattern is indicative of their sublocalization on chromosome 22, thus resulting in a large enrichment factor for the isolation of probes from specific small chromosome subregions. Depending on the local Alu-sequence density, from 3 to 10 independent loci per megabase of genome can thus be identified.

Animals↗
PubMed1995

Refined physical map of the spinal muscular atrophy gene (SMA) region at 5q13 based on YAC and cosmid contiguous arrays.

The gene for the autosomal recessive neurodegenerative disorder spinal muscular atrophy has been mapped to a region of 5q13 flanked proximally by CMS-1 and distally by D5S557. We present a 2-Mb yeast artificial chromosome (YAC) contig constructed from three libraries encompassing the D5S435/D5S629/CMS-1-SMA-D5S557/D5S112 interval. The D5S629/CMS-1-SMA-D5S557 interval is unusual insofar as chromosome 5-specific repetitive sequences are present and many of the simple tandem repeats (STR) are located at multiple loci that are unstable in our YAC clones. A long-range restriction map that demonstrates the SMA-containing interval to be 550 kb is presented. Moreover, a 210-kb cosmid array from both a YAC-specific and a chromosome 5-specific cosmid library encompassing the multilocus STRs CATT-1, CMS-1, D5F149, D5F150, and D5F153 has been assembled. We have recently reported strong linkage disequilibrium with Type I SMA for two of these STRs, indicating that the gene is located in close proximity to or within our cosmid clone array.

Base Sequence↗
PubMed1994

Screening cosmid libraries with oligonucleotides corresponding to splice-site consensus sequences.

To facilitate the identification of genes within genomic DNA, we have developed a method based on the use of short oligonucleotides designed from the consensus sequences of splice sites. We describe here the hybridization and washing conditions under which such oligonucleotides can be used to screen cosmid libraries. We confirm the presence of genes within cosmids identified by screening with one oligonucleotide by showing that DNA isolated from such cosmids will hybridize to another splice-site oligonucleotide.

Animals↗
PubMed1998

A cosmid and cDNA fine physical map of a human chromosome 13q14 region frequently lost in B-cell chronic lymphocytic leukemia and identification of a new putative tumor suppressor gene, Leu5.

B-cell chronic lymphocytic leukemia (B-CLL) is a human hematological neoplastic disease often associated with the loss of a chromosome 13 region between RB1 gene and locus D13S25. A new tumor suppressor gene (TSG) may be located in the region. A cosmid contig has been constructed between the loci D13S1168 (WI9598) and D13S25 (H2-42), which corresponds to the minimal region shared by B-CLL associated deletions. The contig includes more than 200 LANL and ICRF cosmid clones covering 620 kb. Three cDNAs likely corresponding to three different genes have been found in the minimally deleted region, sequenced and mapped against the contigged cosmids. cDNA clone 10k4 as well as a chimeric clone 13g3, codes for a zinc-finger domain of the RING type and shares homology to some known genes involved in tumorigenesis (RET finger protein, BRCA1) and embryogenesis (MID1). We have termed the gene corresponding to 10k4/13g3 clones LEU5. This is the first gene with homology to known TSGs which has been found in the region of B-CLL rearrangements.

Amino Acid Sequence↗
PubMed1999

Rapid isolation of genes from an indexed genomic library of C. cinereus in a novel pab1+ cosmid.

In this study we present an indexed genomic library of homokaryon AmutBmut constructed within a novel cosmid carrying pab1+ as a selectable Coprinus marker. The average insert size per cosmid comprises 41 kb. We screened the library and detected copies of known (a1-2, beta-tub, cgl1, ras, trp1) and of new Coprinus genes (cac, lac1, lac2, lac3). Screening was performed either by Southern blot hybridisation or more efficiently by non-radioactive PCR amplification. We successfully applied PCR with specific and with degenerate primers, multiplex PCR and colony PCR in library screening. Our results suggest a new, more efficient pooling strategy for future high throughput screenings to be used in PCR with pooled cosmid DNAs, or in a less laborious approach using pooled Escherichia coli colonies for PCR.

Amino Acid Sequence↗
PubMed2003

Cosmid cloning and sample sequencing of the genome of the uncultivable mollicute, Western X-disease phytoplasma, using DNA purified by pulsed-field gel electrophoresis.

Western X-disease (WX) phytoplasma is an uncultivable, intracellular pathogen of plants and insects with an AT-rich genome of 670 kb. As part of the genome sequencing project of WX phytoplasma, we have cloned approximately 50% of its genome into the pcosRW2 cosmid vector using DNA purified from pulsed-field gels. One of the cosmid clones with an insert of 24.6 kb was sequenced, which along with the cosmid end sequences, represents 60 kb of unique sequence from the WX phytoplasma genome. The putative genes identified in this sequence represent a wide variety of functions and many had not been previously identified in a phytoplasma.

Chromosome Mapping↗
PubMed1992

Fluorescence in situ hybridization mapping of human chromosome 19: mapping and verification of cosmid contigs formed by random restriction enzyme fingerprinting.

Automated restriction enzyme fingerprinting of 7900 cosmids from chromosome 19 and calculation of the likelihood of their overlap based on shared fragments have resulted in the assembly of 743 sets of overlapping cosmids (contigs). We have mapped 22% of the formed contigs (n = 165) and all of the contigs with minimal tiling paths exceeding 6 members (n = 50) to chromosomal bands by fluorescence in situ hybridization using DNA from at least one member cosmid. The estimated average size of the formed contigs is 60-70 kb. Thus, members of a correctly formed contig are expected to lie close to each other in metaphase and interphase chromatin. Therefore, we tested the contig assembly process by comparing the band assignment of two or more members selected from each of 97 contigs. Forty-two of these contigs were further characterized for valid assembly by determining the proximity of members in interphase chromatin. Using these tests, we surveyed a total of 431 joins counted along the minimal tiling path (280 in interphase as well as metaphase) and found 6 erroneous joins, one in each of 6 contigs (6% of tested).

Chromosomes, Human, Pair 19↗
PubMed2002

Rescue of a pathogenic Marek's disease virus with overlapping cosmid DNAs: use of a pp38 mutant to validate the technology for the study of gene function.

Marek's disease virus (MDV) genetics has lagged behind that of other herpesviruses because of the lack of tools for the introduction of site-specific mutations into the genome of highly cell-associated oncogenic strains. Overlapping cosmid clones have been successfully used for the introduction of mutations in other highly cell-associated herpesviruses. Here we describe the development of overlapping cosmid DNA clones from a very virulent oncogenic strain of MDV. Transfection of these cosmid clones into MDV-susceptible cells resulted in the generation of a recombinant MDV (rMd5) with biological properties similar to the parental strain. To demonstrate the applicability of this technology for elucidation of gene function of MDV, we have generated a mutant virus lacking an MDV unique phosphoprotein, pp38, which has previously been associated with the maintenance of transformation in MDV-induced tumor cell lines. Inoculation of Marek's disease-susceptible birds with the pp38 deletion mutant virus (rMd5 Delta pp38) revealed that pp38 is involved in early cytolytic infection in lymphocytes but not in the induction of tumors. This powerful technology will speed the characterization of MDV gene function, leading to a better understanding of the molecular mechanisms of MDV pathogenesis. In addition, because Marek's disease is a major oncogenic system, the knowledge obtained from these studies may shed light on the oncogenic mechanisms of other herpesviruses.

Animals↗
PubMed1997

Use of the cosmid adenoviral vector cloning system for the in vitro construction of recombinant adenoviral vectors.

The large size of the adenoviral genome unfortunately precludes there being many unique, useful restriction sites available for in vitro manipulation. Two methods have been developed for the construction of recombinant adenoviral vectors to date: in vivo homologous recombination or direct ligation in vitro. The efficiency of either the direct ligation method or the homologous recombination method is low because of the large size of the recombinant adenoviral vectors. To circumvent these problems, we have chosen to use the cosmid vector system to facilitate the assembly of recombinant adenoviral vectors. In this paper, we demonstrate for the first time that recombinant adenoviral vectors can be efficiently constructed in vitro by the cosmid vector system. With this method, it is possible to amplify the recombinant adenoviral vector DNA sufficiently to transfect 293 cells. The cosmid adenoviral vector cloning method for in vitro construction of the full-length recombinant adenoviral vectors represented here is simple and efficient and should facilitate the development of recombinant adenoviral vectors for human gene therapy.

Adenoviridae↗
PubMed1996

An improved cosmid vector for the nested deletion method using the bacteriophage T3 DNA packaging system.

We constructed a new cosmid vector suitable for the previously developed nested deletion method which used the in vitro DNA packaging system of bacteriophage T3. The first step of this method is linearization of a cosmid clone to be packaged, and we previously introduced cleavage at the cos site using lambda-Terminase, but optimization of the reaction conditions was required for complete digestion because of its instability. In the newly constructed vector, pAT5, the sites of 4 different restriction enzymes, Sse8387I, Asc I, Fse I and Pme I, each of which recognizes an 8-bp sequence (8-base cutter) were introduced in the vicinity of the cos site. In addition, the species of restriction sites for cloning were increased to broaden its application. The cosmid clone constructed by this new vector could be linearized at one of the 8-base cutter sites which are assumed to rarely occur in the genome, and followed by in vitro packaging, nested deletion clones were successfully prepared.

Bacteriophage T3↗
PubMed2001

Characterization of the S-locus region of almond (Prunus dulcis): analysis of a somaclonal mutant and a cosmid contig for an S haplotype.

Almond has a self-incompatibility system that is controlled by an S locus consisting of the S-RNase gene and an unidentified "pollen S gene." An almond cultivar "Jeffries," a somaclonal mutant of "Nonpareil" (S(c)S(d)), has a dysfunctional S(c) haplotype both in pistil and pollen. Immunoblot and genomic Southern blot analyses detected no S(c) haplotype-specific signal in Jeffries. Southern blot showed that Jeffries has an extra copy of the S(d) haplotype. These results indicate that at least two mutations had occurred to generate Jeffries: (1) deletion of the S(c) haplotype and (2) duplication of the S(d) haplotype. To analyze the extent of the deletion in Jeffries and gain insight into the physical limit of the S locus region, approximately 200 kbp of a cosmid contig for the S(c) haplotype was constructed. Genomic Southern blot analyses showed that the deletion in Jeffries extends beyond the region covered by the contig. Most cosmid end probes, except those near the S(c)-RNase gene, cross-hybridized with DNA fragments from different S haplotypes. This suggests that regions away from the S(c)-RNase gene can recombine between different S haplotypes, implying that the cosmid contig extends to the borders of the S locus.

Base Sequence↗
PubMedDate not supplied

A cosmid specific for sequences encoding a microtubule-associated protein, MAP1B, contains a polymorphic microsatellite and maps to bovine chromosome 20q14.

A clone for the bovine gene MAP1B was isolated from a bovine cosmid library with a probe obtained by cross-species PCR. The single positive cosmid clone was localized by FISH to chromosome region 20q14. Analysis of the cosmid revealed the presence of a microsatellite motif with a two-allele polymorphism detectable by PCR amplification of genomic DNA. However, the analysis of this polymorphism in a bovine family affected by SMA indicated absence of very close linkage of the phenotype for bovine SMA with MAP1B.

Animals↗
PubMedDate not supplied

Use of cosmid-derived and chromosome-specific canine microsatellites.

The majority of microsatellite markers being used to generate the emerging genetic linkage maps of the dog are derived from small-insert, random clones. While such markers are easy to generate, they have the disadvantage that they cannot easily be physically mapped by fluorescence in situ hybridization (FISH), making it difficult to assess the extent of genome coverage represented by such maps. In contrast, microsatellite markers from large-insert libraries enable the linkage groups within which they fall to be physically anchored to specific chromosomes. One aim of our work is to identify at least one microsatellite-containing cosmid clone for each canine chromosome, to ensure that linkage groups exist for all chromosomes. This is particularly important for a species with as complex a karyotype as the dog. Locating two cosmids on each chromosome would allow the orientation of the linkage groups to be established. Chromosomal locations of cosmid clones containing microsatellites have been determined by FISH and confirmed using canine chromosome-specific paints. Microsatellite sequences have been genotyped on the DogMap reference family. Microsatellites derived from flow-sorted, chromosome-specific libraries represent another source of useful markers. Initial studies have been carried out on the canine X chromosome, on which markers were underrepresented in our initial studies.

Animals↗
PubMed1987

Cosmid mapping of the human chorionic gonadotropin beta subunit genes by field-inversion gel electrophoresis.

A cosmid clone containing the entire hCG beta gene cluster has been isolated. The restriction map of this clone has been determined by an indirect-end-label FIGE (field inversion gel electrophoresis) method. Analysis of this cosmid clone shows that there are 6 hCG beta genes in human genomic DNA. A previously uncloned portion of the hCG beta cluster, termed the "gap" region, has been shown not to contain any sequences homologous to the hCG beta cDNA. The restriction mapping method employed in this study takes advantage of the superior resolution of FIGE for high molecular weight DNA fragments in the size range 15-50 kb. This method is broadly applicable and permits rapid and accurate restriction mapping for extended regions of genomic DNA that have been cloned into cosmid or lambda vectors.

Chorionic Gonadotropin↗
PubMed1988

Randomly picked cosmid clones overlap the pyrB and oriC gap in the physical map of the E. coli chromosome.

Sets of overlapping cosmid clones generated by random sampling and fingerprinting methods complement data at pyrB (96.5') and oriC (84') in the published physical map of E. coli. A new cloning strategy using sheared DNA, and a low copy, inducible cosmid vector were used in order to reduce bias in libraries, in conjunction with micro-methods for preparing cosmid DNA from a large number of clones. Our results are relevant to the design of the best approach to the physical mapping of large genomes.

Chromosome Mapping↗
PubMed1991

A test case for physical mapping of human genome by repetitive sequence fingerprints: construction of a physical map of a 420 kb YAC subcloned into cosmids.

A rapid and safe method of Yeast Artificial Chromosome (YAC) physical mapping by cosmid 'fingerprinting' is presented. YACs are subcloned into cosmids which are prepared without previous separation of cloned DNA from host DNA. Groups of overlapping clones are detected according to their restriction fragments size and intensity after hybridization with total human DNA. To test this approach, a cosmid library was constructed from total DNA of a yeast strain containing a 420 kb YAC. A single contig of 84 clones was obtained with a minimal detectable overlap of 60% i.e. a 9.2 fold representative library. Large scale physical mapping of YACs would take full advantage of the DNA preparation procedure employed in this work and allows to take into account restriction fragment intensities.

Blotting, Southern↗
PubMed1996

Mapping the human Y chromosome by fingerprinting cosmid clones.

We have used Y-specific cosmid clones in a random fingerprinting approach to build contigs on the human Y chromosome. Clones derived from two libraries have been analyzed. The construction of one library is described here, the second was the Y chromosome-specific library LLOYNCO3 "M" (Lawrence Livermore National Laboratory). To date, we have fingerprinted 4430 cosmids: 377 contigs have been constructed containing from 2 to 39 clones. Along with the singletons, we estimate that we have covered 72.5% of the euchomatic portion of the Y chromosome with fingerprinted clones. Sequence tagged sites are being used to anchor cosmids and contigs onto the YAC framework.

Base Sequence↗