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At least 811 records · Page 45Linked to original sources
PubMed1990

Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea.

The 18.1-kilobase plasmid pSE211 integrates into the chromosome of Saccharopolyspora erythraea at a specific attB site. Restriction analysis of the integrated plasmid, pSE211int, and adjacent chromosomal sequences allowed identification of attP, the plasmid attachment site. Nucleotide sequencing of attP, attB, attL, and attR revealed a 57-base-pair sequence common to all sites with no duplications of adjacent plasmid or chromosomal sequences in the integrated state, indicating that integration takes place through conservative, reciprocal strand exchange. An analysis of the sequences indicated the presence of a putative gene for Phe-tRNA at attB which is preserved at attL after integration has occurred. A comparison of the attB site for a number of actinomycete plasmids is presented. Integration at attB was also observed when a 2.4-kilobase segment of pSE211 containing attP and the adjacent plasmid sequence was used to transform a pSE211- host. Nucleotide sequencing of this segment revealed the presence of two complete open reading frames (ORFs) and a segment of a third ORF. The ORF adjacent to attP encodes a putative polypeptide 437 amino acids in length that shows similarity, at its C-terminal domain, to sequences of site-specific recombinases of the integrase family. The adjacent ORF encodes a putative 98-amino-acid basic polypeptide that contains a helix-turn-helix motif at its N terminus which corresponds to domains in the Xis proteins of a number of bacteriophages. A proposal for the function of this polypeptide is presented. The deduced amino acid sequence of the third ORF did not reveal similarities to polypeptide sequences in the current data banks.

Amino Acid Sequence↗
PubMed1995

Characterization of genetic elements required for site-specific integration of Lactobacillus delbrueckii subsp. bulgaricus bacteriophage mv4 and construction of an integration-proficient vector for Lactobacillus plantarum.

Temperate phage mv4 integrates its DNA into the chromosome of Lactobacillus delbrueckii subsp. bulgaricus strains via site-specific recombination. Nucleotide sequencing of a 2.2-kb attP-containing phage fragment revealed the presence of four open reading frames. The larger open reading frame, close to the attP site, encoded a 427-amino-acid polypeptide with similarity in its C-terminal domain to site-specific recombinases of the integrase family. Comparison of the sequences of attP, bacterial attachment site attB, and host-phage junctions attL and attR identified a 17-bp common core sequence, where strand exchange occurs during recombination. Analysis of the attB sequence indicated that the core region overlaps the 3' end of a tRNA(Ser) gene. Phage mv4 DNA integration into the tRNA(Ser) gene preserved an intact tRNA(Ser) gene at the attL site. An integration vector based on the mv4 attP site and int gene was constructed. This vector transforms a heterologous host, L. plantarum, through site-specific integration into the tRNA(Ser) gene of the genome and will be useful for development of an efficient integration system for a number of additional bacterial species in which an identical tRNA gene is present.

Amino Acid Sequence↗
PubMed2003

STAT5 and Oct-1 form a stable complex that modulates cyclin D1 expression.

Signal transducer and activator of transcription 5 (STAT5) is activated by numerous cytokines that control blood cell development. STAT5 was also shown to actively participate in leukemogenesis. Among the target genes involved in cell growth, STAT5 had been shown to activate cyclin D1 gene expression. We now show that thrombopoietin-dependent activation of the cyclin D1 promoter depends on the integrity of a new bipartite proximal element that specifically binds STAT5A and -B transcription factors. We demonstrate that the stable recruitment of STAT5 to this element in vitro requires the integrity of an adjacent octamer element that constitutively binds the ubiquitous POU homeodomain protein Oct-1. We observe that cytokine-activated STAT5 and Oct-1 form a unique complex with the cyclin D1 promoter sequence. We find that STAT5 interacts with Oct-1 in vivo, following activation by different cytokines in various cellular contexts. This interaction involves a small motif in the carboxy-terminal region of STAT5 which, remarkably, is similar to an Oct-1 POU-interacting motif present in two well-known partners of Oct-1, namely, OBF-1/Bob and SNAP190. Our data offer new insights into the transcriptional regulation of the key cell cycle regulator cyclin D1 and emphasize the active roles of both STAT5 and Oct-1 in this process.

Animals↗
PubMed1983

Relationship between chromatic induction and spatial variables: an integrated explanation in terms of element-contribution function.

Chromatic induction as a function of separation and as a function of area was determined by a hue-cancellation procedure. Both functions obtained were expressed by exponential functions with similar exponential coefficients. This led to the derivation of an element-contribution function, based on a linear summation model, that could explain both the relationship between chromatic induction and separation and that between chromatic induction and area. The effects of separation and area on chromatic induction could readily be determined in terms of an element-contribution function. In addition, the induction area that is due to a blue inducing stimulus was larger than those that are due to the other inducing stimuli, suggesting that the summation area of the blue response was larger than those of the other chromatic responses.

Adult↗
PubMed1992

A fast track to IAIMS: the Vanderbilt University strategy.

In July 1991, Vanderbilt University Medical Center (VUMC) initiated a fast track approach to the implementation of an Integrated Academic Information Management System (IAIMS). The fast track approach has four elements: 1) an integrated organizational structure combining various operational information management units and the academic informatics program into a single entity to enhance efficiency; 2) technology transfer and network access to remote resources in preference to de novo development; 3) parallel IAIMS planning and infrastructure construction; 4) restriction of the scope of the initial IAIMS to permit a manageable implementation project. The fast track approach is intended to provide a truly functional IAIMS within a time period (7 years) associated with other major construction projects such as the building of a replacement hospital.

Integrated Advanced Information Management Systems↗
PubMed1998

[A new formulation of death: definition, criteria and diagnostic tests].

OBJECTIVE: To present a new formulation of human death based on neurological considerations. DEVELOPMENT: One of the reasons there is still controversy over a new formulation of human death which is acceptable to society, is that many authors do not suitably integrate three fundamental aspects which should be included in such a formulation: definition, criteria and diagnostic tests. We review the physiopathological mechanisms for generation of consciousness and discuss the three fundamental criteria presented by different authors in recent decades: the whole encephalum, brainstem death and neocortical criteria. We conclude that there are major contradictions in the three criteria with regard to satisfactory integration of the elements, definition, criteria and diagnostic tests. We therefore present a new formulation of human death. DEFINITION: irreversible loss of consciousness, since this gives the essential human attributes, and is the most integrating function of the organism. CRITERIA: cortico-subcortical connections for the generation of both components of consciousness (capacity and content). DIAGNOSTIC TESTS: no waking response to stimuli (capacity), no cognitive nor affective functions (content). CONCLUSIONS: We present a new formulation of human death on a neurological basis which permits satisfactory integration of the three fundamental elements, definition, criteria and diagnostic tests, and so offers a suitable starting point from which man may start to understand death.

Brain↗
PubMed2000

Isolation and analysis of a circular form of the IncJ conjugative transposon-like elements, R391 and R997: implications for IncJ incompatibility.

The incompatibility between the chromosomally integrating, conjugative transposon-like, IncJ elements R997 (ampicillin resistant) and R391 (kanamycin resistant) was examined by constructing strains harbouring both elements. Unusually, recA(+) strains harbouring the resistance determinants of both elements could be isolated but all strains lacked detectable extrachromosomal DNA. The phenotypic characteristics and transfer patterns observed suggested the formation of recombinant hybrids rather than strains harbouring both elements independently. Formation of strains harbouring two IncJ elements in a recA background was thus examined and resulted in the visualisation of extrachromosomal DNA. When R391 was transferred to a recA strain containing integrated R997, both elements co-existed stably and resulted in the isolation of a plasmid of 93.9 kb. When R997 was transferred to a recA strain harbouring an integrated R391, a plasmid of 85 kb was isolated. Comparison of restriction patterns for both elements revealed many common and several distinct fragments indicating a close physical relationship. These data suggest that although IncJ elements normally integrate at a unique site in the Escherichia coli chromosome, they possess the ability for autonomous replication which becomes manifest in a recA background when this site is occupied. This observation has implications for the nature of the incompatibility associated with IncJ elements and also provides a reliable method for isolating IncJ elements for molecular characterisation.

Ampicillin Resistance↗
PubMed1996

The recombination signals for adeno-associated virus site-specific integration.

The adeno-associated virus (AAV) genome integrates site specifically into a defined region of human chromosome 19 (termed AAVS1). Using a functional assay for AAV integration into AAVS1 DNA propagated as an episome, we obtained evidence that a 33-nucleotide AAVS1 DNA sequence contains the minimum signal required for targeted integration. The recombination signal comprises a DNA-binding motif for the AAV regulatory Rep protein [Rep binding site (RBS)] separated by an eight-nucleotide spacer from a sequence that can act as a substrate for Rep endonucleolytic activity [terminal resolution site (TRS)]. Mutations in either the AAVS1-encoded RBS or TRS elements abort targeted integration. Since both the RBS and TRS elements are present in the viral origin of replication and are required for AAV replication, targeted integration into chromosome 19 AAVS1 DNA may involve a replicative type of recombination that is discussed. An additional chromosome 19 element, which is responsible for DNA rearrangements in episomes propagating AAVS1 DNA, was identified and shown not to be required for AAV episomal integration, despite its location adjacent to the recombination signal.

Base Sequence↗
PubMed1986

[The administration of knowledge. The biological and the social in the training of health personnel in Latin America].

The article starts with the concept of the management of knowledge, a component of the mission of PAHO as formulated in 1982. The purpose of the article is to consider what ideas have been formulated on the biological and social elements in medicine and how, and to what extent, they have been put into practice. The first part of the document discusses the theory of medicine and the social sciences, and the biological and social nature of the health-disease process. The second part traces the historical development of the biological and social approaches in relation to the degree to which these elements have been isolated and integrated in instruction. The first stage, the decade of the fifties, was characterized by the influence of the Flexner Report: instruction was organized in a cycle of the basic and clinical sciences; there was almost complete separation between medicine and society, and seminars in the Hemisphere proposed the inclusion of an integrated approach. The second stage, the decade of the sixties, was one of the great advances in theory and practice. Hemispheric meetings among health authorities, professional associations and groups of social scientists, physicians, and educators explicitly expounded the need for integration of the social and biological elements into medical education. The biological basis of study plans was reinforced as well. The third stage, the decade of the seventies, was one of consolidation of social medicine in the profession and the intensification of studies in that discipline. The idea then emerged of interdependence between medical education, medical practice, and the organization of health services in a social context. The authors examine the years of the eighties as an unfinished stage of culmination of the integration of the social and biological elements in medicine with inclusion of the idea of the physician's commitment to society.

Biology↗
PubMed2005

Rapid contour integration in macaque monkeys.

Integration of oriented elements into a contour has been investigated extensively in human psychophysics whereas electrophysiological experiments exploring the neuronal mechanism of contour integration were most often done with macaque monkeys. To bridge the gap between human psychophysics and physiology we estimated spatial and temporal constraints of contour integration in two macaque monkeys. Our results show that contour integration in monkeys depends in a similar way on element distance and alignment between contour path and contour elements as in human subjects. The grouping process was surprisingly fast: In a backward masking experiment we show that a stimulus duration of 30-60 ms is sufficient to perceive a contour and to identify its shape.

Animals↗
PubMedDate not supplied

Biokinetic and toxicodynamic modelling and its role in toxicological research and risk assessment.

Toxicological risk assessment for chemicals is still mainly based on highly standardised protocols for animal experimentation and exposure assessment. However, developments in our knowledge of general physiology, in chemicobiological interactions and in (computer-supported) modelling, have resulted in a tremendous change in our understanding of the molecular mechanisms underlying the toxicity of chemicals. This permits the development of biologically based models, in which the biokinetics as well as the toxicodynamics of compounds can be described. In this paper, the possibilities are discussed of developing systems in which the systemic (acute and chronic) toxicities of chemicals can be quantified without the heavy reliance on animal experiments. By integrating data derived from different sources, predictions of toxicity can be made. Key elements in this integrated approach are the evaluation of chemical functionalities representing structural alerts for toxic actions, the construction of biokinetic models on the basis of non-animal data (for example, tissue-blood partition coefficients, in vitro biotransformation parameters), tests or batteries of tests for determining basal cytotoxicity, and more-specific tests for evaluating tissue or organ toxicity. It is concluded that this approach is a useful tool for various steps in toxicological hazard and risk assessment, especially for those forms of toxicity for which validated in vitro and other non-animal tests have already been developed.

Animal Use Alternatives↗
PubMed1997

Do the integrases of LTR-retrotransposons and class II element transposases have a common ancestor?

The integrases of retrotransposons (class I) and retroviruses and the transposases of bacterial type elements (class II) were compared. The DDE signature that is crucial for the integration of these elements is present in most of them, except for the non-LTR retrotransposons and members of the hAT and P super-families. Alignment of this region was used to infer the relationships between class II elements, retrotransposons, and retroviruses. The mariner-Tc1 and the Pogo-Fot1 super-families were found to be closely related and probably monophyletic, as were LTR retrotransposons and retroviruses. The IS elements of bacteria were clustered in several families, some of them being closely related to the transposase of the mariner-Tc1 super-family or to the LTR retrotransposon and retrovirus integrases. These results plus that of Xiong and Eickbush (1990) were used to develop an evolutionary history suggesting a common ancestral origin(s) for the integrases and transposases containing the DDE signature. The position of the telomeric elements (Het-A and TART) was assessed by comparing their gag and reverse transcriptase domains (when present) to those of group II introns and non-LTR retrotransposons. This preliminary analysis suggests that telomeric elements may be derived from non-LTR retrotransposons.

Amino Acid Sequence↗
PubMed1997

The RIB element in the goaG-pspF intergenic region of Escherichia coli.

The sequence (2,700 bp) between the aldH and pspF genes of Escherichia coli was determined. The pspF gene encodes a sigma54 transcriptional activator of the phage shock protein (psp) operon (pspA to pspE). Downstream of the pspF transcribed region are two open reading frames (ORFs), ordL and goaG, convergently oriented with respect to pspF. These two ORFs, together with the adjacent aldH gene, may constitute a novel operon (aldH-ordL-goaG). The goaG-pspF intergenic region contains a complex extragenic mosaic element, RIB. The structure of this RIB element, which belongs to the BIME-1 family, is Y(REP1) > 16 < Z1(REP2), where Y and Z1 are palindromic units and the central 16 bases contain an L motif with an ihf consensus sequence. DNA fragments containing the L motif of the psp RIB element effectively bind integration host factor (IHF), while the Y palindromic unit (REP1) of the same RIB element binds DNA gyrase weakly. Computer prediction of the pspF mRNA secondary structure suggested that the transcribed stem-loop structures formed by the 3'-flanking region of the pspF transcript containing the RIB element can stabilize and protect pspF mRNA. Analysis of pspF steady-state mRNA levels showed that transcripts with an intact RIB element are much more abundant than those truncated at the 3' end by deletion of either the entire RIB element or a single Z1 sequence (REP2). Thus, the pspF 3'-flanking region containing the RIB element has an important role in the stabilization of the pspF transcript.

Antigens, Bacterial↗
PubMed2004

Efficient transformation of the beetle Tribolium castaneum using the Minos transposable element: quantitative and qualitative analysis of genomic integration events.

Genetic transformation in insects holds great promise as a tool for genetic manipulation in species of particular scientific, economic, or medical interest. A number of transposable elements have been tested recently as potential vectors for transformation in a range of insects. Minos is one of the most promising elements because it appears to be active in diverse species and has the capacity to carry large inserts. We report here the use of the Minos element as a transformation vector in the red flour beetle Tribolium castaneum (Coleoptera), an important species for comparative developmental and pest management studies. Transgenic G(1) beetles were recovered from 32.4% of fertile G(0)'s injected with a plasmid carrying a 3xP3-EGFP-marked transposon and in vitro synthesized mRNA encoding the Minos transposase. This transformation efficiency is 2.8-fold higher than that observed when using a plasmid helper. Molecular and genetic analyses show that several independent insertions can be recovered from a single injected parent, but that the majority of transformed individuals carry single Minos insertions. These results establish Minos as one of the most efficient vectors for genetic transformation in insects. In combination with piggyBac-based transgenesis, our work allows the introduction of sophisticated multicomponent genetic tools in Tribolium.

Animals↗
PubMed2001

Precise excision of bacteriophage Mu DNA.

The temperate bacteriophage Mu is a transposable element that can integrate randomly into bacterial DNA, thereby creating mutations. Mutants due to an integrated Mu prophage do not give rise to revertants, as if Mu, unlike other transposable elements, were unable to excise precisely. In the present work, starting with a lacZ::Muc62(Ts) strain unable to form Lac+ colonies, we cloned a lacZ+ gene in vivo on a mini-Mu plasmid, under conditions of prophage induction. In all lac+ plasmids recovered, the wild-type sequence was restored in the region where the Mu prophage had been integrated. The recovery of lacZ+ genes shows that precise excision of Mu does indeed take place; the absence of Lac+ colonies suggests that precise excision events are systematically associated with loss of colony-forming ability.

Bacteriophage mu↗
PubMed1986

Nucleotide sequence of the BamHI repetitive sequence, including the HindIII fundamental unit, as a possible mobile element from the Japanese monkey Macaca fuscata.

Clustered repeat units produced by BamHI digestion of genomic DNA from the Japanese monkey Macaca fuscata [JMr(BamHI)] were sequenced by dideoxy DNA sequencing. The nucleotide sequences of several individual repeats showed that the BamHI repeat contains the 170-bp HindIII element as an integral part, and that it has more than 90% homology with the HindIII repeat element [AGMr(HindIII)] found in the genomic DNA of the African green monkey. In the JMr(BamHI) repeat unit, the 170-bp HindIII element is flanked by a 6-bp inverted repeat, which is part of a 22-bp direct repeat. This latter repeat of 22-bp asymmetrically overlaps the border between the internal AGMr(HindIII)-like region and adjacent regions of the JMr(BamHI) repeat. A similar structural feature of the BamHI repeat unit has been found in the genomic DNA of the baboon, but not in that of the African green monkey. These results show clearly that the BamHI repeat of the modern Japanese monkey originated as a result of insertion of an AGMr(HindIII) element into a certain site(s) of the genomic DNA of an ancestor of the modern Japanese monkey before Macaca-Cercocebus divergence.

Animals↗
PubMed2006

The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties.

Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties.

Aminophenols↗
PubMed1995

Genotypic effects, maternal effects and grand-maternal effects of immobilized derivatives of the transposable element mariner.

The baseline rate of spontaneous integration of the autonomous mariner element Mos1 into the germline of Drosophila melanogaster is estimated as 16 +/- 5% (mean +/- SE) among fertile G0 flies. However, the transformation rate is reduced approximately 20-fold in Mos1 constructs with exogenous DNA in the size range 5-12 kb inserted into the SacI site. To provide alternative Mos1 helper plasmids for transformation experiments, two types of Mos1-promoter fusions were constructed: hsp-70:Mos1 and hsp26-Sgs3:Mos1. The former has the Mos1 coding region driven by the hsp70 heat-shock promoter; the latter has it driven by the basal Sgs3 promoter under the control of the hsp26 female-germline specific transcriptional regulator. When introduced into D. melanogaster by P-element-mediated germline transformation, these elements are unable to transpose or excise in the presence of autonomous Mos1-related elements (they are "marooned") because the 5' inverted repeat of Mos1 is missing. As expected, the hsp26-Sgs3:Mos1 fusions exhibit a significantly greater rate of germline excision of a target mariner element than do the hsp70:Mos1 fusions. Unexpectedly, the rate of excision of target mariner elements induced by hsp26-Sgs3:Mos1 is the same in the male germline as in the female germline. Both hsp:Mos1 fusions show strong germline expression and a maternal effect of the mariner transposase. A significant grand-maternal effect of the hsp:Mos1 fusions was also detected as a result of a maternal effect on the germline of the F1 progeny. Among flies carrying the promoter fusions inherited maternally, about three-quarters of the overall rate of germline excision derives from the direct genotypic effect and about one-quarter results from the grand-maternal effect. Despite the strong somatic expression of the hsp:Mos1 fusions, mariner transformants carrying a white+ reporter gene at the SacI site remained stable in the soma.

Animals↗