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At least 1,207 records · Page 67Linked to original sources
PubMed1996

Salmonella typhimurium fimbrial phase variation and FimA expression.

Bacteria in a nonfimbriate phase because of continuous aeration of liquid cultures produce FimA in amounts similar to those produced by fimbriate bacteria. However, relatively low FimA production was observed in nonfimbriate-phase cultures obtained by growth on solid media or by anaerobic incubation. Regardless of the fimbrial phase of Salmonella typhimurium, the fimA promoter region was always oriented in the direction that might allow fimA transcription.

Anaerobiosis↗
PubMed1998

Intracisternal A-particle element transposition into the murine beta-glucuronidase gene correlates with loss of enzyme activity: a new model for beta-glucuronidase deficiency in the C3H mouse.

The severity of human mucopolysaccharidosis type VII (MPS VII), or Sly syndrome, depends on the relative activity of the enzyme beta-glucuronidase. Loss of beta-glucuronidase activity can cause hydrops fetalis, with in utero or postnatal death of the patient. In this report, we show that beta-glucuronidase activity is not detectable by a standard fluorometric assay in C3H/HeOuJ (C3H) mice homozygous for a new mutation, gusmps2J. These gusmps2J/gusmps2J mice are born and survive much longer than the previously characterized beta-glucuronidase-null B6.C-H-2(bm1)/ByBir-gusmps (gusmps/gusmps) mice. Northern blot analysis of liver from gusmps2J/gusmps2J mice demonstrates a 750-bp reduction in size of beta-glucuronidase mRNA. A 5.4-kb insertion in the Gus-sh nucleotide sequence from these mice was localized by Southern blot analysis to intron 8. The ends of the inserted sequences were cloned by inverse PCR and revealed an intracisternal A-particle (IAP) element inserted near the 3' end of the intron. The sequence of the long terminal repeat (LTR) regions of the IAP most closely matches that of a composite LTR found in transposed IAPs previously identified in the C3H strain. The inserted IAP may contribute to diminished beta-glucuronidase activity either by interfering with transcription or by destabilizing the message. The resulting phenotype is much less severe than that previously described in the gusmps/gusmps mouse and provides an opportunity to study MPS VII on a genetic background that clearly modulates disease severity.

Animals↗
PubMed1986

Short repeated elements in the upstream regulatory region of the SUC2 gene of Saccharomyces cerevisiae.

Expression of secreted invertase from the SUC2 gene is regulated by carbon catabolite repression. Previously, an upstream regulatory region that is required for derepression of secreted invertase was identified and shown to confer glucose-repressible expression to the heterologous promoter of a LEU2-lacZ fusion. In this paper we show that tandem copies of a 32-base pair (bp) sequence from the upstream regulatory region activate expression of the same LEU2-lacZ fusion. The level of expression increased with the number of copies of the element, but was independent of their orientation; the expression from constructions containing four copies of the sequence was only twofold lower than that when the entire SUC2 upstream regulatory region was present. This activation was not significantly glucose repressible. The 32-bp sequence includes a 7-bp motif with the consensus sequence (A/C)(A/G)GAAAT that is repeated at five sites within the upstream regulatory region. Genetic evidence supporting the functional significance of this repeated motif was obtained by pseudoreversion of a SUC2 deletion mutant lacking part of the upstream region, including two copies of the 7-bp element. In three of five pseudorevertants, the mutations that restored high-level SUC2 expression altered one of the remaining copies of the 7-bp element.

Base Sequence↗
PubMedDate not supplied

[Noncoding sequences of the eukaryotic genome as an additional protection of genes from chemical mutagens].

A quantitative model was developed that detects a new function of noncoding sequences in the eukaryotic genome, namely, the protection of coding sequences from chemical (mainly endogenous) mutagens. It was shown that, under common ecological conditions, the number of nucleotides damaged by mutagens in coding sequences of the genome is inversely proportional to the size of their noncoding counterparts. Noncoding sequences can differently protect single genetic loci from chemical mutagens by the formation of specific spatial structures of the protected loci in the interphase nuclei. The significant differences in genome sizes between species (paradox C) can be explained by different contributions of noncoding sequences to the total effect of genome protection from endogenous chemical mutagens.

Animals↗
PubMed1996

Magnetic resonance guidance of percutaneous ethanol injection in liver.

RATIONALE AND OBJECTIVES: Percutaneous ethanol injection (PEI) is used as a form of treatment for cancer, particularly malignant hepatic tumors. Little is known about the intratumoral distributions of ethanol following PEI. We assessed, using magnetic resonance (MR) imaging, the distribution of ethanol in liver and the concentration of ethanol needed to kill tumor cells in vivo. METHODS: MR imaging studies were performed using phantoms of alcohol, ex vivo bovine liver, and healthy human volunteers. A variety of pulse sequences were tested for their ability to maximize the signal intensity from alcohol while minimizing the signal from liver tissues as well as the regions of necrosis following ethanol injection. A cell culture model of in vitro cytotoxicity was developed to predict the target concentration of alcohol necessary for killing tumor cells. RESULTS: At 1.5 T, we found that an inversion-recovery spin-echo sequence using an inversion time of 250 msec and an echo time of 150 msec in combination with water saturation pulses effectively suppressed the tissue water signal from human liver while obtaining a clear signal from the ethanol. The cytotoxicity experiments suggested that a concentration of 20% or more ethanol is sufficient to completely kill all the tumor cells. CONCLUSION: A critical concentration of ethanol (e.g., 10%) is necessary for full tumoricidal effect. MR imaging should be able to determine the volume of distribution and the intratumoral concentrations of ethanol, thus potentially allowing researchers to achieve the requisite concentrations for maximal tumoricidal effects.

Animals↗
PubMed2000

Nucleotide sequence of alpha-galactosidase MEL gene from Zygosaccharomyces mrakii.

The region encompassing the alpha-galactosidase MELr gene was amplified from Zygosaccharomyces mrakii IFO 1835(T) by inverse-PCR and then sequenced. The nucleotide sequence of this region revealed a single open reading frame of 1410 bp encoding a 470 amino acid protein with a molecular weight of 51,909. The similarity of the deduced mature protein to other yeast alpha-galactosidases was 63.3% to Zygosaccharomyces cidri, 71.5% to Torulaspora delbrueckii, and 70. 7-73.9% to Saccharomyces species. The nucleotide and amino acid sequences are deposited in the DDBJ/EMBL/GenBank database under Accession Number AB030209.

Fungal Proteins↗
PubMed2006

Fluid-attenuated inversion-recovery SSFP imaging.

PURPOSE: To describe and evaluate a fast, fluid-suppressed 2D multislice steady-state free precession (SSFP) neuroimaging sequence. MATERIALS AND METHODS: We developed a fast fluid-attenuated inversion-recovery SSFP sequence for use in neuroimaging. The inversion time (TI) was optimized to yield good cerebrospinal fluid (CSF) suppression while conserving white matter (WM)/lesion contrast across a broad range of flip angles. Multiple SSFP acquisitions were combined using the sum-of-squares (SOS) method to maximize SNR efficiency while minimizing SSFP banding artifacts. We compared our fluid-attenuated inversion-recovery (FLAIR) SSFP sequence with FLAIR fast spin-echo (FSE) in both normal subjects and a volunteer with multiple sclerosis. SNR measurements were performed to ascertain the SNR efficiency of each sequence. RESULTS: Our FLAIR SSFP sequence demonstrated excellent CSF suppression and good gray matter (GM)/WM contrast. Coverage of the entire brain (5-mm slices, 24-cm FOV, 256 x 192 matrix) was achieved with FLAIR SSFP in less than half the scan time of a corresponding FLAIR FSE sequence with similar SNR, yielding improvements of more than 50% in SNR efficiency. Axial scans of a volunteer with multiple sclerosis show clearly visible plaques and very good visualization of brain parenchyma. CONCLUSION: We have demonstrated the feasibility of a very fast fluid-suppressed neuroimaging technique using SSFP.

Algorithms↗
PubMed2000

Evidence from mutational specificity studies that yeast DNA polymerases delta and epsilon replicate different DNA strands at an intracellular replication fork.

Although polymerases delta and epsilon are required for DNA replication in eukaryotic cells, whether each polymerase functions on a separate template strand remains an open question. To begin examining the relative intracellular roles of the two polymerases, we used a plasmid-borne yeast tRNA gene and yeast strains that are mutators due to the elimination of proofreading by DNA polymerases delta or epsilon. Inversion of the tRNA gene to change the sequence of the leading and lagging strand templates altered the specificities of both mutator polymerases, but in opposite directions. That is, the specificity of the polymerase delta mutator with the tRNA gene in one orientation bore similarities to the specificity of the polymerase epsilon mutator with the tRNA gene in the other orientation, and vice versa. We also obtained results consistent with gene orientation having a minor influence on mismatch correction of replication errors occurring in a wild-type strain. However, the data suggest that neither this effect nor differential replication fidelity was responsible for the mutational specificity changes observed in the proofreading-deficient mutants upon gene inversion. Collectively, the data argue that polymerases delta and epsilon each encounter a different template sequence upon inversion of the tRNA gene, and so replicate opposite strands at the plasmid DNA replication fork.

Alleles↗
PubMed2003

Identification of functional lox sites in the plastid genome.

Our objective was to test whether or not cyclization recombination (CRE), the P1 phage site-specific recombinase, induces genome rearrangements in plastids. Testing was carried out in tobacco plants in which a DNA sequence, located between two inversely oriented locus of X-over of P1 (loxP) sites, underwent repeated cycles of inversions as a means of monitoring CRE activity. We report here that CRE mediates deletions between loxP sites and plastid DNA sequences in the 3'rps12 gene leader (lox-rps12) or in the psbA promoter core (lox-psbA). We also observed deletions between two directly oriented lox-psbA sites, but not between lox-rps12 sites. Deletion via duplicated rRNA operon promoter (Prrn) sequences was also frequent in CRE-active plants. However, CRE-mediated recombination is probably not directly involved, as no recombination junction between loxP and Prrn could be observed. Tobacco plants carrying deleted genomes as a minor fraction of the plastid genome population were fertile and phenotypically normal, suggesting that the absence of deleted genome segments was compensated by gene expression from wild-type copies. The deleted plastid genomes disappeared in the seed progeny lacking CRE. Observed plastid genome rearrangements are specific to engineered plastid genomes, which contain at least one loxP site or duplicated psbA promoter sequences. The wild-type plastid genome is expected to be stable, even if CRE is present in the plastid.

3' Untranslated Regions↗
PubMed1989

Direct evidence for intrastrand DNA inversion of kappa immunoglobulin gene segments in two murine plasmacytomas.

The products of kappa immunoglobulin gene recombination have been characterized in two murine plasmacytomas to examine the relationship between V-J products and reciprocal elements. By cloning, sequencing, hybridization, and application of the polymerase chain reaction, we have established the direct relationship of the kappa recombination products in these cells. The results provide stronger support for the intrastrand mechanism of kappa gene recombination as well as demonstrating a role for secondary, corrective recombinations.

Amino Acid Sequence↗
PubMed1992

A general method for chimerization of monoclonal antibodies by inverse polymerase chain reaction which conserves authentic N-terminal sequences.

Chimerization of antibodies (Ab) by cloning the V (variable) regions encoding the light and heavy chains with degenerate oligodeoxyribonucleotide primers matching to framework region 1 and to the joining regions, leads to Ab with altered amino acids at the N-terminus compared to those of the parental Ab. This is due to N-terminal framework 1 sequences in the expression vectors [Larrick et al., Bio/Technology 7 (1989) 937-938; Le Boeuf et al., Gene (1989) 371-377; Orlandi et al., Proc. Natl. Acad. Sci. USA 86 (1989) 3833-3837]. This might lead to Ab with altered affinity to the antigen due to interaction of framework sequences with complementarity determining regions. Moreover, some V regions may be refractory to cloning by this procedure. Here, we describe a method to circumvent these potential problems. The V regions for both chains of the Ab are cloned by inverse polymerase chain reaction (PCR) with primers matching the known constant region sequences of the Ab. After sequencing, PCR fragments corresponding to the V regions of both chains are inserted in-frame into appropriate expression vectors leading to Ab with unaltered N-terminal sequences after expression in mammalian cells. The procedure is illustrated with an Ab directed against the beta chain of the human interleukin-2 receptor.

Amino Acid Sequence↗
PubMed1996

Characterisation of the novel junctions of two minichromosomes of Leishmania major.

The minichromosomes M210 and M230 of Leishmania major are linear amplicons which have an inverted repeat structure. We report here the molecular cloning of the megabasic chromosome region where M210 and M230 recombination points are located. The analysis of this chromosomal region revealed a 374 bp fragment directly repeated 3 times, which was also repeated elsewhere in the genome. DNA fragments containing the novel junctions of the minichromosomes M210 and M230 have been likewise cloned. The nucleotide sequence of these fragments was determined and compared with their corresponding DNAs in the source chromosome. It revealed that M210 contains a central 226 bp non-repeated fragment, whereas the central fragment of M230 was 5 kb long. A 9 bp sequence which was repeated in inverted orientation around the recombination points of M230 was found. M210 showed instead an A + T rich DNA which could be implicated in its generation.

Animals↗
PubMed1998

Neisseria gonorrhoeae contains multiple copies of a gene that may encode a site-specific recombinase and is associated with DNA rearrangements.

A 960-bp ORF potentially encoding a site-specific recombinase has been cloned from Neisseria gonorrhoeae MS11-A. This ORF was designated pivNg on the basis of similarity of the deduced amino acid sequence to the Piv proteins of Moraxella spp. that are site-specific invertases. Southern hybridization and sequence analysis revealed that there were multiple copies of pivNg sequence within the genomes of N. gonorrhoeae strains tested, but not in several other neisserial species. Southern hybridization and sequence analysis further suggested that pivNg sequences may be associated with genomic rearrangements.

Amino Acid Sequence↗
PubMedDate not supplied

A spherical rotation coordinate system for the description of three-dimensional joint rotations.

Three-dimensional joint rotations in human movement analysis have been mainly described by Euler/Cardan angles. Due to sequence dependence, each combination of three Euler/Cardan angles defines a single pattern of joint rotation. When the rotation pattern is unknown, it needs to be considered using a particular sequence of Euler/Cardan angles to represent joint rotations. In this paper a spherical rotation coordinate system is developed for describing three-dimensional joint rotations using a method of rotation involving two steps: a long axis rotation and a pure axial rotation. Two angles of the classical spherical coordinate system--longitude and latitude--are used to describe long axis rotations in this newly proposed coordinate system. The spherical rotation coordinate system uses a radial rotation angle to describe pure axial rotation of a limb segment whereas the classical spherical coordinate system uses a radial displacement to describe motion of a point. An application of the spherical rotation coordinate system is given to define three-dimensional rotations of the glenohumeral joint. A mathematical proof shows that the long axis rotation and axial rotation are sequence independent. Two numerical examples are investigated which demonstrate that the spherical rotation angles can be uniquely determined in both forward and inverse kinematics without considering sequences rotations.

Biomedical Engineering↗
PubMed1992

DNA inversions between short inverted repeats in Escherichia coli.

Using site-specific mutagenesis in vitro, we have constructed Escherichia coli strains that allow the detection of the inversion of an 800-bp segment in the lac region. The invertible segment is bounded by inverted repeats of either 12 or 23 bp. Inversions occurring at these inverted repeats will restore the Lac+ phenotype. Inversions can be detected at both short homologies at frequencies ranging from 0.5 x 10(-8) to 1 x 10(-7). These events, which have been verified by DNA sequence analysis, are reduced up to 1000-fold in strains deficient for either RecA, RecB or RecC. They are not reduced in strains deficient in the RecF, J pathway. These results show that the RecB,C,D system can mediate rearrangements at short sequence repeats, and probably plays a major role in cellular rearrangements.

Base Sequence↗
PubMed1983

Genome fusion mediated by the site specific DNA inversion system of bacteriophage P1.

The genome of bacteriophage P1 contains a segment which is invertible by site specific recombination between sequences near the outside ends of the inverted repeats which flank it. Immediately adjacent to this C segment is the coding sequence for cin, the enzyme catalyzing inversion. We show that multicopy plasmids carrying cin and the sequences at which it acts (cix) can form dimers in the absence of the host recA function. Further, such plasmids can be cotransduced with P1 markers at high frequency from recA lysogens, indicating cointegration with the P1 genome. It is thus demonstrated that a system whose primary role is the inversion of a specific DNA segment can also mediate intermolecular recombination.

Bacterial Proteins↗
PubMed1993

Deletions with inversions: report of a mutation and review of the literature.

Herein we report a 10.9 kb deletion and a 95 bp inversion in a patient with severe hemophilia B (factor IXHB209). With the addition of factor IXHB209, three of six characterized deletions in the factor IX gene are now known to include inversions. A high frequency of combined deletions and inversions has not previously been described in a human gene.

Base Sequence↗