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Isolation and characterization of the Adh2 5' region from Petunia hybrida.

The Adh2 gene from Petunia hybrida has been difficult to clone; exons 1 to 8 were isolated using PCR after unsuccessful screening of three genomic libraries. A combination of inverse and direct PCR strategies has been used to isolate upstream regions of Adh2. Here we report the cloning strategy for the nucleotide sequence of the 5' region of Adh2 from P. hybrida, the locations of the transcriptional start site and putative TATA box, as well as comparative analyses of the upstream regions of petunia Adh2, other Adh genes and other genes induced by hypoxia.

Alcohol Dehydrogenase↗

DNA probes for the identification of members of the Simulium damnosum complex (Diptera: Simuliidae).

Genomic libraries in plasmid have been constructed from various sibling species of blackflies of the Simulium damnosum complex from West Africa. Three cloned repetitive sequences, which show variation in copy number between sibling species, have been isolated. These clones can be used as probes for the dot-blot identification of larvae, pupae or adults into the three main West African subcomplexes, i.e. damnosum, squamosum and sanctipauli subcomplexes. The sequences also show some intraspecific variation in copy number.

Animals↗

The Chironomus thummi genome contains a non-LTR retrotransposon.

Nineteen recombinant phages containing DNA from the region of Balbiani ring a (BRa), which develops on chromosome IV in cells of the special lobe of the Chironomus thummi salivary gland, were isolated from a Chironomus thummi genomic library. Three of the clones contained transposable element sequences that hybridized to more than 100 sites on all four Chironomus chromosomes, including constant and variable sites. Two handogous clones, lambda 24 (which lacks the transposable element) and lambda 43 (which contains this insertion) were investigated by nucleotide sequence analysis. The complete nucleotide sequence of the 4.8 kb transposable element from Chironomus thummi (NLR1Cth) is reported here. This element contains two overlapping open reading frames of 1887 (ORF1) and 2649 bp (ORF2). Three cysteine motifs are found in the sequence of ORF1. Sequence similarity was found between ORF2 and known genes of viruses and transposable elements which encode reverse transcriptase. The NLR1Cth element has no long terminal repeats and is flanked by short direct repeats of the sequence TATCACTGACAAC. A 24 bp poly(dA) sequence was found at the 3' end of the element. Based upon its structural organization and comparative analysis of its nucleotide sequence we suggest that this NLR1Cth element belongs to the class of non-LTR retrotransposons. The genomic clone pC6.10 was previously obtained by microdissection and cloning of DNA from polytene chromosome IV of Chironomus thummi. A 2.4 kb insertion contained part of the 3' terminal region of the NLR1Cth element, but this differed in sequence from the first copy by several nucleotide substitutions and a shorter poly (dA) tract at the 3' end.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes.

We cloned and sequenced the Vicia sativa 25S-18S rDNA intergenic spacer (IGS) and the satellite repeat S12, thought to be related to the spacer sequence. The spacer was shown to contain three types of subrepeats (A, B, and C) with monomers of 173 bp (A), 10 bp (B), and 66 bp (C), separated by unique or partially duplicated sequences. Two spacer variants were detected in V. sativa that differed in length (2990 and 3168 bp) owing to an extra copy of the subrepeat A. The A subrepeats were also shown to be highly homologous to the satellite repeat S12, which is located in large clusters on chromosomes 4, 5, and 6, and is not associated with the rDNA loci. Sequencing of additional S12 clones retrieved from a shotgun genomic library allowed definition of three subfamilies of this repeat based on minor differences in their nucleotide sequences. Two of these subfamilies could be discriminated from the rest of the S12 sequences as well as from the IGS A subrepeats using specific oligonucleotide primers that labeled only a subset of the S12 loci when used in the primed in situ DNA labeling (PRINS) reaction on mitotic chromosomes. These experiments showed that, in spite of the high overall similarity of the IGS A subrepeats and the S12 satellite repeats, there are S12 subfamilies that are divergent from the common consensus and are present at only some of the chromosomes containing the S12 loci. Thus, the subfamilies may have evolved at these loci following the spreading of the A subrepeats from the IGS to genomic regions outside the rDNA clusters.

Base Sequence↗

DNA profiling of Bursaphelenchus species.

A 1190-bp DNA fragment, designated X14, was isolated from a Bursaphelenchus xylophilus (isolate J10) genomic library. Used as a probe for DNA profiling, this fragment identifies the pinewood nematode (Bursaphelenchus spp.) at both the species and isolate level. The DNA profiles of a number of different species and isolates hybridised with the X14 probe, are presented. The nucleotide sequence of the 1190-bp probe was determined. Secondary structure analysis identified a large imperfect inverted repeat (IR) element within the probe which could form a large stem-loop structure in the RNA.

Animals↗

Use of repetitive DNA probes as physical mapping strategy in Caenorhabditis elegans.

A method for linking genomic sequences cloned in yeast artificial chromosomes (YACs) has been tested using Caenorhabditis elegans as a model system. Yeast clones carrying YACs with repeated sequences were selected from a C. elegans genomic library, total DNA was digested with restriction enzymes, transferred to nylon membranes and probed with a variety of repetitive DNA probes. YAC clones that overlap share common bands with one or more repetitive DNA probes. In 159 YAC clones tested with one restriction enzyme and six probes 28 overlapping clones were detected. The advantages and limitations of this method for construction of YAC physical maps is discussed.

Animals↗

Efficient transformation of Claviceps purpurea using pyrimidine auxotrophic mutants: cloning of the OMP decarboxylase gene.

A homologous transformation system was developed for the phytopathogenic fungus Claviceps purpurea. Orotidine-5'-monophosphate decarboxylase (OMPD)-deficient mutants were obtained by UV mutagenesis and selection for resistance against 5-fluoroorotate. These mutants could be complemented well by the corresponding genes of Aspergillus niger (pyrA) and Neurospora crassa (pyr4), yielding significantly higher transformation rates (and lower copy numbers per transformant) than the phleomycin resistance system. The homologous OMPD gene was isolated from a lambda genomic library by heterologous hybridization with the pyr4 gene of N. crassa, identified by complementation of Aspergillus and Claviceps mutants, and used to confirm homologous integration in Claviceps. The pyr transformation system also proved to be very efficient in cotransformation experiments using the bacterial beta-glucuronidase gene (uidA) as a reporter gene, which was also efficiently expressed during the parasitic cycle: honeydew produced by plants infected with pyr/uidA cotransformants was shown to contain significant levels of beta-glucuronidase activity.

Blotting, Southern↗

Molecular cloning and serological characterization of a new Plasmodium vivax recombinant antigen which contains apolipoprotein B-100 like sequences.

We have isolated a new recombinant antigen 'PV12' of Plasmodium vivax by immunological screening of the genomic library. The antigen shows a sequence homology with human apolipoprotein B-100. A large number of P. vivax infected individuals (79%) were seropositive against this antigen. The probable function of this antigen could be to evade the host defence system (i) by inactivating the perforin of natural killer cells and (ii) by engaging the host immune system to produce antibodies against this decoy antigen.

Amino Acid Sequence↗

Molecular cloning and sequence analysis of rat bradykinin B2 receptor gene.

The bradykinin B2 receptor mediates the effect of kinin. In order to understand the structure and regulation of its expression, we have cloned and sequenced the gene encoding the rat bradykinin B2 receptor and its 5' flanking region from a rat genomic library. The B2 receptor gene spans 7.3 kb in length and contains three exons which are separated by two introns. It encodes a peptide of 366 amino acids. The transcription initiation site was mapped by the primer extension assay. A variant TATA box sequence, an IL-6 response element and a cAMP response element were identified in the 5' flanking region of the rat bradykinin B2 receptor gene.

Amino Acid Sequence↗

Molecular cloning and characterization of a Candida tsukubaensis alpha-glucosidase gene in the yeast Saccharomyces cerevisiae.

The molecular cloning of an alpha-glucosidase gene isolated from a Candida tsukubaensis (CBS 6389) genomic library in Saccharomyces cervisiae is reported. The cloned gene is contained within a 6.2 kb Sau3A DNA fragment and directs the synthesis and secretion of an amylolytic enzyme into the extracellular medium of the recombinant host, S. cerevisiae. The cloned enzyme was found to have an unusually broad substrate specificity and is capable of hydrolysing alpha-1,2, alpha-1,3, alpha-1,4 and alpha-1,6 linked, as well as aryl and alkyl, D-glucosides. On the basis of its substrate specificity profile, the cloned enzyme was classified as an alpha-glucosidase (E.C. 3.2.1.20). It has a pH optimum in the range 4.2-4.6, a temperature optimum of 58 degrees C and is readily inactivated at pasteurization temperature (60 degrees C). Southern blot analysis failed to reveal any homology between the cloned gene and genomic DNA isolated from other well characterized amylolytic yeasts. A rapid plate-assay, based on the utilization of a chromogenic substrate X-alpha-D-glucoside to detect the expression of the cloned alpha-glucosidase in S. cerevisiae transformants, was developed.

Blotting, Southern↗

Cloning of genomic and complementary DNA encoding insect pheromone binding proteins: evidence for microdiversity.

Genomic DNA from the silk moth Antheraea pernyi bearing the gene of a pheromone binding protein has been isolated from a partial genomic library using specific cDNA probes. The DNA spans 3.5 kilobases, contains three exons and two intervening sequences that interrupt the protein coding region of the gene. A DNA fragment of a second gene was isolated and the complete primary structure of a corresponding cDNA clone was unravelled. The expression of two different genes, giving rise to different pheromone binding proteins, implies a more specific function of these proteins than was hitherto assumed.

Amino Acid Sequence↗

The turkey prolactin-encoding gene and its regulatory region.

Overlapping prolactin (Prl) lambda clones were isolated from a turkey genomic library. The 6.7-kb turkey Prl gene consists of five exons. Major transcription start points were located by primer extension 51-53 nucleotides upstream from the Met start codon. No estrogen response element (ERE) was found, but two regions similar to mammalian Pit-1/GHF-1-binding sites were identified by computer analysis. This suggests that transcription of the turkey Prl gene may be regulated by Pit-1/GHF-1, and not by the estrogen receptor.

Amino Acid Sequence↗

A combined physical and genetic map of Pseudomonas aeruginosa PAO.

A combined physical and genetic map of Pseudomonas aeruginosa PAO was constructed by pulsed-field gel electrophoresis and Southern hybridization using cosmid clones from a genomic library carrying known genes. A total of 37 SpeI restriction fragments have been mapped on the 5862 kb genome, and fragment contiguity demonstrated by hybridization with clones from a SpeI junction fragment library and fragments obtained by partial SpeI digestion, both derived from the P. aeruginosa PAO chromosome.

Blotting, Southern↗

Characterisation of a novel repetitive DNA sequence from Mycobacterium bovis.

We report characterisation of three copies of a novel repeat sequence isolated from a Mycobacterium bovis genomic library. The repeat occurs within open reading frames, potentially encoding a conserved tandem array of a pentapeptide sequence with the consensus X-Gly-Asn-X-Gly. The tandem array is present up to five times in M. bovis and it is proposed that they may occur in a family of genes expressing functionally related proteins. We postulate that these proteins may play a role in binding of M. bovis to host cell receptors.

Amino Acid Sequence↗

Structure and transcription of the gene for translation elongation factor 1 subunit alpha of zebrafish (Danio rerio).

The zebrafish gene for translation elongation factor 1 alpha (EF1 alpha) was isolated from a phage Lambda genomic library and sequence and structure determined. One gene copy of EF1 alpha per haploid set of chromosomes was found and no processed pseudogenes. A highly active promoter region was localized to a 277 bp PstI/PvuII fragment beginning 240 bp upstream from the tsp, but no transcription enhancing, or silencing activity was observed within 1 kbp upstream, or downstream from the promoter. Expression of EF1 alpha appears to be developmentally regulated.

Animals↗

Purification, characterization, and molecular analysis of thermostable cellulases CelA and CelB from Thermotoga neapolitana.

Two thermostable endocellulases, CelA and CelB, were purified from Thermotoga neapolitana. CelA (molecular mass, 29 kDa; pI 4.6) is optimally active at pH 6.0 at 95 degreesC, while CelB (molecular mass, 30 kDa; pI 4.1) has a broader optimal pH range (pH 6.0 to 6.6) at 106 degreesC. Both enzymes are characterized by a high level of activity (high Vmax value and low apparent Km value) with carboxymethyl cellulose; the specific activities of CelA and CelB are 1,219 and 1,536 U/mg, respectively. With p-nitrophenyl cellobioside the Vmax values of CelA and CelB are 69.2 and 18.4 U/mg, respectively, while the Km values are 0.97 and 0.3 mM, respectively. The major end products of cellulose hydrolysis, glucose and cellobiose, competitively inhibit CelA, and CelB. The Ki values for CelA are 0.44 M for glucose and 2.5 mM for cellobiose; the Ki values for CelB are 0.2 M for glucose and 1.16 mM for cellobiose. CelB preferentially cleaves larger cellooligomers, producing cellobiose as the end product; it also exhibits significant transglycosylation activity. This enzyme is highly thermostable and has half-lives of 130 min at 106 degreesC and 26 min at 110 degreesC. A single clone encoding the celA and celB genes was identified by screening a T. neapolitana genomic library in Escherichia coli. The celA gene encodes a 257-amino-acid protein, while celB encodes a 274-amino-acid protein. Both proteins belong to family 12 of the glycosyl hydrolases, and the two proteins are 60% similar to each other. Northern blots of T. neapolitana mRNA revealed that celA and celB are monocistronic messages, and both genes are inducible by cellobiose and are repressed by glucose.

Amino Acid Sequence↗

A cytogenetically anchored genetic map of bovine chromosome 1 obtained by integrating flow-sorted chromosome-derived microsatellite markers into the international bovine map.

A genomic library was constructed from a peak of flow-sorted bovine chromosomes 1 + X after PCR amplification. Forty-three bovine chromosome 1 microsatellites were isolated, genetically mapped and integrated in the international genetic map. In addition, BAC clones from a goat BAC library were identified for five markers (DVEPC119, INRA011, BM4307, KAP8 and MAF64). These goat BACs could be mapped by FISH onto bovine chromosome 1 to bands 1q44-->q45, 1q25, 1q21, 1q12 and 1q14-->q21, respectively. This map reduces the average interval between consecutive markers on the international bovine genetic map from 5.5 cM to 2.5 cM, and provides a good starting point for positional cloning projects in cattle, sheep or goats.

Animals↗

Molecular cloning of a gene encoding porcine interferon-beta.

A gene encoding the porcine interferon-beta (poIFN-beta) was cloned from a genomic library. The sequence of a potential intronless coding region as well as 1,265 bp of the 5'- and 277 bp of the 3'-flanking regions is presented. The gene is predicted to encode a mature protein of 165 amino acids and a signal peptide of 21 amino acids. This probable poIFN-beta shows high homology (63%) with human (hu) IFN-beta at the amino acid level, but less with porcine (po) IFN-alpha 1 (32%). It contains three cysteines and three potential N-glycosylation sites. A region of the 5' flank (-116 to -159) of the gene is homologous to the IFN gene regulatory element (IRE) of the huIFN-beta gene which mediates virus inducibility. Southern blot analysis indicates that the poIFN-beta gene is present as a single copy in the porcine genome. Its expression in porcine peripheral blood leukocytes stimulated in vitro by pseudorabies virus (PRV) was demonstrated at the RNA level both by Northern blot analysis and by in situ hybridization. The latter approach in addition detected only about one IFN-beta mRNA-containing cell per 2,000 PRV-stimulated porcine leukocytes, a frequency in the same range as that for leukocytes containing IFN-alpha mRNA.

Amino Acid Sequence↗