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Artículos de revistas sobre el tema "Insertion elements"

Autor: Grafiati

Publicado: 4 de junio de 2021

Última modificación: 28 de enero de 2023

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1

Olmeda-López, Héctor, Andrés Corral-Lugo, and Michael J. McConnell. "Effect of Subinhibitory Concentrations of Antibiotics and Disinfectants on ISAba-Mediated Inactivation of Lipooligosaccharide Biosynthesis Genes in Acinetobacter baumannii." Antibiotics 10, no. 10 (October 16, 2021): 1259. http://dx.doi.org/10.3390/antibiotics10101259.

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Inactivation of the lipooligosaccharide (LOS) biosynthesis genes lpxA, lpxC and lpxD by ISAba insertion elements results in high-level resistance to colistin in A. baumannii. In the present study, we quantify the rate of spontaneous insertional inactivation of LOS biosynthesis genes by ISAba elements in the ATCC 19606-type strain and two multidrug clinical isolates. Using insertional inactivation of lpxC by ISAba11 in the ATCC 19606 strain as a model, we determine the effect of several subinhibitory concentrations of the antibiotics, namely tetracycline, ciprofloxacin, meropenem, kanamycin and

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2

Vieira, C., and C. Biémont. "Selection against transposable elements in D. simulans and D. melanogaster." Genetical Research 68, no. 1 (August 1996): 9–15. http://dx.doi.org/10.1017/s0016672300033838.

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SummaryThe insertion site numbers of the transposable elements (TEs) copia, mdgl, 412 and gypsy were determined in various natural populations of Drosophila melanogaster and D. simulans by in situ hybridization. We showed that, while all elements except gypsy had many insertion sites scattered over the chromosomes in D. melanogaster, only the 412 element in D. simulans presented a high number of insertions, and this number was lower than in D. melanogaster. This low 412 site number per genome in D. simulans was associated with a lower proportion of insertions on the X chromosome in comparison

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3

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 f

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4

Carlson, Corey M., Adam J. Dupuy, Sabine Fritz, Kevin J. Roberg-Perez, Colin F. Fletcher, and David A. Largaespada. "Transposon Mutagenesis of the Mouse Germline." Genetics 165, no. 1 (September 1, 2003): 243–56. http://dx.doi.org/10.1093/genetics/165.1.243.

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Abstract Sleeping Beauty is a synthetic “cut-and-paste” transposon of the Tc1/mariner class. The Sleeping Beauty transposase (SB) was constructed on the basis of a consensus sequence obtained from an alignment of 12 remnant elements cloned from the genomes of eight different fish species. Transposition of Sleeping Beauty elements has been observed in cultured cells, hepatocytes of adult mice, one-cell mouse embryos, and the germline of mice. SB has potential as a random germline insertional mutagen useful for in vivo gene trapping in mice. Previous work in our lab has demonstrated transpositio

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5

Hesselbarth, Judith, Christiane Werckenthin, Babett Liebisch, and S. Schwarz. "Insertion elements in Staphylococcus intermedius." Letters in Applied Microbiology 20, no. 3 (March 1995): 180–83. http://dx.doi.org/10.1111/j.1472-765x.1995.tb00421.x.

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6

LADEVEZE, VERONIQUE, IBO GALINDO, NICOLE CHAMINADE, LUIS PASCUAL, GEORGES PERIQUET, and FRANCOISE LEMEUNIER. "Transmission pattern of hobo transposable element in transgenic lines of Drosophila melanogaster." Genetical Research 71, no. 2 (April 1998): 97–107. http://dx.doi.org/10.1017/s0016672398003127.

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This study is an attempt to trace the fate of hobo elements in the genomes of E strains of Drosophila melanogaster that have been transfected with pHFL1, a plasmid containing an autonomous hobo. Such long-term population studies (over 105 generations) could be very useful for better understanding the population and genomic dynamics of transposable elements and their pattern of insertions. Molecular analyses of hobo elements in the transfected lines were performed using Southern blots of XhoI-digested genomic DNAs. The complete element was observed in all six injected lines. In two lines we obs

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7

Appelt, Jens U., Frank A. Giordano, Marcel Zimmermann, Stephan Weinhard, Nadja Grund, Agnes Hotz-Wagenblatt, W. Jens Zeller, Heike Allgayer, Stefan Fruehauf, and Stephanie Laufs. "Genes Involved in Acute Leukemias Are Favored Targets of HIV Vector Integration." Blood 110, no. 11 (November 16, 2007): 3738. http://dx.doi.org/10.1182/blood.v110.11.3738.3738.

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Abstract Insertional mutagenesis and development of leukemia following retroviral gene therapy has created intense interest in assessing the safety of viral vectors for further gene therapy trials. Using the gtsg.org database we analyzed more than 14,900 different viral integration sites of ASLV, FIV, FV, HIV, MLV and SIV based vectors in terms of insertions into fragile sites, cancer genes, transcription factor binding sites, CpG islands, and repetitive elements (SINE, LINE, LTR elements). When we compared these data with our newly generated random set, containing 1,000,000 random integration

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8

Vincent, A., and T. D. Petes. "Mitotic and meiotic gene conversion of Ty elements and other insertions in Saccharomyces cerevisiae." Genetics 122, no. 4 (August 1, 1989): 759–72. http://dx.doi.org/10.1093/genetics/122.4.759.

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Abstract We examined meiotic and mitotic gene conversion events involved in deletion of Ty elements and other insertions from the genome of the yeast Saccharomyces cerevisiae. We found that Ty elements and one other insertion were deleted by mitotic gene conversion less frequently than point mutations at the same loci. One non-Ty insertion similar in size to Ty, however, did not show this bias. Mitotic conversion events deleting insertions were more frequently associated with crossing over than those deleting point mutations. In meiosis, conversion events duplicating the element were more comm

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9

Haandrikman, A. J., C. van Leeuwen, J. Kok, P. Vos, W. M. de Vos, and G. Venema. "Insertion elements on lactococcal proteinase plasmids." Applied and Environmental Microbiology 56, no. 6 (1990): 1890–96. http://dx.doi.org/10.1128/aem.56.6.1890-1896.1990.

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10

Aigner, Martin, and Douglas B. West. "Sorting by insertion of leading elements." Journal of Combinatorial Theory, Series A 45, no. 2 (July 1987): 306–9. http://dx.doi.org/10.1016/0097-3165(87)90022-7.

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11

Eraclio, Giovanni, Giovanni Ricci, and Maria Grazia Fortina. "Insertion sequence elements in Lactococcus garvieae." Gene 555, no. 2 (January 2015): 291–96. http://dx.doi.org/10.1016/j.gene.2014.11.019.

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12

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-glob

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13

Eanes, Walter F., Cedric Wesley, Jody Hey, David Houle, and James W. Ajioka. "The fitness consequences of P element insertion in Drosophila melanogaster." Genetical Research 52, no. 1 (August 1988): 17–26. http://dx.doi.org/10.1017/s0016672300027269.

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SummaryIn this study we estimate the frequency at which P-element insertion events, as identified by in situ hybridization, generate lethal and mild viability mutations. The frequency of lethal mutations generated per insertion event was 0·004. Viability dropped an average of 1% per insertion event. Our results indicate that it is deletions and rearrangements resulting from the mobilization of P elements already in place and not the insertions per se that cause the drastic effects on viability and fitness observed in most studies of P–M dysgenesis-derived mutations. Elements of five other fami

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14

Roseman, R. R., E. A. Johnson, C. K. Rodesch, M. Bjerke, R. N. Nagoshi, and P. K. Geyer. "A P element containing suppressor of hairy-wing binding regions has novel properties for mutagenesis in Drosophila melanogaster." Genetics 141, no. 3 (November 1, 1995): 1061–74. http://dx.doi.org/10.1093/genetics/141.3.1061.

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Abstract P elements are widely used as insertional mutagens to tag genes, facilitating molecular cloning and analyses. We modified a P element so that it carried two copies of the suppressor of Hairy-wing [su(Hw)] binding regions isolated from the gypsy transposable element. This transposon was mobilized, and the genetic consequences of its insertion were analyzed. Gene expression can be altered by the su(Hw) protein as a result of blocking the interaction between enhancer/silencer elements and their promoter. These effects can occur over long distances and are general. Therefore, a composite

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15

Zidi, Marwa, Khouloud Klai, Johann Confais, Benoît Chénais, Aurore Caruso, Françoise Denis, Maha Khemakhem, and Nathalie Casse. "Genome-Wide Screening of Transposable Elements in the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), Revealed Insertions with Potential Insecticide Resistance Implications." Insects 13, no. 5 (April 19, 2022): 396. http://dx.doi.org/10.3390/insects13050396.

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Transposable elements (TEs) are genetically mobile units that move from one site to another within a genome. These units can mediate regulatory changes that can result in massive changes in genes expression. In fact, a precise identification of TEs can allow the detection of the mechanisms involving these elements in gene regulation and genome evolution. In the present study, a genome-wide analysis of the Hemipteran pest Bemisia tabaci was conducted using bioinformatics tools to identify, annotate and estimate the age of TEs, in addition to their insertion sites, within or near of the defensom

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16

Chen, Jiann-Hwa, Wen-Ben Hsu, and Jiing-Luen Hwang. "Two Amino Acid Residues of Transposase Contributing to Differential Transposability of IS1 Elements inEscherichia coli." Journal of Bacteriology 180, no. 19 (October 1, 1998): 5279–83. http://dx.doi.org/10.1128/jb.180.19.5279-5283.1998.

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ABSTRACT Escherichia coli W3110 contains four types of IS1 elements in the chromosome. Using an insertion element entrapping system, we collected 116 IS1 plasmid insertion mutants, which resulted from a minimum of 26 independent IS1 insertion events. All of them had insertions of IS1 of the IS1A (IS1E and IS1G) type. Inspection of the transposase sequences of the four IS1 types and the IS1 of the resistance plasmid R100 showed that two amino acid residues, His-193 and Leu-217 of transposase, might contribute to differential transposability of IS1 elements in W3110. The two amino acid residues

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17

Mahillon, Jacques, and Michael Chandler. "Insertion Sequences." Microbiology and Molecular Biology Reviews 62, no. 3 (September 1, 1998): 725–74. http://dx.doi.org/10.1128/mmbr.62.3.725-774.1998.

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SUMMARY Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at

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18

Natsoulis, G., W. Thomas, M. C. Roghmann, F. Winston, and J. D. Boeke. "Ty1 transposition in Saccharomyces cerevisiae is nonrandom." Genetics 123, no. 2 (October 1, 1989): 269–79. http://dx.doi.org/10.1093/genetics/123.2.269.

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Abstract A large collection of Ty1 insertions in the URA3 and LYS2 loci was generated using a GAL1-Ty1 fusion to augment the transposition frequency. The sites of insertion of most of these Ty elements were sequenced. There appears to be a gradient of frequency of insertion from the 5' end (highest frequency) to the 3' end (lowest frequency) of both loci. In addition we observed hotspots for transposition. Twelve of the 82 Ty1 insertions in the URA3 locus were inserted in exactly the same site. Hotspots were also observed in the LYS2 locus. All hotspots were in the transcribed part of the gene

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19

Dalby, B., A. J. Pereira, and L. S. Goldstein. "An inverse PCR screen for the detection of P element insertions in cloned genomic intervals in Drosophila melanogaster." Genetics 139, no. 2 (February 1, 1995): 757–66. http://dx.doi.org/10.1093/genetics/139.2.757.

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Abstract We developed a screening approach that utilizes an inverse polymerase chain reaction (PCR) to detect P element insertions in or near previously cloned genes in Drosophila melanogaster. We used this approach in a large scale genetic screen in which P elements were mobilized from sites on the X chromosome to new autosomal locations. Mutagenized flies were combined in pools, and our screening approach was used to generate probes corresponding to the sequences flanking each site of insertion. These probes then were used for hybridization to cloned genomic intervals, allowing individuals c

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20

Baek, Jin-Eon, Woo-Young Chin, Ji-Woong Choi, Tae-Hyun Eom, Young-Cheol Jeon, and Yang Lee. "INSERTION-OF-FACTORS-PROPERTY ON NILPOTENT ELEMENTS." Bulletin of the Korean Mathematical Society 49, no. 2 (March 31, 2012): 381–94. http://dx.doi.org/10.4134/bkms.2012.49.2.381.

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21

Naas, T. "S2 Insertion sequences, transposons and repeated elements." International Journal of Antimicrobial Agents 29 (March 2007): S1. http://dx.doi.org/10.1016/s0924-8579(07)70008-0.

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22

Aprianto, Dedi, and I. Nyoman Subudiartha. "INSERTING THE SASAKNESE LOCAL WISDOMS IN ENGLISH CURRICULUM DEVELOPMENT FOR VOCATIONAL HIGH SCHOOLS." EXPOSURE : JURNAL PENDIDIKAN BAHASA INGGRIS 9, no. 2 (November 15, 2020): 352–69. http://dx.doi.org/10.26618/exposure.v9i2.4194.

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This study is the process of English curriculum development aims at analyzing the targets needs, learning needs, and the patterns of local wisdom insertion. This study was conducted through Focused Group Discussion (FGD), semi-structured interview, and content analsysis were used for 12 vocational school teachers and 2 officals of the state and private government institutions (The Department of Education and Culture, NTB Province the Institute of ROWOT Nusantara Lombok). Necessity, the results of the target need analysis on local knowledge and language competence for developing skills and abil

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23

DÍAZ-GONZÁLEZ, JULIA, J. FERNANDO VÁZQUEZ, JESÚS ALBORNOZ, and ANA DOMÍNGUEZ. "Long-term evolution of the roo transposable element copy number in mutation accumulation lines of Drosophila melanogaster." Genetics Research 93, no. 3 (May 6, 2011): 181–87. http://dx.doi.org/10.1017/s0016672311000103.

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SummaryThe rate of insertion of transposable elements (TEs) is a fundamental parameter to understand both their dynamics and role in the evolution of the eukaryotic genome. Nonetheless, direct estimates of insertion rates are scarce because transposition is in general a rare phenomenon. A great deal of our previous work on transposition was based on a set of long-term mutation accumulation (MA) lines of Drosophila melanogaster started in 1987 (Oviedo lines), where roo was found highly active, with a rate of insertion of 7×10−4 insertions per element and generation, as compared with other 15 TE

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Lauermann, Vit, Monika Hermankova, and Jef D. Boeke. "Increased Length of Long Terminal Repeats Inhibits Ty1 Transposition and Leads to the Formation of Tandem Multimers." Genetics 145, no. 4 (April 1, 1997): 911–22. http://dx.doi.org/10.1093/genetics/145.4.911.

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The Ty1 retrotransposon of Saccharomyces cerevisiae is bounded by long-terminal repeats (LTRs). We have constructed a variety of Ty1 elements in which the LTR length has been increased from the normal length of 334 bp to &gt;2 kb. Although small insertions in the LTR have minimal effects on transposition frequency, larger insertions dramatically reduce it. Nevertheless, elements with long LTRs are incorporated into the genome at a low frequency. Most of these rare insertion events represent Ty1 tandem (head to tail) multimers.

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25

Ajioka, James W., and Walter F. Eanes. "The accumulation of P-elements on the tip of the X chromosome in populations of Drosophila melanogaster." Genetical Research 53, no. 1 (February 1989): 1–6. http://dx.doi.org/10.1017/s0016672300027798.

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SummaryLittle information exists about the mechanisms that determine the fate of mobile elements in natural populations. In this study we catalogue the distribution of 638 P-elements across 114 X chromosomes in samples drawn from three natural populations of Drosophila melanogaster. There is an extremely high occurrence of elements at the tip relative to the rest of the euchromatic chromosome. We demonstrate that the distribution of de novo insertions of the P-element on a specific laboratory chromosome is markedly different; no P-elements were recovered at the tip in the 243 insertion events

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26

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 si

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Staddon, Jack H., Edward M. Bryan, Dawn A. Manias, and Gary M. Dunny. "Conserved Target for Group II Intron Insertion in Relaxase Genes of Conjugative Elements of Gram-Positive Bacteria." Journal of Bacteriology 186, no. 8 (April 15, 2004): 2393–401. http://dx.doi.org/10.1128/jb.186.8.2393-2401.2004.

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ABSTRACT The lactococcal group II intron Ll.ltrB interrupts the ltrB relaxase gene within a region that encodes a conserved functional domain. Nucleotides essential for the homing of Ll.ltrB into an intronless version of ltrB are found exclusively at positions required to encode amino acids broadly conserved in a family of relaxase proteins of gram-positive bacteria. Two of these relaxase genes, pcfG from the enterococcal plasmid pCF10 and the ORF4 gene in the streptococcal conjugative transposon Tn5252, were shown to support Ll.ltrB insertion into the conserved motif at precisely the site pre

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28

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 trans

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29

Woodford, Neil, Antoinette-Mary A. Adebiyi, Marie-France I. Palepou, and Barry D. Cookson. "Diversity of VanA Glycopeptide Resistance Elements in Enterococci from Humans and Nonhuman Sources." Antimicrobial Agents and Chemotherapy 42, no. 3 (March 1, 1998): 502–8. http://dx.doi.org/10.1128/aac.42.3.502.

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ABSTRACT Elements mediating VanA glycopeptide resistance in 106 diverse enterococci from humans and nonhuman sources were compared with the prototype VanA transposon, Tn1546, in Enterococcus faecium BM4147. The isolates included 64 from individual patients at 15 hospitals in the United Kingdom (isolated between 1987 and 1996) and 42 from nonhuman sources in the United Kingdom (27 from raw meat, 7 from animal feces, and 8 from sewage). VanA elements were assigned to 24 groups (designated groups A to X) with primers that amplified 10 overlapping fragments of Tn1546. Ten groups of elements were f

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Storer, Jessica M., Jerilyn A. Walker, Catherine E. Rockwell, Grayce Mores, Thomas O. Beckstrom, Joseph D. Orkin, Amanda D. Melin, Kimberley A. Phillips, Christian Roos, and Mark A. Batzer. "Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics." Genes 13, no. 4 (March 24, 2022): 572. http://dx.doi.org/10.3390/genes13040572.

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Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposo

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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

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Zhang, Zhongge, Ming Ren Yen, and Milton H. Saier. "Precise Excision of IS5 from the Intergenic Region between the fucPIK and the fucAO Operons and Mutational Control of fucPIK Operon Expression in Escherichia coli." Journal of Bacteriology 192, no. 7 (January 22, 2010): 2013–19. http://dx.doi.org/10.1128/jb.01085-09.

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ABSTRACT Excision of transposable genetic elements from host DNA occurs at low frequencies and is usually imprecise. A common insertion sequence element in Escherichia coli, IS5, has been shown to provide various benefits to its host by inserting into specific sites. Precise excision of this element had not previously been demonstrated. Using a unique system, the fucose (fuc) regulon, in which IS5 insertion and excision result in two distinct selectable phenotypes, we have demonstrated that IS5 can precisely excise from its insertion site, restoring the wild-type phenotype. In addition to prec

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Backus, Ad. "Het Intergenerationele Codewisseling-Continuum Binnen De Turkse Gemeenschap in Nederland." Spreken in moedertaal en vreemde taal 54 (January 1, 1996): 25–37. http://dx.doi.org/10.1075/ttwia.54.03bac.

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New data on Turkish-Dutch codeswitching (CS) have uncovered patterns not previously attested in this language pair. It turns out that three different generations within the immigrant community switch in three different ways. For the first generation, CS mostly concerns the occasional insertion of Dutch nouns in Turkish sentences. The intermediate generation switches much more frequently and in a much more varied way. The second generation also practices a lot of CS, but the type of switching is virtually always of an alternational, not insertional, nature. Insertional CS further seems to lend

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Payer, Lindsay M., Jared P. Steranka, Wan Rou Yang, Maria Kryatova, Sibyl Medabalimi, Daniel Ardeljan, Chunhong Liu, Jef D. Boeke, Dimitri Avramopoulos, and Kathleen H. Burns. "Structural variants caused by Alu insertions are associated with risks for many human diseases." Proceedings of the National Academy of Sciences 114, no. 20 (May 2, 2017): E3984—E3992. http://dx.doi.org/10.1073/pnas.1704117114.

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Interspersed repeat sequences comprise much of our DNA, although their functional effects are poorly understood. The most commonly occurring repeat is the Alu short interspersed element. New Alu insertions occur in human populations, and have been responsible for several instances of genetic disease. In this study, we sought to determine if there are instances of polymorphic Alu insertion variants that function in a common variant, common disease paradigm. We cataloged 809 polymorphic Alu elements mapping to 1,159 loci implicated in disease risk by genome-wide association study (GWAS) (P <

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Sadler, Michael, Melanie R. Mormile, and Ronald L. Frank. "Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans." Genes 11, no. 5 (April 29, 2020): 484. http://dx.doi.org/10.3390/genes11050484.

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Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying st

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Guiamatsia, I., Brian G. Falzon, and G. A. O. Davies. "Automatic Insertion of Cohesive Elements for Delamination Modelling." Key Engineering Materials 383 (June 2008): 53–66. http://dx.doi.org/10.4028/www.scientific.net/kem.383.53.

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Composite damage modelling with cohesive elements has initially been limited to the analysis of interface damage or delamination. However, their use is also being extended to the analysis of inplane tensile failure arising from matrix or fibre fracture. These interface elements are typically placed at locations where failure is likely to occur, which infers a certain a priori knowledge of the crack propagation path(s). In the case of a crack jump for example, the location of the jump is usually not obvious, and the simulation would require the placement of cohesive elements at all element face

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Bedzyk, L. A., N. B. Shoemaker, K. E. Young, and A. A. Salyers. "Insertion and excision of Bacteroides conjugative chromosomal elements." Journal of Bacteriology 174, no. 1 (1992): 166–72. http://dx.doi.org/10.1128/jb.174.1.166-172.1992.

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Pfeifer, Felicitas. "Insertion elements and genome organization of Halobacterium halobium." Systematic and Applied Microbiology 7, no. 1 (March 1986): 36–40. http://dx.doi.org/10.1016/s0723-2020(86)80121-7.

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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

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40

Brown, A. R., A. C. Townsley, and S. G. B. Amyes. "Diversity of Tn1546 Elements in Clinical Isolates of Glycopeptide-Resistant Enterococci from Scottish Hospitals." Antimicrobial Agents and Chemotherapy 45, no. 4 (April 1, 2001): 1309–11. http://dx.doi.org/10.1128/aac.45.4.1309-1311.2001.

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ABSTRACT The Tn1546-related elements of 48 Van glycopetide-resistant enterococci were compared. Ten distinct Tn1546 types were identified with variation primarily due to IS1542 and IS1216V-like insertions. Clonal isolates frequently differed in their Tn1546 type, indicating instability of Tn1546-related elements. A putative hybrid promoter was identified, generated upstream ofvanR by the insertion of IS1542. The presence of this hybrid promoter was associated with constitutive expression of the van genes and elevated teicoplanin resistance.

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Tang, Zuojian, Jared P. Steranka, Sisi Ma, Mark Grivainis, Nemanja Rodić, Cheng Ran Lisa Huang, Ie-Ming Shih, et al. "Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer." Proceedings of the National Academy of Sciences 114, no. 5 (January 17, 2017): E733—E740. http://dx.doi.org/10.1073/pnas.1619797114.

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Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq). We

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Morozova, Maria S. "Albanian Elements in the Slavic speech of Golo Bordo Bilinguals: Code-Mixing or Borrowing?" Slovene 9, no. 2 (2020): 372–94. http://dx.doi.org/10.31168/2305-6754.2020.9.2.16.

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The article considers contact-related phenomena found in the Slavic speech of bilinguals in the multiethnic region of Golo Bordo, Northeastern Albania. Most inhabitants of the Slavic part of the region master the local Western Macedonian dialect and the literary Albanian language. The material for the study includes dialect texts previously published in [Steinke, Ylli 2008; Соболев et al. 2013], examples from [Asenova 2016] and field materials collected by the author. Particular attention is paid to the insertion of Albanian nouns and verbs in the Macedonian speech of bilinguals. The article a

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Wright, Stephen I., Quang Hien Le, Daniel J. Schoen, and Thomas E. Bureau. "Population Dynamics of anAc-like Transposable Element in Self- and Cross-Pollinating Arabidopsis." Genetics 158, no. 3 (July 1, 2001): 1279–88. http://dx.doi.org/10.1093/genetics/158.3.1279.

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AbstractTheoretical models predict that the mating system should be an important factor driving the dynamics of transposable elements in natural populations due to differences in selective pressure on both element and host. We used a PCR-based approach to examine the abundance and levels of insertion polymorphism of Ac-III, a recently identified Ac-like transposon family, in natural populations of the selfing plant Arabidopsis thaliana and its close outcrossing relative, Arabidopsis lyrata. Although several insertions appeared to be ancient and shared between species, there is strong evidence

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Storer, Jessica M., Jerilyn A. Walker, Lydia C. Rewerts, Morgan A. Brown, Thomas O. Beckstrom, Scott W. Herke, Christian Roos, and Mark A. Batzer. "Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics." Genes 13, no. 11 (November 8, 2022): 2069. http://dx.doi.org/10.3390/genes13112069.

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Owl monkeys (genus Aotus), or “night monkeys” are platyrrhine primates in the Aotidae family. Early taxonomy only recognized one species, Aotus trivirgatus, until 1983, when Hershkovitz proposed nine unique species designations, classified into red-necked and gray-necked species groups based predominately on pelage coloration. Recent studies questioned this conventional separation of the genus and proposed designations based on the geographical location of wild populations. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. A scaffold

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45

Kwong, Shiyang, Anthony E. Woods, Peter J. Mirtschin, Ruowen Ge, and R. Kini. "The recruitment of blood coagulation factor X into snake venom gland as a toxin." Thrombosis and Haemostasis 102, no. 09 (2009): 469–78. http://dx.doi.org/10.1160/th09-03-0162.

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SummaryTrocarin D is a prothrombin activator from the Tropidechis carinatus venom. It is a functional and structural homologue to mammalian blood coagulation factor Xa.Trocarin D is hypothesised to have evolved from its factor X counterpart (TrFX) through gene duplication and recruitment.The genes of trocarin D and TrFX have significant sequence identities, except for insertions/deletions in their intron 1 and promoter regions. In trocarin D intron 1 region, there are three insertions and two deletions. In trocarin D promoter region, there is a novel 264 bp insertion which has potential cis-el

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Grech, Leanne, Daniel C. Jeffares, Christoph Y. Sadée, María Rodríguez-López, Danny A. Bitton, Mimoza Hoti, Carolina Biagosch, et al. "Fitness Landscape of the Fission Yeast Genome." Molecular Biology and Evolution 36, no. 8 (May 11, 2019): 1612–23. http://dx.doi.org/10.1093/molbev/msz113.

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Abstract The relationship between DNA sequence, biochemical function, and molecular evolution is relatively well-described for protein-coding regions of genomes, but far less clear in noncoding regions, particularly, in eukaryote genomes. In part, this is because we lack a complete description of the essential noncoding elements in a eukaryote genome. To contribute to this challenge, we used saturating transposon mutagenesis to interrogate the Schizosaccharomyces pombe genome. We generated 31 million transposon insertions, a theoretical coverage of 2.4 insertions per genomic site. We applied a

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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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Huff, Chad D., Jinchuan Xing, Alan R. Rogers, David Witherspoon, and Lynn B. Jorde. "Mobile elements reveal small population size in the ancient ancestors of Homo sapiens." Proceedings of the National Academy of Sciences 107, no. 5 (January 19, 2010): 2147–52. http://dx.doi.org/10.1073/pnas.0909000107.

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The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimat

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Cancian, Mariana, Tiago Minuzzi Freire da Fontoura Gomes, and Elgion Lucio Silva Loreto. "Somatic Mobilization: High Somatic Insertion Rate of mariner Transposable Element in Drosophila simulans." Insects 13, no. 5 (May 12, 2022): 454. http://dx.doi.org/10.3390/insects13050454.

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Although transposable elements (TEs) are usually silent in somatic tissues, they are sometimes mobilized in the soma and can potentially have biological consequences. The mariner element is one of the TEs involved in somatic mobilization (SM) in Drosophila and has a high rate of somatic excision. It is also known that temperature is an important factor in the increase of the mariner element SM in the fly. However, it is important to emphasize that excision is only one step of TE transposition, and the final step in this process is insertion. In the present study, we used an assay based on sequ

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Wright, David A., and Daniel F. Voytas. "Potential Retroviruses in Plants: Tat1 Is Related to a Group of Arabidopsis thaliana Ty3/gypsy Retrotransposons That Encode Envelope-Like Proteins." Genetics 149, no. 2 (June 1, 1998): 703–15. http://dx.doi.org/10.1093/genetics/149.2.703.

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Abstract Tat1 was originally identified as an insertion near the Arabidopsis thaliana SAM1 gene. We provide evidence that Tat1 is a retrotransposon and that previously described insertions are solo long terminal repeats (LTRs) left behind after the deletion of coding regions of full-length elements. Three Tat1 insertions were characterized that have retrotransposon features, including a primer binding site complementary to an A. thaliana asparagine tRNA and an open reading frame (ORF) with ~44% amino acid sequence similarity to the gag protein of the Zea mays retrotransposon Zeon-1. Tat1 eleme

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