Relevant bibliographies by topics / Insertion elements, DNA

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Academic literature on the topic 'Insertion elements, DNA'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2023

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Journal articles on the topic "Insertion elements, DNA"

1

Hoogland, Christine, and Christian Biémont. "Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number." Genetics 144, no. 1 (September 1, 1996): 197–204. http://dx.doi.org/10.1093/genetics/144.1.197.

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Abstract Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.
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Wuitschick, Jeffrey D., Paul R. Lindstrom, Alison E. Meyer, and Kathleen M. Karrer. "Homing Endonucleases Encoded by Germ Line-Limited Genes in Tetrahymena thermophila Have APETELA2 DNA Binding Domains." Eukaryotic Cell 3, no. 3 (June 2004): 685–94. http://dx.doi.org/10.1128/ec.3.3.685-694.2004.

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ABSTRACT Three insertion elements were previously found in a family of germ line-limited mobile elements, the Tlr elements, in the ciliate Tetrahymena. Each of the insertions contains an open reading frame (ORF). Sequence analysis of the deduced proteins encoded by the elements suggests that they are homing endonucleases. The genes are designated TIE1-1, TIE2-1, and TIE3-1 for Tetrahymena insertion-homing endonuclease. The endonuclease motif occupies the amino terminal half of each TIE protein. The C-terminal regions of the proteins are similar to the APETELA2 DNA binding domain of plant transcription factors. The TIE1 and TIE3 elements belong to families of repeated sequences in the germ line micronuclear genome. Comparison of the genes and the deduced proteins they encode suggests that there are at least two distinct families of homing endonuclease genes, each of which appears to be preferentially associated with a specific region of the Tlr elements. The TIE1 and TIE3 elements and their cognates undergo programmed elimination from the developing somatic macronucleus of Tetrahymena. The possible role of homing endonuclease-like genes in the DNA breakage step in developmentally programmed DNA elimination in Tetrahymena is discussed.
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Ryan, Margret, Jerry D. Johnson, and Lee A. Bulla Jr. "Insertion sequence elements in Bacillus thuringiensis subsp. darmstadiensis." Canadian Journal of Microbiology 39, no. 7 (July 1, 1993): 649–58. http://dx.doi.org/10.1139/m93-094.

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Two variants of insertion sequence IS231, named IS231G and H, were isolated from Bacillus thuringiensis subsp. darmstadiensis 73-E-10-2 (BTD2), an isolate toxic to dipteran insects, and characterized by DNA sequence analysis. They are encoded consecutively as direct repeats on an EcoRI fragment of 5.6 kilo base pairs. Direct tandem repeats of IS231 elements have not been previously reported. Both elements are closely related to other members of the IS231 family that have been isolated from B. thuringiensis strains toxic to lepidopteran as well as to dipteran insects. A close correlation exists between the evolutionary relationships of the IS231 sequences determined to date and the toxicity spectrum of the host cell. Probing of BTD2 DNA with a radiolabeled IS231G fragment demonstrated that IS231 elements are located on 55- and 34-MDa plasmids as well as on chromosomal DNA. Chromosomal DNA, but not plasmids, from BTD2 also hybridizes to another, unrelated insertion sequence, IS240, from B. thuringiensis subsp. israelensis, an isolate toxic to dipteran insects. BTD2, therefore, contains IS elements once thought to reside exclusively in either dipteran- or lepidopteran-specific subspecies of B. thuringiensis.Key words: IS231, IS240, mobile elements.
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Chalker, D. L., and S. B. Sandmeyer. "Transfer RNA genes are genomic targets for de Novo transposition of the yeast retrotransposon Ty3." Genetics 126, no. 4 (December 1, 1990): 837–50. http://dx.doi.org/10.1093/genetics/126.4.837.

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Abstract Insertions of the yeast element Ty3 resulting from induced retrotransposition were characterized in order to identify the genomic targets of transposition. The DNA sequences of the junctions between Ty3 and flanking DNA were determined for two insertions of an unmarked element. Each insertion was at position -17 from the 5' end of a tRNA-coding sequence. Ninety-one independent insertions of a marked Ty3 element were studied by Southern blot analysis. Pairs of independent insertions into seven genomic loci accounted for 14 of these insertions. The DNA sequence flanking the insertion site was determined for at least one member of each pair of integrated elements. In each case, insertion was at position -16 or -17 relative to the 5' end of one of seven different tRNA genes. This proportion of genomic loci used twice for Ty3 integration is consistent with that predicted by a Poisson distribution for a number of genomic targets roughly equivalent to the estimated number of yeast tRNA genes. In addition, insertions upstream of the same tRNA gene in one case were at different positions, but in all cases were in the same orientation. Thus, genomic insertions of Ty3 in a particular orientation are apparently specified by the target, while the actual position of the insertion relative to the tRNA-coding sequence can vary slightly.
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Yin, Bin, and David A. Largaespada. "PCR-based procedures to isolate insertion sites of DNA elements." BioTechniques 43, no. 1 (July 2007): 79–84. http://dx.doi.org/10.2144/000112474.

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6

Paskewitz, Susan M., and Frank H. Collins. "Site-specific ribosomal DNA insertion elements inAnopheles gambiaeandA.arbiensis: nucleotide sequence of gene-element boundaries." Nucleic Acids Research 17, no. 20 (1989): 8125–33. http://dx.doi.org/10.1093/nar/17.20.8125.

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7

Voelker, R. A., J. Graves, W. Gibson, and M. Eisenberg. "Mobile element insertions causing mutations in the Drosophila suppressor of sable locus occur in DNase I hypersensitive subregions of 5'-transcribed nontranslated sequences." Genetics 126, no. 4 (December 1, 1990): 1071–82. http://dx.doi.org/10.1093/genetics/126.4.1071.

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Abstract The locations of 16 mobile element insertions causing mutations at the Drosophila suppressor of sable [su(s)] locus were determined by restriction mapping and DNA sequencing of the junction sites. The transposons causing the mutations are: P element (5 alleles), gypsy (3 alleles), 17.6, HMS Beagle, springer, Delta 88, prygun, Stalker, and a new mobile element which was named roamer (2 alleles). Four P element insertions occur in 5' nontranslated leader sequences, while the fifth P element and all 11 non-P elements inserted into the 2053 nucleotide, 5'-most intron that is spliced from the 5' nontranslated leader approximately 100 nucleotides upstream of the translation start. Fifteen of the 16 mobile elements inserted within a approximately 1900 nucleotide region that contains seven 100-200-nucleotide long DNase I-hypersensitive subregions that alternate with DNase I-resistant intervals of similar lengths. The locations of these 15 insertion sites correlate well with the roughly estimated locations of five of the DNase I-hypersensitive subregions. These findings suggest that the features of chromatin structure that accompany gene activation may also make the DNA susceptible to insertion of mobile elements.
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Gosselin, Sophia P., Danielle R. Arsenault, Catherine A. Jennings, and Johann Peter Gogarten. "The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination." Genes 14, no. 2 (January 21, 2023): 288. http://dx.doi.org/10.3390/genes14020288.

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Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction–modification systems). We found that the methylase family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages.
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Woods, Wayne G., Katrina Ngui, and Michael L. Dyall-Smith. "An Improved Transposon for the Halophilic ArchaeonHaloarcula hispanica." Journal of Bacteriology 181, no. 22 (November 15, 1999): 7140–42. http://dx.doi.org/10.1128/jb.181.22.7140-7142.1999.

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ABSTRACT An improved transposon (ThD73) for Haloarcula hispanica is described. Based on the halobacterial insertion sequence ISH28, it showed little target sequence specificity but was biased toward a lower G+C content. Twenty randomly selected ThD73 mutants were analyzed, and the DNA flanking their insertions revealed several recognizable sequences, including two (unrelated) ISH elements.
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Hargrove, Phillip W., Steven Kepes, Hideki Hanawa, Cheng Cheng, Geoff Neale, Arthur W. Nienhuis, and Derek A. Persons. "Assessment of Changes in Gene Expression Caused by Insertions of a Globin Lentiviral Vector Containing Globin Regulatory Elements or a Lentiviral Vector Containing Retroviral LTR Elements." Blood 104, no. 11 (November 16, 2004): 497. http://dx.doi.org/10.1182/blood.v104.11.497.497.

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Abstract The development of lymphoid leukemia in two children with X-SCID who underwent gene therapy was partially due to activation of the LMO-2 proto-oncogene by the retroviral LTR of the vector which inserted nearby (Hacein-Bey-Abina et al., Science 2003), highlighting the importance of vector design on the potential to activate genes near vector integration sites. As gene therapy vectors for other blood disorders are evaluated, it seems prudent to assess the safety issues regarding insertion for each particular vector in appropriate pre-clinical models. We have focused on developing γ-globin lentiviral vectors for gene therapy of the hemoglobin disorders and have documented correction of a murine model of β-thalassemia in the absence of observable adverse events (Persons et al., Blood 2003; Hanawa et al., Blood 2004). To more thoroughly evaluate the potential for vector-induced genotoxicity, we have examined whether self-inactivating (SIN) γ-globin lentiviral vectors containing erythroid-specific, β-globin locus enhancer elements can alter the expression of genes nearby the vector insertion site, as the retroviral LTR did in the X-SCID trial. To ascertain whether an integrated globin vector could influence endogenous transcriptional activity in erythroid precursors, 15 clonal spleen colony erythroblast populations (≥ 95% erythroid) containing lentiviral globin vector insertions and 15 untransduced control clones were derived from bone marrow cells of β-thalassemic mice. The transcriptional profile of each clone was determined using the Affymetrix Mouse 430A microarray (representing ~15,000 genes). Expression of 4500–6000 genes was observed in all samples. Ligation-mediated PCR was used to obtain the vector-genomic DNA junction sequences, allowing identification of vector insertion locations in 13 of the clones using the NCBI database. Of these, 6 globin vector clones had 16 genes, including N-ras, which were located within 100kb of the vector insertion site and were represented on the array. Only one gene, D3Jfr1, encoding a “cold shock” DNA binding protein and which was disrupted by an intronic vector insertion, had a change in signal value relative to the mean signal value of the controls. Real time RT-PCR confirmed a 4-fold reduction in expression of this gene. Both microarray and real time RT-PCR demonstrated that expression of N-ras was unchanged. For comparison, 15 clones with insertions of a lentiviral vector containing the MSCV retroviral LTR, were also derived, along with 10 additional mock control clones. We are currently analyzing the expression of some 116 genes that lie within 300kb of the vector insertions, relative to the mean expression level in the 25 mock transduced clones. Additionally, we have expanded analysis of the globin vector clones to evaluate changes in expression of 107 genes located within 300kb of the vector insertions. These data should prove useful to assess whether integrated SIN globin lentiviral vectors containing erythroid-specific regulatory elements have a propensity to alter transcriptional activity in the progeny of genetically modified hematopoietic stem cells, relative to vectors containing viral LTR elements.
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Dissertations / Theses on the topic "Insertion elements, DNA"

1

Harris, Linda Janice. "Characterization of the Caenorhabditis elegans var. Bristol (strain N2) Tc1 elements and related transposable elements in Caenorhabditis briggsae." Thesis, University of British Columbia, 1988. http://hdl.handle.net/2429/28838.

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The regulation and evolution of the inverted repeat transposable element Tel, found in the nematode Caenorhabditis elegans, was studied. The stability of Tel elements in the N2 strain genome was investigated by cloning seventeen N2 Tel elements. To examine their structural integrity, sixteen cloned N2 Tel elements were restriction mapped and, in the case of some variants, their DNA was partially sequenced. Two restriction site variants, Tcl(Eco).12 and Tcl(Hpa-).9, were found. Tel(1.5).10b had lost 89 bp from one end, while Tcl(1.7).28 contained a 55 bp insertion. Two additional elements, Tcl(0.9).2 and Tcl(0.9).14, had different internal deletions. Each element was about 900 bp in length. The majority of Tel elements cloned from the N2 strain were found to have identical restriction maps. Somatic excision of Tel elements in the N2 genome was demonstrated. Tel elements in N2 are apparently both structurally and functionally intact. Nevertheless, mobilization of Tel elements in the N2 germline is restricted. Two new transposable element families, Barney (also known as TCbl) and TCb2, were discovered in a closely related nematode, Caenorhabditis briggsae due to Tel identity. These two families, distinguished through differential inter-element hybridization, showed multiple banding differences between strains. The open reading frames (ORFs) of Tel and Barney share 71% DNA sequence and 74% amino acid sequence identity. The putative terminus of Barney exhibits 68% identity with the 54 bp terminal repeat of Tel. Partial sequencing of TCb2 revealed that its ORF is equally diverged from Barney and Tel. The basis of the sequence heterogeneity observed in the C. briggsae transposons and not in the C. elegans transposons could be due to either horizontal transfer or alternate paths of divergence. Significant sequence identity was found between Tel, Barney, and HB1 (a transposable element from Drosophila melanogaster) within their coding regions and terminal repeats. These sequence similarities define a subclass of inverted repeat transposable elements inhabiting two different phylla, Arthropoda and Nematoda.
Medicine, Faculty of
Medical Genetics, Department of
Graduate
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Raghavan, Rahul. "Mobile genetic elements in coxiella burnetii friends, foes or just indifferent? /." [Missoula, Mont.] : The University of Montana, 2008. http://etd.lib.umt.edu/theses/available/etd-12092008-141715/unrestricted/umi-umt-1105.pdf.

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Fobert, Pierre R. (Pierre Rheal) Carleton University Dissertation Biology. "Characterization of chromosomal sites of T-DNA integration by activation of a promoterless B-glucuronidase (GUS) gene linked to the T-DNA right border repeat." Ottawa, 1992.

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Bhangale, Tushar. "Small insertion-deletion polymorphisms in the human genome : characterization and automation of detection by resequencing /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/8044.

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Pillai, Suresh Divakaran. "Ecology and genetic stability of Tn5 mutants of bean rhizobia in Sonoran desert soils." Diss., The University of Arizona, 1989. http://hdl.handle.net/10150/184823.

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Five transposon Tn5 mutants of bean rhizobia (Rhizobium leguminosarum b.v. phaseoli) and the wild type strain were used in ecological studies to evaluate the efficacy of transposon Tn5 as a phenotypic marker in rhizobia for ecological studies in two Sonoran desert soils. All mutants possessed chromosomal insertions of the transposable element. Survival of each mutant strain was compared to that of the wild type strain under non stress, moisture stress and temperature stress conditions in Pima silty clay loam and Brazil to sandy loam. The genetic stability of Tn5 in terms of transposition of the element within the chromosome and the Tn5 coded antibiotic resistant phenotype was determined in cells recovered throughout the survival period. Under non stress conditions, the viable Tn5 mutant population decreased in size. Two mutants showed significantly (p < 0.01) lower populations than the wild type at the end of 30 days in the silty clay loam. In the sandy loam, four of the five mutant populations were significantly lower than the wild type. Tn5 was genetically stable in both soils. Under moisture stress conditions, the decline of the Tn5 mutant and wild type populations corresponded to a decline in soil moisture content. The finer textured soil afforded more protection to the cells than the coarse textured soil. There were no indications of Tn5 instability under moisture stress. In both soils under temperature stress, sizes of all populations declined rapidly and after 12 days, the mutant cells when screened using the Tn5 coded markers were significantly less in numbers than the wild type indicating a loss of Tn5 coded antibiotic resistance phenotype. There were no significant differences in numbers between wild type and mutant cells when screened using only the intrinsic markers. DNA:DNA hybridizations confirmed that the lack of Tn5 coded antibiotic resistance phenotype was probably not due to a deletion or transposition of the element. Under non stress conditions Tn5 is a useful ecological marker, but each Tn5 mutant has to be evaluated independently under specific environmental conditions to determine the efficacy of Tn5 as an ecological marker.
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Liu, Xiulan. "Characterisation of antibiotic resistance gene clusters and their mobility within a collection of multi-drug resistant Salmonella spp." School of Biological Sciences - Faculty of Science, 2009. http://ro.uow.edu.au/theses/3043.

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One hundred and thirty-six Salmonella enterica strains, isolated from humans, animals, environmental and plant sources in Australia from 23 serovars, were examined for the streptomycin resistance gene strA and strB, the sulfonamide resistance gene sul2, and the tetracycline resistance gene tetA(A) and tetA(B). Thirteen strains were identified as containing the strA-strB genes located on the transposon Tn5393. S. enterica serovar Hadar accounted for 11 of these strains, 6 of which were isolated from humans and 5 were from ducks. This investigation is therefore the first report of the Tn5393 transposon being detected in bacterial strains from a human source in Australia.RSF1010 plasmids were identified and extracted from 4 S. enterica strains, and were further confirmed by restriction enzyme profiling using PstI, SspI and EcoRV. Small non-conjugative plasmid p9123 was extracted and characterised from 3 of the S. enterica strains and also confirmed by restriction enzyme digestion. An RSF1010-like plasmid was also identified in 3 of the strains. This plasmid was found to be approximately 2.6 kb larger than RSF1010, and possibly derived from the RSF1010 plasmid via insertion of the tetracycline resistance gene tetA(A) between strB and mobC genes.An IS26-strB-strA-sul2-repC-repA-IS26 antibiotic resistance region was identified in 33 S. enterica strains, among these were 23 serovar Typhimurium isolates, 8 serovar Bovismorbificans, 1 serovar Senftenberg and 1 isolate where the serovar could not be conclusively identified. The 23 Typhimurium strains were further characterised by PCR and Southern hybridisation analysis using a blaTEM gene probe. The analysis identified two classes of antibiotic resistance gene clusters. Eleven S. enterica serovar Typhimurium strains harboured an IS26-strB-strA-sul2-repC-repA-IS26-blaTEM-1-IS26 antibiotic resistance gene cluster and another 10 S. enterica serovar Typhimurium strains contained an IS26-strB-strA-sul2-repC-repA-IS26-blaTEM-1 gene cluster, without the IS26 element downstream of the blaTEM-1 gene. Two strains contain elements of these gene clusters but further investigation is needed to fully identify these.Further linkage PCR amplifications revealed that the IS26-strB-strA-sul2-repC-repA-IS26-blaTEM-1-IS26 antibiotic resistance gene cluster was possibly inserted into the 3P-CS of a class 1 integron (In4 type) and truncated the 3P-CS region. Three derivatives were identified, of which the dfrA5-intI1 type was most commonly found downstream of the blaTEM-1-IS26 region. Southern hybridisation analysis using an IS200 gene probe revealed that strains which contain different antibiotic resistance gene clusters also display different but related IS200 profiles.The antibiotic resistance gene clusters of 19 S. enterica serovar Typhimurium strains were transferred to an E. coli 294 Rifr recipient either by direct mating or triparental mating methods. These experiments confirmed that the antibiotic resistance gene clusters were located on conjugative or mobilisable plasmids. The antibiotic resistance gene clusters of 4 S. enterica serovar Typhimurium strains could not be transferred to the E. coli 294 Rifr recipient. These experimental results suggest that the antibiotic resistance gene cluster of IS26-strB-strA-sul2-repC-repA-IS26-blaTEM-1-IS26 might move as one genetic element between distinct plasmid backbones.
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Signorelli, Katherine Louise. "Characterization of an insertional mutation in a line of transgenic mice /." Access full-text from WCMC, 1989. http://proquest.umi.com/pqdweb?did=744576231&sid=1&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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Richter, Grace Yukiko. "Molecular characterization of specificity and activity of the transposable element IS801." Thesis, 1995. http://hdl.handle.net/1957/34682.

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1S801 is a transposable element isolated from Pseudomonas syringae pathovar (pv.) phaseolicola, the causal agent of halo blight of bean. Fragments of the element are present in multiple copies on an indigenous plasmid, pMMC7105, of strain LR781, and have been implicated as sites of homologous recombination leading to imprecise excision of the chromosomally integrated form of the plasmid. The element, which has been completely sequenced, is 1512 base pairs in length and is unusual among transposable elements in that it does not have direct or inverted repeats in its termini. The terminal regions of the element were uncoupled from the two major open reading frames, and trans-acting activity of the putative transposase was demonstrated in Escherichia coli (recA). An alignment of the sequences of thirteen insertions defined the precise borders of the element, and demonstrated that it does not duplicate its targets upon insertion. The target specificity of IS801 is similar to, but more degenerate than, the target specificity of two transposable elements to which it is closely related, IS91 and IS1294. The consensus derived from the aligned target sequences is G/C-A/G-A-C/G, and the target tetramer is found immediately adjacent to the right terminus of the element upon transposition. IS91 was demonstrated to mobilize 1S801, but not with the specificity characteristic of 1S801. The structure of 1S801 and the characteristics of IS91-activated transposition of 1S801 are discussed in light of a proposed model for IS91 transposition, and it is suggested that 1S801 could have been derived from IS91 by a modification of its left end. Remnants of IS801 are present near avirulence genes of various P. syringae pathovars, suggesting that the element has been involved in genetic rearrangements in the vicinity of these loci.
Graduation date: 1996
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Brezinsky, Laura. "Molecular and evolutionary characterization of the transposable element Uhu from Hawaiian Drosophila." Thesis, 1990. http://hdl.handle.net/10125/9397.

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Shim, Je-Seop. "Studies on the agrocin 84 plasmid of `Agrobacterium radiobacter`." 1987. http://web4.library.adelaide.edu.au/theses/09PH/09phs5565.pdf.

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Books on the topic "Insertion elements, DNA"

1

Barbara, McClintock. The discovery and characterization of transposable elements: The collected papers of Barbara McClintock. New York: Garland Pub., 1987.

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Wisconsin-Madison), International Symposium on Plant Transposable Elements (1987 University of. Plant transposable elements. New York: Plenum Press, 1988.

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Mobile DNA: Finding treasure in junk. Upper Saddle River, New Jersey: FT Press, 2011.

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Richter, Grace Yukiko. Molecular characterization of specificity and activity of the transposable element IS801. 1995.

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H, Saedler, and Gierl A, eds. Transposable elements. Berlin: Springer-Verlag, 1996.

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E, Lambert Michael, McDonald John F. 1947-, Weinstein I. Bernard, Cold Spring Harbor Laboratory, and Abbott Laboratories, eds. Eukaryotic transposable elements as mutagenic agents. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory, 1988.

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Sniegowski, Paul D. Transposable elements and polymorphic inversions in Drosophila melanogaster. 1993.

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Lambert, Michael E., and John F. McDonald. Eukaryotic Transposable Elements As Mutagenic Agents (Banbury Report) (Banbury Report). Cold Spring Harbor Laboratory Pr, 1988.

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Plant DNA infectious agents. Wien: Springer-Verlag, 1987.

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Plant Transposable Elements Topics in Current Genetics. Springer, 2012.

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Book chapters on the topic "Insertion elements, DNA"

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Wessler, Susan R., George Baran, and Marguerite Varagona. "Alterations in Gene Expression Mediated by DNA Insertions in the waxy Gene of Maize." In Plant Transposable Elements, 293–303. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4684-5550-2_22.

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Zhou, Bo, Michael S. Haney, Xiaowei Zhu, Reenal Pattni, Alexej Abyzov, and Alexander E. Urban. "Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants." In Methods in Molecular Biology, 173–90. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7778-9_11.

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Cassidy, Annelise, and Stephane Pelletier. "Emerging CRISPR Technologies." In CRISPR Technology [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.106652.

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The discovery and implementation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas) systems for genome editing has revolutionized biomedical research and holds great promise for the treatment of human genetic disorders. In addition to the popular CRISPR-Cas9 and CRISPR-Cpf1 systems for genome editing, several additional Class I and Class 2 CRISPR-Cas effectors have been identified and adapted for genome editing and transcriptome modulation. Here we discuss current and emerging CRISPR-based technologies such as Cascade-Cas3, CRISPR-associated transposases (CAST), CRISPR-Cas7–11, and CRISPR-Cas13 for genome and transcriptome modification. These technologies allow for the removal or insertion of large DNA elements, the modulation of gene expression at the transcriptional level, and the editing of RNA transcripts, expanding the capabilities of current technologies.
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da Silva, Maelin, Daniele Aparecida Matoso, Vladimir Pavan Margarido, Eliana Feldberg, and Roberto Ferreira Artoni. "Composition and Nature of Heterochromatin in the Electrical Fish (Knifefishes) Gymnotus (Gymnotiformes: Gymnotidae)." In Cytogenetics - Classical and Molecular Strategies for Analysing Heredity Material. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97673.

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Fishes of the genus Gymnotus have been suggested as a good model for biogeographic studies in the South American continent. In relation to heterochromatin, species of this genus have blocks preferably distributed in the centromeric region. The content of these regions has been shown to be variable, with description of transposable elements, pseudogenes of 5S rDNA and satellite sequences. In G. carapo Clade, although geographically separated, species with 2n = 54 chromosomes share the distribution of many 5S rDNA sites, a unique case within the genus. Here, repetitive DNA sequences from G. sylvius (2n = 40) and G. paraguensis (2n = 54) were isolated and mapped to understand their constitution. The chromosome mapping by FISH showed an exclusive association in the centromeres of all chromosomes. However, the cross-FISH did not show positive signs of interspecific hybridization, indicating high levels of heterochromatic sequence specificity. In addition, COI-1 sequences were analyzed in some species of Gymnotus, which revealed a close relationship between species of clade 2n = 54, which have multiple 5S rDNA sites. Possibly, the insertion of retroelements or pseudogenization and dispersion of this sequence occurred before the geographic dispersion of the ancestor of this clade from the Amazon region to the hydrographic systems of Paraná-Paraguay, a synapomorphy for the group.
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Conference papers on the topic "Insertion elements, DNA"

1

Deviprasad, T., and T. Kesavadas. "VPAVE: An Interactive Tool for Validating Assembly Components in Virtual Environment Using Finite Element Simulation." In ASME 1999 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1999. http://dx.doi.org/10.1115/imece1999-0165.

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Abstract Assembly is a geometric problem and its success depends on the quality of the mating parts. Design for Assembly (DFA) takes care of the issues such as part handling, insertion and mating, and other features that make assembly an easier and cost effective task. Practical considerations like part deformation during manufacturing, wear and tear of machines and jigs, and other constraints like cost and technical limitations contribute significantly to dimensional and form errors. These factors are usually not accounted for during the DFA, as the data is not as yet available. This results in improper assembly and part rejection at a later stage. One approach of solving this problem is to develop a virtual prototype, which captures the real manufacturing variables by modeling the process impact on the assembled components. The work presented here tries to look at a few issues concerning validation of the virtual prototype (VP) of a manufactured component before assembly. A Virtual Prototype Assembly Validation Environment dubbed VPAVE was developed to test virtual prototypes of manufactured component in a Virtual Environment for assembly process. We have demonstrated by an example that the VPAVE based validation during DFA can prevent difficulties that may arise during the actual assembly process due to the influence of the production process of the components.
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Yoon, Kyungmin, Chansu Jang, and Jooil Yoon. "A Study on Doppler Weighting Factor for Control Element Assembly Ejection Accident by Using Newly Developed Nuclear Design Code and Non-LOCA Methodology." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-65996.

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Among Reactivity Initiated Accidents (RIAs) for Pressurized Water Reactor (PWR), Control Element Assembly Ejection (CEAE) accident causes the rapid positive reactivity insertion to the core. It causes an asymmetric power distortion which results in the rising of local fuel temperature, fuel pellet thermal expansion and cladding ballooning or rupture. In the CEAE accident, Doppler feedback has a profound effect because the negative reactivity insertion due to the rise of fuel temperature reduces the core power after rapid power excursion. But the Doppler reactivity can’t be calculated properly in the safety analysis code, using point kinetics model, because the point kinetics model is not able to consider spatial-time effect of the sudden rise in local fuel temperature on Doppler feedback calculation during CEAE accident. And then the excessively high core power which results from the underestimated Doppler feedback would make more severe results such as PCMI fuel failure, fuel cladding rupture and serious DNB fuel failure. Therefore, Doppler Weighting Factor (DWF) is needed for the safety analysis of CEAE accident to compensate a missing spatial-time effect on Doppler feedback calculation. In this study, the adequacy of the application of DWF for APR1400 was evaluated by using nuclear design code called ASTRA (Advanced Static and Transient Reactor Analyzer)[1] and a methodology called ISAM (Integrated Safety Analysis Methodology)[2]. ASTRA is the 3D nuclear design code newly developed by KNF and has various functions such as the static core design, the transient core analysis and the operational support. ISAM is the methodology which is newly developed by KNF to perform the Non-LOCA safety analysis by using RETRAN[3] code which is widely used in the transient analysis and based on the point kinetics model.
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Reports on the topic "Insertion elements, DNA"

1

Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
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