[The nature of specificity of integrating the IS50 element in Escherichia coli].
Explore the source record for details and available documents.
Base Sequence↗
SEARCH · Search PubMed
Results for “integrative element”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Tandem insertions of Alu elements.
Alu elements are non-autonomous, non-LTR retroposons that represent the most abundant mobile elements in the human genome (1.1 x 10(6) copies/genome). They preferentially insert adjacent to existing Alu elements. It has been proposed that Alu elements utilize LINE-1 machinery for their retroposition. The LINE-1 endonuclease cleaves at a loose consensus sequence. We have utilized a bioinformatics approach to show the order of insertion of pairs of young (Y) and old (S or J) Alu subfamily members. Our data suggest that the consensus LINE-1 endonuclease cleavage site used for insertion of the old Alu elements can be reused for integration of the younger ones inserting adjacent to them. However, there is also a preference at the 3' end of Alu into a non-ideal cleavage site that may represent unique properties of the A-tail for integration. Alu elements inserting adjacent to one another may suggest the saturation of the optimal integration sites with existing Alu elements, rather than any innate preference for Alu elements to integrate adjacent to other Alus.
Alu Elements↗
Predictors of adolescent sexual behavior and intention: a theory-guided systematic review.
PURPOSE: To better understand why adolescents initiate sexual activity at early ages, we conducted a systematic literature review guided by eight key elements outlined in an integrative theoretical framework. METHODS: Using the matrix method for literature reviews, we extracted-from 69 published studies-statistically significant and nonsignificant findings (related to the attempted prediction/explanation of adolescents' sexual behavior and intention) and organized them using the various integrative model elements. We also assessed these publications' methodological quality including each study's deployment of theory, appropriate design, and data analytic/reporting techniques. RESULTS: Three integrative theoretical framework elements-intention, perceived norms, and an environmental constraint variable, time home alone-emerged as stable predictors of sexual behavior outcomes in this body of literature. This analysis revealed, however, a literature that has remained rather stagnant regarding its methodological quality, over time. CONCLUSIONS: Implications for adolescent sexual health promotion practice and research are discussed.
Adolescent↗
Genomic and functional analyses of SXT, an integrating antibiotic resistance gene transfer element derived from Vibrio cholerae.
SXT is representative of a family of conjugative-transposon-like mobile genetic elements that encode multiple antibiotic resistance genes. In recent years, SXT-related conjugative, self-transmissible integrating elements have become widespread in Asian Vibrio cholerae. We have determined the 100-kb DNA sequence of SXT. This element appears to be a chimera composed of transposon-associated antibiotic resistance genes linked to a variety of plasmid- and phage-related genes, as well as to many genes from unknown sources. We constructed a nearly comprehensive set of deletions through the use of the one-step chromosomal gene inactivation technique to identify SXT genes involved in conjugative transfer and chromosomal excision. SXT, unlike other conjugative transposons, utilizes a conjugation system related to that encoded by the F plasmid. More than half of the SXT genome, including the composite transposon-like structure that contains its antibiotic resistance genes, was not required for its mobility. Two SXT loci, designated setC and setD, whose predicted amino acid sequences were similar to those of the flagellar regulators FlhC and FlhD, were found to encode regulators that activate the transcription of genes required for SXT excision and transfer. Another locus, designated setR, whose gene product bears similarity to lambdoid phage CI repressors, also appears to regulate SXT gene expression.
Bacteriophages↗
Transfer RNA genes: landmarks for integration of mobile genetic elements in Dictyostelium discoideum.
In prokaryotes and eukaryotes mobile genetic elements frequently disrupt the highly conservative structures of chromosomes, which are responsible for storage of genetic information. The factors determining the site for integration of such elements are still unknown. Transfer RNA (tRNA) genes are associated in a highly significant manner with different putative mobile genetic elements in the cellular slime mold Dictyostelium discoideum. These results suggest that tRNA genes in D. discoideum, and probably tRNA genes generally in lower eukaryotes, may function as genomic landmarks for the integration of different transposable elements in a strictly position-specific manner.
Base Sequence↗
[Site of integration of IS1-element responsible for expression of the yeast ADE1 gene in Escherichia coli].
Cloned yeast ADE1 gene is expressed in Escherichia coli, due to integration of the IS1 bacterial element into the non-coding 5' region. Primary structure analysis of the integration site of IS1 element demonstrated that this site is situated in a region flanked by two inverted repeats of yeast DNA which are homologous to the right end of the IS1 element. The region up-stream (5') to the left inverted repeat is AT-rich.
DNA Transposable Elements↗
Dysfunction in visual object recognition of patients with unilateral brain damage under the element presentation condition.
The ability of integrating visual elements of 12 patients with right hemisphere damage (RHD), 14 patients with left hemisphere damage (LHD), and 20 normal young adults was investigated to specify the visual dysfunction processes of patients with unilateral brain damage. Both RHD and LHD groups demonstrated clear deficit in recognizing the familiar objects of which elements were cyclically presented at various time intervals. Moreover, in the nonsequentail element presentation condition the spatial and temporal integration of the RHD group was impaired relative to the LHD and normal groups. The visual degradations of patients with brain damage were discussed from the point of view of information processing stage as well as serial and parallel processing.
Adult↗
The chromosomal integration site of the Streptomyces element pSAM2 overlaps a putative tRNA gene conserved among actinomycetes.
The pSAM2 element of Streptomyces ambofaciens integrates site-specifically in the genome of different Streptomyces species by recombination between a 58 bp sequence common to the plasmid (attP) and the chromosome (attB). Southern hybridization analysis showed that sequences similar to the pSAM2 attB site were found in other actinomycetes (Mycobacterium, Nocardia, Micromonospora) as well as unrelated bacteria (Bacillus circulans, Escherichia coli, Clostridium botulinum, Bordetella pertussis, and Legionella pneumophila). Hybridizing fragments from B. circulans and Mycobacterium tuberculosis were cloned and sequenced. Comparison of these sequences with the sequence of the integration zone of S. ambofaciens revealed a conserved region of 76 bp which overlapped with the attB site. This conserved sequence was similar to the Salmonella typhimurium and E. coli tRNA(pro1) genes as well as a number of eucaryotic tRNA genes and had a proline-tRNA-like cloverleaf structure. Furthermore, the Streptomyces lividans attB site of the Streptomyces glaucescens element pIJ408 was also found to overlap a potential tRNA gene (tRNA(thr)). We note here that these two putative tRNA genes as well as those which overlap the attB site of the elements SLP1 of Streptomyces coelicolor and pMEA100 of Nocardia mediterranei all contain the site where integrative recombination takes place. These presumptive actinomycete tRNA genes lack the 3' terminal CCA sequence found in most procaryotic tRNA genes.
Actinomycetales↗
Identity by descent and DNA sequence variation of human SINE and LINE elements.
To test the hypothesis that Alu and L1 elements are genetic characters that are essentially homoplasy-free, we sequenced a total of five human L1 elements and eleven recently integrated Alu elements from 160 chromosomes (80 individuals representing four diverse human populations). Analysis of worldwide samples at L1 loci revealed 292 segregating sites and a nucleotide diversity of 0.0050. For Ya5 Alu loci, there were 129 segregating sites and nucleotide diversity was estimated at 0.0045. The Alu and L1 sequence diversity varied element to element. No completely or partially deleted Alu or L1 alleles were identified during the analysis. These data suggest that mobile element insertions are identical by descent characters for the study of human population genetics.
Black or African American↗
Analysis of piezoelectric strip waveguides based on the effective index and pseudospectral element methods.
Integrated acousto-optical circuits in LiNbO3 are attractive devices for applications especially in advanced WDM systems. In order to increase the scale of integration and to reduce the RF driving power of these devices, one promising approach is to use acoustical waveguides with smaller lateral dimensions. In this paper the combination of a pseudospectral elements method (PSEM) and an effective index method (EIM) for the analysis of film-loaded surface acoustic waveguides (SAWG's) is presented. Numerical results demonstrate the exponential rate of convergence of the PSEM and agree with the computations performed via the transverse resonance technique. Due to the exponential rate of convergence of the PSEM and to a mapping transformation in the substrate, the piezoelectric problem in the depth direction of the structures is evaluated by a low number of Legendre polynomials. The method is applied to the analysis of several layered SAWG's of practical interest for AO devices, such as metal/SiO2/X - YLiNbO3, in which the metal is either Au, Al, In, or Ti.
Journal Article↗
Measurements of scattered light on a microchip flow cytometer with integrated polymer based optical elements.
Flow cytometry is widely used for analyzing microparticles, such as cells and bacteria. In this paper, we report an innovative microsystem, in which several different optical elements (waveguides, lens and fiber-to-waveguide couplers) are integrated with microfluidic channels to form a complete microchip flow cytometer. All the optical elements, the microfluidic system, and the fiber-to-waveguide couplers were defined in one layer of polymer (SU-8, negative photoresist) by standard photolithography. With only a single mask procedure required, all the fabrication and packaging processes can be finished in one day. Polystyrene beads were measured in the microchip flow cytometer, and three signals (forward scattering, large angle scattering and extinction) were measured simultaneously for each bead. To our knowledge this is the first time forward scattered light and incident light extinction were measured in a microsystem using integrated optics. The microsystem can be applied for analyzing different kinds of particles and cells, and can easily be integrated with other microfluidic components.
Equipment Design↗
Foreign DNA introduced by calcium phosphate is integrated into repetitive DNA elements of the mouse L cell genome.
We investigated the sites of integration of exogenous DNA fragments introduced by DNA-mediated gene transfer. Mouse Ltk- cells were transformed with the herpes simplex virus thymidine kinase gene and pBR322 DNA by the calcium phosphate precipitation method. Some of the integrated exogenous DNA sequences were recovered from the stable tk+ transformants in the form of plasmids that were capable of propagation in bacteria. Four plasmids derived from two cloned cell lines were analyzed in detail by nucleotide sequencing and hybridization techniques. These plasmids contained a total of seven cellular-exogenous DNA junctions. In all cases, there was no sequence homology between the exogenous and cellular DNA sequences adjacent to the joining sites, and no specific exogenous or cellular sequences occurred at the junctions. Rearrangement or deletion of Ltk- DNA was always associated with the integration of exogenous DNA. All of the assignable cellular sequences at the junctions were repetitive sequences. Two of these sequences were from the MIF-1 repetitive sequence family, and a third consisted of a 40-base pair simple copolymer of alternating deoxyadenosine-deoxythymidine. Our results suggest that repetitive sequences are relatively favorable sites for the integration of exogenous DNA.
Animals↗
Effect of short interspersed element sequences on the integration and expression of a reporter gene in the preimplantation-stage mouse embryos.
Based on the assumption that foreign DNA sequences may have increased chance of integration into the host genome if they are flanked by high copy-numbered genomic sequences such as SINEs (short interspersed elements), we investigated the integration frequency of Lac Z reporter gene flanked by a fused B1/B2 in an in vivo system using pronuclear microinjection technique in the mouse. The SINE-flanked DNA showed a 4-fold increased integration frequency of the reporter gene than the control DNA (63% vs. 16%). Moreover, the level of beta-galactosidase expression, estimated from the X-Gal staining intensity in transgenic embryos, was greatly higher in SINE-carrying DNA. These results suggest that the SINE sequences can serve a very useful tool in improving the efficiency of current transgenic animal technology.
Animals↗
Site-specific insertion of biologically functional adventitious genes into the Streptomyces lividans chromosome.
We report that transformation of Streptomyces lividans with cloned DNA of the SLP1 genetic element results in integration of the element at the same chromosomal locus (attB) normally occupied by SLP1 in its original host, Streptomyces coelicolor, and in S. lividans that has received SLP1 by mating. We constructed SLP1 derivatives that can integrate foreign DNA at the attB site and used these to introduce adventitious DNA sequences into the S. lividans chromosome. We also identified three regions of SLP1 essential for its integration and demonstrated that integration of the SLP1 element does not require expression of functions necessary for stable maintenance or transfer of extrachromosomal forms of SLP1.
Cloning, Molecular↗
Pkc1 and the upstream elements of the cell integrity pathway in Saccharomyces cerevisiae, Rom2 and Mtl1, are required for cellular responses to oxidative stress.
In this study we analyze the participation of the PKC1-MAPK cell integrity pathway in cellular responses to oxidative stress in Saccharomyces cerevisiae. Evidence is presented demonstrating that only Pkc1 and the upstream elements of the cell integrity pathway are essential for cell survival upon treatment with two oxidizing agents, diamide and hydrogen peroxide. Mtl1 is characterized for the first time as a cell-wall sensor of oxidative stress. We also show that the actin cytoskeleton is a cellular target for oxidative stress. Both diamide and hydrogen peroxide provoke a marked depolarization of the actin cytoskeleton, being Mtl1, Rom2 and Pkc1 functions all required to restore the correct actin organization. Diamide induces the formation of disulfide bonds in newly secreted cell-wall proteins. This mainly provokes structural changes in the cell outer layer, which activate the PKC1-MAPK pathway and hence the protein kinase Slt2. Our results led us to the conclusion that Pkc1 activity is required to overcome the effects of oxidative stress by: (i) enhancing the machinery required to repair the altered cell wall and (ii) restoring actin cytoskeleton polarity by promoting actin cable formation.
Base Sequence↗
Derepression of excision of integrative and potentially conjugative elements from Streptococcus thermophilus by DNA damage response: implication of a cI-related repressor.
A DNA-damaging agent, mitomycin C, derepresses the site-specific excision of two integrative and potentially conjugative elements from Streptococcus thermophilus, ICESt1 and ICESt3. The regulation pathway involves a repressor related to phage lambda cI repressor. It could also involve a putative regulator related to another type of phage repressors, the "cI-like" repressors.
DNA Damage↗
CREB is one component of the binding complex of the Ces-2/E2A-HLF binding element and is an integral part of the interleukin-3 survival signal.
The Ces-2/E2A-HLF binding element (CBE) is recognized by Caenorhabditis elegans death specification gene product Ces-2 and human acute lymphocytic leukemia oncoprotein E2A-HLF. In an attempt to identify a cellular CBE-binding protein(s) that may be involved in apoptosis regulation in mammals, multiple nuclear binding complexes of CBE were identified in various mammalian cell lines and tissues by electrophoretic mobility shift assay. Cyclic AMP (cAMP)-responsive element (CRE)-binding protein (CREB) was present in one major CBE complex of Ba/F3 and TF-1 cells, and both in vitro-translated and Escherichia coli-synthesized CREB bound to CBE. Activation of CREB by cAMP-elevating chemicals or the catalytic subunit of protein kinase A (PKAc) resulted in induction of the CBE-driven reporter gene. Stimulation of Ba/F3 cells with interleukin-3 (IL-3) promptly induced phosphorylation of CREB at serine(133) partially via a PKA-dependent pathway. Consistently, Ba/F3 cell survival in the absence of IL-3 was prolonged by activation of PKA. Conversely, treatment of cells with a PKA inhibitor or expression of the dominant negative forms of the regulatory subunit type I of PKA and CREB overrode the survival activity of IL-3. Last, the bcl-2 gene was demonstrated to be one candidate cellular target of the CREB-containing CBE complex, as mutations in the CRE and CBE sites significantly reduced the IL-3 inducibility of the bcl-2 promoter. Together, our results suggest that CREB is one cellular counterpart of Ces-2/E2A-HLF and is part of IL-3 dependent apoptosis regulation in hematopoietic cells.
Animals↗
Services for mentally ill homeless persons: street-level integration.
The key elements of a systems integration approach to delivery of human services are reviewed in terms of their application to services for mentally ill homeless persons. The example of a mental health outreach project illustrates the service- and systems-integrating influences of clinical case management with this population, and the ability of a "bottom-up" street-level approach to improve coordination and service accessibility for clients in general is discussed.
Community Health Workers↗