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At least 1,297 records · Page 72Linked to original sources
PubMed2000

Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes.

The complete genome sequences of two closely related organisms--two Helicobacter pylori strains--have recently become available. Comparison of these genomes at single base pair level has suggested the presence of a mechanism for bacterial gene mobility--insertion with long target duplications. This mechanism is formally similar to classical transposon insertion, but the duplication is much longer, often in the range of 100bp. Restriction and/or modification enzyme genes are often within or adjacent to the insertion. A similar process may have mediated insertion of the cag(+) pathogenicity island in H. pylori. A similar structure was identified in comparisons between Neisseria meningitidis and Neisseria gonorrhoeae genomes. We hypothesize that this mechanism, as well as two other types of polymorphism linked with restriction-modification genes (insertion accompanied by target deletion and a tripartite structure composed of substitution/inversion/deletion), have resulted from attack by restriction enzymes on the chromosome.

Base Sequence↗
PubMed1985

Long internal inverted repeat in a yeast viral double-stranded RNA.

The Saccharomyces cerevisiae viruses are non-infectious double-stranded (ds) RNA viruses present in most laboratory strains of yeast. Their genome consists of one or more dsRNAs separately encapsidated in particles composed mainly of one polypeptide, which has a Mr of 88 kdaltons in the best-studied viral subtype. A large viral dsRNA (L1, of 4.7 kb) encodes the capsid polypeptide. We have determined the sequences of a number of cDNA clones homologous to portions of L1 and mapped them by a novel heteroduplex technique. Several of these clones originate from a region of L1 2.3-2.5 kb from the 5' end of the plus strand that contains stop codons in all three reading frames in the plus strand. We therefore suspect that the capsid polypeptide gene lies in the 5' 2.3-2.6 kb of the plus strand. One of the cloned cDNAs has an inverted repeat of 170 bp that appears to be present in its parental RNA. The inverted repeat in L1 is the longest known inverted repeat in a viral dsRNA and the only known non-terminal inverted repeat. It might serve the function of creating two mRNAs from one viral dsRNA.

Amino Acid Sequence↗
PubMed2001

Indirect and direct evidence for DNA double-strand breaks in hypermutating immunoglobulin genes.

The generation of a diverse antigen receptor repertoire is fundamental for the functionality of the adaptive immune system. While the V(D)J recombination process that generates the primary antigen receptor repertoire is understood in great detail, it is still unclear by which mechanism immunoglobulin (Ig) genes are further diversified by somatic hypermutation. Using mouse strains that carry a non-functional, pre-defined V(H)D(H)J(H) gene segment in their IgH locus we demonstrate DNA double-strand breaks (DSBs) in and around V(H)D(H)J(H) in B cells undergoing somatic hypermutation. The generation of these DSBs depends on transcriptional activity, and their distribution along the V(H)D(H)J(H) segment parallels that of point mutations in the hypermutation domain. Furthermore, similar to hot spots of somatic hypermutation, 50-60% of all DSBs occur preferentially at RGYW motifs. DSBs may transiently dissociate the Ig promoter from the intronic enhancer to block further transcription and to initiate an error-prone non-homologous DSB repair pathway. In accord with this model large deletions are frequently produced, along with point mutations, in a V(H)D(H)J(H) segment inserted together with its promoter into the IgH locus in inverted orientation. Our data suggest that DSBs are reaction intermediates of the mechanism underlying somatic hypermutation.

Animals↗
PubMed1989

TraJ protein of plasmid RP4 binds to a 19-base pair invert sequence repetition within the transfer origin.

Transfer of plasmid RP4 during bacterial conjugation requires the plasmid-encoded TraJ protein, which binds to the transfer origin (Fürste, J. P., Pansegrau, W., Ziegelin, G., Kröger, M., and Lanka, E. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 1771-1775). As indicated by traJ mutants, the TraJ protein is a constituent of the relaxosome, the initiation complex of transfer DNA replication. The traJ gene maps adjacent to the transfer origin (oriT). The structural gene consists of a 372-base pair sequence encoding a polypeptide of 122 amino acids (13,282 Da). TraJ was purified from an Escherichia coli strain overproducing the protein. DNA footprinting experiments involving DNase I demonstrated that the purified protein binds to the right arm of a 19-base pair inverted repeat within oriT. Hydroxyl radical footprints of the DNA-protein complex revealed that TraJ protein is bound to only one side of the DNA helix.

Amino Acid Sequence↗
PubMed1992

Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations.

Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and has been used extensively for inducing mutations. In Arabidopsis, two methods for the isolation of genes identified on the basis of mutant phenotypes--genomic subtraction and chromosome walking--either rely on or are greatly facilitated by the availability of these types of mutations. This article gives a detailed characterization of ionizing radiation-induced mutations in plants. The Arabidopsis genes encoding chalcone flavanone isomerase (CHI) and dihydroflavonol 4-reductase (DFR) were cloned and found to correspond to two transparent testa loci. A CHI allele, generated by fast-neutron irradiation, consisted of an inversion within the gene. A 272-bp fragment from 38 centimorgans away on the same chromosome was transferred to one end of this inversion. A DFR allele, induced by x-irradiation, contained two deletions and an inversion of the 2.8-centimorgan intervening region. Sequence analysis of the break points in both mutants indicate that repair of radiation-induced damage involves mechanisms similar or identical to those that mediate the integration of foreign sequences into the genome. The chromosome rearrangements found in these mutants have important implications for the use of ionizing radiation-induced alleles in classical and molecular genetic experiments in plants.

Alcohol Oxidoreductases↗
PubMed2002

Intraportal venous flow distribution: evaluation with single breath-hold ECG-triggered three-dimensional half-Fourier fast spin-echo MR imaging and a selective inversion-recovery tagging pulse.

OBJECTIVE: The purpose of this study was to evaluate the intraportal blood flow distribution from splenic and superior mesenteric veins with an unenhanced MR angiographic technique using single breath-hold ECG-triggered three-dimensional (3D) half-Fourier fast spin-echo sequence and selective inversion-recovery tagging pulse. SUBJECTS AND METHODS: Seventeen healthy volunteers were included in this prospective study. After obtaining regular single breath-hold ECG-triggered 3D half-Fourier fast spin-echo images without applying a tagging pulse, we placed the selective inversion-recovery tagging pulse on the superior mesenteric vein (TAG-A), the splenic vein (TAG-B), or on both (TAG-C) to study the inflow correlation of tagged or marked blood into the portal vein. MR images were evaluated subjectively by three reviewers. RESULTS: On MR images obtained using the TAG-A pulse to suppress the signal flow from the superior mesenteric vein into the portal vein, the most common pattern of signal loss was observed on the right half of the main portal vein (8/17 subjects). Conversely, on the MR images obtained using the TAG-B pulse, signal loss of the left half of the main portal vein was the most common pattern (11/17 subjects). Signal reduction from the splenic venous flow in the left portal vein was significantly greater than that from the superior mesenteric venous flow (p<0.05). CONCLUSION: The unenhanced MR angiographic technique using single breath-hold ECG-triggered 3D half-Fourier fast spin echo with selective inversion-recovery tagging pulse has the potential to assess the intraportal blood flow distribution from the splenic and superior mesenteric veins.

Adult↗
PubMed2000

["Mode for mutation" in the natural population of Drosophila melanogaster from Umani is caused by distribution of a hobo-induced inversion in the regulatory region of the yellow gene].

A mutation outburst of the yellow gene occurred in a Drosophila melanogaster population from the town of Uman' from 1982 to 1991 and was associated with the instability of several alleles. Molecular genetic analysis revealed a deletion variant of the hobo transposable element in the same site of the regulatory region of yellow in the mutant alleles and their derivatives. The outburst of the yellow-2 mutations was attributed to the spreading of the X chromosome, which contained an inversion of the yellow regulatory region, through the population. Reinversion resulted in the wild-type phenotype. Crossing lines carrying the inversion with laboratory line C(1)DX, ywf induced instability of the yellow alleles, which was associated with duplication or multiplication of a fragment of the yellow gene. Most derivative lines eventually became stable. The loss of instability was not associated with phenotypic changes; molecular genetic changes included a loss of the duplicated sequences or a deletion of the inverted regulatory region of the yellow gene.

Animals↗
PubMed1991

Biologically active synthetic fragments of human basic fibroblast growth factor (bFGF): identification of two Asp-Gly-Arg-containing domains involved in the mitogenic activity of bFGF in endothelial cells.

Synthetic peptides derived from the amino acid sequence of human basic fibroblast growth factor (bFGF) have been assayed for the capacity to exert bFGF agonist and antagonist activities in cultured endothelial cells. bFGF fragments A and C, which correspond to the sequences bFGF (38-61) and bFGF (82-101), induce a limited but statistically significant increase in cell number when administered to cultures of fetal bovine aortic endothelial GM 7373 cells and adult bovine aortic endothelial cells. The two peptides also exert a partial antagonist activity when GM 7373 cells are stimulated to proliferate by bFGF, but they do not affect cell proliferation induced by serum, epidermal growth factor (EGF), phorbol ester (TPA), or 1,2-diacylglycerol (diC8). Moreover, antibodies raised against peptides A and C specifically quench the mitogenic activity of bFGF. Peptides A and C contain the amino acid sequence Asp-Gly-Arg (DGR), which is the inverse of the cell adhesion signal sequence RGD recognized by integrins. DGR- and RGD-containing tetra- and heptapeptides inhibit the mitogenic activity exerted by bFGF and by the two active bFGF fragments. They do not affect cell proliferation induced by acidic FGF, EGF, serum, TPA, and diC8. However, neither peptides A and C, their corresponding antibodies, nor DGR-and RGD-containing peptides inhibit the binding of 125I-bFGF to its low and high affinity binding sites. The data suggest that amino acid residues 38-61 and 82-101, both containing a core DGR sequence, represent two "activation" domains of bFGF. Both domains are involved in the modulation of the mitogenic activity of bFGF without interacting directly with the bFGF receptor.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗
PubMed2005

Short tau inversion recovery and proton density-weighted fat suppressed sequences for the evaluation of osteoarthritis of the knee with a 1.0 T dedicated extremity MRI: development of a time-efficient sequence protocol.

Aim of this study was to develop a time-efficient sequence protocol for a 1.0 T dedicated MR system to be used for whole-organ scoring of osteoarthritis (OA). Thirty-four knees were examined using a protocol that included fat suppressed fast spin echo proton density weighted sequences (PDFS) in three planes plus a coronal STIR sequence. Two radiologists scored each knee by consensus for five OA features. In separate sessions, all knees were scored using three different combinations of sequences: (1) all four sequences (reference protocol, 16 min 31 s scanning time), (2) three PDFS sequences without STIR ("No STIR", 12 min 25 s scanning time) and (3) sagittal and axial PDFS sequences plus a coronal STIR sequence ("No PDFS", 11 min 49 s scanning time). Agreement of the readings using both subsets of sequences compared to the reference protocol was evaluated using weighted kappa statistics. kappa-coefficients showed good or excellent agreement for both sequence subsets in comparison to the reference protocol for all assessed features. kappa-coefficients for No PDFS/No STIR: bone marrow abnormalities (0.74/0.67), subarticular cysts (0.84/0.63), marginal osteophytes (0.77/0.71), menisci (0.75/0.79), tibial cartilage (0.71/0.78). Optimization of sequence protocols consisting of three sequences results in time savings and cost efficiency in imaging of knee OA without loss of information over a more time consuming protocol.

Female↗
PubMed1992

Effects of myocardial electrotonic interaction on the sequence of excitation and repolarisation and on T wave polarity. Computer modelling experiments.

A computer model of a 3-dimensional rectangular block of myocardial tissue (3969 cells) has been used to investigate the influence on excitation and repolarisation sequences and on the modelled electrocardiographic T wave of (a) electrotonic interaction, (b) intrinsic distribution of refractoriness, and (c) the speed of repolarisation of action potentials. The model allowed electrotonic interactions to be investigated separately during the depolarisation and repolarisation phases. Scales of 14 values of the strength of electrotonic interaction during the depolarisation phase, 14 values of the strength of electrotonic interaction during the repolarisation phase, 3 shapes of action potential, and 5 distributions of tissue refractoriness were selected and all 2940 combinations were examined. In each experiment, the tissue model was artificially excited and the resulting excitation and repolarisation sequences were simulated. The results of the study suggested that electrotonic interactions between excited cells can cause non-uniform speed of propagation which, by means of the phase shifts of action potentials, contributes to the inversion of the repolarisation sequence and to the physiologic orientation of T waves. Experiments with this model did not support the hypothesis that simple electrotonic smoothing of the differences in repolarisation phases due to the excitation phase shift of action potentials reverses the repolarisation sequence and explains T wave polarity.

Action Potentials↗
PubMed2025

Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow.

The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for nonmodel species, including reference genomes and recombination maps, have constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside-a nonmodel fish with extensive local adaptation across a steep latitudinal gradient-as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci found exclusively within large haploblocks harboring inversions and smaller peaks overlapping putative centromeric regions. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeric regions appeared differentiated because of low recombination and diversity, with no indication of elevated divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.

Gene Flow↗
PubMed2004

Oligosyndactylism mice have an inversion of chromosome 8.

The radiation-induced mutation Oligosyndactylism (Os) is associated with limb and kidney defects in heterozygotes and with mitotic arrest and embryonic lethality in homozygotes. We reported that the cell cycle block in Os and in the 94-A/K transgene-induced mutations is due to disruption of the Anapc10 (Apc10/Doc1) gene. To understand the genetic basis of the limb and kidney abnormalities in Os mice we characterized the structural changes of chromosome 8 associated with this mutation. We demonstrate that the Os chromosome 8 has suffered two breaks that are 5 cM ( approximately 10 Mb) apart and the internal fragment delineated by the breaks is in an inverted orientation on the mutant chromosome. While sequences in proximity to the distal break are present in an abnormal Os-specific Anapc10 hybrid transcript, transcription of these sequences in normal mice is low and difficult to detect. Transfer of the Os mutation onto an FVB/N background indicated that the absence of dominant effects in 94-A/K mice is not due to strain background effects on the mutation. Further analysis of this mutation will determine if a gene interrupted by the break or a long-range effect of the rearrangement on neighboring genes is responsible for the dominant effects of Os.

Animals↗
PubMed2004

Tyrosine site-specific recombinases mediate DNA inversions affecting the expression of outer surface proteins of Bacteroides fragilis.

The chromosome of Bacteroides fragilis has been shown to undergo 13 distinct DNA inversions affecting the expression of capsular polysaccharides and mediated by a serine site-specific recombinase designated Mpi. In this study, we demonstrate that members of the tyrosine site-specific recombinase family, conserved in B. fragilis, mediate additional DNA inversions of the B. fragilis genome. These DNA invertases flip promoter regions in their immediate downstream region. The genetic organization of the genes regulated by these invertible promoter regions suggests that they are operons and many of the products are predicted to be outer membrane proteins. Phenotypic analysis of a deletion mutant of one of these DNA invertases, tsr15 (aapI), which resulted in the promoter region for the downstream genes being locked ON, confirmed the synthesis of multiple surface proteins by this operon. In addition, this deletion mutant demonstrated an autoaggregative phenotype and showed significantly greater adherence than wild-type organisms in a biofilm assay, suggesting a possible functional role for these phase-variable outer surface proteins. This study demonstrates that DNA inversion is a universal mechanism used by this commensal microorganism to phase vary expression of its surface molecules and involves at least three conserved DNA invertases from two evolutionarily distinct families.

Amino Acid Sequence↗
PubMed1995

[Inversion activity in the resolution of transposons Tn5053 and Tn402 possessing a nonstandardly organized res-region].

The classical bacterial site-specific systems of DNA resolution are characterized, despite their considerable divergence, by a regularly arranged res region represented as a triad of res sites. DNA resolution (deletion) is carried out more efficiently than DNA inversion, primarily due to this structure. In this report, the ratio of deletion to inversion activities is evaluated for the resolution systems of Tn5053 and Tn402, which belong to a novel family and possess an irregularly arranged res region. By this criterion, the system studied is shown to be similar to the classical ones. These data suggest that in the course of evolution of the resolvase systems, the same degree of recombination specialization could be attained by different arrangement of the res region.

Amino Acid Sequence↗