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Results for “integrative element”

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At least 109 records · Page 6Linked to original sources
PubMed2002

Common physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements.

Sleeping Beauty (SB) is the most active Tc1/mariner-type transposable element in vertebrates, and is therefore a valuable vector for transposon mutagenesis in vertebrate models and for human gene therapy. We have analyzed factors affecting target site selection of SB in mammalian cells, by generating transposition events from extrachromosomal plasmids to chromosomes. In contrast to the local hopping observed when transposition is induced from a chromosomal context, mapping of 138 unique SB insertions on human chromosomes showed a fairly random genomic distribution, and a 35% occurrence of transposition into genes. Inspection of the DNA flanking the sites of element integration revealed significant differences from random DNA in both primary sequence and physical properties. The consensus sequence of SB target sites was found to be a palindromic AT-repeat, ATATATAT, in which the central TA is the canonical target site. We found however, that target site selection is determined primarily on the level of DNA structure, and not by specific base-pair interactions. Computational analyses revealed that insertion sites tend to have a bendable structure and a palindromic pattern of potential hydrogen-bonding sites in the major groove of the DNA. These features appear conserved in the Tc1/mariner family of transposons and in other, distantly related elements that share a common catalytic domain of the transposase, and integrate fairly randomly. No similar target site preference was found for non-randomly integrating elements. Our results suggest common factors influencing target site selection of a wide range of transposable elements.

Animals↗
PubMed1995

Gene disruptions using P transposable elements: an integral component of the Drosophila genome project.

Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome. DNA flanking the insertions is sequenced, thereby placing an extensive series of genetic markers on the physical genomic map and associating insertions with specific open reading frames and genes. Insertions from the collection now lie within or near most Drosophila genes, greatly reducing the time required to identify new mutations and analyze gene functions. Information revealed from these studies about P element site specificity is being used to target the remaining open reading frames.

Animals↗
PubMed2025

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years.

Mobile genetic elements (MGEs), including plasmids, phages and genome islands, are major sources of bacterial genetic diversity. The small plasmid pT181 confers tetracycline resistance in bacterial pathogen Staphylococcus aureus via an efflux pump, TetK. pT181 was one of the earliest sequenced S. aureus plasmids, and has been isolated in both clinical and livestock-associated strains for decades, both as an independent replicon and integrated in the chromosome as part of staphylococcal cassette chromosome mec (SCCmec). Bacterial genome analysis tools and high-quality sequences with metadata are publicly available, but these resources remain underleveraged for examining historical data, especially when studying the spread of MGEs across a species and over time. Using publicly available reads and metadata, we explored the evolution of pT181 over almost seven decades of samples to identify temporal trends in sequence evolution, copy number changes, and spread across S. aureus and beyond. pT181 was prevalent across S. aureus (found in 9.5% of 83,366 genomes tested), with a conserved sequence outside of three hypervariable regions. The history of pT181 since 1954 is characterized by spread across strains, significant variation in plasmid copy number of the independent replicon, and increasing frequency of integration of the plasmid into the S. aureus chromosome. We have identified multiple chromosomal integration locations of the plasmid, including outside of the previously characterized SCCmec. We find that pT181 has been transferred across staphylococcaceae and into a Gram-negative species. The repeated integration of pT181 into the chromosome may indicate co-evolution of the plasmid and the host, potentially to facilitate increased antibiotic resistance.

Journal Article↗
PubMed2001

A full-length and potentially active LINE element is integrated polymorphically within the IGL locus in a genomically unstable region of chromosome 22.

Leukemic cells of a patient diagnosed with chronic myeloid leukemia (CML) showed a complex BCR-ABL1 rearrangement hidden within a normal appearing karyotype. Previous molecular studies had established that the 3' BCR had recombined at a novel site within the variable region of the immunoglobulin lambda locus ( IGL). A segment of DNA mapping very close to the site of the IGL/3' BCR recombination recognized a previously undescribed insertion polymorphism. A combination of molecular hybridization studies and long-range polymerase chain reaction was used to isolate a 6-kb full-length long interspersed nuclear element (LINE or L1), here designated L1(IGL), which occupies 19% of alleles in the general population. Although unclonable, DNA sequence analysis by a primer walking approach established that L1(IGL) has features characteristic of an actively retrotransposing element. The L1(IGL) element has a 5' untranslated region, two open reading frames (ORF-1 and ORF-2), a 3' untranslated region and terminates in a poly-A tail. We compared the DNA sequence and the predicted amino acid sequence of L1(IGL) with a consensus sequence compiled from seven reported active L1 elements. This analysis indicated that L1(IGL) has high potential for involvement in as yet undetermined somatically and constitutionally acquired disease, not only through recombination mechanisms, but also through retrotransposition events. This full-length L1 element maps close within the IGLlocus to L1.2, one of only nine active L1 elements that have been reported so far. L1(IGL) and L1.2 map within a wider and well-recognized region of genomic instability on chromosome 22.

Base Sequence↗
PubMed1987

Peptide-hormone- and serotonin-immunoreactive tumour cells in carcinoma of the prostate.

In order to establish the extent of neuroendocrine differentiation and the occurrence of neurohormonal peptides in the neoplastic cells of prostatic carcinomas, silver-staining and immunocytochemical techniques were used. All gave satisfactory results. The incidence of the neuroendocrine cells seemed to be higher in the fresh "Bouin-fixed" biopsy specimens than in the conventionally "formalin-fixed" specimens from archival paraffin blocks. All carcinomas demonstrated argyrophil cells as an integral element of the tumour. In highly differentiated carcinomas (grade I) these cells were scattered focally, intermingled with non-argyrophil cells in typical adenocarcinomas; their incidence was estimated to be about the same as in benign prostatic hyperplasia. Most of them were immunoreactive with antisera raised against serotonin and/or TSH (thyroid stimulating hormone). In moderately and poorly differentiated (grades II-III) carcinomas, however, the argyrophil cells were more numerous and showed greater variation in growth pattern; only occasionally they displayed a typical carcinoid-like structure. Moderately and poorly differentiated carcinomas also showed a greater variation in the number and kinds of peptide immunoreactivities than the highly differentiated carcinomas. In addition to serotonin- and TSH-immunoreactive cells as the most prevalent type, now also human chorionic gonadotrophin (HCG-alpha), adrenocorticotropic hormone (ACTH), leu-enkephalin, beta-endorphin, somatostatin, glucagon and calcitonin immunoreactive cells could be found within certain tumour areas and often with a distinctly patchy distribution. In two cases, where the tumour cells in the metastases were also investigated, they were found to be both argyrophil and immunoreactive with the same antisera as those of the primary tumour. Our findings emphasise the fact that prostatic carcinomas are more complex and heterogenous than previously thought, exhibiting endocrine differentiation as an integral element of virtually all prostatic adenocarcinomas.

Adenocarcinoma↗
PubMed2024

It's complicated: relationships between integrative and conjugative elements and their bacterial hosts.

Integrative and conjugative elements (ICEs) are typically found integrated in a bacterial host chromosome. They can excise, replicate, and transfer from cell to cell. Many contain genes that confer phenotypes to host cells, including antibiotic resistances, specialized metabolisms, phage defense, and symbiosis or pathogenesis determinants. Recent studies revealed that at least three ICEs (ICEclc, Tn916, and TnSmu1) cause growth arrest or death of host cells upon element activation. This review highlights the complex interactions between ICEs and their hosts, including the recent examples of the significant costs to host cells. We contrast two examples of killing, ICEclc and Tn916, in which killing, respectively, benefits or impairs conjugation and emphasize the importance of understanding the impacts of ICE-host relationships on conjugation. ICEs are typically only active in a small fraction of cells in a population, and we discuss how phenotypes normally occurring in a small subset of host cells can be uncovered.

Conjugation, Genetic↗
PubMed2002

Computer-integrated finite element modeling of human middle ear.

The objective of this study was to produce an improved finite element (FE) model of the human middle ear and to compare the model with human data. We began with a systematic and accurate geometric modeling technique for reconstructing the middle ear from serial sections of a freshly frozen temporal bone. A geometric model of a human middle ear was constructed in a computer-aided design (CAD) environment with particular attention to geometry and microanatomy. Using the geometric model, a working FE model of the human middle ear was created using previously published material properties of middle ear components. This working FE model was finalized by a cross-calibration technique, comparing its predicted stapes footplate displacements with laser Doppler interferometry measurements from fresh temporal bones. The final FE model was shown to be reasonable in predicting the ossicular mechanics of the human middle ear.

Acoustic Stimulation↗
PubMed1997

TraM of plasmid R1 controls transfer gene expression as an integrated control element in a complex regulatory network.

Site-directed mutagenesis was used to investigate the functions of the traM gene in plasmid R1-mediated bacterial conjugation. Three mutant alleles, a null mutation, a sense mutation and a stop mutation, were recombined back into the R1-16 plasmid, a transfer-derepressed (finO-) variant of plasmid R1. The frequency of conjugative transfer of the traM null mutant derivative of R1-16 was 10(7)-fold lower than that of the isogenic parent plasmid, showing the absolute requirement for this gene in conjugative transfer of plasmid R1. Measurements of the abundance of plasmid specified traJ, traA and traM mRNAs, TraM protein levels, and complementation studies indicated that the traM gene of plasmid R1 has at least two functions in conjugation: (i) positive control of transfer gene expression; and (ii) a function in a process distinct from gene expression. Since expression of the negatively autoregulated traM gene is itself affected positively by the expression of the transfer operon genes, this gene constitutes a decisive element within a regulatory circuit that co-ordinates expression of the genes necessary for horizontal DNA transfer. Based on our studies, we present a novel model for the regulation of the transfer genes of plasmid R1 that might also be applicable to other IncF plasmids.

Alleles↗
PubMed2003

Integrating trace element metabolism from the cell to the whole organism.

The redox chemistry of copper (Cu) makes this both a powerful enzyme catalyst and a dangerous reactant that generates hydroxyl radical. Although virtually all cells from microbes to mammals must acquire Cu to drive important biochemical reactions, the potential toxicity of Cu demands an exquisite level of vectorial transport and homeostatic control. Our laboratory is interested in how organisms acquire Cu through the action of high-affinity plasma membrane Cu transporters of the copper transport protein (Ctr) class of proteins. We have isolated Ctr Cu transporters from baker's yeast and fission yeast and from flies, mice and mammals. This review will focus on understanding how the Ctr high-affinity Cu transport proteins function, from their biochemical mechanism of action in yeast and cultured metazoan cells to their roles in Cu delivery and mammalian embryonic development.

Animals↗
PubMed1986

Computer security: a necessary element of integrated information systems.

The Matheson Report sees the medical library as playing a key role in a network of interlocking information bases that will extend from central repositories of medical information to each physician's personal records. It appears, however, that the role of security in this vision has not been fully delineated. This paper discusses problems in maintaining the security of confidential medical information, the state of the applicable law, and techniques for security (with special emphasis on the UNIX operating system). It is argued that the absence of security threatens any plan to build an information network, as there will be resistance to any system that may give intruders access to confidential data.

Computers↗