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At least 1,135 records · Page 63Linked to original sources
PubMed1989

Identification and mapping of the sulphate permease promoter region in Escherichia coli.

The cys329::lac fusion linking the lacZ gene to the regulatory region of cys locus involved in sulphate transport in E. coli, was cloned and localized within the restriction map of cysA region. The region containing the cysB-dependent promoter governing the expression of sulphate transport system was identified and the direction of transcription from this promoter has been established. Two complementation groups specified by different mutations in cysA region of E. coli were found.

Escherichia coli↗
PubMed1993

Physical mapping of Xq24-25 around loci closely linked to the X-linked lymphoproliferative syndrome locus: an overlapping YAC map and linkage between DXS12, DXS42, and DXS37.

We have localized several markers in the Xq24-25 region containing DXS12, DXS42 and DXS37 which are closely linked to the X-linked lymphoproliferative syndrome (XLP) locus. A 850-kb restriction map has been established by mapping overlapping YACs and showed that DXS12 and DXS42 are physically linked within about 50 kb. DXS37 is separated from these two loci at a maximum distance of 3,700 kb. Several new probes have been generated which will contribute to further physical mapping of this region.

Chromosome Walking↗
PubMed2004

In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction.

UNLABELLED: We have developed a website, www.in-silico.com, which runs a software program that performs three basic tasks in completely sequenced bacterial genomes by in silico analysis: PCR amplification, amplified fragment length polymorphism (AFLP-PCR) and endonuclease restriction. For PCR, after selection of the genome and introduction of primers, fragment size, DNA sequence and corresponding open reading frame (ORF) identity of the resulting PCR product is computed. Plasmids of sequenced species may be included in the analysis. Theoretical AFLP-PCR analyzes similar parameters, and includes a suggestion tool providing a list of commercial restriction enzyme pairs yielding up to 50 amplicons in the selected genome. Endonuclease restriction analysis of complete genomes and plasmids calculates the number of restriction sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, pulsed field gel electrophoresis image and restriction maps are illustrated. Other tools that have been included in this site are ORF search by name and DNA to protein translation as well as restriction digestion of user-defined DNA sequences. AVAILABILITY: This is a new molecular biology resource freely available over the Internet at http://www.in-silico.com

Algorithms↗
PubMed1996

Evolution of the frequency (frq) clock locus in Ascomycete fungi.

The frequency (frq) locus of Neurospora crassa plays a key role in the organization of circadian rhythms. Similar timing systems have been found in nearly all eukaryotes as well as some prokaryotes; thus, frq may be an excellent gene with which to conduct evolutionary studies. To investigate, we used the cloned frq locus from ascomycete fungi representing two classical taxonomic classes and three orders to examine two open questions in ascomycete evolution. Class Pyrenomycetidae is represented by several species of Neurospora, Sordaria fimicola, and Chromocrea spinulosa; class Loculoascomycetidae is represented by the marine fungus Leptosphaeria australiensis. Generation of detailed restriction maps of homologs from the Neurospora species allows analysis of evolutionary relationships among these closely related species. A maximum-parsimony tree based on these restriction data suggests that Neurospora tetrasperma groups more closely with Neurospora sitophila than with Neurospora crassa using the homothallic species Neurospora galapagosensis as an outgroup. A maximum-parsimony tree derived using amino acid sequences from Neurospora crassa, Sordaria fimicola, Chromocrea spinulosa, and Leptosphaeria australiensis surprisingly suggests that Leptosphaeria austral should be classified within Pyrenomycetes rather than in a separate class. This suggestion is based on the observations that Leptosphaeria groups with Chromocrea on an evolutionary tree, is more closely related to Neurospora and Sordaria than is Chromocrea, and shares a conserved intron with Chromocrea. Together, these data show that frq is a useful gene with which to conduct evolutionary studies.

Amino Acid Sequence↗
PubMed1997

Isolation and characterization of two plasmids from Bifidobacterium longum.

In order to develop a cloning vector system which can be used in Bifidobacterium sp., we screened about 100 bifidobacteria from the faeces of adults and children. Among them, only one strain, identified as B. longum KJ, was shown to contain extrachromosomal DNAs. Bifidobacterium longum KJ showed multiple plasmid DNA bands which were resolved to be multimers of two plasmids designated pKJ36 and pKJ50. These plasmids were cloned into the Escherichia coli vector pUC19 as pMS36 and pMS50, respectively, and restriction-mapped.

Adult↗
PubMed1990

Physical and genetic analysis of the phosphoenolpyruvate carboxykinase (pckA) locus from Escherichia coli K12.

An 8 kb BamHI fragment of the Escherichia coli K12 chromosome has been cloned which complemented the pheotype of CRM+ pckA mutants with inactive phosphoenolpyruvate (PEP) carboxykinase. The pckA+ clones expressed levels of enzyme activity elevated up to 30-fold and produced a Mr 55,000 product in maxicells, which co-electrophoresed with purified PEP carboxykinase. The cloned fragment expressed the pckA, ompR and envZ gene products in maxicells. The order of genes on the chromosome inferred from restriction mapping, was (74 min)...pckA envZ ompR...(75 min). Transcription of the pckA gene cloned on multicopy plasmids increased in stationary phase and was also regulated by catabolite repression. The transcriptional control region has been located by genetic fusions to the chloramphenicol acetyltransferase (cat) gene and pckA was transcribed in the direction of envZ (clockwise direction on the chromosome).

Carboxy-Lyases↗
PubMed1989

Analysis of the Om(1D) locus in Drosophila ananassae.

From the ca;px stock, which is the progenitor of Om mutants caused by insertions of the tom retrotransposon, 50 kb of genomic DNA including the Om(1D) locus was cloned by tom tagging and chromosome walking. Southern blot analyses of six Om(1D) mutants exposed one or two tom elements inserted at five nonrandom sites within an 18-kb distal segment of the restriction map; the phenotypic uniformity between these mutants was not affected by variations in the position, number or orientation of their inserts. Spontaneous revertants or more extreme derivatives of Om(1D) alleles were nonlinearly associated with losses or gains of tom inserts. Seven of eight radiation induced derivatives of Om(1D) mutants had one breakpoint of a chromosome rearrangement in polytene section 13A which includes the Om(1D) locus. Two Om(1D) derivatives, a spontaneous revertant and an induced extreme allele, were associated with overlapping deficiencies which define a region that is likely to contain the Om(1D) coding seguences proximal to the tom insertion sites. Incidental results confirm the previously indicated homology of the Om(1D) locus with the Bar locus of Drosophila melanogaster.

Animals↗
PubMedDate not supplied

[Restriction fragment length polymorphism of the 5'-region of the bovine ribosomal spacer repeat].

The restriction map of bovine 28S rRNA gene and adjacent 5'-spacer region was determined. The high level of intragenomic and population length polymorphism of EcoRI-BamHI restriction fragment was demonstrated to originated from the 3'-end of 28S rDNA and 5'-spacer of rDNA repeat. This polymorphism is more pronounced than the ones revealed in human and murine rDNA repeats and could be compared with genomic fingerprints obtained by M13 or minisatellite DNA hybridization probes. From family blot-panel analysis we concluded that in progeny only parental sets of length variants were inherited and that the copy number of definite variants does not change in the progeny as well. From these results it was proposed that the definite sets of linked in genome length variants are inherited independently from each other.

Alleles↗
PubMed1987

Large scale physical mapping in the q27 region of the human X chromosome: the coagulation factor IX gene and the mcf.2 transforming sequence are separated by at most 270 kilobase pairs and are surrounded by several 'HTF islands'.

In spite of the large amount of genetic data obtained on the X chromosome and of the availability of many cloned sequences little is known about the physical map of this chromosome. The construction of large-scale restriction maps is now possible with pulsed field gel methods and data has recently been obtained in the region of band Xq28. We present here results of physical mapping in the Xq27 region, i.e. proximal to the fragile site at Xq27.3 associated with mental retardation, and show physical linkage between the coagulation factor IX gene and the mcf.2 transforming sequence recently localized to Xq27. Our data also indicate partial methylation of some sites in this region, and locate several 'HTF islands', i.e. CpG-rich, unmethylated sequences, containing several sites for 'rare cutter' enzymes, which are believed to be associated with expressed 'housekeeping' genes.

Base Composition↗
PubMed1999

Human epidermal differentiation complex in a single 2.5 Mbp long continuum of overlapping DNA cloned in bacteria integrating physical and transcript maps.

Terminal differentiation of keratinocytes involves the sequential expression of several major proteins which can be identified in distinct cellular layers within the mammalian epidermis and are characteristic for the maturation state of the keratinocyte. Many of the corresponding genes are clustered in one specific human chromosomal region 1q21. It is rare in the genome to find in such close proximity the genes belonging to at least three structurally different families, yet sharing spatial and temporal expression specificity, as well as interdependent functional features. This DNA segment, termed the epidermal differentiation complex, contains 27 genes, 14 of which are specifically expressed during calcium-dependent terminal differentiation of keratinocytes (the majority being structural protein precursors of the cornified envelope) and the other 13 belong to the S100 family of calcium binding proteins with possible signal transduction roles in the differentiation of epidermis and other tissues. In order to provide a bacterial clone resource that will enable further studies of genomic structure, transcriptional regulation, function and evolution of the epidermal differentiation complex, as well as the identification of novel genes, we have constructed a single 2.45 Mbp long continuum of genomic DNA cloned as 45 p1 artificial chromosomes, three bacterial artificial chromosomes, and 34 cosmid clones. The map encompasses all of the 27 genes so far assigned to the epidermal differentiation complex, and integrates the physical localization of these genes at a high resolution on a complete NotI and SalI, and a partial EcoRI restriction map. This map will be the starting resource for the large-scale genomic sequencing of this region by The Sanger Center, Hinxton, U.K.

Bacteria↗
PubMed1991

Molecular cloning of a gene region from Bradyrhizobium japonicum essential for lipopolysaccharide synthesis.

The gene region cloned from a lipopolysaccharide (LPS) mutant carrying the Tn5 and flanking DNA sequences was used as a probe to screen a gene bank prepared from wild-type Bradyrhizobium japonicum strain 61A101C and to isolate the corresponding wild-type LPS-gene region. By cross-hybridization experiments the LPS-gene region did not appear to be closely linked to previously cloned nodulation genes. A detailed restriction map of the LPS-gene region (5.5-kb EcoRI genomic fragment) was established and the mutation site was localized to be in a 300-bp PvuI/PstI restriction fragment. In genomic Southern-blot analysis of various rhizobia, the LPS-gene region was found to be conserved among all the slow-growing bradyrhizobia, but not the fast-growing rhizobia. The different groups of slow-growing bradyrhizobia are polymorphic for restriction-fragment length at the LPS-gene region.

Blotting, Southern↗
PubMed1991

Cloning of a human alpha(1,3)-fucosyltransferase gene that encodes ELFT but does not confer ELAM-1 recognition on Chinese hamster ovary cell transfectants.

In previous studies, Chinese hamster ovary (CHO) cell genomic DNA transfectants that expressed a human alpha(1,3)-fucosyltransferase (alpha(1,3)Fuc-T) gene were isolated and shown to possess a common approximately 7.5-kilobase (kb) EcoRI fragment that hybridized to an Alu probe (Potvin, B., Kumar, R., Howard, D. R., and Stanley, P. (1990) J. Biol. Chem. 265, 1615-1622). One of these transfectants was used to make a genomic DNA library in lambda ZAP-II from EcoRI-digested, size-selected (6-8 kb) DNA, and plaques that hybridized to an Alu probe were purified. After in vivo excision, two plasmids with DNA inserts greater than or equal to 6 kb were obtained and one of these (D2.1) conferred human alpha(1,3)-Fuc-T activity on CHO transfectants. A partial restriction map of this clone revealed an approximately 3.6-kb PstI fragment that contained an Alu sequence. This fragment was subcloned into pGEM-3Zf(+) and compared by restriction analyses with a previously described approximately 3.6-kb PstI DNA fragment isolated from a human peripheral blood lymphocyte library and shown to encode an alpha(1,3)-Fuc-T gene (Lowe, J. B., Stoolman, L. M., Nair, R. P., Larsen, R. D., Berhend, T. L., and Marks, R. M. (1990) Cell 63, 475-484). Both approximately 3.6-kb fragments gave identical restriction patterns. In addition, they both caused CHO transfectants to synthesize the Lex determinant Gal beta(1,4)[Fuc alpha(1,3)]GlcNAc beta 1 but not the alpha(2,3)-sialyl-Lex determinant. As expected, these transfectants did not bind to ELAM-1 on activated endothelial cells, since sialyl-Lex is a carbohydrate ligand recognized by ELAM-1. Surprisingly, however, an open reading frame encoded within the approximately 3.6-kb PstI fragment had a sequence identical to that of ELFT, an alpha(1,3)-Fuc-T previously reported to confer ELAM-1 binding on a previously reported to confer ELAM-1 binding on a CHO transfectant (Goelz, S. E., Hession, C., Goff, D., Griffiths, B., Tizard, R., Newman, B., Chi-Rosso, G., and Lobb, R., (1990) Cell 63, 1349-1356). Possible explanations for these apparently disparate results are discussed.

Amino Acid Sequence↗
PubMed1989

[Organization of Bsp-repeats in the fox genome].

Bsp repeats comprise approximately 1% of silver for total DNA and are preferentially localized in centromeric regions. Two of Bsp fragments cloned earlier, such as non-homologous rsV1 and rsV3, make up together a Bsp unit (680 bp) and possess a set of sites known to have regulatory functions in eucaryotic genomes. In this work, tandem organization of Bsp repeats is demonstrated. A stretched Bsp sequence (approximately 1460 bp, dimeric form) flanked by BamHI sites was cloned and its restriction map was plotted. With use of rsV1 and rsV3 probes the new sequence exhibited linked structure: rsV1-rsV3-rsV1-rsV3-rsV1. Blot-hybridization with the restriction fragments of fox total DNA suggested hierarchical order of Bsp clustes in the genome. It is supposed that the processes of selective amplification of individual fragments had been of real importance during evolution of Bsp repeats.

Animals↗
PubMed1992

Long-range mapping of the gene for the human alpha 5(IV) collagen chain at Xq22-q23.

The X-linked kidney disorder known as Alport syndrome (AS) has been shown to be due to mutations in the gene for an alpha 5 chain of type IV collagen that maps to Xq22-23. Using overlapping cDNA clones that represent approximately 90% of this gene and pulsed-field gel electrophoresis, we have constructed a 2.4-Mb long-range restriction map around the locus. All of the cDNA clones lie within a 360-kb segment of DNA bounded by CpG islands that contain sites for the rare-cutting enzymes BssHII, MluI, NotI, NruI, SalI, and SfiI. High-resolution PFGE mapping with XhoI shows that the gene is at least 110 kb in size and is one of the largest collagen genes characterized to date. This map will prove useful in the characterization of mutations in individuals affected with AS and will also provide information as to the location of other genes in the region.

Cell Line↗
PubMed1989

The linear 20 kb mitochondrial genome of Pandorina morum (Volvocaceae, Chlorophyta).

A physical restriction map of the mitochondrial genome from one clone (TCC 854) of the sexually isolated populations (syngens) of the morphologically uniform species Pandorina morum Bory has been constructed using restriction endonucleases Ava I, Bam HI, Bgl II, Eco RI, Kpn I, and Pst I. The 20 kb linear genome can easily be separated from plastid DNA, nuclear satellite rDNA, and main band (nuclear) DNA on a Hoechst/CsCl buoyant density gradient. The Pandorina mitochondrial DNA shows sufficient similarity to the 16 kb mitochondrial genome of Chlamydomonas reinhardtii to cross-hybridize, and also hybridizes with a probe containing maize mitochondrial 18S rRNA genes. Double digests, self-probing, and Bal31 exonuclease experiments suggest that 1.8 to 3.3 kb of sequence is repeated at each end of the genome as an inverted repeat. Mitochondrial genome sizes of other P. morum syngens were found to range from ca. 20 to ca. 38 kb. The mitochondrial genome should be valuable for taxonomic studies; it can be used for comparative organellar studies; and it should be of interest to compare with that of other plant and animal mitochondrial genomes.

Biological Evolution↗
PubMed1991

Heterozygosity in tetraploid potatoes revealed by rDNA polymorphism analysis of their dihaploid progenies: a contribution to chromosome assignment.

Restriction map and organization of rDNA was inferred from analysis of dihaploid progenies of two tetraploid genotypes of cultivated potato. Each tetraploid genotype was characterized by a specific distribution of different types of rDNA repetition units on their four homologous chromosomes II. The genotypes were heterozygous and differed by the kind of units carried by each chromosome II. Models for the generation of the observed organization are discussed and supported by first cloning studies.

Blotting, Southern↗
PubMed1991

Stable length polymorphism of up to 260 kb at the tip of the short arm of human chromosome 16.

We have completed a long-range restriction map of the terminal region of the short arm of human chromosome 16 (16p13.3) by physically linking a distal genetic locus (alpha-globin) with two recently isolated probes to telomere-associated repeats (TelBam3.4 and TelBam-11). Comparison of 47 chromosomes has revealed major polymorphic length variation in this region: we have identified three alleles in which the alpha-globin genes lie 170 kb, 350 kb, or 430 kb from the telemere. The two most common alleles contain different terminal segments, starting 145 kb distal to the alpha-globin genes. Beyond this boundary these alleles are nonhomologous, yet each contains sequences related to other (different) chromosome termini. This chromosome size polymorphism has probably arisen by occasional exchanges between the subtelomeric regions of nonhomologous chromosomes; analogous length variation is likely to be present at other human telomeres.

Base Sequence↗
PubMed1991

Cloning and partial characterization of genes for ribosomal ribonucleic acid in Lactococcus lactis subsp. lactis.

A cosmid gene library of the genome of Lactococcus lactis subsp. lactis 712 was probed for the presence of 16S rRNA genes, using 32P 5' end-labelled 16S rRNA fragments. Cosmid DNA from positive clones responsible for hybridisation was subcloned into a high copy number vector and a restriction map was constructed. The location of the 16S, 23S and 5S rRNA genes was determined on this map. Transcriptional promoter activity was identified upstream of the 5' end of the 16S rRNA gene. By probing L. lactis 712 chromosomal DNA cut with a range of restriction endonucleases, with a conserved oligonucleotide to the 5' end of the 16S rRNA gene, 6 copies of rRNA genes were identified.

Base Sequence↗