Random mutagenesis of the hyperthermophilic archaeon Pyrococcus furiosus using in vitro mariner transposition and natural transformation.

PubMed

Guschinskaya, Natalia; Brunel, Romain; Tourte, Maxime; Lipscomb, Gina L; Adams, Michael W W; Oger, Philippe; Charpentier, Xavier

2016-11-08

Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P. furiosus COM1 strain and of in vitro Mariner-based transposition. A transposon bearing a genetic marker is randomly transposed in vitro in genomic DNA that is then used for natural transformation of P. furiosus. A small-scale transposition reaction routinely generates several hundred and up to two thousands transformants. Southern analysis and sequencing showed that the obtained mutants contain a single and random genomic insertion. Polyploidy has been reported in Thermococcales and P. furiosus is suspected of being polyploid. Yet, about half of the mutants obtained on the first selection are homozygous for the transposon insertion. Two rounds of isolation on selective medium were sufficient to obtain gene conversion in initially heterozygous mutants. This transposition mutagenesis strategy will greatly facilitate functional exploration of the Thermococcales genomes.

Transposon mutagenesis of Xylella fastidiosa by electroporation of Tn5 synaptic complexes.

PubMed

Guilhabert, M R; Hoffman, L M; Mills, D A; Kirkpatrick, B C

2001-06-01

Pierce's disease, a lethal disease of grapevine, is caused by Xylella fastidiosa, a gram-negative, xylem-limited bacterium that is transmitted from plant to plant by xylem-feeding insects. Strains of X. fastidiosa also have been associated with diseases that cause tremendous losses in many other economically important plants, including citrus. Although the complete genome sequence of X. fastidiosa has recently been determined, the inability to transform or produce transposon mutants of X. fastidiosa has been a major impediment to understanding pathogen-, plant-, and insect-vector interactions. We evaluated the ability of four different suicide vectors carrying either Tn5 or Tn10 transposons as well as a preformed Tn5 transposase-transposon synaptic complex (transposome) to transpose X. fastidiosa. The four suicide vectors failed to produce any detectable transposition events. Electroporation of transposomes, however, yielded 6 x 10(3) and 4 x 10(3) Tn5 mutants per microg of DNA in two different grapevine strains of X. fastidiosa. Molecular analysis showed that the transposition insertions were single, independent, stable events. Sequence analysis of the Tn5 insertion sites indicated that the transpositions occur randomly in the X. fastidiosa genome. Transposome-mediated mutagenesis should facilitate the identification of X. fastidiosa genes that mediate plant pathogenicity and insect transmission.

The Arabidopsis thaliana mobilome and its impact at the species level.

PubMed

Quadrana, Leandro; Bortolini Silveira, Amanda; Mayhew, George F; LeBlanc, Chantal; Martienssen, Robert A; Jeddeloh, Jeffrey A; Colot, Vincent

2016-06-03

Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles.

FB elements can promote exon shuffling: a promoter-less white allele can be reactivated by FB mediated transposition in Drosophila melanogaster.

PubMed

Moschetti, R; Marsano, R M; Barsanti, P; Caggese, C; Caizzi, R

2004-05-01

Foldback ( FB) elements are transposable elements found in many eukaryotic genomes; they are thought to contribute significantly to genome plasticity. In Drosophila melanogaster, FBs have been shown to be involved in the transposition of large chromosomal regions and in the genetic instability of some alleles of the white gene. In this report we show that FB mediated transposition of w(67C23), a mutation that deletes the promoter of the white gene and its first exon, containing the start codon, can restore expression of the white gene. We have characterized three independent events in which a 14-kb fragment from the w(67C23) locus was transposed into an intron region in three different genes. In each case a local promoter drives the expression of white, producing a chimeric mRNA. These findings suggest that, on an evolutionary timescale, FB elements may contribute to the creation of new genes via exon shuffling.

Vector for IS element entrapment and functional characterization based on turning on expression of distal promoterless genes.

PubMed

Szeverényi, I; Hodel, A; Arber, W; Olasz, F

1996-09-26

We constructed and characterized a novel trap vector for rapid isolation of insertion sequences. The strategy used for the isolation of IS elements is based on the ability of many IS elements to turn on the expression of otherwise silent genes distal to some sites of insertion. The simple transposition of an IS element can sometimes cause the constitutive expression of promoterless antibiotic resistance genes resulting in selectable phenotypes. The trap vector pAW1326 is based on a pBR322 replicon, it carries ampicillin and streptomycin resistance genes, and also silenced genes that confer chloramphenicol and kanamycin resistance once activated. The trap vector pAW1326 proved to be efficient and 85 percent of all isolated mutations were insertions. The majority of IS elements resident in the studied Escherichia coli strains tested became trapped, namely IS2, IS3, IS5, IS150, IS186 and Tn1000. We also encountered an insertion sequence, called IS10L/R-2, which is a hybrid of the two IS variants IS10L and IS10R. IS10L/R-2 is absent from most E. coli strains, but it is detectable in some strains such as JM109 which had been submitted to Tn10 mutagenesis. The distribution of the insertion sequences within the trap region was not random. Rather, the integration of chromosomal mobile genetic elements into the offered target sequence occurred in element-specific clusters. This is explained both by the target specificity and by the specific requirements for the activation of gene transcription by the DNA rearrangement. The employed trap vector pAW1326 proved to be useful for the isolation of mobile genetic elements, for a demonstration of their transposition activity as well as for the further characterization of some of the functional parameters of transposition.

Anterior Transposition of Anomalous Tortuous Vertebral Artery Causing Cervical Radiculopathy: A Report of 2 Cases and Review of Literature.

PubMed

Wang, Doris D; Burkhardt, Jan-Karl; Magill, Stephen T; Lawton, Michael T

2017-05-01

Cervical radiculopathy secondary to compression from vertebral artery (VA) tortuosity is a rare entity. We describe successful transposition through an anterolateral approach of tortuous VA loops causing cervical radiculopathy. Two patients with cervical radiculopathy (first case at C5-6 and second case at C3-4) secondary to anomalous VA loop compression underwent anterolateral approaches to the cervical spine for decompression and VA transposition. The anterior transverse foramina were drilled to unroof the VA loop, which was dissected free from the exiting nerve root. In both cases, the affected cervical nerve root was successfully decompressed with both radiographic and clinical improvements in radiculopathy symptoms. We found 8 other cases of VA transposition via either an anterolateral approach or a posterolateral approach described in the literature. Our second case of anterolateral VA transposition at the C3-4 level is the first case at this level and the highest level reported in the literature. Decompression using an anterolateral approach with direct microvascular transposition of the VA is a safe and effective treatment of this pathology and addresses the cause of radiculopathy more directly than the posterolateral approach. Copyright © 2017 Elsevier Inc. All rights reserved.

The Arabidopsis thaliana mobilome and its impact at the species level

PubMed Central

Quadrana, Leandro; Bortolini Silveira, Amanda; Mayhew, George F; LeBlanc, Chantal; Martienssen, Robert A; Jeddeloh, Jeffrey A; Colot, Vincent

2016-01-01

Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles. DOI: http://dx.doi.org/10.7554/eLife.15716.001 PMID:27258693

Search for Rare Copy-Number Variants in Congenital Heart Defects Identifies Novel Candidate Genes and a Potential Role for FOXC1 in Patients With Coarctation of the Aorta.

PubMed

Sanchez-Castro, Marta; Eldjouzi, Hadja; Charpentier, Eric; Busson, Pierre-François; Hauet, Quentin; Lindenbaum, Pierre; Delasalle-Guyomarch, Béatrice; Baudry, Adrien; Pichon, Olivier; Pascal, Cécile; Lefort, Bruno; Bajolle, Fanny; Pezard, Philippe; Schott, Jean-Jacques; Dina, Christian; Redon, Richard; Gournay, Véronique; Bonnet, Damien; Le Caignec, Cédric

2016-02-01

Congenital heart defects are the most frequent malformations among newborns and a frequent cause of morbidity and mortality. Although genetic variation contributes to congenital heart defects, their precise molecular bases remain unknown in the majority of patients. We analyzed, by high-resolution array comparative genomic hybridization, 316 children with sporadic, nonsyndromic congenital heart defects, including 76 coarctation of the aorta, 159 transposition of the great arteries, and 81 tetralogy of Fallot, as well as their unaffected parents. We identified by array comparative genomic hybridization, and validated by quantitative real-time polymerase chain reaction, 71 rare de novo (n=8) or inherited (n=63) copy-number variants (CNVs; 50 duplications and 21 deletions) in patients. We identified 113 candidate genes for congenital heart defects within these CNVs, including BTRC, CHRNB3, CSRP2BP, ERBB2, ERMARD, GLIS3, PLN, PTPRJ, RLN3, and TCTE3. No de novo CNVs were identified in patients with transposition of the great arteries in contrast to coarctation of the aorta and tetralogy of Fallot (P=0.002; Fisher exact test). A search for transcription factor binding sites showed that 93% of the rare CNVs identified in patients with coarctation of the aorta contained at least 1 gene with FOXC1-binding sites. This significant enrichment (P<0.0001; permutation test) was not observed for the CNVs identified in patients with transposition of the great arteries and tetralogy of Fallot. We hypothesize that these CNVs may alter the expression of genes regulated by FOXC1. Foxc1 belongs to the forkhead transcription factors family, which plays a critical role in cardiovascular development in mice. These data suggest that deregulation of FOXC1 or its downstream genes play a major role in the pathogenesis of coarctation of the aorta in humans. © 2015 American Heart Association, Inc.

Testicular expressed genes are missing in familial X-Linked Kallmann syndrome due to two large different deletions in daughter's X chromosomes.

PubMed

Hershkovitz, Eli; Loewenthal, Neta; Peretz, Asaf; Parvari, Ruti

2008-01-01

X-linked Kallmann syndrome (KS) is caused mainly by point mutations, in the KAL1 gene. Large deletions >1 Mb are rare events in the human population and commonly result in contiguous gene syndromes. A search for the mutation causing KS carried out on two pairs of first-degree cousins of 2 sisters. Two different apparently independent deletions were found. The deleted sequences encompass the KAL1 gene and four known additional genes exclusively expressed in testis. Two of these genes belong to the FAM9 gene family, which shares some homology with the SCYP3 gene, previously implicated in azoospermia. One of the events causing the deletion may have been mediated by an L1 transposition, the other by a non-homologous end joining. Such non-homologous recombinations have not yet been reported in the KAL genomic region and thus this area may be more prone to deletions than previously expected. This is the first report on genetic characterization of KS with a deletion of solely testis-expressed genes. The absence of these genes may have unfavorable implications for the patients regarding future fertility. (c) 2008 S. Karger AG, Basel

Insertion sequence transposition determines imipenem resistance in Acinetobacter baumannii.

PubMed

Kuo, Han-Yueh; Chang, Kai-Chih; Liu, Chih-Chin; Tang, Chuan Yi; Peng, Jhih-Hua; Lu, Chia-Wei; Tu, Chi-Chao; Liou, Ming-Li

2014-10-01

This study employed genomewide analysis to investigate potential resistance mechanisms in Acinetobacter baumannii following imipenem exposure. Imipenem-selected mutants were generated from the imipenem-susceptible strain ATCC 17978 by multistep selection resistance. Antibiotic susceptibilities were examined, and the selected mutants originated from the ATCC 17978 strain were confirmed by pulsed-field gel electrophoresis. The genomic sequence of a resistant mutant was analyzed using a next-generation sequencing platform, and genetic recombination was further confirmed by PCR. The result showed that phenotypic resistance was observed with carbapenem upon exposure to various concentrations of imipenem. Genomewide analysis showed that ISAba1 transposition was initiated by imipenem exposure at concentrations up to 0.5 mg/L. Transposition of ISAba1 upstream of blaOXA-95 was detected in all the selected mutants. The expression of blaOXA-95 was further analyzed by quantitative PCR, and the results demonstrated that a 200-fold increase in gene expression was required for resistance to imipenem. This study concluded that imipenem exposure at a concentration of 0.5 mg/L mediated the transposition of ISAba1 upstream of the blaOXA-95 gene and resulted in the overexpression of blaOXA-95 gene, which may play a major role in the resistance to imipenem in A. baumannii.

Rapid and efficient introduction of a foreign gene into bacterial artificial chromosome-cloned varicella vaccine by Tn7-mediated site-specific transposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somboonthum, Pranee; Koshizuka, Tetsuo; Okamoto, Shigefumi

2010-06-20

Using a rapid and reliable system based on Tn7-mediated site-specific transposition, we have successfully constructed a recombinant Oka varicella vaccine (vOka) expressing the mumps virus (MuV) fusion protein (F). The backbone of the vector was our previously reported vOka-BAC (bacterial artificial chromosome) genome. We inserted the transposon Tn7 attachment sequence, LacZ{alpha}-mini-attTn7, into the region between ORF12 and ORF13 to generate a vOka-BAC-Tn genome. The MuV-F expressing cassette was transposed into the vOka-BAC genome at the mini-attTn7 transposition site. MuV-F protein was expressed in recombinant virus, rvOka-F infected cells. In addition, the MuV-F protein was cleaved in the rvOka-F infected cellsmore » as in MuV-infected cells. The growth of rvOka-F was similar to that of the original recombinant vOka without the F gene. Thus, we show that Tn7-mediated transposition is an efficient method for introducing a foreign gene expression cassette into the vOka-BAC genome as a live virus vector.« less

Reconstitutional Mutagenesis of the Maize P Gene by Short-Range Ac Transpositions

PubMed Central

Moreno, M. A.; Chen, J.; Greenblatt, I.; Dellaporta, S. L.

1992-01-01

The tendency for Ac to transpose over short intervals has been utilized to develop insertional mutagenesis and fine structure genetic mapping strategies in maize. We recovered excisions of Ac from the P gene and insertions into nearby chromosomal sites. These closely linked Ac elements reinserted into the P gene, reconstituting over 250 unstable variegated alleles. Reconstituted alleles condition a variety of variegation patterns that reflect the position and orientation of Ac within the P gene. Molecular mapping and DNA sequence analyses have shown that reinsertion sites are dispersed throughout a 12.3-kb chromosomal region in the promoter, exons and introns of the P gene, but in some regions insertions sites were clustered in a nonrandom fashion. Transposition profiles and target site sequence data obtained from these studies have revealed several features of Ac transposition including its preference for certain target sites. These results clearly demonstrate the tendency of Ac to transpose to nearby sites in both proximal and distal directions from the donor site. With minor modifications, reconstitutional mutagenesis should be applicable to many Ac-induced mutations in maize and in other plant species and can possibly be extended to other eukaryotic transposon systems as well. PMID:1325389

Heterogeneic dynamics of the structures of multiple gene clusters in two pathogenetically different lines originating from the same phytoplasma.

PubMed

Arashida, Ryo; Kakizawa, Shigeyuki; Hoshi, Ayaka; Ishii, Yoshiko; Jung, Hee-Young; Kagiwada, Satoshi; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

2008-04-01

Phytoplasmas are phloem-limited plant pathogens that are transmitted by insect vectors and are associated with diseases in hundreds of plant species. Despite their small sizes, phytoplasma genomes have repeat-rich sequences, which are due to several genes that are encoded as multiple copies. These multiple genes exist in a gene cluster, the potential mobile unit (PMU). PMUs are present at several distinct regions in the phytoplasma genome. The multicopy genes encoded by PMUs (herein named mobile unit genes [MUGs]) and similar genes elsewhere in the genome (herein named fundamental genes [FUGs]) are likely to have the same function based on their annotations. In this manuscript we show evidence that MUGs and FUGs do not cluster together within the same clade. Each MUG is in a cluster with a short branch length, suggesting that MUGs are recently diverged paralogs, whereas the origin of FUGs is different from that of MUGs. We also compared the genome structures around the lplA gene in two derivative lines of the 'Candidatus Phytoplasma asteris' OY strain, the severe-symptom line W (OY-W) and the mild-symptom line M (OY-M). The gene organizations of the nucleotide sequences upstream of the lplA genes of OY-W and OY-M were dramatically different. The tra5 insertion sequence, an element of PMUs, was found only in this region in OY-W. These results suggest that transposition of entire PMUs and PMU sections has occurred frequently in the OY phytoplasma genome. The difference in the pathogenicities of OY-W and OY-M might be caused by the duplication and transposition of PMUs, followed by genome rearrangement.

Development of a high-frequency in vivo transposon mutagenesis system for Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942.

PubMed

Watabe, Kazuyuki; Mimuro, Mamoru; Tsuchiya, Tohru

2014-11-01

Synechocystis sp. PCC 6803 (Synechocystis) is the first sequenced photosynthetic organism and has two advantages: natural transformation and light-activated heterotrophic growth. Such characteristics have mainly promoted reverse genetic analysis in this organism, however, to date approximately 50% of genes are still annotated as 'unknown protein' or 'hypothetical protein'. Therefore, forward genetic analysis is required for the identification of significant genes responsible for photosynthesis and other physiological phenomena among the genes of unknown function. The in vivo transposon mutagenesis system is one of the major methods for random mutagenesis. However, present in vivo transposon mutagenesis systems for cyanobacteria face problems such as relatively low frequency of transposition and repeated transposition in the host cells. In this study, we constructed vectors based on a mini-Tn5-derived vector that was designed to prevent repeated transposition. Our vectors carry a hyperactive transposase and optimized recognition sequence of transposase, which were reported to enhance frequency of transposition. Using the vector, we succeeded in highly frequent transposition (9×10(-3) per recipient cell) in Synechocystis. Transposon insertion sites of 10 randomly selected mutants indicated that the insertion sites spread throughout the genome with low sequence dependency. Furthermore, one of the 10 mutants exhibited the slow-growing phenotype, and the mutant was functionally complemented by using our expression vector. Our system also worked with another model cyanobacterium, Synechococcus elongatus PCC 7942, with high frequency. These results indicate that the developed system can be applied to the forward genetic analysis of a broad range of cyanobacteria. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Mandibular Symmetrical Bilateral Canine-Lateral Incisors Transposition: Its Early Diagnosis and Treatment Considerations.

PubMed

Shapira, Yehoshua; Finkelstein, Tamar; Kadry, Rana; Schonberger, Shirley; Shpack, Nir

2016-01-01

Bilateral mandibular tooth transposition is a relatively rare dental anomaly caused by distal migration of the mandibular lateral incisors and can be detected in the early mixed dentition by radiographic examination. Early diagnosis and interceptive intervention may reduce the risk of possible transposition between the mandibular canine and lateral incisor. This report illustrates the orthodontic management of bilateral mandibular canine-lateral incisor transposition. Correct positioning of the affected teeth was achieved on the left side while teeth on the right side were aligned in their transposed position. It demonstrates the outcome of good alignment of the teeth in the dental arch.

Vector modifications to eliminate transposase expression following piggyBac-mediated transgenesis

PubMed Central

Chakraborty, Syandan; Ji, HaYeun; Chen, Jack; Gersbach, Charles A.; Leong, Kam W.

2014-01-01

Transgene insertion plays an important role in gene therapy and in biological studies. Transposon-based systems that integrate transgenes by transposase-catalyzed “cut-and-paste” mechanism have emerged as an attractive system for transgenesis. Hyperactive piggyBac transposon is particularly promising due to its ability to integrate large transgenes with high efficiency. However, prolonged expression of transposase can become a potential source of genotoxic effects due to uncontrolled transposition of the integrated transgene from one chromosomal locus to another. In this study we propose a vector design to decrease post-transposition expression of transposase and to eliminate the cells that have residual transposase expression. We design a single plasmid construct that combines the transposase and the transpositioning transgene element to share a single polyA sequence for termination. Consequently, the separation of the transposase element from the polyA sequence after transposition leads to its deactivation. We also co-express Herpes Simplex Virus thymidine kinase (HSV-tk) with the transposase. Therefore, cells having residual transposase expression can be eliminated by the administration of ganciclovir. We demonstrate the utility of this combination transposon system by integrating and expressing a model therapeutic gene, human coagulation Factor IX, in HEK293T cells. PMID:25492703

Impaired Development of Left Anterior Heart Field by Ectopic Retinoic Acid Causes Transposition of the Great Arteries

PubMed Central

Narematsu, Mayu; Kamimura, Tatsuya; Yamagishi, Toshiyuki; Fukui, Mitsuru; Nakajima, Yuji

2015-01-01

Background Transposition of the great arteries is one of the most commonly diagnosed conotruncal heart defects at birth, but its etiology is largely unknown. The anterior heart field (AHF) that resides in the anterior pharyngeal arches contributes to conotruncal development, during which heart progenitors that originated from the left and right AHF migrate to form distinct conotruncal regions. The aim of this study is to identify abnormal AHF development that causes the morphology of transposition of the great arteries. Methods and Results We placed a retinoic acid–soaked bead on the left or the right or on both sides of the AHF of stage 12 to 14 chick embryos and examined the conotruncal heart defect at stage 34. Transposition of the great arteries was diagnosed at high incidence in embryos for which a retinoic acid–soaked bead had been placed in the left AHF at stage 12. Fluorescent dye tracing showed that AHF exposed to retinoic acid failed to contribute to conotruncus development. FGF8 and Isl1 expression were downregulated in retinoic acid–exposed AHF, and differentiation and expansion of cardiomyocytes were suppressed in cultured AHF in medium supplemented with retinoic acid. Conclusions The left AHF at the early looped heart stage, corresponding to Carnegie stages 10 to 11 (28 to 29 days after fertilization) in human embryos, is the region of the impediment that causes the morphology of transposition of the great arteries. PMID:25929268

Infrequent transposition of Ac in lettuce, Lactuca sativa.

PubMed

Yang, C H; Ellis, J G; Michelmore, R W

1993-08-01

The maize transposable element Activator (Ac) is being used to develop a transposon mutagenesis system in lettuce, Lactuca sativa. Two constructs containing the complete Ac from the waxy-m7 locus of maize were introduced into lettuce and monitored for activity using Southern analysis and PCR amplification of the excision site. No transposition of Ac was detected in over 32 transgenic R1 plants, although these constructs were known to provide frequent transposition in other species. Also, no transposition was observed in later generations. In subsequent experiments, transposition was detected in lettuce calli using constructs that allowed selection for excision events. In these constructs, the neomycin phosphotransferase II gene was interrupted by either Ac or Ds. Excision was detected as the ability of callus to grow on kanamycin. Synthesis of the transposase from the cDNA of Ac expressed from the T-DNA 2' promoter resulted in more frequent excision of Ds than was observed with the wild-type Ac. No excision was observed with Ds in the absence of the transposase. The excision events were confirmed by amplification of the excision site by PCR followed by DNA sequencing. Excision and reintegration were also confirmed by Southern analysis. Ac/Ds is therefore capable of transposition in at least calli of lettuce.

Characterization of growth and reproduction performance, transgene integration, expression and transmission patterns in transgenic pigs produced by piggyBac transposition-mediated gene transfer

PubMed Central

Zeng, Fang; Li, Zicong; Cai, Gengyuan; Gao, Wenchao; Jiang, Gelong; Liu, Dewu; Urschitz, Johann; Moisyadi, Stefan; Wu, Zhenfang

2016-01-01

Previously we successfully produced a group of EGFP-expressing founder transgenic pigs by a newly developed efficient and simple pig transgenesis method based on cytoplasmic injection of piggyBac plasmids. In this study, we investigated the growth and reproduction performance, and characterized the transgene insertion, transmission and expression patterns in transgenic pigs generated by piggyBac transposition. Results showed that transgene has no injurious effect on the growth and reproduction of transgenic pigs. Multiple copies of monogenic EGFP transgene were inserted at noncoding sequences of host genome, and passed from founder transgenic pigs to their transgenic offspring in segregation or linkage manner. The EGFP transgene was ubiquitously expressed in transgenic pigs, and its expression intensity was associated with transgene copy number but not related to its promoter DNA methylation level. To the best of our knowledge, this is first study that fully described the growth and reproduction performance, transgene insertion, expression and transmission profiles in transgenic pigs produced by piggyBac system. It not only demonstrates that piggyBac transposition-mediated gene transfer is an effective and favourable approach for pig transgenesis, but also provides scientific information for understanding the transgene insertion, expression and transmission patterns in transgenic animals produced by piggyBac transposition. PMID:27565868

Riboregulation of bacterial and archaeal transposition.

PubMed

Ellis, Michael J; Haniford, David B

2016-05-01

The coexistence of transposons with their hosts depends largely on transposition levels being tightly regulated to limit the mutagenic burden associated with frequent transposition. For 'DNA-based' (class II) bacterial transposons there is growing evidence that regulation through small noncoding RNAs and/or the RNA-binding protein Hfq are prominent mechanisms of defense against transposition. Recent transcriptomics analyses have identified many new cases of antisense RNAs (asRNA) that potentially could regulate the expression of transposon-encoded genes giving the impression that asRNA regulation of DNA-based transposons is much more frequent than previously thought. Hfq is a highly conserved bacterial protein that plays a central role in posttranscriptional gene regulation and stress response pathways in many bacteria. Three different mechanisms for Hfq-directed control of bacterial transposons have been identified to date highlighting the versatility of this protein as a regulator of bacterial transposons. There is also evidence emerging that some DNA-based transposons encode RNAs that could regulate expression of host genes. In the case of IS200, which appears to have lost its ability to transpose, contributing a regulatory RNA to its host could account for the persistence of this mobile element in a wide range of bacterial species. It remains to be seen how prevalent these transposon-encoded RNA regulators are, but given the relatively large amount of intragenic transcription in bacterial genomes, it would not be surprising if new examples are forthcoming. WIREs RNA 2016, 7:382-398. doi: 10.1002/wrna.1341 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

A Genetic and Molecular Analysis of the 46c Chromosomal Region Surrounding the Fmrfamide Neuropeptide Gene in Drosophila Melanogaster

PubMed Central

O'Brien, M. A.; Roberts, M. S.; Taghert, P. H.

1994-01-01

We have analyzed the FMRFamide neuropeptide gene region of Drosophila melanogaster. This gene maps to the 46C region of chromosome 2R; this interval previously was not well characterized. For this genetic and molecular analysis, we have used X-ray mutagenesis, EMS mutagenesis, and the recently reported local P element transposition method. We identified four overlapping deletions, two of which have proximal breakpoints that define a 50-60-kb region surrounding the FMRFamide gene in 46C. To this small region, we mapped three lethal complementation groups; 10 additional lethal complementation groups were mapped to more distal regions of 46CD. One of these groups corresponds to even-skipped, the other 12 are previously unidentified. Using various lines of evidence we excluded the possibility that FMRFamide corresponds to any of the three lethal complementation groups mapping to its immediate 50-60-kb vicinity. The positions of two of the three lethal complementation groups were identified with P elements using a local transposition scheme. The third lethal complementation group was excluded as being FMRFamide mutants by sequence analysis and by immunocytochemistry with proFMRFamide precursor-specific antibodies. This analysis has (1) provided a genetic map of the 46CD chromosomal region and a detailed molecular map of a portion of the 46C region and (2) provided additional evidence of the utility of local transposition for targeting nearby genes. PMID:8056304

An indicator gene to demonstrate intracellular transposition of defective retroviruses.

PubMed Central

Heidmann, T; Heidmann, O; Nicolas, J F

1988-01-01

An indicator gene for detection and quantitation of RNA-mediated transposition was constructed (neoRT). It was inserted into a Moloney murine leukemia provirus (Mo-MLV) deleted for the envelope gene to test for intracellular transposition of defective retroviruses [Mo-MLV(neo)RT]. NeoRT contains the selectable neo gene (which confers resistance to the drug G418), inactivated by a polyadenylylation sequence inserted between the neo promotor and coding sequence. The polyadenylylation sequence is flanked (on the antisense strand of the DNA) by a donor and an acceptor splice site so as to be removed upon passage of the provirus through an RNA intermediate. 3T3 cells transfected with the defective Mo-MLV(neo)RT provirus are sensitive to G418. After trans-complementation with Mo-MLV, viral transcripts confer resistance to G418 upon infection of test cells. In the resistant cells, the polyadenylylation sequence has been removed, as a result in most cases of precise splicing of the intronic domain. Retrotransposition of the defective Mo-MLV(neo)RT provirus was demonstrated by submitting transfected G418-sensitive clones to selection. Between 1 and 10 G418-resistant clones were obtained per 10(7) cells. Several possess additional copies, with evidence for precise removal of the intronic domain. By using target test cells in coculture experiments, extracellular intermediates of retrotransposition could not be detected. Images PMID:2832848

Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture.

PubMed

Masuta, Yukari; Nozawa, Kosuke; Takagi, Hiroki; Yaegashi, Hiroki; Tanaka, Keisuke; Ito, Tasuku; Saito, Hideyuki; Kobayashi, Hisato; Matsunaga, Wataru; Masuda, Seiji; Kato, Atsushi; Ito, Hidetaka

2017-02-01

A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation. The heat activation of ONSEN transcripts was not significantly up-regulated in tissue culture compared with that in heat-stressed seedlings, indicating that the transposition of ONSEN was regulated independently of the transcript level. RdDM-related genes were up-regulated by heat stress in both tissue culture and seedlings. The level of DNA methylation of ONSEN did not show any change in tissue culture, and the amount of ONSEN-derived small RNAs was not affected by heat stress. The results indicated that the transposition of ONSEN was regulated by an alternative mechanism in addition to the RdDM-mediated epigenetic regulation in tissue culture. We applied the tissue culture-induced transposition of ONSEN to Japanese radish, an important breeding species of the family Brassicaceae. Several new insertions were detected in a regenerated plant derived from heat-stressed tissues and its self-fertilized progeny, revealing the possibility of molecular breeding without genetic modification. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Spontaneous germline excision of Tol1, a DNA-based transposable element naturally occurring in the medaka fish genome.

PubMed

Watanabe, Kohei; Koga, Hajime; Nakamura, Kodai; Fujita, Akiko; Hattori, Akimasa; Matsuda, Masaru; Koga, Akihiko

2014-04-01

DNA-based transposable elements are ubiquitous constituents of eukaryotic genomes. Vertebrates are, however, exceptional in that most of their DNA-based elements appear to be inactivated. The Tol1 element of the medaka fish, Oryzias latipes, is one of the few elements for which copies containing an undamaged gene have been found. Spontaneous transposition of this element in somatic cells has previously been demonstrated, but there is only indirect evidence for its germline transposition. Here, we show direct evidence of spontaneous excision in the germline. Tyrosinase is the key enzyme in melanin biosynthesis. In an albino laboratory strain of medaka fish, which is homozygous for a mutant tyrosinase gene in which a Tol1 copy is inserted, we identified de novo reversion mutations related to melanin pigmentation. The gamete-based reversion rate was as high as 0.4%. The revertant fish carried the tyrosinase gene from which the Tol1 copy had been excised. We previously reported the germline transposition of Tol2, another DNA-based element that is thought to be a recent invader of the medaka fish genome. Tol1 is an ancient resident of the genome. Our results indicate that even an old element can contribute to genetic variation in the host genome as a natural mutator.

Macrovascular Decompression of the Brainstem and Cranial Nerves: Evolution of an Anteromedial Vertebrobasilar Artery Transposition Technique.

PubMed

Choudhri, Omar; Connolly, Ian D; Lawton, Michael T

2017-08-01

Tortuous and dolichoectatic vertebrobasilar arteries can impinge on the brainstem and cranial nerves to cause compression syndromes. Transposition techniques are often required to decompress the brainstem with dolichoectatic pathology. We describe our evolution of an anteromedial transposition technique and its efficacy in decompressing the brainstem and relieving symptoms. To present the anteromedial vertebrobasilar artery transposition technique for macrovascular decompression of the brainstem and cranial nerves. All patients who underwent vertebrobasilar artery transposition were identified from the prospectively maintained database of the Vascular Neurosurgery service, and their medical records were reviewed retrospectively. The extent of arterial displacement was measured pre- and postoperatively on imaging. Vertebrobasilar arterial transposition and macrovascular decompression was performed in 12 patients. Evolution in technique was characterized by gradual preference for the far-lateral approach, use of a sling technique with muslin wrap, and an anteromedial direction of pull on the vertebrobasilar artery with clip-assisted tethering to the clival dura. With this technique, mean lateral displacement decreased from 6.6 mm in the first half of the series to 3.8 mm in the last half of the series, and mean anterior displacement increased from 0.8 to 2.5 mm, with corresponding increases in satisfaction and relief of symptoms. Compressive dolichoectatic pathology directed laterally into cranial nerves and posteriorly into the brainstem can be corrected with anteromedial transposition towards the clivus. Our technique accomplishes this anteromedial transposition from an inferolateral surgical approach through the vagoaccessory triangle, with sling fixation to clival dura using aneurysm clips. Copyright © 2017 by the Congress of Neurological Surgeons

Amplification of the 1731 LTR retrotransposon in Drosophila melanogaster cultured cells: origin of neocopies and impact on the genome.

PubMed

Maisonhaute, Claude; Ogereau, David; Hua-Van, Aurélie; Capy, Pierre

2007-05-15

Transposable elements (TEs), represent a large fraction of the eukaryotic genome. In Drosophila melanogaster, about 20% of the genome corresponds to such middle repetitive DNA dispersed sequences. A fraction of TEs is composed of elements showing a retrovirus-like structure, the LTR-retrotransposons, the first TEs to be described in the Drosophila genome. Interestingly, in D. melanogaster embryonic immortal cell culture genomes the copy number of these LTR-retrotransposons was revealed to be higher than the copy number in the Drosophila genome, presumably as the result of transposition of some copies to new genomic locations [Potter, S.S., Brorein Jr., W.J., Dunsmuir, P., Rubin, G.M., 1979. Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila. Cell 17, 415-427; Junakovic, N., Di Franco, C., Best-Belpomme, M., Echalier, G., 1988. On the transposition of copia-like nomadic elements in cultured Drosophila cells. Chromosoma 97, 212-218]. This suggests that so many transpositions modified the genome organisation and consequently the expression of targeted genes. To understand what has directed the transposition of TEs in Drosophila cell culture genomes, a search to identify the newly transposed copies was undertaken using 1731, a LTR-retrotransposon. A comparison between 1731 full-length elements found in the fly sequenced genome (y(1); cn(1)bw(1), sp(1) stock) and 1731 full-length elements amplified by PCR in the two cell line was done. The resulting data provide evidence that all 1731 neocopies were derived from a single copy slightly active in the Drosophila genome and subsequently strongly activated in cultured cells; and that this active copy is related to a newly evolved genomic variant (Kalmykova, A.I., et al., 2004. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol. Biol. Evol. 21, 2281-2289). Moreover, neocopies are shown to be inserted in different sets of genes in the two cell lines suggesting they might be involved in the biological and physiological differences observed between Kc and S2 cell lines.

Bipedicled strap muscle transposition for vocal fold deficit after laser cordectomy in early glottic cancer patients.

PubMed

Su, Chih-Ying; Chuang, Hui-Ching; Tsai, Shang-Shyue; Chiu, Jeng-Fen

2005-03-01

In treating early glottic carcinomas, the outcomes of endoscopic laser cordectomy have been proven to be valuable in local control, survival, and vocal function preservation. In some extended cases, however, laser cordectomy may leave patients with poor vocal function because of vocal fold deficit. This work assesses the vocal outcome of medialization laryngoplasty with bipedicled strap muscle transposition for vocal fold deficit resulting from laser cordectomy in early glottic cancer patients. A prospective clinical series. Thirteen early glottic cancer patients who had vocal fold deficit caused by previous laser cordectomy underwent medialization laryngoplasty with bipedicled strap muscle transposition. The thyroid lamina on the cordectomy side was paramedially separated. The inner perichondrium was circumspectly raised from the overlying thyroid cartilage. After separating the thyrohyoid and cricothyroid membranes, the lamina was retracted laterally. A bipedicled strap muscle flap was then transposed into the area between the lamina and the paraglottic soft tissue. The thyroid cartilages were carefully sutured back in position. All patients received pre- and postoperative voice assessments comprising laryngostroboscopy and vocal function studies. Vocal enhancement was present in 92% (12/13) of patients after medialization laryngoplasty with strap muscle transposition. The glottal closure and maximal phonation time were noticeably improved by surgery. No dyspnea or other significant complications were observed in any patients. The outcomes show that bipedicled strap muscle transposition is a prosthesis-free, safe, and valuable laryngoplastic technique for correcting glottal incompetence caused by endoscopic laser cordectomy in early glottic cancer patients.

A bacterial genome in transition - an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus

PubMed Central

2011-01-01

Background Insertion sequence (IS) elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont Amoebophilus asiaticus contains an unusually large number of transposase genes (n = 354; 23% of all genes). Results The transposase genes in the A. asiaticus genome can be assigned to 16 different IS elements termed ISCaa1 to ISCaa16, which are represented by 2 to 24 full-length copies, respectively. Despite this high IS element load, the A. asiaticus genome displays a GC skew pattern typical for most bacterial genomes, indicating that no major rearrangements have occurred recently. Additionally, the high sequence divergence of some IS elements, the high number of truncated IS element copies (n = 143), as well as the absence of direct repeats in most IS elements suggest that the IS elements of A. asiaticus are transpositionally inactive. Although we could show transcription of 13 IS elements, we did not find experimental evidence for transpositional activity, corroborating our results from sequence analyses. However, we detected contiguous transcripts between IS elements and their downstream genes at nine loci in the A. asiaticus genome, indicating that some IS elements influence the transcription of downstream genes, some of which might be important for host cell interaction. Conclusions Taken together, the IS elements in the A. asiaticus genome are currently in the process of degradation and largely represent reflections of the evolutionary past of A. asiaticus in which its genome was shaped by their activity. PMID:21943072

Efficient Sleeping Beauty DNA Transposition From DNA Minicircles

PubMed Central

Sharma, Nynne; Cai, Yujia; Bak, Rasmus O; Jakobsen, Martin R; Schrøder, Lisbeth Dahl; Mikkelsen, Jacob Giehm

2013-01-01

DNA transposon-based vectors have emerged as new potential delivery tools in therapeutic gene transfer. Such vectors are now showing promise in hematopoietic stem cells and primary human T cells, and clinical trials with transposon-engineered cells are on the way. However, the use of plasmid DNA as a carrier of the vector raises safety concerns due to the undesirable administration of bacterial sequences. To optimize vectors based on the Sleeping Beauty (SB) DNA transposon for clinical use, we examine here SB transposition from DNA minicircles (MCs) devoid of the bacterial plasmid backbone. Potent DNA transposition, directed by the hyperactive SB100X transposase, is demonstrated from MC donors, and the stable transfection rate is significantly enhanced by expressing the SB100X transposase from MCs. The stable transfection rate is inversely related to the size of circular donor, suggesting that a MC-based SB transposition system benefits primarily from an increased cellular uptake and/or enhanced expression which can be observed with DNA MCs. DNA transposon and transposase MCs are easily produced, are favorable in size, do not carry irrelevant DNA, and are robust substrates for DNA transposition. In accordance, DNA MCs should become a standard source of DNA transposons not only in therapeutic settings but also in the daily use of the SB system. PMID:23443502

Role of Ovarian Transposition Based on the Dosimetric Effects of Craniospinal Irradiation on the Ovaries: A Case Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, James D.; Hitchen, Christine; Vlachaki, Maria T.

2007-10-01

In this study, we present a case of laparoscopic ovarian transposition to preserve ovarian function in an adult female patient treated with craniospinal irradiation for standard risk medulloblastoma. The prescribed dose to the craniospinal axis was 2340 cGy at 180 cGy per fraction and was delivered with 6-MV photons. Before ovarian transposition, magnetic resonance imaging (MRI) of the pelvis was obtained for localization of the ovaries and was registered with the planning computed tomography (CT) scan. Surgical clips allowed for CT localization of the ovaries after transposition. As a result of ovarian transposition, mean and maximum radiation doses decreased frommore » 983 to 68 cGy and 1624 to 84 cGy for the left ovary and from 166 to 87 cGy and 723 to 103 cGy for the right ovary, respectively. Review of the literature indicates that such radiation doses are below the threshold that causes ovarian dysfunction and infertility. We conclude that ovarian localization with an MRI of the pelvis can be offered to females undergoing craniospinal irradiation. Transposition of the ovaries provides an option to preserve ovarian function in cases where the ovaries would otherwise be included within the radiation field.« less

Anatomical considerations of fascial release in ulnar nerve transposition: a concept revisited.

PubMed

Mahan, Mark A; Gasco, Jaime; Mokhtee, David B; Brown, Justin M

2015-11-01

Surgical transposition of the ulnar nerve to alleviate entrapment may cause otherwise normal structures to become new sources of nerve compression. Recurrent or persistent neuropathy after anterior transposition is commonly attributable to a new distal compression. The authors sought to clarify the anatomical relationship of the ulnar nerve to the common aponeurosis of the humeral head of the flexor carpi ulnaris (FCU) and flexor digitorum superficialis (FDS) muscles following anterior transposition of the nerve. The intermuscular septa of the proximal forearm were explored in 26 fresh cadaveric specimens. The fibrous septa and common aponeurotic insertions of the flexor-pronator muscle mass were evaluated in relation to the ulnar nerve, with particular attention to the effect of transposition upon the nerve in this region. An intermuscular aponeurosis associated with the FCU and FDS muscles was present in all specimens. Transposition consistently resulted in angulation of the nerve during elbow flexion when this fascial septum was not released. The proximal site at which the nerve began to traverse this fascial structure was found to be an average of 3.9 cm (SD 0.7 cm) from the medial epicondyle. The common aponeurosis encountered between the FDS and FCU muscles represents a potential site of posttransposition entrapment, which may account for a subset of failed anterior transpositions. Exploration of this region with release of this structure is recommended to provide an unconstrained distal course for a transposed ulnar nerve.

Globin gene structure in a reptile supports the transpositional model for amniote α- and β-globin gene evolution.

PubMed

Patel, Vidushi S; Ezaz, Tariq; Deakin, Janine E; Graves, Jennifer A Marshall

2010-12-01

The haemoglobin protein, required for oxygen transportation in the body, is encoded by α- and β-globin genes that are arranged in clusters. The transpositional model for the evolution of distinct α-globin and β-globin clusters in amniotes is much simpler than the previously proposed whole genome duplication model. According to this model, all jawed vertebrates share one ancient region containing α- and β-globin genes and several flanking genes in the order MPG-C16orf35-(α-β)-GBY-LUC7L that has been conserved for more than 410 million years, whereas amniotes evolved a distinct β-globin cluster by insertion of a transposed β-globin gene from this ancient region into a cluster of olfactory receptors flanked by CCKBR and RRM1. It could not be determined whether this organisation is conserved in all amniotes because of the paucity of information from non-avian reptiles. To fill in this gap, we examined globin gene organisation in a squamate reptile, the Australian bearded dragon lizard, Pogona vitticeps (Agamidae). We report here that the α-globin cluster (HBK, HBA) is flanked by C16orf35 and GBY and is located on a pair of microchromosomes, whereas the β-globin cluster is flanked by RRM1 on the 3' end and is located on the long arm of chromosome 3. However, the CCKBR gene that flanks the β-globin cluster on the 5' end in other amniotes is located on the short arm of chromosome 5 in P. vitticeps, indicating that a chromosomal break between the β-globin cluster and CCKBR occurred at least in the agamid lineage. Our data from a reptile species provide further evidence to support the transpositional model for the evolution of β-globin gene cluster in amniotes.

Loss-of-function of a ubiquitin-related modifier promotes the mobilization of the active MITE mPing.

PubMed

Tsukiyama, Takuji; Teramoto, Shota; Yasuda, Kanako; Horibata, Akira; Mori, Nanako; Okumoto, Yutaka; Teraishi, Masayoshi; Saito, Hiroki; Onishi, Akiko; Tamura, Kanako; Tanisaka, Takatoshi

2013-05-01

Miniature inverted-repeat transposable elements (MITEs) are widespread in both prokaryotic and eukaryotic genomes, where their copy numbers can attain several thousands. Little is known, however, about the genetic factor(s) affecting their transpositions. Here, we show that disruption of a gene encoding ubiquitin-like protein markedly enhances the transposition activity of a MITE mPing in intact rice plants without any exogenous stresses. We found that the transposition activity of mPing is far higher in the lines harboring a non-functional allele at the Rurm1 (Rice ubiquitin-related modifier-1) locus than in the wild-type line. Although the alteration of cytosine methylation pattern triggers the activation of transposable elements under exogenous stress conditions, the methylation degrees in the whole genome, the mPing-body region, and the mPing-flanking regions of the non-functional Rurm1 line were unchanged. This study provides experimental evidence for one of the models of genome shock theory that genetic accidents within cells enhance the transposition activities of transposable elements.

Inferior Alveolar Nerve Lateralization and Transposition for Dental Implant Placement. Part II: a Systematic Review of Neurosensory Complications.

PubMed

Abayev, Boris; Juodzbalys, Gintaras

2015-01-01

This article, the second in a two-part series, continues the discussion of inferior alveolar nerve lateralization/transposition for dental implant placement. The aim of this article is to review the scientific literature and clinical reports in order to analyse the neurosensory complications, risks and disadvantages of lateralization/transposition of the inferior alveolar nerve followed by implant placement in an edentulous atrophic posterior mandible. A comprehensive review of the current literature was conducted according to the PRISMA guidelines by accessing the NCBI PubMed and PMC databases, as well as academic sites and books. The articles were searched from January 1997 to July 2014. Articles in English language, which included adult patients between 18 - 80 years of age who had minimal residual bone above the mandibular canal and had undergone inferior alveolar nerve (IAN) repositioning, with minimum 6 months of follow-up, were included. A total of 21 studies were included in this review. Ten were related to IAN transposition, 7 to IAN lateralization and 4 to both transposition and lateralization. The IAN neurosensory disturbance function was present in most patients (99.47% [376/378]) for 1 to 6 months. In total, 0.53% (2/378) of procedures the disturbances were permanent. Inferior alveolar nerve repositioning is related to initial transient change in sensation in the majority of cases. The most popular causes of nerve damage are spatula-caused traction in the mucoperiosteal flap, pressure due to severe inflammation or retention of fluid around the nerve and subsequent development of transient ischemia, and mandibular body fracture.

Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans

PubMed Central

Rogers, Rebekah L.

2015-01-01

Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5′-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution. PMID:26399483

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.

PubMed

Imprialou, Martha; Kahles, André; Steffen, Joshua G; Osborne, Edward J; Gan, Xiangchao; Lempe, Janne; Bhomra, Amarjit; Belfield, Eric; Visscher, Anne; Greenhalgh, Robert; Harberd, Nicholas P; Goram, Richard; Hein, Jotun; Robert-Seilaniantz, Alexandre; Jones, Jonathan; Stegle, Oliver; Kover, Paula; Tsiantis, Miltos; Nordborg, Magnus; Rätsch, Gunnar; Clark, Richard M; Mott, Richard

2017-04-01

To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred Arabidopsis thaliana genomes, we identified 6502 segregating structural variants. Remarkably, 25% of these were transpositions. While many structural variants cannot be delineated precisely, we validated 83% of 44 predicted transposition breakpoints by polymerase chain reaction. We show that specific structural variants may be causative for quantitative trait loci for germination and resistance to infection by the fungus Albugo laibachii , isolate Nc14. Further we show that the phenotypic heritability attributable to read-mapping anomalies differs from, and, in the case of time to germination and bolting, exceeds that due to standard genetic variation. Genes within structural variants are also more likely to be silenced or dysregulated. This approach complements the prevalent strategy of structural variant discovery in fewer individuals sequenced at high coverage. It is generally applicable to large populations sequenced at low-coverage, and is particularly suited to mapping transpositions. Copyright © 2017 by the Genetics Society of America.

Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia.

PubMed

Wang, Ningning; Wang, Hongyan; Wang, Hui; Zhang, Di; Wu, Ying; Ou, Xiufang; Liu, Shuang; Dong, Zhenying; Liu, Bao

2010-08-26

It is widely recognized that interspecific hybridization may induce "genome shock", and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants. A prominent component involved in the genome shock is reactivation of cryptic transposable elements (TEs) in the hybrid genome, which is often associated with alteration in the elements' epigenetic modifications like cytosine DNA methylation. We have previously reported that introgressants derived from hybridization between Oryza sativa (rice) and Zizania latifolia manifested substantial methylation re-patterning and rampant mobilization of two TEs, a copia retrotransposon Tos17 and a MITE mPing. It was not known however whether other types of TEs had also been transpositionally reactivated in these introgressants, their relevance to alteration in cytosine methylation, and their impact on expression of adjacent cellular genes. We document in this study that the Dart TE family was transpositionally reactivated followed by stabilization in all three studied introgressants (RZ1, RZ2 and RZ35) derived from introgressive hybridization between rice (cv. Matsumae) and Z. latifolia, while the TEs remained quiescent in the recipient rice genome. Transposon-display (TD) and sequencing verified the element's mobility and mapped the excisions and re-insertions to the rice chromosomes. Methylation-sensitive Southern blotting showed that the Dart TEs were heavily methylated along their entire length, and moderate alteration in cytosine methylation patterns occurred in the introgressants relative to their rice parental line. Real-time qRT-PCR quantification on the relative transcript abundance of six single-copy genes flanking the newly excised or inserted Dart-related TE copies indicated that whereas marked difference in the expression of all four genes in both tissues (leaf and root) were detected between the introgressants and their rice parental line under both normal and various stress conditions, the difference showed little association with the presence or absence of the newly mobilized Dart-related TEs. Introgressive hybridization has induced transpositional reactivation of the otherwise immobile Dart-related TEs in the parental rice line (cv. Matsumae), which was accompanied with a moderate alteration in the element's cytosine methylation. Significant difference in expression of the Dart-adjacent genes occurred between the introgressants and their rice parental line under both normal and various abiotic stress conditions, but the alteration in gene expression was not coupled with the TEs.

Size matters: versatile use of PiggyBac transposons as a genetic manipulation tool.

PubMed

Kim, Adele; Pyykko, Ilmari

2011-08-01

Transposons have been promising elements for gene integration, and the Sleeping Beauty (SB) system has been the major one for many years, although there have been several other transposon systems available, for example, Tol2. However, recently another system known as PiggyBac (PB) has been introduced and developed for fulfilling the same purposes, for example, mutagenesis, transgenesis and gene therapy and in some cases with improved transposition efficiency and advantages over the Sleeping Beauty transposon system, although improved hyperactive transposase has highly increased the transposition efficacy for SB. The PB systems have been used in many different scientific research fields; therefore, the purpose of this review is to describe some of these versatile uses of the PiggyBac system to give readers an overview on the usage of PiggyBac system.

Tn5099, a xylE promoter probe transposon for Streptomyces spp.

PubMed Central

Hahn, D R; Solenberg, P J; Baltz, R H

1991-01-01

Tn5099, a promoter probe transposon for Streptomyces spp., was constructed by inserting a promoterless xylE gene and a hygromycin resistance gene into IS493. Tn5099 transposed into different sites in the Streptomyces griseofuscus genome, and the xylE reporter gene was expressed in some of the transposition mutants. Strains containing Tn5099 insertions that gave regulated expression of the xylE gene were identified. Images PMID:1653213

Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.

PubMed

Galindo-González, Leonardo; Mhiri, Corinne; Grandbastien, Marie-Angèle; Deyholos, Michael K

2016-12-07

Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression. We demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.

Correction to: Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling.

PubMed

Zannas, Anthony S; Arloth, Janine; Carrillo-Roa, Tania; Iurato, Stella; Röh, Simone; Ressler, Kerry J; Nemeroff, Charles B; Smith, Alicia K; Bradley, Bekh; Heim, Christine; Menke, Andreas; Lange, Jennifer F; Brückl, Tanja; Ising, Marcus; Wray, Naomi R; Erhardt, Angelika; Binder, Elisabeth B; Mehta, Divya

2018-05-23

Upon publication of the original article [1] it was highlighted by the authors that a transposition error affected Additional file 1, causing the misplacement of several columns and rendering the table difficult to read. This transposition does not influence any of the results nor analyses presented in the paper and has since been formally noted in this correction article; the corrected file is available here as an Additional File. The publisher apologizes for this error.

Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element

PubMed Central

Benson, Meredith A.; Ohneck, Elizabeth A.; Ryan, Chanelle; Alonzo, Francis; Smith, Hannah; Narechania, Apurva; Kolokotronis, Sergios-Orestis; Satola, Sarah W.; Uhlemann, Anne-Catrin; Sebra, Robert; Deikus, Gintaras; Shopsin, Bo; Planet, Paul J.; Torres, Victor J.

2014-01-01

SUMMARY Staphylococcus aureus has evolved as a pathogen that causes a range of diseases in humans. There are two dominant modes of evolution thought to explain most of the virulence differences between strains. First, virulence genes may be acquired from other organisms. Second, mutations may cause changes in the regulation and expression of genes. Here we describe an evolutionary event in which transposition of an IS element has a direct impact on virulence gene regulation resulting in hypervirulence. Whole genome analysis of a methicillin-resistant S. aureus (MRSA) strain USA500 revealed acquisition of a transposable element (IS256) that is absent from close relatives of this strain. Of the multiple copies of IS256 found in the USA500 genome, one was inserted in the promoter sequence of repressor of toxins (Rot), a master transcriptional regulator responsible for the expression of virulence factors in S. aureus. We show that insertion into the rot promoter by IS256 results in the derepression of cytotoxin expression and increased virulence. Taken together, this work provides new insight into evolutionary strategies by which S. aureus is able to modify its virulence properties and demonstrates a novel mechanism by which horizontal gene transfer directly impacts virulence through altering toxin regulation. PMID:24962815

Barbara McClintock, Jumping Genes, and Transposition

Science.gov Websites

genetics, to which McClintock made seminal contributions both experimental and conceptual, has come to (CSHL) Top Some links on this page may take you to non-federal websites. Their policies may differ from

Miniature Transposable Sequences Are Frequently Mobilized in the Bacterial Plant Pathogen Pseudomonas syringae pv. phaseolicola

PubMed Central

Bardaji, Leire; Añorga, Maite; Jackson, Robert W.; Martínez-Bilbao, Alejandro; Yanguas-Casás, Natalia; Murillo, Jesús

2011-01-01

Mobile genetic elements are widespread in Pseudomonas syringae, and often associate with virulence genes. Genome reannotation of the model bean pathogen P. syringae pv. phaseolicola 1448A identified seventeen types of insertion sequences and two miniature inverted-repeat transposable elements (MITEs) with a biased distribution, representing 2.8% of the chromosome, 25.8% of the 132-kb virulence plasmid and 2.7% of the 52-kb plasmid. Employing an entrapment vector containing sacB, we estimated that transposition frequency oscillated between 2.6×10−5 and 1.1×10−6, depending on the clone, although it was stable for each clone after consecutive transfers in culture media. Transposition frequency was similar for bacteria grown in rich or minimal media, and from cells recovered from compatible and incompatible plant hosts, indicating that growth conditions do not influence transposition in strain 1448A. Most of the entrapped insertions contained a full-length IS801 element, with the remaining insertions corresponding to sequences smaller than any transposable element identified in strain 1448A, and collectively identified as miniature sequences. From these, fragments of 229, 360 and 679-nt of the right end of IS801 ended in a consensus tetranucleotide and likely resulted from one-ended transposition of IS801. An average 0.7% of the insertions analyzed consisted of IS801 carrying a fragment of variable size from gene PSPPH_0008/PSPPH_0017, showing that IS801 can mobilize DNA in vivo. Retrospective analysis of complete plasmids and genomes of P. syringae suggests, however, that most fragments of IS801 are likely the result of reorganizations rather than one-ended transpositions, and that this element might preferentially contribute to genome flexibility by generating homologous regions of recombination. A further miniature sequence previously found to affect host range specificity and virulence, designated MITEPsy1 (100-nt), represented an average 2.4% of the total number of insertions entrapped in sacB, demonstrating for the first time the mobilization of a MITE in bacteria. PMID:22016774

Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola.

PubMed

Bardaji, Leire; Añorga, Maite; Jackson, Robert W; Martínez-Bilbao, Alejandro; Yanguas-Casás, Natalia; Murillo, Jesús

2011-01-01

Mobile genetic elements are widespread in Pseudomonas syringae, and often associate with virulence genes. Genome reannotation of the model bean pathogen P. syringae pv. phaseolicola 1448A identified seventeen types of insertion sequences and two miniature inverted-repeat transposable elements (MITEs) with a biased distribution, representing 2.8% of the chromosome, 25.8% of the 132-kb virulence plasmid and 2.7% of the 52-kb plasmid. Employing an entrapment vector containing sacB, we estimated that transposition frequency oscillated between 2.6×10(-5) and 1.1×10(-6), depending on the clone, although it was stable for each clone after consecutive transfers in culture media. Transposition frequency was similar for bacteria grown in rich or minimal media, and from cells recovered from compatible and incompatible plant hosts, indicating that growth conditions do not influence transposition in strain 1448A. Most of the entrapped insertions contained a full-length IS801 element, with the remaining insertions corresponding to sequences smaller than any transposable element identified in strain 1448A, and collectively identified as miniature sequences. From these, fragments of 229, 360 and 679-nt of the right end of IS801 ended in a consensus tetranucleotide and likely resulted from one-ended transposition of IS801. An average 0.7% of the insertions analyzed consisted of IS801 carrying a fragment of variable size from gene PSPPH_0008/PSPPH_0017, showing that IS801 can mobilize DNA in vivo. Retrospective analysis of complete plasmids and genomes of P. syringae suggests, however, that most fragments of IS801 are likely the result of reorganizations rather than one-ended transpositions, and that this element might preferentially contribute to genome flexibility by generating homologous regions of recombination. A further miniature sequence previously found to affect host range specificity and virulence, designated MITEPsy1 (100-nt), represented an average 2.4% of the total number of insertions entrapped in sacB, demonstrating for the first time the mobilization of a MITE in bacteria.

Mobility of the maize suppressor-mutator element in transgenic tobacco cells.

PubMed Central

Masson, P; Fedoroff, N V

1989-01-01

Maize Suppressor-mutator (Spm) transposable elements have been introduced into tobacco cells and a visual assay for Spm activity has been developed using a bacterial beta-glucuronidase gene. The Spm element is mobile in tobacco and can trans-activate excision of a transposition-defective Spm (dSpm) element either from a different site on the same transforming Ti plasmid or from a second plasmid. An Spm element expressed from the stronger cauliflower mosaic virus 35S promoter trans-activates transposition of a dSpm element earlier after its introduction into tobacco cells than an element expressed from its own promoter. Images PMID:2538837

Conceptual Variation or Incoherence? Textbook Discourse on Genes in Six Countries

NASA Astrophysics Data System (ADS)

Gericke, Niklas M.; Hagberg, Mariana; dos Santos, Vanessa Carvalho; Joaquim, Leyla Mariane; El-Hani, Charbel N.

2014-02-01

The aim of this paper is to investigate in a systematic and comparative way previous results of independent studies on the treatment of genes and gene function in high school textbooks from six different countries. We analyze how the conceptual variation within the scientific domain of Genetics regarding gene function models and gene concepts is transformed via the didactic transposition into school science textbooks. The results indicate that a common textbook discourse on genes and their function exist in textbooks from the different countries. The structure of science as represented by conceptual variation and the use of multiple models was present in all the textbooks. However, the existence of conceptual variation and multiple models is implicit in these textbooks, i.e., the phenomenon of conceptual variation and multiple models are not addressed explicitly, nor its consequences and, thus, it ends up introducing conceptual incoherence about the gene concept and its function within the textbooks. We conclude that within the found textbook-discourse ontological aspects of the academic disciplines of genetics and molecular biology were retained, but without their epistemological underpinnings; these are lost in the didactic transposition. These results are of interest since students might have problems reconstructing the correct scientific understanding from the transformed school science knowledge as depicted within the high school textbooks. Implications for textbook writing as well as teaching are discussed in the paper.

Integration Profile and Safety of an Adenovirus Hybrid-Vector Utilizing Hyperactive Sleeping Beauty Transposase for Somatic Integration

PubMed Central

Zhang, Wenli; Muck-Hausl, Martin; Wang, Jichang; Sun, Chuanbo; Gebbing, Maren; Miskey, Csaba; Ivics, Zoltan; Izsvak, Zsuzsanna; Ehrhardt, Anja

2013-01-01

We recently developed adenovirus/transposase hybrid-vectors utilizing the previously described hyperactive Sleeping Beauty (SB) transposase HSB5 for somatic integration and we could show stabilized transgene expression in mice and a canine model for hemophilia B. However, the safety profile of these hybrid-vectors with respect to vector dose and genotoxicity remains to be investigated. Herein, we evaluated this hybrid-vector system in C57Bl/6 mice with escalating vector dose settings. We found that in all mice which received the hyperactive SB transposase, transgene expression levels were stabilized in a dose-dependent manner and that the highest vector dose was accompanied by fatalities in mice. To analyze potential genotoxic side-effects due to somatic integration into host chromosomes, we performed a genome-wide integration site analysis using linker-mediated PCR (LM-PCR) and linear amplification-mediated PCR (LAM-PCR). Analysis of genomic DNA samples obtained from HSB5 treated female and male mice revealed a total of 1327 unique transposition events. Overall the chromosomal distribution pattern was close-to-random and we observed a random integration profile with respect to integration into gene and non-gene areas. Notably, when using the LM-PCR protocol, 27 extra-chromosomal integration events were identified, most likely caused by transposon excision and subsequent transposition into the delivered adenoviral vector genome. In total, this study provides a careful evaluation of the safety profile of adenovirus/Sleeping Beauty transposase hybrid-vectors. The obtained information will be useful when designing future preclinical studies utilizing hybrid-vectors in small and large animal models. PMID:24124483

Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants.

PubMed

Wicke, Susann; Costa, Andrea; Muñoz, Jesùs; Quandt, Dietmar

2011-11-01

Among eukaryotes two types of nuclear ribosomal DNA (nrDNA) organization have been observed. Either all components, i.e. the small ribosomal subunit, 5.8S, large ribosomal subunit, and 5S occur tandemly arranged or the 5S rDNA forms a separate cluster of its own. Generalizations based on data derived from just a few model organisms have led to a superimposition of structural and evolutionary traits to the entire plant kingdom asserting that plants generally possess separate arrays. This study reveals that plant nrDNA organization into separate arrays is not a distinctive feature, but rather assignable almost solely to seed plants. We show that early diverging land plants and presumably streptophyte algae share a co-localization of all rRNA genes within one repeat unit. This raises the possibility that the state of rDNA gene co-localization had occurred in their common ancestor. Separate rDNA arrays were identified for all basal seed plants and water ferns, implying at least two independent 5S rDNA transposition events during land plant evolution. Screening for 5S derived Cassandra transposable elements which might have played a role during the transposition events, indicated that this retrotransposon is absent in early diverging vascular plants including early fern lineages. Thus, Cassandra can be rejected as a primary mechanism for 5S rDNA transposition in water ferns. However, the evolution of Cassandra and other eukaryotic 5S derived elements might have been a side effect of the 5S rDNA cluster formation. Structural analysis of the intergenic spacers of the ribosomal clusters revealed that transposition events partially affect spacer regions and suggests a slightly different transcription regulation of 5S rDNA in early land plants. 5S rDNA upstream regulatory elements are highly divergent or absent from the LSU-5S spacers of most early divergent land plant lineages. Several putative scenarios and mechanisms involved in the concerted relocation of hundreds of 5S rRNA gene copies are discussed. Copyright © 2011 Elsevier Inc. All rights reserved.

Flamenco, a gene controlling the gypsy retrovirus of drosophila melanogaster

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prud`homme, N.; Gans, M.; Masson, M.

1995-02-01

Gypsy is an endogenous retrovirus of Drosophila melanogaster. It is table and does not transpose with detectable frequencies in most Drosophila strains. However, we have characterized unstable strains, known as MG, in which it transposes at high frequency. These stocks contain more copies of gypsy than usual stocks. Transposition results in mutations in several genes such as ovo and cut. They are stable and are due to gypsy insertions. Integrations into the ovo{sup D1} female sterile-dominant mutation result in a null allele of the gene and occurrence of fertile females. This phenomenon, known as the ovo{sup D1} reversion assay, canmore » be used to quantitate gypsy activity. We have shown that the properties of MG strains result from mutation of a host gene that we called flamenco (flam). It has a strict maternal effect on gypsy mobilization: transposition occurs at high frequency only in the germ line of the progeny of females homozygous for mutations of the gene. It is located at position 65.9 (20A1-3) on the X chromosome. The mutant allele present in MG strains is essentially recessive. Flamenco seems to control the infective properties of gypsy. 40 refs., 10 figs., 6 tabs.« less

Successful replacement of the systemic tricuspid valve with a mechanical valve in a 3-month-old boy with congenitally corrected transposition of the great arteries having a dysplastic tricuspid valve.

PubMed

Asada, Dai; Ikeda, Kazuyuki; Yamagishi, Masaaki

2017-04-01

There are a few reports of successful replacement of the left-sided systemic tricuspid valve with a mechanical valve in small infants with congenitally corrected transposition of the great arteries having Ebstein's anomaly. Tricuspid valve replacement is the preferred option when pulmonary artery banding, performed as a prelude to performing the double-switch operation, is not feasible because of severe heart failure caused by tricuspid regurgitation.

Sternocleidomastoid muscle flap used for repairing the dead space after supraomohyoid neck dissection

PubMed Central

Li, Jinzhong; Han, Zhengxue

2015-01-01

Surgical site infection (SSI) is a common complication followed neck dissection and dead space is a common reason of SSI. The present study is aimed to explore whether the sternocleidomastoid muscle (SCM) flap transposition to repair the dead space in level II of neck could decrease the postoperative SSI in patients with oral squamous cell carcinoma (OSCC) underwent supraomohyoid neck dissection (SOND). Ninety-six patients with cT2-3N0 OSCC who underwent extended resection of primary cancer combined SOND and reconstructed with free flap from March 2011 to October 2014 in our department were included. Forty-eight cases underwent SCM transposition to repair the potential dead space in level II of the neck, the other 48 cases did not. The two groups were matched at age, gender, concomitant diseases, and perioperative treatments. All the patients underwent exhaustive hemostasis and careful placement of negative pressure drainage. The wound healing was observed on 7 days postoperatively. The SSI rates of neck between the two groups were compared using Fisher’s exact test. The dead space in level II was observed in all the neck wounds after SOND. The neck wounds healed by primary intention in 46 cases underwent SCM flap transposition, and in 39 cases underwent routine SOND only. Two cases with SCM flap transposition and 9 cases in the group without SCM flap transposition presented SSI in neck. There was significant difference in the SSI rate between the two groups (P = 0.0248). The dead space in level II could be an important cause of SSI in neck followed SOND. Repairing of the dead space in level II using SCM flap transposition reduce the SSI rate of neck followed SOND. PMID:25785129

Sternocleidomastoid muscle flap used for repairing the dead space after supraomohyoid neck dissection.

PubMed

Li, Jinzhong; Han, Zhengxue

2015-01-01

Surgical site infection (SSI) is a common complication followed neck dissection and dead space is a common reason of SSI. The present study is aimed to explore whether the sternocleidomastoid muscle (SCM) flap transposition to repair the dead space in level II of neck could decrease the postoperative SSI in patients with oral squamous cell carcinoma (OSCC) underwent supraomohyoid neck dissection (SOND). Ninety-six patients with cT2-3N0 OSCC who underwent extended resection of primary cancer combined SOND and reconstructed with free flap from March 2011 to October 2014 in our department were included. Forty-eight cases underwent SCM transposition to repair the potential dead space in level II of the neck, the other 48 cases did not. The two groups were matched at age, gender, concomitant diseases, and perioperative treatments. All the patients underwent exhaustive hemostasis and careful placement of negative pressure drainage. The wound healing was observed on 7 days postoperatively. The SSI rates of neck between the two groups were compared using Fisher's exact test. The dead space in level II was observed in all the neck wounds after SOND. The neck wounds healed by primary intention in 46 cases underwent SCM flap transposition, and in 39 cases underwent routine SOND only. Two cases with SCM flap transposition and 9 cases in the group without SCM flap transposition presented SSI in neck. There was significant difference in the SSI rate between the two groups (P = 0.0248). The dead space in level II could be an important cause of SSI in neck followed SOND. Repairing of the dead space in level II using SCM flap transposition reduce the SSI rate of neck followed SOND.

Lateral femoral cutaneous nerve transposition: Renaissance of an old concept in the light of new anatomy.

PubMed

Hanna, Amgad S

2017-04-01

Meralgia paresthetica causes pain in the anterolateral thigh. Most surgical procedures involve nerve transection or decompression. We conducted a cadaveric study to determine the feasibility of lateral femoral cutaneous nerve (LFCN) transposition. In three cadavers, the LFCN was exposed in the thigh and retroperitoneum. The two layers of the LFCN canal superficial and deep to the nerve were opened. The nerve was then mobilized medially away from the ASIS, by cutting the septum medial to sartorius. It was possible to mobilize the nerve for 2 cm medial to the ASIS. The nerve acquired a much straighter course with less tension. A new technique of LFCN transposition is presented here as an anatomical feasibility study. The surgical technique is based on the new understanding of the LFCN canal. Clin. Anat. 30:409-412, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells.

PubMed

Dewannieux, Marie; Heidmann, Thierry

2005-06-03

SINEs are short interspersed nucleotide elements with transpositional activity, present at a high copy number (up to a million) in mammalian genomes. They are 80-400 bp long, non-coding sequences which derive either from the 7SL RNA (e.g. human Alus, murine B1s) or tRNA (e.g. murine B2s) polymerase III-driven genes. We have previously demonstrated that Alus very efficiently divert the enzymatic machinery of the autonomous L1 LINE (long interspersed nucleotide element) retrotransposons to transpose at a high rate. Here we show, using an ex vivo assay for transposition, that both B1 and B2 SINEs can be mobilized by murine LINEs, with the hallmarks of a bona fide retrotransposition process, including target site duplications of varying lengths and integrations into A-rich sequences. Despite different phylogenetic origins, transposition of the tRNA-derived B2 sequences is as efficient as that of the human Alus, whereas that of B1s is 20-100-fold lower despite a similar high copy number of these elements in the mouse genome. We provide evidence, via an appropriate nucleotide substitution within the B1 sequence in a domain essential for its intracellular targeting, that the current B1 SINEs are not optimal for transposition, a feature most probably selected for the host sake in the course of evolution.

A New Member of the Sin3 Family of Corepressors Is Essential for Cell Viability and Required for Retroelement Propagation in Fission Yeast

PubMed Central

Dang, Van Dinh; Benedik, Michael J.; Ekwall, Karl; Choi, Jeannie; Allshire, Robin C.; Levin, Henry L.

1999-01-01

Tf1 is a long terminal repeat (LTR)-containing retrotransposon that propagates within the fission yeast Schizosaccharomyces pombe. LTR-retrotransposons possess significant similarity to retroviruses and therefore serve as retrovirus models. To determine what features of the host cell are important for the proliferation of this class of retroelements, we screened for mutations in host genes that reduced the transposition activity of Tf1. We report here the isolation and characterization of pst1+, a gene required for Tf1 transposition. The predicted amino acid sequence of Pst1p possessed high sequence homology with the Sin3 family of proteins, known for their interaction with histone deacetylases. However, unlike the SIN3 gene of Saccharomyces cerevisiae, pst1+ is essential for cell viability. Immunofluorescence microscopy indicated that Pst1p was localized in the nucleus. Consistent with the critical role previously reported for Sin3 proteins in the histone acetylation process, we found that the growth of the strain with the pst1-1 allele was supersensitive to the specific histone deacetylase inhibitor trichostatin A. However, our analysis of strains with the pst1-1 mutation was unable to detect any changes in the acetylation of specific lysines of histones H3 and H4 as measured in bulk chromatin. Interestingly, the pst1-1 mutant strain produced wild-type levels of Tf1-encoded proteins and cDNA, indicating that the defect in transposition occurred after reverse transcription. The results of immunofluorescence microscopy showed that the nuclear localization of the Tf1 capsid protein was disrupted in the strain with the pst1-1 mutation, indicating an important role of pst1+ in modulating the nuclear import of Tf1 virus-like particles. PMID:10022921

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements on Drosophila

PubMed Central

Lee, Yuh Chwen G.; Langley, Charles H.

2012-01-01

Transposable elements (TEs) are considered to be genomic parasites and their interactions with their hosts have been likened to the coevolution between host and other nongenomic, horizontally transferred pathogens. TE families, however, are vertically inherited as integral segments of the nuclear genome. This transmission strategy has been suggested to weaken the selective benefits of host alleles repressing the transposition of specific TE variants. On the other hand, the elevated rates of TE transposition and high incidences of deleterious mutations observed during the rare cases of horizontal transfers of TE families between species could create at least a transient process analogous to the influence of horizontally transmitted pathogens. Here, we formally address this analogy, using empirical and theoretical analysis to specify the mechanism of how host–TE interactions may drive the evolution of host genes. We found that host TE-interacting genes actually have more pervasive evidence of adaptive evolution than immunity genes that interact with nongenomic pathogens in Drosophila. Yet, both our theoretical modeling and empirical observations comparing Drosophila melanogaster populations before and after the horizontal transfer of P elements, which invaded D. melanogaster early last century, demonstrated that horizontally transferred TEs have only a limited influence on host TE-interacting genes. We propose that the more prevalent and constant interaction with multiple vertically transmitted TE families may instead be the main force driving the fast evolution of TE-interacting genes, which is fundamentally different from the gene-for-gene interaction of host–pathogen coevolution. PMID:22997235

Inversions and inverted transpositions as the basis for an almost universal "format" of genome sequences.

PubMed

Albrecht-Buehler, Guenter

2007-09-01

In genome duplexes that exceed 100 kb the frequency distributions of their trinucleotides (triplet profiles) are the same in both strands. This remarkable symmetry, sometimes called Chargaff's second parity rule, is not the result of base pairing, but can be explained as the result of countless inversions and inverted transpositions that occurred throughout evolution (G. Albrecht-Buehler, 2006, Proc. Natl. Acad. Sci. USA 103, 17828-17833). Furthermore, comparing the triplet profiles of genomes from a large number of different taxa and species revealed that they were not only strand-symmetrical, but even surprisingly similar to one another (majority profile; G. Albrecht-Buehler, 2007, Genomics 89, 596-601). The present article proposes that the same inversion/transposition mechanism(s) that created the strand symmetry may also explain the existence of the majority profile. Thus they may be key factors in the creation of an almost universal "format" in which genome sequences are written. One may speculate that this universality of genome format may facilitate horizontal gene transfer and, thus, accelerate evolution.

The Role of Transposable Elements in Speciation

PubMed Central

Serrato-Capuchina, Antonio; Matute, Daniel R.

2018-01-01

Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species. PMID:29762547

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles

PubMed Central

Steczkiewicz, Kamil; Ginalski, Krzysztof

2017-01-01

Abstract Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a “cut-and-paste” fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species’ lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition. PMID:29228286

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

PubMed

Kang, Jong-Soo; Lee, Byoung Yoon; Kwak, Myounghai

2017-01-01

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

Unexpected genetic heterogeneity for primary ciliary dyskinesia in the Irish Traveller population.

PubMed

Casey, Jillian P; McGettigan, Paul A; Healy, Fiona; Hogg, Claire; Reynolds, Alison; Kennedy, Breandan N; Ennis, Sean; Slattery, Dubhfeasa; Lynch, Sally A

2015-02-01

We present a study of five children from three unrelated Irish Traveller families presenting with primary ciliary dyskinesia (PCD). As previously characterized disorders in the Irish Traveller population are caused by common homozygous mutations, we hypothesised that all three PCD families shared the same recessive mutation. However, exome sequencing showed that there was no pathogenic homozygous mutation common to all families. This finding was supported by histology, which showed that each family has a different type of ciliary defect; transposition defect (family A), nude epithelium (family B) and absence of inner and outer dynein arms (family C). Therefore, each family was analysed independently using homozygosity mapping and exome sequencing. The affected siblings in family A share a novel 1 bp duplication in RSPH4A (NM_001161664.1:c.166dup; p.Arg56Profs*11), a radial-spoke head protein involved in ciliary movement. In family B, we identified three candidate genes (CCNO, KCNN3 and CDKN1C), with a 5-bp duplication in CCNO (NM_021147.3:c.258_262dup; p.Gln88Argfs*8) being the most likely cause of ciliary aplasia. This is the first study to implicate CCNO, a DNA repair gene reported to be involved in multiciliogenesis, in PCD. In family C, we identified a ∼3.5-kb deletion in DYX1C1, a neuronal migration gene previously associated with PCD. This is the first report of a disorder in the relatively small Irish Traveller population to be caused by >1 disease gene. Our study identified at least three different PCD genes in the Irish Traveller population, highlighting that one cannot always assume genetic homogeneity, even in small consanguineous populations.

Relationship between interatrial communication, ductus arteriosus, and pulmonary flow patterns in fetuses with transposition of the great arteries: prediction of neonatal desaturation.

PubMed

Vaujois, Laurence; Boucoiran, Isabelle; Preuss, Christophe; Brassard, Myriam; Houde, Christine; Fouron, Jean C; Raboisson, Marie-Josée

2017-09-01

The relationship between interatrial communication, ductus arteriosus, and pulmonary flow in transposition of the great arteries and intact ventricular septum may help predict postnatal desaturation. Echocardiographic data of 45 fetuses with transposition of the great arteries and intact ventricular septum and 50 age-matched controls were retrospectively reviewed. Interatrial communication, left and right ventricular output, flow in the ductus arteriosus, as well as effective pulmonary flow were measured. Patients were divided into two groups on the basis of postnatal saturations: group 1 had saturations ⩽50% and group 2 >50%. Of 45 fetuses, 13 (26.7%) were classified into group 1. Compared with fetuses in group 2, they had a smaller interatrial communication (2.9 versus 4.0 mm, p=0.004) and more retrograde diastolic flow in the ductus arteriosus (92 versus 23%, p=0.002). Both groups showed a significant decrease in ductal flow compared with controls. Patients in group 2 had a higher effective pulmonary flow compared with controls. There was a mild correlation between left ventricular output and size of the interatrial communication (Spearman's rank correlation 0.44). A retrograde diastolic flow is present in most of the fetuses with postnatal desaturation. Fetuses with transposition of the great arteries have a lower flow through the ductus arteriosus compared with controls. Fetuses without restrictive foramen ovale have higher effective pulmonary flow. Peripheral pulmonary vasodilatation due to higher oxygen saturation in pulmonary arteries in the case of transposition of the great arteries could be one possible cause.

Sequence, assembly and annotation of the maize W22 genome

USDA-ARS?s Scientific Manuscript database

Since its adoption by Brink and colleagues in the 1950s and 60s, the maize W22 inbred has been utilized extensively to understand fundamental genetic and epigenetic processes such recombination, transposition and paramutation. To maximize the utility of W22 in gene discovery, we have Illumina sequen...

Horizontal transfer of potential mobile units in phytoplasmas

PubMed Central

Ku, Chuan; Lo, Wen-Sui; Kuo, Chih-Horng

2013-01-01

Phytoplasmas are uncultivated phytopathogenic bacteria that cause diseases in a wide range of economically important plants. Through secretion of effector proteins, they are able to manipulate their plant hosts to facilitate their multiplication and dispersal by insect vectors. The genome sequences of several phytoplasmas have been characterized to date and a group of putative composite transposons called potential mobile units (PMUs) are found in these highly reduced genomes. Recently, our team reported the genome sequence and comparative analysis of a peanut witches’ broom (PnWB) phytoplasma, the first representative of the phytoplasma 16SrII group. Comparisons between the species phylogeny and the phylogenies of the PMU genes revealed that the PnWB PMU is likely to have been transferred from the 16SrI group. This indicates that PMUs are not only the DNA unit for transposition within a genome, but also for horizontal transfer among divergent phytoplasma lineages. Given the association of PMUs with effector genes, the mobility of PMUs across genomes has important implications for phytoplasma ecology and evolution. PMID:24251068

Negative effect of the 5'-untranslated leader sequence on Ac transposon promoter expression.

PubMed

Scortecci, K C; Raina, R; Fedoroff, N V; Van Sluys, M A

1999-08-01

Transposable elements are used in heterologous plant hosts to clone genes by insertional mutagenesis. The Activator (Ac) transposable element has been cloned from maize, and introduced into a variety of plants. However, differences in regulation and transposition frequency have been observed between different host plants. The cause of this variability is still unknown. To better understand the activity of the Ac element, we analyzed the Ac promoter region and its 5'-untranslated leader sequence (5' UTL). Transient assays in tobacco NT1 suspension cells showed that the Ac promoter is a weak promoter and its activity was localized by deletion analyses. The data presented here indicate that the core of the Ac promoter is contained within 153 bp fragment upstream to transcription start sites. An important inhibitory effect (80%) due to the presence of the 5' UTL was found on the expression of LUC reporter gene. Here we demonstrate that the presence of the 5' UTL in the constructs reduces the expression driven by either strong or weak promoters.

Horizontal transfer of potential mobile units in phytoplasmas.

PubMed

Ku, Chuan; Lo, Wen-Sui; Kuo, Chih-Horng

2013-09-01

Phytoplasmas are uncultivated phytopathogenic bacteria that cause diseases in a wide range of economically important plants. Through secretion of effector proteins, they are able to manipulate their plant hosts to facilitate their multiplication and dispersal by insect vectors. The genome sequences of several phytoplasmas have been characterized to date and a group of putative composite transposons called potential mobile units (PMUs) are found in these highly reduced genomes. Recently, our team reported the genome sequence and comparative analysis of a peanut witches' broom (PnWB) phytoplasma, the first representative of the phytoplasma 16SrII group. Comparisons between the species phylogeny and the phylogenies of the PMU genes revealed that the PnWB PMU is likely to have been transferred from the 16SrI group. This indicates that PMUs are not only the DNA unit for transposition within a genome, but also for horizontal transfer among divergent phytoplasma lineages. Given the association of PMUs with effector genes, the mobility of PMUs across genomes has important implications for phytoplasma ecology and evolution.

A 1.375-approximation algorithm for sorting by transpositions.

PubMed

Elias, Isaac; Hartman, Tzvika

2006-01-01

Sorting permutations by transpositions is an important problem in genome rearrangements. A transposition is a rearrangement operation in which a segment is cut out of the permutation and pasted in a different location. The complexity of this problem is still open and it has been a 10-year-old open problem to improve the best known 1.5-approximation algorithm. In this paper, we provide a 1.375-approximation algorithm for sorting by transpositions. The algorithm is based on a new upper bound on the diameter of 3-permutations. In addition, we present some new results regarding the transposition diameter: we improve the lower bound for the transposition diameter of the symmetric group and determine the exact transposition diameter of simple permutations.

Ac-immobilized, a stable source of Activator transposase that mediates sporophytic and gametophytic excision of Dissociation elements in maize.

PubMed

Conrad, Liza J; Brutnell, Thomas P

2005-12-01

We have identified and characterized a novel Activator (Ac) element that is incapable of excision yet contributes to the canonical negative dosage effect of Ac. Cloning and sequence analysis of this immobilized Ac (Ac-im) revealed that it is identical to Ac with the exception of a 10-bp deletion of sequences at the left end of the element. In screens of approximately 6800 seeds, no germinal transpositions of Ac-im were detected. Importantly, Ac-im catalyzes germinal excisions of a Ds element resident at the r1 locus resulting in the recovery of independent transposed Ds insertions in approximately 4.5% of progeny kernels. Many of these transposition events occur during gametophytic development. Furthermore, we demonstrate that Ac-im transactivates multiple Ds insertions in somatic tissues including those in reporter alleles at bronze1, anthocyaninless1, and anthocyaninless2. We propose a model for the generation of Ac-im as an aberrant transposition event that failed to generate an 8-bp target site duplication and resulted in the deletion of Ac end sequences. We also discuss the utility of Ac-im in two-component Ac/Ds gene-tagging programs in maize.

Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula.

PubMed

d'Erfurth, Isabelle; Cosson, Viviane; Eschstruth, Alexis; Lucas, Helene; Kondorosi, Adam; Ratet, P

2003-04-01

The tobacco element, Tnt1, is one of the few active retrotransposons in plants. Its transposition is activated during protoplast culture in tobacco and tissue culture in the heterologous host Arabidopsis thaliana. Here, we report its transposition in the R108 line of Medicago truncatula during the early steps of the in vitro transformation-regeneration process. Two hundred and twenty-five primary transformants containing Tnt1 were obtained. Among them, 11.2% contained only transposed copies of the element, indicating that Tnt1 transposed very early and efficiently during the in vitro transformation process, possibly even before the T-DNA integration. The average number of insertions per transgenic line was estimated to be about 15. These insertions were stable in the progeny and could be separated by segregation. Inspection of the sequences flanking the insertion sites revealed that Tnt1 had no insertion site specificity and often inserted in genes (one out of three insertions). Thus, our work demonstrates the functioning of an efficient transposable element in leguminous plants. These results indicate that Tnt1 can be used as a powerful tool for insertion mutagenesis in M. truncatula.

Deconstruction of the (Paleo)Polyploid Grapevine Genome Based on the Analysis of Transposition Events Involving NBS Resistance Genes

PubMed Central

Cestaro, Alessandro; Sterck, Lieven; Fontana, Paolo; Van de Peer, Yves; Viola, Roberto; Velasco, Riccardo; Salamini, Francesco

2012-01-01

Plants have followed a reticulate type of evolution and taxa have frequently merged via allopolyploidization. A polyploid structure of sequenced genomes has often been proposed, but the chromosomes belonging to putative component genomes are difficult to identify. The 19 grapevine chromosomes are evolutionary stable structures: their homologous triplets have strongly conserved gene order, interrupted by rare translocations. The aim of this study is to examine how the grapevine nucleotide-binding site (NBS)-encoding resistance (NBS-R) genes have evolved in the genomic context and to understand mechanisms for the genome evolution. We show that, in grapevine, i) helitrons have significantly contributed to transposition of NBS-R genes, and ii) NBS-R gene cluster similarity indicates the existence of two groups of chromosomes (named as Va and Vc) that may have evolved independently. Chromosome triplets consist of two Va and one Vc chromosomes, as expected from the tetraploid and diploid conditions of the two component genomes. The hexaploid state could have been derived from either allopolyploidy or the separation of the Va and Vc component genomes in the same nucleus before fusion, as known for Rosaceae species. Time estimation indicates that grapevine component genomes may have fused about 60 mya, having had at least 40–60 mya to evolve independently. Chromosome number variation in the Vitaceae and related families, and the gap between the time of eudicot radiation and the age of Vitaceae fossils, are accounted for by our hypothesis. PMID:22253773

Didactic Transposition in Mathematics Textbooks.

ERIC Educational Resources Information Center

Kang, Wan; Kilpatrick, Jeremy

1992-01-01

Didactic transposition theory asserts that bodies of knowledge are designed not to be taught but to be used. Discusses didactic transposition, the transposition of knowledge regarded as a tool to be used to knowledge as something to be learned in mathematics textbooks. (14 references) (MDH)

Performance Analysis of Transposition Models Simulating Solar Radiation on Inclined Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Yu; Sengupta, Manajit

2016-06-02

Transposition models have been widely used in the solar energy industry to simulate solar radiation on inclined photovoltaic panels. Following numerous studies comparing the performance of transposition models, this work aims to understand the quantitative uncertainty in state-of-the-art transposition models and the sources leading to the uncertainty. Our results show significant differences between two highly used isotropic transposition models, with one substantially underestimating the diffuse plane-of-array irradiances when diffuse radiation is perfectly isotropic. In the empirical transposition models, the selection of the empirical coefficients and land surface albedo can both result in uncertainty in the output. This study can bemore » used as a guide for the future development of physics-based transposition models and evaluations of system performance.« less

[Plant transposable elements and their application in genetics and biotechnology].

PubMed

Ovcharenko, O O; Rudas, V A; Kuchuk, M V

2006-01-01

Data concerning plant transposable elements and their contribution to plant genome evolution are reviewed. Much attention is focused on utilization of transgenic plants as heterologous hosts of transposons for investigation of transposition mechanisms and gene cloning. Probable ways of the use of plant transposons as genetic tools in biotechnology are discussed.

Report on the Conference on Transposition and Genome Engineering 2015 (TGE 2015): advancing cutting-edge genomics technology in the ancient city of Nara.

PubMed

Woltjen, Knut; Yamamoto, Takashi; Kokubu, Chikara; Takeda, Junji

2016-05-01

From November 17 to 20 in 2015, the Conference on Transposition and Genome Engineering 2015 (TGE 2015) was held at Nara Kasugano International Forum-IRAKA-in Nara, Japan, located at the center of Nara Park. All of the presentations were carried out at Nohgaku hall in Nara Kasugano International Forum-IRAKA. Participation totaled 148 persons (30 international, 118 domestic), who were able to engage in lively scientific discussions over the 4-day period. The guest speaker list consisted of many top-notch international researchers, an achievement for which the conference received praise from the attendees. There were 36 oral presentations including the keynote lecture (22 presentations from guest speakers, complemented with 14 selected from abstract submissions). Additionally, there were 46 poster presentations. The conference uniquely combined research mainly from two different genomics approaches: (i) transposon technology allowing random genomic integration followed by gene discovery-related phenotypes and (ii) genome editing technology with designer nuclease allowing precise modification of a gene-of-interest. © 2016 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Demonstration of retrotransposition of the Tf1 element in fission yeast.

PubMed

Levin, H L; Boeke, J D

1992-03-01

Tf1, a retrotransposon from fission yeast, has LTRs and coding sequences resembling the protease, reverse transcriptase and integrase domains of retroviral pol genes. A unique aspect of Tf1 is that it contains a single open reading frame whereas other retroviruses and retrotransposons usually possess two or more open reading frames. To determine whether Tf1 can transpose, we overproduced Tf1 transcripts encoded by a plasmid copy of the element marked with a neo gene. Approximately 0.1-4.0% of the cell population acquired chromosomally inherited resistance to G418. DNA blot analysis demonstrated that such strains had acquired both Tf1 and neo specific sequences within a restriction fragment of the same size; the size of this restriction fragment varied between different isolates. Structural analysis of the cloned DNA flanking the Tf1-neo element of two transposition candidates with the same regions in the parent strain showed that the ability to grow on G418 was due to transposition of Tf1-neo and not other types of recombination events.

A major insertion accounts for a significant proportion of mutations underlying human lipoprotein lipase deficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langlois, S.; Kastelein, J.J.; Hayden, M.R.

1989-02-01

Lipoprotein lipase is an important enzyme involved in triacylglycerol metabolism. Primary LPL deficiency is a genetic disorder that is usually manifested by a severe elevation in triacylglycerol levels. The authors have used a recently isolated LPL cDNA clone to study 15 probands from 11 families with this inherited disorder. Surprisingly, 7 of the probands from 4 families, of different ancestries, had a similar insertion in their LPL gene. In contrast to other human genetic disorders, where insertions are rare causes of mutation, this insertion accounts for a significant proportion of the alleles causing LPL deficiency. Detailed restriction mapping of themore » insertion revealed that it was unlikely to be a duplication of neighboring DNA and that it was not similar to the consensus sequence of human L1 repetitive elements. This suggests that there must be other mechanisms of insertional mutagenesis in human genetic disease besides transposition of mobile L1 repetitive elements.« less

A large inversion in the linear chromosome of Streptomyces griseus caused by replicative transposition of a new Tn3 family transposon.

PubMed

Murata, M; Uchida, T; Yang, Y; Lezhava, A; Kinashi, H

2011-04-01

We have comprehensively analyzed the linear chromosomes of Streptomyces griseus mutants constructed and kept in our laboratory. During this study, macrorestriction analysis of AseI and DraI fragments of mutant 402-2 suggested a large chromosomal inversion. The junctions of chromosomal inversion were cloned and sequenced and compared with the corresponding target sequences in the parent strain 2247. Consequently, a transposon-involved mechanism was revealed. Namely, a transposon originally located at the left target site was replicatively transposed to the right target site in an inverted direction, which generated a second copy and at the same time caused a 2.5-Mb chromosomal inversion. The involved transposon named TnSGR was grouped into a new subfamily of the resolvase-encoding Tn3 family transposons based on its gene organization. At the end, terminal diversity of S. griseus chromosomes is discussed by comparing the sequences of strains 2247 and IFO13350.

Genetic engineering and improvement of a Zymomonas mobilis for arabinose utilization and its performance on pretreated corn stover hydrolyzate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chou, Yat -Chen; Linger, Jeffrey; Yang, Shihui

In this paper, a glucose, xylose and arabinose utilizing Zymomonas mobilis strain was constructed by incorporating arabinose catabolic pathway genes, araBAD encoding L-ribulokinase, L-arabinose isomerase and L-ribulose-5-phosphate- 4-epimerase in a glucose, xylose co-fermenting host, 8b, using a transposition integration approach. Further improvement on this arabinose-capable integrant, 33C was achieved by applying a second transposition to create a genomic knockout (KO) mutant library. Using arabinose as a sole carbon source and a selection pressure, the KO library was subjected to a growth-enrichment process involving continuous sub-culturing for over 120 generations. Strain 13-1-17, isolated from such process demonstrated significant improvement in metabolizingmore » arabinose in a dilute acid pretreated, saccharified corn stover slurry. Through Next Generation Sequencing (NGS) analysis, integration sites of the transposons were identified. Furthermore, multiple additional point mutations (SNPs: Single Nucleotide Polymorphisms) were discovered in 13-1-17, affecting genes araB and RpiB in the genome. Finally, we speculate that these mutations may have impacted the expression of the enzymes coded by these genes, ribulokinase and Ribose 5-P-isomerase, thus attributing to the improvement of the arabinose utilization.« less

Genetic engineering and improvement of a Zymomonas mobilis for arabinose utilization and its performance on pretreated corn stover hydrolyzate

DOE PAGES

Chou, Yat -Chen; Linger, Jeffrey; Yang, Shihui; ...

2015-04-28

In this paper, a glucose, xylose and arabinose utilizing Zymomonas mobilis strain was constructed by incorporating arabinose catabolic pathway genes, araBAD encoding L-ribulokinase, L-arabinose isomerase and L-ribulose-5-phosphate- 4-epimerase in a glucose, xylose co-fermenting host, 8b, using a transposition integration approach. Further improvement on this arabinose-capable integrant, 33C was achieved by applying a second transposition to create a genomic knockout (KO) mutant library. Using arabinose as a sole carbon source and a selection pressure, the KO library was subjected to a growth-enrichment process involving continuous sub-culturing for over 120 generations. Strain 13-1-17, isolated from such process demonstrated significant improvement in metabolizingmore » arabinose in a dilute acid pretreated, saccharified corn stover slurry. Through Next Generation Sequencing (NGS) analysis, integration sites of the transposons were identified. Furthermore, multiple additional point mutations (SNPs: Single Nucleotide Polymorphisms) were discovered in 13-1-17, affecting genes araB and RpiB in the genome. Finally, we speculate that these mutations may have impacted the expression of the enzymes coded by these genes, ribulokinase and Ribose 5-P-isomerase, thus attributing to the improvement of the arabinose utilization.« less

Investigation of tooth transposition in a non-syndromic Turkish anatolian population: characteristic features and associated dental anomalies.

PubMed

Celikoglu, Mevlut; Miloglu, Ozkan; Oztek, Ozkan

2010-09-01

The aims of this study were to investigate the frequency and characteristics of dental transpositions and to evaluate associated dental anomalies in a large sample of Turkish Anatolian population. A retrospective study was performed using panoramic radiographs of 6983 patients (4092 females and 2891 males) ranging in age from 12 to 27 subjected to Faculty of Dentistry at the University of Ataturk (Erzurum, Turkey) between 2005 and 2008. For each patient with tooth transposition we recorded the demographic variables (including age, sex), history of trauma, type, classification, and location of tooth transpositions, and associated dental anomalies. The Pearson chi-squared test was used to determine potential differences in the distribution of tooth transposition when stratified by gender. Tooth transposition was detected in 19 subjects (0.27%), with a 2.2:1 female male ratio (P=0.38). The most commonly observed transposition was maxillary canine-lateral incisor (60%). The frequencies of complete and incomplete transpositions were equal (10/10) and it was more common in the left side than in the right side (11/9). Of the 19 subjects, 10.5% had a peg shaped lateral incisor, 21.1% one congenitally missing tooth excluding third molar. Supernumerary tooth, impacted teeth excluding third molars, transmigrated tooth, and dilacerations were also observed. The frequency of tooth transposition was 0.27% in a Turkish Anatolian population and maxillary canine-lateral incisor was the most frequently observed transposition. Retained primary teeth were the most frequently observed dental anomaly in all types of tooth transposition.

Internal limiting membrane flap transposition for surgical repair of macular holes in primary surgery and in persistent macular holes.

PubMed

Leisser, Christoph; Hirnschall, Nino; Döller, Birgit; Varsits, Ralph; Ullrich, Marlies; Kefer, Katharina; Findl, Oliver

2018-03-01

Classical or temporal internal limiting membrane (ILM) flap transposition with air or gas tamponade are current trends with the potential to improve surgical results, especially in cases with large macular holes. A prospective case series included patients with idiopathic macular holes or persistent macular holes after 23-G pars plana vitrectomy (PPV) and ILM peeling with gas tamponade. In all patients, 23-G PPV and ILM peeling with ILM flap transposition with gas tamponade and postoperative face-down position was performed. In 7 of 9 eyes, temporal ILM flap transposition combined with pedicle ILM flap could be successfully performed and macular holes were closed in all eyes after surgery. The remaining 2 eyes were converted to pedicle ILM flap transposition with macular hole closure after surgery. Three eyes were scheduled as pedicle ILM flap transposition due to previous ILM peeling. In 2 of these eyes, the macular hole could be closed with pedicle ILM flap transposition. In 3 eyes, free ILM flap transposition was performed and in 2 of these eyes macular hole could be closed after surgery, whereas in 1 eye a second surgery, performed as pedicle ILM flap transposition, was performed and led to successful macular hole closure. Use of ILM flaps in surgical repair of macular hole surgery is a new option of treatment with excellent results independent of the diameter of macular holes. For patients with persistent macular holes, pedicle ILM flap transposition or free ILM flap transposition are surgical options.

Permanent magnet machine with windings having strand transposition

DOEpatents

Qu, Ronghai; Jansen, Patrick Lee

2009-04-21

This document discusses, among other things, a stator with transposition between the windings or coils. The coils are free from transposition to increase the fill factor of the stator slots. The transposition at the end connections between an inner coil and an outer coil provide transposition to reduce circulating current loss. The increased fill factor reduces further current losses. Such a stator is used in a dual rotor, permanent magnet machine, for example, in a compressor pump, wind turbine gearbox, wind turbine rotor.

Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy

PubMed Central

2011-01-01

Background DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery. Results We have observed that (1) the Tol2 transposase (but not piggyBac) is highly sensitive to molecular engineering; (2) the piggyBac donor with only the 40 bp 3'-and 67 bp 5'-terminal repeat domain is sufficient for effective transposition; and (3) a small amount of piggyBac transposases results in robust transposition suggesting the piggyBac transpospase is highly active. Performing genome-wide target profiling on data sets obtained by retrieving chromosomal targeting sequences from individual clones, we have identified several piggyBac and Tol2 hotspots and observed that (4) piggyBac and Tol2 display a clear difference in targeting preferences in the human genome. Finally, we have observed that (5) only sites with a particular sequence context can be targeted by either piggyBac or Tol2. Conclusions The non-overlapping targeting preference of piggyBac and Tol2 makes them complementary research tools for manipulating mammalian genomes. PiggyBac is the most promising transposon-based vector system for achieving site-specific targeting of therapeutic genes due to the flexibility of its transposase for being molecularly engineered. Insights from this study will provide a basis for engineering piggyBac transposases to achieve site-specific therapeutic gene targeting. PMID:21447194

Transposition of maxillary canine to central incisor site: aetiology, treatment options and case report.

PubMed

Ali, Zohaib; Jaisinghani, Aneel C; Waring, David; Malik, Ovais

2014-09-01

Dental transposition is relatively infrequent anomaly of the developing dentition. This article focuses on canine transposition and explores the aetiology, diagnosis and treatment of this challenging anomaly. Specifically, the management of a case of canine transposition involving an unerupted maxillary central incisor is described. © 2014 British Orthodontic Society.

Genome-Wide Transposon Mutagenesis in Pathogenic Leptospira Species▿ ‡

PubMed Central

Murray, Gerald L.; Morel, Viviane; Cerqueira, Gustavo M.; Croda, Julio; Srikram, Amporn; Henry, Rebekah; Ko, Albert I.; Dellagostin, Odir A.; Bulach, Dieter M.; Sermswan, Rasana W.; Adler, Ben; Picardeau, Mathieu

2009-01-01

Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner-based transposon Himar1 to generate the first defined mutants in L. interrogans. In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans. This library provides a valuable resource for the study of gene function in L. interrogans. Combined with the genome sequences of L. interrogans, this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans. PMID:19047402

Genome-wide transposon mutagenesis in pathogenic Leptospira species.

PubMed

Murray, Gerald L; Morel, Viviane; Cerqueira, Gustavo M; Croda, Julio; Srikram, Amporn; Henry, Rebekah; Ko, Albert I; Dellagostin, Odir A; Bulach, Dieter M; Sermswan, Rasana W; Adler, Ben; Picardeau, Mathieu

2009-02-01

Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner-based transposon Himar1 to generate the first defined mutants in L. interrogans. In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans. This library provides a valuable resource for the study of gene function in L. interrogans. Combined with the genome sequences of L. interrogans, this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans.

Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing.

PubMed

Miyao, Akio; Nakagome, Mariko; Ohnuma, Takako; Yamagata, Harumi; Kanamori, Hiroyuki; Katayose, Yuichi; Takahashi, Akira; Matsumoto, Takashi; Hirochika, Hirohiko

2012-01-01

Somaclonal variation is a phenomenon that results in the phenotypic variation of plants regenerated from cell culture. One of the causes of somaclonal variation in rice is the transposition of retrotransposons. However, many aspects of the mechanisms that result in somaclonal variation remain undefined. To detect genome-wide changes in regenerated rice, we analyzed the whole-genome sequences of three plants independently regenerated from cultured cells originating from a single seed stock. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were detected in the genomes of the regenerated plants. The transposition of only Tos17 among 43 transposons examined was detected in the regenerated plants. Therefore, the SNPs and indels contribute to the somaclonal variation in regenerated rice in addition to the transposition of Tos17. The observed molecular spectrum was similar to that of the spontaneous mutations in Arabidopsis thaliana. However, the base change ratio was estimated to be 1.74 × 10(-6) base substitutions per site per regeneration, which is 248-fold greater than the spontaneous mutation rate of A. thaliana.

Parallel approach on sorting of genes in search of optimal solution.

PubMed

Kumar, Pranav; Sahoo, G

2018-05-01

An important tool for comparing genome analysis is the rearrangement event that can transform one given genome into other. For finding minimum sequence of fission and fusion, we have proposed here an algorithm and have shown a transformation example for converting the source genome into the target genome. The proposed algorithm comprises of circular sequence i.e. "cycle graph" in place of mapping. The main concept of algorithm is based on optimal result of permutation. These sorting processes are performed in constant running time by showing permutation in the form of cycle. In biological instances it has been observed that transposition occurs half of the frequency as that of reversal. In this paper we are not dealing with reversal instead commencing with the rearrangement of fission, fusion as well as transposition. Copyright © 2017 Elsevier Inc. All rights reserved.

Methods of Transposition of Nurses between Wards

NASA Astrophysics Data System (ADS)

Miyazaki, Shigeji; Masuda, Masakazu

In this paper, a computer-implemented method for automating the transposition of a hospital’s nursing staff is proposed. The model is applied to the real case example ‘O’ hospital, which performs a transposition of its nursing staff once a year. Results are compared with real data obtained from this hospital’s current manual transposition system. The proposed method not only significantly reduces the time taken to construct the transposition, thereby significantly reducing management labor costs, but also is demonstrated to increase nurses’ levels of satisfaction with the process.

An extremely rare clinical entity: congenitally corrected transposition with situs ınversus and single coronary artery presented with complete atrioventricular block in a young man.

PubMed

Cirakoglu, Omer Faruk; Bayraktar, Ali; Sayin, Muhammet Rasit

2018-05-01

Congenitally corrected transposition of the great arteries is a rare form of CHD. Situs inversus is a much less common variant of a congenitally corrected transposition of the great arteries. In rare cases, transposition events may be accompanied by various cardiac anomalies. However, situs inversus patients with congenitally corrected transposition, single coronary artery anomaly, and atrioventricular block together have not been reported previously. This combination of abnormalities is presented as a first in the literature.

Diagnosing Model Errors in Simulations of Solar Radiation on Inclined Surfaces: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Yu; Sengupta, Manajit

2016-06-01

Transposition models have been widely used in the solar energy industry to simulate solar radiation on inclined PV panels. Following numerous studies comparing the performance of transposition models, this paper aims to understand the quantitative uncertainty in the state-of-the-art transposition models and the sources leading to the uncertainty. Our results suggest that an isotropic transposition model developed by Badescu substantially underestimates diffuse plane-of-array (POA) irradiances when diffuse radiation is perfectly isotropic. In the empirical transposition models, the selection of empirical coefficients and land surface albedo can both result in uncertainty in the output. This study can be used as amore » guide for future development of physics-based transposition models.« less

Diagnosing Model Errors in Simulation of Solar Radiation on Inclined Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Yu; Sengupta, Manajit

2016-11-21

Transposition models have been widely used in the solar energy industry to simulate solar radiation on inclined PV panels. Following numerous studies comparing the performance of transposition models, this paper aims to understand the quantitative uncertainty in the state-of-the-art transposition models and the sources leading to the uncertainty. Our results show significant differences between two highly used isotropic transposition models with one substantially underestimating the diffuse plane-of-array (POA) irradiances when diffuse radiation is perfectly isotropic. In the empirical transposition models, the selection of empirical coefficients and land surface albedo can both result in uncertainty in the output. This study canmore » be used as a guide for future development of physics-based transposition models.« less

The Evolution of SINEs and LINEs in the genus Chironomus (Diptera).

PubMed

Papusheva, Ekaterina; Gruhl, Mary C; Berezikov, Eugene; Groudieva, Tatiana; Scherbik, Svetlana V; Martin, Jon; Blinov, Alexander; Bergtrom, Gerald

2004-03-01

Genomic DNA amplification from 51 species of the family Chironomidae shows that most contain relatives of NLRCth1 LINE and CTRT1 SINE retrotransposons first found in Chironomus thummi. More than 300 cloned PCR products were sequenced. The amplified region of the reverse transcriptase gene in the LINEs is intact and highly conserved, suggesting active elements. The SINEs are less conserved, consistent with minimal/no selection after transposition. A mitochondrial gene phylogeny resolves the Chironomus genus into six lineages (Guryev et al. 2001). LINE and SINE phylogenies resolve five of these lineages, indicating their monophyletic origin and vertical inheritance. However, both the LINE and the SINE tree topologies differ from the species phylogeny, resolving the elements into "clusters I-IV" and "cluster V" families. The data suggest a descent of all LINE and SINE subfamilies from two major families. Based on the species phylogeny, a few LINEs and a larger number of SINEs are cladisitically misplaced. Most misbranch with LINEs or SINEs from species with the same families of elements. From sequence comparisons, cladistically misplaced LINEs and several misplaced SINEs arose by convergent base substitutions. More diverged SINEs result from early transposition and some are derived from multiple source SINEs in the same species. SINEs from two species (C. dorsalis, C. pallidivittatus), expected to belong to the clusters I-IV family, branch instead with cluster V family SINEs; apparently both families predate separation of cluster V from clusters I-IV species. Correlation of the distribution of active SINEs and LINEs, as well as similar 3' sequence motifs in CTRT1 and NLRCth1, suggests coevolving retrotransposon pairs in which CTRT1 transposition depends on enzymes active during NLRCth1 LINE mobility.

Hybrid Adeno-Associated Viral Vectors Utilizing Transposase-Mediated Somatic Integration for Stable Transgene Expression in Human Cells

PubMed Central

Zhang, Wenli; Solanki, Manish; Müther, Nadine; Ebel, Melanie; Wang, Jichang; Sun, Chuanbo; Izsvak, Zsuzsanna; Ehrhardt, Anja

2013-01-01

Recombinant adeno-associated viral (AAV) vectors have been shown to be one of the most promising vectors for therapeutic gene delivery because they can induce efficient and long-term transduction in non-dividing cells with negligible side-effects. However, as AAV vectors mostly remain episomal, vector genomes and transgene expression are lost in dividing cells. Therefore, to stably transduce cells, we developed a novel AAV/transposase hybrid-vector. To facilitate SB-mediated transposition from the rAAV genome, we established a system in which one AAV vector contains the transposon with the gene of interest and the second vector delivers the hyperactive Sleeping Beauty (SB) transposase SB100X. Human cells were infected with the AAV-transposon vector and the transposase was provided in trans either by transient and stable plasmid transfection or by AAV vector transduction. We found that groups which received the hyperactive transposase SB100X showed significantly increased colony forming numbers indicating enhanced integration efficiencies. Furthermore, we found that transgene copy numbers in transduced cells were dose-dependent and that predominantly SB transposase-mediated transposition contributed to stabilization of the transgene. Based on a plasmid rescue strategy and a linear-amplification mediated PCR (LAM-PCR) protocol we analysed the SB100X-mediated integration profile after transposition from the AAV vector. A total of 1840 integration events were identified which revealed a close to random integration profile. In summary, we show for the first time that AAV vectors can serve as template for SB transposase mediated somatic integration. We developed the first prototype of this hybrid-vector system which with further improvements may be explored for treatment of diseases which originate from rapidly dividing cells. PMID:24116154

Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii

PubMed Central

Jaeckisch, Nina; Yang, Ines; Wohlrab, Sylke; Glöckner, Gernot; Kroymann, Juergen; Vogel, Heiko; Cembella, Allan; John, Uwe

2011-01-01

Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79–97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins. PMID:22164224

A Model of Evolution of Development Based on Germline Penetration of New “No-Junk” DNA

PubMed Central

Fontana, Alessandro; Wróbel, Borys

2012-01-01

There is a mounting body of evidence that somatic transposition may be involved in normal development of multicellular organisms and in pathology, especially cancer. Epigenetic Tracking (ET) is an abstract model of multicellular development, able to generate complex 3-dimensional structures. Its aim is not to model the development of a particular organism nor to merely summarise mainstream knowledge on genetic regulation of development. Rather, the goal of ET is to provide a theoretical framework to test new postulated genetic mechanisms, not fully established yet in mainstream biology. The first proposal is that development is orchestrated through a subset of cells which we call driver cells. In these cells, the cellular state determines a specific pattern of gene activation which leads to the occurrence of developmental events. The second proposal is that evolution of development is affected by somatic transposition events. We postulate that when the genome of a driver cell does not specify what developmental event should be undertaken when the cell is in a particular cellular state, somatic transposition events can reshape the genome, build new regulatory regions, and lead to a new pattern of gene activation in the cell. Our third hypothesis, not supported yet by direct evidence, but consistent with some experimental observations, is that these new “no-junk” sequences—regulatory regions created by transposable elements at new positions in the genome—can exit the cell and enter the germline, to be incorporated in the genome of the progeny. We call this mechanism germline penetration. This process allows heritable incorporation of novel developmental events in the developmental trajectory. In this paper we will present the model and link these three postulated mechanisms to biological observations. PMID:24704981

Unilateral and bilateral dental transpositions in the maxilla-dental and skeletal findings in 63 individuals.

PubMed

Danielsen, J C; Karimian, K; Ciarlantini, R; Melsen, B; Kjær, I

2015-12-01

This was to elucidate dental and skeletal findings in individuals with unilateral and bilateral maxillary dental transpositions. The sample comprised of radiographic materials from 63 individuals with maxillary dental transpositions from the Departments of Odontology at the Universities of Copenhagen and Aarhus and by the Danish municipal orthodontic service. The cases were divided into three groups: unilateral transposition of the canine and first premolar (Type 1U), bilateral transposition of canine and first premolar (Type 1B), and unilateral transposition of canine and lateral incisor (Type 2). The dentitions were analysed regarding agenesis and dental morphological anomalies on panoramic radiographs, and craniofacial aspects were cephalometrically analysed on profile images The results were statistically evaluated. All groups demonstrated increased occurrences of agenesis (Type 1U and Type 1B: 31 agenesis in 15 patients; and Type 2 three agenesis in three patients). Taurodontic root morphology was most dominant in Type 1U. Peg-shaped lateral incisors showed an increased occurrence, though not in Type 1U. Skeletally, Type 1B and Type 1U demonstrated maxillary retrognathia (more pronounced in Type 1B). Type 2 showed a significant posterior inclination of the maxilla. Transpositions of maxillary canines involve dental and skeletal deviations. Dental deviations were predominantly taurodontic root morphology and agenesis. Regarding skeletal deviations, bilateral transpositions of the canines and the first premolars are associated with skeletal changes. Unilateral transpositions are possibly a localised deviation with minor or no skeletal involvements. The results indicate a possible difference in the aetiologies of unilateral and bilateral transpositions.

Mucin gene expression in human urothelium and in intestinal segments transposed into the urinary tract.

PubMed

N'Dow, J; Pearson, J P; Bennett, M K; Neal, D E; Robson, C N

2000-10-01

The repertoire of mucin (MUC) gene expression in the normal human urothelium is poorly defined and the alterations in MUC gene expression following transposition of intestinal segments into the urinary tract has not previously been studied. The aims of this study were to define MUC gene expression in the normal human urothelium; and in transposed intestinal segments. Non-isotopic in-situ hybridization was carried out using eight digoxigenin labeled oligonucleotide mucin gene probes (MUC 1 - 7). Immunohistochemistry using NCL-MUC1 and NCL-MUC2 monoclonal antibodies was performed on sections of paraffin-embedded tissues. Twenty-seven patients were investigated (normal human urothelium, n = 6; transposed ileal segments, n = 14 and normal ileal controls, n = 7). MUC1 and MUC4 were the predominant mucin genes expressed in the normal urothelium with MUC3 being expressed in a third of cases studied; MUC2, 5AC, 5B, 6 and 7 were not expressed. Despite the morphological changes seen in transposed ileal segments, MUC2 and MUC3 continued to be expressed in these segments albeit in a disorganised fashion. Both MUC1 and MUC4 were up-regulated in transposed ileal segments, genes expressed by the normal human urothelium. All eight mucin genes were expressed in an area of pyloric-type metaplasia found in one transposed ileal segment. In patients with clam enterocystoplasty there was evidence of increasing up-regulation of MUC2, 3, 4 and 5AC expression in the urothelium toward the anastomotic site. Transposition of ileal segments into the urinary tract results in up-regulation of MUC1 and MUC4, the predominant MUC genes expressed in the human bladder. The clinical implication of the up-regulation of some MUC genes toward the anastomotic site in patients with an enteroplasty and the aberrant expression of MUC5AC - MUC7 by transposed segments is at present unclear.

Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements.

PubMed

Nakagome, Mariko; Solovieva, Elena; Takahashi, Akira; Yasue, Hiroshi; Hirochika, Hirohiko; Miyao, Akio

2014-03-14

Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS. We have developed a program with a new algorithm to detect the transpositions from NGS data. In the process of tool development, we used next-generation sequence (NGS) data of derivative lines (ttm2 and ttm5) of japonica rice cv. Nipponbare, regenerated through cell culture. The new program, called a transposon insertion finder (TIF), was applied to detect the de novo transpositions of Tos17 in the regenerated lines. TIF searched 300 million reads of a line within 20 min, identifying 4 and 12 de novo transposition in ttm2 and ttm5 lines, respectively. All of the transpositions were confirmed by PCR/electrophoresis and sequencing. Using the program, we also detected new transposon insertions of P-element from NGS data of Drosophila melanogaster. TIF operates to find the transposition of any elements provided that target site duplications (TSDs) are generated by their transpositions.

Primary structure and mapping of the hupA gene of Salmonella typhimurium.

PubMed Central

Higgins, N P; Hillyard, D

1988-01-01

In bacteria, the complex nucleoid structure is folded and maintained by negative superhelical tension and a set of type II DNA-binding proteins, also called histonelike proteins. The most abundant type II DNA-binding protein is HU. Southern blot analysis showed that Salmonella typhimurium contained two HU genes that corresponded to Escherichia coli genes hupA (encoding HU-2 protein) and hupB (encoding HU-1). Salmonella hupA was cloned, and the nucleotide sequence of the gene was determined. Comparison of hupA of E. coli and S. typhimurium revealed that the HU-2 proteins were identical and that there was high conservation of nucleotide sequences outside the coding frames of the genes. A 300-member genomic library of S. typhimurium was constructed by using random transposition of MudP, a specialized chimeric P22-Mu phage that packages chromosomal DNA unidirectionally from its insertion point. Oligonucleotide hybridization against the library identified one MudP insertion that lies within 28 kilobases of hupA; the MudP was 12% linked to purH at 90.5 min on the standard map. Plasmids expressing HU-2 had a surprising phenotype; they caused growth arrest when they were introduced into E. coli strains bearing a himA or hip mutation. These results suggest that IHF and HU have interactive roles in bacteria. Images PMID:3056912

Developmental origin of limb size variation in lizards.

PubMed

Andrews, Robin M; Skewes, Sable A

2017-05-01

In many respects, reptile hatchlings are fully functional, albeit miniature, adults. This means that the adult morphology must emerge during embryonic development. This insight emphasizes the connection between the mechanisms that generate phenotypic variation during embryonic development and the action of selection on post-hatching individuals. To determine when species-specific differences in limb and tail lengths emerge during embryonic development, we compared allometric patterns of early limb growth of four distantly related species of lizards. The major questions addressed were whether early embryonic limb and tail growth is characterized by the gradual (continuous allometry) or by the abrupt emergence (transpositional allometry) of size differences among species. Our observations supported transpositional allometry of both limbs and tails. Species-specific differences in limb and tail length were exhibited when limb and tail buds first protruded from the body wall. Genes known to be associated with early limb development of tetrapods are obvious targets for studies on the genetic mechanisms that determine interspecific differences in relative limb length. Broadly comparative studies of gene regulation would facilitate understanding of the mechanisms underlying adaptive variation in limb size, including limb reduction and loss, of squamate reptiles. © 2017 Wiley Periodicals, Inc.

Germline Transgenic Pigs by Sleeping Beauty Transposition in Porcine Zygotes and Targeted Integration in the Pig Genome

PubMed Central

Garrels, Wiebke; Mátés, Lajos; Holler, Stephanie; Dalda, Anna; Taylor, Ulrike; Petersen, Björn; Niemann, Heiner; Izsvák, Zsuzsanna; Ivics, Zoltán; Kues, Wilfried A.

2011-01-01

Genetic engineering can expand the utility of pigs for modeling human diseases, and for developing advanced therapeutic approaches. However, the inefficient production of transgenic pigs represents a technological bottleneck. Here, we assessed the hyperactive Sleeping Beauty (SB100X) transposon system for enzyme-catalyzed transgene integration into the embryonic porcine genome. The components of the transposon vector system were microinjected as circular plasmids into the cytoplasm of porcine zygotes, resulting in high frequencies of transgenic fetuses and piglets. The transgenic animals showed normal development and persistent reporter gene expression for >12 months. Molecular hallmarks of transposition were confirmed by analysis of 25 genomic insertion sites. We demonstrate germ-line transmission, segregation of individual transposons, and continued, copy number-dependent transgene expression in F1-offspring. In addition, we demonstrate target-selected gene insertion into transposon-tagged genomic loci by Cre-loxP-based cassette exchange in somatic cells followed by nuclear transfer. Transposase-catalyzed transgenesis in a large mammalian species expands the arsenal of transgenic technologies for use in domestic animals and will facilitate the development of large animal models for human diseases. PMID:21897845

Assessment of uncertainty in the numerical simulation of solar irradiance over inclined PV panels: New algorithms using measurements and modeling tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Yu; Sengupta, Manajit; Dooraghi, Mike

Development of accurate transposition models to simulate plane-of-array (POA) irradiance from horizontal measurements or simulations is a complex process mainly because of the anisotropic distribution of diffuse solar radiation in the atmosphere. The limited availability of reliable POA measurements at large temporal and spatial scales leads to difficulties in the comprehensive evaluation of transposition models. This paper proposes new algorithms to assess the uncertainty of transposition models using both surface-based observations and modeling tools. We reviewed the analytical derivation of POA irradiance and the approximation of isotropic diffuse radiation that simplifies the computation. Two transposition models are evaluated against themore » computation by the rigorous analytical solution. We proposed a new algorithm to evaluate transposition models using the clear-sky measurements at the National Renewable Energy Laboratory's (NREL's) Solar Radiation Research Laboratory (SRRL) and a radiative transfer model that integrates diffuse radiances of various sky-viewing angles. We found that the radiative transfer model and a transposition model based on empirical regressions are superior to the isotropic models when compared to measurements. We further compared the radiative transfer model to the transposition models under an extensive range of idealized conditions. Our results suggest that the empirical transposition model has slightly higher cloudy-sky POA irradiance than the radiative transfer model, but performs better than the isotropic models under clear-sky conditions. Significantly smaller POA irradiances computed by the transposition models are observed when the photovoltaics (PV) panel deviates from the azimuthal direction of the sun. The new algorithms developed in the current study have opened the door to a more comprehensive evaluation of transposition models for various atmospheric conditions and solar and PV orientations.« less

Assessment of uncertainty in the numerical simulation of solar irradiance over inclined PV panels: New algorithms using measurements and modeling tools

DOE PAGES

Xie, Yu; Sengupta, Manajit; Dooraghi, Mike

2018-03-20

Development of accurate transposition models to simulate plane-of-array (POA) irradiance from horizontal measurements or simulations is a complex process mainly because of the anisotropic distribution of diffuse solar radiation in the atmosphere. The limited availability of reliable POA measurements at large temporal and spatial scales leads to difficulties in the comprehensive evaluation of transposition models. This paper proposes new algorithms to assess the uncertainty of transposition models using both surface-based observations and modeling tools. We reviewed the analytical derivation of POA irradiance and the approximation of isotropic diffuse radiation that simplifies the computation. Two transposition models are evaluated against themore » computation by the rigorous analytical solution. We proposed a new algorithm to evaluate transposition models using the clear-sky measurements at the National Renewable Energy Laboratory's (NREL's) Solar Radiation Research Laboratory (SRRL) and a radiative transfer model that integrates diffuse radiances of various sky-viewing angles. We found that the radiative transfer model and a transposition model based on empirical regressions are superior to the isotropic models when compared to measurements. We further compared the radiative transfer model to the transposition models under an extensive range of idealized conditions. Our results suggest that the empirical transposition model has slightly higher cloudy-sky POA irradiance than the radiative transfer model, but performs better than the isotropic models under clear-sky conditions. Significantly smaller POA irradiances computed by the transposition models are observed when the photovoltaics (PV) panel deviates from the azimuthal direction of the sun. The new algorithms developed in the current study have opened the door to a more comprehensive evaluation of transposition models for various atmospheric conditions and solar and PV orientations.« less

P Element Transposition Contributes Substantial New Variation for a Quantitative Trait in Drosophila Melanogaster

PubMed Central

Torkamanzehi, A.; Moran, C.; Nicholas, F. W.

1992-01-01

The P-M system of transposition in Drosophila melanogaster is a powerful mutator for many visible and lethal loci. Experiments using crosses between unrelated P and M stocks to assess the importance of transposition-mediated mutations affecting quantitative loci and reponse to selection have yielded unrepeatable or ambiguous results. In a different approach, we have used a P stock produced by microinjection of the ry(506) M stock. Selection responses were compared between transposition lines that were initiated by crossing M strain females with males from the ``co-isogenic'' P strain, and ry(506) M control lines. Unlike previous attempts to quantify the effects of P element transposition, there is no possibility of P transposition in the controls. During 10 generations of selection for the quantitative trait abdominal bristle number, none of the four control lines showed any response to selection, indicative of isogenicity for those loci affecting abdominal bristle number. In contrast, three of the four transposition lines showed substantial response, with regression of cumulative response on cumulative selection differential ranging from 15% to 25%. Transposition of P elements has produced new additive genetic variance at a rate which is more than 30 times greater than the rate expected from spontaneous mutation. PMID:1317317

Maxillary canine-first premolar bilateral transposition in a Class III patient: A case report.

PubMed

Potrubacz, Maciej Iancu; Tepedino, Michele; Chimenti, Claudio

2016-05-01

Tooth transposition is a rare dental anomaly that often represents a challenge for the clinician. The case of a girl with skeletal Class III malocclusion and concomitant maxillary canine-first premolar bilateral transposition, followed from 7 to 17 years of age, is presented. After a first phase of treatment aimed at resolving the Class III malocclusion, the transposition was maintained and the case finalized with a multibracket appliance.

Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra

PubMed Central

Shewaramani, Sonal; Finn, Thomas J.; Kassen, Rees; Rainey, Paul B.

2017-01-01

Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements. The anaerobically grown populations displayed a mutation rate nearly twice that of the aerobic populations, showed distinct asymmetric mutational strand biases, and greater insertion element activity. Consistent with mutation rate and spectra observations, genes for transposition and recombination repair associated with SVs were up-regulated during anaerobic growth. Together, these results define differences in mutational spectra affecting the evolution of facultative anaerobes. PMID:28103245

Sorting signed permutations by short operations.

PubMed

Galvão, Gustavo Rodrigues; Lee, Orlando; Dias, Zanoni

2015-01-01

During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the most common operations are reversals, which are responsible for reversing the order and orientation of a sequence of genes, and transpositions, which are responsible for switching the location of two contiguous portions of a genome. The problem of computing the minimum sequence of operations that transforms one genome into another - which is equivalent to the problem of sorting a permutation into the identity permutation - is a well-studied problem that finds application in comparative genomics. There are a number of works concerning this problem in the literature, but they generally do not take into account the length of the operations (i.e. the number of genes affected by the operations). Since it has been observed that short operations are prevalent in the evolution of some species, algorithms that efficiently solve this problem in the special case of short operations are of interest. In this paper, we investigate the problem of sorting a signed permutation by short operations. More precisely, we study four flavors of this problem: (i) the problem of sorting a signed permutation by reversals of length at most 2; (ii) the problem of sorting a signed permutation by reversals of length at most 3; (iii) the problem of sorting a signed permutation by reversals and transpositions of length at most 2; and (iv) the problem of sorting a signed permutation by reversals and transpositions of length at most 3. We present polynomial-time solutions for problems (i) and (iii), a 5-approximation for problem (ii), and a 3-approximation for problem (iv). Moreover, we show that the expected approximation ratio of the 5-approximation algorithm is not greater than 3 for random signed permutations with more than 12 elements. Finally, we present experimental results that show that the approximation ratios of the approximation algorithms cannot be smaller than 3. In particular, this means that the approximation ratio of the 3-approximation algorithm is tight.

Cardiac haemangioma associated with a duct-dependent congenital heart disease in a newborn infant.

PubMed

Djordjevic, Stefan A; Glumac, Sofija; Kalanj, Jasna

2017-07-01

Cardiac haemangiomas are exceedingly rare; however, they can cause significant haemodynamic impairment and disturbances in heart rhythm. Rarely, cardiac tumours may also coexist with congenital heart lesions. We present an extremely unusual case of a cardiac haemangioma in the setting of complex transposition of the great arteries that caused functional tricuspid atresia. To our knowledge, this is the first such case described in the literature.

The challenge of staphylococcal pacemaker endocarditis in a patient with transposition of the great arteries endocarditis in congenital heart disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ch'ng, Julie; Chan, William; Lee, Paul

2003-06-01

Staphylococcus aureus is a leading cause of septicaemia and infective endocarditis. The overall incidence of staphylococcal bacteraemia is increasing, contributing to 16% of all hospital-acquired bacteraemias. The use of cardiac pacemakers has revolutionized the management of rhythm disturbances, yet this has also resulted in a group of patients at risk of pacemaker lead endocarditis and seeding in the range of 1% to 7%. We describe a 26-year-old man with transposition of the great arteries who had a pacemaker implanted and presented with S. aureus septicaemia 2 years postpacemaker implantation and went on to develop pacemaker lead endocarditis. This report illustratesmore » the risk of endocarditis in the population with congenital heart disease and an intracardiac device.« less

RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies

PubMed Central

Hamidou Soumana, Illiassou; Klopp, Christophe; Ravel, Sophie; Nabihoudine, Ibouniyamine; Tchicaya, Bernadette; Parrinello, Hugues; Abate, Luc; Rialle, Stéphanie; Geiger, Anne

2015-01-01

Trypanosoma brucei gambiense (Tbg), causing the sleeping sickness chronic form, completes its developmental cycle within the tsetse fly vector Glossina palpalis gambiensis (Gpg) before its transmission to humans. Within the framework of an anti-vector disease control strategy, a global gene expression profiling of trypanosome infected (susceptible), non-infected, and self-cured (refractory) tsetse flies was performed, on their midguts, to determine differential genes expression resulting from in vivo trypanosomes, tsetse flies (and their microbiome) interactions. An RNAseq de novo assembly was achieved. The assembled transcripts were mapped to reference sequences for functional annotation. Twenty-four percent of the 16,936 contigs could not be annotated, possibly representing untranslated mRNA regions, or Gpg- or Tbg-specific ORFs. The remaining contigs were classified into 65 functional groups. Only a few transposable elements were present in the Gpg midgut transcriptome, which may represent active transpositions and play regulatory roles. One thousand three hundred and seventy three genes differentially expressed (DEGs) between stimulated and non-stimulated flies were identified at day-3 post-feeding; 52 and 1025 between infected and self-cured flies at 10 and 20 days post-feeding, respectively. The possible roles of several DEGs regarding fly susceptibility and refractoriness are discussed. The results provide new means to decipher fly infection mechanisms, crucial to develop anti-vector control strategies. PMID:26617594

Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae

PubMed Central

Li, Zhigang; Hu, Songnian; Yao, Nan; Dean, Ralph A.; Zhao, Wensheng; Shen, Mi; Zhang, Haiwang; Li, Chao; Liu, Liyuan; Cao, Lei; Xu, Xiaowen; Xing, Yunfei; Hsiang, Tom; Zhang, Ziding; Xu, Jin-Rong; Peng, You-Liang

2012-01-01

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus. PMID:22876203

Syllable Transposition Effects in Korean Word Recognition

ERIC Educational Resources Information Center

Lee, Chang H.; Kwon, Youan; Kim, Kyungil; Rastle, Kathleen

2015-01-01

Research on the impact of letter transpositions in visual word recognition has yielded important clues about the nature of orthographic representations. This study investigated the impact of syllable transpositions on the recognition of Korean multisyllabic words. Results showed that rejection latencies in visual lexical decision for…

Evaluation of global horizontal irradiance to plane-of-array irradiance models at locations across the United States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lave, Matthew; Hayes, William; Pohl, Andrew

2015-02-02

We report an evaluation of the accuracy of combinations of models that estimate plane-of-array (POA) irradiance from measured global horizontal irradiance (GHI). This estimation involves two steps: 1) decomposition of GHI into direct and diffuse horizontal components and 2) transposition of direct and diffuse horizontal irradiance (DHI) to POA irradiance. Measured GHI and coincident measured POA irradiance from a variety of climates within the United States were used to evaluate combinations of decomposition and transposition models. A few locations also had DHI measurements, allowing for decoupled analysis of either the decomposition or the transposition models alone. Results suggest that decompositionmore » models had mean bias differences (modeled versus measured) that vary with climate. Transposition model mean bias differences depended more on the model than the location. Lastly, when only GHI measurements were available and combinations of decomposition and transposition models were considered, the smallest mean bias differences were typically found for combinations which included the Hay/Davies transposition model.« less

Orthodontic treatment of the transposition of a maxillary canine and a first premolar: a case report.

PubMed

Teresa, Dinoi Maria; Stefano, Mummolo; Annalisa, Monaco; Enrico, Marchetti; Vincenzo, Campanella; Giuseppe, Marzo

2015-03-01

Transposition is an anomaly of tooth position, the most frequent of which involves the canine and the first maxillary premolar. We describe the orthodontic treatment of a unilateral transposition of an upper canine and an upper right first premolar in the permanent dentition. A 12-year-old Caucasian boy presented with transposition of his upper right canine and upper right first premolar. He had combined surgical-orthodontic treatment to correct the transposition and to obtain a Class I relationship between the molar and canine. This treatment resolved the dental crowding and achieved good functional and aesthetic results. In transposition, the choice of the most suitable treatment depends on the occlusion, level of dental crowding, aesthetics, position of the radicular apices, and the specific needs of the patient. In this case, orthodontic alignment of the transposed teeth into their physiological position achieved all of our objectives and our patient was satisfied with the aesthetic results obtained.

Comparison of hemihypoglossal-facial nerve transposition with a cross-facial nerve graft and muscle transplant for the rehabilitation of facial paralysis using the facial clima method.

PubMed

Hontanilla, Bernardo; Vila, Antonio

2012-02-01

To compare quantitatively the results obtained after hemihypoglossal nerve transposition and microvascular gracilis transfer associated with a cross facial nerve graft (CFNG) for reanimation of a paralysed face, 66 patients underwent hemihypoglossal transposition (n = 25) or microvascular gracilis transfer and CFNG (n = 41). The commissural displacement (CD) and commissural contraction velocity (CCV) in the two groups were compared using the system known as Facial clima. There was no inter-group variability between the groups (p > 0.10) in either variable. However, intra-group variability was detected between the affected and healthy side in the transposition group (p = 0.036 and p = 0.017, respectively). The transfer group had greater symmetry in displacement of the commissure (CD) and commissural contraction velocity (CCV) than the transposition group and patients were more satisfied. However, the transposition group had correct symmetry at rest but more asymmetry of CCV and CD when smiling.

Performance Analysis of Transposition Models Simulating Solar Radiation on Inclined Surfaces: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Yu; Sengupta, Manajit

2016-06-01

Transposition models are widely used in the solar energy industry to simulate solar radiation on inclined photovoltaic (PV) panels. These transposition models have been developed using various assumptions about the distribution of the diffuse radiation, and most of the parameterizations in these models have been developed using hourly ground data sets. Numerous studies have compared the performance of transposition models, but this paper aims to understand the quantitative uncertainty in the state-of-the-art transposition models and the sources leading to the uncertainty using high-resolution ground measurements in the plane of array. Our results suggest that the amount of aerosol optical depthmore » can affect the accuracy of isotropic models. The choice of empirical coefficients and the use of decomposition models can both result in uncertainty in the output from the transposition models. It is expected that the results of this study will ultimately lead to improvements of the parameterizations as well as the development of improved physical models.« less

An unusual Tn21-like transposon containing an ars operon is present in highly arsenic-resistant strains of the biomining bacterium Acidithiobacillus caldus.

PubMed

Tuffin, I Marla; de Groot, Peter; Deane, Shelly M; Rawlings, Douglas E

2005-09-01

A transposon, TnAtcArs, that carries a set of arsenic-resistance genes was isolated from a strain of the moderately thermophilic, sulfur-oxidizing, biomining bacterium Acidithiobacillus caldus. This strain originated from a commercial plant used for the bio-oxidation of gold-bearing arsenopyrite concentrates. Continuous selection for arsenic resistance over many years had made the bacterium resistant to high concentrations of arsenic. Sequence analysis indicated that TnAtcArs is 12 444 bp in length and has 40 bp terminal inverted repeat sequences and divergently transcribed resolvase and transposase genes that are related to the Tn21-transposon subfamily. A series of genes consisting of arsR, two tandem copies of arsA and arsD, two ORFs (7 and 8) and arsB is situated between the resolvase and transposase genes. Although some commercial strains of At. caldus contained the arsDA duplication, when transformed into Escherichia coli, the arsDA duplication was unstable and was frequently lost during cultivation or if a plasmid containing TnAtcArs was conjugated into a recipient strain. TnAtcArs conferred resistance to arsenite and arsenate upon E. coli cells. Deletion of one copy of arsDA had no noticeable effect on resistance to arsenite or arsenate in E. coli. ORFs 7 and 8 had clear sequence similarity to an NADH oxidase and a CBS-domain-containing protein, respectively, but their deletion did not affect resistance to arsenite or arsenate in E. coli. TnAtcArs was actively transposed in E. coli, but no increase in transposition frequency in the presence of arsenic was detected. Northern hybridization and reporter gene studies indicated that although ArsR regulated the 10 kb operon containing the arsenic-resistance genes in response to arsenic, ArsR had no effect on the regulation of genes associated with transposition activity.

Macrovascular Decompression of Facial Nerve With Anteromedial Transposition of a Dolichoectatic Vertebral Artery: 3-Dimensional Operative Video.

PubMed

Tabani, Halima; Yousef, Sonia; Burkhardt, Jan-Karl; Gandhi, Sirin; Benet, Arnau; Lawton, Michael T

2018-05-21

Most cranial nerve compression syndromes (ie, trigeminal neuralgia and hemifacial spasm) are caused by small arteries impinging on a nerve and are relieved by microvascular decompression. Rarely, cranial nerve compression syndromes can be caused by large artery impingement and can be relieved by macrovascular decompression. When present, this compression often occurs in association with degenerative atherosclerosis in the vertebral arteries (VA) and basilar artery. Conservative treatment is recommended for mild forms, but surgical transposition of the VA away from the root entry zone (REZ) can be considered. This video demonstrates macrovascular decompression of a dolichoectatic VA in a 74-yr-old female with refractory left hemifacial spasm. After obtaining IRB approval, patient consent was sought for the procedure. With the patient in three-quarter-prone position, a far-lateral craniotomy was performed. The dentate ligament was cut to free the VA, and the suprahypoglossal portion of the vagoaccessory triangle was widened. VA compressed the REZ of the facial nerve, but was mobilized anteromedially off the REZ. A muslin sling was wrapped around the VA and its tail brought down to the clival dura, which was punctured with a 19-gauge needle and enlarged with a dissector. The sling was pulled anteromedially to this puncture site and secured to the dura with an aneurysm clip, relieving the REZ of all compression. The patient tolerated the procedure with mild, transient hoarseness and her hemifacial spasm resolved completely. This case demonstrates the macrovascular decompression technique with anteromedial transposition of the vertebrobasilar artery, which can also be used for trigeminal neuralgia.

Ovarian transposition in young women and fertility sparing.

PubMed

Mossa, B; Schimberni, M; Di Benedetto, L; Mossa, S

2015-09-01

Ovarian transposition is a highly effective surgical procedure used to preserve ovarian function in premenopausal patients with cancers requiring postoperative or primary pelvic radiotherapy. Pelvic irradiation determines severe damage of ovarian DNA and iatrogenic ovarian failure with premature menopause, necessity of long-term hormone replacement therapy and infertility. We conducted an extensive research of the literature in Medline between January 2000 and April 2015 using the key-words "ovarian transposition radiotherapy", "radiotherapy gonadal function", radiotherapy fertility sparing". The population included young women with normal ovarian function affected by cancers that required pelvic radiotherapy. We have examined 32 articles reporting on 1189 women undergoing ovarian transposition. Median age was 32.5 years, follow up was median 48 months. The procedure has been performed in patients less than 40 years of age. Surgery has been achieved by laparotomy or laparoscoy. We have analyzed effects of radiotherapy on ovarian function. The proportion of women treated by ovarian transposition preserved ovarian function was 70%. About 86% of patients did not develop ovarian cysts and in 98-99% of cases did not occur any metastatic disease. Ovarian transposition is associated with significant preservation of ovarian function and a low frequency of complications as cysts and metastasis. In 31% of cases the procedure can fail. Further studies are needed to evaluate the efficacy of ovarian transposition and the follow up. Ovarian transposition should be discussed at the time of cancer diagnosis in every premenopausal woman requiring pelvic radiotherapy.

[Diagnosis and treatment of strabismus caused by nasal endoscopic surgery].

PubMed

Ai, L K; Wu, X; Wang, J N; Li, J; Wu, Y; Zhou, J; Song, W X; Guo, R L

2017-12-11

Objective: Strabismus with diplopia is the main orbital complication of functional endoscopic sinus surgery (FESS). This study was to analyze clinical findings, treatment and outcomes of such cases. Methods: Retrospective case series. Twenty-three cases were divided into 3 groups based on the disease severity: group A, partial transection of the medial rectus muscle, group B, complete transection of the medical rectus, group C, transection of the medial rectus combined with the other orbital injuries. Complete ophthalmology examinations, including eye alignment, eye motility, force duction test, force generation test, general eye exam, and medical imaging (orbital CT or MRI), were performed for each case. The treatment included botulinum toxin (Botox) injection to the lateral rectus muscle, transposition of the vertical rectus muscle, and orbital surgery if needed. Results: In group A with Botox injection, all the cases achieved single vision in primary position, but still remained some adduction weakness. In group B treated by vertical transposition surgery combined with Botox, 22% of the cases got single vision in primary gaze. In group C, even with more efforts of treatment, the cases with orbital injury can only get cosmetic improvement, and diplopia and adduction dysfunction were found in most cases. Conclusions: Due to the variety of the complications of FESS, force duction test is a crucial exam to detect the direction and severity of synechia in the orbit, which will give solid information to surgery approach as well as prognosis. Botox injection at early stage will minimize the contraction of antagonist lateral rectus, helping to postpone the transposition surgery which may cause anterior segment ischemia when performed right after the medial rectus transection injury. Botox may even reduce the synechia by minimizing the scarring process. Partial vertical rectus transposition combined with muscle resection may effectively correct the eye misalignment in primary gaze and improve eye motility. The prognosis of FESS induced orbital complications is quite related with the severity of the injury. Botox combined with surgery may help medial rectus transection cases to achieve single vision in primary gaze, but when there is any other orbital injury, treatment may only improve cosmetic appearance. (Chin J Ophthalmol, 2017, 53: 917-923) .

The Cohesive Population Genetics of Molecular Drive

PubMed Central

Ohta, Tomoko; Dover, Gabriel A.

1984-01-01

The long-term population genetics of multigene families is influenced by several biased and unbiased mechanisms of nonreciprocal exchanges (gene conversion, unequal exchanges, transposition) between member genes, often distributed on several chromosomes. These mechanisms cause fluctuations in the copy number of variant genes in an individual and lead to a gradual replacement of an original family of n genes (A) in N number of individuals by a variant gene (a). The process for spreading a variant gene through a family and through a population is called molecular drive. Consideration of the known slow rates of nonreciprocal exchanges predicts that the population variance in the copy number of gene a per individual is small at any given generation during molecular drive. Genotypes at a given generation are expected only to range over a small section of all possible genotypes from one extreme (n number of A) to the other (n number of a). A theory is developed for estimating the size of the population variance by using the concept of identity coefficients. In particular, the variance in the course of spreading of a single mutant gene of a multigene family was investigated in detail, and the theory of identity coefficients at the state of steady decay of genetic variability proved to be useful. Monte Carlo simulations and numerical analysis based on realistic rates of exchange in families of known size reveal the correctness of the theoretical prediction and also assess the effect of bias in turnover. The population dynamics of molecular drive in gradually increasing the mean copy number of a variant gene without the generation of a large variance (population cohesion) is of significance regarding potential interactions between natural selection and molecular drive. PMID:6500260

Replacing and Additive Horizontal Gene Transfer in Streptococcus

PubMed Central

Choi, Sang Chul; Rasmussen, Matthew D.; Hubisz, Melissa J.; Gronau, Ilan; Stanhope, Michael J.; Siepel, Adam

2012-01-01

The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes in one lineage to be replaced by homologs from another lineage (“replacing HGT”) and events that result in the addition of substantial new genomic material (“additive HGT”). Here in, we make use of the distinct phylogenetic signatures of replacing and additive HGTs in a genome-wide study of the important human pathogen Streptococcus pyogenes (SPY) and its close relatives S. dysgalactiae subspecies equisimilis (SDE) and S. dysgalactiae subspecies dysgalactiae (SDD). Using recently developed statistical models and computational methods, we find evidence for abundant gene flow of both kinds within each of the SPY and SDE clades and of reduced levels of exchange between SPY and SDD. In addition, our analysis strongly supports a pronounced asymmetry in SPY–SDE gene flow, favoring the SPY-to-SDE direction. This finding is of particular interest in light of the recent increase in virulence of pathogenic SDE. We find much stronger evidence for SPY–SDE gene flow among replacing than among additive transfers, suggesting a primary influence from homologous recombination between co-occurring SPY and SDE cells in human hosts. Putative virulence genes are correlated with transfer events, but this correlation is found to be driven by additive, not replacing, HGTs. The genes affected by additive HGTs are enriched for functions having to do with transposition, recombination, and DNA integration, consistent with previous findings, whereas replacing HGTs seen to influence a more diverse set of genes. Additive transfers are also found to be associated with evidence of positive selection. These findings shed new light on the manner in which HGT has shaped pathogenic bacterial genomes. PMID:22617954

The cohesive population genetics of molecular drive.

PubMed

Ohta, T; Dover, G A

1984-10-01

The long-term population genetics of multigene families is influenced by several biased and unbiased mechanisms of nonreciprocal exchanges (gene conversion, unequal exchanges, transposition) between member genes, often distributed on several chromosomes. These mechanisms cause fluctuations in the copy number of variant genes in an individual and lead to a gradual replacement of an original family of n genes (A) in N number of individuals by a variant gene (a). The process for spreading a variant gene through a family and through a population is called molecular drive. Consideration of the known slow rates of nonreciprocal exchanges predicts that the population variance in the copy number of gene a per individual is small at any given generation during molecular drive. Genotypes at a given generation are expected only to range over a small section of all possible genotypes from one extreme (n number of A) to the other (n number of a). A theory is developed for estimating the size of the population variance by using the concept of identity coefficients. In particular, the variance in the course of spreading of a single mutant gene of a multigene family was investigated in detail, and the theory of identity coefficients at the state of steady decay of genetic variability proved to be useful. Monte Carlo simulations and numerical analysis based on realistic rates of exchange in families of known size reveal the correctness of the theoretical prediction and also assess the effect of bias in turnover. The population dynamics of molecular drive in gradually increasing the mean copy number of a variant gene without the generation of a large variance (population cohesion) is of significance regarding potential interactions between natural selection and molecular drive.

Breakup of a homeobox cluster after genome duplication in teleosts

PubMed Central

Mulley, John F.; Chiu, Chi-hua; Holland, Peter W. H.

2006-01-01

Several families of homeobox genes are arranged in genomic clusters in metazoan genomes, including the Hox, ParaHox, NK, Rhox, and Iroquois gene clusters. The selective pressures responsible for maintenance of these gene clusters are poorly understood. The ParaHox gene cluster is evolutionarily conserved between amphioxus and human but is fragmented in teleost fishes. We show that two basal ray-finned fish, Polypterus and Amia, each possess an intact ParaHox cluster; this implies that the selective pressure maintaining clustering was lost after whole-genome duplication in teleosts. Cluster breakup is because of gene loss, not transposition or inversion, and the total number of ParaHox genes is the same in teleosts, human, mouse, and frog. We propose that this homeobox gene cluster is held together in chordates by the existence of interdigitated control regions that could be separated after locus duplication in the teleost fish. PMID:16801555

The Intermediate-Hue Transposition of Children After Same-Different and Seriation Pretraining

ERIC Educational Resources Information Center

Buss, Judith Liane; Rabinowtiz, F. Michael

1973-01-01

Findings were: it did not matter whether the seriation involved the hues used in subsequent tasks or other hues; the presence or absence of reinforcement during perceptual pretraining did not affect pretraining, training, or transposition behavior; and seriation pretraining produced increased transposition in the intermediate-hue problem.…

Transposition-mediated DNA re-replication in maize

PubMed Central

Zhang, Jianbo; Zuo, Tao; Wang, Dafang; Peterson, Thomas

2014-01-01

Every DNA segment in a eukaryotic genome normally replicates once and only once per cell cycle to maintain genome stability. We show here that this restriction can be bypassed through alternative transposition, a transposition reaction that utilizes the termini of two separate, nearby transposable elements (TEs). Our results suggest that alternative transposition during S phase can induce re-replication of the TEs and their flanking sequences. The DNA re-replication can spontaneously abort to generate double-strand breaks, which can be repaired to generate Composite Insertions composed of transposon termini flanking segmental duplications of various lengths. These results show how alternative transposition coupled with DNA replication and repair can significantly alter genome structure and may have contributed to rapid genome evolution in maize and possibly other eukaryotes. DOI: http://dx.doi.org/10.7554/eLife.03724.001 PMID:25406063

Gene Mutations and Genomic Rearrangements in the Mouse as a Result of Transposon Mobilization from Chromosomal Concatemers

PubMed Central

Geurts, Aron M; Collier, Lara S; Geurts, Jennifer L; Oseth, Leann L; Bell, Matthew L; Mu, David; Lucito, Robert; Godbout, Susan A; Green, Laura E; Lowe, Scott W; Hirsch, Betsy A; Leinwand, Leslie A; Largaespada, David A

2006-01-01

Previous studies of the Sleeping Beauty (SB) transposon system, as an insertional mutagen in the germline of mice, have used reverse genetic approaches. These studies have led to its proposed use for regional saturation mutagenesis by taking a forward-genetic approach. Thus, we used the SB system to mutate a region of mouse Chromosome 11 in a forward-genetic screen for recessive lethal and viable phenotypes. This work represents the first reported use of an insertional mutagen in a phenotype-driven approach. The phenotype-driven approach was successful in both recovering visible and behavioral mutants, including dominant limb and recessive behavioral phenotypes, and allowing for the rapid identification of candidate gene disruptions. In addition, a high frequency of recessive lethal mutations arose as a result of genomic rearrangements near the site of transposition, resulting from transposon mobilization. The results suggest that the SB system could be used in a forward-genetic approach to recover interesting phenotypes, but that local chromosomal rearrangements should be anticipated in conjunction with single-copy, local transposon insertions in chromosomes. Additionally, these mice may serve as a model for chromosome rearrangements caused by transposable elements during the evolution of vertebrate genomes. PMID:17009875

Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.

PubMed

Macreadie, I G; Scott, R M; Zinn, A R; Butow, R A

1985-06-01

The optional 1143 bp intron in the yeast mitochondrial 21S rRNA gene (omega +) is nearly quantitatively inserted in genetic crosses into 21S rRNA alleles that lack it (omega -). The intron contains an open reading frame that can encode a protein of 235 amino acids, but no function has been ascribed to this sequence. We previously found an in vivo double-strand break in omega - DNA at or close to the intron insertion site only in zygotes of omega + X omega - crosses that appears with the same kinetics as intron insertion. We now show that mutations in the intron open reading frame that would alter the translation product simultaneously inhibit nonreciprocal omega recombination and the in vivo double-strand break in omega - DNA. These results provide evidence that the open reading frame encodes a protein required for intron transposition and support the role of the double-strand break in the process.

New insights into the transposition mechanisms of IS6110 and its dynamic distribution between Mycobacterium tuberculosis Complex lineages

PubMed Central

Uranga, Santiago; Picó, Ana; Lampreave, Carlos; Cebollada, Alberto; Otal, Isabel

2018-01-01

The insertion Sequence IS6110, only present in the pathogens of the Mycobacterium tuberculosis Complex (MTBC), has been the gold-standard epidemiological marker for TB for more than 25 years, but biological implications of IS6110 transposition during MTBC adaptation to humans remain elusive. By studying 2,236 clinical isolates typed by IS6110-RFLP and covering the MTBC, we remarked a lineage-specific content of IS6110 being higher in modern globally distributed strains. Once observed the IS6110 distribution in the MTBC, we selected representative isolates and found a correlation between the normalized expression of IS6110 and its abundance in MTBC chromosomes. We also studied the molecular regulation of IS6110 transposition and we found a synergistic action of two post-transcriptional mechanisms: a -1 ribosomal frameshift and a RNA pseudoknot which interferes translation. The construction of a transcriptionally active transposase resulted in 20-fold increase of the transposition frequency. Finally, we examined transposition in M. bovis and M. tuberculosis during laboratory starvation and in a mouse infection model of TB. Our results shown a higher transposition in M. tuberculosis, that preferably happens during TB infection in mice and after one year of laboratory culture, suggesting that IS6110 transposition is dynamically adapted to the host and to adverse growth conditions. PMID:29649213

Gastric Transposition for Esophageal Replacement in Children

PubMed Central

Hirschl, Ronald B.; Yardeni, Dani; Oldham, Keith; Sherman, Neil; Siplovich, Leo; Gross, Eitan; Udassin, Raphael; Cohen, Zehavi; Nagar, Hagith; Geiger, James D.; Coran, Arnold G.

2002-01-01

Objective To evaluate the authors’ experience with gastric transposition as a method of esophageal replacement in children with congenital or acquired abnormalities of the esophagus. Summary Background Data Esophageal replacement in children is almost always done for benign disease and thus requires a conduit that will last more than 70 years. The organ most commonly used in the past has been colon; however, most series have been fraught with major complications and conduit loss. For these reasons, in 1985 the authors switched from using colon interpositions to gastric transpositions for esophageal replacement in infants and children. Methods The authors retrospectively reviewed the records of 41 patients with the diagnoses of esophageal atresia (n = 26), corrosive injury (n = 8), leiomyomatosis (n = 5), and refractory gastroesophageal reflux (n = 2) who underwent gastric transposition for esophageal replacement. Results Mean ± SE age at the time of gastric transposition was 3.3 ± 0.6 years. All but two transpositions were performed through the posterior mediastinum without mortality or loss of the gastric conduit despite previous surgery on the gastric fundus in 8 (20%), previous esophageal operations in 15 (37%), and previous esophageal perforations in 6 (15%) patients. Complications included esophagogastric anastomotic leak (n = 15, 36%), which uniformly resolved without intervention; stricture formation (n = 20, 49%), all of which no longer require dilation; and feeding intolerance necessitating jejunal feeding (n = 8, 20%) due to delayed gastric emptying (n = 3), feeding aversion related to the underlying anomaly (n = 1), or severe neurological impairment (n = 4). No redo anastomoses were required. Conclusions Gastric transposition reestablishes effective gastrointestinal continuity with few complications. Oral feeding and appropriate weight gain are achieved in most children. Therefore, gastric transposition is an appropriate alternative for esophageal replacement in infants and children. PMID:12368682

Endoscopic Transmaxillary Transposition of Temporalis Flap for Recurrent Cerebrospinal Fluid Leak Closure.

PubMed

Thomas, Regi; Girishan, Shabari; Chacko, Ari George

2016-12-01

Objective  To describe the technique of endoscopic transmaxillary temporalis muscle flap transposition for the repair of a persistent postoperative sphenoidal cerebrospinal fluid leak. Design  The repair of a recurrent cerebrospinal fluid leak for a patient who had undergone endoscopic transsphenoidal excision of an invasive silent corticotroph Hardy C and Knosp Grade IV pituitary adenoma was undertaken. The patient had completed postoperative radiotherapy for the residual tumor and presented with cerebrospinal fluid leak, 1 year later. The initial two attempts to repair the cerebrospinal fluid leak with free grafts failed. Therefore, an endoscopic transmaxillary transposition of the temporalis muscle flap was attempted to stop the cerebrospinal fluid leak. Results  The endoscopic transmaxillary transposition of the vascularized temporalis muscle flap onto the cerebrospinal fluid leak repair site resulted in successful closure of the cerebrospinal fluid leak. Conclusion  Endoscopic transmaxillary transposition of the temporalis flap resulted in closure of recurrent cerebrospinal fluid leak in a patient with recurrent pituitary adenoma, who had undergone previous surgery and radiotherapy. This technique has advantages over the endoscopic transpterygoid transposition of the same flap and could be used as a complementary technique in selected patients.

Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species

PubMed Central

Legault, Boris A; Lopez-Lopez, Arantxa; Alba-Casado, Jose Carlos; Doolittle, W Ford; Bolhuis, Henk; Rodriguez-Valera, Francisco; Papke, R Thane

2006-01-01

Background Mature saturated brine (crystallizers) communities are largely dominated (>80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present. Results The metagenome of the microbial community of a crystallizer pond has been analyzed by end sequencing a 2000 clone fosmid library and comparing the sequences obtained with the genome sequence of "Haloquadratum walsbyi". The genome of the sequenced strain was retrieved nearly complete within this environmental DNA library. However, many ORF's that could be ascribed to the "Haloquadratum" metapopulation by common genome characteristics or scaffolding to the strain genome were not present in the specific sequenced isolate. Particularly, three regions of the sequenced genome were associated with multiple rearrangements and the presence of different genes from the metapopulation. Many transposition and phage related genes were found within this pool which, together with the associated atypical GC content in these areas, supports lateral gene transfer mediated by these elements as the most probable genetic cause of this variability. Additionally, these sequences were highly enriched in putative regulatory and signal transduction functions. Conclusion These results point to a large pan-genome (total gene repertoire of the genus/species) even in this highly specialized extremophile and at a single geographic location. The extensive gene repertoire is what might be expected of a population that exploits a diverse nutrient pool, resulting from the degradation of biomass produced at lower salinities. PMID:16820057

Analyzing Maize Anther Development Using Transposons

NASA Astrophysics Data System (ADS)

Han, S.

2011-12-01

Over the summer, we tackled two projects in studying more about transposons (moving/jumping genes) such as Mutator genes in corn for this project, and how the plants switch from the stages of mitosis to meiosis without a germ line. We use a transgenic corn line containing RescueMu (an artificial Mutator containing a plasmid in it), so we can keep track of the insertion events. This is a long term project so we haven't come to any final conclusions or results with tracking what happens in Mutator transposition during different stages of corn development but our process shows to work so we continue with what we've been doing.

Object permanence in the Goffin cockatoo (Cacatua goffini).

PubMed

Auersperg, Alice M I; Szabo, Birgit; von Bayern, Auguste M P; Bugnyar, Thomas

2014-02-01

The ability to represent hidden objects plays an important role in the survival of many species. In order to provide an inclusive synopsis of the current benchmark tasks used to test object permanence in animals for a psittacine representative, we tested eight Goffin cockatoos (Cacatua goffini) on Stages 3-6 of Piagetian object permanence as well as derivations of spatial transposition, rotation, and translocation tasks. Subjects instantly solved visible displacement 3b and 4a but showed an extended plateau for solving Stage 5a at a very late age (10 months). Subjects readily solved most invisible displacement tasks including double hidings and four angles (90°, 180°, 270°, and 360°) of rotation and translocations at high performance levels, although Piagetian Stage 6 invisible displacement tasks caused more difficulties for the animals than transposition, rotations, and translocation tasks. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Transposable genetic elements in Spirulina and potential applications for genetic engineering

NASA Astrophysics Data System (ADS)

Hiroyuki, Kojima; Qin, Song; Thankappan, Ajith Kumar; Yoshikazu, Kawata; Shin-Ichi, Yano

1998-03-01

Transposable elements in cyanobacteria are briefly reviewed. Evidence is presented to show that transposable elements in Spirulina platensis is actually reflected on the phenotype change, i e., helical to straight filaments. Transposition intermediates of DNA were isolated from the extrachromosome and the transposition was related to helical variations in Spirulina. Uses of transposable elements for microalgal recombination are discussed based on the transposition mechanism.

Global mapping of transposon location.

PubMed

Gabriel, Abram; Dapprich, Johannes; Kunkel, Mark; Gresham, David; Pratt, Stephen C; Dunham, Maitreya J

2006-12-15

Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

Germinal and Somatic Activity of the Maize Element Activator (Ac) in Arabidopsis

PubMed Central

Keller, J.; Lim, E.; James-Jr., D. W.; Dooner, H. K.

1992-01-01

We have investigated the germinal and somatic activity of the maize Activator (Ac) element in Arabidopsis with the objective of developing an efficient transposon-based system for gene isolation in that plant. Transposition activity was assayed with a chimeric marker that consists of the cauliflower mosaic virus 35S promoter and a bacterial streptomycin phosphotransferase gene (SPT). Somatic activity was detected in seedlings germinated on plates containing streptomycin as green-resistant sectors against a background of white-sensitive cells. Germinal excisions resulted in fully green seedlings. The transposition frequency was extremely low when a single copy of the transposon was present, but appeared to increase with an increase in Ac copy number. Plants that were selected as variegated produced an increased number of green progeny. The methylation state of the Ac elements in lines with either low or high levels of excision was assessed by restriction analysis. No difference was found between these lines, indicating that the degree of methylation did not contribute to the level of Ac activity. Germinal excision events were analyzed molecularly and shown to carry reinserted transposons in about 50% of the cases. In several instances, streptomycin-resistant siblings carried the same transposed Ac element, indicating that excision had occurred prior to meiosis in the parent. We discuss parameters that need to be considered to optimize the use of Ac as a transposon tag in Arabidopsis. PMID:1322854

Target DNA bending by the Mu transpososome promotes careful transposition and prevents its reversal

PubMed Central

Fuller, James R; Rice, Phoebe A

2017-01-01

The transposition of bacteriophage Mu serves as a model system for understanding DDE transposases and integrases. All available structures of these enzymes at the end of the transposition reaction, including Mu, exhibit significant bends in the transposition target site DNA. Here we use Mu to investigate the ramifications of target DNA bending on the transposition reaction. Enhancing the flexibility of the target DNA or prebending it increases its affinity for transpososomes by over an order of magnitude and increases the overall reaction rate. This and FRET confirm that flexibility is interrogated early during the interaction between the transposase and a potential target site, which may be how other DNA binding proteins can steer selection of advantageous target sites. We also find that the conformation of the target DNA after strand transfer is involved in preventing accidental catalysis of the reverse reaction, as conditions that destabilize this conformation also trigger reversal. DOI: http://dx.doi.org/10.7554/eLife.21777.001 PMID:28177285

Reverse Transcription of a Self-Primed Retrotransposon Requires an RNA Structure Similar to the U5-IR Stem-Loop of Retroviruses

PubMed Central

Lin, Jia-Hwei; Levin, Henry L.

1998-01-01

An inverted repeat (IR) within the U5 region of the Rous sarcoma virus (RSV) mRNA forms a structure composed of a 7-bp stem and a 5-nucleotide (nt) loop. This U5-IR structure has been shown to be required for the initiation of reverse transcription. The mRNA of Tf1, long terminal repeat-containing retrotransposon from fission yeast (Schizosaccharomyces pombe) contains nucleotides with the potential to form a U5-IR stem-loop that is strikingly similar to that of RSV. The putative U5-IR stem-loop of Tf1 consists of a 7-bp stem and a 25-nt loop. Results from mutagenesis studies indicate that the U5-IR stem-loop in the mRNA of Tf1 does form and that it is required for Tf1 transposition. Although the loop is required for transposition, we were surprised that the specific sequence of the nucleotides within the loop was unimportant for function. Additional investigation indicates that the loss of transposition activity due to a reduction in the loop size to 6 nt could be rescued by increasing the GC content of the stem. This result indicates that the large loop in the Tf1 mRNA relative to that of the RSV allows the formation of the relatively weak U5-IR stem. The levels of Tf1 proteins expressed and the amounts of Tf1 RNA packaged into the virus-like particles were not affected by mutations in the U5-IR structure. However, all of the mutations in the U5-IR structure that caused defects in transposition produced low amounts of reverse transcripts. A unique feature in the initiation of Tf1 reverse transcription is that, instead of a tRNA, the first 11 nt of the Tf1 mRNA serve as the minus-strand primer. Analysis of the 5′ end of Tf1 mRNA revealed that the mutations in the U5-IR stem-loop that resulted in defects in reverse transcription caused a reduction in the cleavage activity required to generate the Tf1 primer. Our results indicate that the U5-IR stems of Tf1 and RSV are conserved in size, position, and function. PMID:9774699

Distribution of Unlinked Transpositions of a Ds Element from a T-DNA Locus on Tomato Chromosome 4

PubMed Central

Briza, J.; Carroll, B. J.; Klimyuk, V. I.; Thomas, C. M.; Jones, D. A.; Jones, JDG.

1995-01-01

In maize, receptor sites for unlinked transpositions of Activator (Ac) elements are not distributed randomly. To test whether the same is true in tomato, the receptor sites for a Dissociation (Ds) element derived from Ac, were mapped for 26 transpositions unlinked to a donor T-DNA locus on chromosome 4. Four independent transposed Dss mapped to sites on chromosome 4 genetically unlinked to the donor T-DNA, consistent with a preference for transposition to unlinked sites on the same chromosome as opposed to sites on other chromosomes. There was little preference among the nondonor chromosomes, except perhaps for chromosome 2, which carried seven transposed Dss, but these could not be proven to be independent. However, these data, when combined with those from other studies in tomato examining the distribution of transposed Acs or Dss among nondonor chromosomes, suggest there may be absolute preferences for transposition irrespective of the chromosomal location of the donor site. If true, transposition to nondonor chromosomes in tomato would differ from that in maize, where the preference seems to be determined by the spatial arrangement of chromosomes in the interphase nucleus. The tomato lines carrying Ds elements at known locations are available for targeted transposon tagging experiments. PMID:8536985

Cytotype Control of Drosophila Melanogaster P Element Transposition: Genomic Position Determines Maternal Repression

PubMed Central

Misra, S.; Buratowski, R. M.; Ohkawa, T.; Rio, D. C.

1993-01-01

P element transposition in Drosophila is controlled by the cytotype regulatory state: in P cytotype, transposition is repressed, whereas in M cytotype, transposition can occur. P cytotype is determined by a combination of maternally inherited factors and chromosomal P elements in the zygote. Transformant strains containing single elements that encoded the 66-kD P element protein zygotically repressed transposition, but did not display the maternal repression characteristic of P cytotype. Upon mobilization to new genomic positions, some of these repressor elements showed significant maternal repression of transposition in genetic assays, involving a true maternal effect. Thus, the genomic position of repressor elements can determine the maternal vs. zygotic inheritance of P cytotype. Immunoblotting experiments indicate that this genomic position effect does not operate solely by controlling the expression level of the 66-kD repressor protein during oogenesis. Likewise, P element derivatives containing the hsp26 maternal regulator sequence expressed high levels of the 66-kD protein during oogenesis, but showed no detectable maternal repression. These data suggest that the location of a repressor element in the genome may determine maternal inheritance of P cytotype by a mechanism involving more than the overall level of expression of the 66-kD protein in the ovary. PMID:8293979

Inferior Oblique Overaction: Anterior Transposition Versus Myectomy.

PubMed

Rajavi, Zhale; Feizi, Mohadeseh; Behradfar, Narges; Yaseri, Mehdi; Sayanjali, Shima; Motevaseli, Tahmine; Sabbaghi, Hamideh; Faghihi, Mohammad

2017-07-01

To compare the efficacy of inferior oblique myectomy and anterior transposition for correcting inferior oblique overaction (IOOA). This retrospective study was conducted on 56 patients with IOOA who had either myectomy or anterior transposition of the inferior oblique muscle from 2010 to 2015. The authors compared preoperative and postoperative inferior oblique muscle function grading (-4 to +4) as the main outcome measure and vertical and horizontal deviation, dissociated vertical deviation (DVD), and A- and V-pattern between the two surgical groups as secondary outcomes. A total of 99 eyes of 56 patients with a mean age of 5.9 ± 6.5 years were included (47 eyes in the myectomy group and 52 eyes in the anterior transposition group). There were no differences in preoperative best corrected visual acuity, amblyopia, spherical equivalent, and primary versus secondary IOOA between the two groups. Both surgical procedures were effective in reducing IOOA and satisfactory results were similar between the two groups: 61.7% and 67.3% in the myectomy and anterior transposition groups, respectively (P = .56). After adjustment for the preoperative DVD, there was no statistically significant difference between the two groups postoperatively. The preoperative hypertropia was 6 to 14 and 6 to 18 prism diopters (PD) in the myectomy and anterior transposition groups, respectively. After surgery, no patient had a vertical deviation greater than 5 PD. Both the inferior oblique myectomy and anterior transposition procedures are effective in reducing IOOA with similar satisfactory results. DVD and hypertropia were also corrected similarly by these two surgical procedures. [J Pediatr Ophthalmol Strabismus. 2017;54(4):232-237.]. Copyright 2017, SLACK Incorporated.

Hox genes and chordate evolution.

PubMed

Holland, P W; Garcia-Fernàndez, J

1996-02-01

Hox genes are implicated in the control of axial patterning during embryonic development of many, perhaps all, animals. Here we review recent data on Hox gene diversity, genomic organization, and embryonic expression in chordates (including tunicates, amphioxus, hagfish, lampreys, teleosts) plus their putative sister group, the hemichordates. We consider the potential of comparative Hox gene data to resolve some outstanding controversies in chordate phylogeny. The use of Hox gene expression patterns to identify homologies between body plans both within the vertebrates and between the chordate subphyla is also discussed. Homology between the vertebrate hindbrain and an extensive region of amphioxus neural tube is suggested by comparison of Hox-3 homologues and strengthened by new data on amphioxus Hox-1 gene expression reported here. Finally, we give two examples of how Hox genes are giving glimpses into chordate developmental evolution. The first relates changes in Hox gene expression to transposition of vertebral of vertebral identities; the second describes a correlation between vertebrate origins and Hox gene cluster duplication. We suggest that the simultaneous duplication of many classes of genes, often interacting in gene networks, allowed the elaboration of new developmental control mechanisms at vertebrate origins.

Vibrio cholerae InV117, a Class 1 Integron Harboring aac(6′)-Ib and blaCTX-M-2, Is Linked to Transposition Genes

PubMed Central

Soler Bistué, Alfonso J. C.; Martín, Fernando A.; Petroni, Alejandro; Faccone, Diego; Galas, Marcelo; Tolmasky, Marcelo E.; Zorreguieta, Angeles

2006-01-01

A ca. 150-kbp Vibrio cholerae O1 biotype El Tor plasmid includes blaCTX-M-2 and a variant of aac(6′)-Ib within InV117, an orf513-bearing class 1 integron. InV117 is linked to a tnp1696 module in which IRl carries an insertion of IS4321R. The complete structure could be a potential mobile element. PMID:16641475

[Foster Modification of Full Tendon Transposition of Vertical Rectus Muscles for Sixth Nerve Palsy].

PubMed

Heede, Santa

2018-04-11

Since 1907 a variety of muscle transposition procedures for the treatment of abducens nerve palsy has been established internationally. Full tendon transposition of the vertical rectus muscle was initially described by O'Connor 1935 and then augmented by Foster 1997 with addition of posterior fixation sutures on the vertical rectus muscle. Full tendon transposition augmented by Foster belongs to the group of the most powerful surgical techniques to improve the abduction. Purpose of this study was to evaluate the results of full tendon vertical rectus transposition augmented with lateral fixation suture for patients with abducens nerve palsy. Full tendon transpositions of vertical rectus muscles augmented with posterior fixation suture was performed in 2014 on five patients with abducens nerve palsy. Two of the patients received Botox injections in the medial rectus muscle: one of them three months after the surgery and another during the surgery. One of the patients had a combined surgery of the horizontal muscles one year before. On three of the patients, who received a pure transposition surgery, the preoperative deviation at the distance (mean: + 56.6 pd; range: + 40 to + 80 pd) was reduced by a mean of 39.6 pd (range 34 to 50 pd), the abduction was improved by a mean of 3 mm (range 2 to 4 mm). The other two patients, who received besides the transposition procedure additional surgeries of the horizontal muscles, the preoperative deviation at the distance (+ 25 and + 126 pd respectively) was reduced by 20 and 81 pd respectively. The abduction was improved by 4 and 8 mm respectively. After surgery two patients developed a vertical deviation with a maximum of 4 pd. None of the patients had complications or signs of anterior segment ischemia. The elevation and/or depression was only marginally affected. There was no diplopia in up- or downgaze. Full tendon transposition of vertical rectus muscles, augmented with lateral posterior fixation suture is a safe and effective treatment method for abducens nerve palsy and in most cases recession of the medial rectus can be avoided. Upgaze and downgaze are affected very slightly. Diverse studies have shown that the risk of anterior segment ischemia is low. Georg Thieme Verlag KG Stuttgart · New York.

Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).

PubMed

Shi, Huizhen; Dong, Ji; Irwin, David M; Zhang, Shuyi; Mao, Xiuguang

2016-05-01

Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of Astigmatism Induced by Combined Inferior Oblique Anterior Transposition Procedure and Lateral Rectus Recession Alone

PubMed Central

Eum, Sun Jung

2016-01-01

Purpose The purpose of this study is to compare the magnitude and axis of astigmatism induced by a combined inferior oblique (IO) anterior transposition procedure with lateral rectus (LR) recession versus LR recession alone. Methods Forty-six patients were retrospectively analyzed. The subjects were divided into two groups: those having concurrent inferior oblique muscle overaction (IOOA) and intermittent exotropia (group 1, 20 patients) and those having only intermittent exotropia as a control (group 2, 26 patients). Group 1 underwent combined anterior transposition of IO with LR recession and group 2 underwent LR recession alone. Induced astigmatism was defined as the difference between preoperative and postoperative astigmatism using double-angle vector analysis. Cylinder power, axis of induced astigmatism, and spherical equivalent were analyzed at 1 week, 1 month, and 3 months after surgery. Results Larger changes in the axis of induced astigmatism were observed in group 1, with 4.5° incyclotorsion, than in group 2 at 1 week after surgery (axis, 84.5° vs. 91°; p < 0.001). However, there was no statistically significant inter-group difference thereafter. Relaxation and rapid regression in the incyclotorsion of induced astigmatism were observed over-time. Spherical equivalent significantly decreased postoperatively at 1 month in both groups, indicating a myopic shift (p = 0.011 for group 1 and p = 0.019 for group 2) but did not show significant differences at 3 months after surgery (p = 0.107 for group 1 and p = 0.760 for group 2). Conclusions Combined IO anterior transposition procedures caused an increased change in the axis of induced astigmatism, including temporary incyclotorsion, during the first week after surgery. However, this significant difference was not maintained thereafter. Thus, combined IO surgery with LR recession does not seem to produce a sustained astigmatic change, which can be a potential risk factor of postoperative amblyopia or diplopia compared with LR recession alone. PMID:27980365

Comparison of Astigmatism Induced by Combined Inferior Oblique Anterior Transposition Procedure and Lateral Rectus Recession Alone.

PubMed

Eum, Sun Jung; Chun, Bo Young

2016-12-01

The purpose of this study is to compare the magnitude and axis of astigmatism induced by a combined inferior oblique (IO) anterior transposition procedure with lateral rectus (LR) recession versus LR recession alone. Forty-six patients were retrospectively analyzed. The subjects were divided into two groups: those having concurrent inferior oblique muscle overaction (IOOA) and intermittent exotropia (group 1, 20 patients) and those having only intermittent exotropia as a control (group 2, 26 patients). Group 1 underwent combined anterior transposition of IO with LR recession and group 2 underwent LR recession alone. Induced astigmatism was defined as the difference between preoperative and postoperative astigmatism using double-angle vector analysis. Cylinder power, axis of induced astigmatism, and spherical equivalent were analyzed at 1 week, 1 month, and 3 months after surgery. Larger changes in the axis of induced astigmatism were observed in group 1, with 4.5° incyclotorsion, than in group 2 at 1 week after surgery (axis, 84.5° vs. 91°; p < 0.001). However, there was no statistically significant inter-group difference thereafter. Relaxation and rapid regression in the incyclotorsion of induced astigmatism were observed over-time. Spherical equivalent significantly decreased postoperatively at 1 month in both groups, indicating a myopic shift ( p = 0.011 for group 1 and p = 0.019 for group 2) but did not show significant differences at 3 months after surgery ( p = 0.107 for group 1 and p = 0.760 for group 2). Combined IO anterior transposition procedures caused an increased change in the axis of induced astigmatism, including temporary incyclotorsion, during the first week after surgery. However, this significant difference was not maintained thereafter. Thus, combined IO surgery with LR recession does not seem to produce a sustained astigmatic change, which can be a potential risk factor of postoperative amblyopia or diplopia compared with LR recession alone.

The DNA-bending protein HMGB1 is a cellular cofactor of Sleeping Beauty transposition.

PubMed

Zayed, Hatem; Izsvák, Zsuzsanna; Khare, Dheeraj; Heinemann, Udo; Ivics, Zoltán

2003-05-01

Sleeping Beauty (SB) is the most active Tc1/ mariner-type transposon in vertebrates. SB contains two transposase-binding sites (DRs) at the end of each terminal inverted repeat (IR), a feature termed the IR/DR structure. We investigated the involvement of cellular proteins in the regulation of SB transposition. Here, we establish that the DNA-bending, high-mobility group protein, HMGB1 is a host-encoded cofactor of SB transposition. Transposition was severely reduced in mouse cells deficient in HMGB1. This effect was rescued by transient over-expression of HMGB1, and was partially complemented by HMGB2, but not with the HMGA1 protein. Over-expression of HMGB1 in wild-type mouse cells enhanced transposition, indicating that HMGB1 can be a limiting factor of transposition. SB transposase was found to interact with HMGB1 in vivo, suggesting that the transposase may recruit HMGB1 to transposon DNA. HMGB1 stimulated preferential binding of the transposase to the DR further from the cleavage site, and promoted bending of DNA fragments containing the transposon IR. We propose that the role of HMGB1 is to ensure that transposase-transposon complexes are first formed at the internal DRs, and subsequently to promote juxtaposition of functional sites in transposon DNA, thereby assisting the formation of synaptic complexes.

Involvement of a bifunctional, paired-like DNA-binding domain and a transpositional enhancer in Sleeping Beauty transposition.

PubMed

Izsvák, Zsuzsanna; Khare, Dheeraj; Behlke, Joachim; Heinemann, Udo; Plasterk, Ronald H; Ivics, Zoltán

2002-09-13

Sleeping Beauty (SB) is the most active Tc1/mariner-like transposon in vertebrate species. Each of the terminal inverted repeats (IRs) of SB contains two transposase-binding sites (DRs). This feature, termed the IR/DR structure, is conserved in a group of Tc1-like transposons. The DNA-binding region of SB transposase, similar to the paired domain of Pax proteins, consists of two helix-turn-helix subdomains (PAI + RED = PAIRED). The N-terminal PAI subdomain was found to play a dominant role in contacting the DRs. Transposase was able to bind to mutant sites retaining the 3' part of the DRs; thus, primary DNA binding is not sufficient to determine the specificity of the transposition reaction. The PAI subdomain was also found to bind to a transpositional enhancer-like sequence within the left IR of SB, and to mediate protein-protein interactions between transposase subunits. A tetrameric form of the transposase was detected in solution, consistent with an interaction between the IR/DR structure and a transposase tetramer. We propose a model in which the transpositional enhancer and the PAI subdomain stabilize complexes formed by a transposase tetramer bound at the IR/DR. These interactions may result in enhanced stability of synaptic complexes, which might explain the efficient transposition of Sleeping Beauty in vertebrate cells.

"Maxillary lateral incisor partial anodontia sequence": a clinical entity with epigenetic origin.

PubMed

Consolaro, Alberto; Cardoso, Maurício Almeida; Consolaro, Renata Bianco

2017-01-01

The relationship between maxillary lateral incisor anodontia and the palatal displacement of unerupted maxillary canines cannot be considered as a multiple tooth abnormality with defined genetic etiology in order to be regarded as a "syndrome". Neither were the involved genes identified and located in the human genome, nor was it presumed on which chromosome the responsible gene would be located. The palatal maxillary canine displacement in cases of partial anodontia of the maxillary lateral incisor is potentially associated with environmental changes caused by its absence in its place of formation and eruption, which would characterize an epigenetic etiology. The lack of the maxillary lateral incisor in the canine region means removing one of the reference guides for the eruptive trajectory of the maxillary canine, which would therefore, not erupt and /or impact on the palate. Consequently, and in sequence, it would lead to malocclusion, maxillary atresia, transposition, prolonged retention of the deciduous canine and resorption in the neighboring teeth. Thus, we can say that we are dealing with a set of anomalies and multiple sequential changes known as sequential development anomalies or, simply, sequence. Once the epigenetics and sequential condition is accepted for this clinical picture, it could be called "Maxillary Lateral Incisor Partial Anodontia Sequence."

“Maxillary lateral incisor partial anodontia sequence”: a clinical entity with epigenetic origin

PubMed Central

Consolaro, Alberto; Cardoso, Maurício Almeida; Consolaro, Renata Bianco

2017-01-01

ABSTRACT The relationship between maxillary lateral incisor anodontia and the palatal displacement of unerupted maxillary canines cannot be considered as a multiple tooth abnormality with defined genetic etiology in order to be regarded as a “syndrome”. Neither were the involved genes identified and located in the human genome, nor was it presumed on which chromosome the responsible gene would be located. The palatal maxillary canine displacement in cases of partial anodontia of the maxillary lateral incisor is potentially associated with environmental changes caused by its absence in its place of formation and eruption, which would characterize an epigenetic etiology. The lack of the maxillary lateral incisor in the canine region means removing one of the reference guides for the eruptive trajectory of the maxillary canine, which would therefore, not erupt and /or impact on the palate. Consequently, and in sequence, it would lead to malocclusion, maxillary atresia, transposition, prolonged retention of the deciduous canine and resorption in the neighboring teeth. Thus, we can say that we are dealing with a set of anomalies and multiple sequential changes known as sequential development anomalies or, simply, sequence. Once the epigenetics and sequential condition is accepted for this clinical picture, it could be called “Maxillary Lateral Incisor Partial Anodontia Sequence.” PMID:29364376

Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs).

PubMed

Szuplewska, Magdalena; Ludwiczak, Marta; Lyzwa, Katarzyna; Czarnecki, Jakub; Bartosik, Dariusz

2014-01-01

Functional transposable elements (TEs) of several Pseudomonas spp. strains isolated from black shale ore of Lubin mine and from post-flotation tailings of Zelazny Most in Poland, were identified using a positive selection trap plasmid strategy. This approach led to the capture and characterization of (i) 13 insertion sequences from 5 IS families (IS3, IS5, ISL3, IS30 and IS1380), (ii) isoforms of two Tn3-family transposons--Tn5563a and Tn4662a (the latter contains a toxin-antitoxin system), as well as (iii) non-autonomous TEs of diverse structure, ranging in size from 262 to 3892 bp. The non-autonomous elements transposed into AT-rich DNA regions and generated 5- or 6-bp sequence duplications at the target site of transposition. Although these TEs lack a transposase gene, they contain homologous 38-bp-long terminal inverted repeat sequences (IRs), highly conserved in Tn5563a and many other Tn3-family transposons. The simplest elements of this type, designated TIMEs (Tn3 family-derived Inverted-repeat Miniature Elements) (262 bp), were identified within two natural plasmids (pZM1P1 and pLM8P2) of Pseudomonas spp. It was demonstrated that TIMEs are able to mobilize segments of plasmid DNA for transposition, which results in the generation of more complex non-autonomous elements, resembling IS-driven composite transposons in structure. Such transposon-like elements may contain different functional genetic modules in their core regions, including plasmid replication systems. Another non-autonomous element "captured" with a trap plasmid was a TIME derivative containing a predicted resolvase gene and a res site typical for many Tn3-family transposons. The identification of a portable site-specific recombination system is another intriguing example confirming the important role of non-autonomous TEs of the TIME family in shuffling genetic information in bacterial genomes. Transposition of such mosaic elements may have a significant impact on diversity and evolution, not only of transposons and plasmids, but also of other types of mobile genetic elements.

Enhanced rearrangement technique for secure data transmission: case study credit card process

NASA Astrophysics Data System (ADS)

Vyavahare, Tushar; Tekade, Darshana; Nayak, Saurabh; kumar, N. Suresh; Blessy Trencia Lincy, S. S.

2017-11-01

Encryption of data is very important in order to keep the data secure and make secure transactions and transmission of data. Such as online shopping. whenever we give our card details there is possibility of data being hacked or intruded. So to secure that we need to encrypt the data and decryption strategy should be known only to that particular bank. Therefore to achieve this objective RSA algorithm can be used. Where only intended sender and receiver can know about the encryption and decryption of data. To make the RSA technique more secure in this paper we propose the technique we call it Modified RSA. for which a transposition module is designed which uses Row Transposition method to encrypt the data. Before giving the card details to RSA the input will be given to this transposition module which will scrambles the data and rearranges it. Output of transposition will be then provided to the modified RSA which produces the cipher text to send over the network. Use of RSA and the transposition module will provide the dual security to whole system.

Bilateral Breast Enlargement: An Unusual Presentation of Superior Vena Cava Obstruction in a Hemodialysis Patient with Fibrosing Mediastinitis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goo, Dong Erk, E-mail: degoo@hosp.sch.ac.kr; Kim, Yong Jae; Choi, Deuk Lin

2011-02-15

A 67-year-old woman with end-stage renal disease presented with profound edema of both breasts. The presence of a patent hemodialysis basilic transposition fistula and superior vena cava obstruction (SVC), due to fibrosing mediastinitis, was demonstrated by the use of fistulography. Endovascular treatment with a balloon and stent caused immediate resolution of the breast edema.

Dental transposition of canine and lateral incisor and impacted central incisor treatment: A case report

PubMed Central

Gebert, Tarcisio Jacinto; Palma, Vinícius Canavarros; Borges, Alvaro Henrique; Volpato, Luiz Evaristo Ricci

2014-01-01

Introduction Dental transposition and impaction are disorders related to ectopic eruption or failure in tooth eruption, which can affect child physical, mental and social development and may be difficult to be clinically solved. Methods We describe a case of transposition between the upper left canine and lateral incisor associated with impaction of the central incisor on the same side, in a 12-year-old patient. Conservative treatment involving surgical-orthodontic correction of transposed teeth and traction of the central incisor was conducted. Conclusion The option of correcting transposition and orthodontic traction by means of the segmented arch technique with devices such as cantilever and TMA rectangular wire loops, although a complex alternative, was proved to be esthetically and functionally effective. PMID:24713567

Situs Inversus with Levocardia and Congenitally Corrected Transposition of Great Vessels in a 35 year old Male: A Case report

PubMed Central

Ghorbnazadeh, Atefeh; Zirak, Nahid; Fazlinezhad, Afsoon; Moenipour, Aliasghar; Manshadi, Hamid Hoseinikhah; Teshnizi, Mohammad Abbasi

2017-01-01

Situs inversus with levocardia and congenitally corrected transposition of the great arteries represents a relatively very rare congenital condition and most patients are diagnosed in infancy or early age. This case report describes a 35-year old man with congenitally corrected transposition of the great arteries which presented with a five month history of exertional dyspnea. A diagnosis was confirmed by transesophageal echocardiogram, showing situs inversus, levocardia, atrioventricular and ventriculoarterial discordance. He underwent physiologic repair, and was discharged thirty five days after the operation, in a good general condition. Although management of the corrected transposition of the great arteries patients remains controversial, the recommendation is that physiologic repair may be the procedure of choice for some patients, particularly complicated cases. PMID:28243408

Situs Inversus with Levocardia and Congenitally Corrected Transposition of Great Vessels in a 35 year old Male: A Case report.

PubMed

Ghorbnazadeh, Atefeh; Zirak, Nahid; Fazlinezhad, Afsoon; Moenipour, Aliasghar; Manshadi, Hamid Hoseinikhah; Teshnizi, Mohammad Abbasi

2017-01-01

Situs inversus with levocardia and congenitally corrected transposition of the great arteries represents a relatively very rare congenital condition and most patients are diagnosed in infancy or early age. This case report describes a 35-year old man with congenitally corrected transposition of the great arteries which presented with a five month history of exertional dyspnea. A diagnosis was confirmed by transesophageal echocardiogram, showing situs inversus, levocardia, atrioventricular and ventriculoarterial discordance. He underwent physiologic repair, and was discharged thirty five days after the operation, in a good general condition. Although management of the corrected transposition of the great arteries patients remains controversial, the recommendation is that physiologic repair may be the procedure of choice for some patients, particularly complicated cases.

Efficient Generation of Marker-Free Transgenic Rice Plants Using an Improved Transposon-Mediated Transgene Reintegration Strategy1

PubMed Central

Gao, Xiaoqing; Zhou, Jie; Li, Jun; Zou, Xiaowei; Zhao, Jianhua; Li, Qingliang; Xia, Ran; Yang, Ruifang; Wang, Dekai; Zuo, Zhaoxue; Tu, Jumin; Tao, Yuezhi; Chen, Xiaoyun; Xie, Qi; Zhu, Zengrong

2015-01-01

Marker-free transgenic plants can be developed through transposon-mediated transgene reintegration, which allows intact transgene insertion with defined boundaries and requires only a few primary transformants. In this study, we improved the selection strategy and validated that the maize (Zea mays) Activator/Dissociation (Ds) transposable element can be routinely used to generate marker-free transgenic plants. A Ds-based gene of interest was linked to green fluorescent protein in transfer DNA (T-DNA), and a green fluorescent protein-aided counterselection against T-DNA was used together with polymerase chain reaction (PCR)-based positive selection for the gene of interest to screen marker-free progeny. To test the efficacy of this strategy, we cloned the Bacillus thuringiensis (Bt) δ-endotoxin gene into the Ds elements and transformed transposon vectors into rice (Oryza sativa) cultivars via Agrobacterium tumefaciens. PCR assays of the transposon empty donor site exhibited transposition in somatic cells in 60.5% to 100% of the rice transformants. Marker-free (T-DNA-free) transgenic rice plants derived from unlinked germinal transposition were obtained from the T1 generation of 26.1% of the primary transformants. Individual marker-free transgenic rice lines were subjected to thermal asymmetric interlaced-PCR to determine Ds(Bt) reintegration positions, reverse transcription-PCR and enzyme-linked immunosorbent assay to detect Bt expression levels, and bioassays to confirm resistance against the striped stem borer Chilo suppressalis. Overall, we efficiently generated marker-free transgenic plants with optimized transgene insertion and expression. The transposon-mediated marker-free platform established in this study can be used in rice and possibly in other important crops. PMID:25371551

Efficient generation of marker-free transgenic rice plants using an improved transposon-mediated transgene reintegration strategy.

PubMed

Gao, Xiaoqing; Zhou, Jie; Li, Jun; Zou, Xiaowei; Zhao, Jianhua; Li, Qingliang; Xia, Ran; Yang, Ruifang; Wang, Dekai; Zuo, Zhaoxue; Tu, Jumin; Tao, Yuezhi; Chen, Xiaoyun; Xie, Qi; Zhu, Zengrong; Qu, Shaohong

2015-01-01

Marker-free transgenic plants can be developed through transposon-mediated transgene reintegration, which allows intact transgene insertion with defined boundaries and requires only a few primary transformants. In this study, we improved the selection strategy and validated that the maize (Zea mays) Activator/Dissociation (Ds) transposable element can be routinely used to generate marker-free transgenic plants. A Ds-based gene of interest was linked to green fluorescent protein in transfer DNA (T-DNA), and a green fluorescent protein-aided counterselection against T-DNA was used together with polymerase chain reaction (PCR)-based positive selection for the gene of interest to screen marker-free progeny. To test the efficacy of this strategy, we cloned the Bacillus thuringiensis (Bt) δ-endotoxin gene into the Ds elements and transformed transposon vectors into rice (Oryza sativa) cultivars via Agrobacterium tumefaciens. PCR assays of the transposon empty donor site exhibited transposition in somatic cells in 60.5% to 100% of the rice transformants. Marker-free (T-DNA-free) transgenic rice plants derived from unlinked germinal transposition were obtained from the T1 generation of 26.1% of the primary transformants. Individual marker-free transgenic rice lines were subjected to thermal asymmetric interlaced-PCR to determine Ds(Bt) reintegration positions, reverse transcription-PCR and enzyme-linked immunosorbent assay to detect Bt expression levels, and bioassays to confirm resistance against the striped stem borer Chilo suppressalis. Overall, we efficiently generated marker-free transgenic plants with optimized transgene insertion and expression. The transposon-mediated marker-free platform established in this study can be used in rice and possibly in other important crops. © 2015 American Society of Plant Biologists. All Rights Reserved.

Symmetric Stream Cipher using Triple Transposition Key Method and Base64 Algorithm for Security Improvement

NASA Astrophysics Data System (ADS)

Nurdiyanto, Heri; Rahim, Robbi; Wulan, Nur

2017-12-01

Symmetric type cryptography algorithm is known many weaknesses in encryption process compared with asymmetric type algorithm, symmetric stream cipher are algorithm that works on XOR process between plaintext and key, to improve the security of symmetric stream cipher algorithm done improvisation by using Triple Transposition Key which developed from Transposition Cipher and also use Base64 algorithm for encryption ending process, and from experiment the ciphertext that produced good enough and very random.

What makes up plant genomes: The vanishing line between transposable elements and genes.

PubMed

Zhao, Dongyan; Ferguson, Ann A; Jiang, Ning

2016-02-01

The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes. Copyright © 2015 Elsevier B.V. All rights reserved.

Modeling correction of severe urea cycle defects in the growing murine liver using a hybrid recombinant adeno-associated virus/piggyBac transposase gene delivery system.

PubMed

Cunningham, Sharon C; Siew, Susan M; Hallwirth, Claus V; Bolitho, Christine; Sasaki, Natsuki; Garg, Gagan; Michael, Iacovos P; Hetherington, Nicola A; Carpenter, Kevin; de Alencastro, Gustavo; Nagy, Andras; Alexander, Ian E

2015-08-01

Liver-targeted gene therapy based on recombinant adeno-associated viral vectors (rAAV) shows promising therapeutic efficacy in animal models and adult-focused clinical trials. This promise, however, is not directly translatable to the growing liver, where high rates of hepatocellular proliferation are accompanied by loss of episomal rAAV genomes and subsequently a loss in therapeutic efficacy. We have developed a hybrid rAAV/piggyBac transposon vector system combining the highly efficient liver-targeting properties of rAAV with stable piggyBac-mediated transposition of the transgene into the hepatocyte genome. Transposition efficiency was first tested using an enhanced green fluorescent protein expression cassette following delivery to newborn wild-type mice, with a 20-fold increase in stably gene-modified hepatocytes observed 4 weeks posttreatment compared to traditional rAAV gene delivery. We next modeled the therapeutic potential of the system in the context of severe urea cycle defects. A single treatment in the perinatal period was sufficient to confer robust and stable phenotype correction in the ornithine transcarbamylase-deficient Spf(ash) mouse and the neonatal lethal argininosuccinate synthetase knockout mouse. Finally, transposon integration patterns were analyzed, revealing 127,386 unique integration sites which conformed to previously published piggyBac data. Using a hybrid rAAV/piggyBac transposon vector system, we achieved stable therapeutic protection in two urea cycle defect mouse models; a clinically conceivable early application of this technology in the management of severe urea cycle defects could be as a bridging therapy while awaiting liver transplantation; further improvement of the system will result from the development of highly human liver-tropic capsids, the use of alternative strategies to achieve transient transposase expression, and engineered refinements in the safety profile of piggyBac transposase-mediated integration. © 2015 by the American Association for the Study of Liver Diseases.

Transposition of the Greater Arteries (TGA)

MedlinePlus

... Heart Disease Diseases of the arteries, valves, and aorta, as well as cardiac rhythm disturbances Aortic Valve ... Transposition of the Great Arteries Coarctation of the Aorta Truncus Arteriosus Single Ventricle Defects Patent Ductus Arteriosus ...

Gene expression profiles in promoted-growth rice seedlings that germinated from the seeds implanted by low-energy N+ beam

PubMed Central

Ya, Huiyuan; Chen, Qiufang; Wang, Weidong; Chen, Wanguang; Qin, Guangyong; Jiao, Zhen

2012-01-01

The stimulation effect that some beneficial agronomic qualities have exhibited in present-generation plants have also been observed due to ion implantation on plants. However, there is relatively little knowledge regarding the molecular mechanism of the stimulation effects of ion-beam implantation. In order to extend our current knowledge about the functional genes related to this stimulation effect, we have reported a comprehensive microarray analysis of the transcriptome features of the promoted-growth rice seedlings germinating from seeds implanted by a low-energy N+ beam. The results showed that 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNA (including miRNA), secondary metabolites, resistance proteins, peroxidase and chromatin modification, are all involved in the stimulating effects of ion-beam implantation. The divergences of the functional catalog between the vacuum and ion implantation suggest that ion implantation is the principle cause of the ion-beam implantation biological effects, and revealed the complex molecular networks required to adapt to ion-beam implantation stress in plants, including enhanced transposition of transposable elements, promoted ABA biosynthesis and changes in chromatin modification. Our data will extend the current understanding of the molecular mechanisms and gene regulation of stimulation effects. Further research on the candidates reported in this study should provide new insights into the molecular mechanisms of biological effects induced by ion-beam implantation. PMID:22843621

Increase in IS256 transposition in invasive vancomycin heteroresistant Staphylococcus aureus isolate belonging to ST100 and its derived VISA mutants.

PubMed

Di Gregorio, Sabrina; Fernandez, Silvina; Perazzi, Beatriz; Bello, Natalia; Famiglietti, Angela; Mollerach, Marta

2016-09-01

In Staphylococcus aureus, transposition of IS256 has been described to play an important role in biofilm formation and antibiotic resistance. This study describes the molecular characterization of two clinical heterogeneous vancomycin-intermediate S. aureus (hVISA) isolates recovered from the same patient (before and after antibiotic treatment) and two VISA derivatives obtained by serial passages in the presence of vancomycin. Our results showed that antibiotic treatment (in vivo and in vitro) could enhance IS256 transposition, being responsible for the eventual loss of agr function. As far as we know this is the first study that reports the increase of IS256 transposition in isogenic strains after antibiotic treatment in a clinical setting. Copyright © 2016 Elsevier B.V. All rights reserved.

Anterior transposition of the radial nerve--a cadaveric study.

PubMed

Yakkanti, Madhusudhan R; Roberts, Craig S; Murphy, Joshua; Acland, Robert D

2008-01-01

The radial nerve is at risk during the posterior plating of the humerus. The purpose of this anatomic study was to assess the extent of radial nerve dissection required for anterior transposition through the fracture site (transfracture anterior transposition). A cadaver study was conducted approaching the humerus by a posterior midline incision. The extent of dissection of the nerve necessary for plate fixation of the humerus fracture was measured. An osteotomy was created to model a humeral shaft fracture at the spiral groove (OTA classification 12-A2, 12-A3). The radial nerve was then transposed anterior to the humeral shaft through the fracture site. The additional dissection of the radial nerve and the extent of release of soft tissue from the humerus shaft to achieve the transposition were measured. Plating required a dissection of the radial nerve 1.78 cm proximal and 2.13 cm distal to the spiral groove. Transfracture anterior transposition of the radial nerve required an average dissection of 2.24 cm proximal and 2.68 cm distal to the spiral groove. The lateral intermuscular septum had to be released for 2.21 cm on the distal fragment to maintain laxity of the transposed nerve. Transfracture anterior transposition of the radial nerve before plating is feasible with dissection proximal and distal to the spiral groove and elevation of the lateral intermuscular septum. Potential clinical advantages of this technique include enhanced fracture site visualization, application of broader plates, and protection of the radial nerve during the internal fixation.

The Tn7 transposition regulator TnsC interacts with the transposase subunit TnsB and target selector TnsD

PubMed Central

Choi, Ki Young; Spencer, Jeanelle M.; Craig, Nancy L.

2014-01-01

The excision of transposon Tn7 from a donor site and its insertion into its preferred target site, attachment site attTn7, is mediated by four Tn7-encoded transposition proteins: TnsA, TnsB, TnsC, and TnsD. Transposition requires the assembly of a nucleoprotein complex containing all four Tns proteins and the DNA substrates, the donor site containing Tn7, and the preferred target site attTn7. TnsA and TnsB together form the heteromeric Tn7 transposase, and TnsD is a target-selecting protein that binds specifically to attTn7. TnsC is the key regulator of transposition, interacting with both the TnsAB transposase and TnsD-attTn7. We show here that TnsC interacts directly with TnsB, and identify the specific region of TnsC involved in the TnsB–TnsC interaction during transposition. We also show that a TnsC mutant defective in interaction with TnsB is defective for Tn7 transposition both in vitro and in vivo. Tn7 displays cis-acting target immunity, which blocks Tn7 insertion into a target DNA that already contains Tn7. We provide evidence that the direct TnsB–TnsC interaction that we have identified also mediates cis-acting Tn7 target immunity. We also show that TnsC interacts directly with the target selector protein TnsD. PMID:24982178

The Transposon impala Is Activated by Low Temperatures: Use of a Controlled Transposition System To Identify Genes Critical for Viability of Aspergillus fumigatus ▿ †

PubMed Central

Carr, Paul D.; Tuckwell, Danny; Hey, Peter M.; Simon, Laurence; d'Enfert, Christophe; Birch, Mike; Oliver, Jason D.; Bromley, Michael J.

2010-01-01

Genes that are essential for viability represent potential targets for the development of anti-infective agents. However, relatively few have been determined in the filamentous fungal pathogen Aspergillus fumigatus. A novel solution employing parasexual genetics coupled with transposon mutagenesis using the Fusarium oxysporum transposon impala had previously enabled the identification of 20 essential genes from A. fumigatus; however, further use of this system required a better understanding of the mode of action of the transposon itself. Examination of a range of conditions indicated that impala is activated by prolonged exposure to low temperatures. This newly identified property was then harnessed to identify 96 loci that are critical for viability in A. fumigatus, including genes required for RNA metabolism, organelle organization, protein transport, ribosome biogenesis, and transcription, as well as a number of noncoding RNAs. A number of these genes represent potential targets for much-needed novel antifungal drugs. PMID:20097738

Copy number variation as a genetic basis for heterotaxy and heterotaxy-spectrum congenital heart defects.

PubMed

Cowan, Jason R; Tariq, Muhammad; Shaw, Chad; Rao, Mitchell; Belmont, John W; Lalani, Seema R; Smolarek, Teresa A; Ware, Stephanie M

2016-12-19

Genomic disorders and rare copy number abnormalities are identified in 15-25% of patients with syndromic conditions, but their prevalence in individuals with isolated birth defects is less clear. A spectrum of congenital heart defects (CHDs) is seen in heterotaxy, a highly heritable and genetically heterogeneous multiple congenital anomaly syndrome resulting from failure to properly establish left-right (L-R) organ asymmetry during early embryonic development. To identify novel genetic causes of heterotaxy, we analysed copy number variants (CNVs) in 225 patients with heterotaxy and heterotaxy-spectrum CHDs using array-based genotyping methods. Clinically relevant CNVs were identified in approximately 20% of patients and encompassed both known and putative heterotaxy genes. Patients were carefully phenotyped, revealing a significant association of abdominal situs inversus with pathogenic or likely pathogenic CNVs, while d-transposition of the great arteries was more frequently associated with common CNVs. Identified cytogenetic abnormalities ranged from large unbalanced translocations to smaller, kilobase-scale CNVs, including a rare, single exon deletion in ZIC3, a gene known to cause X-linked heterotaxy. Morpholino loss-of-function experiments in Xenopus support a role for one of these novel candidates, the platelet isoform of phosphofructokinase-1 (PFKP) in heterotaxy. Collectively, our results confirm a high CNV yield for array-based testing in patients with heterotaxy, and support use of CNV analysis for identification of novel biological processes relevant to human laterality.This article is part of the themed issue 'Provocative questions in left-right asymmetry'. © 2016 The Author(s).

Coupled external fixator and skin flap transposition for treatment of exposed and nonunion bone.

PubMed

Zhao, Yong-gang; Ding, Jing; Wang, Neng

2011-02-01

To discuss the effect of coupled external fixator and skin flap transposition on exposed and nonunion bones. The data of 12 cases of infected nonunion and exposed bone following open fracture treated in our hospital during the period of March 1998 to June 2008 were analysed. There were 10 male patients, 2 female patients, whose age were between 19-52 years and averaged 28 years. There were 10 tibial fractures and 2 femoral fractures. The course of diseases lasted for 12-39 months with the mean period of 19 months. All the cases were treated by the coupled external fixator and skin flap transposition. Primary healing were achieved in 10 cases and delayed healing in 2 cases in whom the tibia was exposed due to soft tissue defect and hence local flap transposition was performed. All the 12 cases had bony union within 6-12 months after operation with the average time of 8 months. They were followed up for 1-3 years and all fractures healed up with good function and no infection recurrence. The coupled external fixator and skin flap transposition therapy have shown optimal effects on treating infected, exposed and nonunion bones.

Qualitative and Quantitative Assays of Transposition and Homologous Recombination of the Retrotransposon Tf1 in Schizosaccharomyces pombe.

PubMed

Sangesland, Maya; Atwood-Moore, Angela; Rai, Sudhir K; Levin, Henry L

2016-01-01

Transposition and homologous recombination assays are valuable genetic tools to measure the production and integration of cDNA from the long terminal repeat (LTR) retrotransposon Tf1 in the fission yeast (Schizosaccharomyces pombe). Here we describe two genetic assays, one that measures the transposition activity of Tf1 by monitoring the mobility of a drug resistance marked Tf1 element expressed from a multi-copy plasmid and another assay that measures homologous recombination between Tf1 cDNA and the expression plasmid. While the transposition assay measures insertion of full-length Tf1 cDNA mediated by the transposon integrase, the homologous recombination assay measures levels of cDNA present in the nucleus and is independent of integrase activity. Combined, these assays can be used to systematically screen large collections of strains to identify mutations that specifically inhibit the integration step in the retroelement life cycle. Such mutations can be identified because they reduce transposition activity but nevertheless have wild-type frequencies of homologous recombination. Qualitative assays of yeast patches on agar plates detect large defects in integration and recombination, while the quantitative approach provides a precise method of determining integration and recombination frequencies.

Bilateral Superior Labial Mucosal Transposition Flaps to Correct Stenosis of the Nares Following Bilateral Rostral Maxillectomy Combined with Nasal Planum Resection in a Dog.

PubMed

Séguin, Bernard; Steinke, Julia R

2016-04-01

To describe a technique using labial mucosal flaps to correct stenosis of the nares subsequent to bilateral rostral maxillectomy and nasal planum resection. Case report Client-owned dog. A 10-year-old, neutered male Golden Retriever developed repeated stenosis of the nares, at first after bilateral rostral maxillectomy and nasal planum resection, and again after revision surgery. Bilateral, superior labial mucosal transposition flaps were created and interpolated between the nasal mucosa and skin after debridement of scar tissue. The stenosis did not recur after mucosal flap transposition and the dog returned to normal quality of life (last follow-up 25 months postoperative). Single-stage, superior labial mucosal transposition flaps can be used to correct nares stenosis subsequent to previous surgery. © Copyright 2016 by The American College of Veterinary Surgeons.

Known knowns, known unknowns and unknown unknowns in prokaryotic transposition.

PubMed

Siguier, Patricia; Gourbeyre, Edith; Chandler, Michael

2017-08-01

Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of characterised Tn with other types of Tpases and finally, to highlight new potentially mobile DNA species. It is not exhaustive. Examples have been chosen to provide encouragement in the continued exploration of the considerable prokaryotic mobilome especially in light of the current threat to public health posed by the spread of multiple Ab R . Copyright © 2017 Elsevier Ltd. All rights reserved.

Birth of a new gene on the Y chromosome of Drosophila melanogaster

PubMed Central

Carvalho, Antonio Bernardo; Vicoso, Beatriz; Russo, Claudia A. M.; Swenor, Bonnielin; Clark, Andrew G.

2015-01-01

Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes. PMID:26385968

Long interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus.

PubMed

Lakshmikumaran, M S; D'Ambrosio, E; Laimins, L A; Lin, D T; Furano, A V

1985-09-01

The insulin 1, but not the insulin 2, locus is polymorphic (i.e., exhibits allelic variation) in rats. Restriction enzyme analysis and hybridization studies showed that the polymorphic region is 2.2 kilobases upstream of the insulin 1 coding region and is due to the presence or absence of an approximately 2.7-kilobase repeated DNA element. DNA sequence determination showed that this DNA element is a member of a long interspersed repeated DNA family (LINE) that is highly repeated (greater than 50,000 copies) and highly transcribed in the rat. Although the presence or absence of LINE sequences at the insulin 1 locus occurs in both the homozygous and heterozygous states, LINE-containing insulin 1 alleles are more prevalent in the rat population than are alleles without LINEs. Restriction enzyme analysis of the LINE-containing alleles indicated that at least two versions of the LINE sequence may be present at the insulin 1 locus in different rats. Either repeated transposition of LINE sequences or gene conversion between the resident insulin 1 LINE and other sequences in the genome are possible explanations for this.

The morphology of the coronary sinus in patients with congenitally corrected transposition: implications for cardiac catheterisation and re-synchronisation therapy.

PubMed

Aiello, Vera D; Ferreira, Flávia C N; Scanavacca, Mauricio I; Anderson, Robert H; D'Avila, André

2016-02-01

Patients with congenitally corrected transposition frequently benefit from re-synchronisation therapy or ablation procedures. This is likely to require catheterisation of the coronary sinus. Its anatomy, however, is not always appreciated, despite being well-described. With this caveat in mind, we have evaluated its location and structure in hearts with congenitally corrected transposition in order to reinforce the guidance needed by the cardiac interventionist. We dissected and inspected the coronary sinus, the oblique vein of the left atrium, and the left-sided-circumflex venous channel in eight heart specimens with corrected transposition and eight controls, measuring the orifice and length of the sinus and the atrioventricular valves. In two-thirds of the malformed hearts, the sinus deviated from its anticipated course in the atrioventricular groove, ascending obliquely on the left atrial inferior wall to meet the left oblique vein. The maximal deviation coincided in all hearts with the point where the left oblique vein joined the left-sided-circumflex vein to form the coronary sinus. We describe a circumflex vein, rather than the great cardiac vein, as the latter venous channel is right-sided in the setting of corrected transposition. The length of the sinus correlated positively with the diameter of the tricuspid valve (p=0.02). Compared with controls, the left oblique vein in the malformed hearts joined the circumflex venous channel significantly closer to the mouth of the sinus. The unexpected course of the coronary sinus in corrected transposition and the naming of the cardiac veins have important implications for venous cannulation and interpretation of images.

The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription.

PubMed Central

Ke, N; Gao, X; Keeney, J B; Boeke, J D; Voytas, D F

1999-01-01

Retrotransposons and retroviruses replicate by reverse transcription of an mRNA intermediate. Most retroelements initiate reverse transcription from a host-encoded tRNA primer. DNA synthesis typically extends from the 3'-OH of the acceptor stem, which is complementary to sequences on the retroelement mRNA (the primer binding site, PBS). However, for some retrotransposons, including the yeast Ty5 elements, sequences in the anticodon stem-loop of the initiator methionine tRNA (IMT) are complementary to the PBS. We took advantage of the genetic tractability of the yeast system to investigate the mechanism of Ty5 priming. We found that transposition frequencies decreased at least 800-fold for mutations in the Ty5 PBS that disrupt complementarity with the IMT. Similarly, transposition was reduced at least 200-fold for IMT mutations in the anticodon stem-loop. Base pairing between the Ty5 PBS and IMT is essential for transposition, as compensatory changes that restored base pairing between the two mutant RNAs restored transposition significantly. An analysis of 12 imt mutants with base changes outside of the region of complementarity failed to identify other tRNA residues important for transposition. In addition, assays carried out with heterologous IMTs from Schizosaccharomyces pombe and Arabidopsis thaliana indicated that residues outside of the anticodon stem-loop have at most a fivefold effect on transposition. Our genetic system should make it possible to further define the components required for priming and to understand the mechanism by which Ty5's novel primer is generated. PMID:10411136

Inferior alveolar nerve transposition in conjunction with implant placement.

PubMed

Ferrigno, Nicola; Laureti, Mauro; Fanali, Stefano

2005-01-01

The aim of this prospective study was to determine the incidence of neurosensory disturbance and the cumulative survival and success rates of ITI solid-screw implants placed in conjunction with an inferior alveolar nerve (IAN) transposition technique. 46 ITI implants were placed in 15 patients following transposition of the IAN. In 4 patients nerve transpositioning was performed bilaterally, so a total of 19 IAN mobilization surgeries were performed. Neurosensory dysfunction was objectively evaluated by using light touch (LT), pain (PT), and 2-point discrimination (2-DT) tests. In addition, patients were asked to answer a short questionnaire to investigate individual feelings of discomfort and advantages related to this surgical technique. The mean follow-up period was 49.1 months (range, 12 to 78 months). The cumulative implant survival and success rates were 95.7% and 90.5%, respectively. Only 2 implants were lost. Neurosensory disturbance (ie, disturbance registered by the LT, PT, and 2-DT tests) was experienced in 4 of 19 cases. However, at the time of data analysis (12 to 78 months after surgery), all patients indicated that they would go through the surgery again. The IAN transposition technique, when used in the severely atrophied posterior mandible, allowed placement of implants with adequate length and good initial stabilization. All patients felt that they had received significant benefits from their new prostheses. Based on the results of the present study, it can be concluded that lateral nerve transposition can be used as a surgical procedure to enable ITI implant placement in the severely resorbed posterior mandible.

Germ line transformation of the yellow fever mosquito, Aedes aegypti, mediated by transpositional insertion of a piggyBac vector.

PubMed

Lobo, N F; Hua-Van, A; Li, X; Nolen, B M; Fraser, M J

2002-04-01

Mosquito-vectored diseases such as yellow fever and dengue fever continue to have a substantial impact on human populations world-wide. Novel strategies for control of these mosquito vectored diseases can arise through the development of reliable systems for genetic manipulation of the insect vector. A piggyBac vector marked with the Drosophila melanogaster cinnabar (cn) gene was used to transform the white-eyed khw strain of Aedes aegypti. Microinjection of preblastoderm embryos resulted in four families of cinnabar transformed insects. An overall transformation frequency of 4%, with a range of 0% to as high as 13% for individual experiments, was achieved when using a heat-shock induced transposase providing helper plasmid. Southern hybridizations indicated multiple insertion events in three of four transgenic lines, while the presence of duplicated target TTAA sites at either ends of individual insertions confirmed characteristic piggyBac transposition events in these three transgenic lines. The transgenic phenotype has remained stable for more than twenty generations. The transformations effected using the piggyBac element establish the potential of this element as a germ-line transformation vector for Aedine mosquitoes.

Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae.

PubMed

Fléchard, Maud; Gilot, Philippe

2014-07-01

We have referenced and described Streptococcus agalactiae transposable elements encoding DDE transposases. These elements belonged to nine families of insertion sequences (ISs) and to a family of conjugative transposons (TnGBSs). An overview of the physiological impact of the insertion of all these elements is provided. DDE-transposable elements affect S. agalactiae in a number of aspects of its capability to adapt to various environments and modulate the expression of several virulence genes, the scpB-lmB genomic region and the genes involved in capsule expression and haemolysin transport being the targets of several different mobile elements. The referenced mobile elements modify S. agalactiae behaviour by transferring new gene(s) to its genome, by modifying the expression of neighbouring genes at the integration site or by promoting genomic rearrangements. Transposition of some of these elements occurs in vivo, suggesting that by dynamically regulating some adaptation and/or virulence genes, they improve the ability of S. agalactiae to reach different niches within its host and ensure the 'success' of the infectious process. © 2014 The Authors.

Aberrant twinning (diprosopus) associated with anencephaly.

PubMed

Moerman, P; Fryns, J P; Goddeeris, P; Lauweryns, J M; Van Assche, A

1983-10-01

A case of Monocephalus diprosopus, associated with craniorachischisis and duplication of most of the foregut derivates is presented. The major part of the cardiovascular system remained single but the heart exhibited severe defects, including a complete persistent atrioventricular canal, transposition of the great arteries and atresia of the pulmonary valve. This report further supports the hypothesis that certain-types of incomplete twinning and neural tube defects may be caused by a single teratogenic mechanism.

A trans-Dominant Form of Gag Restricts Ty1 Retrotransposition and Mediates Copy Number Control

PubMed Central

Saha, Agniva; Mitchell, Jessica A.; Nishida, Yuri; Hildreth, Jonathan E.; Ariberre, Joshua A.; Gilbert, Wendy V.

2015-01-01

ABSTRACT Saccharomyces cerevisiae and Saccharomyces paradoxus lack the conserved RNA interference pathway and utilize a novel form of copy number control (CNC) to inhibit Ty1 retrotransposition. Although noncoding transcripts have been implicated in CNC, here we present evidence that a truncated form of the Gag capsid protein (p22) or its processed form (p18) is necessary and sufficient for CNC and likely encoded by Ty1 internal transcripts. Coexpression of p22/p18 and Ty1 decreases mobility more than 30,000-fold. p22/p18 cofractionates with Ty1 virus-like particles (VLPs) and affects VLP yield, protein composition, and morphology. Although p22/p18 and Gag colocalize in the cytoplasm, p22/p18 disrupts sites used for VLP assembly. Glutathione S-transferase (GST) affinity pulldowns also suggest that p18 and Gag interact. Therefore, this intrinsic Gag-like restriction factor confers CNC by interfering with VLP assembly and function and expands the strategies used to limit retroelement propagation. IMPORTANCE Retrotransposons dominate the chromosomal landscape in many eukaryotes, can cause mutations by insertion or genome rearrangement, and are evolutionarily related to retroviruses such as HIV. Thus, understanding factors that limit transposition and retroviral replication is fundamentally important. The present work describes a retrotransposon-encoded restriction protein derived from the capsid gene of the yeast Ty1 element that disrupts virus-like particle assembly in a dose-dependent manner. This form of copy number control acts as a molecular rheostat, allowing high levels of retrotransposition when few Ty1 elements are present and inhibiting transposition as copy number increases. Thus, yeast and Ty1 have coevolved a form of copy number control that is beneficial to both “host and parasite.” To our knowledge, this is the first Gag-like retrotransposon restriction factor described in the literature and expands the ways in which restriction proteins modulate retroelement replication. PMID:25609815

Facts about dextro-Transposition of the Great Arteries (d-TGA)

MedlinePlus

... Septal Defect Atrioventricular Septal Defect Coarctation of the Aorta D-Transposition of the Great Arteries Hypoplastic Left ... the heart – the main pulmonary artery and the aorta – are switched in position, or “transposed.” What is ...

Prosthetic valve implantation with preservation of the entire valvular and subvalvular apparatus of the tricuspid valve in congenitally corrected transposition of the great arteries.

PubMed

Ergenoglu, Mehmet U; Yerebakan, Halit; Ozveren, Olcay; Koner, Ozge; Kalangos, Afksendiyos; Demirsoy, Ergun

2011-10-01

Congenitally corrected transposition of the great arteries, which is characterized by atrioventricular and ventriculoarterial discordance, is a rare congenital heart disease. Most of the cases are diagnosed in childhood, owing to associated cardiac anomalies, such as ventricular septal defect, pulmonary stenosis or pulmonary atresia, and Ebstein-like malformation of the tricuspid valve. We present a patient with congenitally corrected transposition of the great arteries who underwent surgical replacement of the tricuspid valve with a bioprosthesis and reconstruction of the left ventricular outflow tract with bovine conduit.

An O([Formula: see text]) algorithm for sorting signed genomes by reversals, transpositions, transreversals and block-interchanges.

PubMed

Yu, Shuzhi; Hao, Fanchang; Leong, Hon Wai

2016-02-01

We consider the problem of sorting signed permutations by reversals, transpositions, transreversals, and block-interchanges. The problem arises in the study of species evolution via large-scale genome rearrangement operations. Recently, Hao et al. gave a 2-approximation scheme called genome sorting by bridges (GSB) for solving this problem. Their result extended and unified the results of (i) He and Chen - a 2-approximation algorithm allowing reversals, transpositions, and block-interchanges (by also allowing transversals) and (ii) Hartman and Sharan - a 1.5-approximation algorithm allowing reversals, transpositions, and transversals (by also allowing block-interchanges). The GSB result is based on introduction of three bridge structures in the breakpoint graph, the L-bridge, T-bridge, and X-bridge that models goodreversal, transposition/transreversal, and block-interchange, respectively. However, the paper by Hao et al. focused on proving the 2-approximation GSB scheme and only mention a straightforward [Formula: see text] algorithm. In this paper, we give an [Formula: see text] algorithm for implementing the GSB scheme. The key idea behind our faster GSB algorithm is to represent cycles in the breakpoint graph by their canonical sequences, which greatly simplifies the search for these bridge structures. We also give some comparison results (running time and computed distances) against the original GSB implementation.

The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon.

PubMed

Lorenzen, Marcé D; Gnirke, Andreas; Margolis, Jonathan; Garnes, Jeffrey; Campbell, Margie; Stuart, Jeffrey J; Aggarwal, Rajat; Richards, Stephen; Park, Yoonseong; Beeman, Richard W

2008-07-22

Maternal-Effect Dominant Embryonic Arrest ("Medea") factors are selfish nuclear elements that combine maternal-lethal and zygotic-rescue activities to gain a postzygotic survival advantage. We show that Medea(1) activity in Tribolium castaneum is associated with a composite Tc1 transposon inserted just downstream of the neurotransmitter reuptake symporter bloated tubules (blot), whose Drosophila ortholog has both maternal and zygotic functions. The 21.5-kb insertion contains defective copies of elongation initiation factor-3, ATP synthase subunit C, and an RNaseD-related gene, as well as a potentially intact copy of a prokaryotic DUF1703 gene. Sequence comparisons suggest that the current distribution of Medea(1) reflects global emanation after a single transpositional event in recent evolutionary time. The Medea system in Tribolium represents an unusual type of intragenomic conflict and could provide a useful vehicle for driving desirable genes into populations.

The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon

PubMed Central

Lorenzen, Marcé D.; Gnirke, Andreas; Margolis, Jonathan; Garnes, Jeffrey; Campbell, Margie; Stuart, Jeffrey J.; Aggarwal, Rajat; Richards, Stephen; Park, Yoonseong; Beeman, Richard W.

2008-01-01

Maternal-Effect Dominant Embryonic Arrest (“Medea”) factors are selfish nuclear elements that combine maternal-lethal and zygotic-rescue activities to gain a postzygotic survival advantage. We show that Medea1 activity in Tribolium castaneum is associated with a composite Tc1 transposon inserted just downstream of the neurotransmitter reuptake symporter bloated tubules (blot), whose Drosophila ortholog has both maternal and zygotic functions. The 21.5-kb insertion contains defective copies of elongation initiation factor-3, ATP synthase subunit C, and an RNaseD-related gene, as well as a potentially intact copy of a prokaryotic DUF1703 gene. Sequence comparisons suggest that the current distribution of Medea1 reflects global emanation after a single transpositional event in recent evolutionary time. The Medea system in Tribolium represents an unusual type of intragenomic conflict and could provide a useful vehicle for driving desirable genes into populations. PMID:18621706

Micro-Plasticity of Genomes As Illustrated by the Evolution of Glutathione Transferases in 12 Drosophila Species

PubMed Central

Saisawang, Chonticha; Ketterman, Albert J.

2014-01-01

Glutathione transferases (GST) are an ancient superfamily comprising a large number of paralogous proteins in a single organism. This multiplicity of GSTs has allowed the copies to diverge for neofunctionalization with proposed roles ranging from detoxication and oxidative stress response to involvement in signal transduction cascades. We performed a comparative genomic analysis using FlyBase annotations and Drosophila melanogaster GST sequences as templates to further annotate the GST orthologs in the 12 Drosophila sequenced genomes. We found that GST genes in the Drosophila subgenera have undergone repeated local duplications followed by transposition, inversion, and micro-rearrangements of these copies. The colinearity and orientations of the orthologous GST genes appear to be unique in many of the species which suggests that genomic rearrangement events have occurred multiple times during speciation. The high micro-plasticity of the genomes appears to have a functional contribution utilized for evolution of this gene family. PMID:25310450

CRISPR regulation of intraspecies diversification by limiting IS transposition and intercellular recombination.

PubMed

Watanabe, Takayasu; Nozawa, Takashi; Aikawa, Chihiro; Amano, Atsuo; Maruyama, Fumito; Nakagawa, Ichiro

2013-01-01

Mobile genetic elements (MGEs) and genetic rearrangement are considered as major driving forces of bacterial diversification. Previous comparative genome analysis of Porphyromonas gingivalis, a pathogen related to periodontitis, implied such an important relationship. As a counterpart system to MGEs, clustered regularly interspaced short palindromic repeats (CRISPRs) in bacteria may be useful for genetic typing. We found that CRISPR typing could be a reasonable alternative to conventional methods for characterizing phylogenetic relationships among 60 highly diverse P. gingivalis isolates. Examination of genetic recombination along with multilocus sequence typing suggests the importance of such events between different isolates. MGEs appear to be strategically located at the breakpoint gaps of complicated genome rearrangements. Of these MGEs, insertion sequences (ISs) were found most frequently. CRISPR analysis identified 2,150 spacers that were clustered into 1,187 unique ones. Most of these spacers exhibited no significant nucleotide similarity to known sequences (97.6%: 1,158/1,187). Surprisingly, CRISPR spacers exhibiting high nucleotide similarity to regions of P. gingivalis genomes including ISs were predominant. The proportion of such spacers to all the unique spacers (1.6%: 19/1,187) was the highest among previous studies, suggesting novel functions for these CRISPRs. These results indicate that P. gingivalis is a bacterium with high intraspecies diversity caused by frequent insertion sequence (IS) transposition, whereas both the introduction of foreign DNA, primarily from other P. gingivalis cells, and IS transposition are limited by CRISPR interference. It is suggested that P. gingivalis CRISPRs could be an important source for understanding the role of CRISPRs in the development of bacterial diversity.

Method and structure for cache aware transposition via rectangular subsections

DOEpatents

Gustavson, Fred Gehrung; Gunnels, John A

2014-02-04

A method and structure for transposing a rectangular matrix A in a computer includes subdividing the rectangular matrix A into one or more square submatrices and executing an in-place transposition for each of the square submatrices A.sub.ij.

A discovery of novel microRNAs in the silkworm (Bombyx mori) genome.

PubMed

Yu, Xiaomin; Zhou, Qing; Cai, Yimei; Luo, Qibin; Lin, Hongbin; Hu, Songnian; Yu, Jun

2009-12-01

MicroRNAs (miRNAs) are pivotal regulators involved in various physiological and pathological processes via their post-transcriptional regulation of gene expressions. We sequenced 14 libraries of small RNAs constructed from samples spanning the life cycle of silkworms, and discovered 50 novel miRNAs previously not known in animals and verified 43 of them using stem-loop RT-PCR. Our genome-wide analyses of 27 species-specific miRNAs suggest they arise from transposable elements, protein-coding genes duplication/transposition and random foldback sequences; which is consistent with the idea that novel animal miRNAs may evolve from incomplete self-complementary transcripts and become fixed in the process of co-adaptation with their targets. Computational prediction suggests that the silkworm-specific miRNAs may have a preference of regulating genes that are related to life-cycle-associated traits, and these genes can serve as potential targets for subsequent studies of the modulating networks in the development of Bombyx mori.

Antioxidant and antigenotoxic properties of CeO2 NPs and cerium sulphate: Studies with Drosophila melanogaster as a promising in vivo model.

PubMed

Alaraby, Mohamed; Hernández, Alba; Annangi, Balasubramanyam; Demir, Esref; Bach, Jordi; Rubio, Laura; Creus, Amadeu; Marcos, Ricard

2015-01-01

Although in vitro approaches are the most used for testing the potential harmful effects of nanomaterials, in vivo studies produce relevant information complementing in vitro data. In this context, we promote the use of Drosophila melanogaster as a suitable in vivo model to characterise the potential risks associated to nanomaterials exposure. The main aim of this study was to evaluate different biological effects associated to cerium oxide nanoparticles (Ce-NPs) and cerium (IV) sulphate exposure. The end-points evaluated were egg-to-adult viability, particles uptake through the intestinal barrier, gene expression and intracellular reactive oxygen species (ROS) production by haemocytes, genotoxicity and antigenotoxicity. Transmission electron microscopy images showed internalisation of Ce-NPs by the intestinal barrier and haemocytes, and significant expression of Hsp genes was detected. In spite of these findings, neither toxicity nor genotoxicity related to both forms of cerium were observed. Interestingly, Ce-NPs significantly reduced the genotoxic effect of potassium dichromate and the intracellular ROS production. No morphological malformations were detected after larvae treatment. This study highlights the importance of D. melanogaster as animal model in the study of the different biological effects caused by nanoparticulated materials, at the time that shows its usefulness to study the role of the intestinal barrier in the transposition of nanomaterials entering via ingestion.

Human Nonsyndromic Hereditary Deafness DFNA17 Is Due to a Mutation in Nonmuscle Myosin MYH9

PubMed Central

Lalwani, Anil K.; Goldstein, Jayne A.; Kelley, Michael J.; Luxford, William; Castelein, Caley M.; Mhatre, Anand N.

2000-01-01

The authors had previously mapped a new locus—DFNA17, for nonsyndromic hereditary hearing impairment—to chromosome 22q12.2-q13.3. DFNA17 spans a 17- to 23-cM region, and MYH9, a nonmuscle–myosin heavy-chain gene, is located within the linked region. Because of the importance of myosins in hearing, MYH9 was tested as a candidate gene for DFNA17. Expression of MYH9 in the rat cochlea was confirmed using reverse transcriptase–PCR and immunohistochemistry. MYH9 was immunolocalized in the organ of Corti, the subcentral region of the spiral ligament, and the Reissner membrane. Sequence analysis of MYH9 in a family with DFNA17 identified, at nucleotide 2114, a G→A transposition that cosegregated with the inherited autosomal dominant hearing impairment. This missense mutation changes codon 705 from an invariant arginine (R) to histidine (H), R705H, within a highly conserved SH1 linker region. Previous studies have shown that modification of amino acid residues within the SH1 helix causes dysfunction of the ATPase activity of the motor domain in myosin II. Both the precise role of MYH9 in the cochlea and the mechanism by which the R705H mutation leads to the DFNA17 phenotype (progressive hearing impairment and cochleosaccular degeneration) remain to be elucidated. PMID:11023810

The Application of a Homologous Recombination Assay Revealed Amino Acid Residues in an LTR-Retrotransposon That Were Critical for Integration

PubMed Central

Atwood, Angela; Choi, Jeannie; Levin, Henry L.

1998-01-01

Retroviruses and their relatives, the LTR-retrotransposons, possess an integrase protein (IN) that is required for the insertion of reverse transcripts into the genome of host cells. Schizosaccharomyces pombe is the host of Tf1, an LTR-retrotransposon with integration activity that can be studied by using techniques of yeast genetics. In this study, we sought to identify amino acid substitutions in Tf1 that specifically affected the integration step of transposition. In addition to seeking amino acid substitutions in IN, we also explored the possibility that other Tf1 proteins contributed to integration. By comparing the results of genetic assays that monitored both transposition and reverse transcription, we were able to seek point mutations throughout Tf1 that blocked transposition but not the synthesis of reverse transcripts. These mutant versions of Tf1 were candidates of elements that possessed defects in the integration step of transposition. Five mutations in Tf1 that resulted in low levels of integration were found to be located in the IN protein: two substitutions in the N-terminal Zn domain, two in the catalytic core, and one in the C-terminal domain. These results suggested that each of the three IN domains was required for Tf1 transposition. The potential role of these five amino acid residues in the function of IN is discussed. Two of the mutations that reduced integration mapped to the RNase H (RH) domain of Tf1 reverse transcriptase. The Tf1 elements with the RH mutations produced high levels of reverse transcripts, as determined by recombination and DNA blot analysis. These results indicated that the RH of Tf1 possesses a function critical for transposition that is independent of the accumulation of reverse transcripts. PMID:9445033

Transposition Complex with Aortic Arch Obstruction: Outcomes of One-Stage Repair Over 10 Years.

PubMed

Choi, Kwang Ho; Sung, Si Chan; Kim, Hyungtae; Lee, Hyung Doo; Ban, Gil Ho; Kim, Geena; Kim, Hee Young

2016-01-01

The surgical management of transposition complex with aortic arch obstruction remains technically demanding due to anatomic complexity. Even in the recent surgical era, there are centers that address this anomaly with a staged strategy. This report presents our experiences with a one-stage repair of transposition complexes with aortic arch obstructions more than the last 10 years. Since 2003, 19 patients with a transposition of the great arteries (TGA, 2 patients) or a double outlet of the right ventricle (DORV, 17 patients) and aortic arch obstruction have undergone one-stage repair of their anomalies. The mean age was 6.7 ± 2.3 days, and the mean body weight was 3.4 ± 0.3 kg. The 2 patients with TGA exhibited coarctation of the aorta. The 17 patients with DORV all exhibited the Taussig-Bing type. The great artery relationships were anteroposterior in 4 patients (21.1%). The coronary artery anatomies were usual (1LCx; 2R) in 8 patients (42.1%). There were 2 early deaths (10.5%). Seven patients (36.8%) required percutaneous interventions. One patient required re-operation for pulmonary valvar stenosis and left pulmonary artery patch angioplasty. The overall survival was 84.2%. The freedom from mortality was 83.5% at 5 years, and the freedom from intervention was 54.4% at 5 years. The one-stage repair of transposition complexes with aortic arch obstructions resulted in an acceptable survival rate and a relatively high incidence of postoperative catheter interventions. Postoperative catheter interventions are highly effective. Transposition complexes combined with aortic arch obstructions can be managed by one-stage repair with good early and midterm results.

Extemporaneous transposition flap for closing two contiguous surgical excision.

PubMed

Boggio, Paolo; Veronese, Federica; Miglino, Benedetta; Graziola, Francesca; Tiberio, Rossana; Colombo, Enrico

2018-08-01

The authors present a surgical procedure to remove two contiguous cutaneous lesions using a single transposition flap and suture line without an evident scar. This method is useful when rhomboid surgical exeresis could not represent the best choice to obtain an optimum aesthetic result.

Curricular Transposition in Citizenship Education

ERIC Educational Resources Information Center

McCowan, Tristan

2008-01-01

The considerable debate in recent years on the aims of citizenship education has not been accompanied by an equally substantial discussion on the educational processes involved. This article puts forward a theoretical framework, referred to as "curricular transposition", for understanding the complex task of realizing normative ideals of…

A Genome-Wide Survey of Genetic Instability by Transposition in Drosophila Hybrids

PubMed Central

Vela, Doris; Fontdevila, Antonio; Vieira, Cristina; García Guerreiro, María Pilar

2014-01-01

Hybridization between species is a genomic instability factor involved in increasing mutation rate and new chromosomal rearrangements. Evidence of a relationship between interspecific hybridization and transposable element mobilization has been reported in different organisms, but most studies are usually performed with particular TEs and do not discuss the real effect of hybridization on the whole genome. We have therefore studied whole genome instability of Drosophila interspecific hybrids, looking for the presence of new AFLP markers in hybrids. A high percentage (27–90%) of the instability markers detected corresponds to TEs belonging to classes I and II. Moreover, three transposable elements (Osvaldo, Helena and Galileo) representative of different families, showed an overall increase of transposition rate in hybrids compared to parental species. This research confirms the hypothesis that hybridization induces genomic instability by transposition bursts and suggests that genomic stress by transposition could contribute to a relaxation of mechanisms controlling TEs in the Drosophila genome. PMID:24586475

Target Capture during Mos1 Transposition*

PubMed Central

Pflieger, Aude; Jaillet, Jerôme; Petit, Agnès; Augé-Gouillou, Corinne; Renault, Sylvaine

2014-01-01

DNA transposition contributes to genomic plasticity. Target capture is a key step in the transposition process, because it contributes to the selection of new insertion sites. Nothing or little is known about how eukaryotic mariner DNA transposons trigger this step. In the case of Mos1, biochemistry and crystallography have deciphered several inverted terminal repeat-transposase complexes that are intermediates during transposition. However, the target capture complex is still unknown. Here, we show that the preintegration complex (i.e., the excised transposon) is the only complex able to capture a target DNA. Mos1 transposase does not support target commitment, which has been proposed to explain Mos1 random genomic integrations within host genomes. We demonstrate that the TA dinucleotide used as the target is crucial both to target recognition and in the chemistry of the strand transfer reaction. Bent DNA molecules are better targets for the capture when the target DNA is nicked two nucleotides apart from the TA. They improve strand transfer when the target DNA contains a mismatch near the TA dinucleotide. PMID:24269942

Target capture during Mos1 transposition.

PubMed

Pflieger, Aude; Jaillet, Jerôme; Petit, Agnès; Augé-Gouillou, Corinne; Renault, Sylvaine

2014-01-03

DNA transposition contributes to genomic plasticity. Target capture is a key step in the transposition process, because it contributes to the selection of new insertion sites. Nothing or little is known about how eukaryotic mariner DNA transposons trigger this step. In the case of Mos1, biochemistry and crystallography have deciphered several inverted terminal repeat-transposase complexes that are intermediates during transposition. However, the target capture complex is still unknown. Here, we show that the preintegration complex (i.e., the excised transposon) is the only complex able to capture a target DNA. Mos1 transposase does not support target commitment, which has been proposed to explain Mos1 random genomic integrations within host genomes. We demonstrate that the TA dinucleotide used as the target is crucial both to target recognition and in the chemistry of the strand transfer reaction. Bent DNA molecules are better targets for the capture when the target DNA is nicked two nucleotides apart from the TA. They improve strand transfer when the target DNA contains a mismatch near the TA dinucleotide.

Molecular Evolution of piRNA and Transposon Control Pathways in Drosophila

PubMed Central

Malone, C.D.; Hannon, G.J.

2011-01-01

The mere prevalence and potential mobilization of transposable elements in eukaryotic genomes present challenges at both the organismal and population levels. Not only is transposition able to alter gene function and chromosomal structure, but loss of control over even a single active element in the germline can create an evolutionary dead end. Despite the dangers of coexistence, transposons and their activity have been shown to drive the evolution of gene function, chromosomal organization, and even population dynamics (Kazazian 2004). This implies that organisms have adopted elaborate means to balance both the positive and detrimental consequences of transposon activity. In this chapter, we focus on the fruit fly to explore some of the molecular clues into the long- and short-term adaptation to transposon colonization and persistence within eukaryotic genomes. PMID:20453205

Surrogate pregnancy in a patient who underwent radical hysterectomy and bilateral transposition of ovaries.

PubMed

Azem, Foad; Yovel, Israel; Wagman, Israel; Kapostiansky, Rita; Lessing, Joseph B; Amit, Ami

2003-05-01

To evaluate IVF-surrogate pregnancy in a patient with ovarian transposition after radical hysterectomy for carcinoma of the cervix. Case report. A maternity hospital in Tel Aviv that is a major tertiary care and referral center. A 29-year-old woman who underwent Wertheim's hysterectomy for carcinoma of the uterine cervix and ovarian transposition before total pelvic irradiation. Standard IVF treatment, transabdominal oocyte retrieval, and transfer to surrogate mother. Outcome of IVF cycle. A twin pregnancy in the first cycle. This is the second reported case of controlled ovarian stimulation and oocyte retrieval performed on a transposed ovary.

[Preliminary evaluation on seroma prevention and treatment with transposition of tissue flaps and arista hemostatic powder].

PubMed

Zhang, Ruming; Tan, Yiwen; Wang, Heqi

2006-12-01

To investigate and evaluate prevention and treatment of seroma by transposition of tissue flaps and Arista hemostatic powder after regional lymph node resection in patients with malignant tumors. Twelve patients (6 males, 6 females; aged 31-81 years, with metastatic tumors underwent prevention and treatment of seroma with the tissue flaps and Arista hemostatic powder spray after regional lymph node resection. The metastatic tumors involved the axilla in 1 patient with breast carcinoma, the iliac and inguinal regions in 2 patients with carcinomas of the uterine cervix and the rectum, and the inguinal region in 9 patients, including 4 patients with malignant fibrous histiocytoma(3 in the thigh, 1 in the leg), 2 patients with squamous carcinomas in the leg, 1 patient with synovial sarcoma in the knee, 1 patient with epithelioid sarcoma in the leg, and 1 patient with malignant melanoma in the foot. As for the lymph node removal therapy. 1 patient underwent axillary lymph node removal, 2 patients underwent lymph node removal in theiliac and inguinal regions, and 9 patients underwent lymph node removal in the inguinal region. Meanwhile, of the 12 patients, 6 patients underwent transposition of sartorius flaps with Arista hemostatic powder, 3 patients underwent transposition of the rectus abdominis myocutaneous flaps (including 2 patients treated with Arista spray befor the wound closure and 1 patient treated by transposition of local skin flaps with Arista spray used again),and 3 patients underwent only the suturing of the wounds combined with Arista. At the same time, of the 12 patients,only 4 patient underwent the transplantation of artificial blood vessels. The follow-up for 2-10 months after operation revealed that 10 patients, who had received the transposition of tissue flaps and the spray of Arista hemostatic powder, had the first intention of the incision heal with seroma cured. Nine patients were given a preventive use of Arista hemostatic powder and therefore no seroma developed. The combined use of the transposition of tissue flaps and Arista hemostatic powder spray achieved a success rate of 100% in the prevention or treatment of seroma. However, 1 patient developed microcirculation disturbance 24 hours after operation and underwent disarticulation of the hip; 1 patient developed pelvic cavity hydrops and died 10 months after operation. The combined use of transposition of tissue flaps and Arista hemostatic powder spray can effectively prevent or treat seroma after regional lymph node removal in a patient with malignant tumor.

Inferior Alveolar Nerve Lateralization and Transposition for Dental Implant Placement. Part I: a Systematic Review of Surgical Techniques

PubMed Central

Juodzbalys, Gintaras

2015-01-01

ABSTRACT Objectives The purpose of this first part of a two-part series was to review the literature concerning the indications, contraindications, advantages, disadvantages and surgical techniques of the lateralization and transposition of the inferior alveolar nerve, followed by the placement of an implant in an edentulous atrophic posterior mandible. Material and Methods A comprehensive review of the current literature was conducted according to the PRISMA guidelines by accessing the NCBI PubMed and PMC database, academic sites and books. The articles were searched from January 1997 to July 2014 and comprised English-language articles that included adult patients between 18 and 80 years old with minimal residual bone above the mandibular canal who had undergone inferior alveolar nerve (IAN) repositioning with a minimum 6 months of follow-up. Results A total of 16 studies were included in this review. Nine were related to IAN transposition, 4 to IAN lateralization and 3 to both transposition and lateralization. Implant treatment results and complications were presented. Conclusions Inferior alveolar nerve lateralization and transposition in combination with the installation of dental implants is sometimes the only possible procedure to help patients to obtain a fixed prosthesis, in edentulous atrophic posterior mandibles. With careful pre-operative surgical and prosthetic planning, imaging, and extremely precise surgical technique, this procedure can be successfully used for implant placement in edentulous posterior mandibular segments. PMID:25937873

Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements

PubMed Central

Peterson, Thomas

2013-01-01

Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated de novo from a maize allele containing two Class II Ac/Ds transposons. The duplication/deletion structures suggest that they were generated by alternative transposition reactions involving the termini of two nearby transposable elements. The deletion/duplication breakpoint junctions contain 8 bp target site duplications characteristic of Ac/Ds transposition events, confirming their formation directly by an alternative transposition mechanism. Tandem direct duplications and reciprocal deletions were generated at a relatively high frequency (∼0.5 to 1%) in the materials examined here in which transposons are positioned nearby each other in appropriate orientation; frequencies would likely be much lower in other genotypes. To test whether this mechanism may have contributed to maize genome evolution, we analyzed sequences flanking Ac/Ds and other hAT family transposons and identified three small tandem direct duplications with the structural features predicted by the alternative transposition mechanism. Together these results show that some class II transposons are capable of directly inducing tandem sequence duplications, and that this activity has contributed to the evolution of the maize genome. PMID:23966872

Pulmonary Arterial Hypertension and Neonatal Arterial Switch Surgery for Correction of Transposition of the Great Arteries.

PubMed

Domínguez Manzano, Paula; Mendoza Soto, Alberto; Román Barba, Violeta; Moreno Galdó, Antonio; Galindo Izquierdo, Alberto

2016-09-01

There are few reports of the appearance of pulmonary arterial hypertension following arterial switch surgery in the neonatal period to correct transposition of the great arteries. We assessed the frequency and clinical pattern of this complication in our series of patients. Our database was reviewed to select patients with transposition of the great arteries corrected by neonatal arterial switch at our hospital and who developed pulmonary hypertension over time. We identified 2 (1.3%) patients with transposition of the great arteries successfully repaired in the first week of life who later experienced pulmonary arterial hypertension. The first patient was a 7-year-old girl diagnosed with severe pulmonary hypertension at age 8 months who did not respond to medical treatment and required lung transplantation. The anatomic pathology findings were consistent with severe pulmonary arterial hypertension. The second patient was a 24-month-old boy diagnosed with severe pulmonary hypertension at age 13 months who did not respond to medical therapy. Pulmonary hypertension is a rare but very severe complication that should be investigated in all patients with transposition of the great arteries who have undergone neonatal arterial switch, in order to start early aggressive therapy for affected patients, given the poor therapeutic response and poor prognosis involved. Copyright © 2016 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Genomic structure of two ras family genes in the slime mold Physarum polycephalum.

PubMed

Trzcińska-Danielewicz, Joanna; Kozlowski, Piotr; Gierdal, Katarzyna; Wiejak, Jolanta; Jagielski, Adam; Toczko, Kazimierz; Fronk, Jan

2002-08-01

Genomic structure of two Physarum polycephalum ras family genes, Ppras2 and Pprap1, has been determined, including the upstream region of the latter. The genes are interrupted by three and four introns, respectively. The first intron of Ppras2 has the same location within the coding sequence as the first intron in another ras homolog from this organism, Ppras1 [Trzcińska-Danielewicz, J., Kozlowski, P., and Toczko, K. (1996). "Cloning and genomic sequence of the Physarum polycephalum Ppras1 gene, a homologue of the ras protooncogene", Gene 169, pp. 143-144]. All introns, ranging from 53 to ca. 460 base pairs, have the canonical 5' and 3' ends, are greatly enriched in pyrimidines in the coding strand and have frequent pyrimidines-only tracts. These latter features seem to be responsible for the difficulties in cloning and sequencing of parts of these genes. Short sequences shared with P. polycephalum transposon-like repeats are common in the introns, indicating a possible role of transposition in intron evolution. In all three ras family genes phase zero introns are located mostly between sequences coding for regular protein secondary structure elements.

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

PubMed Central

Wang, Xi; Weigel, Detlef; Smith, Lisa M.

2013-01-01

Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants. PMID:23408902

Implementation of Super-Encryption with Trithemius Algorithm and Double Transposition Cipher in Securing PDF Files on Android Platform

NASA Astrophysics Data System (ADS)

Budiman, M. A.; Rachmawati, D.; Jessica

2018-03-01

This study aims to combine the trithemus algorithm and double transposition cipher in file security that will be implemented to be an Android-based application. The parameters being examined are the real running time, and the complexity value. The type of file to be used is a file in PDF format. The overall result shows that the complexity of the two algorithms with duper encryption method is reported as Θ (n 2). However, the processing time required in the encryption process uses the Trithemius algorithm much faster than using the Double Transposition Cipher. With the length of plaintext and password linearly proportional to the processing time.

Association of zygotic piRNAs derived from paternal P elements with hybrid dysgenesis in Drosophila melanogaster.

PubMed

Wakisaka, Keiko Tsuji; Ichiyanagi, Kenji; Ohno, Seiko; Itoh, Masanobu

2018-01-01

P -element transposition in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster . Maternally deposited piRNAs suppress P -element transposition in the progeny, linking them to P-M phenotypes; however, the role of zygotic piRNAs derived from paternal P elements is poorly understood. To elucidate the molecular basis of P -element suppression by zygotic factors, we investigated the genomic constitution and P -element piRNA production derived from fathers. As a result, we characterized males of naturally derived Q, M' and P strains, which show different capacities for the P -element mobilizations introduced after hybridizations with M-strain females. The amounts of piRNAs produced in ovaries of F1 hybrids varied among the strains and were influenced by the characteristics of the piRNA clusters that harbored the P elements. Importantly, while both the Q- and M'-strain fathers restrict the P -element mobilization in ovaries of their daughters, the Q-strain fathers supported the production of the highest piRNA expression in the ovaries of their daughters, and the M' strain carries KP elements in transcriptionally active regions directing the highest expression of KP elements in their daughters. Interestingly, the zygotic P -element piRNAs, but not the KP element mRNA, contributed to the variations in P transposition immunity in the granddaughters. The piRNA-cluster-embedded P elements and the transcriptionally active KP elements from the paternal genome are both important suppressors of P element activities that are co-inherited by the progeny. Expression levels of the P -element piRNA and KP -element mRNA vary among F1 progeny due to the constitution of the paternal genome, and are involved in phenotypic variation in the subsequent generation.

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

PubMed Central

Romero-Soriano, Valèria; Garcia Guerreiro, Maria Pilar

2016-01-01

Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii—D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny. PMID:26812285

The Parity Theorem Shuffle

ERIC Educational Resources Information Center

Smith, Michael D.

2016-01-01

The Parity Theorem states that any permutation can be written as a product of transpositions, but no permutation can be written as a product of both an even number and an odd number of transpositions. Most proofs of the Parity Theorem take several pages of mathematical formalism to complete. This article presents an alternative but equivalent…

Character Decomposition and Transposition Processes of Chinese Compound Words in Rapid Serial Visual Presentation.

PubMed

Cao, Hong-Wen; Yang, Ke-Yu; Yan, Hong-Mei

2017-01-01

Character order information is encoded at the initial stage of Chinese word processing, however, its time course remains underspecified. In this study, we assess the exact time course of the character decomposition and transposition processes of two-character Chinese compound words (canonical, transposed, or reversible words) compared with pseudowords using dual-target rapid serial visual presentation (RSVP) of stimuli appearing at 30 ms per character with no inter-stimulus interval. The results indicate that Chinese readers can identify words with character transpositions in rapid succession; however, a transposition cost is involved in identifying transposed words compared to canonical words. In RSVP reading, character order of words is more likely to be reversed during the period from 30 to 180 ms for canonical and reversible words, but the period from 30 to 240 ms for transposed words. Taken together, the findings demonstrate that the holistic representation of the base word is activated, however, the order of the two constituent characters is not strictly processed during the very early stage of visual word processing.

Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda)

USGS Publications Warehouse

Aunins, Aaron W.; Nelms, David L.; Hobson, Christopher S.; King, Timothy L.

2016-01-01

The mitochondrial genomes of three North American stygobiont amphipods Stygobromus tenuis potomacus, S. foliatus and S. indentatus collected from Caroline County, VA, were sequenced using a shotgun sequencing approach on an Illumina NextSeq500 (Illumina Inc., San Diego, CA). All three mitogenomes displayed 13 protein-coding genes, 22 tRNAs and two rRNAs typical of metazoans. While S. tenuis and S. indentatusdisplayed identical gene orders similar to the pancrustacean ground pattern, S. foliatus displayed a transposition of the trnL2-cox2 genes to after atp8-atp6. In addition, a short atp8 gene, longer rrnL gene and large inverted repeat within the Control Region distinguished S. foliatus from S. tenuis potomacus and S. indentatus. Overall, it appears that gene order varies considerably among amphipods, and the addition of these Stygobromus mitogenomes to the existing sequenced amphipod mitogenomes will prove useful for characterizing evolutionary relationships among various amphipod taxa, as well as investigations of the evolutionary dynamics of the mitogenome in general.

Interspecific hybridization as a genomic stressor inducing mobilization of transposable elements in Drosophila

PubMed Central

Guerreiro, Maria Pilar García

2014-01-01

Transposable elements (TEs) are DNA sequences able to be mobilized in host genomes. They are currently recognized as the major mutation inducers because of their insertion in the target, their effect on neighboring regions, or their ectopic recombination. A large number of factors including chemical and physical factors as well as intraspecific crosses have traditionally been identified as inducers of transposition. Besides environmental factors, interspecific crosses have also been proposed as promoters of transposition of particular TEs in plants and different animals. Our previous published work includes a genome-wide survey with the set of genomic TEs and shows that interspecific hybridization between the species Drosophila buzzatii and Drosophila koepferae induces genomic instability by transposition bursts. A high percentage of this instability corresponds to TEs belonging to classes I and II. The detailed study of three TEs (Osvaldo, Helena, and Galileo), representative of the different TE families, shows an increase of transposition in hybrids compared with parental species, that varies depending on the element. This study suggests ample variation in TE regulation mechanisms and the question is why this variation occurs. Interspecific hybridization is a genomic stressor that disrupts the stability of TEs probably contributing to a relaxation of the mechanisms controlling TEs in the Drosophila genome. In this commentary paper we will discuss these results and the molecular mechanisms that could explain these increases of transposition rates observed in interspecific Drosophila hybrids. PMID:25136509

Insertion Sequences

PubMed Central

Mahillon, Jacques; Chandler, Michael

1998-01-01

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 the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

Ovarian preservation with subcutaneous transposition in the setting of cytoreductive surgery

PubMed Central

Tan, Winson Jianhong; Jung, JingJin; Chia, Claramae Shulyn; Teo, Melissa Ching Ching; Toh, Han Chong; Soo, Khee Chee

2013-01-01

INTRODUCTION In recent years, cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) has gained increasing acceptance as a treatment modality for peritoneal carcinomatosis. In female patients, this procedure involves a total hysterectomy and bilateral saphingo-oophorectomy to remove the pelvic peritoneum. We present a case of an unfortunate female adolescent with peritoneal carcinomatosis who underwent cytoreductive surgery and HIPEC. In view of the compelling circumstance, an innovative surgical technique was used to attempt ovarian preservation. PRESENTATION OF CASE A 14 year old girl with carcinoma of the sigmoid colon and peritoneal metastases was offered cytoreductive surgery and hyperthermic intra-peritoneal chemotherapy. In view of her age, ovarian preservation with subcutaneous transposition was performed during cytoreductive surgery. She is currently well 6 months post surgery and has resumed normal menstruation. We review the literature regarding ovarian preservation with subcutaneous transposition and discuss its benefit in pre-menopausal women undergoing peritonectomy and cytoreductive surgery for peritoneal carcinomatosis. DISCUSSION Subcutaneous transposition of the ovary in pre-menopasual patients requiring cytoreductive surgery spares them the sequelae of surgical castration. The subcutaneous location of the transposed ovary conveys advantages such as the ease of ultrasound surveillance and removal in event of disease recurrence. It also retains the possibility of future conception as the transposed ovary can easily be accessed for ovum extraction with assisted reproductive techniques. CONCLUSION Ovarian preservation with subcutaneous transposition is a technique worth considering in the treatment of pre-menopausal women who require cytoreductive surgery for peritoneal carcinomatosis. PMID:23396395

The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster

PubMed Central

Lee, Yuh Chwen G.

2015-01-01

The piwi-interacting RNAs (piRNA) are small RNAs that target selfish transposable elements (TEs) in many animal genomes. Until now, piRNAs’ role in TE population dynamics has only been discussed in the context of their suppression of TE transposition, which alone is not sufficient to account for the skewed frequency spectrum and stable containment of TEs. On the other hand, euchromatic TEs can be epigenetically silenced via piRNA-dependent heterochromatin formation and, similar to the widely known “Position-effect variegation”, heterochromatin induced by TEs can “spread” into nearby genes. We hypothesized that the piRNA-mediated spread of heterochromatin from TEs into adjacent genes has deleterious functional effects and leads to selection against individual TEs. Unlike previously identified deleterious effects of TEs due to the physical disruption of DNA, the functional effect we investigated here is mediated through the epigenetic influences of TEs. We found that the repressive chromatin mark, H3K9me, is elevated in sequences adjacent to euchromatic TEs at multiple developmental stages in Drosophila melanogaster. Furthermore, the heterochromatic states of genes depend not only on the number of and distance from adjacent TEs, but also on the likelihood that their nearest TEs are targeted by piRNAs. These variations in chromatin status probably have functional consequences, causing genes near TEs to have lower expression. Importantly, we found stronger selection against TEs that lead to higher H3K9me enrichment of adjacent genes, demonstrating the pervasive evolutionary consequences of TE-induced epigenetic silencing. Because of the intrinsic biological mechanism of piRNA amplification, spread of TE heterochromatin could result in the theoretically required synergistic deleterious effects of TE insertions for stable containment of TE copy number. The indirect deleterious impact of piRNA-mediated epigenetic silencing of TEs is a previously unexplored, yet important, element for the evolutionary dynamics of TEs. PMID:26042931

Long interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus.

PubMed Central

Lakshmikumaran, M S; D'Ambrosio, E; Laimins, L A; Lin, D T; Furano, A V

1985-01-01

The insulin 1, but not the insulin 2, locus is polymorphic (i.e., exhibits allelic variation) in rats. Restriction enzyme analysis and hybridization studies showed that the polymorphic region is 2.2 kilobases upstream of the insulin 1 coding region and is due to the presence or absence of an approximately 2.7-kilobase repeated DNA element. DNA sequence determination showed that this DNA element is a member of a long interspersed repeated DNA family (LINE) that is highly repeated (greater than 50,000 copies) and highly transcribed in the rat. Although the presence or absence of LINE sequences at the insulin 1 locus occurs in both the homozygous and heterozygous states, LINE-containing insulin 1 alleles are more prevalent in the rat population than are alleles without LINEs. Restriction enzyme analysis of the LINE-containing alleles indicated that at least two versions of the LINE sequence may be present at the insulin 1 locus in different rats. Either repeated transposition of LINE sequences or gene conversion between the resident insulin 1 LINE and other sequences in the genome are possible explanations for this. Images PMID:3016521

Efficient transposition of the retrotransposon Tnt1 in Cucumber (Cucumis sativus L.)

USDA-ARS?s Scientific Manuscript database

The Tnt1 is a type of active DNA retrotransposon originally identified in tobacco. The transposition activity of TNT1 could be activated through tissue culture in other plant species. The insertions of TNT1 in the recipient genome are stable and inheritable in the progeny, which has made it a valuab...

An Evaluation of Frequency Transposition for Hearing-Impaired School-Age Children

ERIC Educational Resources Information Center

Smith, Jenny; Dann, Marilyn; Brown, P. Margaret

2009-01-01

A key objective when fitting hearing aids to children is to maximize the audibility of high frequency speech cues which are critical in the understanding of spoken English. Recent advances in digital signal processing have enabled the development of hearing aids which offer linear frequency transposition as a new way of accessing these important…

The (Homo)Morphism Concept: Didactic Transposition, Meta-Discourse and Thematisation

ERIC Educational Resources Information Center

Hausberger, Thomas

2017-01-01

This article focuses on the didactic transposition of the homomorphism concept and on the elaboration and evaluation of an activity dedicated to the teaching of this fundamental concept in Abstract Algebra. It does not restrict to Group Theory but on the contrary raises the issue of the teaching and learning of algebraic structuralism, thus…

Relational Learning in a Context of Transposition: A Review

ERIC Educational Resources Information Center

Lazareva, Olga F.

2012-01-01

In a typical transposition task, an animal is presented with a single pair of stimuli (for example, S3+S4-, where plus and minus denote reward and nonreward and digits denote stimulus location on a sensory dimension such as size). Subsequently, an animal is presented with a testing pair that contains a previously reinforced or nonreinforced…

Endovascular management of recurrent stenosis following left renal vein transposition for the treatment of Nutcracker syndrome.

PubMed

Baril, Donald T; Polanco, Patricio; Makaroun, Michel S; Chaer, Rabih A

2011-04-01

Nutcracker syndrome is an entity resulting from left renal vein compression by the superior mesenteric artery and the aorta, leading to symptoms of left flank pain and hematuria. Conventional treatment has been surgical, commonly through transposition of the left renal vein to a more caudal location on the inferior vena cava. Additionally, endovascular approaches, primarily via renal vein stenting, have been described for treatment of this syndrome. We report the case of a patient with Nutcracker syndrome who underwent successful left renal vein transposition but then developed recurrent symptoms 10 months postoperatively and was successfully treated with angioplasty and stenting. Copyright © 2011 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

Successful surrogate pregnancy after ovarian transposition, pelvic irradiation and hysterectomy.

PubMed

Zinger, Michael; Liu, James H; Husseinzadeh, Nader; Thomas, Michael A

2004-07-01

Treatment of cervical cancer is often effective but at the cost of the woman's fertility. Ovarian transposition with subsequent oocyte retrieval and surrogate pregnancy can enable these patients to become genetic parents. We present the third reported such case. A 22-year-old woman was diagnosed with bulky, stage IB cervical cancer. Following transposition of both ovaries to the upper abdomen, she underwent pelvic irradiation followed by total abdominal hysterectomy. Eleven years later she presented for assisted reproduction. Two oocytes were retrieved following ovarian stimulation and transcutaneous, abdominal oocyte retrieval. One embryo was transferred to the gestational surrogate, resulting in a single intrauterine pregnancy and successful delivery at term. These procedures can preservefertility while successfully treating cervical cancer.

Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haberle, Rosemarie C.; Fourcade, Matthew L.; Boore, Jeffrey L.

2006-01-09

Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (psbJ) duplicated twice, for a total of 137 genes.Four genes (ycf15, rpl23, infA and accD) are truncated and likelynonfunctional; three others (clpP, ycf1 andmore » ycf2) are so highly divergedthat they may now be pseudogenes. The most conspicuous feature of theTrachelium genome is the presence of eighteen internally unrearrangedblocks of genes that have been inverted or relocated within the genome,relative to the typical gene order of most angiosperm chloroplastgenomes. Recombination between repeats or tRNAs has been suggested as twomeans of chloroplast genome rearrangements. We compared the relativenumber of repeats in Trachelium to eight other angiosperm chloroplastgenomes, and evaluated the location of repeats and tRNAs in relation torearrangements. Trachelium has the highest number and largest repeats,which are concentrated near inversion endpoints or other rearrangements.tRNAs occur at many but not all inversion endpoints. There is likely nosingle mechanism responsible for the remarkable number of alterations inthis genome, but both repeats and tRNAs are clearly associated with theserearrangements. Land plant chloroplast genomes are highly conserved instructure, gene order and content. The chloroplast genomes of ferns, thegymnosperm Ginkgo, and most angiosperms are nearly collinear, reflectingthe gene order in lineages that diverged from lycopsids and the ancestralchloroplast gene order over 350 million years ago (Raubeson and Jansen,1992). Although earlier mapping studies identified a number of taxa inwhich several rearrangements have occurred (reviewed in Raubeson andJansen, 2005), an extraordinary number of chloroplast genome alterationsare concentrated in several families in the angiosperm order Asterales(sensu APGII, Bremer et al., 2003). Gene mapping studies ofrepresentatives of the Campanulaceae (Cosner, 1993; Cosner et al.,1997,2004) and Lobeliaceae (Knox et al., 1993; Knox and Palmer, 1999)identified large inversions, contraction and expansion of the invertedrepeat regions, and several insertions and deletions in the cpDNAs ofthese closely related taxa. Detailed restriction site and gene mapping ofthe chloroplast genome of Trachelium caeruleum (Campanulaceae) identifiedseven to ten large inversions, families of repeats associated withrearrangements, possible transpositions, and even the disruption ofoperons (Cosner et al., 1997). Seventeen other members of theCampanulaceae were mapped and exhibit many additional rearrangements(Cosner et al., 2004). What happened in this lineage that made itsusceptible to so many chloroplast genome rearrangements? How do normallyvery conserved chloroplast genomes change? The cause of rearrangements inthis group is unclear based on the limited resolution available withmapping techniques. Several mechanisms have been proposed to explain howrearrangements occur: recombination between repeats, transposition, ortemporary instability due to loss of the inverted repeat (Raubeson andJansen, 2005). Sequencing whole chloroplast genomes within theCampanulaceae offers a unique opportunity to examine both the extent andmechanisms of rearrangements within a phylogenetic framework.We reporthere the first complete chloroplast genome sequence of a member of theCampanulaceae, Trachelium caeruleum. This work will serve as a benchmarkfor subsequent, comparative sequencing and analysis of other members ofthis family and close relatives, with the goal of further understandingchloroplast genome evolution. We confirmed features previously identifiedthrough mapping, and discovered many additional structural changes,including several partial to entire gene duplications, deterioration ofat least four normally conserved chloroplast genes into gene fragments,and the nature and position of numerous repeat elements at or nearinversion endpoints. The focus of this paper is on analyses of sequencesat or near these rearrangements in Trachelium caeruleum. Inversions arebelieved to occur due to the presence of repeat elements subject tohomologous recombination (Palmer, 1991; Knox et al., 1993). Repeats mayfacilitate inversions or other genome rearrangements (Achaz et al.,2003), and higher incidences of repeats have been correlated with greaternumbers of rearrangements (Rocha, 2003). Alternatively, repeats mayproliferate within a genome asa result of DNA strand repair mechanismsfollowing a rearrangement event such as an inversion. Gene« less

Genome evolution and speciation genetics of clawed frogs (Xenopus and Silurana).

PubMed

Evans, Ben J

2008-05-01

Speciation of clawed frogs occurred through bifurcation and reticulation of evolutionary lineages, and resulted in extant species with different ploidy levels. Duplicate gene evolution and expression in these animals provides a unique perspective into the earliest genomic transformations after vertebrate whole genome duplication (WGD) and suggests that functional constraints are relaxed compared to before duplication but still consistently strong for millions of years following WGD. Additionally, extensive quantitative expression divergence between duplicate genes occurred after WGD. Diversification of clawed frogs was potentially catalyzed by transposition and divergent resolution--processes that occur through different genetic mechanisms but that have analogous implications for genome structure. How sex determination is maintained after genome duplication is fundamental to our understanding of why allopolyploidization is so prevalent in this group, and why clawed frogs violate Haldane's Rule for hybrid sterility. Future studies of expression subfunctionalization in polyploids will shed light on the role and purviews of cis- and trans-regulatory elements in gene regulation.

The Genetics of a Small Chromosome Region of DROSOPHILA MELANOGASTER Containing the Structural Gene for Alcohol Dehydrogenase. IV: Scutoid, an Antimorphic Mutation

PubMed Central

Ashburner, M.; Tsubota, S.; Woodruff, R. C.

1982-01-01

Exchange mapping locates the dominant mutation Scutoid to the right of Adh on chromosome arm 2L of D. melanogaster. However, deletion mapping indicates that Sco is to the left of Adh. The phenotype of Sco is sensitive to mutation, or deletion, of noc+ and of three genes, el, l(2)br22, and l(2)br29 mapping immediately distal to noc. The four contiguous loci, el, l(2)br22, l(2)br29 and noc, although separable by deletion end points, interact, because certain (or all) alleles of these four loci show partial failure of complementation, or even negative complementation. The simplest hypothesis is that Sco is a small reciprocal transposition, the genes noc, osp, and Adh exchanging places with three genes normally mapping proximal to them: l(2)br34, l(2)br35 and rd. The Sco phenotype is thought to result from a position effect at the newly created noc/l(2)br28 junction. PMID:6816673

Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution.

PubMed

Quraishi, Umar Masood; Abrouk, Michael; Murat, Florent; Pont, Caroline; Foucrier, Séverine; Desmaizieres, Gregory; Confolent, Carole; Rivière, Nathalie; Charmet, Gilles; Paux, Etienne; Murigneux, Alain; Guerreiro, Laurent; Lafarge, Stéphane; Le Gouis, Jacques; Feuillet, Catherine; Salse, Jerome

2011-03-01

Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Association between the location of transposed ovary and ovarian function in patients with uterine cervical cancer treated with (postoperative or primary) pelvic radiotherapy.

PubMed

Hwang, Jong Ha; Yoo, Heon Jong; Park, Sae Hyun; Lim, Myong Cheol; Seo, Sang-Soo; Kang, Sokbom; Kim, Joo-Young; Park, Sang-Yoon

2012-06-01

To evaluate the effectiveness of ovarian transposition procedures in preserving ovarian function in relation to the location of the transposed ovaries in patients who underwent surgery with or without pelvic radiotherapy. Retrospective. Uterine cancer center. A total of 53 patients with cervical cancer who underwent ovarian transposition between November 2002 and November 2010. Ovarian transposition to the paracolic gutters with or without radical hysterectomy and lymph node dissection. Preservation of ovarian function, which was assessed by patient's symptoms and serum FSH level. Lateral ovarian transposition was performed in 53 patients. Based on receiver operator characteristic curve analysis, optimum cutoff value of location more than 1.5 cm above the iliac crest was significantly associated with preservation of ovarian function after treatment (area under receiver operator characteristic curve: 0.757, 95% confidence interval [CI]: 0.572-0.943). In univariate analysis, higher location of transposed ovary more than 1.5 cm from the iliac crest was the only independent factor for intact ovarian function (odds ratio 9.91, 95% CI: 1.75-56.3). Multivariate analysis confirmed that the location of transposed ovary (odds ratio 11.72, 95% CI 1.64-83.39) was the most important factor for intact ovarian function. Location of transposed ovary higher than 1.5 cm above the iliac crest is recommended to avoid ovarian failure after lateral ovarian transposition after primary or adjuvant pelvic radiotherapy in cervical cancer. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Auditory Proprioceptive Integration: Effects of Real-Time Kinematic Auditory Feedback on Knee Proprioception

PubMed Central

Ghai, Shashank; Schmitz, Gerd; Hwang, Tong-Hun; Effenberg, Alfred O.

2018-01-01

The purpose of the study was to assess the influence of real-time auditory feedback on knee proprioception. Thirty healthy participants were randomly allocated to control (n = 15), and experimental group I (15). The participants performed an active knee-repositioning task using their dominant leg, with/without additional real-time auditory feedback where the frequency was mapped in a convergent manner to two different target angles (40 and 75°). Statistical analysis revealed significant enhancement in knee re-positioning accuracy for the constant and absolute error with real-time auditory feedback, within and across the groups. Besides this convergent condition, we established a second divergent condition. Here, a step-wise transposition of frequency was performed to explore whether a systematic tuning between auditory-proprioceptive repositioning exists. No significant effects were identified in this divergent auditory feedback condition. An additional experimental group II (n = 20) was further included. Here, we investigated the influence of a larger magnitude and directional change of step-wise transposition of the frequency. In a first step, results confirm the findings of experiment I. Moreover, significant effects on knee auditory-proprioception repositioning were evident when divergent auditory feedback was applied. During the step-wise transposition participants showed systematic modulation of knee movements in the opposite direction of transposition. We confirm that knee re-positioning accuracy can be enhanced with concurrent application of real-time auditory feedback and that knee re-positioning can modulated in a goal-directed manner with step-wise transposition of frequency. Clinical implications are discussed with respect to joint position sense in rehabilitation settings. PMID:29568259

Tilt to horizontal global solar irradiance conversion: application to PV systems data

NASA Astrophysics Data System (ADS)

Housmans, Caroline; Leloux, Jonathan; Bertrand, Cédric

2017-04-01

Many transposition models have been proposed in the literature to convert solar irradiance on the horizontal plane to that on a tilted plane requiring that at least two of the three solar components (i.e. global, direct and diffuse) are known. When only global irradiance measurements are available, the conversion from horizontal to tilted planes is still possible but in this case transposition models have to be coupled with decomposition models (i.e. models that predict the direct and diffuse components from the global one). Here, two different approaches have been considered to solve the reverse process, i.e. the conversion from tilted to horizontal: (i) one-sensor approach and (ii) multi-sensors approach. Because only one tilted plane is involved in the one-sensor approach, a decomposition model need to be coupled with a transposition model to solve the problem. By contrast, at least two tilted planes being considered in the multi-sensors approach, only a transposition model is required to perform the conversion. First, global solar irradiance measurements recorded on the roof of the Royal Meteorological Institute of Belgium's radiation tower in Uccle were used to evaluate the performance of both approaches. Four pyranometers (one mounted in the horizontal plane and three on inclined surfaces with different tilts and orientations) were involved in the validation exercise. Second, the inverse transposition was applied to tilted global solar irradiance values retrieved from the energy production registered at residential PV systems located in the vicinity of Belgian radiometric stations operated by RMI (for validation purposes).

A Review of the Surgical Management of Perineal Hernias in Dogs.

PubMed

Gill, Sukhjit Singh; Barstad, Robert D

2018-05-14

Perineal hernia refers to the failure of the muscular pelvic diaphragm to support the rectal wall, resulting in herniation of pelvic and, occasionally, abdominal viscera into the subcutaneous perineal region. The proposed causes of pelvic diaphragm weakness include tenesmus associated with chronic prostatic disease or constipation, myopathy, rectal abnormalities, and gonadal hormonal imbalances. The most common presentation of perineal hernia in dogs is a unilateral or bilateral nonpainful swelling of the perineum. Clinical signs do occur, but not always. Clinical signs may include constipation, obstipation, dyschezia, tenesmus, rectal prolapse, stranguria, or anuria. The definitive diagnosis of perineal hernia is based on clinical signs and findings of weak pelvic diaphragm musculature during a digital rectal examination. In dogs, perineal hernias are mostly treated by surgical intervention. Appositional herniorrhaphy is sometimes difficult to perform as the levator ani and coccygeus muscles are atrophied and unsuitable for use. Internal obturator muscle transposition is the most commonly used technique. Additional techniques include superficial gluteal and semitendinosus muscle transposition, in addition to the use of synthetic implants and biomaterials. Pexy techniques may be used to prevent rectal prolapse and bladder and prostate gland displacement. Postoperative care involves analgesics, antibiotics, a low-residue diet, and stool softeners.

A Didactic Sequence of Elementary Geometric Optics Informed by History and Philosophy of Science

ERIC Educational Resources Information Center

Maurício, Paulo; Valente, Bianor; Chagas, Isabel

2017-01-01

The concepts and instruments required for the teaching and learning of geometric optics are introduced in the didactic process without a proper didactic transposition. This claim is secured by the ample evidence of both wide- and deep-rooted alternative concepts on the topic. Didactic transposition is a theory that comes from a reflection on the…

Debating trans inclusion in the feminist movement: a trans-positive analysis.

PubMed

Green, Eli R

2006-01-01

The debate over whether or not to allow, accept, and embrace transpeople as a segment of the feminist movement has been a tumultuous one that remains unresolved. Prominent authors have argued both sides of the dispute. This article analyzes the anti-inclusion feminist viewpoint and offers a trans-positive perspective for moving toward a potential resolution of the debate.

The Differential Use of Bilobed and Trilobed Transposition Flaps in Cutaneous Nasal Reconstructive Surgery.

PubMed

Knackstedt, Thomas; Lee, Kachiu; Jellinek, Nathaniel J

2018-05-22

Bilobed and trilobed transposition flaps are versatile random pattern transposition flaps which reliably restore nasal symmetry, topography, light reflex, contour and are frequently used in cutaneous nasal reconstructive surgery. We wish to compare the characteristics of bilobed and trilobed flaps in cutaneous reconstructive surgery and to identify scenarios for their differential use. A retrospective chart review over 7 years of consecutive patients reconstructed with a bilobed or trilobed flap after Mohs micrographic surgery was performed. Statistical analysis of patient and surgery characteristics, anatomic distribution, postprocedural events and need for revisions after both flap types was conducted. One hundred eleven patients with bilobed flaps and 74 patients with trilobed flaps were identified. Bilobed flaps are significantly more frequently used on the inferior nasal dorsum and on the sidewall whereas trilobed flaps are significantly more frequently used on the nasal tip and infratip. No significant difference in postprocedural events (complications, erythema, trapdoor, etc) was noted between the two flap types. Bilobed and trilobed transposition flaps are versatile repairs for nasal reconstruction. Trilobed flaps may be used to repair defects in a more distal nasal location than bilobed flaps. Regardless of flap type, complications are rare.

[Transposition of the cephalic vein in free flap breast reconstruction: Technical note].

PubMed

Silhol, T; Suffee, T; Hivelin, M; Lantieri, L

2018-02-01

Free flaps have become a reliable practice for breast reconstruction. However, the venous congestion is still the most frequent reason of flap failure. It is due to bad quality of the internal mammary veins, a preferential superficial venous outflow of the flap or due to venous thrombosis. The transposition of the cephalic vein could useful in some cases. We describe the surgical technique and suggest an intraoperative algorithm. Seventeen patients (15 DIEP and 2 PAP) were included. Twenty nine point four percent had an unusable internal mammary vein, 23.5% a preferential superficial venous outflow and 47.1% a venous thrombosis. The length of the cephalic vein dissected varied from 15 to 25cm. The mean time of dissection was 39min. There was no flap failure after cephalic vein transposition. The sequelae were one or two scars on the arm without any functional morbidity. The transposition of the cephalic vein is a reliable, less morbid alternative in case of bad quality internal mammary vein with a good quality internal mammary artery, in case of an additional venous outflow necessity or in case of venous thrombosis. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

MaRGEE: Move and Rotate Google Earth Elements

NASA Astrophysics Data System (ADS)

Dordevic, Mladen M.; Whitmeyer, Steven J.

2015-12-01

Google Earth is recognized as a highly effective visualization tool for geospatial information. However, there remain serious limitations that have hindered its acceptance as a tool for research and education in the geosciences. One significant limitation is the inability to translate or rotate geometrical elements on the Google Earth virtual globe. Here we present a new JavaScript web application to "Move and Rotate Google Earth Elements" (MaRGEE). MaRGEE includes tools to simplify, translate, and rotate elements, add intermediate steps to a transposition, and batch process multiple transpositions. The transposition algorithm uses spherical geometry calculations, such as the haversine formula, to accurately reposition groups of points, paths, and polygons on the Google Earth globe without distortion. Due to the imminent deprecation of the Google Earth API and browser plugin, MaRGEE uses a Google Maps interface to facilitate and illustrate the transpositions. However, the inherent spatial distortions that result from the Google Maps Web Mercator projection are not apparent once the transposed elements are saved as a KML file and opened in Google Earth. Potential applications of the MaRGEE toolkit include tectonic reconstructions, the movements of glaciers or thrust sheets, and time-based animations of other large- and small-scale geologic processes.

The impact of dissociation on transposon-mediated disease control strategies.

PubMed

Marshall, John M

2008-03-01

Vector-borne diseases such as malaria and dengue fever continue to be a major health concern through much of the world. The emergence of chloroquine-resistant strains of malaria and insecticide-resistant mosquitoes emphasize the need for novel methods of disease control. Recently, there has been much interest in the use of transposable elements to drive resistance genes into vector populations as a means of disease control. One concern that must be addressed before a release is performed is the potential loss of linkage between a transposable element and a resistance gene. Transposable elements such as P and hobo have been shown to produce internal deletion derivatives at a significant rate, and there is concern that a similar process could lead to loss of the resistance gene from the drive system following a transgenic release. Additionally, transposable elements such as Himar1 have been shown to transpose significantly more frequently when free of exogenous DNA. Here, we show that any transposon-mediated gene drive strategy must have an exceptionally low rate of dissociation if it is to be effective. Additionally, the resistance gene must confer a large selective advantage to the vector to surmount the effects of a moderate dissociation rate and transpositional handicap.

Successful Gene Tagging in Lettuce Using the Tnt1 Retrotransposon from Tobacco

PubMed Central

Mazier, Marianne; Botton, Emmanuel; Flamain, Fabrice; Bouchet, Jean-Paul; Courtial, Béatrice; Chupeau, Marie-Christine; Chupeau, Yves; Maisonneuve, Brigitte; Lucas, Hélène

2007-01-01

The tobacco (Nicotiana tabacum) element Tnt1 is one of the few identified active retrotransposons in plants. These elements possess unique properties that make them ideal genetic tools for gene tagging. Here, we demonstrate the feasibility of gene tagging using the retrotransposon Tnt1 in lettuce (Lactuca sativa), which is the largest genome tested for retrotransposon mutagenesis so far. Of 10 different transgenic bushes carrying a complete Tnt1 containing T-DNA, eight contained multiple transposed copies of Tnt1. The number of transposed copies of the element per plant was particularly high, the smallest number being 28. Tnt1 transposition in lettuce can be induced by a very simple in vitro culture protocol. Tnt1 insertions were stable in the progeny of the primary transformants and could be segregated genetically. Characterization of the sequences flanking some insertion sites revealed that Tnt1 often inserted into genes. The progeny of some primary transformants showed phenotypic alterations due to recessive mutations. One of these mutations was due to Tnt1 insertion in the gibberellin 3β-hydroxylase gene. Taken together, these results indicate that Tnt1 is a powerful tool for insertion mutagenesis especially in plants with a large genome. PMID:17351058

The dorsal transposition flap for congenital contractures of the first web space: a 20-year experience.

PubMed

Friedman, R; Wood, V E

1997-07-01

Fifty-four dorsal transposition flaps were performed in 38 patients (46 hands) for severe congenital thumb web-space contractures. At an average follow-up interval of 6 years, complications or unsatisfactory results had occurred in 100% of symbrachydactyly patients and in 27% of all other patients. Postoperative first web-space angle was augmented an average of 59 degrees with a distal flap two-point discrimination of 8 mm. Mean postoperative pinch and grip strengths were 58% and 72%, respectively, of the normal contralateral hand. Parental satisfaction with the functional results was high, and the aesthetic results were generally acceptable. With the exception of symbrachydactyly patients, the dorsal transposition flap remains an excellent reconstructive option for severe congenital contractures of the thumb web space.

Inadvertent transposition of defibrillator coil terminal pins causing inappropriate ICD therapies.

PubMed

Issa, Ziad F

2008-06-01

We report the case of a 65-year-old man with chronic atrial fibrillation (AF) and severe ischemic cardiomyopathy who underwent implantation of a prophylactic single-chamber implantable cardioverter-defibrillator (ICD). The patient experienced inappropriate ICD therapies due to oversensing of pectoral muscle myopotential secondary to reversal of the defibrillator coil terminal pins in the ICD header. Recognizing this possibility is important to avoid misinterpretation of spontaneous oversensing as hardware failure (e.g., lead fracture or insulation breech) and potentially unnecessary ICD system surgical intervention, including lead extraction.

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beller, H.R.; Legler, T.C.; Kane, S.R.

2011-07-15

Chemolithoautotrophic bacteria can be of industrial and environmental importance, but they present a challenge for systems biology studies, as their central metabolism deviates from that of model organisms and there is a much less extensive experimental basis for their gene annotation than for typical organoheterotrophs. For microbes with sequenced genomes but unconventional metabolism, the ability to create knockout mutations can be a powerful tool for functional genomics and thereby render an organism more amenable to systems biology approaches. In this chapter, we describe a genetic system for Thiobacillus denitrificans, with which insertion mutations can be introduced by homologous recombination andmore » complemented in trans. Insertion mutations are generated by in vitro transposition, the mutated genes are amplified by the PCR, and the amplicons are introduced into T. denitrificans by electroporation. Use of a complementation vector, pTL2, based on the IncP plasmid pRR10 is also addressed.« less

Altruistic functions for selfish DNA.

PubMed

Faulkner, Geoffrey J; Carninci, Piero

2009-09-15

Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this "selfish DNA" or "junk DNA" dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo.

Gastric transposition in infants and children.

PubMed

Cowles, Robert A; Coran, Arnold G

2010-12-01

The loss of esophageal length in long-gap esophageal atresia or obliteration of the esophageal lumen due to stricture may require major operative reconstruction. A number of procedures have been developed to allow anatomic replacement of the esophagus. The gastric transposition requires a single cervical anastomosis and uses a gastric conduit with excellent blood supply. This review illustrates the procedure and discusses its indications, planning, and outcome.

Improving the accuracy of flood forecasting with transpositions of ensemble NWP rainfall fields considering orographic effects

NASA Astrophysics Data System (ADS)

Yu, Wansik; Nakakita, Eiichi; Kim, Sunmin; Yamaguchi, Kosei

2016-08-01

The use of meteorological ensembles to produce sets of hydrological predictions increased the capability to issue flood warnings. However, space scale of the hydrological domain is still much finer than meteorological model, and NWP models have challenges with displacement. The main objective of this study to enhance the transposition method proposed in Yu et al. (2014) and to suggest the post-processing ensemble flood forecasting method for the real-time updating and the accuracy improvement of flood forecasts that considers the separation of the orographic rainfall and the correction of misplaced rain distributions using additional ensemble information through the transposition of rain distributions. In the first step of the proposed method, ensemble forecast rainfalls from a numerical weather prediction (NWP) model are separated into orographic and non-orographic rainfall fields using atmospheric variables and the extraction of topographic effect. Then the non-orographic rainfall fields are examined by the transposition scheme to produce additional ensemble information and new ensemble NWP rainfall fields are calculated by recombining the transposition results of non-orographic rain fields with separated orographic rainfall fields for a generation of place-corrected ensemble information. Then, the additional ensemble information is applied into a hydrologic model for post-flood forecasting with a 6-h interval. The newly proposed method has a clear advantage to improve the accuracy of mean value of ensemble flood forecasting. Our study is carried out and verified using the largest flood event by typhoon 'Talas' of 2011 over the two catchments, which are Futatsuno (356.1 km2) and Nanairo (182.1 km2) dam catchments of Shingu river basin (2360 km2), which is located in the Kii peninsula, Japan.

Comparison of hemihypoglossal nerve versus masseteric nerve transpositions in the rehabilitation of short-term facial paralysis using the Facial Clima evaluating system.

PubMed

Hontanilla, Bernardo; Marré, Diego

2012-11-01

Masseteric and hypoglossal nerve transfers are reliable alternatives for reanimating short-term facial paralysis. To date, few studies exist in the literature comparing these techniques. This work presents a quantitative comparison of masseter-facial transposition versus hemihypoglossal facial transposition with a nerve graft using the Facial Clima system. Forty-six patients with complete unilateral facial paralysis underwent reanimation with either hemihypoglossal transposition with a nerve graft (group I, n = 25) or direct masseteric-facial coaptation (group II, n = 21). Commissural displacement and commissural contraction velocity were measured using the Facial Clima system. Postoperative intragroup commissural displacement and commissural contraction velocity means of the reanimated versus the normal side were first compared using a paired sample t test. Then, mean percentages of recovery of both parameters were compared between the groups using an independent sample t test. Onset of movement was also compared between the groups. Significant differences of mean commissural displacement and commissural contraction velocity between the reanimated side and the normal side were observed in group I but not in group II. Mean percentage of recovery of both parameters did not differ between the groups. Patients in group II showed a significantly faster onset of movement compared with those in group I (62 ± 4.6 days versus 136 ± 7.4 days, p = 0.013). Reanimation of short-term facial paralysis can be satisfactorily addressed by means of either hemihypoglossal transposition with a nerve graft or direct masseteric-facial coaptation. However, with the latter, better symmetry and a faster onset of movement are observed. In addition, masseteric nerve transfer avoids morbidity from nerve graft harvesting. Therapeutic, III.

nanos-Driven expression of piggyBac transposase induces mobilization of a synthetic autonomous transposon in the malaria vector mosquito, Anopheles stephensi.

PubMed

Macias, Vanessa M; Jimenez, Alyssa J; Burini-Kojin, Bianca; Pledger, David; Jasinskiene, Nijole; Phong, Celine Hien; Chu, Karen; Fazekas, Aniko; Martin, Kelcie; Marinotti, Osvaldo; James, Anthony A

2017-08-01

Transposons are a class of selfish DNA elements that can mobilize within a genome. If mobilization is accompanied by an increase in copy number (replicative transposition), the transposon may sweep through a population until it is fixed in all of its interbreeding members. This introgression has been proposed as the basis for drive systems to move genes with desirable phenotypes into target species. One such application would be to use them to move a gene conferring resistance to malaria parasites throughout a population of vector mosquitos. We assessed the feasibility of using the piggyBac transposon as a gene-drive mechanism to distribute anti-malarial transgenes in populations of the malaria vector, Anopheles stephensi. We designed synthetic gene constructs that express the piggyBac transposase in the female germline using the control DNA of the An. stephensi nanos orthologous gene linked to marker genes to monitor inheritance. Two remobilization events were observed with a frequency of one every 23 generations, a rate far below what would be useful to drive anti-pathogen transgenes into wild mosquito populations. We discuss the possibility of optimizing this system and the impetus to do so. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Antioxidant, antimutagenic, and anticarcinogenic effects of Papaver rhoeas L. extract on Saccharomyces cerevisiae.

PubMed

Todorova, Teodora; Pesheva, Margarita; Gregan, Fridrich; Chankova, Stephka

2015-04-01

The aim of this work was to analyze the antioxidant and antimutagenic/anticarcinogenic capacity of Papaver rhoeas L. water extract against standard mutagen/carcinogen methyl methanesulfonate (MMS) and radiomimetic zeocin (Zeo) on a test system Saccharomyces cerevisiae. The following assays were used: 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, quantitative determination of superoxide anion (antireactive oxygen species [antiROS test]), DNA topology assay, D7ts1 test--for antimutagenic--and Ty1 transposition test--for anticarcinogenic effects. Strong pro-oxidative capacity of Zeo was shown to correlate with its well-expressed mutagenic and carcinogenic properties. The mutagenic and carcinogenic effects of MMS were also confirmed. Our data concerning the antioxidant activity of P. rhoeas L. extract revealed that concentration corresponding to IC(50) in the DPPH assay possessed the highest antioxidant activity in the antiROS biological assay. It was also observed that a concentration with 50% scavenging activity expressed the most pronounced antimutagenic properties decreasing Zeo-induced gene conversion twofold, reverse mutation fivefold, and total aberrations fourfold. The same concentration possessed well-expressed anticarcinogenic properties measured as reduction of MMS-induced Ty1 transposition rate fivefold and fourfold when Zeo was used as an inductor. Based on the well-expressed antioxidant, antimutagenic, and anticarcinogenic properties obtained in this work, the P. rhoeas L. extract could be recommended for further investigations and possible use as a food additive.

Assessing Tn5 and Sleeping Beauty for transpositional transgenesis by cytoplasmic injection into bovine and ovine zygotes

PubMed Central

Bevacqua, R. J.; Fernandez-Martin, R.; Canel, N. G.; Gibbons, A.; Texeira, D.; Lange, F.; Vans Landschoot, G.; Savy, V.; Briski, O.; Hiriart, M. I.; Grueso, E.; Ivics, Z.; Taboga, O.; Kues, W. A.; Ferraris, S.

2017-01-01

Transgenic domestic animals represent an alternative to bioreactors for large-scale production of biopharmaceuticals and could also provide more accurate biomedical models than rodents. However, their generation remains inefficient. Recently, DNA transposons allowed improved transgenesis efficiencies in mice and pigs. In this work, Tn5 and Sleeping Beauty (SB) transposon systems were evaluated for transgenesis by simple cytoplasmic injection in livestock zygotes. In the case of Tn5, the transposome complex of transposon nucleic acid and Tn5 protein was injected. In the case of SB, the supercoiled plasmids encoding a transposon and the SB transposase were co-injected. In vitro produced bovine zygotes were used to establish the cytoplasmic injection conditions. The in vitro cultured blastocysts were evaluated for reporter gene expression and genotyped. Subsequently, both transposon systems were injected in seasonally available ovine zygotes, employing transposons carrying the recombinant human factor IX driven by the beta-lactoglobulin promoter. The Tn5 approach did not result in transgenic lambs. In contrast, the Sleeping Beauty injection resulted in 2 lambs (29%) carrying the transgene. Both animals exhibited cellular mosaicism of the transgene. The extraembryonic tissues (placenta or umbilical cord) of three additional animals were also transgenic. These results show that transpositional transgenesis by cytoplasmic injection of SB transposon components can be applied for the production of transgenic lambs of pharmaceutical interest. PMID:28301581

Transposition of Francis turbine cavitation compliance at partial load to different operating conditions

NASA Astrophysics Data System (ADS)

Gomes, J.; Favrel, A.; Landry, C.; Nicolet, C.; Avellan, F.

2017-04-01

Francis turbines operating in part load conditions experience a swirling flow at the runner outlet leading to the development of a precessing cavitation vortex rope in the draft tube. This cavitation vortex rope changes drastically the velocity of pressure waves traveling in the draft tube and may lead to resonance conditions in the hydraulic circuit. The wave speed being strongly related to the cavitation compliance, this research work presents a simple model to explain how it is affected by variations of operating conditions and proposes a method to transpose its values. Even though the focus of this paper is on transpositions within the same turbine scale, the methodology is also expected to be tested for the model to prototype transposition in the future. Comparisons between measurements and calculations are in good agreement.

Imprinted genes and transpositions: epigenomic targets for low dose radiation effects. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jirtle, Randy L.

2012-10-11

The overall hypothesis of this grant application is that low dose ionizing radiation (LDIR) elicits adaptive responses in part by causing heritable DNA methylation changes in the epigenome. This novel postulate was tested by determining if the level of DNA methylation at the Agouti viable yellow (A{sup vy}) metastable locus is altered, in a dose-dependent manner, by low dose radiation exposure (<10 cGy) during early gestation. This information is particularly important to ascertain given the increased use of CT scans in disease diagnosis, increased number of people predicted to live and work in space, and the present concern about radiologicalmore » terrorism. We showed for the first time that LDIR significantly increased DNA methylation at the A{sup vy} locus in a sex-specific manner (p=0.004). Average DNA methylation was significantly increased in male offspring exposed to doses between 0.7 cGy and 7.6 cGy with maximum effects at 1.4 cGy and 3.0 cGy (p<0.01). Offspring coat color was concomitantly shifted towards pseudoagouti (p<0.01). Maternal dietary antioxidant supplementation mitigated both the DNA methylation changes and coat color shift in the irradiated offspring (p<0.05). Thus, LDIR exposure during gestation elicits epigenetic alterations that lead to positive adaptive phenotypic changes that are negated with antioxidants, indicating they are mediated in part by oxidative stress. These findings provide evidence that in the isogenic Avy mouse model epigenetic alterations resulting from LDIR play a role in radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. Our findings not only have significant implications concerning the mechanism of hormesis, but they also emphasize the potential importance of this phenomenon in determining human risk at low radiation doses. Since the epigenetic regulation of genes varies markedly between species, the effect of LDIR on other epigenetically labile genes (e.g. imprinted genes) in animals and humans needs to be defined.« less

Executive Function and Theory of Mind in School-Aged Children after Neonatal Corrective Cardiac Surgery for Transposition of the Great Arteries

ERIC Educational Resources Information Center

Calderon, Johanna; Bonnet, Damien; Courtin, Cyril; Concordet, Susan; Plumet, Marie-Helene; Angeard, Nathalie

2010-01-01

Aim: Cardiac malformations resulting in cyanosis, such as transposition of the great arteries (TGA), have been associated with neurodevelopmental dysfunction. The purpose of this study was to assess, for the first time, theory of mind (ToM), which is a key component of social cognition and executive functions in school-aged children with TGA.…

Novel Biliary Reconstruction Techniques During Liver Transplantation

PubMed Central

Carmody, Ian C.; Romano, John; Bohorquez, Humberto; Bugeaud, Emily; Bruce, David S.; Cohen, Ari J.; Seal, John; Reichman, Trevor W.; Loss, George E.

2017-01-01

Background: Biliary complications remain a significant problem following liver transplantation. Several surgical options can be used to deal with a significant size mismatch between the donor and recipient bile ducts during the biliary anastomosis. We compared biliary transposition to recipient biliary ductoplasty in cadaveric liver transplant. Methods: A total of 33 reconstructions were performed from January 1, 2005 to December 31, 2013. In the biliary transposition group (n=23), 5 reconstructions were performed using an internal stent (5 or 8 French pediatric feeding tube), and 18 were performed without. Of the 10 biliary ductoplasties, 2 were performed with a stent. All patients were managed with standard immunosuppression and ursodiol. Follow-up ranged from 2 months to 5 years. Results: No patients in the biliary transposition group required reoperation; 1 patient had an internal stent removed for recurrent unexplained leukocytosis, and 2 patients required endoscopic retrograde cholangiography and stent placement for evidence of stricture. Three anastomotic leaks occurred in the biliary ductoplasty group, and 2 patients in the biliary ductoplasty group required reoperation for biliary complications. Conclusion: Our results indicate that biliary reconstruction can be performed with either biliary transposition or biliary ductoplasty. These techniques are particularly useful when a significant mismatch in diameter exists between the donor and recipient bile ducts. PMID:28331447

A nucleolus-predominant piggyBac transposase, NP-mPB, mediates elevated transposition efficiency in mammalian cells.

PubMed

Hong, Jin-Bon; Chou, Fu-Ju; Ku, Amy T; Fan, Hsiang-Hsuan; Lee, Tung-Lung; Huang, Yung-Hsin; Yang, Tsung-Lin; Su, I-Chang; Yu, I-Shing; Lin, Shu-Wha; Chien, Chung-Liang; Ho, Hong-Nerng; Chen, You-Tzung

2014-01-01

PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase) codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP) signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB). Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3-4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells.

Unilateral endonasal transcribriform approach with septal transposition for olfactory groove meningioma: can olfaction be preserved?

PubMed

Youssef, A Samy; Sampath, Raghuram; Freeman, Jacob L; Mattingly, Jameson K; Ramakrishnan, Vijay R

2016-10-01

Loss of olfaction has been considered inevitable in endoscopic endonasal resection of olfactory groove meningiomas. Olfaction preservation may be feasible through an endonasal unilateral transcribriform approach, with the option for expansion using septal transposition and contralateral preservation of the olfactory apparatus. An expanded unilateral endonasal transcribriform approach with septal transposition was performed in five cadaver heads. The approach was applied in a surgical case of a 24 × 26-mm olfactory groove meningioma originating from the right cribriform plate with partially intact olfaction. The surgical approach offered adequate exposure to the anterior skull base bilaterally. The nasal/septal mucosa was preserved on the contralateral side. Gross total resection of the meningioma was achieved with the successful preservation of the contralateral olfactory apparatus and preoperative olfaction. Six months later, the left nasal cavity showed no disruption of the mucosal lining and the right side was at the appropriate stage of healing for a harvested nasoseptal flap. One year later, the preoperative olfactory function was intact and favorably viewed by the patient. Objective testing of olfaction showed microsomia. Olfaction preservation may be feasible in the endoscopic endonasal resection of a unilateral olfactory groove meningioma through a unilateral transcribriform approach with septal transposition and preservation of the contralateral olfactory apparatus.

TED, an Autonomous and Rare Maize Transposon of the Mutator Superfamily with a High Gametophytic Excision Frequency[W

PubMed Central

Li, Yubin; Harris, Linda; Dooner, Hugo K.

2013-01-01

Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor. PMID:24038653

TED, an autonomous and rare maize transposon of the mutator superfamily with a high gametophytic excision frequency.

PubMed

Li, Yubin; Harris, Linda; Dooner, Hugo K

2013-09-01

Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor.

Active Transposition in Genomes

PubMed Central

Huang, Cheng Ran Lisa; Burns, Kathleen H.; Boeke, Jef D.

2013-01-01

Transposons are DNA sequences capable of moving in genomes. Early evidence showed their accumulation in many species and suggested their continued activity in at least isolated organisms. In the past decade, with the development of various genomic technologies, it has become abundantly clear that ongoing activity is the rule rather than the exception. Active transposons of various classes are observed throughout plants and animals, including humans. They continue to create new insertions, have an enormous variety of structural and functional impact on genes and genomes, and play important roles in genome evolution. Transposon activities have been identified and measured by employing various strategies. Here, we summarize evidence of current transposon activity in various plant and animal genomes. PMID:23145912

Speciation in Drosophila: from phenotypes to molecules.

PubMed

Orr, H Allen; Masly, J P; Phadnis, Nitin

2007-01-01

Study of the genetics of speciation--and especially of the genetics of intrinsic postzygotic isolation-has enjoyed remarkable progress over the last 2 decades. Indeed progress has been so rapid that one might be tempted to ask if the genetics of postzygotic isolation is now wrapped up. Here we argue that the genetics of speciation is far from complete. In particular, we review 2 topics where recent work has revealed major surprises: 1) the role of meiotic drive in hybrid sterility and 2) the role of gene transposition in speciation. These surprises, and others like them, suggest that evolutionary biologists may understand less about the genetic basis of speciation than seemed likely a few years ago.

Estimation of hysteretic losses for MgB2 tapes under the operating conditions of a generator

NASA Astrophysics Data System (ADS)

Vargas-Llanos, Carlos Roberto; Zermeño, Víctor M. R.; Sanz, Santiago; Trillaud, Frederic; Grilli, Francesco

2016-03-01

Hysteretic losses in the MgB2 wound superconducting coils of a 550 kW synchronous hybrid scaled generator were estimated as part of the European project SUPRAPOWER led by the Spanish Fundación Tecnalia Research & Innovation. Particular interest was given to the losses caused by the magnetic flux ripples in the rotor coils originating from the conventional stator during nominal operation. To compute these losses, a 2D finite element analysis was conducted and Maxwell’s equations written in the H-formulation were solved considering the nonlinear material properties of the conductor materials. The modeled tapes are made of multiple MgB2 filaments embedded in a Ni matrix and soldered to a high purity copper strip and insulated with Dacron braid. Three geometrical models of single tape cross sections of decreasing complexity were studied: (1) the first model reproduced closely the actual cross section obtained from tape micrographs. (2) The second model was obtained from the computed elasto-plastic deformation of a round Ni wire. (3) The third model was based on a simplified cross section with the superconducting filaments bundled in a single elliptical bulky structure. The last geometry allowed the validation of the modeling technique by comparing numerical losses with results from well-established analytical expressions. Additionally, the following cases of filament transpositions of the multi-filamentary tape were studied: no transposition, partial and full transposition; thereby improving understanding of the relevance of the tape fabrication process on the magnitude of the determination of ac losses. Finally, choosing the right level of geometrical detail, the following operational regimes of the machine and its impact on individual superconducting tape losses in the rotor were studied: bias-dc current, ramping current under ramping background field and magnetic flux ripples under dc background current and field.

Artist's concept of scene in Earth orbit during transposition and docking

NASA Technical Reports Server (NTRS)

1975-01-01

An artist's concept depicting a scene in Earth orbit during the Apollo transposition and docking maneuvers of the Apollo Soyuz Test Project (ASTP) mission. The Command/Service Module is moving into position to dock with the Docking Module. This scene will take place some one hour and twenty-three minutes after the Apollo-Saturn 1B liftoff from the Kennedy Space Center on July 15, 1975. The artwork is by Paul Fjeld.

Isolation of the right subclavian artery in a patient with d-transposition of the great arteries.

PubMed

Arunamata, Alisa; Perry, Stanton B; Kipps, Alaina K; Vasanawala, Shreyas S; Axelrod, David M

2015-01-01

Isolation of the right subclavian artery (RSCA) is rare, and this finding in association with d-transposition of the great arteries (d-TGA) is extremely unusual. We present a case of an isolated RSCA in a newborn with d-TGA in whom the clinical presentation was diagnostic. We discuss the imaging modalities used to confirm the diagnosis, the embryological basis of the finding, and the surgical repair.

A matter of emphasis: Linguistic stress habits modulate serial recall.

PubMed

Taylor, John C; Macken, Bill; Jones, Dylan M

2015-04-01

Models of short-term memory for sequential information rely on item-level, feature-based descriptions to account for errors in serial recall. Transposition errors within alternating similar/dissimilar letter sequences derive from interactions between overlapping features. However, in two experiments, we demonstrated that the characteristics of the sequence are what determine the fates of items, rather than the properties ascribed to the items themselves. Performance in alternating sequences is determined by the way that the sequences themselves induce particular prosodic rehearsal patterns, and not by the nature of the items per se. In a serial recall task, the shapes of the canonical "saw-tooth" serial position curves and transposition error probabilities at successive input-output distances were modulated by subvocal rehearsal strategies, despite all item-based parameters being held constant. We replicated this finding using nonalternating lists, thus demonstrating that transpositions are substantially influenced by prosodic features-such as stress-that emerge during subvocal rehearsal.

Effect of beta blockers (carvedilol or metoprolol XL) in patients with transposition of great arteries and dysfunction of the systemic right ventricle.

PubMed

Doughan, Abdul Rahman K; McConnell, Michael E; Book, Wendy M

2007-03-01

This study evaluated the effects of beta blockers (carvedilol and metoprolol XL) on New York Heart Association functional class and systemic right ventricular (RV) function in patients with complete transposition of the great arteries who had systemic RV dysfunction late after atrial inflow correction. A significant improvement in New York Heart Association functional class was found after 4 months of therapy with beta blockers. Functional recovery was significant mostly in those patients with pacemakers who received higher maintenance doses of carvedilol. RV end-diastolic area was significantly greater in untreated patients at the end of the follow-up period, whereas it was unchanged in treated patients. In conclusion, beta blockers prevent RV remodeling, with a concomitant improvement in exercise tolerance in patients with complete transposition of the great arteries and systemic RV dysfunction.

[The effect of modified Nance arch on treating maxillary impacted canine transposed with first premolar].

PubMed

Xu, Qing-chao; Sun, Hao; Lin, Yan; Wang, Xiu-ying; Hu, Rong-dang

2015-10-01

To explore the effect of modified Nance arch on treating maxillary canine-first premolar transposition cases, in which the anchorage and force direction were discussed. Modified Nance arch was applied to 5 cases with maxillary impacted canine-first premolar transposition. First, a lingual knot button was bonded on the surface of the canine crown. Modified Nance arch was decorated with a hook that moved horizontally and buccally. Then the location of the hook was gradually adjusted in order to move the canine cross the root of the first premolar and move the canine to the right position. At last the canine was moved downward by straight wire appliance. Five maxillary transposed canines were fully erupted in their right position, with normal pulp activity and gingival morphology. No obvious root resorption was detected. The mean treatment time was 30 months. Modified Nance arch has advantages in treating canine-first premolar transposition.

[Transposition errors during learning to reproduce a sequence by the right- and the left-hand movements: simulation of positional and movement coding].

PubMed

Liakhovetskiĭ, V A; Bobrova, E V; Skopin, G N

2012-01-01

Transposition errors during the reproduction of a hand movement sequence make it possible to receive important information on the internal representation of this sequence in the motor working memory. Analysis of such errors showed that learning to reproduce sequences of the left-hand movements improves the system of positional coding (coding ofpositions), while learning of the right-hand movements improves the system of vector coding (coding of movements). Learning of the right-hand movements after the left-hand performance involved the system of positional coding "imposed" by the left hand. Learning of the left-hand movements after the right-hand performance activated the system of vector coding. Transposition errors during learning to reproduce movement sequences can be explained by neural network using either vector coding or both vector and positional coding.

Evaluation of various procedures transposing global tilted irradiance to horizontal surface irradiance

NASA Astrophysics Data System (ADS)

Housmans, Caroline; Bertrand, Cédric

2017-02-01

Many transposition models have been proposed in the literature to convert solar irradiance on the horizontal plane to that on a tilted plane. The inverse process, i.e. the conversion from tilted to horizontal is investigated here based upon seven months of in-plane global solar irradiance measurements recorded on the roof of the Royal Meteorological Institute of Belgium's radiation tower in Uccle (Longitude 4.35° E, Latitude 50.79° N). Up to three pyranometers mounted on inclined planes of different tilts and orientations were involved in the inverse transposition process. Our results indicate that (1) the tilt to horizontal irradiance conversion is improved when measurements from more than one tilted pyranometer are considered (i.e. by using a multi-pyranometer approach) and (2) the improvement from using an isotropic model to anisotropic models in the inverse transposition problem is not significant.

Vertical muscle transposition with silicone band belting in VI nerve palsy

PubMed Central

Freitas, Cristina

2016-01-01

A woman aged 60 years developed a Millard-Gubler syndrome after a diagnosis of a cavernous angioma in the median and paramedian areas of the pons. In this context, she presented a right VI nerve palsy, right conjugate gaze palsy, facial palsy and left hemiparesis. To improve the complete VI nerve palsy, we planned a modified transposition approach, in which procedure we made a partial transposition of vertical rectus with a silicone band that was fixated posteriorly. After the procedure, the patient gained the ability to slightly abduct the right eye. We found no compensatory torticollis in the primary position of gaze. There was also an improvement of elevation and depression movements of the right eye. We obtained satisfactory results with a theoretically reversible technique, which is adjustable intraoperatively with no need of muscle detachment, preventing anterior segment ischaemia and allowing simultaneous recession of the medial rectus muscles, if necessary. PMID:27974341

A probabilistic storm transposition approach for estimating exceedance probabilities of extreme precipitation depths

NASA Astrophysics Data System (ADS)

Foufoula-Georgiou, E.

1989-05-01

A storm transposition approach is investigated as a possible tool of assessing the frequency of extreme precipitation depths, that is, depths of return period much greater than 100 years. This paper focuses on estimation of the annual exceedance probability of extreme average precipitation depths over a catchment. The probabilistic storm transposition methodology is presented, and the several conceptual and methodological difficulties arising in this approach are identified. The method is implemented and is partially evaluated by means of a semihypothetical example involving extreme midwestern storms and two hypothetical catchments (of 100 and 1000 mi2 (˜260 and 2600 km2)) located in central Iowa. The results point out the need for further research to fully explore the potential of this approach as a tool for assessing the probabilities of rare storms, and eventually floods, a necessary element of risk-based analysis and design of large hydraulic structures.

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues.

PubMed

De Cecco, Marco; Criscione, Steven W; Peterson, Abigail L; Neretti, Nicola; Sedivy, John M; Kreiling, Jill A

2013-12-01

Transposable elements (TEs) were discovered by Barbara McClintock in maize and have since been found to be ubiquitous in all living organisms. Transposition is mutagenic and organisms have evolved mechanisms to repress the activity of their endogenous TEs. Transposition in somatic cells is very low, but recent evidence suggests that it may be derepressed in some cases, such as cancer development. We have found that during normal aging several families of retrotransposable elements (RTEs) start being transcribed in mouse tissues. In advanced age the expression culminates in active transposition. These processes are counteracted by calorie restriction (CR), an intervention that slows down aging. Retrotransposition is also activated in age-associated, naturally occurring cancers in the mouse. We suggest that somatic retrotransposition is a hitherto unappreciated aging process. Mobilization of RTEs is likely to be an important contributor to the progressive dysfunction of aging cells.

Concerted formation of macromolecular Suppressor–mutator transposition complexes

PubMed Central

Raina, Ramesh; Schläppi, Michael; Karunanandaa, Balasulojini; Elhofy, Adam; Fedoroff, Nina

1998-01-01

Transposition of the maize Suppressor–mutator (Spm) transposon requires two element-encoded proteins, TnpA and TnpD. Although there are multiple TnpA binding sites near each element end, binding of TnpA to DNA is not cooperative, and the binding affinity is not markedly affected by the number of binding sites per DNA fragment. However, intermolecular complexes form cooperatively between DNA fragments with three or more TnpA binding sites. TnpD, itself not a sequence-specific DNA-binding protein, binds to TnpA and stabilizes the TnpA–DNA complex. The high redundancy of TnpA binding sites at both element ends and the protein–protein interactions between DNA-bound TnpA complexes and between these and TnpD imply a concerted transition of the element from a linear to a protein crosslinked transposition complex within a very narrow protein concentration range. PMID:9671711

[Autodermal plastics and transposition of musculus rectus abdominus for giant postoperative hernias].

PubMed

Ianov, V N

2000-01-01

For reduction of postoperative hernia relapses rate the technique of the autodermal plastics and transposition of musculus rectus abdominalis (MRA) was developed. This technique consists of two-sided transection of the lateral abdominal muscles (oblique and transverse) on the pararectal line, transposition of MRA together with their sheaths medially by autodermal continuous lacing to complete adaptation of the edges. Closing of the lateral muscle-aponeurotic defects was carried out with use of the double autodermal grafts which were prepared by Yanov's technique. This technique is indicated for giant postoperative hernias and pronounced diastase of the MRA in people with well developed abdominal muscles. This technique was used in 11 patients without complications after surgery. Long-term results are available for all the patients. The relapses were absent. The technique, developed by us, provides first of all restoration of physiological function of the MRA, and also closing of the abdominal wall muscle-aponeurotic defect.

Spatial transposition gradients in visual working memory.

PubMed

Rerko, Laura; Oberauer, Klaus; Lin, Hsuan-Yu

2014-01-01

In list memory, access to individual items reflects limits of temporal distinctiveness. This is reflected in the finding that neighbouring list items tend to be confused most often. This article investigates the analogous effect of spatial proximity in a visual working-memory task. Items were presented in different locations varying in spatial distance. A retro-cue indicated the location of the item relevant for the subsequent memory test. In two recognition experiments, probes matching spatially close neighbours of the relevant item led to more false alarms than probes matching distant neighbours or non-neighbouring memory items. In two probed-recall experiments, one with simultaneous, the other with sequential memory item presentation, items closer to the cued location were more frequently chosen for recall than more distant items. These results reflect a spatial transposition gradient analogous to the temporal transposition gradient in serial recall and challenge fixed-capacity models of visual working memory (WM).

Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium Castaneum, Is Associated with a Recent Mutation

PubMed Central

Beeman, R. W.; Thomson, M. S.; Clark, J. M.; DeCamillis, M. A.; Brown, S. J.; Denell, R. E.

1996-01-01

A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains. PMID:8722793

Insertional engineering of chromosomes with Sleeping Beauty transposition: an overview.

PubMed

Grabundzija, Ivana; Izsvák, Zsuzsanna; Ivics, Zoltán

2011-01-01

Novel genetic tools and mutagenesis strategies based on the Sleeping Beauty (SB) transposable element are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of its inherent capacity to insert into DNA, the SB transposon can be developed into powerful tools for chromosomal manipulations. Mutagenesis screens based on SB have numerous advantages including high throughput and easy identification of mutated alleles. Forward genetic approaches based on insertional mutagenesis by engineered SB transposons have the advantage of providing insight into genetic networks and pathways based on phenotype. Indeed, the SB transposon has become a highly instrumental tool to induce tumors in experimental animals in a tissue-specific -manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with SB transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models.

Controlled insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model.

PubMed

O'Donnell, Kathryn A; An, Wenfeng; Schrum, Christina T; Wheelan, Sarah J; Boeke, Jef D

2013-07-16

A codon-optimized mouse LINE-1 element, ORFeus, exhibits dramatically higher retrotransposition frequencies compared with its native long interspersed element 1 counterpart. To establish a retrotransposon-mediated mouse model with regulatable and potent mutagenic capabilities, we generated a tetracycline (tet)-regulated ORFeus element harboring a gene-trap cassette. Here, we show that mice expressing tet-ORFeus broadly exhibit robust retrotransposition in somatic tissues when treated with doxycycline. Consistent with a significant mutagenic burden, we observed a reduced number of double transgenic animals when treated with high-level doxycycline during embryogenesis. Transgene induction in skin resulted in a white spotting phenotype due to somatic ORFeus-mediated mutations that likely disrupt melanocyte development. The data suggest a high level of transposition in melanocyte precursors and consequent mutation of genes important for melanoblast proliferation, differentiation, or migration. These findings reveal the utility of a retrotransposon-based mutagenesis system as an alternative to existing DNA transposon systems. Moreover, breeding these mice to different tet-transactivator/reversible tet-transactivator lines supports broad functionality of tet-ORFeus because of the potential for dose-dependent, tissue-specific, and temporal-specific mutagenesis.

Tn5401, a new class II transposable element from Bacillus thuringiensis.

PubMed Central

Baum, J A

1994-01-01

A new class II (Tn3-like) transposable element, designated Tn5401, was recovered from a sporulation-deficient variant of Bacillus thuringiensis subsp. morrisoni EG2158 following its insertion into a recombinant plasmid. Sequence analysis of the insert revealed a 4,837-bp transposon with two large open reading frames, in the same orientation, encoding proteins of 36 kDa (306 residues) and 116 kDa (1,005 residues) and 53-bp terminal inverted repeats. The deduced amino acid sequence for the 36-kDa protein shows 24% sequence identity with the TnpI recombinase of the B. thuringiensis transposon Tn4430, a member of the phage integrase family of site-specific recombinases. The deduced amino acid sequence for the 116-kDa protein shows 42% sequence identity with the transposase of Tn3 but only 28% identity with the TnpA transposase of Tn4430. Two small open reading frames of unknown function, designated orf1 (85 residues) and orf2 (74 residues), were also identified. Southern blot analysis indicated that Tn5401, in contrast to Tn4430, is not commonly found among different subspecies of B. thuringiensis and is not typically associated with known insecticidal crystal protein genes. Transposition was studied with B. thuringiensis by using plasmid pEG922, a temperature-sensitive shuttle vector containing Tn5401. Tn5401 transposed to both chromosomal and plasmid target sites but displayed an apparent preference for plasmid sites. Transposition was replicative and resulted in the generation of a 5-bp duplication at the target site. Transcriptional start sites within Tn5401 were mapped by primer extension analysis. Two promoters, designated PL and PR, direct the transcription of orf1-orf2 and tnpI-tnpA, respectively, and are negatively regulated by TnpI. Sequence comparison of the promoter regions of Tn5401 and Tn4430 suggests that the conserved sequence element ATGTCCRCTAAY mediates TnpI binding and cointegrate resolution. The same element is contained within the 53-bp terminal inverted repeats, thus accounting for their unusual lengths and suggesting an additional role for TnpI in regulating Tn5401 transposition. Images PMID:7514590

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

DOE PAGES

Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan; ...

2017-04-01

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we will need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can bemore » used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.« less

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants1[OPEN

PubMed Central

Zhang, Peifen; Kim, Taehyong; Banf, Michael; Chavali, Arvind K.; Nilo-Poyanco, Ricardo; Bernard, Thomas

2017-01-01

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters. PMID:28228535

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we will need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can bemore » used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.« less

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.

PubMed

Schläpfer, Pascal; Zhang, Peifen; Wang, Chuan; Kim, Taehyong; Banf, Michael; Chae, Lee; Dreher, Kate; Chavali, Arvind K; Nilo-Poyanco, Ricardo; Bernard, Thomas; Kahn, Daniel; Rhee, Seung Y

2017-04-01

Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters. © 2017 American Society of Plant Biologists. All Rights Reserved.

Novel Insights about Class 2 Integrons from Experimental and Genomic Epidemiology▿

PubMed Central

Ramírez, María Soledad; Piñeiro, Silvia; Centrón, Daniela

2010-01-01

In order to contribute to the knowledge of the architecture and epidemiology of class 2 integrons, we performed a class 2 integron molecular survey in which we analyzed 726 isolates in two bacterial populations from environmental and nonepidemiologically related clinical samples, respectively, collected from 1982 to 2007. We recovered the intI2 gene from 130 of 726 isolates, most of which were clinical isolates, and only 1 (a psychrophilic Pseudomonas sp.) was from a water sample. Unlike the widespread distribution of class 1 integrons within Gram-negative bacilli, only Acinetobacter baumannii and Enterobacter cloacae harbored class 2 integrons at a high frequency in our collection. Class 2 integrons with six novel cassette arrays were documented. Characterization of the transposition module of Tn7, the genetic platform in which class 2 integrons have always been reported, showed tns modules with a mosaic genetic structure. A bioinformatic analysis performed with the tns genes present in sequence databases, the finding of intI2 not associated with tns genes, and the genetic examination of novel tns-like genes found in three isolates indicated the possibility of the independent evolution of the two components related to horizontal gene transfer, the class 2 integrons and the Tn7 transposons. PMID:19917745

Detection of a Putative TetR-Like Gene Related to Mycobacterium bovis BCG Growth in Cholesterol Using a gfp-Transposon Mutagenesis System

PubMed Central

Otal, Isabel; Pérez-Herrán, Esther; Garcia-Morales, Lazaro; Menéndez, María C.; Gonzalez-y-Merchand, Jorge A.; Martín, Carlos; García, María J.

2017-01-01

In vitro transposition is a powerful genetic tool for identifying mycobacterial virulence genes and studying virulence factors in relation to the host. Transposon shuttle mutagenesis is a method for constructing stable insertions in the genome of different microorganisms including mycobacteria. Using an IS1096 derivative, we have constructed the Tngfp, a transposon containing a promoterless green fluorescent protein (gfp) gene. This transposon was able to transpose randomly in Mycobacterium bovis BCG. Bacteria with a single copy of the gfp gene per chromosome from an M. bovis BCG::Tngfp library were analyzed and cells exhibiting high levels of fluorescence were detected by flow cytometry. Application of this approach allowed for the selection of a mutant, BCG_2177c::Tngfp (BCG-Tn), on the basis of high level of long-standing fluorescence at stationary phase. This BCG-Tn mutant showed some particular phenotypic features compared to the wild type strain, mainly during stationary phase, when cholesterol was used as a sole carbon source, thus supporting the relationships of the targeted gene with the regulation of cholesterol metabolism in this bacteria. This approach showed that Tngfp is a potentially useful tool for studying the involvement of the targeted loci in metabolic pathways of mycobacteria. PMID:28321208

Site-specific recombination in the chicken genome using Flipase recombinase-mediated cassette exchange.

PubMed

Lee, Hong Jo; Lee, Hyung Chul; Kim, Young Min; Hwang, Young Sun; Park, Young Hyun; Park, Tae Sub; Han, Jae Yong

2016-02-01

Targeted genome recombination has been applied in diverse research fields and has a wide range of possible applications. In particular, the discovery of specific loci in the genome that support robust and ubiquitous expression of integrated genes and the development of genome-editing technology have facilitated rapid advances in various scientific areas. In this study, we produced transgenic (TG) chickens that can induce recombinase-mediated gene cassette exchange (RMCE), one of the site-specific recombination technologies, and confirmed RMCE in TG chicken-derived cells. As a result, we established TG chicken lines that have, Flipase (Flp) recognition target (FRT) pairs in the chicken genome, mediated by piggyBac transposition. The transgene integration patterns were diverse in each TG chicken line, and the integration diversity resulted in diverse levels of expression of exogenous genes in each tissue of the TG chickens. In addition, the replaced gene cassette was expressed successfully and maintained by RMCE in the FRT predominant loci of TG chicken-derived cells. These results indicate that targeted genome recombination technology with RMCE could be adaptable to TG chicken models and that the technology would be applicable to specific gene regulation by cis-element insertion and customized expression of functional proteins at predicted levels without epigenetic influence. © FASEB.

Human Transposon Tectonics

PubMed Central

Burns, Kathleen H.; Boeke, Jef D.

2012-01-01

Mobile DNAs have had a central role in shaping our genome. More than half of our DNA is comprised of interspersed repeats resulting from replicative copy and paste events of retrotransposons. Although most are fixed, incapable of templating new copies, there are important exceptions to retrotransposon quiescence. De novo insertions cause genetic diseases and cancers, though reliably detecting these occurrences has been difficult. New technologies aimed at uncovering polymorphic insertions reveal that mobile DNAs provide a substantial and dynamic source of structural variation. Key questions going forward include the how and how much new transposition events affect human health and disease. PMID:22579280

Inferior gluteal artery myocutaneous island transposition flap reconstruction of irradiated perineal defects.

PubMed

Boccola, Mark A; Rozen, Warren M; Ek, Edmund W; Teh, Bing M; Croxford, Matthew; Grinsell, Damien

2010-07-01

With the progressive use of more radical surgical resections and pre-operative chemo-radiotherapy for locally advanced anorectal cancers, there has become an increasing need for reconstructive options that import well-vascularised tissue of sufficient bulk to the perineum. We present our technique of inferior gluteal artery myocutaneous (IGAM) transposition flaps for reconstruction after extended abdomino-perineal excision (APE) for anorectal cancer. Six consecutive male patients with T2/T3 rectal carcinoma underwent neoadjuvant chemo-radiotherapy followed by extended APE and immediate reconstruction with an islanded IGAM transposition flap. The operative technique and surgical outcomes were assessed with follow-up ranging from 3 to 18 months (median 5 months). In all cases, there were clear histological margins with no flap failures or partial flap losses, and no post-operative hernias. There were no major wound complications, with only one superficial breakdown associated with high body mass index (BMI) and adhesive tape allergy, treated with dressings alone. There was no donor site morbidity evident following flap harvest. The IGAM island transposition flap provides excellent tissue bulk, a large reliable skin paddle and a long pedicle that permits flexible positioning with tension free closure. Our successful results and high patient satisfaction make it a favourable option that should be considered when faced with this reconstructive challenge. Copyright 2009 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

[Pattern of paralysis and reconstructive operations after traumatic brachial plexus lesions].

PubMed

Rühmann, O; Schmolke, S; Carls, J; Wirth, C J

2002-12-01

The aim of this study was to evaluate persistent patterns of paralysis after traumatic brachial plexus lesions. As a result, consecutive reconstructive operations according to our differential therapy concept are presented. Between 04/1994 and 12/2000 in 104 patients with brachial plexus palsy, the grade of muscle power of the affected upper extremities was evaluated prospectively. The neuromuscular patterns of defect showed, in most cases, insufficient muscle power grades of 0-2 for the deltoid muscle (90%), supraspinatus muscle (82%), infraspinatus muscle (93%), elbow flexors (67% to 77%), hand and finger extensors (69% to 71%), and the abductor and extensors of the thumb (67% to 70%). In corresponding frequency, the following operations were performed between 04/1994 and 06/2002: shoulder arthrodesis (n 26), trapezius transfer (n 80), rotation osteotomy of humerus (n 10), triceps to biceps transposition (n 11), transposition of forearm flexors or extensors/Steindler operation (n 12), latissimus transfer (n 7), pectoralis transfer (n 1), teres major transfer (n 1), transposition of forearm flexors to the tendons of extensor digitorum (n 19) and of the extensor pollicis longus (n 9), and wrist arthrodesis (n 5). On malfunction of muscles following brachial plexus lesions, taking into account the individual neuromuscular defect, passive joint function, and bony deformities, different procedures such as muscle transposition, arthrodesis, and corrective osteotomy can be performed to improve function of the upper extremity.

Silent polymorphisms in the RYR1 gene do not modify the phenotype of the p.4898 I>T pathogenic mutation in central core disease: a case report

PubMed Central

2014-01-01

Background Central core disease is a congenital myopathy, characterized by presence of central core-like areas in muscle fibers. Patients have mild or moderate weakness, hypotonia and motor developmental delay. The disease is caused by mutations in the human ryanodine receptor gene (RYR1), which encodes a calcium-release channel. Since the RYR1 gene is huge, containing 106 exons, mutation screening has been limited to three ‘hot spots’, with particular attention to the C-terminal region. Recent next- generation sequencing methods are now identifying multiple numbers of variants in patients, in which interpretation and phenotype prevision is difficult. Case presentation In a Brazilian Caucasian family, clinical, histopathological and molecular analysis identified a new case of central core disease in a 48-year female. Sanger sequencing of the C-terminal region of the RYR1 gene identified two different missense mutations: c.14256 A > C polymorphism in exon 98 and c.14693 T > C in exon 102, which have already been described as pathogenic. Trans-position of the 2 mutations was confirmed because patient’s daughter, mother and sister carried only the exon 98’s mutation, a synonymous variant that was subsequently found in the frequency of 013–0,05 of alleles. Further next generation sequencing study of the whole RYR1 gene in the patient revealed the presence of additional 5 common silent polymorphisms in homozygosis and 8 polymorphisms in heterozygosis. Conclusions Considering that patient’s relatives showed no pathologic phenotype, and the phenotype presented by the patient is within the range observed in other central core disease patients with the same mutation, it was concluded that the c.14256 A > C polymorphism alone is not responsible for disease, and the associated additional silent polymorphisms are not acting as modifiers of the primary pathogenic mutation in the affected patient. The case described above illustrates the present reality where new methods for wide genome screening are becoming more accessible and able to identify a great variety of mutations and polymorphisms of unknown function in patients and their families. PMID:25084811

Genome-scale analysis of positionally relocated genes

PubMed Central

Bhutkar, Arjun; Russo, Susan M.; Smith, Temple F.; Gelbart, William M.

2007-01-01

During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the relocation of individual genes. This latter category, which we will refer to as positionally relocated genes (PRGs), is the subject of this report. Assessment of the magnitude of such PRGs and of possible contributing mechanisms is aided by a comparative analysis of related genomes, where conserved chromosomal organization can aid in identifying genes that have acquired a new location in a lineage of these genomes. Here we utilize two methods to comprehensively identify relocated protein-coding genes in the recently sequenced genomes of 12 species of genus Drosophila. We use exceptions to the general rule of maintenance of chromosome arm (Muller element) association for most Drosophila genes to identify one major class of PRGs. We also identify a partially overlapping set of PRGs among “embedded genes,” located within the extents of other surrounding genes. We provide evidence that PRG movements have at least two different origins: Some events occur via retrotransposition of processed RNAs and others via a DNA-based transposition mechanism. Overall, we identify several hundred PRGs that arose within a lineage of the genus Drosophila phylogeny and provide suggestive evidence that a few thousand such events have occurred within the radiation of the insect order Diptera, thereby illustrating the magnitude of the contribution of PRG movement to chromosomal reorganization during evolution. PMID:17989252

Evaluation of Right Ventricular Myocardial Mechanics Using Velocity Vector Imaging of Cardiac MRI Cine Images in Transposition of the Great Arteries Following Atrial and Arterial Switch Operations.

PubMed

Thattaliyath, Bijoy D; Forsha, Daniel E; Stewart, Chad; Barker, Piers C A; Campbell, Michael J

2015-01-01

The aim of the study was to determine right and left ventricle deformation parameters in patients with transposition of the great arteries who had undergone atrial or arterial switch procedures. Patients with transposition are born with a systemic right ventricle. Historically, the atrial switch operation, in which the right ventricle remains the systemic ventricle, was performed. These patients have increased rates of morbidity and mortality. We used cardiac MRI with Velocity Vector Imaging analysis to characterize and compare ventricular myocardial deformation in patients who had an atrial switch or arterial switch operation. Patients with a history of these procedures, who had a clinically ordered cardiac MRI were included in the study. Consecutive 20 patients (75% male, 28.7 ± 1.8 years) who underwent atrial switch operation and 20 patients (60% male, 17.7 ± 1.9 years) who underwent arterial switch operation were included in the study. Four chamber and short-axis cine images were used to determine longitudinal and circumferential strain and strain rate using Vector Velocity Imaging software. Compared with the arterial switch group, the atrial switch group had decreased right ventricular ejection fraction and increased end-diastolic and end-systolic volumes, and no difference in left ventricular ejection fraction and volumes. The atrial switch group had decreased longitudinal and circumferential strain and strain rate. When compared with normal controls multiple strain parameters in the atrial switch group were reduced. Myocardial deformation analysis of transposition patients reveals a reduction of right ventricular function and decreased longitudinal and circumferential strain parameters in patients with an atrial switch operation compared with those with arterial switch operation. A better understanding of the mechanisms of right ventricle failure in transposition of great arteries may lead to improved therapies and adaptation. © 2015 Wiley Periodicals, Inc.

Regional and global right ventricular dysfunction in asymptomatic or minimally symptomatic patients with congenitally corrected transposition.

PubMed

Tulevski, Igor I; Zijta, Frank M; Smeijers, Anika S; Dodge-Khatami, Ali; van der Wall, Ernst E; Mulder, Barbara J M

2004-04-01

Patients with congenitally corrected transposition are at risk of right ventricular dysfunction and failure. With this in mind, we examined 13 patients with congenitally corrected transposition, 7 not having undergone surgery, and 6 after physiological repair, comparing them with 6 healthy subjects matched for age and sex, using cardiac magnetic resonance imaging, at rest and during dobutamine stress, in order to determine regional and global right ventricular response to stress. At rest, the patients had significantly decreased overall wall motion compared to their healthy peers (7.2 +/- 0.5, versus 9.8 +/- 0.4 mm). During infusion of dobutamine, overall wall motion increased to 12.8 +/- 0.4 mm in the healthy subjects, versus 8.8 +/- 1.0 mm in patients. At the regional level, significant differences in mural motion were found between patients and controls in the anterior (9.5 +/- 1.1, versus 13.2 +/- 0.6 mm), posterior (10.2 +/- 1.6, versus 13.2 +/- 0.8 mm), and septal segments (5.0 +/- 0.8, versus 11.2 +/- 0.6 mm). At rest, overall mural thickening in patients was similar to that of controls, but significantly less in patients during stress. During dobutamine stress, patients showed significantly less regional wall thickening than controls, particularly in the septal (2.7 +/- 0.6, versus 6.0 +/- 0.4 mm, respectively) and in the anterior segments (4.2 +/- 0.6, versus 7.8 +/- 0.6 mm, respectively). Right ventricular ejection fraction strongly correlated with mural motion and thickening, both at rest and during stress. Abnormal regional function in the systemic morphologically right ventricle may occur in patients with congenitally corrected transposition, which strongly correlates with right ventricular ejection fraction. Our findings support the hypothesis that, in patients with congenitally corrected transposition, ischemia of the right ventricular myocardium contributes to the development of right ventricular dysfunction.

Temporalis myofascial flap transfer into the oral cavity without zygomatic arch osteotomy

PubMed Central

Tauro, David P.; Mishra, Madan; Singh, Gaurav

2013-01-01

Among plethora of options, the temporalis myofascial flap remains a workhorse for the maxillofacial reconstruction. The inherent advantages include reliable vascularity, adequate size, and proximity to the defect. Although contemporary surgical techniques provide fair surgical results with low rate of complications, their intraoral transposition involve additional surgical trauma by intentional fracturing of the zygomatic arch. We have proposed herein a simpler technique of temporalis myofascial flap transposition into the oral cavity without zygomatic arch osteotomy. PMID:24665182

Functional and cosmetic outcome of single-digit ray amputation in hand.

PubMed

Bhat, A K; Acharya, A M; Narayanakurup, J K; Kumar, B; Nagpal, P S; Kamath, A

2017-12-01

To assess patient satisfaction, functional and cosmetic outcomes of single-digit ray amputation in hand and identify factors that might affect the outcome. Forty-five patients who underwent ray amputation were evaluated, 37 males and eight females whose mean age was 36.6 years ranging between 15 and 67 years. Twenty-eight patients had dominant hand involvement. Twenty-one patients underwent primary ray amputation, and 24 patients had secondary ray amputation. Eight out of the 23 patients with central digit injuries underwent transposition. Grip strength, pinch strength, tactile sensibility and functional evaluation using Result Assessment Scale (RAS) and DASH score were analysed. Cosmetic assessment was performed using visual analogue scale (VAS) for cosmesis. Median time of assessment after surgery was 20 months. Average loss of grip strength and pinch strength was found to be 43.3 and 33.6%, respectively. Average RAS score was 3.75. Median DASH score was 23.4. Eighty-three percentage of patients had excellent or good cosmesis on the VAS. Transposition causes significant increase in DASH scores for central digit ray amputations but was cosmetically superior. Middle finger ray amputation had the maximum loss of grip strength, and index finger ray amputation had greater loss of pinch strength. Affection of neighbouring digits caused greater grip and pinch loss, and a higher DASH score. Primary ray resection decreased the total disability and eliminated the costs of a second procedure. Following ray amputation, one can predict an approximate 43.3% loss of grip strength and 33.6% loss of pinch strength. The patients can be counselled regarding the expected time off from work, amount of disability and complications after a single-digit ray amputation. Majority of the patients can return to the same occupation after a period of dedicated hand therapy. Therapeutic, Level III.

Genomic Structural Variations Affecting Virulence During Clonal Expansion of Pseudomonas syringae pv. actinidiae Biovar 3 in Europe.

PubMed

Firrao, Giuseppe; Torelli, Emanuela; Polano, Cesare; Ferrante, Patrizia; Ferrini, Francesca; Martini, Marta; Marcelletti, Simone; Scortichini, Marco; Ermacora, Paolo

2018-01-01

Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37). While no phenotype change associated with Tn6212 mobilization could be detected, strains CRAFRU 12.29 and CRAFRU 12.50 did not elicit the hypersensitivity response (HR) on tobacco and eggplant leaves and were limited in their growth in kiwifruit leaves due to insertion of ISPsy31 and ISPsy36 in the hrpS and hrpR genes, respectively, interrupting the hrp cluster. Both strains had been isolated from symptomatic plants, suggesting coexistence of variant strains with reduced virulence together with virulent strains in mixed populations. The structural differences caused by rearrangements of self-genetic elements within European and New Zealand strains were comparable in number and type to those occurring among the European strains, in contrast with the significant difference in terms of nucleotide polymorphisms. We hypothesize a relaxation, during clonal expansion, of the selection limiting the accumulation of deleterious mutations associated with genome structural variation due to transposition of mobile elements. This consideration may be relevant when evaluating strategies to be adopted for epidemics management.

Transposition of a Ds element from a plasmid into the plant genome in Nicotiana plumbaginifolia protoplast-derived cells.

PubMed

Houba-Hérin, N; Domin, M; Pédron, J

1994-07-01

Nicotiana plumbaginifolia haploid protoplasts were co-transformed with two plasmids, one with a NPT-II/Ds element and one with a gene encoding an amino-terminal truncated Ac transposase. It is shown that Ds can efficiently transpose from extrachromosomal DNA to N. plumbaginifolia chromosomes when the Ac transposase gene is present in trans. Ds has been shown to have transposed into the plant genome in a limited number of copies (1.9 copies per genome), for 21/32 transgenic lines tested. The flanking sequences present in the original plasmid are missing in these 21 plants. In only two of 21 plants was part of the transposase construct integrated. By segregation analysis of transgenic progeny, Ds was shown to be present in the heterozygous state in 10 lines even though haploid protoplasts had been originally transformed. This observation could indicate that integration occurred after or during DNA replication that leads to protoplast diploidization.

[Nursing knowledge production: transposition and repercussions on the graduation teaching].

PubMed

Pereira, Wilza Rocha

2013-09-01

The research aimed to analyze the production of knowledge in nursing at a public university, in order to evaluate the impact of that production during the Nursing Graduation. An exploratory and descriptive research has been done in two stages. The first one consisted of gathering the reports of researches executed by the teachers who coordinated them from 2000 to 2009. As a result of this stage, it was mapped the type of studies performed, the themes and the theoretical and methodological references most utilized. During the second stage we studied the current pedagogical project used in the Graduation course, and crossed the data with the previously, to create a dimension to some of the transpositions and applications of the knowledge produced by the researches to the Nursing Graduation course. We concluded that, in different ways, not only the application of the studies has been occurring but also the transposition of ideals that cross through the research groups to which they belong, being able to bring change to nursing education.

Tracking the displacement of objects: a series of tasks with great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, and Pongo pygmaeus) and young children (Homo sapiens).

PubMed

Barth, Jochen; Call, Josep

2006-07-01

The authors administered a series of object displacement tasks to 24 great apes and 24 30-month-old children (Homo sapiens). Objects were placed under 1 or 2 of 3 cups by visible or invisible displacements. The series included 6 tasks: delayed response, inhibition test, A not B, rotations, transpositions, and object permanence. Apes and children solved most tasks performing at comparable levels except in the transposition task, in which apes performed better than children. Ape species performed at comparable levels in all tasks except in single transpositions, in which chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) performed better than gorillas (Gorilla gorilla) and orangutans (Pongo pygmeaus). All species found nonadjacent trials and rotations especially difficult. The number of elements that changed locations, the type of displacement, and having to inhibit predominant reaching responses were factors that negatively affected the subjects' performance.

Fission yeast retrotransposon Tf1 integration is targeted to 5' ends of open reading frames.

PubMed

Behrens, R; Hayles, J; Nurse, P

2000-12-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100-420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed.

Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames

PubMed Central

Behrens, Ralf; Hayles, Jacky; Nurse, Paul

2000-01-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100–420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed. PMID:11095681

Use of the multipurpose transposon Tn KPK2 for the mutational analysis of chromosomal regions upstream and downstream of the sipF gene in Bradyrhizobium japonicum.

PubMed

Müller, P

2004-04-01

The DNA regions upstream and downstream of the Bradyrhizobium japonicum gene sipF were cloned by in vivo techniques and subsequently sequenced. In order to study the function of the predicted genes, a new transposon for in vitro mutagenesis, Tn KPK2, was constructed. This mutagenesis system has a number of advantages over other transposons. Tn KPK2 itself has no transposase gene, making transposition events stable. Extremely short inverted repeats minimize the length of the transposable element and facilitate the determination of the nucleotide sequence of the flanking regions. Since the transposable element carries a promoterless ' phoA reporter gene, the appearance of functional PhoA fusion proteins indicates that Tn KPK2 has inserted in a gene encoding a periplasmic or secreted protein. Although such events are extremely rare, because the transposon has to insert in-frame, in the correct orientation, and at an appropriate location in the target molecule, a direct screening procedure on agar indicator plates permits the identification of candidate clones from large numbers of colonies. In this study, Tn KPK2 was used for the construction of various symbiotic mutants of B. japonicum. One of the mutant strains, A2-10, which is defective in a gene encoding a protein that comigrates with bacterioferritin ( bcpB), was found to induce the formation of small and ineffective nodules.

ISAba1 and Tn6168 acquisition by natural transformation leads to third-generation cephalosporins resistance in Acinetobacter baumannii.

PubMed

Domingues, Sara; Rosário, Natasha; Ben Cheikh, Hadhemi; Da Silva, Gabriela Jorge

2018-05-15

Acinetobacter baumannii has intrinsic beta-lactamase genes, namely ampC and bla OXA-51 -like, which are only strongly expressed when the ISAba1 insertion sequence is upstream the 5' end of the genes. A second ampC gene has also been identified in some clinical A. baumannii strains. The increased expression of these genes leads to resistance to beta-lactams, including third-generation cephalosporins and/or carbapenems. The aim of this work was to assess the involvement of natural transformation in the transfer of chromosomal ampC-associated mobile elements, and related changes in the resistance profile of recipient cells. Natural transformation assays with the naturally competent A. baumannii A118 clinical isolate as recipient cell and the multidrug resistant A. baumannii Ab51 clinical isolate as the source of donor DNA produced transformants. All tested transformants showed integration of the ISAba1 close to the ampC gene. In two transformants, the ISAba1 was acquired by transposition and inserted between the usual folE and the ampC genes. The remaining transformants acquired the ISAba1 adjacent to a second ampC gene, as part of Tn6168, likely by homologous recombination. Our study demonstrates that natural transformation can contribute to the widespread of beta-lactams resistance, and acquisition of non-resistant determinants can lead to changes in the susceptibility profile of A. baumannii strains. Copyright © 2018 Elsevier B.V. All rights reserved.

International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories.

PubMed

Ainouche, Abdelkader; Bétermier, Mireille; Chandler, Mick; Cordaux, Richard; Cristofari, Gaël; Deragon, Jean-Marc; Lesage, Pascale; Panaud, Olivier; Quesneville, Hadi; Vaury, Chantal; Vieira, Cristina; Vitte, Clémentine

2012-10-30

An international conference on Transposable Elements (TEs) was held 21-24 April 2012 in Saint Malo, France. Organized by the French Transposition Community (GDR Elements Génétiques Mobiles et Génomes, CNRS) and the French Society of Genetics (SFG), the conference's goal was to bring together researchers from around the world who study transposition in diverse organisms using multiple experimental approaches. The meeting drew more than 217 attendees and most contributed through poster presentations (117), invited talks and short talks selected from poster abstracts (48 in total). The talks were organized into four scientific sessions, focused on: impact of TEs on genomes, control of transposition, evolution of TEs and mechanisms of transposition. Here, we present highlights from the talks given during the platform sessions. The conference was sponsored by Alliance pour les sciences de la vie et de la santé (Aviesan), Centre national de la recherche scientifique (CNRS), Institut national de la santé et de la recherche médicale (INSERM), Institut de recherche pour le développement (IRD), Institut national de la recherche agronomique (INRA), Université de Perpignan, Université de Rennes 1, Région Bretagne and Mobile DNA. CHAIR OF THE ORGANIZATION COMMITTEE: Jean-Marc Deragon ORGANIZERS: Abdelkader Ainouche, Mireille Bétermier, Mick Chandler, Richard Cordaux, Gaël Cristofari, Jean-Marc Deragon, Pascale Lesage, Didier Mazel, Olivier Panaud, Hadi Quesneville, Chantal Vaury, Cristina Vieira and Clémentine Vitte.

Rapid inactivation of the maize transposable element En/Spm in Medicago truncatula.

PubMed

d'Erfurth, I; Cosson, V; Eschstruth, A; Rippa, S; Messinese, E; Durand, P; Trinh, H; Kondorosi, A; Ratet, P

2003-09-01

Transposable elements have been widely used as mutagens in many organisms. Among them, the maize transposable element En/Spm has been shown to transpose efficiently in several plant species including the model plant Arabidopsis, where it has been used for large-scale mutagenesis. To determine whether we could use this transposon as a mutagen in the model legume plant Medicago truncatula, we tested the activity of the autonomous element, as well as two defective elements, in this plant, and in Arabidopsis as a positive control. In agreement with previous reports, we observed efficient excision of the autonomous En/Spm element in A. thaliana. This element was also active in M. truncatula, but the transposition activity was low and was apparently restricted to the tissue culture step necessary for the production of transgenic plants. The activity of one of the defective transposable elements, dSpm, was very low in A. thaliana and even lower in M. truncatula. The use of different sources of transposases suggested that this defect in transposition was associated with the dSpm element itself. Transposition of the other defective element, I6078, was also detected in M. truncatula, but, as observed with the autonomous element, transposition events were very rare and occurred during tissue culture. These results suggest that the En/Spm element is rapidly inactivated in the regenerated plants and their progeny, and therefore is not suitable for routine insertion mutagenesis in M. truncatula.

Esophageal replacement by gastric transposition: A single surgeon's experience from a tertiary pediatric surgical center.

PubMed

Foster, Jake D; Hall, Nigel J; Keys, S Charles; Burge, David M

2018-06-02

Many pediatric surgeons have limited experience of esophageal replacement. This study reports outcomes of esophageal replacement by gastric transposition performed by a single UK-based pediatric surgeon. Consecutive patients were identified who underwent esophageal replacement by gastric transposition over a 28 year period. Clinical and demographic data were collected. Weight-for-age Z-scores were calculated for esophageal atresia patients. Nineteen patients were identified. Indication in the majority was long-gap esophageal atresia (n = 17; 10 with tracheoesophageal fistula). At surgery, median age was 8.5 months (range 2-55); median weight was 7.4 kg (range 4.0-17.4 kg). A right-sided thoracotomy or transhiatal approach was used. Median postoperative length of stay was 17.5 days (range 7-130); median intensive care stay was three days (range 1-63). There were no deaths. Anastomotic leak rate at 30 days was 10.5% (n = 2). One patient required early stricture dilatation. Median weight-for-age Z-score increased from -2.17 at one year of age to -1.86, -1.70 and -1.93 at 5, 10 and 15 years. Esophageal replacement by gastric transposition offers a potentially life-changing treatment; however, it is associated with significant morbidity. The majority of patients eventually achieve full oral feeding and maintenance of weight gain trajectory. A right-sided approach to the esophagus is feasible. Treatment Study. IV. Copyright © 2018 Elsevier Inc. All rights reserved.

Expanded Transposition Flap Technique for Total and Subtotal Resurfacing of the Face and Neck

PubMed Central

Spence, Robert J.

2007-01-01

Background: The reconstruction of major burn and other deformities resulting from significant soft tissue deficits of the face and neck is a continuing challenge for surgeons who wish to reliably restore facial function and aesthetic appearance. A primary problem is deficiency of well-matched donor skin. Other problems include the unique characteristics of facial skin, the fine anatomic nuances, and the unique functional demands placed on the face. This article describes an expanded shoulder transposition flap that can provide a large amount of both flap and full-thickness skin graft for total and subtotal reconstruction of the face. Methods: An expanded shoulder transposition flap has been used since 1986 for head and neck resurfacing 58 times in 41 patients ranging in age from 2 to 62 years. The details of the technique and the results of the flap including complications are described. Results: The flap proved remarkably reliable and reproducible in resurfacing the peripheral facial aesthetic units. The pedicle skin is often used for grafting of the central face with its finer features. The donor site of the flap is closed primarily. Conclusions: Twenty years' experience with expanded transposition flaps has shown it to be reliable and versatile in the reconstruction of major soft tissue deficits of the face and neck. It is a technique that provides economy of tissue, versatility, and is well within the skill, patience, and courage of most reconstructive surgeons. PMID:17534420

The functionally conserved nucleoporins Nup124p from fission yeast and the human Nup153 mediate nuclear import and activity of the Tf1 retrotransposon and HIV-1 Vpr.

PubMed

Varadarajan, Padmapriya; Mahalingam, Sundarasamy; Liu, Peiyun; Ng, Sarah Boon Hsi; Gandotra, Sheetal; Dorairajoo, Desmond Suresh Kumar; Balasundaram, David

2005-04-01

We report that the fission yeast nucleoporin Nup124p is required for the nuclear import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr. Failure to import Tf1-Gag into the nucleus in a nup124 null mutant resulted in complete loss of Tf1 transposition. Similarly, nuclear import of HIV-1 Vpr was impaired in nup124 null mutant strains and cells became resistant to Vpr's cell-killing activity. On the basis of protein domain similarity, the human nucleoporin Nup153 was identified as a putative homolog of Nup124p. We demonstrate that in vitro-translated Nup124p and Nup153 coimmunoprecipitate Tf1-Gag or HIV-1 Vpr. Though full-length Nup153 was unable to complement the Tf1 transposition defect in a nup124 null mutant, we provide evidence that both nucleoporins share a unique N-terminal domain, Nup124p(AA264-454) and Nup153(AA448-634) that is absolutely essential for Tf1 transposition. Epigenetic overexpression of this domain in a wild-type (nup124(+)) background blocked Tf1 activity implying that sequences from Nup124p and the human Nup153 challenged the same pathway affecting Tf1 transposition. Our results establish a unique relationship between two analogous nucleoporins Nup124p and Nup153 wherein the function of a common domain in retrotransposition is conserved.

Reconstructive operations for the upper limb after brachial plexus palsy.

PubMed

Rühmann, Oliver; Schmolke, Stephan; Bohnsack, Michael; Carls, Jörg; Flamme, Christian; Wirth, Carl Joachim

2004-07-01

Limited function due to paralysis following brachial plexus lesions can be improved by secondary operations of the bony and soft tissue. Between April 1994 and December 2000, 109 patients suffering from arm-plexus lesions underwent a total of 144 reconstructive operations guided by our concept of integrated therapy. The average age at the time of surgery was 32 years (range: 15-59). The following operations were performed: shoulder arthrodesis (23), trapezius transfer (74), rotation osteotomy of humerus (9), triceps to biceps transposition (9), transposition of forearm flexors or extensors (8), latissimus transfer (7), pectoralis transfer (1), teres major transfer (1), transposition of flexor carpi ulnaris to the tendons of extensor digitorum (10), and wrist arthrodesis (2). Prospectively, in all patients, the grade of muscle power of the affected upper extremity was evaluated prior to surgery. The follow-up period for all 144 operations was, on average, 22 months (range: 6-74). By means of operative measures, almost all patients obtained an improvement of shoulder function (100%) and stability (>90%), elbow flexion (85%), and hand, finger, and thumb (100%). When muscles malfunction after brachial plexus lesions, one should take into account the individual neuromuscular defect, passive joint function, and bony deformities; different procedures such as muscle transpositions, arthrodeses, and corrective osteotomies can then be performed to improve function of the upper extremity. Each form of operative treatment presents patients with certain benefits and all are integrated into a total treatment plan for the affected extremity.

Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation

PubMed Central

Garcia, S; Kovařík, A

2013-01-01

In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA locus encoding 18S–5.8S–26S genes (L-type arrangement). Here we used Southern blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the 35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo (∼30% of the species analysed), while the remaining exhibit separate organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short tandems embedded in the 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may be encoded by the same (Ginkgo, Ephedra) or opposite (Podocarpus) DNA strand as the 18S–5.8S–26S genes. In addition, pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have been largely homogenised across the genomes. Phylogenetic relationships based on the comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at least three times in the course of gymnosperm evolution. Frequent transpositions and rearrangements of basic units indicate relatively relaxed selection pressures imposed on genomic organisation of 5S genes in plants. PMID:23512008

Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation.

PubMed

Garcia, S; Kovařík, A

2013-07-01

In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA locus encoding 18S-5.8S-26S genes (L-type arrangement). Here we used Southern blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the 35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo (∼30% of the species analysed), while the remaining exhibit separate organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short tandems embedded in the 26S-18S rDNA intergenic spacer (IGS). The 5S transcript may be encoded by the same (Ginkgo, Ephedra) or opposite (Podocarpus) DNA strand as the 18S-5.8S-26S genes. In addition, pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have been largely homogenised across the genomes. Phylogenetic relationships based on the comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at least three times in the course of gymnosperm evolution. Frequent transpositions and rearrangements of basic units indicate relatively relaxed selection pressures imposed on genomic organisation of 5S genes in plants.

Biological safety concepts of genetically modified live bacterial vaccines.

PubMed

Frey, Joachim

2007-07-26

Live vaccines possess the advantage of having access to induce cell-mediated and antibody-mediated immunity; thus in certain cases they are able to prevent infection, and not only disease. Furthermore, live vaccines, particularly bacterial live vaccines, are relatively cheap to produce and easy to apply. Hence they are suitable to immunize large communities or herds. The induction of both cell-mediated immunity as well as antibody-mediated immunity, which is particularly beneficial in inducing mucosal immune responses, is obtained by the vaccine-strain's ability to colonize and multiply in the host without causing disease. For this reason, live vaccines require attenuation of virulence of the bacterium to which immunity must be induced. Traditionally attenuation was achieved simply by multiple passages of the microorganism on growth medium, in animals, eggs or cell cultures or by chemical or physical mutagenesis, which resulted in random mutations that lead to attenuation. In contrast, novel molecular methods enable the development of genetically modified organisms (GMOs) targeted to specific genes that are particularly suited to induce attenuation or to reduce undesirable effects in the tissue in which the vaccine strains can multiply and survive. Since live vaccine strains (attenuated by natural selection or genetic engineering) are potentially released into the environment by the vaccinees, safety issues concerning the medical as well as environmental aspects must be considered. These involve (i) changes in cell, tissue and host tropism, (ii) virulence of the carrier through the incorporation of foreign genes, (iii) reversion to virulence by acquisition of complementation genes, (iv) exchange of genetic information with other vaccine or wild-type strains of the carrier organism and (v) spread of undesired genes such as antibiotic resistance genes. Before live vaccines are applied, the safety issues must be thoroughly evaluated case-by-case. Safety assessment includes knowledge of the precise function and genetic location of the genes to be mutated, their genetic stability, potential reversion mechanisms, possible recombination events with dormant genes, gene transfer to other organisms as well as gene acquisition from other organisms by phage transduction, transposition or plasmid transfer and cis- or trans-complementation. For this, GMOs that are constructed with modern techniques of genetic engineering display a significant advantage over random mutagenesis derived live organisms. The selection of suitable GMO candidate strains can be made under in vitro conditions using basic knowledge on molecular mechanisms of pathogenicity of the corresponding bacterial species rather than by in vivo testing of large numbers of random mutants. This leads to a more targeted safety testing on volunteers and to a reduction in the use of animal experimentation.

Target sites for the transposition of rat long interspersed repeated DNA elements (LINEs) are not random.

PubMed Central

Furano, A V; Somerville, C C; Tsichlis, P N; D'Ambrosio, E

1986-01-01

The long interspersed repeated DNA family of rats (LINE or L1Rn family) contains about 40,000 6.7-kilobase (kb) long members (1). LINE members may be currently mobile since their presence or absence causes allelic variation at three single copy loci (2, 3): insulin 1, Moloney leukemia virus integration 2 (Mlvi-2) (4), and immunoglobulin heavy chain (Igh). To characterize target sites for LINE insertion, we compared the DNA sequences of the unoccupied Mlvi-2 target site, its LINE-containing allele, and several other LINE-containing sites. Although not homologous overall, the target sites share three characteristics: First, depending on the site, they are from 68% to 86% (A+T) compared to 58% (A+T) for total rat DNA (5). Depending on the site, a 7- to 15-bp target site sequence becomes duplicated and flanks the inserted LINE member. The second is a version (0 or 1 mismatch) of the hexanucleotide, TACTCA, which is also present in the LINE member, in a highly conserved region located just before the A-rich right end of the LINE member. The third is a stretch of alternating purine/pyrimidine (PQ). The A-rich right ends of different LINE members vary in length and composition, and the sequence of a particularly long one suggests that it contains the A-rich target site from a previous transposition. PMID:3012480

Dynamics of genome size evolution in birds and mammals.

PubMed

Kapusta, Aurélie; Suh, Alexander; Feschotte, Cédric

2017-02-21

Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.

Supravalvular aortic stenosis after arterial switch operation.

PubMed

Maeda, Takuya; Koide, Masaaki; Kunii, Yoshifumi; Watanabe, Kazumasa; Kanzaki, Tomohito; Ohashi, Yuko

2016-07-01

Supravalvular aortic stenosis as a late complication of transposition of the great arteries is very rare, and only a few cases have been reported. We describe the case of a 14-year-old girl who developed supravalvular aortic stenosis as a late complication of the arterial switch operation for transposition of the great arteries. The narrowed ascending aorta was replaced with a graft. The right pulmonary artery was transected to approach the ascending aorta which adhered severely to the main pulmonary trunk, and we obtained a good operative field. © The Author(s) 2015.

Bartonella endocarditis with glomerulonephritis in a patient with complete transposition of the great arteries

PubMed Central

Hashemi, Helen; Endicott-Yazdani, Tiana R.; Oguayo, Christopher; Harmon, David M.; Tran, Tuan; Tsai-Nguyen, Ginger; Benavides, Raul; Spak, Cedric W.; Nguyen, Hoang-Lan

2018-01-01

ABSTRACT We describe a patient with history of dextro-transposition of the great vessels, ventricular septal defect, and pulmonary valve replacement who presented with fatigue, prolonged fever, and leg edema. He was found to have kidney injury, pancytopenia, and liver congestion. Echocardiogram revealed thickened leaflets with prolapsing vegetation on the pulmonary valve. Given the negative blood cultures, high Bartonella henselae immunogobulin G titer (≥1:1024) and positive immunoglobulin M titer (≥1:20), he was diagnosed with Bartonella endocarditis complicated with glomerulonephritis. PMID:29686571

Bartonella endocarditis with glomerulonephritis in a patient with complete transposition of the great arteries.

PubMed

Hashemi, Helen; Endicott-Yazdani, Tiana R; Oguayo, Christopher; Harmon, David M; Tran, Tuan; Tsai-Nguyen, Ginger; Benavides, Raul; Spak, Cedric W; Nguyen, Hoang-Lan

2018-01-01

We describe a patient with history of dextro-transposition of the great vessels, ventricular septal defect, and pulmonary valve replacement who presented with fatigue, prolonged fever, and leg edema. He was found to have kidney injury, pancytopenia, and liver congestion. Echocardiogram revealed thickened leaflets with prolapsing vegetation on the pulmonary valve. Given the negative blood cultures, high Bartonella henselae immunogobulin G titer (≥1:1024) and positive immunoglobulin M titer (≥1:20), he was diagnosed with Bartonella endocarditis complicated with glomerulonephritis.

3D Printing to Model Surgical Repair of Complex Congenitally Corrected Transposition of the Great Arteries.

PubMed

Sahayaraj, R Anto; Ramanan, Sowmya; Subramanyan, Raghavan; Cherian, Kotturathu Mammen

2017-01-01

We report the use of three-dimensional (3D) modeling to plan surgery for physiologic repair of congenitally corrected transposition of the great arteries with pulmonary atresia, dextrocardia, and complex intra cardiac anatomy. Based on measurements made from the 3D printed model of the actual patient's anatomy, we anticipated using a composite valved conduit (Dacron tube graft, decellularized bovine jugular vein, and aortic homograft) to establish left ventricle-to-pulmonary artery continuity with relief of stenosis involving the pulmonary artery confluence and bilateral branch pulmonary arteries.

Orthodontic management of bilateral maxillary canine-first premolar transposition and bilateral agenesis of maxillary lateral incisors: a case report.

PubMed

Di Palma, Elena; Di Giuseppe, Biagio; Tepedino, Michele; Chimenti, Claudio

2015-01-01

Maxillary canine-first premolar transposition (Mx.C.P1) is an uncommon dental positional anomaly that may create many orthodontic problems from both esthetic and functional points of view. In this report we show the orthodontic management of a case of Mx.C.P1 associated with bilateral maxillary lateral incisor agenesis and unilateral mandibular second premolar agenesis The patient was treated with a multibracket appliance and the extraction of the lower premolar. treatment was completed without the need for any prosthetic replacement.

Continuous inhaled iloprost in a neonate with d-transposition of the great arteries and severe pulmonary arterial hypertension.

PubMed

Dykes, John C; Torres, Marilyn; Alexander, Plato J

2016-03-01

This report describes the case of a neonate with d-transposition of the great arteries and severe pulmonary arterial hypertension stabilised in the post-operative period with continuous iloprost nebulisation. To our knowledge, this is the first documented method of treating post-operative severe pulmonary arterial hypertension with continuous inhaled iloprost in a patient with complex CHD. We found this method of delivering the drug very effective in stabilising haemodynamic swings in the setting of severe pulmonary arterial hypertension.

Contribution of transposable elements in the plant's genome.

PubMed

Sahebi, Mahbod; Hanafi, Mohamed M; van Wijnen, Andre J; Rice, David; Rafii, M Y; Azizi, Parisa; Osman, Mohamad; Taheri, Sima; Bakar, Mohd Faizal Abu; Isa, Mohd Noor Mat; Noor, Yusuf Muhammad

2018-07-30

Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms. Copyright © 2018 Elsevier B.V. All rights reserved.

[Soft tissue defects treated with perforator flaps].

PubMed

Weum, Sven; de Weerd, Louis; Klein, Steven; Hage, J Joris

2008-01-31

Treatment of soft tissue defects caused by trauma, tumour surgery or pressure sores is a challenge to the reconstructive surgeon. Although contour and function may be restored by tissue transposition, traditional methods often cause significant donor site morbidity. This article describes how increased understanding of vascular anatomy has led to the development of new techniques. The article is based on textbooks of plastic surgery, selected articles and own clinical experience. Pedicled and free perforator flaps represent the latest development in surgical treatment of soft tissue defects. The use of perforator flaps can considerably reduce the disadvantages that are associated with other surgical methods. The use of perforator flaps demands microsurgical skills, but has many advantages. Reliable vascular supply and a good aesthetical result can be combined with minimal donor site morbidity. In many cases this technique may even give sensibility to the reconstructed area.

In-vivo-induced antigenic determinants of Fusobacterium nucleatum subsp. nucleatum.

PubMed

Lee, H-R; Rhyu, I-C; Kim, H-D; Jun, H-K; Min, B-M; Lee, S-H; Choi, B-K

2011-04-01

Fusobacterium nucleatum plays a pivotal role in dental plaque biofilm formation and is known to be involved in chronic inflammatory systemic disease. However, limited knowledge of F. nucleatum genes expressed in vivo interferes with our understanding of pathogenesis. In this study, we identified F. nucleatum genes induced in vivo using in-vivo-induced antigen technology (IVIAT). Among 30,000 recombinant clones screened, 87 reacted reproducibly with pooled sera from 10 patients with periodontitis. The clones encoded for 32 different proteins, of which 28 could be assigned to their functions, which were categorized in translation, transcription, transport, energy metabolism, cell envelope, cellular process, fatty acid and phospholipid metabolism, transposition, cofactor biosynthesis, amino acid biosynthesis, and DNA replication. Putative virulence factors detected were ABC transporter, butyrate-acetoacetate CoA-transferase, hemin receptor, hemolysin, hemolysin-related protein, LysR family transcriptional regulator, serine protease, and transposase. Analysis of immune responses to the in-vivo-induced (ivi) antigens in five patients demonstrated that most were reactive to these proteins, confirming results with pooled sera. IVIAT-identified F. nucleatum genes in this study may accelerate the elucidation of F. nucleatum-mediated molecular pathogenesis. © 2011 John Wiley & Sons A/S.

Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti.

PubMed

Adelman, Zach N; Jasinskiene, Nijole; Vally, K J M; Peek, Corrie; Travanty, Emily A; Olson, Ken E; Brown, Susan E; Stephens, Janice L; Knudson, Dennis L; Coates, Craig J; James, Anthony A

2004-10-01

The Class II transposable element, piggyBac, was used to transform the yellow fever mosquito, Aedes aegypti. In two transformed lines only 15-30% of progeny inherited the transgene, with these individuals displaying mosaic expression of the EGFP marker gene. Southern analyses, gene amplification of genomic DNA, and plasmid rescue experiments provided evidence that these lines contained a high copy number of piggyBac transformation constructs and that much of this DNA consisted of both donor and helper plasmids. A detailed analysis of one line showed that the majority of piggyBac sequences were unit-length donor or helper plasmids arranged in a large tandem array that could be lost en masse in a single generation. Despite the presence of a transposase source and many intact donor elements, no conservative (cut and paste) transposition of piggyBac was observed in these lines. These results reveal one possible outcome of uncontrolled and/or unexpected recombination in this mosquito, and support the conclusion that further investigation is necessary before transposable elements such as piggyBac can be used as genetic drive mechanisms to move pathogen-resistance genes into mosquito populations.

Comparison of augmented and nonaugmented modified Knapp procedure for the treatment of nonrestrictive double elevator palsies.

PubMed

Li, YuePing; Sun, LiLi; Zhang, Wei; Zhao, KanXing

2016-10-01

To compare surgical results of augmented and nonaugmented modified Knapp procedure, for the treatment of nonrestrictive double elevator palsies (DEP). The medical records of patients with congenital DEP were reviewed retrospectively. Patients were divided into three treatment groups: standard transposition (group A), Foster transposition (group B), and resection transposition (group C). Pre- and postoperative vertical deviation in primary position, ocular motility, and binocular vision were compared. Thirty patients were enrolled. The pre- and postoperative deviations in group A were 34.7 Δ ± 8.6 Δ and 6.5 Δ ± 6.5 Δ ; in group B, 38.6 Δ ± 14.6 Δ and 5.7 Δ ± 9.3 Δ ; and in group C, 43.1 Δ ± 10.3 Δ and 8.5 Δ ± 6.1 Δ . The corrected vertical deviation of group B (32.9 Δ  ± 5.7 Δ ) and group C (34.6 Δ  ± 5.0 Δ ) were greater than that of group A (28.1 Δ  ± 3.6 Δ ; P = 0.03, 0.002). The pre- and postoperative measures of upgaze in group A were -3.7 and -1.8; in group B, -4.0 and -1.3; and in group C, -3.6 and -2.0. The average improved upgaze in group B (2.6 ± 0.5) was statistically significantly better than that in group A (1.9 ± 0.6) and group C (1.5 ± 0.5; P = 0.03, 0.002). There was no significant difference in the surgical effect on downgaze in three groups (P > 0.05). The surgical outcome was satisfactory in 19 (63.3%) patients with preoperative vertical devation of ≤40 Δ . All transpositions are reasonably effective in treating vertical deviations of <35 Δ without obviously limiting downgaze in DEP. Augmented procedures could correct greater vertical deviation of 30 Δ -40 Δ . The Foster transposition demonstrates the strongest effect in improving upgaze. Copyright © 2016 American Association for Pediatric Ophthalmology and Strabismus. Published by Elsevier Inc. All rights reserved.

The clustered regularly interspaced short palindromic repeats/associated proteins system for the induction of gene mutations and phenotypic changes in Bombyx mori.

PubMed

Song, Jia; Che, Jiaqian; You, Zhengying; Ye, Xiaogang; Li, Jisheng; Ye, Lupeng; Zhang, Yuyu; Qian, Qiujie; Zhong, Boxiong

2016-12-01

To probe the general phenomena of gene mutations, Bombyx mori, the lepidopterous model organism, was chosen as the experimental model. To easily detect phenotypic variations, the piggyBac system was utilized to introduce two marker genes into the silkworm, and 23.4% transposition efficiency aided in easily breeding a new strain for the entire experiment. Then, the clustered regularly interspaced short palindromic repeats/an associated protein (Cas9) system was utilized. The results showed that the Cas9 system can induce efficient gene mutations and the base changes could be detected since the G 0 individuals in B. mori; and that the mutation rates on different target sites were diverse. Next, the gRNA2-targeted site that generated higher mutation rate was chosen, and the experimental results were enumerated. First, the mutation proportion in G 1 generation was 30.1%, and some gene mutations were not inherited from the G 0 generation; second, occasionally, base substitutions did not lead to variation in the amino-acid sequence, which decreased the efficiency of phenotypic changes compared with that of genotypic changes. These results laid the foundation for better use of the Cas9 system in silkworm gene editing. © The Author 2016. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora

PubMed Central

Horvath, Robert

2017-01-01

Abstract To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population. To explore how effects of TE silencing on gene regulation shapes purifying selection on TEs, we analyzed whole genome sequencing data from 166 individuals of a large population of the outcrossing species Capsella grandiflora. We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates. Our results provide new insights into the processes affecting the accumulation of TEs in an outcrossing species and support the view that epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing. PMID:29036316

Comparison of systemic right ventricular function in transposition of the great arteries after atrial switch and congenitally corrected transposition of the great arteries.

PubMed

Morcos, Michael; Kilner, Philip J; Sahn, David J; Litt, Harold I; Valsangiacomo-Buechel, Emanuela R; Sheehan, Florence H

2017-12-01

In patients with transposition of the great arteries corrected by interatrial baffle (TGA) and those with congenitally corrected transposition of the great arteries (ccTGA) the right ventricle (RV) is subjected to systemic pressure and fails prematurely. Previous studies have demonstrated RV dysfunction may be more pronounced in patients with TGA. The present study sought to compare patients with TGA and ccTGA using three-dimensional (3D) techniques to comprehensively analyze the shape, volume, global and regional function in the systemic RV. We compared RV size, shape, and regional and global function in 25 patients with TGA, 17 patients with ccTGA, and 9 normal subjects. The RVs were reconstructed from cardiac Magnetic Resonance Images for 3D analyses. Compared to normal, the RV in TGA and ccTGA was dilated, rounded, and reduced in function. Compared to each other, TGA and ccTGA patients had similar RV size and shape. Global RV function was lower in TGA than ccTGA when assessed from ejection fraction (EF) (30 ± 7 vs. 35 ± 7, p = 0.02) and from normalized tricuspid annular systolic plane excursion (TAPSE) (0.10 ± 0.04 vs. 0.18 ± 0.04, p < 0.01). Basilar RV function was poorer in the TGA patients when compared to ccTGA. The systemic RVs in both TGA and ccTGA are dilated, spherical, and poorly functioning. Compared to ccTGA, TGA RVs have reduced TAPSE and worse basilar hypokinesis.

Ductal stenting retrains the left ventricle in transposition of great arteries with intact ventricular septum.

PubMed

Sivakumar, Kothandam; Francis, Edwin; Krishnan, Prasad; Shahani, Jagdish

2006-11-01

In late presenters with transposition of the great arteries, intact ventricular septum, and regressing left ventricle, left ventricular retraining by pulmonary artery banding and aortopulmonary shunt is characterized by a stormy postoperative course and high costs. Ductal stenting in the cardiac catheterization laboratory is conceptualized to retrain the left ventricle with less morbidity. Recanalization and transcatheter stenting of patent ductus arteriosus was performed in patients with transposition to induce pressure and volume overload to the regressing left ventricle. Serial echocardiographic monitoring of left ventricular shape, mass, free wall thickness, and volumes was done, and once the left ventricle was adequately prepared, an arterial switch was performed. The ductal stent was removed and the remaining surgical steps were similar to a 1-stage arterial switch operation. Postoperative course, need for inotropic agents, and left ventricular function were monitored. Ductal stenting in 2 patients aged 3 months resulted in improvement of indexed left ventricular mass from 18.9 to 108.5 g/m2, left ventricular free wall thickness from 2.5 to 4.8 mm, and indexed left ventricular volumes from 7.6 to 29.5 mL/m2 within 3 weeks. Both patients underwent arterial switch (bypass times 125 and 158 minutes) uneventfully, needed inotropic agents and ventilatory support for 3 days, and were discharged in 8 and 10 days. Ductal stenting is a less morbid method of left ventricular retraining in transposition of the great arteries with regressed left ventricle. Its major advantages lie in avoiding pulmonary artery distortion and neoaortic valve regurgitation resulting from banding and also in avoiding thoracotomy.

Hybrid endovascular repair in aortic arch pathologies: a retrospective study.

PubMed

Ma, Xiaohui; Guo, Wei; Liu, Xiaoping; Yin, Tai; Jia, Xin; Xiong, Jiang; Zhang, Hongpeng; Wang, Lijun

2010-11-18

The aortic arch presents specific challenges to endovascular repair. Hybrid repair is increasingly evolving as an alternative option for selected patients, and promising initial results have been reported. The aim of this study was to introduce our experiences and evaluate mid-term results of supra aortic transpositions for extended endovascular repair of aortic arch pathologies. From December 2002 to January 2008, 25 patients with thoracic aortic aneurysms and dissections involving the aortic arch were treated with hybrid endovascular treatment in our center. Of the 25 cases, 14 were atherosclerotic thoracic aortic aneurysms and 11 were thoracic aortic dissection. The hybrid repair method included total-arch transpositions (15 cases) or hemi-arch transpositions (10 cases), and endovascular procedures. All hybrid endovascular procedures were completed successfully. Three early residual type-I endoleaks and one type-II endoleak were observed. Stroke occurred in three patients (8%) during the in-hospital stage. The perioperative mortality rate was 4%; one patients died post-operatively from catheter related complications. The average follow-up period was 15 ± 5.8 months (range, 1-41 months). The overall crude survival rate at 15 months was 92% (23/25). During follow-up, new late endoleaks and stent-raft related complications were not observed. One case (4%) developed a unilateral lower limb deficit at 17 days and was readmitted to hospital. In conclusion, the results are encouraging for endovascular aortic arch repair in combination with supra-aortic transposition in high risk cases. Aortic endografting offers good mid-term results. Mid-term results of the hybrid approach in elderly patients with aortic arch pathologies are satisfying.

The Functionally Conserved Nucleoporins Nup124p from Fission Yeast and the Human Nup153 Mediate Nuclear Import and Activity of the Tf1 Retrotransposon and HIV-1 VprV⃞

PubMed Central

Varadarajan, Padmapriya; Mahalingam, Sundarasamy; Liu, Peiyun; Ng, Sarah Boon Hsi; Gandotra, Sheetal; Dorairajoo, Desmond Suresh Kumar; Balasundaram, David

2005-01-01

We report that the fission yeast nucleoporin Nup124p is required for the nuclear import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr. Failure to import Tf1-Gag into the nucleus in a nup124 null mutant resulted in complete loss of Tf1 transposition. Similarly, nuclear import of HIV-1 Vpr was impaired in nup124 null mutant strains and cells became resistant to Vpr's cell-killing activity. On the basis of protein domain similarity, the human nucleoporin Nup153 was identified as a putative homolog of Nup124p. We demonstrate that in vitro–translated Nup124p and Nup153 coimmunoprecipitate Tf1-Gag or HIV-1 Vpr. Though full-length Nup153 was unable to complement the Tf1 transposition defect in a nup124 null mutant, we provide evidence that both nucleoporins share a unique N-terminal domain, Nup124pAA264–454 and Nup153AA448–634 that is absolutely essential for Tf1 transposition. Epigenetic overexpression of this domain in a wild-type (nup124+) background blocked Tf1 activity implying that sequences from Nup124p and the human Nup153 challenged the same pathway affecting Tf1 transposition. Our results establish a unique relationship between two analogous nucleoporins Nup124p and Nup153 wherein the function of a common domain in retrotransposition is conserved. PMID:15659641

IHF-independent assembly of the Tn10 strand transfer transpososome: implications for inhibition of disintegration.

PubMed

Stewart, Barry J; Wardle, Simon J; Haniford, David B

2002-08-15

The frequency of DNA transposition in transposition systems that employ a strand transfer step may be significantly affected by the occurrence of a disintegration reaction, a reaction that reverses the strand transfer event. We have asked whether disintegration occurs in the Tn10 transposition system. We show that disintegration substrates (substrates constituting one half of the strand transfer product) are assembled into a transpososome that mimics the strand transfer intermediate. This strand transfer transpososome (STT) does appear to support an intermolecular disintegration reaction, but only at a very low level. Strikingly, assembly of the STT is not dependent on IHF, a host protein that is required for de novo assembly of all previously characterized Tn10 transpososomes. We suggest that disintegration substrates are able to form both transposon end and target type contacts with transposase because of their enhanced conformational flexibility. This probably allows the conformation of DNA within the complex that prevents the destructive disintegration reaction, and is responsible for relaxing the DNA sequence requirements for STT formation relative to other Tn10 transpososomes.

IHF-independent assembly of the Tn10 strand transfer transpososome: implications for inhibition of disintegration

PubMed Central

Stewart, Barry J.; Wardle, Simon J.; Haniford, David B.

2002-01-01

The frequency of DNA transposition in transposition systems that employ a strand transfer step may be significantly affected by the occurrence of a disintegration reaction, a reaction that reverses the strand transfer event. We have asked whether disintegration occurs in the Tn10 transposition system. We show that disintegration substrates (substrates constituting one half of the strand transfer product) are assembled into a transpososome that mimics the strand transfer intermediate. This strand transfer transpososome (STT) does appear to support an intermolecular disintegration reaction, but only at a very low level. Strikingly, assembly of the STT is not dependent on IHF, a host protein that is required for de novo assembly of all previously characterized Tn10 transpososomes. We suggest that disintegration substrates are able to form both transposon end and target type contacts with transposase because of their enhanced conformational flexibility. This probably allows the conformation of DNA within the complex that prevents the destructive disintegration reaction, and is responsible for relaxing the DNA sequence requirements for STT formation relative to other Tn10 transpososomes. PMID:12169640

[Primary, single-stage arterial switch operations at a newly-established, comprehensive congenital cardiac center performed in the neonatal age and beyond].

PubMed

Király, László; Tamás, Csaba

2015-06-21

Outcome of arterial switch operation for transposition of the great arteries with/without ventricular septal defect is a service key-performance-indicator. The aim of the authors was to assess patient characteristics and parameters in the perioperative course. In the setting of a newly-established, comprehensive tertiary-care center, primary complete repair was performed including associated anomalies, e.g. transverse arch repairs. Patients with d-transposition were grouped according to coexistence of ventricular septal defect. 118 arterial switch operations were performed between 2007 and 2014 with 96.62% survival (114/118). Ventricular septal defect and repair of associated anomalies did not yield worse outcome. Left ventricular re-training with late presentation necessitated mechanical circulatory support for 4.5±1.5 days. D-transposition is suitable for standardization of clinical algorithm and surgical technique. Quality standards contribute to excellent outcomes, minimize complications, and serve as blueprint for other neonatal open-heart procedures. Availability of mechanical circulatory support is key for single-stage left ventricular re-training beyond the neonatal period.

Surgical management of strabismus after rupture of the inferior rectus muscle.

PubMed

Paysse, E A; Saunders, R A; Coats, D K

2000-06-01

Rupture of an inferior rectus muscle is an uncommon problem. The resulting absence of infraduction and large hypertropia that result when the muscle cannot be repaired are challenging to manage surgically. We treated 2 patients who had traumatic rupture of the inferior rectus muscle. Both patients underwent an inferior transposition of the inferior halves of the medial and lateral rectus muscles without disinsertion (modified Jensen transposition procedure). Both patients had a persistent small overcorrection in the primary gaze position. One patient was treated with a second strabismus surgery consisting of a recession of the contralateral superior rectus muscle; the other was treated with prism glasses. Both achieved restoration of depression to approximately 40 degrees and single binocular vision in the primary position at distance, near, and in the reading position. This modified Jensen transposition procedure of the horizontal rectus muscles appears to be highly effective in the treatment of the hypertropia and infraduction deficit produced by rupture of the inferior rectus muscle. It also appears to be suitable for use in situations when other rectus muscles are absent or unavailable for surgical manipulation.

MCMC genome rearrangement.

PubMed

Miklós, István

2003-10-01

As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions and deletions, therefore phylogenetic investigations based on inversions, transpositions and inverted transpositions are less biased by the hypothesis on neutral evolution. Although efficient algorithms exist for obtaining the inversion distance of two signed permutations, there is no reliable algorithm when both inversions and transpositions are considered. Moreover, different type of mutations happen with different rates, and it is not clear how to weight them in a distance based approach. We introduce a Markov Chain Monte Carlo method to genome rearrangement based on a stochastic model of evolution, which can estimate the number of different evolutionary events needed to sort a signed permutation. The performance of the method was tested on simulated data, and the estimated numbers of different types of mutations were reliable. Human and Drosophila mitochondrial data were also analysed with the new method. The mixing time of the Markov Chain is short both in terms of CPU times and number of proposals. The source code in C is available on request from the author.

In vitro fertilization surrogate pregnancy in a patient who underwent radical hysterectomy followed by ovarian transposition, lower abdominal wall radiotherapy, and chemotherapy.

PubMed

Steigrad, Stephen; Hacker, Neville F; Kolb, Bradford

2005-05-01

To describe an IVF surrogate pregnancy from a patient who had a radical hysterectomy followed by excision of a laparoscopic port site implantation with ovarian transposition followed by abdominal wall irradiation and chemotherapy, which resulted in premature ovarian failure from which there was partial recovery. Case report. Tertiary referral university women's hospital in Sydney, Australia and private reproductive medicine clinic in California. A 34-year-old woman who underwent laparoscopy for pelvic pain, shortly afterward followed by radical hysterectomy and pelvic lymph node dissection, who subsequently developed a laparoscopic port site recurrence, which was excised in association with ovarian transposition before abdominal wall irradiation and chemotherapy. Modified IVF treatment, transabdominal oocyte retrieval, embryo cryopreservation in Australia, and transfer to a surrogate mother in the United States. Pregnancy. Miscarriage in the second cycle and a twin pregnancy in the fourth cycle. This is the first case report of ovarian stimulation and oocyte retrieval performed on transposed ovaries after a patient developed premature ovarian failure after radiotherapy and chemotherapy with subsequent partial ovarian recovery.

Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms.

PubMed

Zapata, Luis; Ding, Jia; Willing, Eva-Maria; Hartwig, Benjamin; Bezdan, Daniela; Jiao, Wen-Biao; Patel, Vipul; Velikkakam James, Geo; Koornneef, Maarten; Ossowski, Stephan; Schneeberger, Korbinian

2016-07-12

Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.

Flail Tricuspid Valve in an Adult Patient with Congenitally Corrected Transposition of the Great Arteries.

PubMed

Meloni, Luigi; Abbruzzese, Piero A.; Pirisi, Raimondo; Cherchi, Angelo

1997-01-01

We describe a case of a 50-year-old woman with congenitally corrected transposition of the great vessels, in whom severe left-sided tricuspid (systemic atrioventricular) valve insufficiency was the only associated anomaly. The tricuspid valve was dysplastic and abnormally oriented toward the interventricular septum, without the downward displacement of Ebstein's anomaly. The mechanism of atrioventricular regurgitation was unusual in that it consisted of the rupture of chordae tendineae of both the anterior and septal leaflets. The left-sided tricuspid valve was replaced with a St. Jude prosthesis and the postoperative course was uneventful.

The natural history of congenitally corrected transposition of the great arteries.

PubMed

Huhta, James

2011-01-01

The natural history of congenitally corrected transposition of the great arteries is of clinical/surgical importance once the fetus is born without heart block or signs of heart failure. Without significant tricuspid valve malformation, associated defects such as ventricular septal defect and left ventricular outflow obstruction can be repaired surgically. The mortality and long-term outcome appear to be linked strongly with the severity of tricuspid valve regurgitation. Some patients with an intact ventricular septum and no right ventricular dysfunction will live long lives without detection, and some women will successfully complete pregnancy.

Recurrent invasion and extinction of a selfish gene.

PubMed

Goddard, M R; Burt, A

1999-11-23

Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in populations even when they are of no benefit to the host organism. To test the idea that regular horizontal transmission is necessary for the long-term persistence of these genes, we surveyed 20 species of yeasts for the omega-homing endonuclease gene and associated group I intron. The status of omega could be categorized into three states (functional, nonfunctional, or absent), and status was not clustered on the host phylogeny. Moreover, the phylogeny of omega differed significantly from that of the host, strong evidence of horizontal transmission. Further analyses indicate that horizontal transmission is more common than transposition, and that it occurs preferentially between closely related species. Parsimony analysis and coalescent theory suggest that there have been 15 horizontal transmission events in the ancestry of our yeast species, through simulations indicate that this value is probably an underestimate. Overall, the data support a cyclical model of invasion, degeneration, and loss, followed by reinvasion, and each of these transitions is estimated to occur about once every 2 million years. The data are thus consistent with the idea that frequent horizontal transmission is necessary for the long-term persistence of homing endonuclease genes, and further, that this requirement limits these genes to organisms with easily accessible germ lines. The data also show that mitochondrial DNA sequences are transferred intact between yeast species; if other genes do not show such high levels of horizontal transmission, it would be due to lack of selection, rather than lack of opportunity.

Rapid generation of recombinant Pseudomonas putida secondary metabolite producers using yTREX.

PubMed

Domröse, Andreas; Weihmann, Robin; Thies, Stephan; Jaeger, Karl-Erich; Drepper, Thomas; Loeschcke, Anita

2017-12-01

Microbial secondary metabolites represent a rich source of valuable compounds with a variety of applications in medicine or agriculture. Effective exploitation of this wealth of chemicals requires the functional expression of the respective biosynthetic genes in amenable heterologous hosts. We have previously established the TREX system which facilitates the transfer, integration and expression of biosynthetic gene clusters in various bacterial hosts. Here, we describe the yTREX system, a new tool adapted for one-step yeast recombinational cloning of gene clusters. We show that with yTREX, Pseudomonas putida secondary metabolite production strains can rapidly be constructed by random targeting of chromosomal promoters by Tn5 transposition. Feasibility of this approach was corroborated by prodigiosin production after yTREX cloning, transfer and expression of the respective biosynthesis genes from Serratia marcescens . Furthermore, the applicability of the system for effective pathway rerouting by gene cluster adaptation was demonstrated using the violacein biosynthesis gene cluster from Chromobacterium violaceum , producing pathway metabolites violacein, deoxyviolacein, prodeoxyviolacein, and deoxychromoviridans. Clones producing both prodigiosin and violaceins could be readily identified among clones obtained after random chromosomal integration by their strong color-phenotype. Finally, the addition of a promoter-less reporter gene enabled facile detection also of phenazine-producing clones after transfer of the respective phenazine-1-carboxylic acid biosynthesis genes from Pseudomonas aeruginosa . All compounds accumulated to substantial titers in the mg range. We thus corroborate here the suitability of P. putida for the biosynthesis of diverse natural products, and demonstrate that the yTREX system effectively enables the rapid generation of secondary metabolite producing bacteria by activation of heterologous gene clusters, applicable for natural compound discovery and combinatorial biosynthesis.

Genomic Structural Variations Affecting Virulence During Clonal Expansion of Pseudomonas syringae pv. actinidiae Biovar 3 in Europe

PubMed Central

Firrao, Giuseppe; Torelli, Emanuela; Polano, Cesare; Ferrante, Patrizia; Ferrini, Francesca; Martini, Marta; Marcelletti, Simone; Scortichini, Marco; Ermacora, Paolo

2018-01-01

Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37). While no phenotype change associated with Tn6212 mobilization could be detected, strains CRAFRU 12.29 and CRAFRU 12.50 did not elicit the hypersensitivity response (HR) on tobacco and eggplant leaves and were limited in their growth in kiwifruit leaves due to insertion of ISPsy31 and ISPsy36 in the hrpS and hrpR genes, respectively, interrupting the hrp cluster. Both strains had been isolated from symptomatic plants, suggesting coexistence of variant strains with reduced virulence together with virulent strains in mixed populations. The structural differences caused by rearrangements of self-genetic elements within European and New Zealand strains were comparable in number and type to those occurring among the European strains, in contrast with the significant difference in terms of nucleotide polymorphisms. We hypothesize a relaxation, during clonal expansion, of the selection limiting the accumulation of deleterious mutations associated with genome structural variation due to transposition of mobile elements. This consideration may be relevant when evaluating strategies to be adopted for epidemics management. PMID:29675009

The Chromodomain of Tf1 Integrase Promotes Binding to cDNA and Mediates Target Site Selection▿ †

PubMed Central

Chatterjee, Atreyi Ghatak; Leem, Young Eun; Kelly, Felice D.; Levin, Henry L.

2009-01-01

The long terminal repeat (LTR) retrotransposon Tf1 of Schizosaccharomyces pombe integrates specifically into the promoters of pol II-transcribed genes. Its integrase (IN) contains a C-terminal chromodomain related to the chromodomains that bind to the N-terminal tail of histone H3. Although we have been unable to detect an interaction between histone tails and the chromodomain of Tf1 IN, it is possible that the chromodomain plays a role in directing IN to its target sites. To test this idea, we generated transposons with single amino acid substitutions in highly conserved residues of the chromodomain and created a chromodomain-deleted mutant. The mutations, V1290A, Y1292A, W1305A, and CHDΔ, substantially reduced transposition activity in vivo. Blotting assays showed that there was little or no reduction in the levels of IN or cDNA. By measuring the homologous recombination between cDNA and the plasmid copy of Tf1, we found that two of the mutations did not reduce the import of cDNA into the nucleus, while another caused a 33% reduction. Chromatin immunoprecipitation assays revealed that CHDΔ caused an approximately threefold reduction in the binding of IN to the downstream LTR of the cDNA. These data indicate that the chromodomain contributed directly to integration. We therefore tested whether the chromodomain contributed to selecting insertion sites. Results of a target plasmid assay showed that the deletion of the chromodomain resulted in a drastic reduction in the preference for pol II promoters. Collectively, these data indicate that the chromodomain promotes binding of cDNA and plays a key role in efficient targeting. PMID:19109383

The chromodomain of Tf1 integrase promotes binding to cDNA and mediates target site selection.

PubMed

Chatterjee, Atreyi Ghatak; Leem, Young Eun; Kelly, Felice D; Levin, Henry L

2009-03-01

The long terminal repeat (LTR) retrotransposon Tf1 of Schizosaccharomyces pombe integrates specifically into the promoters of pol II-transcribed genes. Its integrase (IN) contains a C-terminal chromodomain related to the chromodomains that bind to the N-terminal tail of histone H3. Although we have been unable to detect an interaction between histone tails and the chromodomain of Tf1 IN, it is possible that the chromodomain plays a role in directing IN to its target sites. To test this idea, we generated transposons with single amino acid substitutions in highly conserved residues of the chromodomain and created a chromodomain-deleted mutant. The mutations, V1290A, Y1292A, W1305A, and CHDDelta, substantially reduced transposition activity in vivo. Blotting assays showed that there was little or no reduction in the levels of IN or cDNA. By measuring the homologous recombination between cDNA and the plasmid copy of Tf1, we found that two of the mutations did not reduce the import of cDNA into the nucleus, while another caused a 33% reduction. Chromatin immunoprecipitation assays revealed that CHDDelta caused an approximately threefold reduction in the binding of IN to the downstream LTR of the cDNA. These data indicate that the chromodomain contributed directly to integration. We therefore tested whether the chromodomain contributed to selecting insertion sites. Results of a target plasmid assay showed that the deletion of the chromodomain resulted in a drastic reduction in the preference for pol II promoters. Collectively, these data indicate that the chromodomain promotes binding of cDNA and plays a key role in efficient targeting.

Homeland security in the C. elegans germ line: insights into the biogenesis and function of piRNAs.

PubMed

Kasper, Dionna M; Gardner, Kathryn E; Reinke, Valerie

2014-01-01

While most eukaryotic genomes contain transposable elements that can provide select evolutionary advantages to a given organism, failure to tightly control the mobility of such transposable elements can result in compromised genomic integrity of both parental and subsequent generations. Together with the Piwi subfamily of Argonaute proteins, small, non-coding Piwi-interacting RNAs (piRNAs) primarily function in the germ line to defend the genome against the potentially deleterious effects that can be caused by transposition. Here, we describe recent discoveries concerning the biogenesis and function of piRNAs in the nematode Caenorhabditis elegans, illuminating how the faithful production of these mature species can impart a robust defense mechanism for the germ line to counteract problems caused by foreign genetic elements across successive generations by contributing to the epigenetic memory of non-self vs. self.

Analysis of piRNA-mediated silencing of active TEs in Drosophila melanogaster suggests limits on the evolution of host genome defense.

PubMed

Kelleher, Erin S; Barbash, Daniel A

2013-08-01

The Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of transposable element (TE) infection by imposing small-RNA-mediated silencing. Because silencing is targeted by TE-derived piRNAs, piRNA production is posited to be central to the evolution of genome defense. We harnessed genomic data sets from Drosophila melanogaster, including genome-wide measures of piRNA, mRNA, and genomic abundance, along with estimates of age structure and risk of ectopic recombination, to address fundamental questions about the functional and evolutionary relationships between TE families and their regulatory piRNAs. We demonstrate that mRNA transcript abundance, robustness of "ping-pong" amplification, and representation in piRNA clusters together explain the majority of variation in piRNA abundance between TE families, providing the first robust statistical support for the prevailing model of piRNA biogenesis. Intriguingly, we also discover that the most transpositionally active TE families, with the greatest capacity to induce harmful mutations or disrupt gametogenesis, are not necessarily the most abundant among piRNAs. Rather, the level of piRNA targeting is largely independent of recent transposition rate for active TE families, but is rapidly lost for inactive TEs. These observations are consistent with population genetic theory that suggests a limited selective advantage for host repression of transposition. Additionally, we find no evidence that piRNA targeting responds to selection against a second major cost of TE infection: ectopic recombination between TE insertions. Our observations confirm the pivotal role of piRNA-mediated silencing in defending the genome against selfish transposition, yet also suggest limits to the optimization of host genome defense.

Cubital tunnel syndrome: comparative results of a multicenter study of 4 surgical techniques with a mean follow-up of 92 months.

PubMed

Bacle, G; Marteau, E; Freslon, M; Desmoineaux, P; Saint-Cast, Y; Lancigu, R; Kerjean, Y; Vernet, E; Fournier, J; Corcia, P; Le Nen, D; Rabarin, F; Laulan, J

2014-06-01

Cubital tunnel syndrome is the second most frequent entrapment syndrome. Physiopathology is mixed, and treatment options are multiple, none having yet proved superior efficacy. The present retrospective multicenter study compared results and rates of complications and recurrence between the 4 main cubital tunnel syndrome treatments, to identify trends and optimize outcome. Patients presenting with primary clinical cubital tunnel syndrome diagnosed on electroneuromyography were included and operated on using 1 of the following 4 techniques: open or endoscopic in situ decompression, or subcutaneous or submuscular anterior transposition. Four specialized upper-limb surgery centers participated, each systematically performing 1 of the above procedures. Subjective and objective results and rates of complications and recurrence were compared at end of follow-up. Five hundred and two patients were included and 375 followed up for a mean 92 months (range, 9-144 months); 103 were lost to follow-up and 24 died. Whichever the procedure, more than 90% of patients were cured or showed improvement. There was a single case of scar pain at end of follow-up, managed by endoscopic decompression; there were no other long-term complications. None of the 4 techniques aggravated symptoms. There were 6 recurrences by end of follow-up: 1 associated with open in situ decompression and 5 with submuscular transposition. Surgery was effective in treating cubital tunnel syndrome. Submuscular anterior transposition was associated with recurrence. In contrast to literature reports, subcutaneous anterior transposition, which is a reliable and valid technique, was not associated with a higher complication rate than in situ decompression. Level IV. Multicenter retrospective. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Comparison of the dental anomalies found in maxillary canine-first premolar transposition cases with those in palatally displaced canine cases.

PubMed

Scerri, Erica Sultana; McDonald, Fraser; Camilleri, Simon

2016-02-01

To compare the developmental dental anomalies associated with maxillary canine-first premolar (MxCP1) transposition and those of palatally displaced canine (PDC) with each other and with the background prevalence in the Maltese population in order to elucidate whether the two conditions have similar or differing genetic backgrounds. Dental records of 477 subjects with PDC, 57 subjects with MxCP1, and a control group of 500 subjects with no history of a PDC or tooth transposition were compared for canine eruption anomalies and hypodontia. A high frequency of bilateral occurrence was present for both canine malpositions and when unilateral, a trend to right-sided occurrence was evident. The occurrence of transpositions in the PDC group and of PDC in the MxCP1 group was higher than expected. The prevalence of incisor hypodontia was significantly higher in subjects with PDC and MxCP1, as compared to the control group. The size of the MxCP1 group is relatively small. The study population is a small isolated Caucasian population and the results may not be applicable to other populations. There is no significant difference between the MxCP1 and PDC groups in the prevalence or distribution of hypodontia and each of these groups exhibits a higher prevalence of the other canine anomaly. These findings support the theory that PDC and MxCP1 form part of a group of interrelated dental anomalies that share a common genetic basis. © The Author 2015. Published by Oxford University Press on behalf of the European Orthodontic Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Character Decomposition and Transposition Processes in Chinese Compound Words Modulates Attentional Blink.

PubMed

Cao, Hongwen; Gao, Min; Yan, Hongmei

2016-01-01

The attentional blink (AB) is the phenomenon in which the identification of the second of two targets (T2) is attenuated if it is presented less than 500 ms after the first target (T1). Although the AB is eliminated in canonical word conditions, it remains unclear whether the character order in compound words affects the magnitude of the AB. Morpheme decomposition and transposition of Chinese two-character compound words can provide an effective means to examine AB priming and to assess combinations of the component representations inherent to visual word identification. In the present study, we examined the processing of consecutive targets in a rapid serial visual presentation (RSVP) paradigm using Chinese two-character compound words in which the two characters were transposed to form meaningful words or meaningless combinations (reversible, transposed, or canonical words). We found that when two Chinese characters that form a compound word, regardless of their order, are presented in an RSVP sequence, the likelihood of an AB for the second character is greatly reduced or eliminated compared to when the two characters constitute separate words rather than a compound word. Moreover, the order of the report for the two characters is more likely to be reversed when the normal order of the two characters in a compound word is reversed, especially when the interval between the presentation of the two characters is extremely short. These findings are more consistent with the cognitive strategy hypothesis than the resource-limited hypothesis during character decomposition and transposition of Chinese two-character compound words. These results suggest that compound characters are perceived as a unit, rather than two separate words. The data further suggest that readers could easily understand the text with character transpositions in compound words during Chinese reading.

Evolutionary dynamics of autosomal-heterosomal rearrangements in a multiple-X chromosome system of tiger beetles (Cicindelidae)

PubMed Central

Galián, José; Proença, Sónia JR; Vogler, Alfried P

2007-01-01

Background Genetic systems involving multiple X chromosomes have arisen repeatedly in sexually reproducing animals. Tiger beetles (Cicindelidae) exhibit a phylogenetically ancient multiple-X system typically consisting of 2–4 X chromosomes and a single Y. Because recombination rates are suppressed in sex chromosomes, changes in their numbers and movement of genes between sex chromosomes and autosomes, could have important consequences for gene evolution and rates of speciation induced by these rearrangements. However, it remains unclear how frequent these rearrangements are and which genes are affected. Results Karyotype analyses were performed for a total of 26 North American species in the highly diverse genus Cicindela, tallying the number of X chromosomes and autosomes during mitosis and meiosis. The chromosomal location of the ribosomal rRNA gene cluster (rDNA) was used as an easily scored marker for genic turnover between sex chromosomes or autosomes. The findings were assessed in the light of a recent phylogenetic analysis of the group. While autosome numbers remained constant throughout the lineage, sex chromosome numbers varied. The predominant karyotype was n = 9+X1X2X3Y which was also inferred to be the ancestral state, with several changes to X1X2Y and X1X2X3X4Y confined to phylogenetically isolated species. The total (haploid) numbers of rDNA clusters varied between two, three, and six (in one exceptional case), and clusters were localized either on the autosomes, the sex chromosomes, or both. Transitions in rDNA localization and in numbers of rDNA clusters varied independently of each other, and also independently of changes in sex chromosome numbers. Conclusion Changes of X chromosome numbers and transposition of the rDNA locus (and presumably other genes) between autosomes and sex chromosomes in Cicindela occur frequently, and are likely to be the result of fusions or fissions between X chromosomes, rather than between sex chromosomes and autosomes. Yet, translocations between sex chromosomes and autosomes appear to be common, as indicated by the patterns of rDNA localization. Rearranged karyotypes involving multiple sex chromosomes would reduce recombination, and hybrid dysgenesis selects against polymorphic populations. Hence, the high frequency of these rearrangements could be a cause of the great species diversity in Cicindela. PMID:17822542

DNA transposons have colonized the genome of the giant virus Pandoravirus salinus.

PubMed

Sun, Cheng; Feschotte, Cédric; Wu, Zhiqiang; Mueller, Rachel Lockridge

2015-06-12

Transposable elements are mobile DNA sequences that are widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force in genome evolution. However, transposable elements have rarely been documented in viruses, and their contribution to viral genome evolution remains largely unexplored. Pandoraviruses are recently described DNA viruses with genome sizes that exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear to include substantial noncoding intergenic spaces, which provide potential locations for transposable element insertions. However, no mobile genetic elements have yet been reported in pandoravirus genomes. Here, we report a family of miniature inverted-repeat transposable elements (MITEs) in the Pandoravirus salinus genome, representing the first description of a virus populated with a canonical transposable element family that proliferated by transposition within the viral genome. The MITE family, which we name Submariner, includes 30 copies with all the hallmarks of MITEs: short length, terminal inverted repeats, TA target site duplication, and no coding capacity. Submariner elements show signs of transposition and are undetectable in the genome of Pandoravirus dulcis, the closest known relative Pandoravirus salinus. We identified a DNA transposon related to Submariner in the genome of Acanthamoeba castellanii, a species thought to host pandoraviruses, which contains remnants of coding sequence for a Tc1/mariner transposase. These observations suggest that the Submariner MITEs of P. salinus belong to the widespread Tc1/mariner superfamily and may have been mobilized by an amoebozoan host. Ten of the 30 MITEs in the P. salinus genome are located within coding regions of predicted genes, while others are close to genes, suggesting that these transposons may have contributed to viral genetic novelty. Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses. Our findings continue to blur the division between viral and cellular genomes, adhering to the emerging view that the content, dynamics, and evolution of the genomes of giant viruses do not substantially differ from those of cellular organisms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Finnerty, W.R.

We have sought the structural elucidation of the glycolipid biosurfactant. The extracellular glycolipid consists of 1 major component (>90%) plus 6--7 minor molecular species. The deacylated water-soluble backbone is common to all molecular species of the glycolipid. A complex fatty acid composition characterizes the glycolipid and contributes to its surface active character. The water soluble backbone consists of glycerol, trehalose and 3--5 glucose residues. FTIR spectroscopy has confirmed the presence of these polyhydric components. The next major objective has been to clone the genes for glycolipid biosynthesis in Rhodococcus sp. H13-A. Improvements in the E. coli-Rhodococcus shuttle vector, pMVS301, weremore » made prior to the construction and screening of a genomic library in Rhodococcus. A system is being developed for transpositional mutagenesis in Rhodococcus, using Tn917 containing plasmids used successfully in Bacillus sp. for the isolation and analysis of sporulation and developmental genes. We are also actively assessing the utility of this cloning and transformation system which we have developed for Rhodococcus, for use in mycobacterium, a related Actinomycete for which there exists no systems for plasmid transformation or molecular cloning. 8 refs., 1 fig.« less

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

PubMed Central

Muiño, Jose M.; de Bruijn, Suzanne; Pajoro, Alice; Geuten, Koen; Vingron, Martin; Angenent, Gerco C.; Kaufmann, Kerstin

2016-01-01

Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon. PMID:26429922

Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.

PubMed

Lucas, Bronwyn A; Lavi, Eitan; Shiue, Lily; Cho, Hana; Katzman, Sol; Miyoshi, Keita; Siomi, Mikiko C; Carmel, Liran; Ares, Manuel; Maquat, Lynne E

2018-01-30

Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3'-untranslated regions (3'-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3'-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3'-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20-25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

Analysis of strain-specific genes in glutamic acid-producing Corynebacterium glutamicum ssp. lactofermentum AJ 1511.

PubMed

Nishio, Yousuke; Koseki, Chie; Tonouchi, Naoto; Matsui, Kazuhiko; Sugimoto, Shinichi; Usuda, Yoshihiro

2017-07-11

Strains of the bacterium, Corynebacterium glutamicum, are widely used for the industrial production of L-glutamic acid and various other substances. C. glutamicum ssp. lactofermentum AJ 1511, formerly classified as Brevibacterium lactofermentum, and the closely related C. glutamicum ATCC 13032 have been used as industrial strains for more than 50 years. We determined the whole genome sequence of C. glutamicum AJ 1511 and performed genome-wide comparative analysis with C. glutamicum ATCC 13032 to determine strain-specific genetic differences. This analysis revealed that the genomes of the two industrial strains are highly similar despite the phenotypic differences between the two strains. Both strains harbored unique genes but gene transpositions or inversions were not observed. The largest unique region, a 220-kb AT-rich region located between 1.78 and 2.00 Mb position in C. glutamicum ATCC 13032 genome, was missing in the genome of C. glutamicum AJ 1511. The next two largest unique regions were present in C. glutamicum AJ 1511. The first region (413-484 kb position) contains several predicted transport proteins, enzymes involved in sugar metabolism, and transposases. The second region (1.47-1.50 Mb position) encodes restriction modification systems. A gene predicted to encode NADH-dependent glutamate dehydrogenase, which is involved in L-glutamate biosynthesis, is present in C. glutamicum AJ 1511. Strain-specific genes identified in this study are likely to govern phenotypes unique to each strain.

Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells.

PubMed

Luo, Wentian; Galvan, Daniel L; Woodard, Lauren E; Dorset, Dan; Levy, Shawn; Wilson, Matthew H

2017-08-21

Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes without requiring homologous recombination. We systematically compared four different engineered zinc finger proteins (ZFP), four transcription activator-like effector proteins (TALE), CRISPR associated protein 9 (SpCas9) and the catalytically inactive dSpCas9 protein fused to the amino-terminus of the transposase enzyme designed to target the hypoxanthine phosphoribosyltransferase (HPRT) gene located on human chromosome X. Chimeric transposases were evaluated for expression, transposition activity, chromatin immunoprecipitation at the target loci, and targeted knockout of the HPRT gene in human cells. One ZFP-PB and one TALE-PB chimera demonstrated notable HPRT gene targeting. In contrast, Cas9/dCas9-PB chimeras did not result in gene targeting. Instead, the HPRT locus appeared to be protected from transposon integration. Supplied separately, PB permitted highly efficient isolation of Cas9-mediated knockout of HPRT, with zero transposon integrations in HPRT by deep sequencing. In summary, these tools may allow isolation of 'targeted-only' cells, be utilized to protect a genomic locus from transposon integration, and enrich for Cas9-mutated cells. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

PubMed Central

2010-01-01

Background Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis. Results The six Asian Crassostrea mt genomes ranged from 18,226 to 22,446 bp in size, and all coded for 39 genes (12 proteins, 2 rRNAs and 25 tRNAs) on the same strand. Their genomes contained a split of the rrnL gene and duplication of trnM, trnK and trnQ genes. They shared the same gene order that differed from an Atlantic sister species by as many as nine tRNA changes (6 transpositions and 3 duplications) and even differed significantly from S. mordax in protein-coding genes. Phylogenetic analysis indicates that the six Asian Crassostrea species emerged between 3 and 43 Myr ago, while the Atlantic species evolved 83 Myr ago. Conclusions The complete conservation of gene order in the six Asian Crassostrea species over 43 Myr is highly unusual given the remarkable rate of rearrangements in their sister species and other bivalves. It provides strong evidence for the recent speciation of the six Crassostrea species in Asia. It further indicates that changes in mt gene order may not be strictly a function of time but subject to other constraints that are presently not well understood. PMID:21189147

Acquisition and amplification of a testis-expressed autosomal gene, SSL, by the Drosophila Y chromosome

PubMed Central

Kalmykova, Alla I.; Shevelyov, Yury Y.; Dobritsa, Anna A.; Gvozdev, Vladimir A.

1997-01-01

The acquisition of autosomal fertility genes has been proposed to be an important process in human Y chromosome evolution. For example, the Y-linked fertility factor DAZ (Deleted in Azoospermia) appears to have arisen after the transposition and tandem amplification of the autosomal DAZH gene. The Drosophila melanogaster Y chromosome contains tandemly repeated Su(Ste) units that are thought to affect male fertility as suppressors of the homologous X-linked Stellate repeats. Here we report the detection of a testis-expressed autosomal gene, SSL [Su(Ste)-like], that appears to be an ancestor of the Y-linked Su(Ste) units. SSL encodes a casein kinase 2 (CK2) β-subunit-like protein. Its putative ORF shares extensive (45%) homology with the genuine β-subunit of CK2 and retains the conserved C-terminal and Glu/Asp-rich domains that are essential for CK2 holoenzyme regulation. SSL maps within region 60D1–2 of D. melanogaster and D. simulans polytene chromosomes. We present evidence that SSL was derived from the genuine βCK2 gene by reverse transcription. This event resulted in the loss of the first three introns in the coding region of the SSL ancestor gene. Evolutionary analysis indicates that SSL has evolved under selective pressure at the translational level. Its sequence, especially in the 3′ region, is much closer to the Y-linked Su(Ste) tandem repeats than to the βCK2 gene. These results suggest that the acquisition of testis-specific autosomal genes may be important for the evolution of Drosophila as well as human Y chromosomes. PMID:9177211

Dynamics of genome size evolution in birds and mammals

PubMed Central

Feschotte, Cédric

2017-01-01

Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified “accordion” model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives. PMID:28179571

Identification of Male Gametogenesis Expressed Genes from the Scallop Nodipecten subnodosus by Suppressive Subtraction Hybridization and Pyrosequencing

PubMed Central

Llera-Herrera, Raúl; García-Gasca, Alejandra; Abreu-Goodger, Cei; Huvet, Arnaud; Ibarra, Ana M.

2013-01-01

Despite the great advances in sequencing technologies, genomic and transcriptomic information for marine non-model species with ecological, evolutionary, and economical interest is still scarce. In this work we aimed to identify genes expressed during spermatogenesis in the functional hermaphrodite scallop Nodipecten subnodosus (Mollusca: Bivalvia: Pectinidae), with the purpose of obtaining a panel of genes that would allow for the study of differentially transcribed genes between diploid and triploid scallops in the context of meiotic arrest and reproductive sterility. Because our aim was to isolate genes involved in meiosis and other testis maturation-related processes, we generated suppressive subtractive hybridization libraries of testis vs. inactive gonad. We obtained 352 and 177 ESTs by clone sequencing, and using pyrosequencing (454-Roche) we maximized the identified ESTs to 34,276 reads. A total of 1,153 genes from the testis library had a blastx hit and GO annotation, including genes specific for meiosis, spermatogenesis, sex-differentiation, and transposable elements. Some of the identified meiosis genes function in chromosome pairing (scp2, scp3), recombination and DNA repair (dmc1, rad51, ccnb1ip1/hei10), and meiotic checkpoints (rad1, hormad1, dtl/cdt2). Gene expression analyses in different gametogenic stages in both sexual regions of the gonad of meiosis genes confirmed that the expression was specific or increased towards the maturing testis. Spermatogenesis genes included known testis-specific ones (kelch-10, shippo1, adad1), with some of these known to be associated to sterility. Sex differentiation genes included one of the most conserved genes at the bottom of the sex-determination cascade (dmrt1). Transcript from transposable elements, reverse transcriptase, and transposases in this library evidenced that transposition is an active process during spermatogenesis in N. subnodosus. In relation to the inactive library, we identified 833 transcripts with functional annotation related to activation of the transcription and translation machinery, as well as to germline control and maintenance. PMID:24066034

Meeting report for mobile DNA 2010.

PubMed

Chaconas, George; Craig, Nancy; Curcio, M Joan; Deininger, Prescott; Feschotte, Cedric; Levin, Henry; Rice, Phoebe A; Voytas, Daniel F

2010-08-24

An international conference on mobile DNA was held 24-28 April 2010 in Montreal, Canada. Sponsored by the American Society for Microbiology, the conference's goal was to bring together researchers from around the world who study transposition in diverse organisms using multiple experimental approaches. The meeting drew over 190 attendees and most contributed through poster presentations, invited talks and short talks selected from poster abstracts. The talks were organized into eight scientific sessions, which ranged in topic from the evolutionary dynamics of mobile genetic elements to transposition reaction mechanisms. Here we present highlights from the platform sessions with a focus on talks presented by the invited speakers.

[Surrogate mothers and ovarian transposition: two attitudes to be considered in young women with cervical carcinoma. A case report].

PubMed

Giacalone, P L; Sobierajksi, J; Benos, P; Giovannini, N; Laffargue, F; Hédon, B

2003-02-01

In cases of cervical cancer, there are 2 major advantages to preserving the ovaries, with or without transposition: hormone function is maintained during subsequent cancer treatment and patient quality of life is improved. We report the first case of pregnancy in a surrogate mother following stimulation of a transposed ovary before irradiation and chemotherapy for a squamous cell carcinoma of the uterine cervix. Because of the wide dissemination of information on the technical progress in this area, patients are now in a position to make therapeutic choices that are no longer guided by strictly medical considerations.

Compressive Neuropathy of the Ulnar Nerve: A Perspective on History and Current Controversies.

PubMed

Eberlin, Kyle R; Marjoua, Youssra; Jupiter, Jesse B

2017-06-01

The untoward effects resulting from compression of the ulnar nerve have been recognized for almost 2 centuries. Initial treatment of cubital tunnel syndrome focused on complete transection of the nerve at the level of the elbow, resulting in initial alleviation of pain but significant functional morbidity. A number of subsequent techniques have been described including in situ decompression, subcutaneous transposition, submuscular transposition, and most recently, endoscopic release. This manuscript focuses on the historical aspects of each of these treatments and our current understanding of their efficacy. Copyright © 2017 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

The expanding universe of transposon technologies for gene and cell engineering.

PubMed

Ivics, Zoltán; Izsvák, Zsuzsanna

2010-12-07

Transposable elements can be viewed as natural DNA transfer vehicles that, similar to integrating viruses, are capable of efficient genomic insertion. The mobility of class II transposable elements (DNA transposons) can be controlled by conditionally providing the transposase component of the transposition reaction. Thus, a DNA of interest (be it a fluorescent marker, a small hairpin (sh)RNA expression cassette, a mutagenic gene trap or a therapeutic gene construct) cloned between the inverted repeat sequences of a transposon-based vector can be used for stable genomic insertion in a regulated and highly efficient manner. This methodological paradigm opened up a number of avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture, the production of germline transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species, and therapy of genetic disorders in humans. Sleeping Beauty (SB) was the first transposon shown to be capable of gene transfer in vertebrate cells, and recent results confirm that SB supports a full spectrum of genetic engineering including transgenesis, insertional mutagenesis, and therapeutic somatic gene transfer both ex vivo and in vivo. The first clinical application of the SB system will help to validate both the safety and efficacy of this approach. In this review, we describe the major transposon systems currently available (with special emphasis on SB), discuss the various parameters and considerations pertinent to their experimental use, and highlight the state of the art in transposon technology in diverse genetic applications.

Structural Determinants of Sleeping Beauty Transposase Activity

PubMed Central

Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

2016-01-01

Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called “sectors”, which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. PMID:27401040

Foldback intercoil DNA and the mechanism of DNA transposition.

PubMed

Kim, Byung-Dong

2014-09-01

Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as 180° and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed.

Does letter position coding depend on consonant/vowel status? Evidence with the masked priming technique.

PubMed

Perea, Manuel; Acha, Joana

2009-02-01

Recently, a number of input coding schemes (e.g., SOLAR model, SERIOL model, open-bigram model, overlap model) have been proposed that capture the transposed-letter priming effect (i.e., faster response times for jugde-JUDGE than for jupte-JUDGE). In their current version, these coding schemes do not assume any processing differences between vowels and consonants. However, in a lexical decision task, Perea and Lupker (2004, JML; Lupker, Perea, & Davis, 2008, L&CP) reported that transposed-letter priming effects occurred for consonant transpositions but not for vowel transpositions. This finding poses a challenge for these recently proposed coding schemes. Here, we report four masked priming experiments that examine whether this consonant/vowel dissociation in transposed-letter priming is task-specific. In Experiment 1, we used a lexical decision task and found a transposed-letter priming effect only for consonant transpositions. In Experiments 2-4, we employed a same-different task - a task which taps early perceptual processes - and found a robust transposed-letter priming effect that did not interact with consonant/vowel status. We examine the implications of these findings for the front-end of the models of visual word recognition.

Paraspinal Transposition Flap for Reconstruction of Sacral Soft Tissue Defects: A Series of 53 Cases from a Single Institute

PubMed Central

Chattopadhyay, Debarati; Agarwal, Akhilesh Kumar; Guha, Goutam; Bhattacharya, Nirjhar; Chumbale, Pawan K; Gupta, Souradip; Murmu, Marang Buru

2014-01-01

Study Design Case series. Purpose To describe paraspinal transposition flap for coverage of sacral soft tissue defects. Overview of Literature Soft tissue defects in the sacral region pose a major challenge to the reconstructive surgeon. Goals of sacral wound reconstruction are to provide a durable skin and soft tissue cover adequate for even large sacral defects; minimize recurrence; and minimize donor site morbidity. Various musculocutaneous and fasciocutanous flaps have been described in the literature. Methods The flap was applied in 53 patients with sacral soft tissue defects of diverse etiology. Defects ranged in size from small (6 cm×5 cm) to extensive (21 cm×10 cm). The median age of the patients was 58 years (range, 16-78 years). Results There was no flap necrosis. Primary closure of donor sites was possible in all the cases. The median follow up of the patients was 33 months (range, 4-84 months). The aesthetic outcomes were acceptable. There has been no recurrence of pressure sores. Conclusions The authors conclude that paraspinal transposition flap is suitable for reconstruction of large sacral soft tissue defects with minimum morbidity and excellent long term results. PMID:24967044

Delivering the Goods for Genome Engineering and Editing.

PubMed

Skipper, Kristian Alsbjerg; Mikkelsen, Jacob Giehm

2015-08-01

A basic understanding of genome evolution and the life and impact of microorganisms, like viruses and bacteria, has been fundamental in the quest for efficient genetic therapies. The expanding tool box for genetic engineering now contains transposases, recombinases, and nucleases, all created from naturally occurring genome-modifying proteins. Whereas conventional gene therapies have sought to establish sustained expression of therapeutic genes, genomic tools are needed only in a short time window and should be delivered to cells ideally in a balanced "hit-and-run" fashion. Current state-of-the-art delivery strategies are based on intracellular production of protein from transfected plasmid DNA or in vitro-transcribed RNA, or from transduced viral templates. Here, we discuss advantages and challenges of intracellular production strategies and describe emerging approaches based on the direct delivery of protein either by transfer of recombinant protein or by lentiviral protein transduction. With focus on adapting viruses for protein delivery, we describe the concept of "all-in-one" lentiviral particles engineered to codeliver effector proteins and donor sequences for DNA transposition or homologous recombination. With optimized delivery methods-based on transferring DNA, RNA, or protein-it is no longer far-fetched that researchers in the field will indeed deliver the goods for somatic gene therapies.

piggyBac Transposon-Mediated Transgenesis in the Apicomplexan Parasite Eimeria tenella

PubMed Central

Su, Huali; Liu, Xianyong; Yan, Wenchao; Shi, Tuanyuan; Zhao, Xinxin; Blake, Damer P.; Tomley, Fiona M.; Suo, Xun

2012-01-01

piggyBac, a type II transposon that is useful for efficient transgenesis and insertional mutagenesis, has been used for effective and stable transfection in a wide variety of organisms. In this study we investigate the potential use of the piggyBac transposon system for forward genetics studies in the apicomplexan parasite Eimeria tenella. Using the restriction enzyme-mediated integration (REMI) method, E. tenella sporozoites were electroporated with a donor plasmid containing the enhanced yellow fluorescent protein (EYFP) gene flanked by piggyBac inverted terminal repeats (ITRs), an Asc I-linearized helper plasmid containing the transposase gene and the restriction enzyme Asc I. Subsequently, electroporated sporozoites were inoculated into chickens via the cloacal route and transfected progeny oocysts expressing EYFP were sorted by flow cytometry. A transgenic E. tenella population was selected by successive in vivo passage. Southern-blotting analysis showed that exogenous DNA containing the EYFP gene was integrated into the parasite genome at a limited number of integration sites and that the inserted part of the donor plasmid was the fragment located between the 5′ and 3′ ITRs as indicated by primer-specific PCR screening. Genome walking revealed that the insertion sites were TTAA-specific, which is consistent with the transposition characteristics of piggyBac. PMID:22768223

The Long Terminal Repeat Retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe.

PubMed

Esnault, Caroline; Levin, Henry L

2015-08-01

The long terminal repeat (LTR) retrotransposons Tf1 and Tf2 of Schizosaccharomyces pombe are active mobile elements of the Ty3/gypsy family. The mobilization of these retrotransposons depends on particle formation, reverse transcription and integration, processes typical of other LTR retrotransposons. However, Tf1 and Tf2 are distinct from other LTR elements in that they assemble virus-like particles from a single primary translation product, initiate reverse transcription with an unusual self-priming mechanism, and, in the case of Tf1, integrate with a pattern that favors specific promoters of RNA pol II-transcribed genes. To avoid the chromosome instability and genome damage that results from increased copy number, S. pombe applies a variety of defense mechanisms that restrict Tf1 and Tf2 activity. The mRNA of the Tf elements is eliminated by an exosome-based pathway when cells are in favorable conditions whereas nutrient deprivation triggers an RNA interference-dependent pathway that results in the heterochromatization of the elements. Interestingly, Tf1 integrates into the promoters of stress-induced genes and these insertions are capable of increasing the expression of adjacent genes. These properties of Tf1 transposition raise the possibility that Tf1 benefits cells with specific insertions by providing resistance to environmental stress.

Lack of effect of bone morphogenetic protein 2 and 4 gene polymorphisms on bone density in postmenopausal Turkish women.

PubMed

Ozkan, Z S; Deveci, D; Onalan Etem, E; Yüce, H

2010-11-30

We investigated the effect of bone morphogenetic protein 2 and 4 (BMP-2 and -4) gene polymorphisms on bone density in postmenopausal Turkish women with osteoporosis. The frequency of single-nucleotide polymorphisms (SNPs) of BMP-2 and -4 genes was analyzed in 101 osteoporotic-postmenopausal women and 52 postmenopausal women with positive bone mineral density scores. We evaluated the frequency of the thymine→cytosine nucleotide variation at position 538 for BMP-4 and the transposition of adenine→thymine at codon 190 for BMP-2, with PCR. The proportions of genotypes observed for the BMP-2 SNP in the osteoporotic group were AA (47.5%), AT (39.6%), TT (12.9%), and in the non-osteoporotic group they were AA (48.1%), AT (40.4%), TT (11.5%). The corresponding frequencies for the BMP-4 SNP in the osteoporotic group were TT (30.7%), TC (45.5%), CC (23.8%), and in the non-osteoporotic group they were TT (26.9%), TC (40.4%), CC (32.7%). There were no significant differences in the frequencies of these genotypes between the patient and control groups. We conclude that genetic variations in BMP-2 and -4 do not substantially contribute to lumbar spine bone mineral density in postmenopausal Turkish women.

Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase

PubMed Central

Baharoglu, Zeynep; Babosan, Anamaria; Mazel, Didier

2014-01-01

Sub-inhibitory concentrations (sub-MIC) of antibiotics play a very important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated. PMID:24319148

Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase.

PubMed

Baharoglu, Zeynep; Babosan, Anamaria; Mazel, Didier

2014-02-01

Sub-inhibitory concentrations (sub-MIC) of antibiotics play a very important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated.

Heterologous Production and Yield Improvement of Epothilones in Burkholderiales Strain DSM 7029.

PubMed

Bian, Xiaoying; Tang, Biao; Yu, Yucong; Tu, Qiang; Gross, Frank; Wang, Hailong; Li, Aiying; Fu, Jun; Shen, Yuemao; Li, Yue-Zhong; Stewart, A Francis; Zhao, Guoping; Ding, Xiaoming; Müller, Rolf; Zhang, Youming

2017-07-21

The cloning of microbial natural product biosynthetic gene clusters and their heterologous expression in a suitable host have proven to be a feasible approach to improve the yield of valuable natural products and to begin mining cryptic natural products in microorganisms. Myxobacteria are a prolific source of novel bioactive natural products with only limited choices of heterologous hosts that have been exploited. Here, we describe the use of Burkholderiales strain DSM 7029 as a potential heterologous host for the functional expression of myxobacterial secondary metabolites. Using a newly established electroporation procedure, the 56 kb epothilone biosynthetic gene cluster from the myxobacterium Sorangium cellulosum was introduced into the chromosome of strain DSM 7029 by transposition. Production of epothilones A, B, C, and D was detected despite their yields being low. Optimization of the medium, introduction of the exogenous methylmalonyl-CoA biosynthetic pathway, and overexpression of rare tRNA genes resulted in an approximately 75-fold increase in the total yields of epothilones to 307 μg L -1 . These results show that strain DSM 7029 has the potential to produce epothilones with reasonable titers and might be a broadly applicable host for the heterologous expression of other myxobacterial polyketide synthases and nonribosomal peptide synthetases, expediting the process of genome mining.

Generation of a transgenic cashmere goat using the piggyBac transposition system.

PubMed

Bai, Ding-Ping; Yang, Ming-Ming; Qu, Lei; Chen, Yu-Lin

2017-04-15

The development of transgenic technologies in the Cashmere goat (Capra hircus) has the potential to improve the quality of the meat and wool. The piggyBac (PB) transposon system is highly efficient and can be used to transpose specific target genes into the genome. Here, we developed a PB transposon system to produce transgenic Cashmere goat fetal fibroblasts (GFFs) with the enhanced green fluorescent protein (EGFP). We then used the genetically modified GFFs as nuclear donors to generate transgenic embryos by somatic cell nuclear transfer (SCNT). The embryos (n = 40) were implanted into female goats (n = 20). One transgenic kid that expressed EGFP throughout the surface features of its body was born. This result demonstrated the usefulness of PB transposon system in generating transgenic Cashmere goats. Copyright © 2017 Elsevier Inc. All rights reserved.

Drifter, a novel, low copy hAT-like transposon in Fusarium oxysporum is activated during starvation.

PubMed

Rep, Martijn; van der Does, H Charlotte; Cornelissen, Ben J C

2005-06-01

The facultative pathogenic fungus Fusarium oxysporum is known to harbour many different transposable and/or repetitive elements. We have identified Drifter, a novel DNA transposon of the hAT family in F. oxysporum. It was found adjoining SIX1-H, a truncated homolog of the SIX1 avirulence gene in F. oxysporum f. sp. lycopersici. Absence of a target site duplication as well as the 5' part of SIX1-H suggests that transposition of Drifter into the ancestor of SIX1-H was followed by loss of a chromosomal segment through recombination between Drifters. F. oxysporum isolates belonging to various formae speciales harbour between 0 and 5 full-length copies of Drifter and/or one or more copies with an internal deletion. Transcription of Drifter is activated during starvation for carbon or nitrogen.

Insertion sequence diversity in archaea.

PubMed

Filée, J; Siguier, P; Chandler, M

2007-03-01

Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.

[Early hypertrophic scar after surgery on the nasal region: value of long-acting corticosteroid injections].

PubMed

Amici, J-M

2014-01-01

"Pincushioning" is a complication of post-surgical scarring following use of transposition flaps particularly when surgery is performed on the nasal region. The transposition flap technique is very useful for the repair of certain defects of the tip of the nose, the medial canthus or of the ala nasi. The aim of this study is to define the clinical characteristics of this scarring dystrophy, which we propose to call "early hypertrophy scarring", to clarify the nature thereof and to assess the efficacy of intralesional injection of corticosteroids at the first signs of hypertrophy. A prospective, open, non-comparative, single-centre study examined the clinical and histological characteristics of early hypertrophy scarring and the effectiveness of therapy with one or two injections of corticosteroids performed on the 15th day post-operatively and optionally repeated at D45 depending on the outcome. From January 2011 to January 2013, 12 consecutive patients with early hypertrophy scarring were included (ten men and two women - mean age: 64 years). All had undergone surgery for basal cell carcinoma under local anaesthesia with one-stage repair by means of a rhombic flap or a bilobed flap located in the nasal area. Scars were injected strictly intra-lesionally with triamcinolone acetate (40 mg/1 mL) until whitening occurred. A single injection was performed in three cases of rhombic flap while a second injection was given at D45 in the remaining nine cases. Complete regression of the early hypertrophy scarring was obtained in ten of the 12 patients by D90. Incomplete regression was observed but with a marked improvement in the other two patients. Early hypertrophy scarring is distinguished by its clinical characteristics of hypertrophic or keloid scars. Biopsy performed in two cases showed the fibrous but non-fatty nature of early hypertrophy scarring. Biomechanical factors particular to the nasal region and the transposition flap technique could account for the early and excessive collagen production causing early hypertrophy scarring. Early injection of corticosteroids, which was consistently effective in our study, could represent a simple treatment for early hypertrophy scarring, thus avoiding surgical correction. These preliminary results in a small number of patients require confirmation by a comparative, multicentre, prospective controlled study. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

ADP and brucellosis indemnity systems development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanders, W.M.; Harlan, B.L.

1976-01-01

Our initial study of the USDA/TAHC Brucellosis Indemnity Program in Texas has shown that both the efficiency and rate of claim payments can be increased by the application of present day computer technologies. Two main factors contribute to these increases: the number of discrepancies that are caused by poor penmanship, transposition of numbers, and other human errors can be monitored and minimized; and the documented information can be indexed, sorted, and searched faster, more efficiently, and without human error. The overall flow of documentation that is used to control the movement of infected or exposed animals through commerce should bemore » studied. A new system should be designed that fully utilizes present day computer and electronic technologies.« less

Transposition cutaneous flap and split skin mesh graft as combined optimal treatment approach for Giant Neglected multicentric BCC of the Shoulder.

PubMed

Tchernev, Georgi; Pidakev, Ivan

2018-05-31

We report for a 70-year-old cachectic patient - 165 cm, 45 kg, who was admitted for the first time to the dematosurgical unit for a surgical removal of a tumor formation localized in the region of the back from more than 15 years (fig. 1a). In the last few months the lesion has increased significantly in size and causes burning sensation, mild pain and abundant secretion of bloody yellow secretions (fig. 1a). During the dermatological examination a tumor-like formation in the left scapular region was visualized, This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.

PubMed

Tang, Haibao; Bomhoff, Matthew D; Briones, Evan; Zhang, Liangsheng; Schnable, James C; Lyons, Eric

2015-11-11

The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity for studying gene loss and gene transposition. However, the identification of syntenic regions requires complex analyses which must be repeated for pairwise comparisons between any two species. Therefore, as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of target genomes. SynFind is capable of reporting per-gene information, useful for researchers studying specific gene families, as well as genome-wide data sets of syntenic gene and predicted gene locations, critical for researchers focused on large-scale genomic analyses. Inference of syntenic homologs provides the basis for correlation of functional changes around genes of interests between related organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic data from over 15,000 organisms from all domains of life as well as supporting multiple releases of the same organism. SynFind makes use of a powerful job execution framework that promises scalability and reproducibility. SynFind can be accessed at http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Walking tree heuristics for biological string alignment, gene location, and phylogenies

NASA Astrophysics Data System (ADS)

Cull, P.; Holloway, J. L.; Cavener, J. D.

1999-03-01

Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids (proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and aligning strings brings out their shared characteristics. Although string matching is well-understood in the edit-distance model, biological strings with transpositions and inversions violate this model's assumptions. We propose a family of heuristics called walking trees to align biologically reasonable strings. Both edit-distance and walking tree methods can locate specific genes within a large string when the genes' sequences are given. When we attempt to match whole strings, the walking tree matches most genes, while the edit-distance method fails. We also give examples in which the walking tree matches substrings even if they have been moved or inverted. The edit-distance method was not designed to handle these problems. We include an example in which the walking tree "discovered" a gene. Calculating scores for whole genome matches gives a method for approximating evolutionary distance. We show two evolutionary trees for the picornaviruses which were computed by the walking tree heuristic. Both of these trees show great similarity to previously constructed trees. The point of this demonstration is that WHOLE genomes can be matched and distances calculated. The first tree was created on a Sequent parallel computer and demonstrates that the walking tree heuristic can be efficiently parallelized. The second tree was created using a network of work stations and demonstrates that there is suffient parallelism in the phylogenetic tree calculation that the sequential walking tree can be used effectively on a network.

Infraorbital nerve transposition to expand the endoscopic transnasal maxillectomy.

PubMed

Salzano, Giovanni; Turri-Zanoni, Mario; Karligkiotis, Apostolos; Zocchi, Jacopo; Dell'Aversana Orabona, Giovanni; Califano, Luigi; Battaglia, Paolo; Castelnuovo, Paolo

2017-02-01

The infraorbital nerve (ION) is a terminal branch of the maxillary nerve (V2) providing sensory innervation to the malar skin. It is sometimes necessary to sacrifice the ION and its branches to obtain adequate maxillary sinus exposure for radical resection of sinonasal tumors. Consequently, patients suffer temporary or permanent paresthesia, hypoestesthia, and neuralgia of the face. We describe an innovative technique used for preservation of the ION while removing the anterior, superior, and lateral walls of the maxillary sinus through a medial endoscopic transnasal maxillectomy. All patients who underwent transnasal endoscopic maxillectomy with ION transposition in our institute were retrospectively reviewed. Two patients were identified who had been treated for sinonasal cancers using this approach. No major complications were observed. Transient loss of ION function was observed with complete recovery of skin sensory perception within 6 months of surgery. One patient referred to a mild permanent anesthesia of the upper incisors. No diplopia or enophthalmos were encountered in any of the patients. The ION transposition is useful for selected cases of benign and malignant sinonasal tumors that do not infiltrate the ION itself but involve the surrounding portion of the maxillary sinus. Anatomic preservation of the ION seems to be beneficial to the postoperative quality of life of such patients. © 2016 ARS-AAOA, LLC.

Children and adults both see 'pirates' in 'parties': letter-position effects for developing readers and skilled adult readers.

PubMed

Paterson, Kevin B; Read, Josephine; McGowan, Victoria A; Jordan, Timothy R

2015-03-01

Developing readers often make anagrammatical errors (e.g. misreading pirates as parties), suggesting they use letter position flexibly during word recognition. However, while it is widely assumed that the occurrence of these errors decreases with increases in reading skill, empirical evidence to support this distinction is lacking. Accordingly, we compared the performance of developing child readers (aged 8-10 years) against the end-state performance of skilled adult readers in a timed naming task, employing anagrams used previously in this area of research. Moreover, to explore the use of letter position by developing readers and skilled adult readers more fully, we used anagrams which, to form another word, required letter transpositions over only interior letter positions, or both interior and exterior letter positions. The patterns of effects across these two anagram types for the two groups of readers were very similar. In particular, both groups showed similarly slowed response times (and developing readers increased errors) for anagrams requiring only interior letter transpositions but not for anagrams that required exterior letter transpositions. This similarity in the naming performance of developing readers and skilled adult readers suggests that the end-state skilled use of letter position is established earlier during reading development than is widely assumed. © 2014 John Wiley & Sons Ltd.

Letter position coding across modalities: braille and sighted reading of sentences with jumbled words.

PubMed

Perea, Manuel; Jiménez, María; Martín-Suesta, Miguel; Gómez, Pablo

2015-04-01

This article explores how letter position coding is attained during braille reading and its implications for models of word recognition. When text is presented visually, the reading process easily adjusts to the jumbling of some letters (jugde-judge), with a small cost in reading speed. Two explanations have been proposed: One relies on a general mechanism of perceptual uncertainty at the visual level, and the other focuses on the activation of an abstract level of representation (i.e., bigrams) that is shared by all orthographic codes. Thus, these explanations make differential predictions about reading in a tactile modality. In the present study, congenitally blind readers read sentences presented on a braille display that tracked the finger position. The sentences either were intact or involved letter transpositions. A parallel experiment was conducted in the visual modality. Results revealed a substantially greater reading cost for the sentences with transposed-letter words in braille readers. In contrast with the findings with sighted readers, in which there is a cost of transpositions in the external (initial and final) letters, the reading cost in braille readers occurs serially, with a large cost for initial letter transpositions. Thus, these data suggest that the letter-position-related effects in visual word recognition are due to the characteristics of the visual stream.

Nematicidal protease genes screened from a soil metagenomic library to control Radopholus similis mediated by Pseudomonas fluorescens pf36.

PubMed

Chen, Deqiang; Wang, Dongwei; Xu, Chunling; Chen, Chun; Li, Junyi; Wu, Wenjia; Huang, Xin; Xie, Hui

2018-04-01

Controlling Radopholus similis, an important phytopathogenic nematode, is a challenge worldwide. Herein, we constructed a metagenomic fosmid library from the rhizosphere soil of banana plants, and six clones with protease activity were obtained by functionally screening the library. Furthermore, subclones were constructed using the six clones, and three protease genes with nematicidal activity were identified: pase1, pase4, and pase6. The pase4 gene was successfully cloned and expressed, demonstrating that the protease PASE4 could effectively degrade R. similis tissues and result in nematode death. Additionally, we isolated a predominant R. similis-associated bacterium, Pseudomonas fluorescens (pf36), from 10 R. similis populations with different hosts. The pase4 gene was successfully introduced into the pf36 strain by vector transformation and conjugative transposition, and two genetically modified strains were obtained: p4MCS-pf36 and p4Tn5-pf36. p4MCS-pf36 had significantly higher protease expression and nematicidal activity (p < 0.05) than p4Tn5-pf36 in a microtiter plate assay, whereas p4Tn5-pf36 was superior to p4MCS-pf36 in terms of genetic stability and controlling R. similis in growth pot tests. This study confirmed that R. similis is inhibited by the associated bacterium pf36-mediated expression of nematicidal proteases. Herein, a novel approach is provided for the study and development of efficient, environmentally friendly, and sustainable biocontrol techniques against phytonematodes.

Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

PubMed

Campo, Daniel; García-Vázquez, Eva

2012-01-01

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

Effects of morphologic left ventricular pressure on right ventricular geometry and tricuspid valve regurgitation in patients with congenitally corrected transposition of the great arteries.

PubMed

Kral Kollars, Catharine A; Gelehrter, Sarah; Bove, Edward L; Ensing, Gregory

2010-03-01

Congenitally corrected transposition of the great arteries (CCTGA) is associated with tricuspid regurgitation (TR), which has been postulated to arise from the effect of ventricular septal position on the attachments of the tricuspid valve. This study was performed to determine the effect of left ventricular (LV) pressure on right ventricular (RV) and LV geometry and the degree of TR. Serial echocardiograms were reviewed from, 30 patients with CCTGA who underwent pulmonary artery banding to train the morphologic left ventricle (n = 14) or left ventricle-to-pulmonary artery conduit placement and ventricular septal defect closure in conjunction with physiologic repair (n = 16). The degree of TR, the LV/RV pressure ratio, RV and LV sphericity indexes, and tricuspid valve tethering distance and coaptation length were analyzed. After pulmonary artery banding, an increase in LV systolic pressure to > or =2/3 systemic resulted in a decrease in TR from severe to moderate (p = 0.02). The percentage of patients with severe TR decreased from 64% to 18% (p = 0.06). The RV sphericity index decreased (p = 0.05), and the LV sphericity index increased (p = 0.02). After left ventricle-to-pulmonary artery conduit placement, a decrease in LV pressure to < or =1/2 systemic resulted in an increase in TR from none to mild (p = 0.003). In conclusion, these data indicate that LV pressure in patients with CCTGA affects the degree of TR and that septal shift caused by changes in LV and RV pressure is an important mechanism. Copyright 2010. Published by Elsevier Inc.

Triceps brachii muscle reconstruction with a latissimus dorsi muscle flap in a dog.

PubMed

Pavletic, Michael M; Kalis, Russell; Tribou, Patricia; Mouser, Pam J

2015-01-15

A 6-year-old spayed female Border Collie was examined for a severe deformity of the right forelimb. Three months prior to examination, the patient awkwardly fell off the couch and became acutely lame in the right forelimb, progressing to non-weight bearing over the following 72 hours. On physical examination, the dog carried the limb caudally against the thoracic wall, with the shoulder flexed and elbow in extension. The right triceps brachii muscle was atrophied and contracted, resulting in a resistant tension band effect that precluded manipulation of the right elbow joint. The physical changes in the triceps muscle were considered the primary cause of the patient's loss of limb function. Surgical treatment by means of elevation and transposition of the ipsilateral latissimus dorsi muscle was performed. The exposed triceps brachii muscles were transected 3 cm proximal to the tendons of insertion. Via a separate incision, the right latissimus dorsi muscle was elevated and tunneled subcutaneously beneath the interposing skin between the 2 surgical incisions. The muscle was then positioned and sutured to the proximal and distal borders of the divided triceps muscle group. Two weeks later, physical therapy was initiated. After 2 months, the patient regularly walked on the limb most of the time (9/10 steps). The surgical procedure for elevation and transposition of the latissimus dorsi muscle was relatively simple to perform. Physical therapy was an essential component to achieving the successful functional outcome in this case. This technique may be considered for treatment of similar patients in which the triceps muscle group is severely compromised.

Ulnar neuropathy and medial elbow pain in women's fastpitch softball pitchers: a report of 6 cases.

PubMed

Smith, Adam M; Butler, Thomas H; Dolan, Michael S

2017-12-01

Elite-level women's fastpitch softball players place substantial biomechanical strains on the elbow that can result in medial elbow pain and ulnar neuropathic symptoms. There is scant literature reporting the expected outcomes of the treatment of these injuries. This study examined the results of treatment in a series of these patients. We identified 6 female softball pitchers (4 high school and 2 collegiate) with medial elbow pain and ulnar neuropathic symptoms. Trials of conservative care failed in all 6, and they underwent surgical treatment with subcutaneous ulnar nerve transposition. These patients were subsequently monitored postoperatively to determine outcome. All 6 female pitchers had early resolution of elbow pain and neuropathic symptoms after surgical treatment. Long-term follow-up demonstrated that 1 patient quit playing softball because of other injuries but no longer reported elbow pain or paresthesias. One player was able to return to pitching at the high school level but had recurrent forearm pain and neuritis 1 year later while playing a different sport and subsequently stopped playing competitive sports. Four patients continued to play at the collegiate level without further symptoms. Medial elbow pain in women's softball pitchers caused by ulnar neuropathy can be treated effectively with subcutaneous ulnar nerve transposition if nonsurgical options fail. Further study is necessary to examine the role of overuse, proper training techniques, and whether pitching limits may be necessary to avoid these injuries. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Masseteric-facial nerve transposition for reanimation of the smile in incomplete facial paralysis.

PubMed

Hontanilla, Bernardo; Marre, Diego

2015-12-01

Incomplete facial paralysis occurs in about a third of patients with Bell's palsy. Although their faces are symmetrical at rest, when they smile they have varying degrees of disfigurement. Currently, cross-face nerve grafting is one of the most useful techniques for reanimation. Transfer of the masseteric nerve, although widely used for complete paralysis, has not to our knowledge been reported for incomplete palsy. Between December 2008 and November 2013, we reanimated the faces of 9 patients (2 men and 7 women) with incomplete unilateral facial paralysis with transposition of the masseteric nerve. Sex, age at operation, cause of paralysis, duration of denervation, recipient nerves used, and duration of follow-up were recorded. Commissural excursion, velocity, and patients' satisfaction were evaluated with the FACIAL CLIMA and a questionnaire, respectively. The mean (SD) age at operation was 39 (±6) years and the duration of denervation was 29 (±19) months. There were no complications that required further intervention. Duration of follow-up ranged from 6-26 months. FACIAL CLIMA showed improvement in both commissural excursion and velocity of more than two thirds in 6 patients, more than one half in 2 patients and less than one half in one. Qualitative evaluation showed a slight or pronounced improvement in 7/9 patients. The masseteric nerve is a reliable alternative for reanimation of the smile in patients with incomplete facial paralysis. Its main advantages include its consistent anatomy, a one-stage operation, and low morbidity at the donor site. Copyright © 2015 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Right ventricular performance and mass by use of cine MRI late after atrial repair of transposition of the great arteries.

PubMed

Lorenz, C H; Walker, E S; Graham, T P; Powers, T A

1995-11-01

The long-term adaptation of the right ventricle after atrial repair of transposition of the great arteries (TGA) remains a subject of major concern. Cine magnetic resonance imaging (MRI), with its tomographic capabilities, allows unique quantitative evaluation of both right and left ventricular function and mass. Our purpose was to use MRI and an age-matched normal population to examine the typical late adaptation of the right and left ventricles after atrial repair of TGA. Cine MRI was used to study ventricular function and mass in 22 patients after atrial repair of TGA. Images were obtained in short-axis sections from base to apex to derive normalized right and left ventricular mass (RVM and LVM, g/m2), interventricular septal mass (IVSM, g/m2), RV and LV end-diastolic volumes (EDV, mL/m2), and ejection fractions (EF). Results 8 to 23 years after repair were compared with analysis of 24 age- and sex-matched normal volunteers and revealed markedly elevated RVM, decreased LVM and IVSM, normal RV size, and only mildly depressed RVEF. Only 1 of 22 patients had clinical RV dysfunction, and this patient had increased RVM. Cine MRI allows quantitative evaluation of both RV and LV mass and function late after atrial repair of TGA. Longitudinal studies that include these measurements should prove useful in determining the mechanism of late RV failure in these patients. On the basis of these early data, inadequate hypertrophy does not appear to be the cause of late dysfunction in this patient group.

Testicular transposition in children undergoing brachytherapy for bladder and/or prostate rhabdomyosarcoma.

PubMed

de Lambert, Guenolee; Chargari, Cyrus; Minard-Colin, Véronique; Haie-Meder, Christine; Guérin, Florent; Martelli, Hélène

2018-04-13

Fertility preservation is a major goal in treatment of children with cancer. We describe a new technique of testicular transposition (TT) in patients treated with pulse-dose-rate (PDR) brachytherapy as part of the multimodal conservative treatment of bladder neck and/or prostate rhabdomyosarcoma (BP RMS). Medical records of consecutive patients treated between September 2016 and August 2017 were studied. These patients underwent a TT performed during BP RMS surgery by the same suprapubic incision. The external oblique aponeurosis was not incised. The spermatic cord was mobilized up to the external inguinal ring, and the gubernaculum attachments were severed from the scrotum. The testis was then flipped over with care taken to avoid injury of the vessels or the vas, wrapped in a silicone material and sutured under the abdominal skin with a transfixing stitch facing the anterior superior iliac spine. At the end of brachytherapy, the testis was relocated in the scrotum and during the same general anesthesia, plastic tubes and stents were removed. Surgical outcome and dosimetric parameters were examined. Eight patients were identified. Median age was 24 months (range 11-80 months). All had embryonal BP RMS and received chemotherapy according to RMS 2005 protocol prior to local treatment. All patients underwent conservative surgery followed by brachytherapy (60 Gy) and had testicular transposition of one testis. None had surgical complications. After converting doses to biologically equivalent doses in 2-Gy fractions (EQD2), the dose delivered to 75% of the transposed testis was 1.5 GyEQD2 (1-3 GyEQD2), versus 5.4 GyEQD2 (3.9-9.4 Gy EQD2) for the untransposed testis (p < 0.001). Testicular transposition is feasible in order to potentially preserve fertility and future quality of life in children undergoing brachytherapy for BP RMS. Level IV Treatment Study: Case Study with no Comparison Group. Copyright © 2018 Elsevier Inc. All rights reserved.

Outcomes After Superior Rectus Transposition and Medial Rectus Recession Versus Vertical Recti Transposition for Sixth Nerve Palsy.

PubMed

Lee, Yeon-Hee; Lambert, Scott R

2017-05-01

To compare the effectiveness of superior rectus transposition and medial rectus recession (SRT/MRc) vs inferior and superior rectus transposition (VRT) for acquired sixth nerve palsy. Consecutive, interventional case series. The medical records of a consecutive series of patients with acquired sixth nerve palsy who underwent VRT or SRT/MRc by a single surgeon were reviewed. The preoperative and postoperative findings were compared between the 2 groups. Eight patients (mean age, 46.8 years) underwent SRT/MRc and 8 patients underwent VRT (mean age, 51.1 years). Lateral fixation was performed on all but 4 patients in the VRT group. Preoperative esotropia in primary position and abduction deficit were similar in both groups (SRT/MRc, 41.9 prism diopter [PD], -4.6; VRT, 55.6 PD, -4.5; P = .195, 1.0). The SRT/MRc group underwent a mean MR recession of 6 (range, 5-7) mm. Four patients in the VRT later underwent MR recession (mean 5.3 mm, range 5-6 mm). In addition, 5 patients in the VRT group had 1 or more botulinum toxin injections in the medial rectus muscle. No additional procedures were performed in the SRT/MR group. Fewer additional procedures were performed with SRT/MR (SRT/MR, 0; VRT, 1.8 ± 1.2; P < .010). At last follow-up, residual esotropia (SRT/MRc, 7.1 PD; VRT, 10.3 PD; P = .442) was similar in both groups, but abduction was better in the SRT/MRc group (SRT/MR, -3.0 ± 0.7; VRT, -3.8 ± 0.4; P = .038). There were no new persistent vertical deviations or torsional diplopia. Final outcomes were similar with SRT/MRc vs VRT. However, fewer additional surgical procedures were needed with SRT/MR. Copyright © 2017 Elsevier Inc. All rights reserved.

Overall satisfaction, sexual function, and the durability of neophallus dimensions following staged female to male genital gender confirming surgery: the Institute of Urology, London U.K. experience

PubMed Central

Christopher, Nim A.; De Luca, Francesco; Spilotros, Marco; Ralph, David J.

2014-01-01

Background and purpose What factors influence transgender men’s decisions to undergo (and to not undergo) specific genital gender confirming surgeries (GCS) has not been described in the literature. Sexual function outcomes related to clitoral transposition and penile prosthesis placement is also not well described. Durability of neophallus dimensions after phalloplasty has not been described. A better understanding of these factors is necessary for pre-op counseling. We sought to assess patient genital-GCS related satisfaction, regret, pre/post-op sexual function, genital preferences, and genital measurements post-op. Materials and methods We evaluated ten female to male transgender patients who had previously undergone suprapubic pedicle-flap phalloplasty [suprapubic phalloplasty (SP); N=10] and 15 who had undergone radial artery forearm-flap phalloplasty [(RAP); N=15; 5/15 without and 10/15 with cutaneous nerve to clitoral nerve anastomosis] at our center (UK). We queried patients’ surgery related preferences and concerns, satisfaction, and sexual function pre/post-surgery, and accounted for whether patients had undergone clitoral transposition and/or cutaneous-to-clitoral nerve anastomosis. We measured flaccid and (where applicable) erect length and girth using a smart-phone app we designed. Results Mean age at surgery and follow-up for those that underwent SP was 35.1 and 2.23 years, and 34 and 6.8 for those that underwent RAP. Mean satisfaction scores were 9.1/10 and 9/10 for those that underwent SP and RAP, respectively. No patient (0%) regretted starting genital-GCS surgery. All (100%) patients that could achieve orgasm before GCS with clitoral transposition could achieve orgasm after surgery, and the vast majority reported preserved quality of erogenous sensation by our transposition technique. All (100%) RAP and 9/10 SP patients reported masturbation with their phallus. Inflatable penile prosthesis placement was not associated with decreased erogenous sensation/orgasm. Penile dimensions were relatively stable through follow-up for both groups. Our App length measurements correlated with a ruler within ±<4.5%. Conclusions Female-to-male genital-GCS offered in 3-stages was associated with high overall satisfaction and no regret among our sample. Sexual function appears to be preserved after both clitoral transposition and inflatable prosthesis placement, and consolidation of erogenous sensation to the phallus was described as important to all subjects. Discussion of patient’s pre-op sexual function, as well as specific concerns and preferences related to specific genital-GCS surgeries is important. PMID:26816764

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges[W][OA

PubMed Central

Butelli, Eugenio; Licciardello, Concetta; Zhang, Yang; Liu, Jianjun; Mackay, Steve; Bailey, Paul; Reforgiato-Recupero, Giuseppe; Martin, Cathie

2012-01-01

Traditionally, Sicilian blood oranges (Citrus sinensis) have been associated with cardiovascular health, and consumption has been shown to prevent obesity in mice fed a high-fat diet. Despite increasing consumer interest in these health-promoting attributes, production of blood oranges remains unreliable due largely to a dependency on cold for full color formation. We show that Sicilian blood orange arose by insertion of a Copia-like retrotransposon adjacent to a gene encoding Ruby, a MYB transcriptional activator of anthocyanin production. The retrotransposon controls Ruby expression, and cold dependency reflects the induction of the retroelement by stress. A blood orange of Chinese origin results from an independent insertion of a similar retrotransposon, and color formation in its fruit is also cold dependent. Our results suggest that transposition and recombination of retroelements are likely important sources of variation in Citrus. PMID:22427337

Use of the piggyBac transposon to create stable packaging cell lines for the production of clinical-grade self-inactivating γ-retroviral vectors.

PubMed

Feldman, Steven A; Xu, Hui; Black, Mary A; Park, Tristen S; Robbins, Paul F; Kochenderfer, James N; Morgan, Richard A; Rosenberg, Steven A

2014-08-01

Efforts to improve the biosafety of γ-retroviral-mediated gene therapy have resulted in a shift toward the use of self-inactivating (SIN) γ-retroviral vectors. However, scale-up and manufacturing of such vectors requires significant optimization of transient transfection-based processes or development of novel platforms for the generation of stable producer cell clones. To that end, we describe the use of the piggybac transposon to generate stable producer cell clones for the production of SIN γ-retroviral vectors. The piggybac transposon is a universal tool allowing for the stable integration of SIN γ-retroviral constructs into murine (PG13) and human 293-based Phoenix (GALV and RD114, respectively) packaging cell lines without reverse transcription. Following transposition, a high-titer clone is selected for manufacture of a master cell bank and subsequent γ-retroviral vector supernatant production. Packaging cell clones created using the piggybac transposon have comparable titers to non-SIN vectors generated via conventional methods. We describe herein the use of the piggybac transposon for the production of stable packaging cell clones for the manufacture of clinical-grade SIN γ-retroviral vectors for ex vivo gene therapy clinical trials.

Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates.

PubMed

Warren, Ian A; Naville, Magali; Chalopin, Domitille; Levin, Perrine; Berger, Chloé Suzanne; Galiana, Delphine; Volff, Jean-Nicolas

2015-09-01

Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.

A non-invasive in vivo imaging system to study dissemination of bioluminescent Yersinia pestis CO92 in a mouse model of pneumonic plague

PubMed Central

Sha, Jian; Rosenzweig, Jason A.; Kirtley, Michelle L.; van Lier, Christina J.; Fitts, Eric C.; Kozlova, Elena V.; Erova, Tatiana E.; Tiner, Bethany L.; Chopra, Ashok K.

2012-01-01

The gold standard in microbiology for monitoring bacterial dissemination in infected animals has always been viable plate counts. This method, despite being quantitative, requires sacrificing the infected animals. Recently, however, an alternative method of in vivo imaging of bioluminescent bacteria (IVIBB) for monitoring microbial dissemination within the host has been employed. Yersina pestis is a Gram-negative bacterium capable of causing bubonic, septicemic, and pneumonic plague. In this study, we compared the conventional counting of bacterial colony forming units (cfu) in the various infected tissues to IVIBB in monitoring Y. pestis dissemination in a mouse model of pneumonic plague. By using a transposon mutagenesis system harboring the luciferase (luc) gene, we screened approximately 4000 clones and obtained a fully virulent, luc-positive Y. pestis CO92 (Y. pestis-luc2) reporter strain in which transposition occurred within the largest pMT1 plasmid which possesses murine toxin and capsular antigen encoding genes. The aforementioned reporter strain and the wild-type CO92 exhibited similar growth curves, formed capsule based on immunofluorescence microscopy and flow cytometry, and had a similar LD50. Intranasal infection of mice with 15 LD50 of CO92-luc2 resulted in animal mortality by 72 h, and an increasing number of bioluminescent bacteria were observed in various mouse organs over a 24–72 h period when whole animals were imaged. However, following levofloxacin treatment (10 mg/kg/day) for 6 days 24 h post infection, no luminescence was observed after 72 h of infection, indicating that the tested antimicrobial killed bacteria preventing their detection in host peripheral tissues. Overall, we demonstrated that IVIBB is an effective and non-invasive way of monitoring bacterial dissemination in animals following pneumonic plague having strong correlation with cfu, and our reporter CO92-luc2 strain can be employed as a useful tool to monitor the efficacy of antimicrobial countermeasures in real time. PMID:23063826

Preparation of next-generation sequencing libraries using Nextera™ technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition.

PubMed

Caruccio, Nicholas

2011-01-01

DNA library preparation is a common entry point and bottleneck for next-generation sequencing. Current methods generally consist of distinct steps that often involve significant sample loss and hands-on time: DNA fragmentation, end-polishing, and adaptor-ligation. In vitro transposition with Nextera™ Transposomes simultaneously fragments and covalently tags the target DNA, thereby combining these three distinct steps into a single reaction. Platform-specific sequencing adaptors can be added, and the sample can be enriched and bar-coded using limited-cycle PCR to prepare di-tagged DNA fragment libraries. Nextera technology offers a streamlined, efficient, and high-throughput method for generating bar-coded libraries compatible with multiple next-generation sequencing platforms.

Lateralization Technique and Inferior Alveolar Nerve Transposition

PubMed Central

Sanches, Marco Antonio; Ramalho, Gabriel Cardoso; Manzi, Marcello Roberto

2016-01-01

Bone resorption of the posterior mandible can result in diminished bone edge and, therefore, the installation of implants in these regions becomes a challenge, especially in the presence of the mandibular canal and its contents, the inferior alveolar nerve. Several treatment alternatives are suggested: the use of short implants, guided bone regeneration, appositional bone grafting, distraction osteogenesis, inclined implants tangential to the mandibular canal, and the lateralization of the inferior alveolar nerve. The aim was to elucidate the success rate of implants in the lateralization technique and in inferior alveolar nerve transposition and to determine the most effective sensory test. We conclude that the success rate is linked to the possibility of installing implants with long bicortical anchor which favors primary stability and biomechanics. PMID:27433360

Generation of Transgenic Pigs by Cytoplasmic Injection of piggyBac Transposase-Based pmGENIE-3 Plasmids1

PubMed Central

Li, Zicong; Zeng, Fang; Meng, Fanming; Xu, Zhiqian; Zhang, Xianwei; Huang, Xiaoling; Tang, Fei; Gao, Wenchao; Shi, Junsong; He, Xiaoyan; Liu, Dewu; Wang, Chong; Urschitz, Johann; Moisyadi, Stefan; Wu, Zhenfang

2014-01-01

ABSTRACT The process of transgenesis involves the introduction of a foreign gene, the transgene, into the genome of an animal. Gene transfer by pronuclear microinjection (PNI) is the predominant method used to produce transgenic animals. However, this technique does not always result in germline transgenic offspring and has a low success rate for livestock. Alternate approaches, such as somatic cell nuclear transfer using transgenic fibroblasts, do not show an increase in efficiency compared to PNI, while viral-based transgenesis is hampered by issues regarding transgene size and biosafety considerations. We have recently described highly successful transgenesis experiments with mice using a piggyBac transposase-based vector, pmhyGENIE-3. This construct, a single and self-inactivating plasmid, contains all the transpositional elements necessary for successful gene transfer. In this series of experiments, our laboratories have implemented cytoplasmic injection (CTI) of pmGENIE-3 for transgene delivery into in vivo-fertilized pig zygotes. More than 8.00% of the injected embryos developed into transgenic animals containing monogenic and often single transgenes in their genome. However, the CTI technique was unsuccessful during the injection of in vitro-fertilized pig zygotes. In summary, here we have described a method that is not only easy to implement, but also demonstrated the highest efficiency rate for nonviral livestock transgenesis. PMID:24671876

Organizational differences between cytoplasmic male sterile and male fertile Brassica mitochondrial genomes are confined to a single transposed locus.

PubMed Central

L'Homme, Y; Brown, G G

1993-01-01

Comparison of the physical maps of male fertile (cam) and male sterile (pol) mitochondrial genomes of Brassica napus indicates that structural differences between the two mtDNAs are confined to a region immediately upstream of the atp6 gene. Relative to cam mtDNA, pol mtDNA possesses a 4.5 kb segment at this locus that includes a chimeric gene that is cotranscribed with atp6 and lacks an approximately 1kb region located upstream of the cam atp6 gene. The 4.5 kb pol segment is present and similarly organized in the mitochondrial genome of the common nap B.napus cytoplasm; however, the nap and pol DNA regions flanking this segment are different and the nap sequences are not expressed. The 4.5 kb CMS-associated pol segment has thus apparently undergone transposition during the evolution of the nap and pol cytoplasms and has been lost in the cam genome subsequent to the pol-cam divergence. This 4.5 kb segment comprises the single DNA region that is expressed differently in fertile, pol CMS and fertility restored pol cytoplasm plants. The finding that this locus is part of the single mtDNA region organized differently in the fertile and male sterile mitochondrial genomes provides strong support for the view that it specifies the pol CMS trait. Images PMID:8388101

RpA, an extracellular protease similar to the metalloprotease of serralysin family, is required for pathogenicity of Ralstonia pickettii.

PubMed

Chen, C-M; Liu, J-J; Chou, C-W; Lai, C-H; Wu, L-T

2015-10-01

To investigate the biochemical and functional properties of an extracellular protease, RpA, in Ralstonia pickettii WP1 isolated from water supply systems. An extracellular protease was identified and characterized from R. pickettii WP1. A mutant strain WP1M2 was created from strain WP1 by mini-Tn5 transposition. The culture filtrates from WP1M2 had a lower cytotoxic effect than the parental WP1 on several mammalian cell lines. Cloning and sequence analysis revealed the Tn5 transposon inserted at a protease gene (rpA) which is 81% homologous to prtA and aprX genes of Pseudomonas fluorescens. The rpA gene encodes a 482-residue protein showing sequence similarity to metalloproteases of the serralysin family. The RpA protein was expressed in Escherichia coli using a pET expression vector and purified as a 55 kDa molecular weight protein. Furthermore, the protease activity of RpA was inhibited by protease inhibitor and heat treatment. The in vitro cytotoxic activity of R. pickettii culture filtrates was attributed to RpA protease. An extracellular protease, RpA, was identified from R. pickettii WP1 isolated from water supply system. The RpA metalloproteases is required for the pathogenicity of R. pickettii to mammalian cell lines. © 2015 The Society for Applied Microbiology.

The 'double headed slug flap': a simple technique to reconstruct large helical rim defects.

PubMed

Masud, D; Tzafetta, K

2012-10-01

Reconstructing partial defects of the ear can be challenging, balancing the creation of the details of the ear with scarring, morbidity and number of surgical stages. Common causes of ear defects are human bites, tumour excision and burn injuries. Reconstructing defects of the ear with tube pedicled flaps and other local flaps requires an accurate measurement of size of the defect with little room for error, particularly under estimation. We present a simple method of reconstruction for partial defects of the ear using a two-stage technique with post auricular transposition flaps. This allows for under or over estimation of size defects permitting accurate tissue usage giving good aesthetic outcomes. Copyright © 2012 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Historic origin of the "Arcade of Struthers".

PubMed

De Jesus, Ramon; Dellon, A Lee

2003-05-01

John Struthers wrote in 1848 and 1854 about sites of compression of the median nerve from axilla to elbow. He is best known for describing the rare median nerve entrapment by a ligament from a supracondylar process extending to the medial humeral epicondyle. In 1973, observation of ulnar nerve entrapment associated with a midshaft humeral fracture and subsequent anatomic dissections led to the creation of the term "Arcade of Struthers." Review of Struthers' original writings fails to identify either the use of word "arcade" or description of ulnar nerve compression. Review of published anatomic dissections identifies variations in the origin of the medial head of the triceps, not described by Struthers, that may cause failure of an anterior transposition of the ulnar nerve. Continued use of the term "Arcade of Struthers" is historically incorrect.

Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1).

PubMed Central

Fukumori, F; Saint, C P

1997-01-01

A 9,233-bp HindIII fragment of the aromatic amine catabolic plasmid pTDN1, isolated from a derivative of Pseudomonas putida mt-2 (UCC22), confers the ability to degrade aniline on P. putida KT2442. The fragment encodes six open reading frames which are arranged in the same direction. Their 5' upstream region is part of the direct-repeat sequence of pTDN1. Nucleotide sequence of 1.8 kb of the repeat sequence revealed only a single base pair change compared to the known sequence of IS1071 which is involved in the transposition of the chlorobenzoate genes (C. Nakatsu, J. Ng, R. Singh, N. Straus, and C. Wyndham, Proc. Natl. Acad. Sci. USA 88:8312-8316, 1991). Four open reading frames encode proteins with considerable homology to proteins found in other aromatic-compound degradation pathways. On the basis of sequence similarity, these genes are proposed to encode the large and small subunits of aniline oxygenase (tdnA1 and tdnA2, respectively), a reductase (tdnB), and a LysR-type regulatory gene (tdnR). The putative large subunit has a conserved [2Fe-2S]R Rieske-type ligand center. Two genes, tdnQ and tdnT, which may be involved in amino group transfer, are localized upstream of the putative oxygenase genes. The tdnQ gene product shares about 30% similarity with glutamine synthetases; however, a pUC-based plasmid carrying tdnQ did not support the growth of an Escherichia coli glnA strain in the absence of glutamine. TdnT possesses domains that are conserved among amidotransferases. The tdnQ, tdnA1, tdnA2, tdnB, and tdnR genes are essential for the conversion of aniline to catechol. PMID:8990291

Evolution of European Union legislation of herbal medicinal products and its transposition to national legislation in 1965-2007: case Finland.

PubMed

Koski, Sari M; Laitinen-Parkkonen, Pirjo; Airaksinen, Marja

2015-01-01

The study aim was to explore the progress of legislation relating to herbal medicinal products in the European Union and compare it with the corresponding progress of the legislation in Finland in 1965-2007. The study was carried out using content analysis. Data were searched from publicly available European Union directives and national acts. All definitions and safety-related requirements for herbal medicinal products were identified. The transposition of safety-related requirements into the national legislation was studied. Medicinal products from plant origins have been part of the European Union legislation since 1965. Most plant-based products have not initially been regarded as medicinal products but rather as some kind of medicine-like products. The official definition of herbal medicinal products was introduced in Directive 2004/24/EC and implemented into the Finnish legislation with the terminology to recognise herbal medicinal products as part of medicinal products. The current safety-related requirements of medicinal products concern analogously herbal medicinal products. Herbal medicinal products have had different definitions in pharmaceutical legislation over the study period in the European Union and Finland. The current definition places herbal medicinal products more clearly under the medicinal products' legislation. Safety-related requirements are now practically identical for all medicinal products. Transposition of the European Union legislation into the national legislation in Finland is apparent. Copyright © 2013 John Wiley & Sons, Ltd.

Neurotized lateral gastrocnemius muscle transfer for persistent traumatic peroneal nerve palsy: Surgical technique.

PubMed

Leclère, F M; Badur, N; Mathys, L; Vögelin, E

2015-08-01

Persistent traumatic peroneal nerve palsy, following nerve surgery failure, is usually treated by tendon transfer or more recently by tibial nerve transfer. However, when there is destruction of the tibial anterior muscle, an isolated nerve transfer is not possible. In this article, we present the key steps and surgical tips for the Ninkovic procedure including transposition of the neurotized lateral gastrocnemius muscle with the aim of restoring active voluntary dorsiflexion. The transposition of the lateral head of the gastrocnemius muscle to the tendons of the anterior tibial muscle group, with simultaneous transposition of the intact proximal end of the deep peroneal nerve to the tibial nerve of the gastrocnemius muscle by microsurgical neurorrhaphy is performed in one stage. It includes 10 key steps which are described in this article. Since 1994, three clinical series have highlighted the advantages of this technique. Functional and subjective results are discussed. We review the indications and limitations of the technique. Early clinical results after neurotized lateral gastrocnemius muscle transfer appear excellent; however, they still need to be compared with conventional tendon transfer procedures. Clinical studies are likely to be conducted in this area largely due to the frequency of persistant peroneal nerve palsy and the limitations of functional options in cases of longstanding peripheral nerve palsy, anterior tibial muscle atrophy or destruction. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Female Fertility Issues

Cancer.gov

Fertility issues are common in women getting cancer treatment. Fertility preservation options include egg freezing, embryo freezing, ovarian tissue freezing, ovarian shielding and ovarian transposition. Resources, support, and clinical trials are listed.

Esophageal Cancer

MedlinePlus

... Heart Disease Diseases of the arteries, valves, and aorta, as well as cardiac rhythm disturbances Aortic Valve ... Transposition of the Great Arteries Coarctation of the Aorta Truncus Arteriosus Single Ventricle Defects Patent Ductus Arteriosus ...

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

PubMed Central

Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

2014-01-01

Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2–1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2–1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms. PMID:24030599

Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M Integrated in the Chromosome

PubMed Central

Sebra, Robert; Zhuge, Jian; Yin, Changhong; Aguero-Rosenfeld, Maria E.; Schuetz, Audrey N.; Dimitrova, Nevenka; Fallon, John T.

2017-01-01

ABSTRACT The extended-spectrum-β-lactamase (ESBL)- and Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae represent serious and urgent threats to public health. In a retrospective study of multidrug-resistant K. pneumoniae, we identified three clinical isolates, CN1, CR14, and NY9, carrying both blaCTX-M and blaKPC genes. The complete genomes of these three K. pneumoniae isolates were de novo assembled by using both short- and long-read whole-genome sequencing. In CR14 and NY9, blaCTX-M and blaKPC were carried on two different plasmids. In contrast, CN1 had one copy of blaKPC-2 and three copies of blaCTX-M-15 integrated in the chromosome, for which the blaCTX-M-15 genes were linked to an insertion sequence, ISEcp1, whereas the blaKPC-2 gene was in the context of a Tn4401a transposition unit conjugated with a PsP3-like prophage. Intriguingly, downstream of the Tn4401a-blaKPC-2-prophage genomic island, CN1 also carried a clustered regularly interspaced short palindromic repeat (CRISPR)-cas array with four spacers targeting a variety of K. pneumoniae plasmids harboring antimicrobial resistance genes. Comparative genomic analysis revealed that there were two subtypes of type I-E CRISPR-cas in K. pneumoniae strains and suggested that the evolving CRISPR-cas, with its acquired novel spacer, induced the mobilization of antimicrobial resistance genes from plasmids into the chromosome. The integration and dissemination of multiple copies of blaCTX-M and blaKPC from plasmids to chromosome depicts the complex pandemic scenario of multidrug-resistant K. pneumoniae. Additionally, the implications from this study also raise concerns for the application of a CRISPR-cas strategy against antimicrobial resistance. PMID:28438939

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.

PubMed

Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

2014-01-01

Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.

Regional Dissemination of a Trimethoprim-Resistance Gene Cassette via a Successful Transposable Element

PubMed Central

Opintan, Japheth A.; Bishar, Rima A.; Aboderin, A. Oladipo; Newman, Mercy J.; Lamikanra, Adebayo; Okeke, Iruka N.

2012-01-01

Background Antimicrobial resistance is a growing international problem. We observed a 50% increase in the prevalence of trimethoprim resistance among fecal Escherichia coli from healthy Nigerian students between 1998 and 2005, a trend to increase that continued in 2009. Methods and Findings A PCR-based screen revealed that 131 (43.1%) of isolates obtained in Nigeria in 2005 and 2009 carried integron-borne dfrA cassettes. In the case of 67 (51.1%) of these isolates, the cassette was a class 1-integron-borne dfrA7 gene, which has been reported at high prevalence from E. coli isolates from other parts of Africa. Complete sequencing of a 27 Kb dfrA7-bearing plasmid from one isolate located the dfrA7 gene within a Tn21-type transposon. The transposon also contained an IS26-derived bla/sul/str element, encoding resistance to β-lactams, sulphonamides and streptomycin, and mercury resistance genes. Although the plasmid backbone was only found in 12 (5.8%) of trimethoprim-resistant isolates, dfrA7 and other transposon-borne genes were detected in 14 (16.3%) and 32 (26.3%) of trimethoprim resistant isolates collected in Nigeria in 2005 and 2009, respectively. Additionally, 37 (19.3%) of trimethoprim-resistant E. coli isolates collected between 2006 and 2008 from Ghana were positive for the dfrA7 and a transposon marker, but only 4 (2.1%) harbored the plasmid backbone. Conclusions Our data point to transposition as a principal mechanism for disseminating dfrA7 among E. coli from Nigeria and Ghana. On-going intensive use of the affordable broad-spectrum antibacterials is likely to promote selective success of a highly prevalent transposable element in West Africa. PMID:22666464

Making sense out of the emerging complexity inherent in professional development

NASA Astrophysics Data System (ADS)

Prodromou, Theodosia; Robutti, Ornella; Panero, Monica

2017-12-01

This paper reports on a study of the process of professional development for mathematics teachers. The analysis connects two theoretical frameworks: the Meta-Didactical Transposition model developed by Arzarello et al. (2014), which describes the macro level, and, at the micro level, the idea of emergence, which has been around since at least the time of Aristotle and has been defined by Mill (1843), Lewes (1875), Blitz (1992), Huxley and Huxley (1947) and many others. The meta-didactical transposition model considers the evolution of teachers' practices as part of a community process, while the notion of emergence helps us to gain better insights into the details of the practices of individual teachers. This paper focuses on secondary school teachers' learning of new digital technologies to illuminate this theoretical framework.

A highly efficient transposon mutagenesis system for the tomato pathogen Clavibacter michiganensis subsp. michiganensis.

PubMed

Kirchner, O; Gartemann, K H; Zellermann, E M; Eichenlaub, R; Burger, A

2001-11-01

A transposon mutagenesis system for Clavibacter michiganensis subsp. michiganensis was developed based on antibiotic resistance transposons that were derived from the insertion element IS1409 from Arthrobacter sp. strain TM1 NCIB12013. As a prerequisite, the electroporation efficiency was optimized by using unmethylated DNA and treatment of the cells with glycine such that about 5 x 10(6) transformants per microg of DNA were generally obtained. Electroporation of C. michiganensis subsp. michiganensis with a suicide vector carrying transposon Tn1409C resulted in approximately 1 x 10(3) transposon mutants per pg of DNA and thus is suitable for saturation mutagenesis. Analysis of Tn1409C insertion sites suggests a random mode of transposition. Transposition of Tn1409C was also demonstrated for other subspecies of C. michiganensis.

Popliteal tendon transposition for stabilization of the cranial cruciate ligament deficient stifle joint in dogs: an experimental study.

PubMed

Monnet, E; Schwarz, P D; Powers, B

1995-01-01

Popliteal tendon transposition was performed in five dogs with surgically induced cranial cruciate ligament rupture. After a lateral approach to the stifle joint, the popliteal tendon was severed distal to the sesamoid bone and transposed cranially onto the tibial crest to mimic the sagittal orientation of the cranial cruciate ligament. The origin of the popliteal tendon on the lateral femoral condyle was preserved. Lameness was not clinically detectable 2 months after surgery. At 6 months postoperatively, there was minimal radiographic and histopathologic evidence of degenerative joint disease in the stifle joints that had underwent surgery. There was no gross or microscopic evidence of meniscal damage found at necropsy 6 months after surgery. Biomechanical studies are warranted before recommending the procedure.

The Streptococcus pyogenes serotype M49 Nra-Ralp3 transcriptional regulatory network and its control of virulence factor expression from the novel eno ralp3 epf sagA pathogenicity region.

PubMed

Kreikemeyer, Bernd; Nakata, Masanobu; Köller, Thomas; Hildisch, Hendrikje; Kourakos, Vassilios; Standar, Kerstin; Kawabata, Shigetada; Glocker, Michael O; Podbielski, Andreas

2007-12-01

Many Streptococcus pyogenes (group A streptococcus [GAS]) virulence factor- and transcriptional regulator-encoding genes cluster together in discrete genomic regions. Nra is a central regulator of the FCT region. Previous studies exclusively described Nra as a transcriptional repressor of adhesin and toxin genes. Here transcriptome and proteome analysis of a serotype M49 GAS strain and an isogenic Nra mutant of this strain revealed the complete Nra regulon profile. Nra is active in all growth phases tested, with the largest regulon in the transition phase. Almost exclusively, virulence factor-encoding genes are repressed by Nra; these genes include the GAS pilus operon, the capsule synthesis operon, the cytolysin-mediated translocation system genes, all Mga region core virulence genes, and genes encoding other regulators, like the Ihk/Irr system, Rgg, and two additional RofA-like protein family regulators. Surprisingly, our experiments revealed that Nra additionally acts as a positive regulator, mostly for genes encoding proteins and enzymes with metabolic functions. Epidemiological investigations revealed strong genetic linkage of one particular Nra-repressed regulator, Ralp3 (SPy0735), with a gene encoding Epf (extracellular protein factor from Streptococcus suis). In a serotype-specific fashion, this ralp3 epf gene block is integrated, most likely via transposition, into the eno sagA virulence gene block, which is present in all GAS serotypes. In GAS serotypes M1, M4, M12, M28, and M49 this novel discrete genetic region is therefore designated the eno ralp3 epf sagA (ERES) pathogenicity region. Functional experiments showed that Epf is a novel GAS plasminogen-binding protein and revealed that Ralp3 activity counteracts Nra and MsmR regulatory activity. In addition to the Mga and FCT regions, the ERES region is the third discrete chromosomal pathogenicity region. All of these regions are transcriptionally linked, adding another level of complexity to the known GAS growth phase-dependent regulatory network.

The Streptococcus pyogenes Serotype M49 Nra-Ralp3 Transcriptional Regulatory Network and Its Control of Virulence Factor Expression from the Novel eno ralp3 epf sagA Pathogenicity Region▿ †

PubMed Central

Kreikemeyer, Bernd; Nakata, Masanobu; Köller, Thomas; Hildisch, Hendrikje; Kourakos, Vassilios; Standar, Kerstin; Kawabata, Shigetada; Glocker, Michael O.; Podbielski, Andreas

2007-01-01

Many Streptococcus pyogenes (group A streptococcus [GAS]) virulence factor- and transcriptional regulator-encoding genes cluster together in discrete genomic regions. Nra is a central regulator of the FCT region. Previous studies exclusively described Nra as a transcriptional repressor of adhesin and toxin genes. Here transcriptome and proteome analysis of a serotype M49 GAS strain and an isogenic Nra mutant of this strain revealed the complete Nra regulon profile. Nra is active in all growth phases tested, with the largest regulon in the transition phase. Almost exclusively, virulence factor-encoding genes are repressed by Nra; these genes include the GAS pilus operon, the capsule synthesis operon, the cytolysin-mediated translocation system genes, all Mga region core virulence genes, and genes encoding other regulators, like the Ihk/Irr system, Rgg, and two additional RofA-like protein family regulators. Surprisingly, our experiments revealed that Nra additionally acts as a positive regulator, mostly for genes encoding proteins and enzymes with metabolic functions. Epidemiological investigations revealed strong genetic linkage of one particular Nra-repressed regulator, Ralp3 (SPy0735), with a gene encoding Epf (extracellular protein factor from Streptococcus suis). In a serotype-specific fashion, this ralp3 epf gene block is integrated, most likely via transposition, into the eno sagA virulence gene block, which is present in all GAS serotypes. In GAS serotypes M1, M4, M12, M28, and M49 this novel discrete genetic region is therefore designated the eno ralp3 epf sagA (ERES) pathogenicity region. Functional experiments showed that Epf is a novel GAS plasminogen-binding protein and revealed that Ralp3 activity counteracts Nra and MsmR regulatory activity. In addition to the Mga and FCT regions, the ERES region is the third discrete chromosomal pathogenicity region. All of these regions are transcriptionally linked, adding another level of complexity to the known GAS growth phase-dependent regulatory network. PMID:17893125

Long-term results after atrial correction of complete transposition of the great arteries.

PubMed

Merlo, M; de Tommasi, S M; Brunelli, F; Abbruzzese, P A; Crupi, G; Ghidoni, I; Casari, A; Pitì, A; Mamprin, F; Parenzan, L

1991-02-01

This study presents the late results for the first 104 consecutive patients surviving and atrial repair for transposition of the great arteries (TGA) between January 1971 and December 1978 (group 1). Mean follow-up was 12 years (range, 0.1 to 17.7 years). The actuarial survival rate at 18 years was 84.2% (70% confidence limits, 79% to 88%) for simple TGA and 93.7% (70% confidence limits, 84% to 97%) for complex TGA. Nine of the 11 deaths were sudden. Two (2.6%) of the 78 late survivors operated on for simple TGA are in New York Heart Association functional class III or IV versus 4 (26.7%) of the 15 survivors with complex TGA; the other patients are doing very well. To better assess long-term results, we report the findings for randomly obtained electrocardiograms, Holter monitor recordings, radionuclide angiographic studies, and cardiac catheterizations performed in 1987 in a larger group of 159 long-term survivors of atrial repair operated on at Ospedale Riuniti di Bergamo from January 1971 to December 1984 (group 2), which includes all of group 1. The findings confirm that the arterial switch repair is the procedure of choice for complex TGA and that there is a major incidence (approximately 10%) of systemic right ventricular dysfunction and rhythm disturbances after the atrial repair. On the other hand, our late survival rate at 18 years of 84% for simple TGA with 97.5% of the patients in functional class I is a result that should be kept in mind, especially in institutions where the arterial switch is a relatively new approach and presumably is a higher risk to cause early death.

DNA transposon-based gene vehicles - scenes from an evolutionary drive

PubMed Central

2013-01-01

DNA transposons are primitive genetic elements which have colonized living organisms from plants to bacteria and mammals. Through evolution such parasitic elements have shaped their host genomes by replicating and relocating between chromosomal loci in processes catalyzed by the transposase proteins encoded by the elements themselves. DNA transposable elements are constantly adapting to life in the genome, and self-suppressive regulation as well as defensive host mechanisms may assist in buffering ‘cut-and-paste’ DNA mobilization until accumulating mutations will eventually restrict events of transposition. With the reconstructed Sleeping Beauty DNA transposon as a powerful engine, a growing list of transposable elements with activity in human cells have moved into biomedical experimentation and preclinical therapy as versatile vehicles for delivery and genomic insertion of transgenes. In this review, we aim to link the mechanisms that drive transposon evolution with the realities and potential challenges we are facing when adapting DNA transposons for gene transfer. We argue that DNA transposon-derived vectors may carry inherent, and potentially limiting, traits of their mother elements. By understanding in detail the evolutionary journey of transposons, from host colonization to element multiplication and inactivation, we may better exploit the potential of distinct transposable elements. Hence, parallel efforts to investigate and develop distinct, but potent, transposon-based vector systems will benefit the broad applications of gene transfer. Insight and clever optimization have shaped new DNA transposon vectors, which recently debuted in the first DNA transposon-based clinical trial. Learning from an evolutionary drive may help us create gene vehicles that are safer, more efficient, and less prone for suppression and inactivation. PMID:24320156

Community-wide plasmid gene mobilization and selection

PubMed Central

Sentchilo, Vladimir; Mayer, Antonia P; Guy, Lionel; Miyazaki, Ryo; Green Tringe, Susannah; Barry, Kerrie; Malfatti, Stephanie; Goessmann, Alexander; Robinson-Rechavi, Marc; van der Meer, Jan R

2013-01-01

Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions. PMID:23407308

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants.

PubMed

Ferreira de Carvalho, Julie; Oplaat, Carla; Pappas, Nikolaos; Derks, Martijn; de Ridder, Dick; Verhoeven, Koen J F

2016-03-08

Asexual reproduction has the potential to enhance deleterious mutation accumulation and to constrain adaptive evolution. One source of mutations that can be especially relevant in recent asexuals is activity of transposable elements (TEs), which may have experienced selection for high transposition rates in sexual ancestor populations. Predictions of genomic divergence under asexual reproduction therefore likely include a large contribution of transposable elements but limited adaptive divergence. For plants empirical insight into genome divergence under asexual reproduction remains limited. Here, we characterize expression divergence between clone members of a single apomictic lineage of the common dandelion (Taraxacum officinale) to contribute to our knowledge of genome evolution under asexuality. Using RNA-Seq, we show that about one third of heritable divergence within the apomictic lineage is driven by TEs and TE-related gene activity. In addition, we identify non-random transcriptional differences in pathways related to acyl-lipid and abscisic acid metabolisms which might reflect functional divergence within the apomictic lineage. We analyze SNPs in the transcriptome to assess genetic divergence between the apomictic clone members and reveal that heritable expression differences between the accessions are not explained simply by genome-wide genetic divergence. The present study depicts a first effort towards a more complete understanding of apomictic plant genome evolution. We identify abundant TE activity and ecologically relevant functional genes and pathways affecting heritable within-lineage expression divergence. These findings offer valuable resources for future work looking at epigenetic silencing and Cis-regulation of gene expression with particular emphasis on the effects of TE activity on asexual species' genome.

The growth of birdwings

NASA Technical Reports Server (NTRS)

Meunier, K.

1980-01-01

Growth and order allometry is defined and applied to the growth of bird effects of negative wing allometry discussed with regard to body size and flight power. Transposition and evolutionary significance are explained.

Prolonged Expression of Secreted Enzymes in Dogs After Liver-Directed Delivery of Sleeping Beauty Transposons: Implications for Non-Viral Gene Therapy of Systemic Disease.

PubMed

Aronovich, Elena L; Hyland, Kendra A; Hall, Bryan C; Bell, Jason B; Olson, Erik R; Rusten, Myra Urness; Hunter, David W; Ellinwood, N Matthew; McIvor, R Scott; Hackett, Perry B

2017-07-01

The non-viral, integrating Sleeping Beauty (SB) transposon system is efficient in treating systemic monogenic disease in mice, including hemophilia A and B caused by deficiency of blood clotting factors and mucopolysaccharidosis types I and VII caused by α-L-iduronidase (IDUA) and β-glucuronidase (GUSB) deficiency, respectively. Modified approaches of the hydrodynamics-based procedure to deliver transposons to the liver in dogs were recently reported. Using the transgenic canine reporter secreted alkaline phosphatase (cSEAP), transgenic protein in the plasma was demonstrated for up to 6 weeks post infusion. This study reports that immunosuppression of dogs with gadolinium chloride (GdCl 3 ) prolonged the presence of cSEAP in the circulation up to 5.5 months after a single vector infusion. Transgene expression declined gradually but appeared to stabilize after about 2 months at approximately fourfold baseline level. Durability of transgenic protein expression in the plasma was inversely associated with transient increase of liver enzymes alanine transaminase and aspartate transaminase in response to the plasmid delivery procedure, which suggests a deleterious effect of hepatocellular toxicity on transgene expression. GdCl 3 treatment was ineffective for repeat vector infusions. In parallel studies, dogs were infused with potentially therapeutic transposons. Activities of transgenic IDUA and GUSB in plasma peaked at 50-350% of wildtype, but in the absence of immunosuppression lasted only a few days. Transposition was detectable by excision assay only when the most efficient transposase, SB100X, was used. Dogs infused with transposons encoding canine clotting factor IX (cFIX) were treated with GdCl 3 and showed expression profiles similar to those in cSEAP-infused dogs, with expression peaking at 40% wt (2 μg/mL). It is concluded that GdCl 3 can support extended transgene expression after hydrodynamic introduction of SB transposons in dogs, but that alternative regimens will be required to achieve therapeutic levels of transgene products.

Ambiguous genitalia: what prenatal genetic testing is practical?

PubMed

Adam, Margaret P; Fechner, Patricia Y; Ramsdell, Linda A; Badaru, Angela; Grady, Richard E; Pagon, Roberta A; McCauley, Elizabeth; Cheng, Edith Y; Parisi, Melissa A; Shnorhavorian, Margarett

2012-06-01

Concern for ambiguous genitalia or chromosome-phenotype discordance detected in a prenatal setting has increased over the last two decades. Practitioners faced with this prenatal finding have a variety of genetic tests available to them; however, it is unclear to what extent prenatal testing for disorders of sex development (DSD) is useful or practical. We undertook a retrospective review of the medical records of 140 individuals evaluated through the DSD clinic at Seattle Children's Hospital with birthdates from 01/01/1994 through 08/16/2011 to determine the rate of prenatal detection of ambiguous genitalia in individuals with DSD, what prenatal diagnostic workup was undertaken, and the postnatal outcome, including whether a postnatal genetic diagnosis was confirmed. Of all 140 subjects, 34 (24%) were identified prenatally. The most common postnatal diagnoses were penoscrotal hypospadias with transposition of the scrotum with no known genetic cause (24/140; 17%) and 21-hydroxylase deficiency (20/140; 14%). Apart from these, no single diagnosis comprised more than a few cases. Prenatal diagnostic testing varied widely, from no tests to multiple molecular tests with amniotic fluid hormone concentrations. In the absence of other fetal anomalies or growth retardation on ultrasound, prenatal karyotype with fluorescence in situ hybridization for the SRY gene is the most useful test when ambiguous genitalia is suspected. Further prenatal testing for Smith-Lemli-Opitz syndrome in 46,XY individuals and congenital adrenal hyperplasia in 46,XX individuals may be considered. However, targeted molecular testing for rare DSD conditions in the absence of a family history of DSD has a low yield. Copyright © 2012 Wiley Periodicals, Inc.

Integration of replication-defective R68.45-like plasmids into the Pseudomonas aeruginosa chromosome.

PubMed

Reimmann, C; Rella, M; Haas, D

1988-06-01

R68.45 and other similar broad-host-range (IncP) plasmids carrying a tandem repeat of the 2.1 kb insertion element IS21 mobilize the chromosome of many different Gram-negative bacteria. To analyse the structure of R68.45-chromosome cointegrates, whose involvement in the mobilization process had been postulated previously, we selected for the stable integration of R68.45-like plasmids into the Pseudomonas aeruginosa chromosome. Two plasmids were chosen: pME28, a transfer-deficient, mobilizable RP1 derivative with an inactive replication control (trfA) gene, and pME487, an R68.45 derivative with a trfA(ts) mutation causing temperature-sensitive replication. Chromosomally integrated pME28 and pME487 were found to be flanked by single IS21 elements. This structure is in agreement with a 'cut-and-paste' mode of R68.45 transposition. pME28 and pME487 showed a low specificity of insertion but rarely (less than 0.1%) induced auxotrophic mutations. Hfr (high-frequency-of-recombination) donors of P. aeruginosa could be obtained by chromosomal integration of pME487 or pME28; in the latter case, the transfer functions lacking from pME28 had to be provided in trans on an autonomous plasmid. Hfr donors gave higher conjugational linkage and transferred longer stretches of the P. aeruginosa chromosome than did R68.45 donors. This suggests that the integration of R68.45 into the donor chromosome is short-lived in P. aeruginosa.

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

DOE PAGES

Walworth, Nathan; Pfreundt, Ulrike; Nelson, William C.; ...

2015-03-23

Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20–25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. In this paper, we use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% ofmore » the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Finally, our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual “inflation” of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.« less

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

DOE PAGES

Walworth, Nathan G.; Pfreundt, Ulrike; Nelson, William C.; ...

2015-04-07

Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance due to its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and non-pathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus both in culture and in situ. Transcriptome analysis indicates that 86% of the non-coding spacemore » is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and two fold higher than that found in the gene dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium ncRNA secondary structures were predicted between most culture and metagenomic sequences lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high fidelity replication allowed the unusual ‘inflation’ of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.« less

Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome

PubMed Central

Krsticevic, Flavia J.; Schrago, Carlos G.; Carvalho, A. Bernardo

2015-01-01

The autosomal gene Mst77F of Drosophila melanogaster is essential for male fertility. In 2010, Krsticevic et al. (Genetics 184: 295−307) found 18 Y-linked copies of Mst77F (“Mst77Y”), which collectively account for 20% of the functional Mst77F-like mRNA. The Mst77Y genes were severely misassembled in the then-available genome assembly and were identified by cloning and sequencing polymerase chain reaction products. The genomic structure of the Mst77Y region and the possible existence of additional copies remained unknown. The recent publication of two long-read assemblies of D. melanogaster prompted us to reinvestigate this challenging region of the Y chromosome. We found that the Illumina Synthetic Long Reads assembly failed in the Mst77Y region, most likely because of its tandem duplication structure. The PacBio MHAP assembly of the Mst77Y region seems to be very accurate, as revealed by comparisons with the previously found Mst77Y genes, a bacterial artificial chromosome sequence, and Illumina reads of the same strain. We found that the Mst77Y region spans 96 kb and originated from a 3.4-kb transposition from chromosome 3L to the Y chromosome, followed by tandem duplications inside the Y chromosome and invasion of transposable elements, which account for 48% of its length. Twelve of the 18 Mst77Y genes found in 2010 were confirmed in the PacBio assembly, the remaining six being polymerase chain reaction−induced artifacts. There are several identical copies of some Mst77Y genes, coincidentally bringing the total copy number to 18. Besides providing a detailed picture of the Mst77Y region, our results highlight the utility of PacBio technology in assembling difficult genomic regions such as tandemly repeated genes. PMID:25858959

Facts about Truncus Arteriosis

MedlinePlus

... Septal Defect Atrioventricular Septal Defect Coarctation of the Aorta D-Transposition of the Great Arteries Hypoplastic Left ... usual two vessels (the main pulmonary artery and aorta ). What is Truncus Arteriosus Click here to view ...

Transposition of the great arteries

MedlinePlus

... that carry blood away from the heart -- the aorta and the pulmonary artery -- are switched (transposed). ... side of the heart and travels out the aorta to the body. In TGA, venous blood returns ...

AMS fabric and structural record along a strain gradient in an extrusive salt diapir (Kuh-e-Namak, Dashti, Iran)

NASA Astrophysics Data System (ADS)

Zavada, Prokop; Schulmann, Karel; Lexa, Ondrej; Machek, Matej; Roxerova, Zuzana; Kusbach, Vladimir

2016-04-01

The AMS record and the halite fabrics on meso- and micro-scale were studied in detail on a well exposed salt extrusive body in Iran. In the Kuh-e-Namak (Dashti) mountain salt diapir, the deformation structures in colored salt are displayed along longitudinal profiles across the dome and two glaciers that extend from the NE and SW edge of the dome. The profiles from the dome to the frontal parts of the glaciers reveal a continuous strain gradient associated with transposition of the domal salt fabrics by axial fold cleavage development during flow of rock salt over the ridges in the channel. The extruded salt belongs to the Hormuz sequence of Neo-Proterozoic to Early Cambrian age. From central dome towards especially the northern namakier, structural record revealed zonation from; 1) gravitational collapse related recumbent isoclinal folds in the dome, 2) flat normal shears at the edge of the dome, 3) collapsed vertical layering into flat lying transpositional fabric at the toe of the dome, 4) penetrative fold cleavage transposition of earlier fabrics above the topographical ridge in the base of the flow, locally displaying strong transversal constrictional fabrics, 5) banded mylonites with isoclinal rootless folds in subhorizontally banded frontal and marginal domain of the glacier. The AMS fabric in the rock salt is generated primarily by hematite dispersed in the recrystallized halite. The AMS exhibits three main types of fabric symmetry from clustered all directions (K1,K2,K3, orthogonal fabric) to clustered K1 directions with girdle forming K2,K3 axes and clustered K3 directions with girdle of K1 and K2 directions. The AMS fabric clearly reflects the macroscopic fabric transpositions along the entire investigated strain gradient in the rock salt. Magnetic fabrics reveal continuous trends from bimodal to semi-girdle distribution of foliations in folded and cleavage present regions, to magnetic lineation clustering perpendicular to flow in completely refolded domains and to flat lying orthogonal fabric in mylonites at the frontal and marginal edges of the glacier.

What Is a Cardiothoracic Surgeon?

MedlinePlus

... Heart Disease Diseases of the arteries, valves, and aorta, as well as cardiac rhythm disturbances Aortic Valve ... Transposition of the Great Arteries Coarctation of the Aorta Truncus Arteriosus Single Ventricle Defects Patent Ductus Arteriosus ...

Birth Defects Data and Statistics

MedlinePlus

... Septal Defect Atrioventricular Septal Defect Coarctation of the Aorta D-Transposition of the Great Arteries Hypoplastic Left ... Syndrome Disorders Gastroschisis Heart Defects Coarctation of the Aorta Hypoplastic left heart syndrome Tetralogy of Fallot Other ...

Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins

PubMed Central

Filler, Aaron G.

2007-01-01

Background Despite the rising interest in homeotic genes, little has been known about the course and pattern of evolution of homeotic traits across the mammalian radiation. An array of emerging and diversifying homeotic gradients revealed by this study appear to generate new body plans and drive evolution at a large scale. Methodology/Principal Findings This study identifies and evaluates a set of homeotic gradients across 250 extant and fossil mammalian species and their antecedents over a period of 220 million years. These traits are generally expressed as co-linear gradients along the body axis rather than as distinct segmental identities. Relative position or occurrence sequence vary independently and are subject to polarity reversal and mirroring. Five major gradient modification sets are identified: (1)–quantitative changes of primary segmental identity pattern that appeared at the origin of the tetrapods ; (2)–frame shift relation of costal and vertebral identity which diversifies from the time of amniote origins; (3)–duplication, mirroring, splitting and diversification of the neomorphic laminar process first commencing at the dawn of mammals; (4)–emergence of homologically variable lumbar lateral processes upon commencement of the radiation of therian mammals and ; (5)–inflexions and transpositions of the relative position of the horizontal septum of the body and the neuraxis at the emergence of various orders of therian mammals. Convergent functional changes under homeotic control include laminar articular engagement with septo-neural transposition and ventrally arrayed lumbar transverse process support systems. Conclusion/Significance Clusters of homeotic transformations mark the emergence point of mammals in the Triassic and the radiation of therians in the Cretaceous. A cluster of homeotic changes in the Miocene hominoid Morotopithecus that are still seen in humans supports establishment of a new “hominiform” clade and suggests a homeotic origin for the human upright body plan. PMID:17925867

From Greeks to Today: Cipher Trees and Computer Cryptography.

ERIC Educational Resources Information Center

Grady, M. Tim; Brumbaugh, Doug

1988-01-01

Explores the use of computers for teaching mathematical models of transposition ciphers. Illustrates the ideas, includes activities and extensions, provides a mathematical model and includes computer programs to implement these topics. (MVL)

Facts about Hypoplastic Left Heart Syndrome

MedlinePlus

... Septal Defect Atrioventricular Septal Defect Coarctation of the Aorta D-Transposition of the Great Arteries Hypoplastic Left ... is very small. The ascending portion of the aorta is underdeveloped or is too small. Often, babies ...

Genetics Home Reference: critical congenital heart disease

MedlinePlus

... into and out of the heart (including the aorta and pulmonary artery). Still others involve a combination ... defects classified as CCHD include coarctation of the aorta , double-outlet right ventricle, D-transposition of the ...

Understanding pressure: didactical transpositions and pupils' conceptions

NASA Astrophysics Data System (ADS)

Kariotogloy, P.; Psillos, D.; Vallassiades, O.

1990-03-01

Using the concept of pressure two research trends-content analysis and pupils' conceptions of subject matter-are drawn together, in an attempt to understand the issues in teaching and learning specific domains of physics.

Redefining the MED13L syndrome

PubMed Central

Adegbola, Abidemi; Musante, Luciana; Callewaert, Bert; Maciel, Patricia; Hu, Hao; Isidor, Bertrand; Picker-Minh, Sylvie; Le Caignec, Cedric; Delle Chiaie, Barbara; Vanakker, Olivier; Menten, Björn; Dheedene, Annelies; Bockaert, Nele; Roelens, Filip; Decaestecker, Karin; Silva, João; Soares, Gabriela; Lopes, Fátima; Najmabadi, Hossein; Kahrizi, Kimia; Cox, Gerald F; Angus, Steven P; Staropoli, John F; Fischer, Ute; Suckow, Vanessa; Bartsch, Oliver; Chess, Andrew; Ropers, Hans-Hilger; Wienker, Thomas F; Hübner, Christoph; Kaindl, Angela M; Kalscheuer, Vera M

2015-01-01

Congenital cardiac and neurodevelopmental deficits have been recently linked to the mediator complex subunit 13-like protein MED13L, a subunit of the CDK8-associated mediator complex that functions in transcriptional regulation through DNA-binding transcription factors and RNA polymerase II. Heterozygous MED13L variants cause transposition of the great arteries and intellectual disability (ID). Here, we report eight patients with predominantly novel MED13L variants who lack such complex congenital heart malformations. Rather, they depict a syndromic form of ID characterized by facial dysmorphism, ID, speech impairment, motor developmental delay with muscular hypotonia and behavioral difficulties. We thereby define a novel syndrome and significantly broaden the clinical spectrum associated with MED13L variants. A prominent feature of the MED13L neurocognitive presentation is profound language impairment, often in combination with articulatory deficits. PMID:25758992

Redefining the MED13L syndrome.

PubMed

Adegbola, Abidemi; Musante, Luciana; Callewaert, Bert; Maciel, Patricia; Hu, Hao; Isidor, Bertrand; Picker-Minh, Sylvie; Le Caignec, Cedric; Delle Chiaie, Barbara; Vanakker, Olivier; Menten, Björn; Dheedene, Annelies; Bockaert, Nele; Roelens, Filip; Decaestecker, Karin; Silva, João; Soares, Gabriela; Lopes, Fátima; Najmabadi, Hossein; Kahrizi, Kimia; Cox, Gerald F; Angus, Steven P; Staropoli, John F; Fischer, Ute; Suckow, Vanessa; Bartsch, Oliver; Chess, Andrew; Ropers, Hans-Hilger; Wienker, Thomas F; Hübner, Christoph; Kaindl, Angela M; Kalscheuer, Vera M

2015-10-01

Congenital cardiac and neurodevelopmental deficits have been recently linked to the mediator complex subunit 13-like protein MED13L, a subunit of the CDK8-associated mediator complex that functions in transcriptional regulation through DNA-binding transcription factors and RNA polymerase II. Heterozygous MED13L variants cause transposition of the great arteries and intellectual disability (ID). Here, we report eight patients with predominantly novel MED13L variants who lack such complex congenital heart malformations. Rather, they depict a syndromic form of ID characterized by facial dysmorphism, ID, speech impairment, motor developmental delay with muscular hypotonia and behavioral difficulties. We thereby define a novel syndrome and significantly broaden the clinical spectrum associated with MED13L variants. A prominent feature of the MED13L neurocognitive presentation is profound language impairment, often in combination with articulatory deficits.

Development of reconstructive blepharoplasty: the temporofacial rotation flap. Was it first conceived on the Spree, on the Seine, or on the Manzanares?

PubMed

Hinderer, U T

1993-01-01

The development of reconstructive blepharoplasty in the 19th century is analyzed and the techniques classified according to their principles. Besides the main contributions of French, German, and Italian plastic surgeons, those made by two Spanish surgeons are summarized. Argumosa, who published an article on the tempororotation flap two years before Dieffenbach, and Hysern, who developed the first musculocutaneous transposition flaps for eyelid reconstruction, are usually omitted in the literature. After Dieffenbach's publication, German and French surgeons argued about who contributed to the development of plastic surgery in general and to blepharoplasty in particular, while in Spain controversies arose about the importance of Hysern's and Argumosa's contributions. The background and causes of these disputes are analyzed and compared with the present day dissemination and publication of new techniques.

Pelvi-ureteric junction obstruction related to crossing vessels: vascular anatomic variations and implication for surgical approaches.

PubMed

Panthier, Frédéric; Lareyre, Fabien; Audouin, Marie; Raffort, Juliette

2018-03-01

Pelvi-ureteric junction obstruction corresponds to an impairment of urinary transport that can lead to renal dysfunction if not treated. Several mechanisms can cause the obstruction of the ureter including intrinsic factors or extrinsic factors such as the presence of crossing vessels. The treatment of the disease relies on surgical approaches, pyeloplasty being the standard reference. The technique consists in removing the pathologic ureteric segment and renal pelvis and transposing associated crossing vessels if present. The vascular anatomy of the pelvi-ureteric junction is complex and varies among individuals, and this can impact on the disease development and its surgical treatment. In this review, we summarize current knowledge on vascular anatomic variations in the pelvi-ureteric junction. Based on anatomic characteristics, we discuss implications for surgical approaches during pyeloplasty and vessel transposition.

Fungicide-induced transposon movement in Monilinia fructicola.

PubMed

Chen, Fengping; Everhart, Sydney E; Bryson, P Karen; Luo, Chaoxi; Song, Xi; Liu, Xili; Schnabel, Guido

2015-12-01

Repeated applications of fungicides with a single mode of action are believed to select for pre-existing resistant strains in a pathogen population, while the impact of sub-lethal doses of such fungicides on sensitive members of the population is unknown. In this study, in vitro evidence is presented that continuous exposure of Monilinia fructicola mycelium to some fungicides can induce genetic change in form of transposon transposition. Three fungicide-sensitive M. fructicola isolates were exposed in 12 weekly transfers of mycelia to a dose gradient of demethylation inhibitor fungicide (DMI) SYP-Z048 and quinone outside inhibitor fungicide (QoI) azoxystrobin in solo or mixture treatments. Evidence of mutagenesis was assessed by monitoring Mftc1, a multicopy transposable element of M. fructicola, by PCR and Southern blot analysis. Movement of Mftc1 was observed following azoxystrobin and azoxystrobin plus SYP-Z048 treatments in two of the three isolates, but not in the non-fungicide-treated controls. Interestingly, the upstream promoter region of MfCYP51 was a prime target for Mftc1 transposition in these isolates. Transposition of Mftc1 was verified by Southern blot in two of three isolates from another, similar experiment following prolonged, sublethal azoxystrobin exposure, although in these isolates movement of Mftc1 in the upstream MfCYP51 promoter region was not observed. More research is warranted to determine whether fungicide-induced mutagenesis may also happen under field conditions. Copyright © 2015 Elsevier Inc. All rights reserved.

Anterior subcutaneous transposition of ulnar nerve with fascial flap and complete excision of medial intermuscular septum in cubital tunnel syndrome: a prospective patient cohort.

PubMed

Hamidreza, Aslani; Saeid, Abrishami; Mohammadreza, Dehghanfard; Zohreh, Zaferani; Mehdi, Saeidpour

2011-10-01

Regarding the frequency of cubital tunnel syndrome, varieties of treatment modalities, and ambiguity of anterior subcutaneous transposition of ulnar nerve method, we aimed to evaluate the efficacy of this procedure in patients with cubital tunnel syndrome referred to Taleghani hospital between 2006 and 2009. This study was a case series including all referred patients with definite diagnosis of cubital tunnel syndrome, treated by anterior subcutaneous transposition. Treatment results were measured according to modified Bishop rating system, and were ranked into excellent, good, fair, and poor. Variables such as gender, age (less/more than 45 years), causation, and initial severity, determined by Dellon criteria preoperatively, were analyzed by Fisher's exact test. This study was performed on 26 eligible cases including 29 elbows, 38% males and 62.1% females, with mean age of 44.5 years (ranging 23-72 years). In a 12 months follow-up post-operatively, 62% showed excellent, 20.7% good, and 17.3% fair, with no poor result. In a 1-12 months follow-up post-operatively, results showed improvement, and initial severity and old age were demonstrated to significantly affect treatment results (P<0.07). Though considered standard of care, the present study suggests that criteria for surgical techniques of ulnar nerve decompression, e.g. simple decompression vs. more extensive repair as in the present cohort, should be revised by controlled prospective studies. Copyright © 2011 Elsevier B.V. All rights reserved.

Surgical technique of double switch procedure: Senning with arterial switch operation for congenitally corrected transposition of the great arteries with ventricular septal defect.

PubMed

Ilin, Alexey S; Teplov, Pavel V; Sakovich, Valeriy A; Ohye, Richard G

2016-01-01

We present a case of 12-month-old boy with congenitally corrected transposition of great arteries with L-looped ventricles and L-transposition of great arteries and ventricular septal defect. When admitted to the hospital, the patient had the appearance of congestive heart failure due to moderate to severe tricuspid valve regurgitation and right ventricle dysfunction. The pulmonary artery (PA) banding was required first because of low systolic pressure in the morphological left ventricle less than 70% confirmed by catheterization. Three months later, the patient appeared to be a good candidate for anatomical repair and a double switch procedure-Senning with arterial switch-was performed. The early postoperative period was relatively smooth and uneventful. Tricuspid valve insufficiency was resolved immediately after surgery. Mild systolic dysfunction of the left ventricle with mild mitral insufficiency was confirmed by the 2D strain method of echocardiography on the second day of the postoperative period and it improved over the next 21 days. Thirty days later after the procedure, the patient underwent catheterization of his superior vena cava tunnel because of the slightly increased blood flow velocity diagnosed by echocardiography. In 3 months after the surgery, the boy was asymptomatic and was doing well. The patient's functional status was I according to the NYHA classification. © The Author 2016. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

A general heuristic for genome rearrangement problems.

PubMed

Dias, Ulisses; Galvão, Gustavo Rodrigues; Lintzmayer, Carla Négri; Dias, Zanoni

2014-06-01

In this paper, we present a general heuristic for several problems in the genome rearrangement field. Our heuristic does not solve any problem directly, it is rather used to improve the solutions provided by any non-optimal algorithm that solve them. Therefore, we have implemented several algorithms described in the literature and several algorithms developed by ourselves. As a whole, we implemented 23 algorithms for 9 well known problems in the genome rearrangement field. A total of 13 algorithms were implemented for problems that use the notions of prefix and suffix operations. In addition, we worked on 5 algorithms for the classic problem of sorting by transposition and we conclude the experiments by presenting results for 3 approximation algorithms for the sorting by reversals and transpositions problem and 2 approximation algorithms for the sorting by reversals problem. Another algorithm with better approximation ratio can be found for the last genome rearrangement problem, but it is purely theoretical with no practical implementation. The algorithms we implemented in addition to our heuristic lead to the best practical results in each case. In particular, we were able to improve results on the sorting by transpositions problem, which is a very special case because many efforts have been made to generate algorithms with good results in practice and some of these algorithms provide results that equal the optimum solutions in many cases. Our source codes and benchmarks are freely available upon request from the authors so that it will be easier to compare new approaches against our results.

Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate.

PubMed

Nonaka, Lisa; Yamamoto, Tatsuya; Maruyama, Fumito; Hirose, Yuu; Onishi, Yuki; Kobayashi, Takeshi; Suzuki, Satoru; Nomura, Nobuhiko; Masuda, Michiaki; Yano, Hirokazu

2018-01-01

The capture of antimicrobial resistance genes (ARGs) by mobile genetic elements (MGEs) plays a critical role in resistance acquisition for human-associated bacteria. Although aquaculture environments are recognized as important reservoirs of ARGs, intra- and intercellular mobility of MGEs discovered in marine organisms is poorly characterized. Here, we show a new pattern of interspecies ARGs transfer involving a 'non-conjugative' integrative element. To identify active MGEs in a Vibrio ponticus isolate, we conducted whole-genome sequencing of a transconjugant obtained by mating between Escherichia coli and Vibrio ponticus. This revealed integration of a plasmid (designated pSEA1) into the chromosome, consisting of a self-transmissible plasmid backbone of the MOBH group, ARGs, and a 13.8-kb integrative element Tn6283. Molecular genetics analysis suggested a two-step gene transfer model. First, Tn6283 integrates into the recipient chromosome during suicidal plasmid transfer, followed by homologous recombination between the Tn6283 copy in the chromosome and that in the newly transferred pSEA1. Tn6283 is unusual among integrative elements in that it apparently does not encode transfer function and its excision barely generates unoccupied donor sites. Thus, its movement is analogous to the transposition of insertion sequences rather than to that of canonical integrative and conjugative elements. Overall, this study reveals the presence of a previously unrecognized type of MGE in a marine organism, highlighting diversity in the mode of interspecies gene transfer.

A targeted genetic modifier screen links the SWI2/SNF2 protein domino to growth and autophagy genes in Drosophila melanogaster.

PubMed

Kwon, Matt Hyoung; Callaway, Heather; Zhong, Jim; Yedvobnick, Barry

2013-05-20

Targeted genetic studies can facilitate phenotypic analyses and provide important insights into development and other complex processes. The SWI2/SNF2 DNA-dependent ATPase Domino (Dom) of Drosophila melanogaster, a component of the Tip60 acetyltransferase complex, has been associated with a wide spectrum of cellular processes at multiple developmental stages. These include hematopoiesis, cell proliferation, homeotic gene regulation, histone exchange during DNA repair, and Notch signaling. To explore the wider gene network associated with Dom action, we used RNAi directed against domino (dom) to mediate loss-of-function at the wing margin, a tissue that is readily scored for phenotypic changes. Dom RNAi driven through GAL4-UAS elicited dominant wing nicking that responded phenotypically to the dose of dom and other loci known to function with dom. We screened for phenotypic modifiers of this wing phenotype among 2500 transpositions of the EP P element and found both enhancers and suppressors. Several classes of modifier were obtained, including those encoding transcription factors, RNA regulatory proteins, and factors that regulate cell growth, proliferation and autophagy, a lysosomal degradation pathway that affects cell growth under conditions of starvation and stress. Our analysis is consistent with prior studies, suggesting that Dom acts pleiotropically as a positive effector of Notch signaling and a repressor of proliferation. This genetic system should facilitate screens for additional loci associated with Dom function, and complement biochemical approaches to their regulatory activity.

Estimating true evolutionary distances under the DCJ model.

PubMed

Lin, Yu; Moret, Bernard M E

2008-07-01

Modern techniques can yield the ordering and strandedness of genes on each chromosome of a genome; such data already exists for hundreds of organisms. The evolutionary mechanisms through which the set of the genes of an organism is altered and reordered are of great interest to systematists, evolutionary biologists, comparative genomicists and biomedical researchers. Perhaps the most basic concept in this area is that of evolutionary distance between two genomes: under a given model of genomic evolution, how many events most likely took place to account for the difference between the two genomes? We present a method to estimate the true evolutionary distance between two genomes under the 'double-cut-and-join' (DCJ) model of genome rearrangement, a model under which a single multichromosomal operation accounts for all genomic rearrangement events: inversion, transposition, translocation, block interchange and chromosomal fusion and fission. Our method relies on a simple structural characterization of a genome pair and is both analytically and computationally tractable. We provide analytical results to describe the asymptotic behavior of genomes under the DCJ model, as well as experimental results on a wide variety of genome structures to exemplify the very high accuracy (and low variance) of our estimator. Our results provide a tool for accurate phylogenetic reconstruction from multichromosomal gene rearrangement data as well as a theoretical basis for refinements of the DCJ model to account for biological constraints. All of our software is available in source form under GPL at http://lcbb.epfl.ch.

The baculovirus-integrated retrotransposon TED encodes gag and pol proteins that assemble into viruslike particles with reverse transcriptase.

PubMed Central

Lerch, R A; Friesen, P D

1992-01-01

TED is a lepidopteran retrotransposon found inserted within the DNA genome of the Autographa californica nuclear polyhedrosis virus mutant, FP-D. To examine the proteins and functions encoded by this representative of the gypsy family of retrotransposons, the gag- and pol-like open reading frames (ORFs 1 and 2) were expressed in homologous lepidopteran cells by using recombinant baculovirus vectors. Expression of ORF 1 resulted in synthesis of an abundant TED-specific protein (Pr55gag) that assembled into viruslike particles with a diameter of 55 to 60 nm. Expression of ORF 2, requiring a -1 translational frameshift, resulted in synthesis of a protease that mediated cleavage of Pr55gag to generate p37, the major protein component of the resulting particles. Expression of ORF 2 also produced reverse transcriptase that associated with these particles. Both protease and reverse transcriptase activities mapped to domains within ORF 2 that contain sequence similarities with the corresponding functional domains of the pol gene of the vertebrate retroviruses. These results indicated that TED ORFs 1 and 2 functionally resemble the retrovirus gag and pol genes and demonstrated for the first time that an invertebrate member of the gypsy family of elements encodes active forms of the structural and enzymatic functions necessary for transposition via an RNA intermediate. TED integration within the baculovirus genome thus represents one of the first examples of transposon-mediated transfer of host-derived genes to an eukaryotic virus. Images PMID:1371168

Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia.

PubMed

Meyer, C; Pouteau, S; Rouzé, P; Caboche, M

1994-01-01

By Northern blot analysis of nitrate reductase-deficient mutants of Nicotiana plumbaginifolia, we identified a mutant (mutant D65), obtained after gamma-ray irradiation of protoplasts, which contained an insertion sequence in the nitrate reductase (NR) mRNA. This insertion sequence was localized by polymerase chain reaction (PCR) in the first exon of NR and was also shown to be present in the NR gene. The mutant gene contained a 565 bp insertion sequence that exhibits the sequence characteristics of a transposable element, which was thus named dTnp1. The dTnp1 element has 14 bp terminal inverted repeats and is flanked by an 8-bp target site duplication generated upon transposition. These inverted repeats have significant sequence homology with those of other transposable elements. Judging by its size and the absence of a long open reading frame, dTnp1 appears to represent a defective, although mobile, transposable element. The octamer motif TTTAGGCC was found several times in direct orientation near the 5' and 3' ends of dTnp1 together with a perfect palindrome located after the 5' inverted repeat. Southern blot analysis using an internal probe of dTnp1 suggested that this element occurs as a single copy in the genome of N. plumbaginifolia. It is also present in N. tabacum, but absent in tomato or petunia. The dTnp1 element is therefore of potential use for gene tagging in Nicotiana species.

The surgical treatment of ilio-femoral venous obstruction.

PubMed

Illuminati, G; Caliò, F G; D'Urso, A; Mancini, P; Papaspyropoulos, V; Ceccanei, G; Lorusso, R; Vietri, F

2004-01-01

A series of 9 patients of a mean age of 48 years, operated on for compression of the ilio-femoral venous axis is reported. The cause of obstruction was external compression in 3 cases, a retroperitoneal sarcoma in 1 case, and an infrarenal aortic aneurysm in 2. Two patients presented with a Cockett's syndrome, 3 with a chronic ilio-femoral thrombosis, and one with a post-traumatic segmentary stenosis. Treatment consisted in a resection/Dacron grafting of 2 infrarenal aortic aneurysms, one femoro-caval bypass graft, 2 transpositions of the right common iliac artery in the left hypogastric artery for Cockett's syndrome, 3 Palma's operations for chronic thrombosis, and one internal jugular vein interposition for segmentary stenosis. There were no postoperative deaths and no early thromboses of venous reconstructions performed. All the patients were relieved of symptoms during the follow-up period, whose mean length was 38 months. The cause of venous obstruction and the presence of symptoms which are resistant to medical treatment are the main indications to ilio-femoral venous revascularization. The choice of the optimal treatment in each single case yields satisfactory results.

Reproduction and Survival After Cardiac Defect Repair

ClinicalTrials.gov

2016-02-17

Cardiovascular Diseases; Heart Diseases; Defect, Congenital Heart; Aortic Valve Stenosis; Transposition of Great Vessels; Ductus Arteriosus, Patent; Heart Septal Defects, Atrial; Heart Septal Defects, Ventricular; Down Syndrome; Tetralogy of Fallot; Pulmonic Stenosis; Coarctation of Aorta

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kennedy, M.A.; Morris, C.M.; Fitzgerald, P.H.

The human kappa deleting element (Kde) mediates loss of CK and JK genes in B cells. A probe for Kde detects two genomic sequences on Southern blots. The Kde is located 24kb 3{prime} to CK, but the position of the homologous sequence is unknown. The authors in situ hybridized m141-2 to metaphase cells of JC11, a B-cell line bearing a t(2;14)(p11;q32) in which the chromosome 2 breakpoint is within JK or the VK-JK intron. Three peaks of labelled sites were obtained. Southern analysis of BamH1 digested DNA showed that Kde (14kb) and the homologous sequence (3kb) were both intact. Kdemore » accounts for hybridization to 14q+ and the 2p- signal presumably derives from the related sequence. This locates the sequence homologous to Kde upstream from JK, possibly within the VK cluster, and may reflect transposition or some other duplicative event as proposed for the evolution of other regions of the kappa locus.« less

Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells

PubMed Central

Clark, Karl J.; Carlson, Daniel F.; Leaver, Michael J.; Foster, Linda K.; Fahrenkrug, Scott C.

2009-01-01

The Tc1/mariner family of DNA transposons is widespread across fungal, plant and animal kingdoms, and thought to contribute to the evolution of their host genomes. To date, an active Tc1 transposon has not been identified within the native genome of a vertebrate. We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells. In transposition assays, we found that the Passport transposon system improved stable cellular transgenesis by 40-fold, has an apparent preference for insertion into genes, and is subject to overproduction inhibition like other Tc1 elements. Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active. The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements. PMID:19136468

Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells.

PubMed

Clark, Karl J; Carlson, Daniel F; Leaver, Michael J; Foster, Linda K; Fahrenkrug, Scott C

2009-03-01

The Tc1/mariner family of DNA transposons is widespread across fungal, plant and animal kingdoms, and thought to contribute to the evolution of their host genomes. To date, an active Tc1 transposon has not been identified within the native genome of a vertebrate. We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells. In transposition assays, we found that the Passport transposon system improved stable cellular transgenesis by 40-fold, has an apparent preference for insertion into genes, and is subject to overproduction inhibition like other Tc1 elements. Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active. The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements.

Active Site Sharing and Subterminal Hairpin Recognition in a New Class of DNA Transposases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronning, Donald R.; Guynet, Catherine; Ton-Hoang, Bao

2010-07-20

Many bacteria harbor simple transposable elements termed insertion sequences (IS). In Helicobacter pylori, the chimeric IS605 family elements are particularly interesting due to their proximity to genes encoding gastric epithelial invasion factors. Protein sequences of IS605 transposases do not bear the hallmarks of other well-characterized transposases. We have solved the crystal structure of full-length transposase (TnpA) of a representative member, ISHp608. Structurally, TnpA does not resemble any characterized transposase; rather, it is related to rolling circle replication (RCR) proteins. Consistent with RCR, Mg{sup 2+} and a conserved tyrosine, Tyr127, are essential for DNA nicking and the formation of a covalentmore » intermediate between TnpA and DNA. TnpA is dimeric, contains two shared active sites, and binds two DNA stem loops representing the conserved inverted repeats near each end of ISHp608. The cocrystal structure with stem-loop DNA illustrates how this family of transposases specifically recognizes and pairs ends, necessary steps during transposition.« less

Functional mapping of yeast genomes by saturated transposition

PubMed Central

Michel, Agnès H; Hatakeyama, Riko; Kimmig, Philipp; Arter, Meret; Peter, Matthias; Matos, Joao; De Virgilio, Claudio; Kornmann, Benoît

2017-01-01

Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput. DOI: http://dx.doi.org/10.7554/eLife.23570.001 PMID:28481201

Endometrial response to endogenous hormones after pelvic irradiation for genital malignancies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, J.E.; Whitney, C.W.; Zaino, R.

1990-01-01

Two cases are presented which demonstrate histologically an endometrial response to endogenous hormones after pelvic teletherapy and brachytherapy in patients who have undergone lateral ovarian transposition. Reasons for such a response are briefly discussed.

Successful initiation and maintenance of hemodialysis in an adult patient with complete transposition of the great arteries.

PubMed

Yamada, Shunsuke; Yotsueda, Hideki; Taniguchi, Masatomo; Tsuruya, Kazuhiko; Hirakata, Hideki; Iida, Mitsuo

2010-10-01

Cyanotic congenital heart disease (CCHD) is a life-threatening cardiac defect that requires palliative or corrective surgery in early life. Major advances in medical and surgical management have resulted in the survival of CCHD patients to adulthood with or without corrective surgery, though some are at risk of development of end-stage renal disease (ESRD) due to cyanotic nephropathy (CN). There is little or no information on the initiation and maintenance of hemodialysis (HD) in such patients. We present here a case of a 44-year-old man with complete transposition of the great arteries and CN-related ESRD. He had only received a bi-directional Glenn's operation and still suffered persistent severe hypoxemia and impaired cardiac function. ESRD was successfully treated with HD over more than 4 years. The case emphasizes the need for special attention in the selection and initiation of renal replacement therapy.

Primary Prevention of Sudden Cardiac Death in Adults with Transposition of the Great Arteries: A Review of Implantable Cardioverter-Defibrillator Placement

PubMed Central

Cedars, Ari M.

2015-01-01

Transposition of the great arteries encompasses a set of structural congenital cardiac lesions that has in common ventriculoarterial discordance. Primarily because of advances in medical and surgical care, an increasing number of children born with this anomaly are surviving into adulthood. Depending upon the subtype of lesion or the particular corrective surgery that the patient might have undergone, this group of adult congenital heart disease patients constitutes a relatively new population with unique medical sequelae. Among the more common and difficult to manage are cardiac arrhythmias and other sequelae that can lead to sudden cardiac death. To date, the question of whether implantable cardioverter-defibrillators should be placed in this cohort as a preventive measure to abort sudden death has largely gone unanswered. Therefore, we review the available literature surrounding this issue. PMID:26413012

Transposable elements in Drosophila.

PubMed

McCullers, Tabitha J; Steiniger, Mindy

2017-01-01

Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster .

[Active miniature inverted-repeat transposable elements transposon in plants: a review].

PubMed

Hu, Bingjie; Zhou, Mingbing

2018-02-25

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

The Gam protein of bacteriophage Mu is an orthologue of eukaryotic Ku

PubMed Central

di Fagagna, Fabrizio d'Adda; Weller, Geoffrey R.; Doherty, Aidan J.; Jackson, Stephen P.

2003-01-01

Mu bacteriophage inserts its DNA into the genome of host bacteria and is used as a model for DNA transposition events in other systems. The eukaryotic Ku protein has key roles in DNA repair and in certain transposition events. Here we show that the Gam protein of phage Mu is conserved in bacteria, has sequence homology with both subunits of Ku, and has the potential to adopt a similar architecture to the core DNA-binding region of Ku. Through biochemical studies, we demonstrate that Gam and the related protein of Haemophilus influenzae display DNA binding characteristics remarkably similar to those of human Ku. In addition, we show that Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae. These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved. PMID:12524520

Transposable elements in Drosophila

PubMed Central

McCullers, Tabitha J.; Steiniger, Mindy

2017-01-01

ABSTRACT Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster. PMID:28580197

The midline-based nasolabial transposition (MNT) flap: an original single-stage technique for nasal tip reconstruction.

PubMed

Beustes-Stefanelli, Matthieu; O'Toole, Greg; Schertenleib, Pierre

2015-04-01

Nasolabial flaps based on the lateral side of the nose for the reconstruction of lateral nasal defects in a single-stage procedure have been described. Similarly, in midline defects, nasolabial flaps can be used but a 2-stage procedure is classically required. The Midline-based Nasolabial Transposition (MNT) flap is presented as a new single-stage procedure for nasal tip reconstruction. Between 2009 and 2011, an MNT flap was used as a single-stage procedure in 3 cases of large nasal defects of the tip where the forehead flap was either contraindicated or rejected as an option by the patient. There were no complications and a satisfactory aesthetic result was achieved in all cases. The MNT flap is a new single-stage procedure for large nasal tip defects and as such represents an interesting alternative to the classical 2-stage forehead and nasolabial flaps, especially in elderly patients.

Targeting of a Nuclease to Murine Leukemia Virus Capsids Inhibits Viral Multiplication

NASA Astrophysics Data System (ADS)

Natsoulis, Georges; Seshaiah, Partha; Federspiel, Mark J.; Rein, Alan; Hughes, Stephen H.; Boeke, Jef D.

1995-01-01

Capsid-targeted viral inactivation is an antiviral strategy in which toxic fusion proteins are targeted to virions, where they inhibit viral multiplication by destroying viral components. These fusion proteins consist of a virion structural protein moiety and an enzymatic moiety such as a nuclease. Such fusion proteins can severely inhibit transposition of yeast retrotransposon Ty1, an element whose transposition mechanistically resembles retroviral multiplication. We demonstrate that expression of a murine retrovirus capsid-staphylococcal nuclease fusion protein inhibits multiplication of the corresponding murine leukemia virus by 30- to 100-fold. Staphylococcal nuclease is apparently inactive intracellularly and hence nontoxic to the host cell, but it is active extracellularly because of its requirement for high concentrations of Ca2+ ions. Virions assembled in and shed from cells expressing the fusion protein contain very small amounts of intact viral RNA, as would be predicted for nuclease-mediated inhibition of viral multiplication.

A faster 1.375-approximation algorithm for sorting by transpositions.

PubMed

Cunha, Luís Felipe I; Kowada, Luis Antonio B; Hausen, Rodrigo de A; de Figueiredo, Celina M H

2015-11-01

Sorting by Transpositions is an NP-hard problem for which several polynomial-time approximation algorithms have been developed. Hartman and Shamir (2006) developed a 1.5-approximation [Formula: see text] algorithm, whose running time was improved to O(nlogn) by Feng and Zhu (2007) with a data structure they defined, the permutation tree. Elias and Hartman (2006) developed a 1.375-approximation O(n(2)) algorithm, and Firoz et al. (2011) claimed an improvement to the running time, from O(n(2)) to O(nlogn), by using the permutation tree. We provide counter-examples to the correctness of Firoz et al.'s strategy, showing that it is not possible to reach a component by sufficient extensions using the method proposed by them. In addition, we propose a 1.375-approximation algorithm, modifying Elias and Hartman's approach with the use of permutation trees and achieving O(nlogn) time.

Transposition of the maize transposable element Ac in barley (Hordeum vulgare L.).

PubMed

Scholz, S; Lörz, H; Lütticke, S

2001-01-01

Transposition of the maize autonomous element Ac (Activator) was investigated in barley (Hordeum vulgare L.) with the aim of developing a transposon tagging system for the latter. The Ac element was introduced into meristematic tissue of barley by microprojectile bombardment. Transposon activity was then examined in the resulting transgenic plants. Multiple excision events were detected in leaf tissue of all plant lines. The mobile elements generated empty donor sites with small DNA sequence alterations, similar to those found in maize. Reintegration of Ac at independent genomic loci in somatic tissue was demonstrated by isolation of new element-flanking regions by AIMS-PCR (amplification of insertion-mutagenized sites). In addition, transmission of transposed Ac elements to progeny plants was confirmed. The results indicate that the introduced Ac element is able to transpose in barley. This is a first step towards the establishment of a transposon tagging system in this economically important crop.

Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain

PubMed Central

2012-01-01

Background The molecular mechanisms altered by the traditional mutation and screening approach during the improvement of antibiotic-producing microorganisms are still poorly understood although this information is essential to design rational strategies for industrial strain improvement. In this study, we applied comparative genomics to identify all genetic changes occurring during the development of an erythromycin overproducer obtained using the traditional mutate-and- screen method. Results Compared with the parental Saccharopolyspora erythraea NRRL 2338, the genome of the overproducing strain presents 117 deletion, 78 insertion and 12 transposition sites, with 71 insertion/deletion sites mapping within coding sequences (CDSs) and generating frame-shift mutations. Single nucleotide variations are present in 144 CDSs. Overall, the genomic variations affect 227 proteins of the overproducing strain and a considerable number of mutations alter genes of key enzymes in the central carbon and nitrogen metabolism and in the biosynthesis of secondary metabolites, resulting in the redirection of common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, affect global expression profile as demonstrated by a comparative analysis of the parental and overproducer expression profiles. Genomic data, finally, suggest that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes. Conclusions This study helps to clarify the mechanisms underlying antibiotic overproduction providing valuable information about new possible molecular targets for rationale strain improvement. PMID:22401291

Critical components of the pluripotency network are targets for the p300/CBP interacting protein (p/CIP) in embryonic stem cells.

PubMed

Chitilian, J M; Thillainadesan, G; Manias, J L; Chang, W Y; Walker, E; Isovic, M; Stanford, W L; Torchia, J

2014-01-01

p/CIP, also known as steroid receptor coactivator 3 (SRC-3)/Nuclear Receptor Coactivator 3 (NCoA3), is a transcriptional coactivator that binds liganded nuclear hormone receptors, as well as other transcription factors, and facilitates transcription through direct recruitment of accessory factors. We have found that p/CIP is highly expressed in undifferentiated mouse embryonic stem cells (mESCs) and is downregulated during differentiation. siRNA-mediated knockdown of p/CIP decreased transcript levels of Nanog, but not Oct4 or Sox2. Microarray expression analysis showed that Klf4, Tbx3, and Dax-1 are significantly downregulated in mESCs when p/CIP is knocked down. Subsequent chromatin immunoprecipitation (ChIP) analysis demonstrated that Tbx3, Klf4, and Dax-1 are direct transcriptional targets of p/CIP. Using the piggyBac transposition system, a mouse ESC line that expresses Flag-p/CIP in a doxycycline-dependent manner was generated. p/CIP overexpression increased the level of target genes and promoted the formation of undifferentiated colonies. Collectively, these results indicate that p/CIP contributes to the maintenance of ESC pluripotency through direct regulation of essential pluripotency genes. To better understand the mechanism by which p/CIP functions in ESC pluripotency, we integrated our ChIP and transcriptome data with published protein-protein interaction and promoter occupancy data to draft a p/CIP gene regulatory network. The p/CIP gene regulatory network identifies various feed-forward modules including one in which p/CIP activates members of the extended pluripotency network, demonstrating that p/CIP is a component of this extended network. © AlphaMed Press.

Host factors that promote retrotransposon integration are similar in distantly related eukaryotes

PubMed Central

Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak

2017-01-01

Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements. PMID:29232693

Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.

PubMed

Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak; Levin, Henry L

2017-12-01

Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.