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At least 19 recordsLinked to original sources
PubMed1990

Sequence homologies, N sequence insertion and JH gene utilization in VHDJH joining: implications for the joining mechanism and the ontogenetic timing of Ly1 B cell and B-CLL progenitor generation.

Sequence analysis of rearranged VHDJH genes of B lineage cells from various stages of ontogeny indicates that short sequence homologies at the breakpoints of recombination contribute to V region gene assembly. Such homologies are regularly seen at DJH junctions of neonatal pre-B cells, most of which do not contain N sequences. In the same cells, but not at later developmental stages, preferential usage of the JH1 element is observed. After birth, N sequence insertion increases with time and is always more prominent at the VHD border than the DJH border. In pre-B cells from adult animals and in mature B cells, in cases where N sequences were not detectable, sequence homologies at the DJH border were found in only half of the instances. This lower incidence could be due to N sequence addition to one of the recombining DNA ends and/or cellular selection. Inspection of VHDJH junctions for N sequence insertion, sequence homologies at the DJH border and JH1 usage allows the estimation of the timepoint in ontogeny at which particular B cell subsets are seeded into the immune system. Specifically, the present data show that the cells of the Ly1 B cell subset are generated not only neonatally but also beyond the first weeks of life. However, the DJH junctions of the progenitors of chronic B cell leukemias which originate from the same B cell subset resemble those of neonatal pre-B cells, suggesting that these cells have already undergone a transforming event at this early developmental stage.

Animals↗
PubMed1990

Nonpathogenic isolates of Yersinia enterocolitica do not contain functional inv-homologous sequences.

Previous studies have demonstrated a correlation between the ability of isolates of Yersinia enterocolitica to cause disease and to invade tissue culture cells in vitro. Two genes, inv and ail, isolated from a pathogenic strain of Y. enterocolitica have each been shown to confer this invasive phenotype upon Escherichia coli. Eighty pathogenic, invasive isolates studied by Miller et al. (Infect. Immun. 57:121-131, 1989) contained sequences homologous to both of these genes. Thirty-five nonpathogenic, noninvasive isolates similarly studied had no ail homology but carried inv-homologous sequences. We investigated inv-homologous sequences from four nonpathogenic isolates. Recombinant clones of these inv-homologous sequences did not confer the invasive phenotype upon E. coli. No RNA transcripts capable of encoding a full-length Inv protein were detected in the four noninvasive Yersinia strains. When the inv gene from a pathogenic isolate was introduced into two of these strains, the resulting transformants invaded tissue culture cells in vitro. The inv gene was transcribed in a pathogenic Yersinia isolate grown at 30 degrees C but not at all in these cells grown at 37 degrees C. The production of RNA transcripts homologous to inv in transformants was not regulated by temperature to the same degree as was seen for pathogenic isolates. We conclude that the inv gene in nonpathogenic strains of Y. enterocolitica is nonfunctional. Y. enterocolitica isolates epidemiologically linked to disease contain both a functional inv gene and a functional ail gene. Environmental isolates not associated with disease have a nonfunctional inv gene and no ail gene.

Gene Expression Regulation, Bacterial↗
PubMed1991

Multiplex polymerase chain reaction amplification and direct sequencing of homologous sequences: point mutation analysis of the ras genes.

ras proto-oncogenes are activated by point mutation in a wide variety of human and animal tumors, making ras gene analysis a major area of clinical and basic cancer research. Activating point mutations, in each of the three ras genes (Ha-, Ki-, or N-ras), usually occur in one of three specific codons (12, 13, or 61). Thus, an adequate assessment of activating ras gene mutations should include the analysis of at least nine codons. We have developed a rapid method for point mutation analysis of the ras genes, which involves simultaneous (multiplex) PCR amplification of all three homologous ras genes (in the regions surrounding codons 12-13 and codon 61) in a single reaction starting with only 1 microgram of genomic DNA. Although multiplex PCR has been previously used for unrelated sequences, we demonstrate here that multiplex PCR can also be used for highly homologous sequences. Importantly, after coamplification, each of the homologous ras genes can be individually and specifically sequenced even though the other two closely related genes are present in the same template mixture, by using high-stringency conditions permitted by Taq DNA polymerase. An automated multicycle DNA sequencing procedure is used to allow the double-stranded PCR products to be sequenced directly without the need to generate single-stranded templates, further simplifying the protocol. Our multiplex PCR amplification and direct DNA sequencing procedures should greatly facilitate more complete analyses of activating ras gene point mutations, particularly in studies involving many tumor samples.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2000

Search for the most stable folds of protein chains: III. Improvement in fold recognition by averaging over homologous sequences and 3D structures.

Three-dimensional (3D) protein fold recognition by query sequence can be improved using information of fold recognition yielded by the sequences homologous to the query one. This idea is now used more and more widely. Our paper presents its consequent development. We suggest incorporating information both on the sequences homologous to the query protein sequence and the 3D structures homologous to the target (already deciphered) protein folds. We show that both these tricks, and especially their combination reduces errors in fold recognition by the threading method. Proteins 2000;40:494-501.

Amino Acids↗
PubMed1999

Effect of distance between homologous sequences and 3' homology on the frequency of retroviral reverse transcriptase template switching.

Deletion of direct repeats in retroviral genomes provides an in vivo system for analysis of reverse transcriptase (RT) template switching. The effect of distance between direct repeats on the rate of deletion was determined for 16 murine leukemia virus (MLV)-based vectors containing a 701-bp direct repeat of overlapping fragments of the herpes simplex virus thymidine kinase gene (HTK). The direct repeats were separated by spacer fragments of various lengths (0.1 to 3.5 kb). Southern analysis of infected cells after one replication cycle indicated that all vectors in which the distance between homologous sequences was >1,500 bp deleted at very high rates (>90%). In contrast, vectors containing <1,500 bp between homologous sequences exhibited lower frequencies of deletion (37 to 82%). To analyze the pattern of locations at which RT switched templates, restriction site markers were introduced to divide the downstream direct repeat into five regions. RT switched templates within all five regions of the 701-bp direct repeat and the frequency of template switching was greater within the 5' regions in comparison to the 3' regions. The probability of RT switching templates within the 5' regions doubled when the MLV packaging sequence (Psi) was placed between the 701-bp direct repeats. However, Psi did not increase the rate of template switching for shorter direct repeats. These results indicate that linear distance between homologous sequences increases the rate of template switching and suggest that duplex formation between nascent DNA and homologous template sequences 3' of RT promote template switching.

Animals↗
PubMed1997

Minimum length of sequence homology required for in vivo cloning by homologous recombination in yeast.

With efficient homologous recombination in Saccharomyces cerevisiae, a rapid in vivo cloning technique has been available. Here we demonstrated that 30 bp of a homologous sequence at each end of a DNA fragment is sufficient to integrate the fragment into a linearized plasmid in yeast. To obtain a high yield of recombination transformants, however, more than 60 bp are desirable. Interestingly, we observed that 20 bp of homology at one end of a DNA fragment is sufficient for efficient recombination provided that the other end contains 80 bp of homologous sequence. Some applications, including high-throughput transferring of EST inserts to the yeast expression systems for the Human Genome Project, are discussed.

Animals↗
PubMed1988

Restriction fragment length polymorphism and multiple copies of DNA sequences homologous with probes for P-fimbriae and hemolysin genes among uropathogenic Escherichia coli.

Hemolysin and P-fimbriae are two virulence traits frequently found together in uropathogenic Escherichia coli. Previous studies have discovered evidence both for linkage between the genes for these traits and for their duplication in the chromosomes of a limited number of strains. To test whether these observations are characteristic of uropathogenic Escherichia coli, the method of DNA hybridization to DNA restriction fragments separated by electrophoresis and transferred to nylon was used to determine copy number of genes for P-fimbriae (pap) among 51 E. coli strains isolated from symptomatic urinary tract infections. Twenty percent of the strains had more than one copy of pap homologous sequences. Fifteen strains, each representing a unique clone, were examined for the presence of sequences homologous with cloned hemolysin genes (hly). Samples of DNA from 14 of the 15 strains hybridized with hly probes. In eight strains the number of copies of pap equalled the number of copies of hly, including one strain with two apparent copies of each. Five strains appeared to have one more copy of pap than of hly, and one strain had an extra copy of hly.

Autoradiography↗
PubMed1991

X/Y translocations resulting from recombination between homologous sequences on Xp and Yq.

Several regions of sequence homology between the human X and Y chromosomes have been identified. These segments are thought to represent areas of these chromosomes that have engaged in meiotic recombination in relatively recent evolutionary times. Normally, the X and Y chromosomes pair during meiosis and exchange DNA only within the pseudoautosomal region at the distal short arms of both chromosomes. However, it has been suggested that aberrant recombination involving other segments of high homology could be responsible for the production of X/Y translocations. We have studied four X/Y translocation patients using molecular probes detecting homologous sequences on X and Y chromosomes. In one translocation the breakpoints have been isolated and sequenced. The mapping data are consistent with the hypothesis that X/Y translocations arise by homologous recombination. The sequencing data from one translocation demonstrate this directly.

Base Sequence↗
PubMed1980

Nucleotide sequence homology between the heat-labile enterotoxin gene of Escherichia coli and Vibrio cholerae deoxyribonucleic acid.

Isolated deoxyribonucleic acid fragments encoding the heat-labile enterotoxin of Escherichia coli were used to probe for homologous sequences in restricted whole-cell deoxyribonucleic acid from Vibrio cholerae. Significant sequence homology between the heat-labile enterotoxin gene and V. cholerae deoxyribonucleic acid was demonstrated, and apparent differences were observed in the organization of the cholera toxin gene among different strains of V. cholerae.

Base Sequence↗
PubMedDate not supplied

Sequences homologous to the listeriolysin O gene region of Listeria monocytogenes are present in virulent and avirulent haemolytic species of the genus Listeria.

Various parts of the hlyA gene region of Listeria monocytogenes which encodes a major virulence factor, listeriolysin O, have been used to detect the presence of homologous sequences in other species of the genus Listeria. Under low-stringency hybridization conditions, sequences homologous to the hlyA gene and its 5' adjacent regions were detected in the haemolytic and pathogenic species L. ivanovii, and in the haemolytic but non-pathogenic species L. seeligeri. In contrast, the region located downstream from hlyA appeared specific to L. monocytogenes. None of the probes spanning the region revealed homologies between L. monocytogenes and the non-pathogenic and non-haemolytic members of the genus, L. innocua, L. murrayi and L. welshimeri. Among various strains of L. monocytogenes tested, the gene hlyA and its 3' adjacent region appeared well-conserved. In contrast, a restriction length polymorphism was detected in the region located upstream from hlyA with no obvious correlation with the haemolytic phenotype or the serovar of the strains tested.

Bacterial Toxins↗
PubMed1993

Gypsy homologous sequences in Drosophila subobscura (gypsyDS).

Characterization of sequences homologous to the Drosophila melanogaster gypsy transposable element was carried out in Drosophila subobscura (gypsyDS). They were found to be widely distributed among natural populations of this species. From Southern blot and in situ analyses, these sequences appear to be mobile in this species. GypsyDS sequences are located in both euchromatic and heterochromatic regions. A complete gypsyDS sequence was isolated from a D. subobscura genomic library, and a 1.3-kb fragment which aligns with the ORF2 of the D. melanogaster gypsy element was sequenced. Comparisons of this sequence in three species (D. subobscura, D. melanogaster, and D. virilis) indicate that there is greater similarity between the D. subobscura-D. virilis sequences than between D. subobscura and D. melanogaster. Molecular divergence of gypsy sequences between D. virilis and D. subobscura is estimated at 16 MY, whereas the most likely divergence time of these two species is more than 60 MY. These data strongly suggest that gypsy sequences have been horizontally transferred between these species.

Amino Acid Sequence↗
PubMed1979

Deoxyribonucleic acid sequence homologies among bacterial insertion sequence elements and genomes of various organisms.

Plasmid and phage deoxyribonucleic acid (DNA) harboring bacterial insertion sequence (IS) elements IS1, IS2, and IS5 were characterized and used as probes to detect homologous sequences in various procaryotic and eucaryotic genomes. The hybridization method used permits the detection of sequences partially homologous to the elements. Hybridization of the IS-containing probes to each other revealed a region of limited homology between IS1 and IS2. Homologous sequences were then detected by computer analysis of the published IS1 and IS2 nucleotide sequences. The homologous sequence contains a tandemly repeated tetranucleotide sequence which resembles the repeated sequence at the hot spot for spontaneous mutations in the lacI gene (P. J. Farabaugh, U. Schmeissner, M. Hofer, and J. Miller, J. Mol. Biol. 126:847-863, 1978). Homology between the IS elements and various genomes was determined by hybridizing labeled DNA containing IS1, IS2, and IS5 sequences to Southern blots of chromosomal DNA cleaved with restriction endonucleases. IS1 and IS5 appear limited to the enteric bacteria, whereas IS2 sequences can also be detected in Pseudomonas putida, Pseudomonas aeruginosa, and Serratia marcescens. Bacteria which appear not to possess extrachromosomal elements, e.g., Caulobacter crescentus, did not show homology with any insertion sequences tested. In addition, sequences homologous to IS1, IS2, or IS5 were not detected in Saccharomyces cerevisiae, Dictyostelium discoideum, or calf thymus DNA.

Bacteria↗
PubMed1984

Nucleotide sequence homology between the immunoglobulin A1 protease genes of Neisseria gonorrhoeae, Neisseria meningitidis, and Haemophilus influenzae.

Isolated DNA fragments encoding the immunoglobulin A1 (IgA1) protease of Neisseria gonorrhoeae were used as hybridization probes to search for homologous sequences in whole cell DNA from Neisseria meningitidis and Haemophilus influenzae. Significant homology was detected. That the detected homology represented IgA1 protease-specific sequences was confirmed by the cloning of these sequences in Escherichia coli HB101 and demonstrating the expression of IgA1 protease by these transformed cells. Molecular probing of commensal Neisseria and Haemophilus species, which do not elaborate IgA1 protease activity, revealed that they were devoid of sequence homology with the cloned IgA1 protease gene DNA.

Base Sequence↗
PubMed2006

Sequence homology of polymorphic AFLP markers in garlic (Allium sativum L.).

Linkage mapping and genetic diversity studies with DNA markers in plant species assume that comigrating bands are identical, or at least that they have homologous sequences. To test this assumption in a plant with a large genome, sequence identities of 7 polymorphic amplified fragment length polymorphism (AFLP) markers of garlic, previously used to estimate similarity in genetic diversity studies, were characterized. Among 37 diverse garlic clones, 87 bands from these 7 polymorphisms were excised, amplicons were cloned, and 2 to 6 colonies were sequenced from each band, to yield a total of 191 DNA amplicons. Of these 87 bands, 83 bands (95.4%) contained AFLP amplicons that were identical or highly homologous to the typical marker of that band; only 4 bands contained amplicons with little homology to the same-sized amplicons of other garlic clones. Of these 83 bands, 64 (73.6%) contained only highly homologous amplicons (>90% sequence identity), whereas 19 (21.8%) contained both homologous and nonhomologous amplicons, with sequence identities less than 60%. Of the 37 nonhomologous amplicons identified, 25 (67.5%) differed in length from other amplicons in the band. Sequence conservation of AFLP amplicons followed patterns similar to phylogenetic relationships among garlic clones, making them useful for developing simple PCR-based markers in genetic mapping and diversity assessment.

Base Sequence↗
PubMed1999

A P element-homologous sequence in the house fly, Musca domestica.

Sequences homologous to the P transposable element have been identified in Musca domestica. Sequence analysis of a genomic clone (Md-P1) indicates that, although the house fly P element has lost its coding capacity, the basic general structure of drosophilid P elements is present. The house fly P element sequence shares a number of structural features with that from the blow fly, Lucilia cuprina, including a large intron separating exons 1 and 2, two additional introns interrupting exon 2 and the apparent absence of inverted repeat termini. Within a relatively well-conserved central region, the house fly sequence shows 59% similarity to the D. melanogaster P element, but distal regions are more diverged. Southern blot analysis of several strains indicated the presence of at least four P element copies.

Amino Acid Sequence↗
PubMed1985

A sequence from Drosophila DNA cross-hybridizing with a mouse class I H-2 gene: absence of relevant nucleic acid or amino acid sequence homology.

Following serological data (1) showing cross-reactivity of drosophila surface antigens with anti-H-2 and mouse beta 2-microglobulin (beta 2-m) antisera, we have looked for homologous sequences in the drosophila genome by low stringency hybridization with mouse H-2 and beta 2-m probes. A 240 bp drosophila DNA segment cross-hybridizing with a H-2 probe, was isolated and sequenced. No homology at the nucleotide or amino acid levels was found with the mouse probe which was used, except for a perfectly matching 16-mer containing 11 G-C, which might be responsible for the cross-hybridization. Therefore, our present data do not support the existence of class I H-2 and/or beta 2-m related gene sequences in the drosophila genome.

Amino Acid Sequence↗
PubMed1994

(CAC)5 detects DNA fingerprints and sequences homologous to gene transcripts in rice.

In the present report the potential of (CAC)5 is demonstrated for DNA fingerprinting in rice. Based on the fingerprint data, (CAC)5 was estimated to differentiate up to 6.3 x 10(8) genotypes of rice. In a search for homologous sequences in rice transcripts, four oligonucleotide probes, namely, (CAC)5, (GATA)4, (GACA)4, and (TG)10, were used. Among these probes, (CAC)5 showed hybridization to total rice RNA in a tissue-specific manner; while a band at 1.2 kb was common in both seed and leaf RNA, there were additional prominent bands at 1.9 and 2.3 kb in seed and leaf RNA, respectively. When (CAC)5 was hybridized to poly(A)+ RNA, in addition to a band at 1.2 kb in seed and leaf, hybridization was observed only in seed to heterogeneously sized RNAs.

Base Sequence↗
PubMed1992

[The construction of genomic library of Alcaligenes faecalis and cloning of nifH gene sequence homologous to Klebsiella pneumoniae].

A genomic library of Alcaligenes faecalis A-15Hl which possesses rather high nitrogenase activity has been constructed. The total DNA of A. faecalis A-15 Hl was partially digested with Sau3AI. 13-20 kb of fragments recovered from agarose gel were cloned in bacteriophage EM-BL4 vector. A total number of 1.2 x 10(6) of recombinants was obtained. It is much beyond the desired capacity of a library. By using nifH gene of K. pneumoniae from plasmid pGB1 as probe, we have successfully screened the clone containing its homologous sequence. The recombinant bacteriophage DNA was digested with EcoRI. A 3.5 kb of hybridizing band appeared after southern blotting and then was cloned in pUC19 DNA. The result of southern blotting indicated that the recombinant plasmid clone contained nifH gene sequence of A. faecalis. This clone was named as pAFH.

Alcaligenes↗