Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genomic Library”

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.

At least 1,783 records · Page 99Linked to original sources
PubMed2004

The fugitive LTR retrotransposon from the genome of the human blood fluke, Schistosoma mansoni.

Inspection of the nucleotide sequence of bacterial artificial chromosome number 49_J_14 [Le Paslier, M.C., Pierce, R.J., Merlin, F., Hirai, H., Wu, W., Williams, D.L., Johnston, D., LoVerde, P.T., Le Paslier, D., 2000. Construction and characterization of a Schistosoma mansoni bacterial artificial chromosome library. Genomics 65, 87-94] from chromosome 1 of the genome of Schistosoma mansoni (GenBank ) revealed the likely presence of a proviral form of a novel schistosome retrotransposon. The novel element, which we named the fugitive, belonged to the mag-like family of the gypsy-Ty3 clade of long terminal repeat retrotransposons. It was closely related to the mag-like retrotransposon Gulliver from Schistosoma japonicum, but was dissimilar to several other long terminal repeat retrotransposons known from S. mansoni including Boudicca, Saci-1, Saci-2 and Saci-3. The full length fugitive element was 4811 bp constituted of a single read-through open reading frame of 4134 bp flanked at both ends by identical long terminal repeat sequences of 273 bp. The open reading frame encoded retroviral-like gag, with a distinctive double Cys-His motif, and pol polyprotein, with a pol domain order of protease, reverse transcriptase, RNaseH and integrase. Examination of schistosome transcriptome sequences in the public domain revealed that the fugitive was transcribed in at least six developmental stages of S. mansoni, while bioinformatics approaches and Southern hybridisation analysis indicated that as many as 2000 copies of the fugitive were interspersed throughout the schistosome genome.

Amino Acid Sequence↗
PubMed1994

Demonstration of promoter activity and alternative splicing in the region 5' to exon 1 of the APC gene.

Screening of fetal brain and fetal retina complementary DNA (cDNA) libraries and exon-connection experiments using brain cDNA have identified three exons 5' to exon 1 of the adenomatous polyposis coli gene. The exons are termed (from 5'-3') 0.3, 0.1, and 0.2; exons 0.1 and 0.2 are contiguous genomically. Library screening revealed alternatively spliced cDNAs containing the following combinations of 5'-exons: 0.3 + 1 + 2, 0.3 + 2, 0.1 + 0.2 + 1 + 2, and 0.1 + 1 + 2. Exon-connection experiments also identified these four forms in mRNAs from tissues and cultured cell lines, along with two additional forms, 0.1 + 0.2 + 2 and 0.1 + 2. The multiple splice forms may lead to proteins of differing activity; for example, products derived from cDNAs without exon 1 will lack most of a heptad-repeat domain that supports formation of homodimers. No mRNA species combining 0.3 with either 0.1 or 0.2 were identified. The existence of two apparently separate 5'-ends of APC suggests the possibility of two independent promoters. The genomic sequence adjacent to exon 0.3 confers promotor activity when cloned in a chloramphenicol acetyltransferase expression vector and transfected into a colon cancer cell line.

Alternative Splicing↗
PubMed1997

Microsatellite marker development, mapping and applications in rice genetics and breeding.

Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10,000 microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 microsatellite markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trail locus (QTL) analysis, screening of large insert libraries, and marker-assisted selection in breeding. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP markers can be expected to complement existing RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice.

Breeding↗
PubMed2000

Physiological role of the D-amino acid oxidase gene, DAO1, in carbon and nitrogen metabolism in the methylotrophic yeast Candida boidinii.

A methylotrophic yeast, Candida boidinii, exhibits D-amino acid oxidase activity (DAO, EC 1.4.3.3) during its growth on D-alanine as a sole carbon or a nitrogen source. The structural gene (DAO1), encoding DAO, was cloned from a genomic library of C. boidinii. The 1035-bp gene encoded 345 amino acids and the predicted amino acid sequence showed significant similarity to those of DAOs from other organisms. The DAO1 gene was disrupted in the C. boidinii genome by one-step gene disruption. The DAO1-deleted strain did not grow on D-alanine as a carbon source but did grow on D-alanine as a sole nitrogen source (with glucose as the carbon source). These results suggested that, while DAO is critically involved in growth on D-alanine as a carbon source, there should be another enzyme system which metabolizes D-alanine as a nitrogen source in C. boidinii. We also showed that the three C-terminal amino acid sequence of DAO, -AKL was necessary and sufficient for the import of DAO into peroxisomes.

Alanine↗
PubMed1998

Genomic structure and developmental expression of the chicken nonocarboxylate transporter MCT3 gene.

MCT3 is a monocarboxylate transporter that is specifically expressed on the basolateral membrane of retinal pigment epithelial cells (RPE). In these studies the temporal expression of MCT3 during ocular development was examined using Northern blot analysis. A 2.2 kb transcript (MCT3b) was detected in RPE by embryonic day 7 (E7) and was present throughout embryonic development. A 2.45 kb transcript (MCT3a) was expressed at low levels before E11 but its expression increased between E11 and E17. Using 5'-RACE (rapid amplification of cDNA ends) it has demonstrated that MCT3a and MCT3b mRNA had distinct 5'-untranslated sequences but shared the same translation start site. To determine the exon-intron structure and to understand the elements that control the tissue specific and developmental expression of MCT3, the MCT3 gene was cloned and sequenced from a chicken genomic library. The MCT3 gene is distributed over 8 kb of DNA and is composed of 6 exons. Coding sequences for MCT3 are found on exon 2 through exon 5. Comparison of the 5'-RACE sequence with the genomic sequence reveals that the two 5'-untranslated regions of the mRNAs are encoded by distinct exons, 1a and 1b, which are alternatively spliced to exon 2. These data suggest that two forms of MCT3 mRNAs could be generated by two distinct promoters that may be regulated in response to changes in the metabolic activity of the retina during development.

Amino Acid Sequence↗
PubMed1996

Subtype 2 and atypical angiotensin receptors in the human heart.

Angiotensin receptors have been described in the human heart and are suspected to play a central role in remodeling after myocardial infarction and in cardiac hypertrophy. Two subtypes, AT1 and AT2, have so far been described in humans, with AT2 being the dominant subtype in human atria. We have now determined subtype numbers and distribution by binding in ventricular myocardium from patients with end-stage heart failure. We found about 50-80% of subtype AT2 in the right and left ventricles from patients with end-stage heart failure due to coronary artery disease and cardiomyopathy, indicating that AT2 is the dominant angiotensin receptor subtype in the whole human heart. To determine the cellular localization of angiotensin receptors in human myocardium in addition to the known localization on myocytes, smooth muscle cells and endothelial cells, we investigated cardiac fibroblasts. They express an angiotensin receptor with yet incompletely understood binding characteristics which is coupled to proliferation and DNA synthesis. As AT2 is the dominant angiotensin receptor subtype in human heart, we cloned the complete mRNA sequence by a rapid amplification of cDNA ends (RACE) procedure and thereafter the promoter sequence from a human genomic library. Once the sequence of the mRNA and thus exon 1 was obtained by the RACE-PCR, a probe was constructed for the most 5' region of exon 1 and used for screening of a human genomic DNA bank. After cutting of the positive clones with EcoR1 and Not1, a 4000 bp fragment hybridized with the probe and was further sequenced. A functional AT2 promoter, with > 90% homology with the mouse promoter and 35% homology with the human AT1 promoter containing numerous cis-acting sequences for basal (TFIID) and inducible (AP-1, PEA-3, CBF) transcription factors in the first 1000 bp was identified.

DNA↗
PubMed1990

Characterization of a Trypanosoma cruzi specific nuclear repeated sequence.

We report the isolation of three different clones from a Trypanosoma cruzi genomic library bearing a common repeated sequence. This sequence is not tandemly repeated, and is dispersed on many chromosomes. All of the T. cruzi strains tested share this element. On the other hand, it is absent from the genome of other Kinetoplastida. The size of this element is about 10-12 kb, and its copy number is 220 in the T. cruzi Dm 28c genome. A transcript homologous to this sequence is detected in epimastigote forms of the parasite.

Animals↗
PubMed1993

A repetitive element in the genome of Atlantic salmon, Salmo salar.

When Atlantic salmon (Salmo salar) genomic DNA is digested with the restriction endonuclease BglI and the fragments separated by agarose-gel electrophoresis, bands corresponding to approximately 430 and 923 bp are visualized after EtdBr staining. The 923-bp band was excised from a preparative gel and used to screen a salmon genomic library for recombinant phage (re-phage) containing the repeat. The BglI repeat element is tandemly arrayed, and an array from one re-phage has been sequenced. The BglI repeats comprise 2.3% of the S. salar genome and have been found in the vicinity of rDNA genes (encoding ribosomal RNA). Southern blot hybridization detects a homologue of the Atlantic salmon BglI repeat in the brown trout (Salmo trutta) genome, but not in other salmonids. However, a DNA fragment with sequence homology to part of the BglI repeat has recently been isolated from Arctic charr (Salvelinus alpinus; S.E. Hartley and W.S.D., unpublished data). In addition, the BglI repeat detects RFLPs in Atlantic salmon.

Animals↗
PubMed2006

Cloning and characterization of two genes encoding rainbow trout homologues of the IFITM protein family.

To identify genes connected with leucocyte function in rainbow trout a cDNA library derived from head kidney leucocytes exposed to phytohemagglutinin (PHA) was screened. A clone with homology to the previously described human interferon-inducible transmembrane proteins (IFITM) was isolated. This clone was used to screen a trout genomic library identifying two trout IFITM genes. Both genes are composed of two exons, in common with human IFITM genes. The promoter regions of both genes were examined and found to contain interferon, immune and stress-related transcription factor binding sites. Transcripts for both genes were found in most tissues examined. Trout IFITM1 mRNA levels were highest in head kidney, but present in all tissues studied. IFITM2 mRNA levels were highest in gill, heart and liver, and absent in head kidney and blood. In response to conditions mimicking viral infection, transcription of the trout IFITM genes was elevated in a trout spleen macrophage cell line (RTS11) over the examined timecourse (72 h). This study suggests that the organization and transcription of the IFITM genes is well conserved between human and rainbow trout.

Amino Acid Sequence↗
PubMed2002

Genomic sequencing of the bovine T cell receptor beta locus.

The T cell, which plays an integral role in the coordination of the immune system, has a heterodimer receptor (TCR) that can exist in one of the two forms: alpha/beta or gamma/delta. Cells displaying the gamma/delta TCR comprise less than 5% of T cell populations in humans and mice. In the bovine system, however, gamma/delta populations can reach as high as 60%. Differences in T cell populations make the bovine system an excellent candidate for genomic TCR sequencing and multi-species comparisons. In an effort to characterize the bovine TCR loci, a genomic library was screened for the beta TCR gene. A shotgun sequencing library was constructed and preliminary analysis demonstrates that the organization of the bovine TCR beta constant regions is different from both humans and mice. The bovine beta locus appears to have a third constant region. Overall, the genomic characterization of the bovine TCR genes will provide insight into the evolution of T cell receptor.

Animals↗
PubMed1989

Structure of rDNA in the mosquito Anopheles gambiae and rDNA sequence variation within and between species of the A. gambiae complex.

The structure of the rDNA repeating unit of Anopheles gambiae (Diptera: Culicidae) was determined by restriction endonuclease mapping and hybridization analyses on four independent clones obtained from a genomic library of a colony (G3) from the Gambia (West Africa). rDNA gene coding sequences are conserved, but much intragenomic and intraspecific (geographic) variation occurs in the intergenic spacer. Hybridization of subclones from spacer and coding sequences to genomic DNA that was isolated from single mosquitoes from laboratory colonies of four other A. gambiae complex species reveals conservation of coding sequences but concerted evolution in the intergenic spacers.

Africa, Western↗
PubMedDate not supplied

Cloning and characterization of highly polymorphic porcine microsatellites.

A size-fractionated (200-400 bp) porcine genomic library was screened with the dinucleotide motifs (TG)n and (TC)n. The number of TG- and TC-positive clones was 83 and four, respectively, implying that the former motif is more frequent in the porcine genome, as previously reported in other species. Twenty-six TG-clones were sequenced, and the number of repeats varied between 16 and 42 with different compositions of the repetitive sequences; 17 clones had a perfect stretch of TG-repeats, four had imperfect stretches, and five had a compound structure with TG-repeats followed by TC-repeats. Primers for DNA amplification using the polymerase chain reaction (PCR) were synthesized for six loci. Ten unrelated individuals (two wild boars and eight domestic pigs of the Swedish Yorkshire breed) were screened for microsatellite polymorphism. All six microsatellite loci were polymorphic with two to seven alleles and observed heterozygosities in the range of 0.42-0.84; the inheritance of the observed polymorphism was confirmed by family studies. The characteristics of microsatellites make them highly suitable as genetic markers, and these microsatellites were isolated as a part of a pig gene mapping project.

Animals↗
PubMed1987

Identification of restriction-fragment-length polymorphisms in genomic DNA of the lesser snow goose (Anser caerulescens caerulescens).

A genomic library of partially EcoRI-digested DNA from the lesser snow goose, Anser caerulescens caerulescens, was constructed in the phage vector Charon 4. Phage containing only unique sequences were identified by screening plaques with 32P-labeled genomic DNA. Restriction-fragment-length polymorphisms (RFLPs) were identified by probing DNA from 11-13 male birds from the breeding colony at La Perouse Bay. Of the 17 probes examined, all detected RFLPs with at least one of EcoRi, HindIII, Msp1, and Taq1. Several of them identified highly variable regions with multiple alleles. These RFLPs are valuable DNA markers that can be used for (1) the examination of DNA variation, relatedness, and genetic distance and (2) assessing paternity and maternity. These data suggest that there are higher levels of variation of DNA sequence in birds than had previously been thought to exist.

Alleles↗
PubMed1993

Three baculovirus genes involved in late and very late gene expression: ie-1, ie-n, and lef-2.

We developed a method to identify baculovirus genes required for late and very late gene expression that is based on subtraction of clones from an Autographa californica nuclear polyhedrosis virus genomic library which is able to trans activate promoters of reporter plasmids in transient expression assays. Using this assay, we found that three genes located between 83.7 and 7.5 map units of the Autographa californica nuclear polyhedrosis virus genome were involved in expression from the late capsid protein (vp39) and very late polyhedrin (polh) gene promoters. Two of these genes, ie-1 and ie-n, trans regulate early genes in transient expression assays. Although ie-1 was necessary and sufficient for expression from the early promoter in our assay, it was necessary but not sufficient for expression from the vp39 and polh promoters. The presence of ie-n increased expression from the early, late, and very late classes of promoters tested. However, a third gene identified in this region was specifically required for expression from the vp39 and polh promoters. This gene, a previously sequenced 630-nucleotide open reading frame, was renamed lef-2 for late expression factor 2. We also found that other genes in the region between 83.7 and 7.5 map units were not required for expression from the promoters used in this assay, although we did not eliminate the possibility that they subtly modify expression. These genes include pe-38 and me53, early genes with zinc finger-like motifs, and the upstream exon of ie-0, which specifies an alternate form of IE-1.

Animals↗
PubMed1989

Characterization of the human parathyroid hormone-like peptide gene. Functional and evolutionary aspects.

The single-copy gene coding for the human parathyroid hormone-like peptide was isolated from a human placental genomic library. The gene spans 13 kilobases and contains seven exons. Exons I and II encode 5'-noncoding regions; each has its own transcription initiation site, and the two promoters are separated by over 1000 base pairs of genomic DNA. Exon III encodes the prepro-coding region, and exon IV encodes the mature peptide sequence. At the end of exon IV the splice site interrupts codon 139 of the mature peptide. Exon V, which is contiguous with exon IV, encodes a stop codon and a 3'-noncoding region. Exon VI encodes 34 additional amino acids, a stop codon, and a second 3'-noncoding region. Exon VII encodes two extra amino acids, a stop codon, and a third 3'-noncoding region. This genomic organization reveals how the multiple human parathyroid hormone-like peptide RNA transcripts, which have been observed, arise by both alternative splicing out of exons and use of multiple promoters. The mRNAs, which can potentially be formed from the primary transcript of this gene, could have one of three different carboxyl-terminal coding regions. The use of different exons to encode the different functional domains, 5'-noncoding region, pre-pro-coding region, and mature peptide region is identical to the organization of the human parathyroid hormone gene. This strongly suggests a common evolutionary origin of the two genes.

Amino Acid Sequence↗
PubMed1986

Molecular analysis of the human class I alcohol dehydrogenase gene family and nucleotide sequence of the gene encoding the beta subunit.

Human alcohol dehydrogenase (ADH) exists as a heterogeneous group of isozymes capable of oxidizing a wide variety of aliphatic and aromatic alcohols. The five distinct human ADH subunits, each encoded by a separate gene, are differentially expressed during development and are subject to tissue-specific regulation. To analyze the organization and regulation of human ADH genes we first isolated a cDNA clone (pADH12) encoding the 3' portion of the beta ADH gene. In the current study pADH12 was used to screen a human genomic library, and several overlapping and nonoverlapping clones were selected. Hybridization and partial nucleotide sequence analyses of the clones indicated that three full-length human ADH genes encoding the alpha, beta, and gamma subunits were isolated. Human genomic DNA hybridization results indicate that the alpha, beta, and gamma ADH genes form a closely related gene family and suggest that the other known human ADH genes (i.e. those encoding the pi and chi subunits) share a more distant evolutionary relationship. Nucleotide sequence analysis of the beta ADH gene reveals that the coding region is interrupted by eight introns and spans approximately 15 kilobases. A presumptive transcription initiation site for the beta ADH gene was located by S1 nuclease mapping at a position 70 base pairs upstream of the start codon. The 5' flanking region possesses a TATA box promoter element as well as two tandem DNA sequences which display homology to previously examined glucocorticoid-responsive elements.

Alcohol Dehydrogenase↗
PubMed1997

Cloning of GPR37, a gene located on chromosome 7 encoding a putative G-protein-coupled peptide receptor, from a human frontal brain EST library.

A cDNA sequence encoding a putative peptide-specific G-protein-coupled receptor (GPR37) was isolated from a set of human brain frontal lobe expressed sequence tags. The GPR37 cDNA predicts a single open reading frame coding for a 613-amino-acid protein with seven hydrophobic transmembrane domains. The GPR37 genomic sequence was mapped to chromosome 7q31, and it was isolated upon screening of a chromosome 7-specific genomic library. The GPR37 gene spans more than 25 kb and contains two exons and a single intron which interrupts the GPR37 cDNA within the sequence encoding the presumed third transmembrane domain. Northern blot analysis with GPR37 probes revealed a main 3.8-kb mRNA and a less abundant 8-kb mRNA, both expressed in human brain tissues, particularly in corpus callosum, medulla, putamen, and caudate nucleus. The lowest level of expression was detected in cerebellum. The 3.8-kb mRNA is also less abundantly expressed in liver and placenta. Although the ligand for the putative GPR37 receptor has not been identified, its deduced amino acid sequence shows a high degree of homology (approximately 40% in the transmembrane regions) with most mammalian peptide-specific G-protein-coupled receptors and particularly with the human endothelin-B, bombesin-BB1, and bombesin-BB2 receptors.

Adult↗
PubMed1994

Isolation and characterization of a species-specific multicopy DNA sequence from Entamoeba histolytica.

A genomic library of Entamoeba histolytica (pathogenic strain HM-1:IMSS) was screened to detect repetitive DNA clones other than those from the highly abundant ribosomal DNA (rDNA). One such clone (HMc) had a 2.3 kb insert which hybridized with the main genome and not the rDNA circle. Southern hybridization of E. histolytica genomic DNA, digested with EcoR I and probed with HMc, showed multiple bands. The banding pattern was identical in all axenic pathogenic strains tested. Differences, however, existed when the banding pattern of a pathogenic strain was compared with that of a non-pathogenic strain. HMc was present in about 25-30 copies per genome in strain HM-1:IMSS. Nucleotide sequence analysis of HMc revealed a partial open reading frame which hybridized with a 1.35 kb poly A+ transcript in Northern blots. The deduced amino acid sequence did not, however, show significant homology with known proteins. The HMc sequence was found only in E. histolytica as it hybridized with 5 different axenic strains of E. histolytica but did not recognize other closely related species of Entamoeba. It has thus the potential to be used as a species-specific DNA probe.

Amino Acid Sequence↗