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At least 649 records · Page 36Linked to original sources
PubMed1994

A novel multi-gene family of sheep gamma delta T cells.

The WC1 protein is a cell surface constituent of bovine gamma delta T cells and is absent from most or all CD4+, CD8+ T cells and from B cells. It is a single polypeptide chain of 1413 amino acids consisting of 11 non-identical repeats of a 110 amino acid consensus sequence, homologous to the macrophage scavenger receptor cysteine rich (SRCR) domain. A 1059 nucleotide segment of the bovine WC1 cDNA sequence was used as a probe to molecularly clone homologous DNA segments from a sheep genomic library in which the presence of numerous positive plaques was documented. The high representation of such recombinants (1-2/1000 clones) within the library suggested the existence of multiple genes for WC1 (called T19 in sheep) and supported Southern blotting data which revealed an unexpectedly high number of WC1/T19 restriction fragments in sheep genomic DNA. Restriction digests of 27 samples of T19 genomic recombinants were examined by electrophoresis and Southern blotting. All but two pairs of recombinants exhibited non-overlapping restriction digest patterns. Four recombinant DNA samples were partially sequenced and in all cases putative exons were identified and exhibited high homology to appropriate segments of the WC1 cDNA at the levels of both nucleotide and amino acid sequence. Furthermore, multiple nucleotide and amino acid differences occurred between all sequences compared, establishing the existence of a repertoire of non-identical T19 genes, each with the potential to encode a different protein.

Animals↗
PubMed1991

Optimized strategies for sequence-tagged-site selection in genome mapping.

The physical mapping of complex genomes is based on the construction of a genomic library and the determination of the overlaps between the inserts of the mapping clones in order to generate an ordered, cloned representation of nearly all the sequences present in the target genome. Evaluation of the relative efficiency of experimental procedures used to accomplish this goal must minimally include a comparison of the fraction of the genome covered by the ordered arrays (or "contigs"), the average size of the contigs, and the cost, in terms of time and resources, required to generate the map. Sequence-tagged-site (STS) content mapping is one strategy that has been proposed and is being utilized for this type of experiment. This paper describes three STS selection schemes and presents computer simulations of contig-building experiments based on these procedures. The results of these simulations suggest that a nonrandom STS strategy that uses paired probes requires one-third to one-fourth as many STS assays as are required in random and nonpaired approaches, and also results in a map that has both greater genome coverage and a larger average contig size. This strategy promises to reduce the time and cost required to build a high-quality physical map.

Base Sequence↗
PubMed1992

Assignment of the lens intrinsic membrane protein MP19 structural gene to human chromosome 19.

We have isolated and characterized a bovine cDNA clone encoding the bovine lens intrinsic membrane protein, MP19. This cDNA was used as a probe to analyze a panel of Southern blots of human-Chinese hamster somatic cell hybrid DNAs to assign the gene coding for MP19 to its human chromosome. Control human and Chinese hamster DNAs displayed a distinct EcoR1 restriction fragment pattern when hybridized with the bovine MP19 cDNA. When somatic cell hybrid DNAs were restricted with Eco R1 and Southern blots hybridized with the bovine MP19 cDNA, the characteristic human restriction pattern was observed only when human chromosome 19 was present in the hybrid panel. This assignment was confirmed using a human chromosome 19-specific genomic library. A clone from this human chromosome 19-specific library was identified and further characterized. This clone contained a 7.9 kilobase fragment that contained identical DNA sequences with that of the authentic bovine MP19 cDNA, and with a separate human genomic clone containing the MP19 gene.

Amino Acid Sequence↗
PubMed1990

Structure and expression of the human angiotensinogen gene. Identification of a unique and highly active promoter.

We have isolated the human angiotensinogen gene from a genomic library and determined the exon-intron junction sequences. The gene is 12 kilobases long and consists of five exons interrupted by four introns, as a single copy in the human genome. Of particular interest are the positions of the introns in the human angiotensinogen gene which are identical to those in the highly homologous human alpha 1-antitrypsin and alpha 1-antichymotrypsin genes, as well as rat and mouse angiotensinogen genes. Northern blot analysis showed that human hepatoma cells (HepG2) produce a large amount of angiotensinogen mRNA but not human glioma cells (T98G). To assay the promoter activity, the 1.3-kilobase genomic fragment containing the 5'-flanking region, first exon, and a part of first intron at positions -1222 to +44 was fused upstream to the chloramphenicol acetyltransferase gene, then transfected into HepG2 and T98G cells. The gene sequence was active only in HepG2 cells, suggesting the presence of a functional promoter. Analysis of deletion mutants demonstrated that the 76-base pairs region from -32 to +44 containing the TATA box and first exon is the minimal promoter, whose activity is as high as that of the SV40 enhancer-promoter. Since the basal expression of the human angiotensinogen gene is much higher in HepG2 than T98G cells, these results may reflect cell-specific differences in the gene transcription.

Amino Acid Sequence↗
PubMed1991

Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation.

Physical mapping of chromosomes would be facilitated by methods of breaking large DNA into manageable fragments, or cutting uniquely at genetic markers of interest. Key issues in the design of sequence-specific DNA cleaving reagents are the specificity of binding, the generalizability of the recognition motif, and the cleavage yield. Oligonucleotide-directed triple helix formation is a generalizable motif for specific binding to sequences longer than 12 base pairs within DNA of high complexity. Studies with plasmid DNA show that triple helix formation can limit the operational specificity of restriction enzymes to endonuclease recognition sequences that overlap oligonucleotide-binding sites. Triple helix formation, followed by methylase protection, triple helix-disruption, and restriction endonuclease digestion produces near quantitative cleavage at the single overlapping triple helix-endonuclease site. As a demonstration that this technique may be applicable to the orchestrated cleavage of large genomic DNA, we report the near quantitative single-site enzymatic cleavage of the Saccharomyces cerevisiae genome mediated by triple helix formation. The 340-kilobase yeast chromosome III was cut uniquely at an overlapping homopurine-EcoRI target site 27 base pairs long to produce two expected cleavage products of 110 and 230 kilobases. No cleavage of any other chromosome was detected. The potential generalizability of this technique, which is capable of near quantitative cleavage at a single site in at least 14 megabase pairs of DNA, could enable selected regions of chromosomal DNA to be isolated without extensive screening of genomic libraries.

Base Sequence↗
PubMed1990

How to select Plasmodium falciparum pre-erythrocytic antigens in an expression library without defined probe.

The restricted access to Plasmodium falciparum liver stages has greatly limited the analysis of the antigenic content of that stage. Due to the lack of material to perform immunochemical studies, of access to mRNA, and of monoclonal probes, we decided to screen a genomic library with stage-restricted human antibodies. This strategy led to the identification of a large number of DNA fragments encoding both sporozoite specific as well as liver-stage specific epitopes. Following the initial characterization of one liver-stage antigen, further screening was performed by using additional selective human antibodies. These were defined as having a high degree of reactivity with native antigens on either of the two stages while being negative with the already known molecules of the two stages. From this second screening and the study of cross-reactions, several subsets of DNA clones expressing antigens present on the surface of sporozoites, or in liver stages, or in both, could be identified. In exposed individuals a high prevalence of antibodies to several of these antigens was found.

Animals↗
PubMed2003

Temporal transcription of two antennapedia class homeobox genes in the marine copepod Calanus helgolandicus.

DNA sequence information has been obtained for 2 genes implicated in playing critical roles in copepod development. The first ( Cal-antp) was obtained by screening a Calanus helgolandicus genomic library. It shows homology to Antennapedia homeobox genes from a number of organisms including the centipede (76.8% over 250 bp) and the brine shrimp (75.5% over 220 bp). A second sequence (Hox 12) was obtained through reverse transcription polymerase chain reaction (PCR) of a solid-phase cDNA library constructed from Calanus eggs, and subsequent inverse PCR using a genomic DNA template. The Hox 12 sequence is homologous to the Antennapedia class of genes and shares homology with the chicken HoxB3 gene (71% over 187 bp) and with the fruit fly Sex Combs Reduced ( Scr) homeotic gene (66% identity over 223 bp). Using sequence data from Cal-Antp and Hox 12, specific primers were designed to investigate the temporal expression of these genes by PCR analysis of 10 stage-specific cDNA libraries.

Amino Acid Sequence↗
PubMed1990

Organization and structure of the 5' flanking region of the rat serine dehydratase gene.

For study of the mechanisms regulating the induction of serine dehydratase by various hormones in rat liver [Noda et al. (1988) J. Biol. Chem. 263, 14764-14768], we cloned the gene for this enzyme from a rat genomic library. The gene spans about 7.5 kilobases and consists of nine exons and eight introns. The exon-intron boundaries are consistent with the "GT-AG" rule. Southern blot analysis of rat genomic DNA suggested the presence of one copy of serine dehydratase gene per haploid genome. The 5' end of serine dehydratase mRNA is located 148 nucleotides upstream of the initiator methionine codon. ATG, determined by primer extension analysis and S1 nuclease mapping, although an alternative transcription initiation site(s) may be located a few bases downstream. The 5' flanking region of the gene lacks typical TATA and CCAAT sequences, but contains AATAAA and CATT sequences, at -25 to -20 and -54 to -51, respectively. Furthermore, there are five GC box-related sequences. There are three putative glucocorticoid-responsive elements and two copies of the CGTCA motif of the cAMP-responsive element upstream of the promoters. The 5' flanking sequence shows more than 98% homology with that reported by Ogawa et al. [(1988) Proc. Natl. Acad. Sci. U.S.A. 85, 5809-5813], but the first exons have different sequences. Another difference is that a segment of 108 nucleotides is located just upstream of exon 5 in the sequence reported here, but is included as an exon in the sequence of Ogawa et al. The possibility to producing two species of serine dehydratase mRNAs from a single gene by transcription from different sites and alternative splicing is discussed.

Animals↗
PubMed1994

Charomid cloning vectors meet the pedipalpal chelae: single-locus minisatellite DNA probes for paternity assignment in the harlequin beetle-riding pseudoscorpion.

We describe the first application of the charomid-cloning method for developing single-locus minisatellite DNA probes in a terrestrial arthropod. From a genomic library of the neotropical pseudoscorpion, Cordylochernes scorpioides, we have isolated two probes with heterozygosities exceeding 95%. These probes yielded single-locus patterns after only low stringency washing and in the absence of genomic competitor DNA. Analysis of three pedigrees indicated germline stability and showed no evidence of linkage between the loci. Patterns of allelic transmission generally conformed closely to Mendelian expectations but large offspring numbers did enable detection of one example of significant bias in allele inheritance. Two test cases are presented to illustrate the clarity and power with which these probes can establish paternity: (i) a female mated to three unrelated males, and (ii) a female mated to two of her brothers. In both cases, a single probe could be used to assign the paternity of all offspring.

Animals↗
PubMed1994

The use of microsatellite analysis in population biology: background, methods and potential applications.

A promising technique currently emerging for population studies is the analysis of microsatellite DNAs. Microsatellite alleles offer several advantages over other types of molecular markers. They are abundant, highly variable, and can be assayed from minute quantities of DNA using PCR. Their major disadvantage is that it is usually necessary to screen genomic libraries to identify and characterize microsatellite loci for each species under investigation. The first goal of this chapter is to summarize background information having implications for population studies. This information comes primarily from human genome literature and is therefore not easily accessible to many population biologists. Secondly, because microsatellite analysis uses molecular approaches that are new to most population biologists, we attempt to provide a rationale and overview of methodology. Finally, we review population studies to date that have used microsatellite analysis and offer our perspective on the potential for future studies.

Animals↗
PubMed1991

Isolation of the spinach nitrite reductase gene promoter which confers nitrate inducibility on GUS gene expression in transgenic tobacco.

Nitrite reductase is the second enzyme in the nitrate assimilatory pathway. The transcription of this gene is regulated by nitrate as well as a variety of other environmental and developmental factors. Genomic clones containing the entire nitrite reductase gene have been isolated from a spinach genomic library and sequenced. The sequence is identical in the transcribed region to a previously isolated spinach NiR cDNA clone (Back et al., 1988) except for the presence of three introns. The analysis of the genomic clones and DNA blot hybridization demonstrates that there is a single NiR gene per haploid genome in spinach. This is in contrast to what has been found for other plant species. The transcription initiation site has been determined by S1 mapping and the 5' upstream region has been used to regulate the GUS reporter gene in transgenic tobacco plants. This gene was found to be regulated by the addition of nitrate in the transgenic plants.

Amino Acid Sequence↗
PubMed1996

Isolation and chromosomal distribution of natural Z-DNA-forming sequences in Halobacterium halobium.

Conditions favoring left-handed Z-DNA such as high salinity (> 4 ), high negative DNA supercoiling, and GC-rich DNA [statistically favoring d(CG)n repeat sequences], are all found in the extremely halophilic archaeum (archaebacterium) Halobacterium halobium. In order to identify and study Z-DNA regions of the H. halobium genome, an affinity chromatography method with high Z-DNA selection efficiency was developed. Supercoiled plasmids were incubated with a Z-DNA-specific antibody (Z22) and passed over a protein A-agarose column, and the bound plasmids were eluted using an ethidium bromide gradient. In control experiments using mixtures of pUC12 (Z-negative) and a d(CG)5-containing (Z-positive) pUC12 derivative, up to 4,000-fold enrichment of the Z-DNA-containing plasmid was demonstrated per cycle of the Z-DNA selection procedure. The selection efficiency was determined by transformation of Escherichia coli DH5alpha with eluted plasmids and blue-white screening on X-gal plates. Twenty recombinant plasmids containing Z-DNA-forming sequences of H. halobium were isolated from a genomic library using affinity chromatography. Z-DNA-forming sequences in selected plasmids were identified by bandshift and antibody footprinting assays using Z22 monoclonal antibody. Alternating purine-pyrimidine sequences ranging from 8 base pairs (bp) to 13 bp with at least a 6-bp alternating d(GC) stretch were found in the Z22 antibody binding regions of isolated plasmids. The distribution of Z-DNA-forming sequences in the Halobacterium salinarum GRB chromosome was analyzed by dot-blot hybridization of an ordered cosmid library using the cloned H. halobium Z-DNA segments as probe. Among the 11 Z-DNA segments tested, five were found to be clustered in a 100-kilobase pair region of the genome, whereas six others were distributed throughout the rest of the genome.

Base Sequence↗
PubMedDate not supplied

Expression of reverse transcriptase genes in Fulvia fulva.

Antibodies raised against intercellular fluid antigens isolated from diseased tomato leaves have revealed that the fungal pathogen Fulvia fulva expresses genes for a fungal reverse transcriptase (RNA-dependent DNA polymerase). This enzyme is required for the replication of retroviruses and retroviral-like transposable elements and could provide a mechanism for increasing the mutation rate of fungal pathogens, perhaps explaining their ability to evolve new races rapidly. We report here the DNA sequence of a 225-bp clone from a lambda gt11 genomic library of F. fulva. This clone, designated P5, exhibits a high degree of sequence homology with the reverse transcriptase (pol) gene of the Drosophila melanogaster copia-like retrotransposon 17.6. Southern blot analysis of genomic DNA of F. fulva showed that P5-related sequences are moderately reiterated with 30-100 copies, some of which exhibit restriction fragment length polymorphism in different races of the pathogen. Western blot analysis of extracts from F. fulva with antibodies raised to purified reverse transcriptase (from human immunodeficiency virus-1) revealed immunoreactive proteins. Reverse transcriptase previously has been detected in a variety of organisms including yeast, insects, protozoa, and mammals, but to our knowledge, this is the first report of its occurrence in filamentous fungi.

Amino Acid Sequence↗
PubMed1997

Heterologous expression of heterotrophic nitrification genes.

Paracoccus denitrificans is a heterotrophic organism capable of oxidizing ammonia to nitrite during growth on an organic carbon and energy source. This pathway, termed heterotrophic nitrification, requires the concerted action of an ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). The genes required for heterotrophic nitrification have been isolated by introducing a Pa. denitrificans genomic library into Pseudomonas putida and screening for the accumulation of nitrite. In contrast to the situation in chemolithoautotrophic ammonia oxidizers, the genes encoding AMO and HAO are present in single linked copies in the genome of Pa. denitrificans. AMO from Pa. denitrificans expressed in Ps. putida is capable of oxidizing ethene (ethylene) to epoxyethane (ethylene oxide), which is indicative of a relaxed substrate specificity. Further, when expressed in the methylotroph Methylobacterium extorquens AM1, the AMO endows on this organism the ability to grow on ethene and methane. Thus, the Pa. denitrificans AMO is capable of oxidizing methane to methanol, as is the case for the AMO from Nitrosomonas europaea. The heterotrophic nitrification genes are moderately toxic in M. extorquens, more toxic in Ps. putida, and non-toxic in Escherichia coli. Toxicity is due to the activity of the gene products in M. extorquens, and both expression and activity in Ps. putida. This is the first time that the genes encoding an active AMO have been expressed in a heterologous host.

Ammonia↗
PubMed1995

Simple plaque hybridization method for the detection of differentially represented repetitive DNA.

A differential DNA hybridization method of detecting moderately repetitive strain-specific or species-specific DNA is described. Two Drosophila melanogaster strains, one with and one without transposable elements, were utilized as a model system to demonstrate the effectiveness of this procedure. A genomic library was constructed from flies of the pi 2 strain, which contains both P and hobo transposable elements. Duplicate plaque lifts of this library were probed with DNA from the same strain and with DNA from the Canton-S strain, which contains neither of these two families of transposable elements. Plaques that hybridized stronger to the genomic DNA that contained elements were noted, and then the filters were stripped and reprobed with P and hobo element DNA. Many of the differentially hybridizing plaques were shown to contain DNA homologous to one of the two known elements. This method should allow the isolation and cloning of any repetitive DNA present in one species or isolate, but absent or present in reduced copy number in another species or isolate. By analogy to the recent invasion of D. melanogaster by P elements, such differentially represented DNA is likely to represent recently invading transposable elements that are actively mobile.

Animals↗
PubMed1993

Cloning and characterization of the tandemly arranged bovine lymphotoxin and tumour necrosis factor-alpha genes.

The screening of a bovine genomic library with a human tumour necrosis factor-alpha (TNF-alpha) cDNA probe resulted in the isolation of a 7.2 kb DNA fragment containing the entire bovine TNF-alpha gene. Analysis of this genomic clone showed that it also contains the bovine lymphotoxin (LT, TNF-beta) gene. Comparison to published sequences of human, murine, ovine and rabbit counterparts allowed us to delineate the coding sequences, the promoters and the enhancers of these two genes. Sequences involved in the regulation of translation and in the mRNA stability were found in the 3' untranslated regions.

Amino Acid Sequence↗
PubMed1999

A PCR-based method for isolation of genomic DNA flanking a known DNA sequence.

We describe a simple PCR-based method for the isolation of genomic DNA that lies adjacent to a known DNA sequence. The method is based on the directional cloning of digested genomic DNA into the multiple cloning site of a pUC-based plasmid to generate a limited genomic library. The library is plated onto a number of selective LA plates which are incubated overnight, and recombinant plasmid DNA is then isolated from resistant colonies pooled from each plate. PCR amplification is performed on the pooled recombinant plasmid DNAs using primers specific for the pUC vector and the known genomic sequence. The combination of efficient directional cloning and bacterial transformation gives relative enrichment for the genomic sequence of interest and generates a simple DNA template, enabling easy amplification by PCR.

DNA↗
PubMed1996

Trypanosoma cruzi elongation factor 1-alpha: nuclear localization in parasites undergoing apoptosis.

The cloning and sequencing of the gene coding for Trypanosoma cruzi elongation factor 1 alpha (TcEF-1 alpha) was performed by screening a T. cruzi genomic library with a probe obtained through the polymerase chain reaction (PCR) amplification of T. cruzi DNA using two oligonucleotides deduced from the sequence of T. brucei EF-1 alpha. Southern blot analysis of T. cruzi digested genomic DNA and Northern blot hybridized with the labeled probe revealed that one copy of TcEF-1 alpha exist in the genome of the parasite. Indirect immunofluorescence technique using anti-EF-1 alpha antibodies and epimastigotes harvested after different days of in vitro culture showed that EF-1 alpha is localised in the cytoplasm of the parasites from the exponential growth phase. Surprisingly, during the stationary phase (ageing parasites), EF-1 alpha was found in the nucleus. Furthermore, treatment of parasites with the antibiotic drug geneticin (G418) which induces the death of epimastigotes by apoptosis showed selective localization of EF-1 alpha in the nucleus of dying parasites. This observation supports the notion already reported in the case of mammalian cells that EF-1 alpha could participate in the transcription processes and possibly in the case of T. cruzi, in the expression regulation of genes involved in the control of cell death. The possible transfection and genomic manipulation of T. cruzi may provide a model to study the role of TcEF-1 alpha in this phenomenon.

Amino Acid Sequence↗