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At least 703 records · Page 39Linked to original sources
PubMed1995

Molecular cloning and sequencing of the gene encoding a sheep arginine vasopressin type 1a receptor.

The gene for the sheep arginine vasopressin type 1a (V1a) receptor subtype was cloned from a genomic library. The deduced amino acid sequence shows characteristics of a G-protein coupled receptor and high sequence identity to human and rat V1a receptor sequences (81% and 73%, respectively). Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed a tissue distribution consistent with a type V1a receptor. The genomic DNA (7.1 kb) contains a 1586 bp intron between the putative 6th and 7th transmembrane domains.

Amino Acid Sequence↗
PubMed2000

Listeriolysin O as a reporter to identify constitutive and in vivo-inducible promoters in the pathogen Listeria monocytogenes.

Listeria monocytogenes is a facultative intracellular gram-positive bacterium capable of growing in the cytoplasm of infected host cells. Bacterial escape from the phagosomal vacuole of infected cells is mainly mediated by the pore-forming hemolysin listeriolysin O (LLO) encoded by hly. LLO-negative mutants of L. monocytogenes are avirulent in the mouse model. We have developed a genetic system with hly as a reporter gene allowing the identification of both constitutive and in vivo-inducible promoters of this pathogen. Genomic libraries were created by randomly inserting L. monocytogenes chromosomal fragments upstream of the promoterless hly gene cloned into gram-positive and gram-negative shuttle vectors and expressed in an LLO-negative mutant strain. With this hly-based promoter trap system, combined with access to the L. monocytogenes genome database, we identified 20 in vitro-transcribed genes, including genes encoding (i) p60, a previously known virulence gene, (ii) a putative new hemolysin, and (iii) two proteins of the general protein secretion pathway. By using the hly-based system as an in vivo expression technology tool, nine in vivo-induced loci of L. monocytogenes were identified, including genes encoding (i) the previously known in vivo-inducible phosphatidylinositol phospholipase C and (ii) a putative N-acetylglucosamine epimerase, possibly involved in teichoic acid biosynthesis. The use of hly as a reporter is a simple and powerful alternative to classical methods for transcriptional analysis to monitor promoter activity in L. monocytogenes.

Amino Acid Sequence↗
PubMed2003

Structural analysis of a Lotus japonicus genome. V. Sequence features and mapping of sixty-four TAC clones which cover the 6.4 mb regions of the genome.

We determined the nucleotide sequences of 64 TAC (transformation-competent artificial chromosome) clones selected from genomic libraries of Lotus japonicus accession Miyakojima MG-20 based on the sequence information of expressed sequence tags (ESTs), cDNAs, genes and DNA markers from L. japonicus and other legumes. The length of the DNA regions sequenced in this study was 6,370,255 bp, and the total length of the L. japonicus genome sequenced so far is 32,537,698 bp together with the nucleotide sequences of 256 TAC clones previously reported. Five hundred forty-eight potential protein-encoding genes with known or predicted functions, 127 gene segments and 224 pseudogenes were assigned to the newly sequenced regions by computer prediction and similarity searches against the sequences in protein and EST databases. Based on the nucleotide sequences of the clones, simple sequence repeat length polymorphism (SSLP) or derived cleaved amplified polymorphic sequence (dCAPS) markers were generated, and each clone was genetically localized onto the linkage map of two accessions of L. japonicus, MG-20 and Gifu B-129. The sequence data, gene information and mapping information are available through the World Wide Web at http://www.kazusa.or.jp/lotus/.

Base Sequence↗
PubMed1999

Genomic structure of phage B40-8 of Bacteroides fragilis.

Very few data are available on the molecular biology of Bacteroides fragilis bacteriophages, which have been considered in several studies as indicators of faecal contamination. Phage B40-8, initially isolated from an urban sewage sample using a strain of B. fragilis (HSP40) isolated from a clinical specimen, was chosen in this study as a prototype for morphological and molecular studies. Like most of the phages infective for B. fragilis, B40-8 belongs to the Siphoviridae family. Its genome has been found to be a double-stranded DNA molecule, of approximately 51.7 kb, containing a rather low percentage (38.9 mol%) of G + C. The ends of the molecule appeared not to be cohesive but permuted, with a terminal redundancy of 7.3%. A genomic map was constructed. Three major proteins (MP) out of 15 peptides in the SDS-PAGE profile were selected for N-terminal sequencing. From these data, degenerate probes were designed to locate the ORFs in the genomic map. Immunodetection by electron microscopy revealed that MP1 and MP3 were structural proteins of the phage head and that MP2 was a constituent of the tail. A genomic library of the phage was prepared, and a clone including the MP2 ORF was identified and sequenced.

Amino Acid Sequence↗
PubMed2006

[Length polymorphism of integrated copies of R1 and R2 retrotransposons in the German cockroach (Blattella germanica) as a potential marker for population and phylogenetic studies].

Using polymerase chain reaction technique with primers flanking target sites of retrotransposons R1 and R2, integrated copies of these transposable elements were amplified in various cockroach species (Blattodea). It was shown that each species has a unique pattern of "5'-undertranscripts" with the definite set of amplified fragments of different lengths. Intraspecies polymorphism was revealed in analysis of German cockroach specimens obtained upon individual mating. This is the first report providing results of identifying, cloning, and sequencing extended fragments (5'-truncated copies) of Blatella germanica R1 and R2 retrotransposons. It may be assumed that patterns of 5'-truncated copies of R1 and R2 elements can be used as markers in population and phylogenetic studies. Moreover, cloned and sequenced fragments will be employed in our further studies for screening of the German cockroach genomic library in order to detect full-length copies in this class transposable elements.

Animals↗
PubMed1996

Diversity of the Tcra-V3 gene family in BALB/c mice.

Southern analysis of Eco RI-digested BALB/c liver DNA reveals four T-cell receptor Tcra-V3-hybridizing DNA fragments, which are of sizes 18.0, 12.0, 8.0, and 2.1 kilobases, respectively. These four Tcra-V3-hybridizing genomic DNA were isolated from a BALB/c genomic library. Restriction and Southern analysis of the genomic DNA clones showed that each of the Tcra-V3-hybridizing Eco RI DNA fragments harbors only a single Tcra-V3 gene. The DNA sequences of coding regions of the four Tcra-V3 family members were determined. These sequences show very limited divergence from one another. Comparisons of BALB/c Tcra-V3 sequences with published Tcra-V3 sequences expressed in different strains of mice reveal substantial allelic polymorphism. Sequence similarity searches retrieved homologous rat, cattle, and human genes. The scarcity of coding sequence divergence among members of the Tcra-V3 family and the more substantial allelic polymorphism may be general features of the T-cell receptor V-alpha chain-encoding gene families.

Amino Acid Sequence↗
PubMed1993

Analysis of the gene family encoding the Entamoeba histolytica galactose-specific adhesin 170-kDa subunit.

The 170-kDa or heavy subunit of the galactose binding adhesin of Entamoeba histolytica is seminal in target cell binding and lysis. To determine the existence and complexity of the 170-kDa subunit gene family, hgl, an amebic genomic library in lambda phage was hybridized with DNA fragments from the 5' or 3' ends of hgl1. Termini from three distinct heavy subunit genes were identified including hgl1, hgl2, and a third, unreported gene designated hgl3. The open reading frame of hgl3 was sequenced in its entirety. Non-stringent hybridization of a genomic Southern blot with heavy subunit specific DNA labeled only those bands predicted by hgl1-3. The amino acid sequence of hgl3 was 95.2% identical to hgl1 and 89.4% identical to hgl2. All 97 cysteine residues present in the heavy subunit were conserved in hgl1-3. Analysis of amebic RNA showed that all three heavy subunit genes were expressed in the amebae and that hgl message became less abundant as the amebae entered a stationary growth phase.

Amino Acid Sequence↗
PubMed1989

Maize phosphoenolpyruvate carboxylase involved in C4 photosynthesis: nucleotide sequence analysis of the 5' flanking region of the gene.

To clone the genomic DNA fragment containing the putative promoter region of the gene for phosphoenolpyruvate carboxylase [EC 4.1.1.31] involved in C4 photosynthesis (C4-type PEPC), maize genomic libraries were screened. On probing with a 384-bp fragment from the N-terminal coding region of the maize cDNA for C4-type PEPC, four EcoRI-fragments differing in the restriction map were cloned, reflecting the presence of a small gene family. Southern blot analyses were carried out on the genomic DNA and the cloned DNA fragments using several segments of the cDNA for C4-type PEPC as probes. The results indicated that the C4-type PEPC is encoded by a single gene and the cloned 7.0-kb fragment was derived from this gene. The transcription start site, as determined in a primer extension experiment, was located at about 4 kb downstream of the 5' end of the cloned fragment. The nucleotide sequence was determined for the region which extended about 1 kb upstream from the transcription start site and possible signal sequences related to gene expression were found, including four classes of direct repeats. The sequences of the corresponding regions of the other two cloned fragments (8.9 and 12.9 kb) which strongly hybridized with the 384-bp probe were very similar to each other, but they were quite different in the 5' upstream region from the sequence of the gene for C4-type PEPC.

Base Sequence↗
PubMed1992

Development of a species-specific DNA probe for Mycoplasma capricolum.

A specific DNA probe for the detection and identification of Mycoplasma capricolum, one of the causative agents of contagious agalactia syndrome, was selected from a genomic library. It consists of a 900bp RsaI genomic fragment of M. capricolum (reference strain), cloned into the EcoRV site of the plasmid Bluescript. By using the appropriate stringency this radiolabelled probe reacts specifically with M. capricolum when tested by dot blot hybridization against various mycoplasmal DNAs. The current level of sensitivity of the 32P-labelled 900bp RsaI probe is 500 pg of homologous DNA, corresponding to 5 x 10(4) mycoplasmas. A non radioactive labelling method, using the digoxigenin-11-dUTP, was also tested. The specificity of the digoxigenin-labelled probe was equivalent to that obtained with the radioactive probe. However the sensitivity of detection decreased to 1 ng of homologous DNA detected, corresponding to 1 x 10(5) mycoplasmas. Tests performed with milk samples have demonstrated that the radioactive 900 bp RsaI probe indeed detected M. capricolum contained in milk. A positive signal was obtained when 10(5) M. capricolum were present in the spot.

Animals↗
PubMed1997

Fission yeast dihydrolipoamide dehydrogenase gene is involved in G1/S cell cycle progression.

Using functional complementation with a Schizosaccharomyces pombe genomic library, we have isolated a clone complementing a G1/S phase progression defective mutant. The newly isolated temperature-sensitive mutant, cyj150, showed elongated morphology at a restrictive temperature of 36 degrees C and DNA content analysis of the mutant indicated a defect in cell cycle progression at the G1/S phase. Sequence analysis of the genomic and cDNA clones complementing this elongated phenotype at 36 degrees C show that it encodes a protein that has 50% amino acid identity with dihydrolipoamide dehydrogenase from Saccharomyces cerevisiae and garden pea. Alignment of the deduced amino acid sequence of S. pombe dihydrolipoamide dehydrogenase (dld1+) with glutathione reductase and mercuric reductase revealed extensive homologies throughout the primary sequence and protein structure, and contained amino acid sequences of the active site region conserved from prokaryote to higher eukaryote. Gene disruption and tetrad analysis showed that dld1+ is an essential gene for cell viability. Northern analysis indicates that transcriptional expression of this gene is not fluctuated according to the cell cycle. However, it is certain that malfunction of this Dld1 protein blocks the progression of cell cycle from G1 to S phase. The sequence of the dld1+ gene is available in EMBL/GenBank under Accession Number L40360.

Amino Acid Sequence↗
PubMed2002

Development of a Brucella suis specific hybridisation probe and PCR which distinguishes B. suis from Brucella abortus.

A genomic library was prepared from Brucella suis DNA (MboI digested) and cloned into the BamHI site of pUC18. Colony hybridisation using a probe prepared from purified B. suis DNA labelled with alpha 32P was carried out to identify colonies of interest. About 20 colonies, which gave an intense signal upon hybridisation with whole B. suis genomic DNA as a probe, were selected. Because of the high degree of DNA homology between B. suis and Brucella abortus, a short probe was chosen as it would more likely give species specificity. Of seven fragments selected to probe whole B. suis, B. abortus, and Yersinia enterocolitica DNA, one was found to hybridise with B. suis only. The probe was sequenced in two directions and sense and anti sense primers of 25bp in length were chosen to yield a product of 421bp. After optimisation of the PCR, a product of 420bp was obtained with B. suis template DNA and two bands of 420 and 650bp were detected with B. abortus template DNA. This is the first reported PCR of the Brucella genome where a single pair of primers will discriminate between B. suis and B. abortus. No band was observed when the two primers were used to amplify E. coli, Y. enterocolitica, Enterobacter cloacae, Staphylococcus aureus, Streptococcus uberis, Corynebacterium bovis, or Serratia marcescens template DNA.

Animals↗
PubMedDate not supplied

A general coverage theory for shotgun DNA sequencing.

The classical theory of shotgun DNA sequencing accounts for neither the placement dependencies that are a fundamental consequence of the forward-reverse sequencing strategy, nor the edge effect that arises for small to moderate-sized genomic targets. These phenomena are relevant to a number of sequencing scenarios, including large-insert BAC and fosmid clones, filtered genomic libraries, and macro-nuclear chromosomes. Here, we report a model that considers these two effects and provides both the expected value of coverage and its variance. Comparison to methyl-filtered maize data shows significant improvement over classical theory. The model is used to analyze coverage performance over a range of small to moderately-sized genomic targets. We find that the read pairing effect and the edge effect interact in a non-trivial fashion. Shorter reads give superior coverage per unit sequence depth relative to longer ones. In principle, end-sequences can be optimized with respect to template insert length; however, optimal performance is unlikely to be realized in most cases because of inherent size variation in any set of targets. Conversely, single-stranded reads exhibit roughly the same coverage attributes as optimized end-reads. Although linking information is lost, single-stranded data should not pose a significant assembly liability if the target represents predominantly low-copy sequence. We also find that random sequencing should be halted at substantially lower redundancies than those now associated with larger projects. Given the enormous amount of data generated per cycle on pyro-sequencing instruments, this observation suggests devising schemes to split each run cycle between twoor more projects. This would prevent over-sequencing and would further leverage the pyrosequencing method.

Computational Biology↗
PubMed1990

Multiple forms of chicken alpha 3(VI) collagen chain generated by alternative splicing in type A repeated domains.

Type VI collagen is a structurally unique component widely distributed in connective tissues. Its molecular structure consists of monomers that have the potential to assemble intracellularly into dimers and tetramers which, once secreted, can form microfilaments by end-to-end association. Individual monomers are composed of chains of Mr = approximately 140,000 (alpha 1 and alpha 2) and greater than 300,000 (alpha 3). Type VI collagen molecules contain a short triple helix with large globular domains at both ends. These domains are made for their greatest part of repetitive units similar to type A repeats of von Willebrand Factor. The alpha 3(VI) chain, contributing most of the mass of the NH2-terminal globule, appeared heterogenous both at the mRNA and protein level. Several alpha 3(VI)-specific clones that lack the sequences corresponding to repeats A8 and A6 were isolated from a chicken aorta cDNA library. Northern blot hybridization of poly (A+)-enriched RNA from chicken gizzard with cDNA fragments corresponding to several individual type A repeats showed that A8- and A6-specific probes did not hybridize to the lower Mr transcripts. Clones spanning approximately 20 kb of the 5'-end of the alpha 3(VI) gene were isolated from a chicken genomic library and subjected to analysis by restriction mapping, Southern blotting, and selective sequencing of the intron-exon boundaries. At the most 5'-end of the gene an additional type A repeat (A9), previously undetected in cDNA clones, was identified. Furthermore, it was determined that the presumed signal peptide and repeats A9 through A6 are encoded within individual exons. Reverse transcription and polymerase chain reaction of aorta RNA suggested that a mechanism of alternative mRNA splicing by a phenomenon of exon skipping generates alpha 3(VI) isoform variants that contain different numbers of type A repeats. Immunohistochemistry of frozen sections of chicken embryo tissues with repeat-specific mAbs showed that an antibody directed against a conditional exon has a more restricted tissue distribution compared to an antibody against a constitutive exon.

Amino Acid Sequence↗
PubMed1995

Human liver mitochondrial carnitine palmitoyltransferase I: characterization of its cDNA and chromosomal localization and partial analysis of the gene.

Using the cDNA for rat liver mitochondrial carnitine palmitoyltransferase I (CPT I; EC 2.3.1.21) as a probe, we isolated its counterpart as three overlapping clones from a human liver cDNA library. Both the nucleotide sequence of the human cDNA and the predicted primary structure of the protein (773 aa) proved to be very similar to those of the rat enzyme (82% and 88% identity, respectively). The CPT I mRNA size was also found to be the same (approximately 4.7 kb) in both species. Screening of a human genomic library with the newly obtained cDNA yielded a positive clone of approximately 6.5 kb which, upon partial analysis, was found to contain at least two complete exons linked by a 2.3-kb intron. Oligonucleotide primers specific to upstream and downstream regions of one of the exon/intron junctions were tested in PCRs with DNA from a panel of somatic cell hybrids, each containing a single human chromosome. The results allowed unambiguous assignment of the human liver CPT I gene to the q (long) arm of chromosome 11. Additional experiments established that liver and fibroblasts express the same isoform of mitochondrial CPT I, legitimizing the use of fibroblast assays in the differential diagnosis of the "muscle" and "hepatic" forms of CPT deficiency. The data provide insights into the structure of a human CPT I isoform and its corresponding gene and establish unequivocally that CPT I and CPT II are distinct gene products. Availability of the human CPT I cDNA should open the way to an understanding of the genetic basis of inherited CPT I deficiency syndromes, how the liver CPT I gene is regulated, and which tissues other than liver express this particular variant of the enzyme.

Amino Acid Sequence↗
PubMed1990

Selective amplification of an mRNA and related pseudogene for a human ADP-ribosylation factor, a guanine nucleotide-dependent protein activator of cholera toxin.

ADP-ribosylation factors (ARFs) are approximately 20-kDa proteins that act as GTP-dependent allosteric activators of cholera toxin. With deoxyinosine-containing degenerate oligonucleotide primers corresponding to conserved GTP-binding domains in ARFs, the polymerase chain reaction (PCR) was used to amplify simultaneously from human DNA portions of three ARF genes that include codons for 102 amino acids, with intervening sequences. Amplification products that differed in size because of differences in intron sizes were separated by agarose gel electrophoresis. One amplified DNA contained no introns and had a sequence different from those of known ARFs. Based on this sequence, selective oligonucleotide probes were prepared and used to isolate clone psi ARF 4, a putative ARF pseudogene, from a human genomic library in lambda phage EMBL3. Reverse transcription-PCR was then used to clone from human poly(A)+ RNA the cDNA corresponding to the expressed homolog of psi ARF 4, referred to as human ARF 4. It appears that psi ARF 4 arose during human evolution by integration of processed ARF 4 mRNA into the genome. Human ARF 4 differs from previously identified mammalian ARFs 1, 2, and 3. Hybridization of ARF 4-specific oligonucleotide probes with human, bovine, and rat RNA revealed a single 1.8-kilobase mRNA, which was clearly distinguished from the 1.9-kilobase mRNA for ARF 1 in these tissues. The PCR provides a powerful tool for investigating diversity in this and other multigene families, especially with primers targeted at domains believed to have functional significance.

ADP-Ribosylation Factors↗
PubMed1995

Highly repetitive DNA sequence elements from Orseolia oryzae (Wood-Mason) discriminate between the Indian isolates and the Asian rice gall midge and the paspalum midge.

We described multicopy DNA clones isolated from a partial genomic library of Orseolia oryzae, based on reverse genomic hybridization, suitable for studying genetic variation in the Asian rice gall midge and other isomorphic species. Three clones produced monomorphic DNA band patterns between biotypes of O. oryzae but polymorphic patterns were produced between O. oryzae and O. fluvialis, the paspalum midge. These probes detect changes in the repetitive sequence structure between species and constitute the first genetic markers for distinguishing between field isolates of rice gall midge and related species of Orseolia. These will be useful in identifying and perhaps eradicating alternative hosts for this pest, and detecting early-season outbreaks of O. oryzae from light trap collections.

Animals↗
PubMed1993

Canine distemper terminal and intergenic non-protein coding nucleotide sequences: completion of the entire CDV genome sequence.

Sequences critical for the transcription and replication functions of canine distemper virus (CDV) RNA polymerase were analyzed. The sequence was obtained from polymerase chain reaction (PCR) products using either c-DNA clones from a genomic library as template or in most instances genomic CDV RNA. Clones coding for the precise 3'- and 5'-ends of the CDV genome were sequenced and the results confirmed by additional PCR experiments. The virtual identity of terminal sequences and spacing at the two noncoding ends speak to the importance of these areas in replication and transcription. The sequence for each of the CDV gene boundaries was defined and all were compared to related viruses. This report completes the sequence determination of the CDV genome.

Base Sequence↗
PubMed1995

Features of the hmg 1 subfamily of genes encoding HMG-CoA reductase in potato.

3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes a key step in isoprenoid metabolism leading to a range of compounds that are important for the growth, development and health of the plant. We have isolated 7 classes of genomic clones encoding HMGR from a potato genomic library. Comparison of nucleic acid sequences reveals a high degree of identity between all seven classes of clones and the potato hmg 1 gene described by Choi et al. (Plant Cell 4: 1333, 1992), indicating that all are members of the same subfamily in potato. A representative member (hmg 1.2) of the most abundant class of genomic clones was selected for further characterization. Transgenic tobacco and potato containing the beta-glucuronidase (GUS) reporter gene under the control of the hmg 1.2 promoter expressed GUS activity constitutively at a low level in many plant tissues. High levels of GUS activity were observed only in the pollen. GUS assays of isolated pollen, correlations of GUS activity with the HMGR activity of anthers, hmg 1.2 promoter deletion studies, and segregation analysis of the expression of hmg 1.2::GUS among the R2 pollen of R1 progeny plants demonstrated that the hmg 1.2 promoter controls pollen expression.

Amino Acid Sequence↗