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At least 1,261 records · Page 70Linked to original sources
PubMed1999

Abnormalities at 14q32.1 in T cell malignancies involve two oncogenes.

The TCL1 oncogene on human chromosome 14q32.1 is involved in the development of T cell leukemia in humans. Its expression in these leukemias is activated by chromosomal translocations and inversions at 14q32.1. Here we report the isolation and characterization of a new member of the TCL1 gene family, TCL1b, located approximately 16 kb centromeric of TCL1. The 1.2-kb TCL1b cDNA encodes a 14-kDa protein of 128 aa and shows 60% similarity to Tcl1. Expression profiles of TCL1 and TCL1b genes are very similar: both genes are expressed at very low levels in normal bone marrow and peripheral lymphocytes but are activated in T cell leukemia by rearrangements of the 14q32.1 region. Thus, translocations and inversions at 14q32. 1 in T cell malignancies involve two oncogenes.

Amino Acid Sequence↗
PubMed2005

The Shigella flexneri serotype Y vaccine candidate SFL124 originated from a serotype 2a background.

Shigella flexneri is endemic in most developing countries and responsible for the highest mortality rate among the Shigella species. The attenuated serotype Y S. flexneri strain SFL124 has been used as the parental strain for the development of recombinant vaccines expressing multiple O-antigen structures. During the development of one such multivalent vaccine, a region of gtrII homology was found in SFL124. Sequencing and analysis of this region revealed the presence of an insertion element interrupted serotype 2a serotype-conversion locus in the serotype Y vaccine strain SFL124. The data presented suggests that SFL124 has derived from a serotype 2a background.

Base Sequence↗
PubMed1992

Recombination in vitro between herpes simplex virus type 1 a sequences.

We have partially purified an activity from extracts of cells infected with herpes simplex virus type 1 that mediates recombination between repeated copies of the 317-base-pair a sequence of herpes simplex virus type 1. Recombination leads to deletion of a lacZ indicator gene situated between two directly repeated copies of the a sequence and is scored by transformation of lacZ- Escherichia coli. The two products of the reaction can be observed directly by restriction enzyme digestion and Southern blot analysis. The recombinase activity is also detectable, but at a lower level, in uninfected cell extracts. The DNA substrate must contain the two a sequences arranged in direct orientation to generate the lacZ deletion. However, when the a sequences are arranged in inverted orientation, an inversion results. A substrate with two homologous sequences of size and G + C content similar to the a sequence undergoes recombination at a much lower frequency. The reaction requires a divalent cation (Mg2+ or Mn2+) but not ATP or any other nucleoside triphosphate. The simple requirements and specificity for the a sequence suggest that the recombination may proceed by a site-specific mechanism.

Animals↗
PubMed2001

[Karyotypes and chromosome polymorphism of two phytophilous species of chironomids--Glyptotendipes mancunianus and G.imbecillis (Diptera, Chironomidae].

Detailed cytophotomaps of polytene chromosomes have been made for Glyptotendipes mancunianus (2n = 8) and G. imbecillis (2n = 8). In the karyotype of G. imbecillis a greater quantity of a near-centromere heterochromatin is noted. In the karyopool of G. mancunianus 10 sequences are revealed. Specimens with heterozygous inversions make 39%, the average number of heterozygous inversions per specimen is 0.34. In the karyopool of G. imbecillis 11 sequences have been met. Specimens with heterozygous inversions make 69%, the average number of heterozygous inversions per specimen is 1.68.

Animals↗
PubMed1994

Cloning of polygalacturonase (PG) cDNA and inhibition effects of its antisense RNA on the expression of PG gene in transgenic tomato plants.

We have amplified a 1.5-kb PG cDNA including its complete open reading frame, using two primers specific to PG gene and PCR technique. Its fidelity and correctness were confirmed by restriction mapping and partial DNA sequencing. The PG gene was then inserted into a binary vector, pBin437, in an inverted orientation between the 35S promoter with duplicated enhancers and the Nos3' transcriptional termination sequence, and the resulting plasmid pBPG was introduced into LBA 4404. The A. tumefaciens harboring pBPG was used to transform tomato plants. Sixty kanamycin-resistant transformants were selected. PCR detection showed two-third of the transformed plants tested (30 plants) contain the exogenous PG gene. The PG activity assay and SDS-PAGE analysis of proteins from ripening fruit cell wall showed that the PG activity in transgenic tomato plants were inhibited in different extent. One of them, plant 3, gave only 7% PG activity compared with the control (100%). These results suggest that the expression of the anti-PG gene has effectively inhibited the expression of endogenous PG gene. The effect of low-level PG activity on tomato fruit ripening and storage is being investigated.

Base Sequence↗
PubMedDate not supplied

Signal suppression of normal liver tissue by phase corrected inversion recovery: a screening technique.

A new pulse sequence characterized by simultaneous multislice spin echo (SE) and short inversion time (TI) with inversion recovery (STIR) acquisitions is demonstrated. For the STIR component, a repetition time of 1,000 ms and TI of 210 ms were chosen to suppress the signal from normal liver at 0.5 T and create a fast sequence suitable for screening purposes. Phase correction of the STIR with the SE's signal as a reference resulted in high contrast real IR images that were free of phase error artifact. In 13 min the entire liver could be imaged in 14 adjacent slices, each slice portrayed in an ensemble of four images: a T1-weighted SE image, IR real and modulus images, and a T1 map. Forty-one patients with liver pathology and 10 normal volunteers were examined with the sequence implemented on a commercially available 0.5 T imager (Gyroscan; Phillips). Images demonstrated high liver-lesion contrast and sensitivity to liver lesions. Lesions of less than 1 cm in diameter and lymphomatous lesions, commonly occult to magnetic resonance, were detected.

Humans↗
PubMed1995

Inverse protein folding by the residue pair preference profile method: estimating the correctness of alignments of structurally compatible sequences.

The residue pair preference profile (R3P) method is an inverse folding method that combines environmental profiles and pair preference profiles. The method uses statistical preferences for residue pairs which score the likelihood of finding a profiled residue to be paired with a residue within its local environment. All pairs are characterized by their dihedral angles, secondary structure and number of neighboring residues as a function of residue type. Each residue pair preference is expressed for all 20 amino acids of the profiled residue and is weighted by the compatibility of the environment residue with its own local environment. The R3P method produces an initial profile-sequence alignment which is then refined by converting the initial profile into a profile of a target sequence threaded into the structure of the initial profile. We have tested this method by evaluating alignments of sequences with known 3-D structures using structural superposition alignments as reference. R3P-sequence alignments are > or = 50% correct on average for sequences whose 3-D structure pairs superimpose with an r.m.s. deviation of < or = 1.97 A. The average improvement in correctness during this iterative refinement is 14%. The R3P-sequence alignments are compared with sequence-sequence and 3-D profile-sequence alignments. When all three methods are combined, on average > or = 50% of the alignments are correct for pairs of 3-D structures that superimpose within 2.12 A. A 3-D model of HisA is predicted with the combined method.

Aldose-Ketose Isomerases↗
PubMed2002

Pattern of segmental recombination in the distal inversion of mouse t haplotypes.

To examine genetic exchange between t haplotypes and their wild-type homologs, four previously identified mouse Chromosome (Chr) 17 variants termed mosaic haplotypes were analyzed in detail. Three of these haplotypes-one from a Mus musculus population in Bulgaria, one from a Mus domesticus population in Chile, and one from a M. domesticus population in Germany-display properties indicative of the t complex. All four haplotypes are exceptional because they are characterized by the presence of a few wild-type DNA markers in the distal inversion [In(17)4] of a t haplotype chromosome: thus, they are classified as mosaic t haplotypes. The mosaic pattern for each haplotype is distinct, however. We compared the mosaic haplotypes with each other, and with several well-characterized laboratory t haplotypes, by analyzing several DNA markers in the In(17)4 region of the t complex, where all of the mosaicism occurs. We used a combination of high-resolution restriction mapping, DNA sequencing, and analysis of new DNA markers to classify the haplotypes. This analysis shows that segmental exchange, either by gene conversion or double crossing-over, has occurred at molecular markers in the vicinity of a gene, Dnahc8, that is a candidate for the t complex distorter locus Tcd2. While it is unclear whether segmental exchanges have included the Tcd2 gene, it is apparent that several independent recombination events have occurred in In(17)4 during the recent evolution of t haplotypes.

Animals↗
PubMed1993

A gene for a myosin peptide is disrupted by the inv(16)(p13q22) in acute nonlymphocytic leukemia M4Eo.

Chromosome 16 aberrations are well known in acute nonlymphocytic leukemia (ANLL). The most frequent chromosome 16 aberration in ANLL subtype M4Eo is the inv(16)(p13q22). Recently, we showed that in 5 inv(16) patients with ANLL M4Eo the short arm breakpoints are clustered within a 14-kb genomic EcoRI fragment. We report here the identification of a gene situated in the 14-kb fragment. The gene, which codes for a myosin peptide, is disrupted by the inversion of chromosome 16 in the 5 patients. To the best of our knowledge, this is the first report of a myosin gene disrupted in leukemia.

Base Sequence↗
PubMed1989

The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals.

The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp. Predicted genes have been identified along with open reading frames (ORFs) conserved between rice and the previously sequenced chloroplast genomes, a dicot, tobacco (Nicotiana tabacum), and a liverwort (Marchantia polymorpha). The same complement of 30 tRNA and 4 rRNA genes has been conserved between rice and tobacco. Most ORFs extensively conserved between N. tabacum and M. polymorpha are also conserved intact in rice. However, several such ORFs are entirely absent in rice, or present only in severely truncated form. Structural changes are also apparent in the genome relative to tobacco. The inverted repeats, characteristic of chloroplast genome structure, have expanded outward to include several genes present only once per genome in tobacco and liverwort and the large single copy region has undergone a series of inversions which predate the divergence of the cereals. A chimeric tRNA pseudogene overlaps an apparent endpoint of the largest inversion, and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.

Amino Acid Sequence↗
PubMed2000

Evolutionary significance of an unusual chloroplast DNA inversion found in two basal angiosperm lineages.

Two basal lineages of flowering plants possess an intergenic inversion in the chloroplast inverted repeat (IR), a region of the genome from which there have been few previous reports of this class of structural mutation. The size of the inversion (approximately 200 bp) places it in a class not previously seen in the plastid genome. The two lineages with the rearrangement, representatives of the orders Laurales and Nymphaeales, are not closely related and the inversion therefore probably arose independently in each group. The inversion is bordered by short, but highly conserved, inverted repeat motifs that were most likely associated with the inversion process. A stem-loop structure that involves these motifs may play a functional role in mRNA stability. It is seen in all optimal or nearly optimal predicted RNA foldings of the intergenic region.

Base Sequence↗
PubMed1997

Purification, characterization and gene sequence analysis of a novel cytochrome c co-induced with reductive dechlorination activity in Desulfomonile tiedjei DCB-1.

The sulfate-reducing bacterium, Desulfomonile tiedjei DCB-1, conserves energy for growth from reductive dechlorination of 3-chlorobenzoate via halorespiration. To understand this respiratory process better, we examined electron carriers from different cellular compartments of D. tiedjei. A 50-kDa cytochrome from the membrane fraction was found to be co-induced with dechlorination activity. This inducible cytochrome was extracted from the membrane fractions by Tris-HCl buffer containing ammonium sulfate at 35% saturation and was purified to electrophoretic homogeneity by phenyl superose, Mono Q, and hydroxyapatite chromatography. The purified cytochrome had a high-spin absorption spectrum. In a pH titration experiment, the absorption spectrum of the inducible cytochrome shifted to low spin at pH 13.2. The midpoint potential of the inducible cytochrome at pH 7.0 was -342 mV. The NH2-terminal amino acid sequence of the inducible cytochrome was determined and was used to obtain inverse PCR products containing the sequence of the gene encoding the inducible cytochrome. The ORF was 1398 bp and coded for a protein of 52.6 kDa. Two c-type heme-binding domains were identified in the COOH-terminal half of the protein. A putative signal peptide of 26 residues was found at the NH2-terminal end. The protein sequence was not found to have substantial sequence similarity to any other sequence in GenBank. We conclude that this is a c-type cytochrome substantially different from previously characterized c-type cytochromes.

Amino Acid Sequence↗
PubMed1982

Construction and characterization of new cloning vehicles. VI. Plasmid pBR329, a new derivative of pBR328 lacking the 482-base-pair inverted duplication.

The 4150-bp plasmid pBR329 was constructed by the the insertion into pBR327 of an 877-bp DNA fragment carrying the Cmr gene from pBR328. This new cloning vector does not contain the 482-bp inverted duplication that has been reported to be present in pBR325 and pBR328 (Prentki et al., 1981). In pBR329 the Cmr gene lacks its original promoter but is transcribed counterclockwise toward the Apr gene by a promoter located to the right of the HindIII site in the Tcr gene.

Base Sequence↗
PubMed1990

Upstream regulatory sequence for transcriptional activator XylR in the first operon of xylene metabolism on the TOL plasmid.

Transcription of the first operon coding for m-xylene-degrading enzymes on the TOL plasmid of Pseudomonas putida is activated by the xylR gene product in the presence of m-xylene. The operon has the consensus sequence of the ntr/nif promoters at -24 and -12 regions, and the transcription is dependent on an RNA polymerase containing a sigma factor NtrA (RpoN or sigma 54). Deletion derivatives of the upstream sequence of the operon promoter were made in vitro and connected with the xylE gene on a plasmid. Their promoter activities were analyzed in Escherichia coli by monitoring catechol 2,3-dioxygenase activity, the xylE gene product. A cis-acting DNA element was identified, which is required for activation of the operon promoter by XylR protein in the presence of the inducer. This regulatory sequence of about 40 base-pairs in length was located 150 base-pairs upstream from the transcription start site. Analysis of the mutants containing insertions between the upstream regulatory sequence and the promoter sequence demonstrated strong dependence of the activation upon helical periodicity of DNA. The regulatory sequence functioned in the inverse orientation or at a distance of more than 1 x 10(3) base-pairs upstream from the promoter though less efficient. These results indicated that this upstream regulatory sequence might be the binding site for XylR protein. DNA-loop formation through protein-protein interaction between XylR protein attached to the upstream sequence and the NtrA-containing RNA polymerase bound by the promoter sequence was suggested for activation of the operon transcription. A sequence similar to the regulatory sequence of the first operon of xylene metabolism was found in the upstream region of the xylS gene, which is also activated by XylR protein in the presence of m-xylene.

Base Sequence↗
PubMed1994

Haemophilia A: database of nucleotide substitutions, deletions, insertions and rearrangements of the factor VIII gene, second edition.

A large number of different mutations in the factor VIII (F8) gene have been identified as a cause of haemophilia A. This compilation lists known single base-pair substitutions, deletions and insertions in the F8 gene and reviews the status of the inversional events which account for a substantial proportion of mutations causing severe haemophilia A.

Base Sequence↗