SEARCH · Search PubMed
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
We constructed a cosmid vector, pSW206, which should be useful for the construction of genomic libraries of Actinobacillus pleuropneumoniae (Apl) DNA. pSW206 is based on the broad-host-range plasmid RK2 and can be introduced into Apl by conjugation.
Chitin synthase genes of the arbuscular mycorrhizal fungus Glomus versiforme were sought in an investigation of the molecular basis of fungal growth. Three DNA fragments (Gvchs1, Gvchs2 and Gvchs3) corresponding to the conserved regions of distinct chitin synthase (chs) genes were amplified by means of the polymerase chain reaction (PCR) with two sets of degenerate primers. Gvchs1 and Gvchs2 encode two class I chitin synthases, whereas Gvchs3 encodes a class IV chitin synthase. A genomic library was used to obtain the Gvchs3 complete gene (1194 amino acids), which shows a very close similarity to the class IV chitin synthase from Neurospora crassa.
We have examined several tumors from South African patients with hepatitis B virus (HBV)-associated hepatocellular carcinoma for the presence of integrated viral DNA. In contrast with our findings in patients from Taiwan, few copies of the viral genome were integrated in each tumor. Furthermore, Southern hybridization showed similarities in integration patterns between different tumors. We are presently constructing genomic libraries from selected single-copy tumors in order to make a more detailed analysis of HBV DNA integration at the molecular level.
We have identified, genetically mapped and physically delineated the chromosomal location of a new rice blast resistance locus, designated Pi-CO39(t). This locus confers resistance to Magnaporthe grisea isolates carrying the AVR1-CO39 avirulence locus. The AVR1-CO39 locus is conserved in non-rice (cereals and grasses)-infecting isolates of M. grisea, making Pi-CO39(t) useful for engineering M. grisea resistance in rice and other cereals. The resistance in the rice line CO39 was inherited as a single dominant locus in segregating populations derived from F(2) and F(3) crosses between disease-resistant (CO39) and susceptible (51583) rice genotypes. Microsatellite, RFLP and resistance gene analog (RGA) markers were used to map the Pi-CO39(t) locus to a 1.2-cM interval between the probenazole-responsive ( RPR1) gene (0.2 cM) and RFLP marker S2712 (1.0 cM) on the short arm of rice chromosome 11. RFLP markers G320 and F5003, and resistance gene analogs RGA8, RGA38 and RGACO39 were tightly linked to the Pi-CO39(t) locus (no recombination detected in a sample of ~2400 gametes). A large-insert genomic library of CO39 was constructed in the binary plant transformation vector pCLD04541. A library screen using RGA8, RGA38 and probes derived from the ends of CO39 clones, as well as BAC end probes from the corresponding locus in the rice cv. Nipponbare, resulted in the assembly of three CO39 contigs of 180 kb, 110 kb and 145 kb linked to the Pi-CO39(t) locus. A 650-kb contig was also constructed representing the susceptible locus, pi-CO39(t), in the Nipponbare genome. The two genomes are highly divergent with respect to additions, deletions and translocations at the Pi-CO39(t) locus, as revealed by the presence or absence of mapping markers.
A gene (lap) coding for a Lactococcus lactis ssp. cremoris Wg2 aminopeptidase was cloned from genomic libraries of size-fractionated lactococcal DNA. The 5' end of the lap gene was isolated by using a polymerase chain reaction hybridization probe of 77 nucleotides (nt) synthesized from two degenerate primers derived from the N-terminal amino acid (aa) sequence of the lactococcal lysine-aminopeptidase (LAP). The remaining part(s) of the gene were recovered by a search for overlapping sequences in Southern blots of variably restricted genomic DNA. The complete nt sequence of the lap gene has been determined. A large open reading frame of 2538 nt is predicted to encode a polypeptide of 846 aa (approx. 95.3 kDa; pI, 5.93). A recombinant plasmid containing the lap gene with its flanking sequences was shown to direct in vivo synthesis of LAP activity in Escherichia coli, indicating that the cloned DNA fragment is the lap gene. Primer extension analysis of lap mRNA and Northern blot hybridization indicated the gene transcript to be approx. 3.0 kb in size with a 5'-untranslated region of 19-22 nt. Comparison of the deduced aa sequence indicates that the LAP has extensive homology with the super family of Zn(2+)-metallohydrolases and shows identity in the core deca-peptide consensus sequence for the Zn(2+)-binding motif of these enzymes.
A seed and flower color marker (P), nine seed protein, nine isozyme and 224 restriction fragment length polymorphism marker loci were used to construct a linkage map of the common bean, Phaseolus vulgaris L. (n = 11). The mapping population consisted of a backcross progeny between the Mesoamerican breeding line 'XR-235-1-1' and the Andean cultivar 'Calima'; the former was used as the recurrent parent. A bean PstI genomic library enriched for single copy sequences (95%) was the source of DNA probes. Sixty percent of the probes tested detected polymorphisms between the parental genotypes with at least one of the four restriction enzymes used here (DraI, EcoRI, EcoRV and HindIII). The computer software Mapmaker was used to determine the linkage relationships and linear order of segregating markers. These markers assorted into 11 linkage groups covering 960 cM of the bean genome. Partial linkage data were used to estimate the total length of the genome at 1200 cM. This estimate and that for the physical size of the genome yield an average ratio of 530 kb/cM. The relatively small size of the genome makes this crop species a good candidate for the isolation of genes via chromosome walking techniques.
Di-nucleotide microsatellites were isolated from a genomic library of a tropical tree species, Dryobalanops lanceolata, in Sarawak, for the purpose of using them as hypervariable genetic markers to study the pollen-mediated gene flow. Among 1600 recombinant clones, in total 20 clones gave positive signals when hybridized with oligonucleotides with the three different repeat motifs, GT, CA and CT. Estimations of abundance of (GT)n/(CA)n and (GA)n/(CT)n dinucleotide repeats in D. lanceolata genome revealed to be one in every 84 kb and 80 kb, respectively. Among six sequenced microsatellite loci, one was selected to synthesize PCR primers to amplify the microsatellite. PCR product size of the locus was variable among different individuals, which is attributed to the different number of di-nucleotide repeats. The same microsatellite genotype was detected in the trunk and canopy of a single large tree, indicating the utility of trunk tissue as the source of DNA for the population genetic study of tropical tree species, the canopy of which is usually difficult to approach.
A gene encoding ovine interferon alpha (IFN alpha) was identified from an ovine liver genomic library. Based on nucleotide and deduced amino acid sequencing analyses, this gene appears to code for an IFN of the alpha II family different from the ovine embryonic IFNs found to date.
We isolated the gene encoding the brain specific snRNP-associated polypeptide "N" from a rat genomic library. Some intronless genes have previously been reported for this polypeptide in the rat. In contrast, our gene consists of at least nine exons (the last exon(s) encoding the 3'-end of the mRNA has not been isolated). The second intron of the gene is probably so long as to hamper the cloning of the complete gene into a single phage vector. Therefore, we used polymerase chain reaction amplification of the rat genome with oligonucleotides designed on the basis of known cDNA sequences that allowed us to isolate and clone the first two exons at the 5'-end of the gene. Primer extension studies revealed multiple transcription start sites, all of them contained within the first exon. The intron/exon organization coincides with the alternative splicing events suggested by the sequences of the various cDNA species isolated so far. As also reported by others, genomic Southern analysis suggests the presence of other genomic regions containing sequences strongly hybridizing to the cDNA. We isolated and characterized two of these regions. They contain sequences very similar to the cDNA, not interrupted by introns and flanked by a polyA tail at their 3'-ends; hence they are considered two different pseudogenes.
An agar plate freezing assay is described based on the incorporation of fluorescein dye in agar medium. Upon addition of fluorescein the medium becomes transparent. This facilitates the monitoring of the ice nucleation event in vivo and the subsequent in situ selection of transformed ice nucleating bacteria. In comparison with known assays for the screening of transformants, the proposed assay is very accurate and reproducible. It may be applied in environmental samples screening for ice nucleating organisms, or in cDNA or genomic libraries for identifying novel ice nucleation genes. It may also prove useful in comparative studies of the ice nucleation activity, e.g. in directed evolution experiments involving ice nucleation genes.
Secreted and cell envelope-associated proteins are important to both Mycobacterium tuberculosis pathogenesis and the generation of protective immunity to M. tuberculosis. We used an in vitro Tn552'phoA transposition system to identify exported proteins of M. tuberculosis. The system is simple and efficient, and the transposon inserts randomly into target DNA. M. tuberculosis genomic libraries were targeted with Tn552'phoA transposons, and these libraries were screened in M. smegmatis for active PhoA translational fusions. Thirty-two different M. tuberculosis open reading frames were identified; eight contain standard signal peptides, six contain lipoprotein signal peptides, and seventeen contain one or more transmembrane domains. Four of these proteins had not yet been assigned as exported proteins in the M. tuberculosis databases. This collection of exported proteins includes factors that are known to participate in the immune response of M. tuberculosis and proteins with homologies, suggesting a role in pathogenesis. Nine of the proteins appear to be unique to mycobacteria and represent promising candidates for factors that participate in protective immunity and virulence. This technology of creating comprehensive fusion libraries should be applicable to other organisms.
A genomic library of L. monocytogenes was constructed using lambda Zap II-Eco RI and screened with a monoclonal antibody which is specific for a Listeria cell surface protein. Three positive clones each contained a 6.5 kb insert which in E. coli could express the same Listeria protein. The 6.5 kb insert was further digested with Hin dIII and the smaller fragments were subcloned into a plasmid vector (pBluescript) and screened with 32P-labelled genomic DNA from L. monocytogenes or L. innocua. Three clones which were positive with L. monocytogenes and negative with L. innocua were screened and each contained a 2.1 kb insert. The 2.1 kb insert was partly sequenced and some candidate oligomer probes from the sequences were selected and compared with sequences in a Genbank computer search. One such oligomer probe (T7-list) was confirmed to be specific for L. monocytogenes. The probe hybridized with all 28 strains of L. monocytogenes tested, but not with any of six other Listeria species nor 11 other bacteria tested. Using this probe-primer, a PCR method was developed which could detect as few as 2 cfu of L. monocytogenes in pure cultures, and as few as 4-10 cfu of L. monocytogenes when inoculated into foods.
Identifying and selectively breeding for improved traits is one of the ultimate goals of genetic research in agriculturally important species. Genome characterization and analysis are important first steps in this process. Genetic linkage maps based on the linear order of polymorphic DNA markers are typically developed through statistical analysis of inheritance patterns in pedigreed families. To develop microsatellite markers for further improvement of the turkey genetic linkage map, small-insert genomic libraries were screened for tandem repeats. Oligonuclotide primers were designed to amplify 164 microsatellite-containing fragments from genomic DNA. Genetic polymorphisms at 154 markers were determined by genotyping the F(1) individuals of two resource populations. Markers determined as segregating in the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) reference population were used to genotype F(2) individuals and a two-point linkage analysis was performed.
One-armed PCR (OA-PCR) is a novel technique that allows amplification of genomic DNA from a single region of known sequence. Previously described methods are either limited to cDNA or require extensive manipulation of template prior to amplification. In OA-PCR, DNA from a small insert phage Fugu genomic library is amplified using two sequence-specific primers and a tailed vector primer. Single, specific products of between 70 bp and 1.9 kb (mean 600 bp) have been obtained following two rounds of amplification and directly sequenced without cloning. The optimum parameters have been investigated: primer pairs of 18-24 bp, separated by between 0 and 500 bp, have successfully amplified a specific product. OA-PCR represents a rapid, simple method to extend genomic sequence into noncoding and regulatory sequences. In addition, degenerate OA-PCR primer pairs have allowed cross-species amplification of novel Fugu gene homologues.
Development of a subunit vaccine for Mycobacterium tuberculosis (Mtb) is likely to be dependent on the identification of T cell antigens that induce strong proliferation and interferon gamma production from healthy purified protein derivative (PPD)(+) donors. We have developed a sensitive and rapid technique for screening an Mtb genomic library expressed in Escherichia coli using Mtb-specific CD4(+) T cells. Using this technique, we identified a family of highly related Mtb antigens. The gene of one family member encodes a 9.9-kD antigen, termed Mtb9.9A. Recombinant Mtb9.9A protein, expressed and purified from E. coli, elicited strong T cell proliferation and IFN-gamma production by peripheral blood mononuclear cells from PPD(+) but not PPD(-) individuals. Southern blot analysis and examination of the Mtb genome sequence revealed a family of highly related genes. A T cell line from a PPD(+) donor that failed to react with recombinant Mtb9.9A recognized one of the other family members, Mtb9.9C. Synthetic peptides were used to map the T cell epitope recognized by this line, and revealed a single amino acid substitution in this region when compared with Mtb9.9A. The direct identification of antigens using T cells from immune donors will undoubtedly be critical for the development of vaccines to several intracellular pathogens.
Two unique but homologous receptors for the neutrophil chemoattractant, IL-8 have been cloned (designated IL-8RA and IL-8RB), each of which binds IL-8 with high affinity. IL-8RA mRNA expression was found to be regulated by granulocyte-CSF and LPS. In an attempt to understand the tissue-specific expression and to identify transcriptional regulatory elements, we have cloned, sequenced, and characterized the human IL-8RA gene. A lambda-DASH clone encoding the entire human IL-8RA gene was isolated by screening a genomic library with a PCR-generated cDNA. After mapping, subcloning, and sequencing several restriction fragments, a 9.2-kb continuous DNA sequence was obtained. As the sizes of the published cDNA (1.9 kb) and the mRNA determined by Northern blot analysis (2.1 kb) were not in agreement, a full-length cDNA was cloned by using a modified rapid amplification of cDNA ends technique. We identified a 5'-untranslated region of 119 bp. After comparison with the genomic sequence, we found the gene consisted of two exons interrupted by an intron of 1.7 kb. A 1050-bp ORF was encoded entirely in the second exon together with a 834-bp 3'-untranslated region. The immediate GC-rich 5'-flanking region upstream of exon 1 could serve as a constitutively active promoter in chloramphenicol-acetyl-transferase-expression assays. Expression analysis of additional upstream regions suggested the presence of silencer elements between positions -841 and -280. In conclusion, cloning a full-length cDNA permitted us to clone the human IL-8RA gene, identify the genomic structure, and characterize the promoter region.
Three distinct clones from a Salmonella typhimurium genomic library were identified which suppressed the copper-sensitive (Cu(s)) phenotype of cutF mutants of Escherichia coli. One of these clones, pCUTFS2, also increased the copper tolerance of cutA, -C, and -E mutants, as well as that of a lipoprotein diacylglyceryl transferase (lgt) mutant of E. coli. Characterization of pCUTFS2 revealed that the genes responsible for suppression of copper sensitivity (scs) reside on a 4.36-kb DNA fragment located near 25.4 min on the S. typhimurium genome. Sequence analysis of this fragment revealed four open reading frames (ORF120, ORF627, ORF207, and ORF168) that were organized into two operons. One operon consisted of a single gene, scsA (ORF120), whereas the other operon contained the genes scsB (ORF627), scsC (ORF207), and scsD (ORF168). Comparison of the deduced amino acid sequences of the predicted gene products showed that ScsB, ScsC, and ScsD have significant homology to thiol-disulfide interchange proteins (CutA2, DipZ, CycZ, and DsbD) from E. coli and Haemophilus influenzae, to an outer membrane protein (Com1) from Coxiella burnetii, and to thioredoxin and thioredoxin-like proteins, respectively. The two operons were subcloned on compatible plasmids, and complementation analyses indicated that all four proteins are required for the increased copper tolerance of E. coli mutants. In addition, the scs locus also restored lipoprotein modification in lgt mutants of E. coli. Sequence analyses of the S. typhimurium scs genes and adjacent DNAs revealed that the scs locus is flanked by genes with high homology to the cbpA (predicted curved DNA-binding protein) and agp (acid glucose phosphatase) genes of E. coli located at 22.90 min (1,062.07 kb) and 22.95 min (1,064.8 kb) of the E. coli chromosome, respectively. However, examination of the E. coli chromosome revealed that these genes are absent at this locus and no evidence has thus been obtained for the occurrence of the scs locus elsewhere on the genome.
The genomic library of alkalophilic thermophilic Bacillus was constructed in E.coli. A single recombinant [pATB 507 I] out of 10,000 colonies showed growth at 50 degrees C, which produced large, opaque and mucilaginous colonies on LB. The IMViC biochemical tests suggested that the strain was E.coli, and scanning electron microscopy revealed increased cell length. The plasmid DNA from the thermophilic recombinant showed multiple bands. The cured strain showed ampicillin resistance (10 micrograms/ml) and presence of insert DNA in the genome, as revealed by southern blot analysis. The thermophilic trait was transformable with 10(-4) frequency of expression amongst the pATB 507I transformants. The hybridization of E.coli genomic DNA with labeled genomic DNA from alkalophilic thermophilic Bacillus suggested that the genetic recombination(s) of the insert DNA was an essential prerequisite for expression of thermophilic trait. The conjugative plasmid (RP4) mediated mobilization of thermophilic trait resulted in thermophilic conjugants after 2 h incubation. Southern blot analysis revealed that a single locus [5.6 kb Bam HI fragment] was involved in the transfer of thermophilic trait.