Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “mobile elements”

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.

At least 541 records · Page 30Linked to original sources

Circular copies of mobile dispersed genetic elements in cultured Drosophila melanogaster cells.

Extrachromosomal supercoiled circular copies of mobile dispersed genetic elements mdg1, mdg3 and copia have been isolated from 67J25D and Kc lines of cultured Drosophila melanogaster cells. With the exception of the copia element in the line Kc, all circular molecules contain only one long terminal repeat. Both whole-length circular copies and molecules with deletion from the internal segment of the copia element have been detected in the line 67J25D. Mdg3-specific circular molecules in the line Kc are represented by the deleted molecules only. Similar copies of mdg3 are also present in chromosomal DNA of flies and cultured cells. The analysis of the mdg3 transcription in both cell lines suggests that extrachromosomal molecules of mdg may be created by reverse transcription.

Animals↗

Mobile dispersed genetic element MDG1 of Drosophila melanogaster: structural organization.

The whole-length mobile dispersed genetic element mdg1 has been cloned from D. melanogaster genome. It contains DNA fragments described earlier as Dm225 and Dm234, Mdg1 is 7.2 kb long and framed with two direct repeats of 300-400 base pairs each. Mdg1 family is represented by about 25 copies in the genome of flies and by 200 copies in the genome of cultured cell line 67J25D. Virtually all the copies in the genome of D. melanogaster have the same restriction map. Oligo(dA)-oligo(dT) regions were found within mdg1.

Animals↗

[An increase in transposition frequency of copia-like elements in isogenic crosses with a balancer line].

Distribution spectra of mdg1, Dm412, copia, and B104 in a descending series of isogenic scute lines of Drosophila melanogaster were analyzed. Transpositions of mobile elements occurring during isogenization were shown to be the main source of insertion site polymorphism detected in daughter lines. Isogenization resulted in a significant increase in transposition frequency (approximately approximately 10(-2) per site per genome per generation).

Animals↗

Genetic instability in Drosophila melanogaster: the genetics of an MR element that makes complete P insertion mutations.

An MR element that maps to a specific locus in chromosome 3 of Drosophila melanogaster has the unusual feature of producing complete P (a mobile element) sequence mutations at several X chromosome loci. This MR also increases the frequency of mitotic recombination. Evidence is given for the transposition of MR. The complete P insertion mutations are autonomously unstable and are capable of causing otherwise stable incomplete (defective) P insertion mutations to revert. These results complement the analysis of P element functions with a synthetic complete P derivative. The genetic basis for the mutational-mitotic recombinational components of "hybrid dysgenesis" is conveniently explicable in terms of MR elements present in the genomes of flies present in the wild.

Animals↗

Chloramphenicol resistance in Clostridium difficile is encoded on Tn4453 transposons that are closely related to Tn4451 from Clostridium perfringens.

The chloramphenicol resistance gene catD from Clostridium difficile was shown to be encoded on the transposons Tn4453a and Tn4453b, which were structurally and functionally related to Tn4451 from Clostridium perfringens. Tn4453a and Tn4453b excised precisely from recombinant plasmids, generating a circular form, as is the case for Tn4451. Evidence that this process is mediated by Tn4453-encoded tnpX genes was obtained from experiments which showed that in trans these genes complemented a Tn4451tnpX delta 1 mutation for excision. Nucleotide sequencing showed that the joint of the circular form generated by the excision of Tn4453a and Tn4453b was similar to that from Tn4451. These results suggest that the Tn4453-encoded TnpX proteins bind to similar DNA target sequences and function in a manner comparable to that of TnpX from Tn4453. Furthermore, it has been shown that Tn4453a and Tn4453b can be transferred to suitable recipient cells by RP4 and therefore are mobilizable transposons. It is concluded that, like Tn4451, they must encode a functional tnpZ gene and a target oriT or RSA site. The finding that related transposable elements are present in C. difficile and C. perfringens has implications for the evolution and dissemination of antibiotic resistance genes and the mobile elements on which they are found within the clostridia.

Base Sequence↗

[Induction of unstable mutations in Drosophila melanogaster by microinjection of oncogenic virus DNA into the embryo polar plasma. Insertional nature of mutations].

We have demonstrated that mutations induced in Drosophila melanogaster by the microinjections of adenovirus Sa7 DNA in early embryos are of insertional nature. The role of insertional elements is played by the Drosophila transposons, but not by the virus DNA. The ability of oncoviral DNA to induce transpositions of mobile elements in recipient genome is the molecular basis of this system of genetic instability.

Adenoviridae↗

Mobile surgical hospital design: lessons from 5th MASH surgical packages for Operations Desert Shield/Desert Storm.

Operations Desert Shield/Desert Storm defined and tested a number of assumptions about the abilities of the Mobile Army Surgical Hospital. These assumptions involved the adequacies of mobility, both strategic and tactical, the number of hospital beds, surgical capability, and set-up time. This article reviews the characteristics, staffing, and surgical abilities of the four types of surgical packages deployed by the 5th Mobile Army Surgical Hospital in response to the changing patient care and tactical situation. These packages were the Forward Surgical Team, Forward Surgical Element, Mobile Army Surgical Hospital(-), and Mobile Army Surgical Hospital. Seven variables as they relate to hospital weight and cubic space are introduced. Mobility and surgical ability are emphasized as the first and second highest priority to consider in a proposed methodology when developing Mobile Army Surgical Hospitals.

Middle East↗

Mobilized retrotransposon Tos17 of rice by alien DNA introgression transposes into genes and causes structural and methylation alterations of a flanking genomic region.

Tos17 is a copia-like endogenous retrotransposon of rice, which can be activated by various stresses such as tissue culture and alien DNA introgression. To confirm element mobilization by introgression and to study possible structural and epigenetic effects of Tos17 insertion on its target sequences, we isolated all flanking regions of Tos17 in an introgressed rice line (Tong35) that contains minute amount of genomic DNA from wild rice (Zizania latifolia). It was found that there has been apparent but limited mobilization of Tos17 in this introgression line, as being reflected by increased but stable copy number of the element in progeny of the line. Three of the five activated copies of the element have transposed into genes. Based on sequence analysis and Southern blot hybridization with several double-enzyme digests, no structural change in Tos17 could be inferred in the introgression line. Cytosine methylation status at all seven CCGG sites within Tos17 was also identical between the introgression line and its rice parent (Matsumae)-all sites being heavily methylated. In contrast, changes in structure and cytosine methylation patterns were detected in one of the three low-copy genomic regions that flank newly transposed Tos17, and all changes are stably inherited through selfed generations.

3' Flanking Region↗

Distribution and characterization of plasmid-related sequences in the chromosomal DNA of different thermophilic Methanobacterium strains.

The genomes of several thermophilic members of the genus Methanobacterium were analyzed for homology to the related restriction-modification plasmids pFV1 and pFZ1 from M. thermoformicicum strains THF and Z-245, respectively. Two plasmid regions, designated FR-I and FR-II, could be identified with chromosomal counterparts in six Methanobacterium strains. Multiple copies of the pFV1-specific element FR-I were detected in the M. thermoformicicum strains CSM3, FF1, FF3 and M. thermoautotrophicum delta H. Sequence analysis showed that one FR-I element had been integrated in almost identical sequence contexts into the chromosomes of the strains CSM3 and delta H. Comparison of the FR-I elements from these strains with that from pFV1 revealed that they consisted of two subfragments, boxI (1118 bp) and boxII (383 bp), the order of which is variable. Each subfragment was identical on the sequence level with the corresponding plasmid-borne element and was flanked by terminal direct repeats with the consensus sequence A(A/T)ATTT. These results suggest that FR-I represents a mobile element. FR-II was located on both plasmids pFV1 and pFZ1, and on the chromosome of M. thermoformicicum strains THF, CSM3 and HN4. Comparison of the nucleotide sequences of the two plasmid FR-II copies and that from the chromosome of strain CSM3 showed that the FR-II segments were approximately 2.5-3.0 kb in size and contained large open reading frames (ORFs) that may encode highly related proteins with an as yet unknown function.

Amino Acid Sequence↗

The Jak/Stat pathway and urokinase receptor signaling in human aortic vascular smooth muscle cells.

The binding of urokinase plasminogen activator (uPA) to its specific receptor (uPAR) facilitates migration of vascular smooth muscle cells (VSMC). However, the signaling cascade utilized by the urokinase receptor is only incompletely understood. We investigated intracellular uPA/uPAR signaling in human aortic VSMC from the cell membrane to the nucleus. uPA binding to VSMC induced a rapid and pronounced increase in tyrosine phosphorylation of several proteins with molecular masses of 53-60, 85-90, and 130-140 kDa. By using co-immunoprecipitation techniques and in vitro kinase assays, the uPAR-associated proteins were identified as Janus (Jak) and Src non-receptor protein-tyrosine kinases (PTK) Jak1, Tyk2, and p59(fyn), p53/56(lyn), p53/59(hck), and p55(fgr). Furthermore, uPA induced a time-dependent reversible translocation of the Stat1 (signal transducer and activator of transcription) protein to the VSMC nuclei, as shown by confocal microscopy studies. Using an electrophoretic mobility shift assay, we then demonstrated that Stat1 is rapidly activated in response to stimulation with uPA and specifically binds to the DNA regulatory elements GAS (interferon-gamma activation site) and ISRE (interferon-stimulated response element). Mobility supershift experiments confirmed DNA-protein complexes containing Stat1 protein. Migration experiments with double immunofluorescence staining revealed polarization of uPAR, and colocalization with Jak1 and Tyk2 to the leading edge of the migrating cells. Under the same conditions, Jak2, Jak3, and the Src-PTKs remained randomly distributed over the entire body of the cells. Our studies therefore suggest that, in VSMC, the uPAR-signaling complex utilizes at least two different mechanisms, a direct signaling pathway utilizing the Jak/Stat cascade and a second signal transduction mechanism via Src-like protein-tyrosine kinases. uPA-induced signaling via Jak/Stat is most likely involved in the regulation of cell migration, while the functional purpose of the uPA-associated Src-PTK activation remains to be elucidated.

Cell Movement↗

Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440.

A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.

Adaptation, Physiological↗

Characterization of the global transcriptional responses to different types of DNA damage and disruption of replication in Bacillus subtilis.

DNA damage and perturbations in DNA replication can induce global transcriptional responses that can help organisms repair the damage and survive. RecA is known to mediate transcriptional responses to DNA damage in several bacterial species by inactivating the repressor LexA and phage repressors. To gain insight into how Bacillus subtilis responds to various types of DNA damage, we measured the effects of DNA damage and perturbations in replication on mRNA levels by using DNA microarrays. We perturbed replication either directly with p-hydroxyphenylazo-uracil (HPUra), an inhibitor of DNA polymerase, or indirectly with the DNA-damaging reagents mitomycin C (MMC) and UV irradiation. Our results indicate that the transcriptional responses to HPUra, MMC, and UV are only partially overlapping. recA is the major transcriptional regulator under all of the tested conditions, and LexA appears to directly repress the expression of 63 genes in 26 operons, including the 18 operons previously identified as LexA targets. MMC and HPUra treatments caused induction of an integrative and conjugative element (ICEBs1) and resident prophages (PBSX and SPbeta), which affected the expression of many host genes. Consistent with previous results, the induction of these mobile elements required recA. Induction of the phage appeared to require inactivation of LexA. Unrepaired UV damage and treatment with MMC also affected the expression of some of the genes that are controlled by DnaA. Furthermore, MMC treatment caused an increase in origin-proximal gene dosage. Our results indicate that different types of DNA damage have different effects on replication and on the global transcriptional profile.

Bacillus Phages↗

Insertional mutagenesis by transposable elements in the mammalian genome.

Several mammalian repetitive transposable genetic elements were characterized in recent years, and their role in mutagenesis is delineated in this review. Two main groups have been described: elements with symmetrical termini such as the murine IAP sequences and the human THE 1 elements and elements characterized by a poly-A rich tail at the 3' end such as the SINE and LINE sequences. The characteristic property of such mobile elements to spread and integrate in the host genome leads to insertional mutagenesis. Both germline and somatic mutations have been documented resulting from the insertion of the various types of mammalian repetitive transposable genetic elements. As foreseen by Barbara McClintock, such genetic events can cause either the activation or the inactivation of specific genes, resulting in their identification via an altered phenotype. Several disease states, such as hemophilia and cancer, are the result of this apparent aspect of genome instability.

Animals↗

The geochemistry of river particulates from the continental USA: major elements.

River particulates have been collected from twenty-three rivers from throughout the continental USA. The rivers drain mostly large basins (basin areas range from 2.1 x 10(3) to 2970 x 10(3) km2) composed of mixed lithologies, and spanning a wide range of climatic conditions as evidenced by a large variation in air and ground water temperatures, precipitation, and runoff. Suspended particulates have been analyzed for organic and inorganic carbon, as well as the major elements Al, Fe, Mn, K, Si, Ca, Mg, and Na. Also determined were suspended sediment loads at the time of sampling, particle surface areas, and grain size distributions. Five-year average river water chemistry and suspended sediment concentrations, obtained from USGS water supply reports, are also included as supporting information. Particle chemistry systematically varies with rates of runoff, with high runoff rivers transporting the most heavily altered particulates and low runoff rivers carrying the least altered. Degrees of alteration are indicated by the extent to which the refractory, nonmobile elements Al and Fe are concentrated into the particulates and the extent to which the most easily weathered elements Na, Ca, and Mg have been leached. Overall, the susceptibility of elements towards leaching is consistent with numerous previous descriptions of element mobility on weathering. A simple predictive model has been developed to explore and explain the observed trends between particle composition and river runoff. Thus, the elemental composition of riverine particulates may be given by the expression PCOi = [(Propi)TM-DCOi]/SS, where PCOi is the concentration of element i (as the oxide) in a riverine particulate, Propi is the proportion of i (as the oxide) in unweathered rock, DCOi is the dissolved concentration of i (as the equivalent oxide), TM is the total rock derived mass dissolved in river water, and SS is suspended sediment concentration. To utilize this equation, a model was first developed to predict the concentration of river solutes with the input of temperature, precipitation, and a limited number of weathering parameters. Combining this solute model with the above predictive equation for particle composition, it was discovered that the observed trends between particle composition and runoff require the special circumstance of decreasing SS with increasing runoff. Hence, the composition of river particulates depends both on the climate parameters of runoff and temperature (as they control dissolved river chemistry) and the nonclimate parameters including elevation, relief, tectonics, and basin area that control the SS load of rivers.

Climate↗

Evolutionary conservation and molecular characteristics of repetitive sequences of Drosophila koepferae.

Thirteen middle repetitive DNA clones obtained from the genome of Drosophila koepferae have been tested for their evolutionary conservation in the other seven species of the buzzatii and martensis clusters (repleta group). All but two of these clones exhibit qualitatively similar patterns of hybridization in the eight species. The average interspecific hybridization signal is 85 per cent of that found intraspecifically, ranging from 73 to 93 per cent. Partial sequencing of six of these clones has shown sequences related to the retrotransposon Gypsy, first characterized in D. melanogaster, as well as to the Anopheles gambiae LINE elements T1Ag and Q. A fragment of a hitherto unknown, short inverted repeat transposable element has also been found. The evolutionary conservation of repetitive D. koepferae sequences seems to be related to the high proportion of simple DNA and inactive mobile elements in the genome of this species.

Amino Acid Sequence↗

The transposable portion of the genome of Drosophila algonquin is very different from that in D. melanogaster.

Four clones containing different transposable elements were isolated from a genomic library of Drosophila algonquin. Each clone was hybridized to salivary-gland chromosomes of three lines of D. algonquin and two lines of D. affinis. The estimated copy number in D. algonquin of the four element families varied from 59 to 333. The occupancy per site varied from 0.64 to 0.75. Thus the transposable portion of the D. algonquin genome is dominated by a few high-copy-number elements, each characterized by high occupancies. The copy number and occupancy values were very similar in D. affinis. This differs from the situation in D. melanogaster mobile middle-repetitive DNA, which has at least 30 and perhaps as many as 100 different families of mobile elements, with copy numbers ranging from 5 to 100. When several lines have been examined, elements in D. melanogaster are revealed to have very low occupancies. The four D. algonquin elements do not hybridize with D. melanogaster DNA, but they did hybridize with 15 obscura-group species, thereby revealing a pattern that is consistent with concerted evolution.

Animals↗

Evidence of participation of cytoskeleton of heart muscle cells during the invasion of Trypanosoma cruzi.

The participation of heart muscle cells (HMC) cytoskeleton during its interaction with Trypanosoma cruzi was investigated. Pre-treatment of heart muscle cells with cytochalasin B (CB) or D (CD) prior to 1 and 3 h of interaction with T. cruzi inhibited the uptake of parasites by about 65% and 75%. T. cruzi was not able to invade fixed HMC, and fixed parasites were not internalized in either normal and CD-treated HMC. Transmission electron microscopy showed cell membrane projections of HMC enclosing the parasite during the invasion process after short periods of interaction (5 to 30 min). During the parasite internalization process, sarcolemma extensions were observed inside the cytoplasmic vacuole, suggesting that the endocytic event may involve internalization of a "self membrane". Images of cytoskeleton elements mobilization during T. cruzi penetration of HMC were obtained following treatment of cells with Triton X-100. Our results suggest an active involvement of HMC cytoskeleton elements during the interiorization of metacyclic forms of T. cruzi.

Animals↗