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).

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.

Transposable elements as a molecular evolutionary force

NASA Technical Reports Server (NTRS)

Fedoroff, N. V.

1999-01-01

This essay addresses the paradoxes of the complex and highly redundant genomes. The central theses developed are that: (1) the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy; (2) the special contribution of transposable elements is to modularize the genome; and (3) the labilizing forces of recombination and transposition are just barely contained, giving a dynamic genetic system of ever increasing complexity that verges on the chaotic.

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

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

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

Regional frequency analysis of extreme rainfall for the Baltimore Metropolitan region based on stochastic storm transposition

NASA Astrophysics Data System (ADS)

Zhou, Z.; Smith, J. A.; Yang, L.; Baeck, M. L.; Wright, D.; Liu, S.

2017-12-01

Regional frequency analyses of extreme rainfall are critical for development of engineering hydrometeorology procedures. In conventional approaches, the assumptions that `design storms' have specified time profiles and are uniform in space are commonly applied but often not appropriate, especially over regions with heterogeneous environments (due to topography, water-land boundaries and land surface properties). In this study, we present regional frequency analyses of extreme rainfall for Baltimore study region combining storm catalogs of rainfall fields derived from weather radar and stochastic storm transposition (SST, developed by Wright et al., 2013). The study region is Dead Run, a small (14.3 km2) urban watershed, in the Baltimore Metropolitan region. Our analyses build on previous empirical and modeling studies showing pronounced spatial heterogeneities in rainfall due to the complex terrain, including the Chesapeake Bay to the east, mountainous terrain to the west and urbanization in this region. We expand the original SST approach by applying a multiplier field that accounts for spatial heterogeneities in extreme rainfall. We also characterize the spatial heterogeneities of extreme rainfall distribution through analyses of rainfall fields in the storm catalogs. We examine the characteristics of regional extreme rainfall and derive intensity-duration-frequency (IDF) curves using the SST approach for heterogeneous regions. Our results highlight the significant heterogeneity of extreme rainfall in this region. Estimates of IDF show the advantages of SST in capturing the space-time structure of extreme rainfall. We also illustrate application of SST analyses for flood frequency analyses using a distributed hydrological model. Reference: Wright, D. B., J. A. Smith, G. Villarini, and M. L. Baeck (2013), Estimating the frequency of extreme rainfall using weather radar and stochastic storm transposition, J. Hydrol., 488, 150-165.

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

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

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

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

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.

Transposable Elements as Stress Adaptive Capacitors Induce Genomic Instability in Fungal Pathogen Magnaporthe oryzae

PubMed Central

Chadha, Sonia; Sharma, Mradul

2014-01-01

A fundamental problem in fungal pathogenesis is to elucidate the evolutionary forces responsible for genomic rearrangements leading to races with fitter genotypes. Understanding the adaptive evolutionary mechanisms requires identification of genomic components and environmental factors reshaping the genome of fungal pathogens to adapt. Herein, Magnaporthe oryzae, a model fungal plant pathogen is used to demonstrate the impact of environmental cues on transposable elements (TE) based genome dynamics. For heat shock and copper stress exposed samples, eight TEs belonging to class I and II family were employed to obtain DNA profiles. Stress induced mutant bands showed a positive correlation with dose/duration of stress and provided evidences of TEs role in stress adaptiveness. Further, we demonstrate that genome dynamics differ for the type/family of TEs upon stress exposition and previous reports of stress induced MAGGY transposition has underestimated the role of TEs in M. oryzae. Here, we identified Pyret, MAGGY, Pot3, MINE, Mg-SINE, Grasshopper and MGLR3 as contributors of high genomic instability in M. oryzae in respective order. Sequencing of mutated bands led to the identification of LTR-retrotransposon sequences within regulatory regions of psuedogenes. DNA transposon Pot3 was identified in the coding regions of chromatin remodelling protein containing tyrosinase copper-binding and PWWP domains. LTR-retrotransposons Pyret and MAGGY are identified as key components responsible for the high genomic instability and perhaps these TEs are utilized by M. oryzae for its acclimatization to adverse environmental conditions. Our results demonstrate how common field stresses change genome dynamics of pathogen and provide perspective to explore the role of TEs in genome adaptability, signalling network and its impact on the virulence of fungal pathogens. PMID:24709911

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PubMed Central

Diez, Concepcion M.; Meca, Esteban; Tenaillon, Maud I.; Gaut, Brandon S.

2014-01-01

Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. PMID:24743518

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.

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

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.

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

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.

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

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.

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.

A complex structure in the mRNA of Tf1 is recognized and cleaved to generate the primer of reverse transcription.

PubMed

Lin, J H; Levin, H L

1997-01-15

All retroviruses and LTR-containing retrotransposons are thought to require specific tRNA molecules to serve as primers of reverse transcription. An exception is the LTR-containing retrotransposon Tf1, isolated from Schizosaccharomyces pombe. Instead of requiring a tRNA, the reverse transcriptase of Tf1 uses the first 11 bases of the Tf1 transcript as the primer for reverse transcription. The primer is generated by a cleavage that occurs between bases 11 and 12 of the Tf1 mRNA. Sequence analysis of the 5' untranslated region of the Tf1 mRNA resulted in the identification of a region with the potential to form an RNA structure of 89 bases that included the primer binding site and the first 11 bases of the Tf1 mRNA. Systematic mutagenesis of this region revealed 34 single-point mutants in the structure that resulted in reduced transposition activity. The defects in transposition correlated with reduced level of Tf1 reverse transcripts as determined by DNA blot analysis. Evidence that the RNA structure did form in vivo included the result that strains with second site mutations that restored complementarity resulted in increased levels of reverse transcripts and Tf1 transposition. The majority of the mutants defective for reverse transcription were unable to cleave the Tf1 mRNA between bases 11 and 12. These data indicate that formation of an extensive RNA structure was required for the cleavage reaction that generated the primer for Tf1 reverse transcription.

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

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes

PubMed Central

Gallus, Susanne; Janke, Axel

2017-01-01

Abstract Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. PMID:28985298

The industrial melanism mutation in British peppered moths is a transposable element.

PubMed

Van't Hof, Arjen E; Campagne, Pascal; Rigden, Daniel J; Yung, Carl J; Lingley, Jessica; Quail, Michael A; Hall, Neil; Darby, Alistair C; Saccheri, Ilik J

2016-06-02

Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria-typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of 'jumping genes' as a source of major phenotypic novelty.

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.

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.

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.

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

Unstable transpositions of his4 in yeast.

PubMed Central

Greer, H; Fink, G R

1979-01-01

Unstable transpositions in yeast have been selected in which the his4C gene from chromosome III is inserted into chromosome XII. This event is associated with the generation of a recessive lethal mutation, resulting from the integration of his4C into an essential gene. Strains with these transpositions are viable as diploids or aneuploids for chromosome XII. The event that generates the transpositions does not lead reciprocally to a deletion on chromosome III, implying that synthesis of a new copy of his4C and subsequent transposition may have occurred. The his4C transpositions are unstable and give rise to C- segregants at a high frequency, as a result of either precise excision of the his4C gene (restoring function of the gene into which insertion had occurred) or chromosome loss. PMID:386353

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

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

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.

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.

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes.

PubMed

Grabundzija, Ivana; Messing, Simon A; Thomas, Jainy; Cosby, Rachel L; Bilic, Ilija; Miskey, Csaba; Gogol-Döring, Andreas; Kapitonov, Vladimir; Diem, Tanja; Dalda, Anna; Jurka, Jerzy; Pritham, Ellen J; Dyda, Fred; Izsvák, Zsuzsanna; Ivics, Zoltán

2016-03-02

Helitron transposons capture and mobilize gene fragments in eukaryotes, but experimental evidence for their transposition is lacking in the absence of an isolated active element. Here we reconstruct Helraiser, an ancient element from the bat genome, and use this transposon as an experimental tool to unravel the mechanism of Helitron transposition. A hairpin close to the 3'-end of the transposon functions as a transposition terminator. However, the 3'-end can be bypassed by the transposase, resulting in transduction of flanking sequences to new genomic locations. Helraiser transposition generates covalently closed circular intermediates, suggestive of a replicative transposition mechanism, which provides a powerful means to disseminate captured transcriptional regulatory signals across the genome. Indeed, we document the generation of novel transcripts by Helitron promoter capture both experimentally and by transcriptome analysis in bats. Our results provide mechanistic insight into Helitron transposition, and its impact on diversification of gene function by genome shuffling.

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

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…

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.

PubMed

Lammers, Fritjof; Gallus, Susanne; Janke, Axel; Nilsson, Maria A

2017-10-01

Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

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.

A TALE of transposition: Tn3-like transposons play a major role in the spread of pathogenicity determinants of Xanthomonas citri and other xanthomonads.

PubMed

Ferreira, Rafael Marini; de Oliveira, Amanda Carolina P; Moreira, Leandro M; Belasque, José; Gourbeyre, Edith; Siguier, Patricia; Ferro, Maria Inês T; Ferro, Jesus A; Chandler, Michael; Varani, Alessandro M

2015-02-17

Members of the genus Xanthomonas are among the most important phytopathogens. A key feature of Xanthomonas pathogenesis is the translocation of type III secretion system (T3SS) effector proteins (T3SEs) into the plant target cells via a T3SS. Several T3SEs and a murein lytic transglycosylase gene (mlt, required for citrus canker symptoms) are found associated with three transposition-related genes in Xanthomonas citri plasmid pXAC64. These are flanked by short inverted repeats (IRs). The region was identified as a transposon, TnXax1, with typical Tn3 family features, including a transposase and two recombination genes. Two 14-bp palindromic sequences within a 193-bp potential resolution site occur between the recombination genes. Additional derivatives carrying different T3SEs and other passenger genes occur in different Xanthomonas species. The T3SEs include transcription activator-like effectors (TALEs). Certain TALEs are flanked by the same IRs as found in TnXax1 to form mobile insertion cassettes (MICs), suggesting that they may be transmitted horizontally. A significant number of MICs carrying other passenger genes (including a number of TALE genes) were also identified, flanked by the same TnXax1 IRs and delimited by 5-bp target site duplications. We conclude that a large fraction of T3SEs, including individual TALEs and potential pathogenicity determinants, have spread by transposition and that TnXax1, which exhibits all of the essential characteristics of a functional transposon, may be involved in driving MIC transposition. We also propose that TALE genes may diversify by fork slippage during the replicative Tn3 family transposition. These mechanisms may play a crucial role in the emergence of Xanthomonas pathogenicity. Xanthomonas genomes carry many insertion sequences (IS) and transposons, which play an important role in their evolution and architecture. This study reveals a key relationship between transposons and pathogenicity determinants in Xanthomonas. We propose that several transposition events mediated by a Tn3-like element carrying different sets of passenger genes, such as different type III secretion system effectors (including transcription activation-like effectors [TALEs]), were determinant in the evolution and emergence of Xanthomonas pathogenicity. TALE genes are DNA-binding effectors that modulate plant transcription. We also present a model for generating TALE gene diversity based on fork slippage associated with the replicative transposition mechanism of Tn3-like transposons. This may provide a mechanism for niche adaptation, specialization, host-switching, and other lifestyle changes. These results will also certainly lead to novel insights into the evolution and emergence of the various diseases caused by different Xanthomonas species and pathovars. Copyright © 2015 Marini Ferreira et al.

Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species

PubMed Central

Kim, Jae-Heup; Antunes, Agostinho; Luo, Shu-Jin; Menninger, Joan; Nash, William G.; O’Brien, Stephen J.; Johnson, Warren E.

2006-01-01

Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2 – telomeric region vs. D2 – centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 kb vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species. PMID:16380222

Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species.

PubMed

Kim, Jae-Heup; Antunes, Agostinho; Luo, Shu-Jin; Menninger, Joan; Nash, William G; O'Brien, Stephen J; Johnson, Warren E

2006-02-01

Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2-telomeric region vs. D2-centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species.

Short- and Long-term Evolutionary Dynamics of Bacterial Insertion Sequences: Insights from Wolbachia Endosymbionts

PubMed Central

Cerveau, Nicolas; Leclercq, Sébastien; Leroy, Elodie; Bouchon, Didier; Cordaux, Richard

2011-01-01

Transposable elements (TE) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Long-term TE evolution can readily be reconstructed in eukaryotes, thanks to many degraded copies constituting genomic fossil records of past TE proliferations. By contrast, bacterial genomes usually experience high sequence turnover and short TE retention times, thereby obscuring ancient TE evolutionary patterns. We found that Wolbachia bacterial genomes contain 52–171 insertion sequence (IS) TEs. IS account for 11% of Wolbachia wRi, which is one of the highest IS genomic coverage reported in prokaryotes to date. We show that many IS groups are currently expanding in various Wolbachia genomes and that IS horizontal transfers are frequent among strains, which can explain the apparent synchronicity of these IS proliferations. Remarkably, >70% of Wolbachia IS are nonfunctional. They constitute an unusual bacterial IS genomic fossil record providing direct empirical evidence for a long-term IS evolutionary dynamics following successive periods of intense transpositional activity. Our results show that comprehensive IS annotations have the potential to provide new insights into prokaryote TE evolution and, more generally, prokaryote genome evolution. Indeed, the identification of an important IS genomic fossil record in Wolbachia demonstrates that IS elements are not always of recent origin, contrary to the conventional view of TE evolution in prokaryote genomes. Our results also raise the question whether the abundance of IS fossils is specific to Wolbachia or it may be a general, albeit overlooked, feature of prokaryote genomes. PMID:21940637

Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts.

PubMed

Cerveau, Nicolas; Leclercq, Sébastien; Leroy, Elodie; Bouchon, Didier; Cordaux, Richard

2011-01-01

Transposable elements (TE) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Long-term TE evolution can readily be reconstructed in eukaryotes, thanks to many degraded copies constituting genomic fossil records of past TE proliferations. By contrast, bacterial genomes usually experience high sequence turnover and short TE retention times, thereby obscuring ancient TE evolutionary patterns. We found that Wolbachia bacterial genomes contain 52-171 insertion sequence (IS) TEs. IS account for 11% of Wolbachia wRi, which is one of the highest IS genomic coverage reported in prokaryotes to date. We show that many IS groups are currently expanding in various Wolbachia genomes and that IS horizontal transfers are frequent among strains, which can explain the apparent synchronicity of these IS proliferations. Remarkably, >70% of Wolbachia IS are nonfunctional. They constitute an unusual bacterial IS genomic fossil record providing direct empirical evidence for a long-term IS evolutionary dynamics following successive periods of intense transpositional activity. Our results show that comprehensive IS annotations have the potential to provide new insights into prokaryote TE evolution and, more generally, prokaryote genome evolution. Indeed, the identification of an important IS genomic fossil record in Wolbachia demonstrates that IS elements are not always of recent origin, contrary to the conventional view of TE evolution in prokaryote genomes. Our results also raise the question whether the abundance of IS fossils is specific to Wolbachia or it may be a general, albeit overlooked, feature of prokaryote genomes.

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

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

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

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

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.

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

Prevertebral corridor: posterior pathway for reconstruction of the ventral skull base.

PubMed

Durmaz, Abdullah; Fernandez-Miranda, Juan; Snyderman, Carl H; Rivera-Serrano, Carlos; Tosun, Fuat

2011-05-01

Regional vascularized flaps, such as the pericranial and temporoparietal fascia flaps, are currently used for reconstruction of skull base defects after endoscopic endonasal surgery whenever local vascularized flaps, such as the nasoseptal flap, are not available. Two different transposition pathways, infratemporal transpterygoid and subfrontal, have been proposed for regional flaps. The objective of this study was to describe and assess the feasibility of the transposition of a vascularized pedicled flap from the occipital galeopericranium via the prevertebral space corridor into the nasopharynx. Ten heads were injected with colored silicone. An endoscopic endonasal anterior craniofacial resection and panclival approach were performed in each specimen. The occipital flap was harvested using a previously described technique. The prevertebral corridor, extending from the neck to the nasopharynx, was dissected superficial to the paraspinal muscles. Computed tomography-based image guidance was used to assess the relationship between the corridor and adjacent neurovascular structures. Length of the corridor and pedicle and area of the donor flap were measured. The flap was harvested and successfully transposed into the nasopharynx using the proposed corridor in all studied specimens (10 heads, 20 sides). All flaps provided complete coverage of the skull base defects. The average length of the pedicle was 70.5 (SD, 6.5) mm, and the average length and width of the flap were 99.9 (SD, 14.6) mm and 59.3 (SD, 10.9) mm, respectively. The average length of the prevertebral corridor was 49.7 (SD, 4.8) mm. The occipital flap has favorable anatomic characteristics for use in skull base reconstruction. Transposition of the flap via the prevertebral corridor is a suitable option for vascularized reconstruction of expanded endonasal skull base defects when other local or regional flaps are not available. Additional clinical studies are necessary to define its role in endoscopic endonasal surgery.

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.

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.

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

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

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

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

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.

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

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.

Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective.

PubMed

Luo, Shiqi; Lu, Jian

2017-06-01

Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established "transposition-selection" population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) were demonstrated to be master repressors of TE activities in Drosophila. The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The interaction between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysgenesis for the I-R and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms. Copyright © 2017 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Production and hosting by Elsevier B.V. All rights reserved.

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

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.

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

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

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.

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.

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.

Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria).

PubMed

Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

2012-01-01

Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution.

Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

PubMed Central

Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

2012-01-01

Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution. PMID:22359677

[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.

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.

The Evolution of Mobile DNAs: When Will Transposons Create Phylogenies That Look As If There Is a Master Gene?

PubMed Central

Brookfield, John F. Y.; Johnson, Louise J.

2006-01-01

Some families of mammalian interspersed repetitive DNA, such as the Alu SINE sequence, appear to have evolved by the serial replacement of one active sequence with another, consistent with there being a single source of transposition: the “master gene.” Alternative models, in which multiple source sequences are simultaneously active, have been called “transposon models.” Transposon models differ in the proportion of elements that are active and in whether inactivation occurs at the moment of transposition or later. Here we examine the predictions of various types of transposon model regarding the patterns of sequence variation expected at an equilibrium between transposition, inactivation, and deletion. Under the master gene model, all bifurcations in the true tree of elements occur in a single lineage. We show that this property will also hold approximately for transposon models in which most elements are inactive and where at least some of the inactivation events occur after transposition. Such tree shapes are therefore not conclusive evidence for a single source of transposition. PMID:16790583

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.

In Situ Localization of Ribosomal Sites in Peckoltia and Ancistomus (Loricariidae: Hypostominae) from the Amazon Basin.

PubMed

Pety, Ananda Marques; Cardoso, Adauto Lima; Nagamachi, Cleusa Yoshiko; Pieczarka, Julio Cesar; de Sousa, Leandro Melo; Noronha, Renata Coelho Rodrigues

2018-06-01

Loricariidae is a diverse group of fish from the neotropical region, occupying a wide variety of freshwater environments. Cytogenetic data have brought important insights into Loricariidae diversity because they help validate undescribed species as well as our understanding of inter- and intraspecific diversity. However, conventional cytogenetic approaches are limited in their ability to detect variability in some lineages, as seen in the Peckoltia clade, owing to their apparent conserved karyotype. Thus, the aim of this work was to map 5S and 18S ribosomal (rDNA) sites in five species of Peckoltia and one species of Ancistomus from the Amazon basin, and discusses the mechanisms of organization and diversification of these clusters. The species analyzed were found to have 2n = 52 and share KF = 38 m-sm +14st-a chromosomes, except Peckoltia vittata with KF = 34 m-sm +18st-a. Extensive variations in the number and location of 5S and 18S rDNA sites were observed among species. These data indicate that inversions are not the most important events in karyotype evolution in this group, and should prove useful in identifying the species studied here. In addition to inversions, transpositions are important evolutionary events that are involved at least in rDNA clusters spreading in Peckoltia and probably in other species of Hypostominae.

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.

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.

Intramolecular transposition by a synthetic IS50 (Tn5) derivative

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

Tomcsanyi, T.; Phadnis, S.H.; Berg, D.E.

1990-11-01

We report the formation of deletions and inversions by intramolecular transposition of Tn5-derived mobile elements. The synthetic transposons used contained the IS50 O and I end segments and the transposase gene, a contraselectable gene encoding sucrose sensitivity (sacB), antibiotic resistance genes, and a plasmid replication origin. Both deletions and inversions were associated with loss of a 300-bp segment that is designated the vector because it is outside of the transposon. Deletions were severalfold more frequent than inversions, perhaps reflecting constraints on DNA twisting or abortive transposition. Restriction and DNA sequence analyses showed that both types of rearrangements extended from onemore » transposon end to many different sites in target DNA. In the case of inversions, transposition generated 9-bp direct repeats of target sequences.« less

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.

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

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 ...

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.

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.

A Modular Mind? A Test Using Individual Data from Seven Primate Species

PubMed Central

Amici, Federica; Barney, Bradley; Johnson, Valen E.; Call, Josep; Aureli, Filippo

2012-01-01

It has long been debated whether the mind consists of specialized and independently evolving modules, or whether and to what extent a general factor accounts for the variance in performance across different cognitive domains. In this study, we used a hierarchical Bayesian model to re-analyse individual level data collected on seven primate species (chimpanzees, bonobos, orangutans, gorillas, spider monkeys, brown capuchin monkeys and long-tailed macaques) across 17 tasks within four domains (inhibition, memory, transposition and support). Our modelling approach evidenced the existence of both a domain-specific factor and a species factor, each accounting for the same amount (17%) of the observed variance. In contrast, inter-individual differences played a minimal role. These results support the hypothesis that the mind of primates is (at least partially) modular, with domain-specific cognitive skills undergoing different evolutionary pressures in different species in response to specific ecological and social demands. PMID:23284816

The group II intron maturase: a reverse transcriptase and splicing factor go hand in hand.

PubMed

Zhao, Chen; Pyle, Anna Marie

2017-12-01

The splicing of group II introns in vivo requires the assistance of a multifunctional intron encoded protein (IEP, or maturase). Each IEP is also a reverse-transcriptase enzyme that enables group II introns to behave as mobile genetic elements. During splicing or retro-transposition, each group II intron forms a tight, specific complex with its own encoded IEP, resulting in a highly reactive holoenzyme. This review focuses on the structural basis for IEP function, as revealed by recent crystal structures of an IEP reverse transcriptase domain and cryo-EM structures of an IEP-intron complex. These structures explain how the same IEP scaffold is utilized for intron recognition, splicing and reverse transcription, while providing a physical basis for understanding the evolutionary transformation of the IEP into the eukaryotic splicing factor Prp8. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements

PubMed Central

Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; de Kochko, Alexandre; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

2015-01-01

A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes. PMID:25573958

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide.

PubMed

Tabata, Michiro; Ohhata, Satoshi; Nikawadori, Yuki; Kishida, Kouhei; Sato, Takuya; Kawasumi, Toru; Kato, Hiromi; Ohtsubo, Yoshiyuki; Tsuda, Masataka; Nagata, Yuji

2016-12-01

γ-Hexachlorocyclohexane (γ-HCH) is a recalcitrant man-made chlorinated pesticide. Here, the complete genome sequences of four γ-HCH-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-HCH degrader, were compared. Together with several experimental data, we showed that (i) all the four strains carry almost identical linA to linE genes for the conversion of γ-HCH to maleylacetate (designated "specific" lin genes), (ii) considerably different genes are used for the metabolism of maleylacetate in one of the four strains, and (iii) the linKLMN genes for the putative ABC transporter necessary for γ-HCH utilization exhibit structural divergence, which reflects the phylogenetic relationship of their hosts. Replicon organization and location of the lin genes in the four genomes are significantly different with one another, and that most of the specific lin genes are located on multiple sphingomonad-unique plasmids. Copies of IS6100, the most abundant insertion sequence in the four strains, are often located in close proximity to the specific lin genes. Analysis of the footprints of target duplication upon IS6100 transposition and the experimental detection of IS6100 transposition strongly suggested that the IS6100 transposition has caused dynamic genome rearrangements and the diversification of lin-flanking regions in the four strains. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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.

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

A Remote Sensing-Based Tool for Assessing Rainfall-Driven Hazards

PubMed Central

Wright, Daniel B.; Mantilla, Ricardo; Peters-Lidard, Christa D.

2018-01-01

RainyDay is a Python-based platform that couples rainfall remote sensing data with Stochastic Storm Transposition (SST) for modeling rainfall-driven hazards such as floods and landslides. SST effectively lengthens the extreme rainfall record through temporal resampling and spatial transposition of observed storms from the surrounding region to create many extreme rainfall scenarios. Intensity-Duration-Frequency (IDF) curves are often used for hazard modeling but require long records to describe the distribution of rainfall depth and duration and do not provide information regarding rainfall space-time structure, limiting their usefulness to small scales. In contrast, RainyDay can be used for many hazard applications with 1-2 decades of data, and output rainfall scenarios incorporate detailed space-time structure from remote sensing. Thanks to global satellite coverage, RainyDay can be used in inaccessible areas and developing countries lacking ground measurements, though results are impacted by remote sensing errors. RainyDay can be useful for hazard modeling under nonstationary conditions. PMID:29657544

A Remote Sensing-Based Tool for Assessing Rainfall-Driven Hazards.

PubMed

Wright, Daniel B; Mantilla, Ricardo; Peters-Lidard, Christa D

2017-04-01

RainyDay is a Python-based platform that couples rainfall remote sensing data with Stochastic Storm Transposition (SST) for modeling rainfall-driven hazards such as floods and landslides. SST effectively lengthens the extreme rainfall record through temporal resampling and spatial transposition of observed storms from the surrounding region to create many extreme rainfall scenarios. Intensity-Duration-Frequency (IDF) curves are often used for hazard modeling but require long records to describe the distribution of rainfall depth and duration and do not provide information regarding rainfall space-time structure, limiting their usefulness to small scales. In contrast, RainyDay can be used for many hazard applications with 1-2 decades of data, and output rainfall scenarios incorporate detailed space-time structure from remote sensing. Thanks to global satellite coverage, RainyDay can be used in inaccessible areas and developing countries lacking ground measurements, though results are impacted by remote sensing errors. RainyDay can be useful for hazard modeling under nonstationary conditions.

A Remote Sensing-Based Tool for Assessing Rainfall-Driven Hazards

NASA Technical Reports Server (NTRS)

Wright, Daniel B.; Mantilla, Ricardo; Peters-Lidard, Christa D.

2017-01-01

RainyDay is a Python-based platform that couples rainfall remote sensing data with Stochastic Storm Transposition (SST) for modeling rainfall-driven hazards such as floods and landslides. SST effectively lengthens the extreme rainfall record through temporal resampling and spatial transposition of observed storms from the surrounding region to create many extreme rainfall scenarios. Intensity-Duration-Frequency (IDF) curves are often used for hazard modeling but require long records to describe the distribution of rainfall depth and duration and do not provide information regarding rainfall space-time structure, limiting their usefulness to small scales. In contrast, Rainy Day can be used for many hazard applications with 1-2 decades of data, and output rainfall scenarios incorporate detailed space-time structure from remote sensing. Thanks to global satellite coverage, Rainy Day can be used in inaccessible areas and developing countries lacking ground measurements, though results are impacted by remote sensing errors. Rainy Day can be useful for hazard modeling under nonstationary conditions.

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.

Minos as a novel Tc1/mariner-type transposable element for functional genomic analysis in Aspergillus nidulans.

PubMed

Evangelinos, Minoas; Anagnostopoulos, Gerasimos; Karvela-Kalogeraki, Iliana; Stathopoulou, Panagiota M; Scazzocchio, Claudio; Diallinas, George

2015-08-01

Transposons constitute powerful genetic tools for gene inactivation, exon or promoter trapping and genome analyses. The Minos element from Drosophila hydei, a Tc1/mariner-like transposon, has proved as a very efficient tool for heterologous transposition in several metazoa. In filamentous fungi, only a handful of fungal-specific transposable elements have been exploited as genetic tools, with the impala Tc1/mariner element from Fusarium oxysporum being the most successful. Here, we developed a two-component transposition system to manipulate Minos transposition in Aspergillus nidulans (AnMinos). Our system allows direct selection of transposition events based on re-activation of niaD, a gene necessary for growth on nitrate as a nitrogen source. On average, among 10(8) conidiospores, we obtain up to ∼0.8×10(2) transposition events leading to the expected revertant phenotype (niaD(+)), while ∼16% of excision events lead to AnMinos loss. Characterized excision footprints consisted of the four terminal bases of the transposon flanked by the TA target duplication and led to no major DNA rearrangements. AnMinos transposition depends on the presence of its homologous transposase. Its frequency was not significantly affected by temperature, UV irradiation or the transcription status of the original integration locus (niaD). Importantly, transposition is dependent on nkuA, encoding an enzyme essential for non-homologous end joining of DNA in double-strand break repair. AnMinos proved to be an efficient tool for functional analysis as it seems to transpose in different genomic loci positions in all chromosomes, including a high proportion of integration events within or close to genes. We have used Minos to obtain morphological and toxic analogue resistant mutants. Interestingly, among morphological mutants some seem to be due to Minos-elicited over-expression of specific genes, rather than gene inactivation. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

PubMed Central

Grzebelus, Dariusz; Lasota, Slawomir; Gambin, Tomasz; Kucherov, Gregory; Gambin, Anna

2007-01-01

Background Transposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. The presence of an ORF coding for the DDE/DDD transposase, required for transposition, is characteristic for the autonomous PIF/Harbinger-like elements. Based on the above features, PIF/Harbinger-like elements were identified in several plant genomes and divided into several evolutionary lineages. Availability of a significant portion of Medicago truncatula genomic sequence allowed for mining PIF/Harbinger-like elements, starting from a single previously described element MtMaster. Results Twenty two putative autonomous, i.e. carrying an ORF coding for TPase and complete terminal inverted repeats, and 67 non-autonomous PIF/Harbinger-like elements were found in the genome of M. truncatula. They were divided into five families, MtPH-A5, MtPH-A6, MtPH-D,MtPH-E, and MtPH-M, corresponding to three previously identified and two new lineages. The largest families, MtPH-A6 and MtPH-M were further divided into four and three subfamilies, respectively. Non-autonomous elements were usually direct deletion derivatives of the putative autonomous element, however other types of rearrangements, including inversions and nested insertions were also observed. An interesting structural characteristic – the presence of 60 bp tandem repeats – was observed in a group of elements of subfamily MtPH-A6-4. Some families could be related to miniature inverted repeat elements (MITEs). The presence of empty loci (RESites), paralogous to those flanking the identified transposable elements, both autonomous and non-autonomous, as well as the presence of transposon insertion related size polymorphisms, confirmed that some of the mined elements were capable for transposition. Conclusion The population of PIF/Harbinger-like elements in the genome of M. truncatula is diverse. A detailed intra-family comparison of the elements' structure proved that they proliferated in the genome generally following the model of abortive gap repair. However, the presence of tandem repeats facilitated more pronounced rearrangements of the element internal regions. The insertion polymorphism of the MtPH elements and related MITE families in different populations of M. truncatula, if further confirmed experimentally, could be used as a source of molecular markers complementary to other marker systems. PMID:17996080

Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

PubMed Central

Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

2013-01-01

Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa. PMID:23372772

Molecular analysis and genomic organization of major DNA satellites in banana (Musa spp.).

PubMed

Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

2013-01-01

Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.

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.

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.

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.

The Saccharomyces cerevisiae DNA recombination and repair functions of the RAD52 epistasis group inhibit Ty1 transposition.

PubMed Central

Rattray, A J; Shafer, B K; Garfinkel, D J

2000-01-01

RNA transcribed from the Saccharomyces cerevisiae retrotransposon Ty1 accumulates to a high level in mitotically growing haploid cells, yet transposition occurs at very low frequencies. The product of reverse transcription is a linear double-stranded DNA molecule that reenters the genome by either Ty1-integrase-mediated insertion or homologous recombination with one of the preexisting genomic Ty1 (or delta) elements. Here we examine the role of the cellular homologous recombination functions on Ty1 transposition. We find that transposition is elevated in cells mutated for genes in the RAD52 recombinational repair pathway, such as RAD50, RAD51, RAD52, RAD54, or RAD57, or in the DNA ligase I gene CDC9, but is not elevated in cells mutated in the DNA repair functions encoded by the RAD1, RAD2, or MSH2 genes. The increase in Ty1 transposition observed when genes in the RAD52 recombinational pathway are mutated is not associated with a significant increase in Ty1 RNA or proteins. However, unincorporated Ty1 cDNA levels are markedly elevated. These results suggest that members of the RAD52 recombinational repair pathway inhibit Ty1 post-translationally by influencing the fate of Ty1 cDNA. PMID:10655210

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

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.

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.

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.

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.

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

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

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.

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.

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.

Characterization of a Chlamydomonas Transposon, Gulliver, Resembling Those in Higher Plants

PubMed Central

Ferris, P. J.

1989-01-01

While pursuing a chromosomal walk through the mt(+) locus of linkage group VI of Chlamydomonas reinhardtii, I encountered a 12-kb sequence that was found to be present in approximately 12 copies in the nuclear genome. Comparison of various C. reinhardtii laboratory strains provided evidence that the sequence was mobile and therefore a transposon. One of two separate natural isolates interfertile with C. reinhardtii, C. smithii (CC-1373), contained the transposon, but at completely different locations in its nuclear genome than C. reinhardtii; and a second, CC-1952 (S1-C5), lacked the transposon altogether. Genetic analysis indicated that the transposon was found at dispersed sites throughout the genome, but had a conserved structure at each location. Sequence homology between the termini was limited to an imperfect 15-bp inverted repeat. An 8-bp target site duplication was created by insertion; transposon sequences were completely removed upon excision leaving behind both copies of the target site duplication, with minor base changes. The transposon contained an internal region of unique repetitive sequence responsible for restriction fragment length heterogeneity among the various copies of the transposon. In several cases it was possible to identify which of the dozen transposons in a given strain served as the donor when a transposition event occurred. The transposon often moved into a site genetically linked to the donor, and transposition appeared to be nonreplicative. Thus the mechanism of transposition and excision of the transposon, which I have named Gulliver, resembles that of certain higher plant transposons, like the Ac transposon of maize. PMID:2570007

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.

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.

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.

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

PubMed

Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

2015-12-01

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

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

Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome.

PubMed

Gorshkova, Natalya V; Lobanova, Juliya S; Tokmakova, Irina L; Smirnov, Sergey V; Akhverdyan, Valerii Z; Krylov, Alexander A; Mashko, Sergey V

2018-03-01

A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10 -4 per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition-amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.

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.

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

Copy and paste: the impact of a new non-L1 retroposon on the gonosomal heterochromatin of Microtus agrestis.

PubMed

Neitzel, H; Kalscheuer, V; Singh, A P; Henschel, S; Sperling, K

2002-01-01

Mobile elements are most abundant in the mammalian genome, comprising at least 40-50% of the DNA. They are differentiated into two most prominent families: the LINE elements, which are preferentially located in the G-bands, and SINES, which are clustered in the R-bands. We report here a novel mammalian non-L1-retroposon, which invaded the genome of Microtus agrestis in a very short time from an evolutionary viewpoint. No relevant sequence homology could be demonstrated to known sequences in the NCBI database. However, cross-hybridizing sequences exist in the genomes of all other Microtus species analyzed, but not in Mus musculus, indicating the recent evolutionary origin of this element. This retroposon is enriched in the entire heterochromatin of the X and Y chromosomes, but is also interspersed in autosomal locations in euchromatic portions of the genome. We show that the retroposon is heavily transcribed from the heterochromatin during female meiosis prerequisite for the subsequent retrotransposition. The estimated rate of retrotransposition is at least 1-2 x 10(-2) per generation, which is hundred-fold higher than that of the majority of invertebrate retroposons and also higher than the transposition rate of a murine L1 element, which was calculated to be 3 x 10(-3) per generation. Copyright 2002 S. Karger AG, Basel

[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.

Graph theory analysis of cortical thickness networks in adolescents with d-transposition of the great arteries.

PubMed

Watson, Christopher G; Stopp, Christian; Newburger, Jane W; Rivkin, Michael J

2018-02-01

Adolescents with d-transposition of the great arteries (d-TGA) who had the arterial switch operation in infancy have been found to have structural brain differences compared to healthy controls. We used cortical thickness measurements obtained from structural brain MRI to determine group differences in global brain organization using a graph theoretical approach. Ninety-two d-TGA subjects and 49 controls were scanned using one of two identical 1.5-Tesla MRI systems. Mean cortical thickness was obtained from 34 regions per hemisphere using Freesurfer. A linear model was used for each brain region to adjust for subject age, sex, and scanning location. Structural connectivity for each group was inferred based on the presence of high inter-regional correlations of the linear model residuals, and binary connectivity matrices were created by thresholding over a range of correlation values for each group. Graph theory analysis was performed using packages in R. Permutation tests were performed to determine significance of between-group differences in global network measures. Within-group connectivity patterns were qualitatively different between groups. At lower network densities, controls had significantly more long-range connections. The location and number of hub regions differed between groups: controls had a greater number of hubs at most network densities. The control network had a significant rightward asymmetry compared to the d-TGA group at all network densities. Using graph theory analysis of cortical thickness correlations, we found differences in brain structural network organization among d-TGA adolescents compared to controls. These may be related to the white matter and gray matter differences previously found in this cohort, and in turn may be related to the cognitive deficits this cohort presents.

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 comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize.

PubMed

Theuri, J; Phelps-Durr, T; Mathews, S; Birchler, J

2005-01-01

Bacterial Artificial Chromosomes (BACs) derived from the B chromosome, based on homology with the B specific sequence, were subcloned and sequenced. Analysis of DNA sequence data indicated the presence of 23 common retroelements, as well as novel sequences of B chromosome origin. Generally, where the same retrotransposon type was observed in both A and B chromosomes, there were more copies per unit of sequence in the B centromeric region (the major site of B repeat) than in the A centromere, except for Huck-1. Based on previous estimates of the age of the major burst of transposition into the maize genome, the oldest retrotransposons (Ji-6 and Tekay, approximately 5.0 and 5.2 million years ago, respectively) were found in the B centromere region only, while the next two oldest (Huck-1 and Opie-1) were found in both the A and B sequences. Phylogenetic analysis of Opie retroelements from both A and B centromeres indicated that some of the B Opie centromeric sequences share a more recent common ancestor with A Opie retroelements than they do with other B Opie centromeric sequences. These results imply that the supernumerary maize B chromosome has coexisted with the A chromosomes during that period of transposition. They also support the hypothesis that the B chromosome had its origins from A chromosome elements, or that alternative origins, such as being donated to the maize genome in a wide species cross, preceded six million years ago, because the spectrum of retrotransposons in the two chromosomes is quite similar.

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.

DNA methylation inhibits expression and transposition of the Neurospora Tad retrotransposon.

PubMed

Zhou, Y; Cambareri, E B; Kinsey, J A

2001-06-01

Tad is a LINE-like retrotransposon of the filamentous fungus Neurospora crassa. We have analyzed both expression and transposition of this element using strains with a single copy of Tad located in the 5' noncoding sequences of the am (glutamate dehydrogenase) gene. Tad in this position has been shown to carry a de novo cytosine methylation signal which causes reversible methylation of both Tad and am upstream sequences. Here we find that methylation of the Tad sequences inhibits both Tad expression and transposition. This inhibition can be relieved by the use of 5-azacytidine, a drug which reduces cytosine methylation, or by placing the Tad/am sequences in a dim-2 genetic background.

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.

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.

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.

Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution.

PubMed

Toro, Nicolás; Martínez-Abarca, Francisco; Molina-Sánchez, María D; García-Rodríguez, Fernando M; Nisa-Martínez, Rafael

2018-01-01

Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti , the nitrogen-fixing endosymbiont of legumes of genus Medicago , harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation.

Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution

PubMed Central

Toro, Nicolás; Martínez-Abarca, Francisco; Molina-Sánchez, María D.; García-Rodríguez, Fernando M.; Nisa-Martínez, Rafael

2018-01-01

Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti, the nitrogen-fixing endosymbiont of legumes of genus Medicago, harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation. PMID:29670598

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.

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

Excision of Sleeping Beauty transposons: parameters and applications to gene therapy

PubMed Central

Liu, Geyi; Aronovich, Elena L.; Cui, Zongbin; Whitley, Chester B.; Hackett, Perry B.

2007-01-01

A major problem in gene therapy is the determination of the rates at which gene transfer has occurred. Our work has focused on applications of the Sleeping Beauty (SB) transposon system as a non-viral vector for gene therapy. Excision of a transposon from a donor molecule and its integration into a cellular chromosome are catalyzed by SB transposase. In this study, we used a plasmid-based excision assay to study the excision step of transposition. We used the excision assay to evaluate the importance of various sequences that border the sites of excision inside and outside the transposon in order to determine the most active sequences for transposition from a donor plasmid. These findings together with our previous results in transposase binding to the terminal repeats suggest that the sequences in the transposon-junction of SB are involved in steps subsequent to DNA binding but before excision, and that they may have a role in transposase–transposon interaction. We found that SB transposons leave characteristically different footprints at excision sites in different cell types, suggesting that alternative repair machineries operate in concert with transposition. Most importantly, we found that the rates of excision correlate with the rates of transposition. We used this finding to assess transposition in livers of mice that were injected with the SB transposon and transposase. The excision assay appears to be a relatively quick and easy method to optimize protocols for delivery of genes in SB transposons to mammalian chromosomes in living animals. PMID:15133768

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 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.

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.

Comparative Genomics of the Mating-Type Loci of the Mushroom Flammulina velutipes Reveals Widespread Synteny and Recent Inversions

PubMed Central

van Peer, Arend F.; Park, Soon-Young; Shin, Pyung-Gyun; Jang, Kab-Yeul; Yoo, Young-Bok; Park, Young-Jin; Lee, Byoung-Moo; Sung, Gi-Ho; James, Timothy Y.; Kong, Won-Sik

2011-01-01

Background Mating-type loci of mushroom fungi contain master regulatory genes that control recognition between compatible nuclei, maintenance of compatible nuclei as heterokaryons, and fruiting body development. Regions near mating-type loci in fungi often show adapted recombination, facilitating the generation of novel mating types and reducing the production of self-compatible mating types. Compared to other fungi, mushroom fungi have complex mating-type systems, showing both loci with redundant function (subloci) and subloci with many alleles. The genomic organization of mating-type loci has been solved in very few mushroom species, which complicates proper interpretation of mating-type evolution and use of those genes in breeding programs. Methodology/Principal Findings We report a complete genetic structure of the mating-type loci from the tetrapolar, edible mushroom Flammulina velutipes mating type A3B3. Two matB3 subloci, matB3a that contains a unique pheromone and matB3b, were mapped 177 Kb apart on scaffold 1. The matA locus of F. velutipes contains three homeodomain genes distributed over 73 Kb distant matA3a and matA3b subloci. The conserved matA region in Agaricales approaches 350 Kb and contains conserved recombination hotspots showing major rearrangements in F. velutipes and Schizophyllum commune. Important evolutionary differences were indicated; separation of the matA subloci in F. velutipes was diverged from the Coprinopsis cinerea arrangement via two large inversions whereas separation in S. commune emerged through transposition of gene clusters. Conclusions/Significance In our study we determined that the Agaricales have very large scale synteny at matA (∼350 Kb) and that this synteny is maintained even when parts of this region are separated through chromosomal rearrangements. Four conserved recombination hotspots allow reshuffling of large fragments of this region. Next to this, it was revealed that large distance subloci can exist in matB as well. Finally, the genes that were linked to specific mating types will serve as molecular markers in breeding. PMID:21799803

Evolutionary characterization of the West Nile Virus complete genome.

PubMed

Gray, R R; Veras, N M C; Santos, L A; Salemi, M

2010-07-01

The spatial dynamics of the West Nile Virus epidemic in North America are largely unknown. Previous studies that investigated the evolutionary history of the virus used sequence data from the structural genes (prM and E); however, these regions may lack phylogenetic information and obscure true evolutionary relationships. This study systematically evaluated the evolutionary patterns in the eleven genes of the WNV genome in order to determine which region(s) were most phylogenetically informative. We found that while the E region lacks resolution and can potentially result in misleading conclusions, the full NS3 or NS5 regions have strong phylogenetic signal. Furthermore, we show that geographic structure of WNV infection within the US is more pronounced than previously reported in studies that used the structural genes. We conclude that future evolutionary studies should focus on NS3 and NS5 in order to maximize the available sequences while retaining maximal interpretative power to infer temporal and geographic trends among WNV strains. Copyright 2010 Elsevier Inc. All rights reserved.

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.

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).

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.

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.

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

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.

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

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 Sycp1 loci of the mouse genome: successive retropositions of a meiotic gene during the recent evolution of the genus.

PubMed

Sage, J; Yuan, L; Martin, L; Mattei, M G; Guénet, J L; Liu, J G; Hoög, C; Rassoulzadegan, M; Cuzin, F

1997-08-15

The murine Sycp1 gene is expressed at the early stages of meiosis. We show that it is composed of a number of small exons and localized on mouse chromosome 3. In the laboratory strains, two retrogenes were also identified. The first one (Sycp1-ps1), on chromosome 7, has accumulated point mutations and deletions and is not transcribed. A second retrogene (Sycp1-ps2), on chromosome 8, is inserted within the continuity of a moderately repeated element, in an intron of another gene (Cad11). The two retroposition events can be dated to distinct periods in the evolution of the Muridae. Sycp1-ps2 has kept features indicative of a relatively recent origin, namely a nearly intact coding region, a poly(A) tail, and 14-bp terminal repeats. Its recent origin was confirmed by the fact that it is found in all the laboratory strains of mice, but neither in a recent isolate from Mus musculus domesticus wild stocks nor in the closely related subspecies M. musculus musculus, M. m. molossinus, M. m. castaneus, and M. m. bactrianus. Appearance of the more ancient Sycp1-ps1 retrogene is concomitant with the radiation of the genus. It is present in various Mus species (M. spretus, M. spicilegus, M. macedonicus, and M. cookii), but neither in the rat nor in the more closely related Pyromis genus. Transposition of retrotranscripts during meiosis and their hereditary establishment thus appear to occur relatively frequently. They may, therefore, play a significant role in the evolutionary process.

Visions of the past and dreams of the future in the Orient: the Irano-Turanian region from classical botany to evolutionary studies.

PubMed

Manafzadeh, Sara; Staedler, Yannick M; Conti, Elena

2017-08-01

Ever since the 19th century, the immense arid lands of the Orient, now called the Irano-Turanian (IT) floristic region, attracted the interest of European naturalists with their tremendous plant biodiversity. Covering approximately 30% of the surface of Eurasia (16000000 km 2 ), the IT region is one of the largest floristic regions of the world. The IT region represents one of the hotspots of evolutionary and biological diversity in the Old World, and serves as a source of xerophytic taxa for neighbouring regions. Moreover, it is the cradle of the numerous species domesticated in the Fertile Crescent. Over the last 200 years, naturalists outlined different borders for the IT region. Yet, the delimitation and evolutionary history of this area remain one of the least well-understood fields of global biogeography, even though it is crucial to explaining the distribution of life in Eurasia. No comprehensive review of the biogeographical delimitations nor of the role of geological and climatic changes in the evolution of the IT region is currently available. After considering the key role of floristic regions in biogeography, we review the history of evolving concepts about the borders and composition of the IT region over the past 200 years and outline a tentative circumscription for it. We also summarise current knowledge on the geological and climatic history of the IT region. We then use this knowledge to generate specific evolutionary hypotheses to explain how different geological, palaeoclimatic, and ecological factors contributed to range expansion and contraction, thus shaping patterns of speciation in the IT region over time and space. Both historical and ecological biogeography should be applied to understand better the floristic diversification of the region. This will ultimately require evolutionary comparative analyses based on integrative phylogenetic, geological, climatic, ecological, and species distribution studies on the region. Furthermore, an understanding of evolutionary and ecological processes will play a major role in regional planning for protecting biodiversity of the IT region in facing climatic change. With this review, we aim to introduce the IT floristic region to a broader audience of evolutionary, ecological and systematic biologists, thus promoting cutting-edge research on this area and raising awareness of this vast and diverse, yet understudied, part of the world. © 2016 Cambridge Philosophical Society.

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.

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.

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia

PubMed Central

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M.

2016-01-01

Abstract Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints. PMID:28175287

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.

PubMed

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M; Ruiz-Herrera, Aurora

2016-12-01

Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.

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.

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.

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.

PubMed

Nuttle, Xander; Giannuzzi, Giuliana; Duyzend, Michael H; Schraiber, Joshua G; Narvaiza, Iñigo; Sudmant, Peter H; Penn, Osnat; Chiatante, Giorgia; Malig, Maika; Huddleston, John; Benner, Chris; Camponeschi, Francesca; Ciofi-Baffoni, Simone; Stessman, Holly A F; Marchetto, Maria C N; Denman, Laura; Harshman, Lana; Baker, Carl; Raja, Archana; Penewit, Kelsi; Janke, Nicolette; Tang, W Joyce; Ventura, Mario; Banci, Lucia; Antonacci, Francesca; Akey, Joshua M; Amemiya, Chris T; Gage, Fred H; Reymond, Alexandre; Eichler, Evan E

2016-08-11

Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage--a pattern unlikely to have arisen so rapidly in the absence of selection (P < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11. rearrangement show that more than 96% of breakpoints occur within the H. sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the H. sapiens lineage about 282 ka simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.

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.

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

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

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.

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.

Is mammalian chromosomal evolution driven by regions of genome fragility?

PubMed Central

Ruiz-Herrera, Aurora; Castresana, Jose; Robinson, Terence J

2006-01-01

Background A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. Results Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. Conclusion These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity. PMID:17156441

Evolution of intrinsic disorder in eukaryotic proteins.

PubMed

Ahrens, Joseph B; Nunez-Castilla, Janelle; Siltberg-Liberles, Jessica

2017-09-01

Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.

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.

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.

[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).

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

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.

Expansion of the neck reconstituted the shoulder-diaphragm in amniote evolution.

PubMed

Hirasawa, Tatsuya; Fujimoto, Satoko; Kuratani, Shigeru

2016-01-01

The neck acquired flexibility through modifications of the head-trunk interface in vertebrate evolution. Although developmental programs for the neck musculoskeletal system have attracted the attention of evolutionary developmental biologists, how the heart, shoulder and surrounding tissues are modified during development has remained unclear. Here we show, through observation of the lateral plate mesoderm at cranial somite levels in chicken-quail chimeras, that the deep part of the lateral body wall is moved concomitant with the caudal transposition of the heart, resulting in the infolding of the expanded cervical lateral body wall into the thorax. Judging from the brachial plexus pattern, an equivalent infolding also appears to take place in mammalian and turtle embryos. In mammals, this infolding process is particularly important because it separates the diaphragm from the shoulder muscle mass. In turtles, the expansion of the cervical lateral body wall affects morphogenesis of the shoulder. Our findings highlight the cellular expansion in developing amniote necks that incidentally brought about the novel adaptive traits. © 2015 The Authors Development, Growth & Differentiation published by John Wiley & Sons Australia, Ltd on behalf of Japanese Society of Developmental Biologists.

Organizational topology of brain and its relationship to ADHD in adolescents with d-transposition of the great arteries.

PubMed

Schmithorst, Vincent J; Panigrahy, Ashok; Gaynor, J William; Watson, Christopher G; Lee, Vince; Bellinger, David C; Rivkin, Michael J; Newburger, Jane W

2016-08-01

Little is currently known about the impact of congenital heart disease (CHD) on the organization of large-scale brain networks in relation to neurobehavioral outcome. We investigated whether CHD might impact ADHD symptoms via changes in brain structural network topology in a cohort of adolescents with d-transposition of the great arteries (d-TGA) repaired with the arterial switch operation in early infancy and referent subjects. We also explored whether these effects might be modified by apolipoprotein E (APOE) genotype, as the APOE ε2 allele has been associated with worse neurodevelopmental outcomes after repair of d-TGA in infancy. We applied graph analysis techniques to diffusion tensor imaging (DTI) data obtained from 47 d-TGA adolescents and 29 healthy referents to construct measures of structural topology at the global and regional levels. We developed statistical mediation models revealing the respective contributions of d-TGA, APOE genotype, and structural network topology on ADHD outcome as measured by the Connors ADHD/DSM-IV Scales (CADS). Changes in overall network connectivity, integration, and segregation mediated worse ADHD outcomes in d-TGA patients compared to healthy referents; these changes were predominantly in the left and right intrahemispheric regional subnetworks. Exploratory analysis revealed that network topology also mediated detrimental effects of the APOE ε4 allele but improved neurobehavioral outcomes for the APOE ε2 allele. Our results suggest that disruption of organization of large-scale networks may contribute to neurobehavioral dysfunction in adolescents with CHD and that this effect may interact with APOE genotype.

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.

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.

Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice

PubMed Central

Ngezahayo, Frédéric; Xu, Chunming; Wang, Hongyan; Jiang, Lily; Pang, Jinsong; Liu, Bao

2009-01-01

Background mPing is an endogenous MITE in the rice genome, which is quiescent under normal conditions but can be induced towards mobilization under various stresses. The cellular mechanism responsible for modulating the activity of mPing remains unknown. Cytosine methylation is a major epigenetic modification in most eukaryotes, and the primary function of which is to serve as a genome defense system including taming activity of transposable elements (TEs). Given that tissue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes, it provides a tractable system to investigate the possible relationship between the two phenomena. Results mPing transposition and cytosine methylation alteration were measured in callus and regenerated plants in three rice (ssp. indica) genotypes, V14, V27 and R09. All three genotypes showed transposition of mPing, though at various frequencies. Cytosine methylation alteration occurred both at the mPing-flanks and at random loci sampled globally in callus and regenerated plants of all three genotypes. However, a sharp difference in the changing patterns was noted between the mPing-flanks and random genomic loci, with a particular type of methylation modification, i.e., CNG hypermethylation, occurred predominantly at the mPing-flanks. Pearson's test on pairwise correlations indicated that mPing activity is positively correlated with specific patterns of methylation alteration at random genomic loci, while the element's immobility is positively correlated with methylation levels of the mPing's 5'-flanks. Bisulfite sequencing of two mPing-containing loci showed that whereas for the immobile locus loss of CG methylation in the 5'-flank was accompanied by an increase in CHG methylation, together with an overall increase in methylation of all three types (CG, CHG and CHH) in the mPing-body region, for the active locus erasure of CG methylation in the 5'-flank was not followed by such a change. Conclusion Our results documented that tissue culture-induced mPing activity in rice ssp. indica is correlated with alteration in cytosine methylation patterns at both random genomic loci and the elements' flanks, while the stability of mPing positively correlates with enhanced methylation levels of both the flanks and probably the elements per se. Thus, our results implicate a possible role of cytosine methylation in maintaining mPing stability under normal conditions, and in releasing the element's activity as a consequence of epigenetic perturbation in a locus-specific manner under certain stress conditions. PMID:19604382

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.

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.

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.

Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus.

PubMed

Zhu, Li-Ping; Yue, Xin-Jing; Han, Kui; Li, Zhi-Feng; Zheng, Lian-Shuai; Yi, Xiu-Nan; Wang, Hai-Long; Zhang, You-Ming; Li, Yue-Zhong

2015-07-22

Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear. We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants. With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes.

[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.

Survival and health in liveborn infants with transposition of great arteries--a population-based study.

PubMed

Garne, Ester; Loane, Maria A; Nelen, Vera; Bakker, Marian K; Gener, Blanca; Abramsky, Lenore; Addor, Marie-Claude; Queisser-Luft, Annette

2007-01-01

To describe treatment, survival, and morbidity for liveborn infants with isolated transposition of great arteries (TGA). Population-based data from 7 European registries of congenital malformations (EUROCAT). Ninety-seven infants were diagnosed with isolated TGA and livebirth prevalence was 2.0 per 10,000 livebirths. The majority of infants were treated with prostaglandins (83%) and 57% had a catheter atrial septostomia performed. Arterial switch surgery was performed in 78 infants, other or unknown type of surgery was performed in 3 cases, and for 6 infants there was no information on surgery. At 1 year of age 69 infants were alive (71%) and 24 (25%) were dead (4 unknown). There were 10 deaths before surgery and 58% of all deaths took place during the first week. There was no statistically significant regional difference in mortality. Eight infants diagnosed prenatally all survived to 1 year and only 71% of infants diagnosed after birth survived (P = 0.08). Data on morbidity at 1 year of age was available for 57 infants. Fifty-one infants were reported with normal health and development. In this population-based study survival for liveborn infants with TGA is lower than in studies published from tertiary centers. Outcome for survivors at 1 year of age seems favorable.

Diagnosis and management of Transposition of great arteries within a pediatric cardiology network with the aid of telemedicine: A case report from Brazil.

PubMed

Galdino, Millena M; Hazin, Sheila Mv; de Araújo, Juliana Ss; Regis, Cláudio T; Rodrigues, Klecida N; Mourato, Felipe A; Mattos, Sandra da Silva

2016-04-01

We present a case of a newborn from a remote, underserved area in the inland of Paraíba, a state from Northeast Brazil. She presented with clinical cyanosis at birth. With the aid of telemedicine, a neonatologist under online cardiology supervision performed a screening echocardiogram. The session established the diagnosis of simple transposition of the great vessels in the baby's first few hours of life. During the same telemedicine session, the necessary arrangements for transferal to a larger maternity center took place. The baby was maintained stable on prostaglandins and was subsequently transferred to a tertiary cardiac center in the neighboring State, Pernambuco. She underwent anatomical correction at day 10, presented no surgical or postoperative complications, and was discharged home at the age of 21 days. She is now over three years old and continues her follow-up care mostly at her hometown, with local pediatricians under online supervision by a cardiologist in a virtual outpatient clinic. The establishment of a Pediatric Cardiology Network, with the aid of telemedicine, can produce a major impact on the access to specialized health care for poor regions of developing countries. © The Author(s) 2015.

Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms

PubMed Central

Chavda, Kalyan D.; Chen, Liang; Fouts, Derrick E.; Sutton, Granger; Brinkac, Lauren; Jenkins, Stephen G.; Bonomo, Robert A.

2016-01-01

ABSTRACT Knowledge regarding the genomic structure of Enterobacter spp., the second most prevalent carbapenemase-producing Enterobacteriaceae, remains limited. Here we sequenced 97 clinical Enterobacter species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed blaKPC-2, 40 had blaKPC-3, 2 had blaKPC-4, and 2 had blaNDM-1. Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional Enterobacter genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups—18 groups (A to R) in the Enterobacter cloacae complex and Enterobacter aerogenes. Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant Enterobacter spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of blaKPC-harboring plasmids between different phylogenomic groups, and repeated transposition of the blaKPC gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique blaKPC-harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant Enterobacter spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this genus. PMID:27965456

The relative importance of regional, local, and evolutionary factors structuring cryptobenthic coral-reef assemblages

NASA Astrophysics Data System (ADS)

Ahmadia, Gabby N.; Tornabene, Luke; Smith, David J.; Pezold, Frank L.

2018-03-01

Factors shaping coral-reef fish species assemblages can operate over a wide range of spatial scales (local versus regional) and across both proximate and evolutionary time. Niche theory and neutral theory provide frameworks for testing assumptions and generating insights about the importance of local versus regional processes. Niche theory postulates that species assemblages are an outcome of evolutionary processes at regional scales followed by local-scale interactions, whereas neutral theory presumes that species assemblages are formed by largely random processes drawing from regional species pools. Indo-Pacific cryptobenthic coral-reef fishes are highly evolved, ecologically diverse, temporally responsive, and situated on a natural longitudinal diversity gradient, making them an ideal group for testing predictions from niche and neutral theories and effects of regional and local processes on species assemblages. Using a combination of ecological metrics (fish density, diversity, assemblage composition) and evolutionary analyses (testing for phylogenetic niche conservatism), we demonstrate that the structure of cryptobenthic fish assemblages can be explained by a mixture of regional factors, such as the size of regional species pools and broad-scale barriers to gene flow/drivers of speciation, coupled with local-scale factors, such as the relative abundance of specific microhabitat types. Furthermore, species of cryptobenthic fishes have distinct microhabitat associations that drive significant differences in assemblage community structure between microhabitat types, and these distinct microhabitat associations are phylogenetically conserved over evolutionary timescales. The implied differential fitness of cryptobenthic fishes across varied microhabitats and the conserved nature of their ecology are consistent with predictions from niche theory. Neutral theory predictions may still hold true for early life-history stages, where stochastic factors may be more important in explaining recruitment. Overall, through integration of ecological and evolutionary techniques, and using multiple spatial scales, our study offers a unique perspective on factors determining coral-reef fish assemblages.

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.

[Pulley for strengthening a muscle replacement operation across two joints in brachial plexus lesion: description of the surgical technique].

PubMed

Berger, A; Schaller, E; Becker, M H

1994-01-01

The reconstruction of lost muscle functions in cases of brachial plexus lesion is possible even in those cases where primary nerve reconstruction was not performed or unsuccessful. If there are only few motor nerves available, we prefer free latissimus dorsi transplantation or pedicled latissimus dorsi transposition for replacement of biceps and finger flexors. The combination of elbow flexion and finger flexion becomes possible when the transposed motor is passed around a suitable pulley in the elbow region like the flexor carpi ulnaris or carpi radialis.

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

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.

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

PubMed Central

Hou, Beiwei; Luo, Jing; Zhang, Yusi; Niu, Zhitao; Xue, Qingyun; Ding, Xiaoyu

2017-01-01

The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species’ diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange. PMID:28262789

A model of professional competences in mathematics to update mathematical and didactic knowledge of teachers

NASA Astrophysics Data System (ADS)

Díaz, Verónica; Poblete, Alvaro

2017-07-01

This paper describes part of a research and development project carried out in public elementary schools. Its objective was to update the mathematical and didactic knowledge of teachers in two consecutive levels in urban and rural public schools of Region de Los Lagos and Region de Los Rios of southern Chile. To that effect, and by means of an advanced training project based on a professional competences model, didactic interventions based on types of problems and types of mathematical competences with analysis of contents and learning assessment were designed. The teachers' competence regarding the didactic strategy used and its results, as well as the students' learning achievements are specified. The project made possible to validate a strategy of lifelong improvement in mathematics, based on the professional competences of teachers and their didactic transposition in the classroom, as an alternative to consolidate learning in areas considered vulnerable in two regions of the country.

[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.

Transposition behavior of nonautonomous a hAT superfamily transposon nDart in rice (Oryza sativa L.).

PubMed

Fujino, Kenji; Sekiguchi, Hiroshi

2011-08-01

Transposable elements (TEs) have a significant impact on the evolution of gene function and genome structures. An endogenous nonautonomous transposable element nDart was discovered in an albino mutant that had an insertion in the Mg-protoporphyrin IX methyltransferase gene in rice. In this study, we elucidated the transposition behavior of nDart, the frequency of nDart transposition and characterized the footprint of nDart. Novel independent nDart insertions in backcrossed progenies were detected by DNA blotting analysis. In addition, germinal excision of nDart occurred at very low frequency compared with that of somatic excision, 0-13.3%, in the nDart1-4(3-2) and nDart1-A loci by a locus-specific PCR strategy. A total of 253 clones from somatic excision at five nDart loci in 10 varieties were determined. nDart rarely caused deletions beyond target site duplication (TSD). The footprint of nDart contained few transversions of nucleotides flanking to both sides of the TSD. The predominant footprint of nDart was an 8-bp addition. Precise excision of nDart was detected at a rate of only 2.2%, which occurred at two loci among the five loci examined. Furthermore, the results in this study revealed that a highly conserved mechanism of transposition is involved between maize Ac/Ds and rice Dart/nDart, which are two-component transposon systems of the hAT superfamily transposons in plant species.

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.

Derepression of the Plant Chromovirus LORE1 Induces Germline Transposition in Regenerated Plants

PubMed Central

Fukai, Eigo; Umehara, Yosuke; Sato, Shusei; Endo, Makoto; Kouchi, Hiroshi; Hayashi, Makoto; Stougaard, Jens; Hirochika, Hirohiko

2010-01-01

Transposable elements represent a large proportion of the eukaryotic genomes. Long Terminal Repeat (LTR) retrotransposons are very abundant and constitute the predominant family of transposable elements in plants. Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements. These elements contain chromodomains in their integrases, which suggests a preference for insertion into heterochromatin. In turn, this preference might have contributed to the patterning of heterochromatin observed in host genomes. Despite their potential importance for our understanding of plant genome dynamics and evolution, the regulatory mechanisms governing the behavior of chromoviruses and their activities remain largely uncharacterized. Here, we report a detailed analysis of the spatio-temporal activity of a plant chromovirus in the endogenous host. We examined LORE1a, a member of the endogenous chromovirus LORE1 family from the model legume Lotus japonicus. We found that this chromovirus is stochastically de-repressed in plant populations regenerated from de-differentiated cells and that LORE1a transposes in the male germline. Bisulfite sequencing of the 5′ LTR and its surrounding region suggests that tissue culture induces a loss of epigenetic silencing of LORE1a. Since LTR promoter activity is pollen specific, as shown by the analysis of transgenic plants containing an LTR::GUS fusion, we conclude that male germline-specific LORE1a transposition in pollen grains is controlled transcriptionally by its own cis-elements. New insertion sites of LORE1a copies were frequently found in genic regions and show no strong insertional preferences. These distinctive novel features of LORE1 indicate that this chromovirus has considerable potential for generating genetic and epigenetic diversity in the host plant population. Our results also define conditions for the use of LORE1a as a genetic tool. PMID:20221264

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.

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.

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.

The Evolutionary Tempo of Sex Chromosome Degradation in Carica papaya.

PubMed

Wu, Meng; Moore, Richard C

2015-06-01

Genes on non-recombining heterogametic sex chromosomes may degrade over time through the irreversible accumulation of deleterious mutations. In papaya, the non-recombining male-specific region of the Y (MSY) consists of two evolutionary strata corresponding to chromosomal inversions occurring approximately 7.0 and 1.9 MYA. The step-wise recombination suppression between the papaya X and Y allows for a temporal examination of the degeneration progress of the young Y chromosome. Comparative evolutionary analyses of 55 X/Y gene pairs showed that Y-linked genes have more unfavorable substitutions than X-linked genes. However, this asymmetric evolutionary pattern is confined to the oldest stratum, and is only observed when recently evolved pseudogenes are included in the analysis, indicating a slow degeneration tempo of the papaya Y chromosome. Population genetic analyses of coding sequence variation of six Y-linked focal loci in the oldest evolutionary stratum detected an excess of nonsynonymous polymorphism and reduced codon bias relative to autosomal loci. However, this pattern was also observed for corresponding X-linked loci. Both the MSY and its corresponding X-specific region are pericentromeric where recombination has been shown to be greatly reduced. Like the MSY region, overall selective efficacy on the X-specific region may be reduced due to the interference of selective forces between highly linked loci, or the Hill-Robertson effect, that is accentuated in regions of low or suppressed recombination. Thus, a pattern of gene decay on the X-specific region may be explained by relaxed purifying selection and widespread genetic hitchhiking due to its pericentromeric location.

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

pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements

PubMed Central

Xiang, Xiaoyu; Huang, Xiaoxing; Wang, Haina; Huang, Li

2015-01-01

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading. PMID:25686154

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements.

PubMed

Xiang, Xiaoyu; Huang, Xiaoxing; Wang, Haina; Huang, Li

2015-02-12

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.

Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back

PubMed Central

Makarova, Kira S.

2017-01-01

Abstract The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-CRISPR-associated proteins (Cas) systems of bacterial and archaeal adaptive immunity show multifaceted evolutionary relationships with at least five classes of mobile genetic elements (MGE). First, the adaptation module of CRISPR-Cas that is responsible for the formation of the immune memory apparently evolved from a Casposon, a self-synthesizing transposon that employs the Cas1 protein as the integrase and might have brought additional cas genes to the emerging immunity loci. Second, a large subset of type III CRISPR-Cas systems recruited a reverse transcriptase from a Group II intron, providing for spacer acquisition from RNA. Third, effector nucleases of Class 2 CRISPR-Cas systems that are responsible for the recognition and cleavage of the target DNA were derived from transposon-encoded TnpB nucleases, most likely, on several independent occasions. Fourth, accessory nucleases in some variants of types I and III toxin and type VI effectors RNases appear to be ultimately derived from toxin nucleases of microbial toxin–antitoxin modules. Fifth, the opposite direction of evolution is manifested in the recruitment of CRISPR-Cas systems by a distinct family of Tn7-like transposons that probably exploit the capacity of CRISPR-Cas to recognize unique DNA sites to facilitate transposition as well as by bacteriophages that employ them to cope with host defense. Additionally, individual Cas proteins, such as the Cas4 nuclease, were recruited by bacteriophages and transposons. The two-sided evolutionary connection between CRISPR-Cas and MGE fits the “guns for hire” paradigm whereby homologous enzymatic machineries, in particular nucleases, are shuttled between MGE and defense systems and are used alternately as means of offense or defense. PMID:28985291

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

Liposarcoma of the chest wall. Transformation of dedifferentiated liposarcoma from a recurrent lipoma.

PubMed

Bicakcioglu, Pinar; Sak, Serpil D; Tastepe, Abdullah I

2012-08-01

Liposarcoma is the second most common soft tissue sarcoma after malignant fibrous histiocytoma in adults. It is frequently found in the extremities and retroperitoneum; rarely it can be seen in the chest wall. We report a rare case of giant liposarcoma originating from the chest wall representing a transformation of a relapsing lipoma in the same region. We performed chest wall resection, reconstruction with latissimus dorsi muscle transposition via posterolateral thoracotomy. The patient received 4 series of adjuvant chemotherapy after the postoperative diagnosis of dedifferentiated liposarcoma. The patient had no postoperative complication and has remained disease-free for 30 months.

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.

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.

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

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.

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.

Transcriptional activity of transposable elements in coelacanth.

PubMed

Forconi, Mariko; Chalopin, Domitille; Barucca, Marco; Biscotti, Maria Assunta; De Moro, Gianluca; Galiana, Delphine; Gerdol, Marco; Pallavicini, Alberto; Canapa, Adriana; Olmo, Ettore; Volff, Jean-Nicolas

2014-09-01

The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity. © 2013 Wiley Periodicals, Inc.

Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion.

PubMed

Vaschetto, Luis María

2018-04-01

In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.

Even parasites have parasites: oscillatory population dynamics of mobile genetic elements in your genome

NASA Astrophysics Data System (ADS)

Xue, Chi; Goldenfeld, Nigel

Transposable elements (TEs), or transposons, are a class of mobile genetic elements that can either move or duplicate themselves in the genome, sometimes interfering with gene expression as a result. Some TEs can code all necessary enzymes for their transposition and are thus autonomous, while non-autonomous TEs are parasitic and must depend on the machinery of autonomous ones. I present and solve a stochastic model to describe the dynamics of non-autonomous/autonomous pairs of retrotransposons in the human genome that proliferate by a copy-and-paste mechanism. We predict noise-induced persistent oscillations in their copy numbers, analogous to predator-prey dynamics in an ecosystem. We discuss if it is experimentally feasible to measure these phenomena in the laboratory and to observe them over evolutionary time through bioinformatics. This work shows that it is fruitful to regard the genome as an ecosystem that is host to diverse interacting populations. This work was partially supported by the National Science Foundation through Grant No. PHY-1430124, and by the National Aeronautics and Space Administration Astrobiology Institute (NAI) under Cooperative Agreement No. NNA13AA91A.

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.

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

PubMed Central

Sheng, Zizhang; Schramm, Chaim A.; Connors, Mark; Morris, Lynn; Mascola, John R.; Kwong, Peter D.; Shapiro, Lawrence

2016-01-01

Accumulation of somatic mutations in antibody variable regions is critical for antibody affinity maturation, with HIV-1 broadly neutralizing antibodies (bnAbs) generally requiring years to develop. We recently found that the rate at which mutations accumulate decreases over time, but the mechanism governing this slowing is unclear. In this study, we investigated whether natural selection and/or mutability of the antibody variable region contributed significantly to observed decrease in rate. We used longitudinally sampled sequences of immunoglobulin transcripts of single lineages from each of 3 donors, as determined by next generation sequencing. We estimated the evolutionary rates of the complementarity determining regions (CDRs), which are most significant for functional selection, and found they evolved about 1.5- to 2- fold faster than the framework regions. We also analyzed the presence of AID hotspots and coldspots at different points in lineage development and observed an average decrease in mutability of less than 10 percent over time. Altogether, the correlation between Darwinian selection strength and evolutionary rate trended toward significance, especially for CDRs, but cannot fully explain the observed changes in evolutionary rate. The mutability modulated by AID hotspots and coldspots changes correlated only weakly with evolutionary rates. The combined effects of Darwinian selection and mutability contribute substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineages. PMID:27191167

Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response.

PubMed

Wheeler, Bayly S

2013-12-01

Transposons are mobile genetic elements that are a major constituent of most genomes. Organisms regulate transposable element expression, transposition, and insertion site preference, mitigating the genome instability caused by uncontrolled transposition. A recent burst of research has demonstrated the critical role of small non-coding RNAs in regulating transposition in fungi, plants, and animals. While mechanistically distinct, these pathways work through a conserved paradigm. The presence of a transposon is communicated by the presence of its RNA or by its integration into specific genomic loci. These signals are then translated into small non-coding RNAs that guide epigenetic modifications and gene silencing back to the transposon. In addition to being regulated by the host, transposable elements are themselves capable of influencing host gene expression. Transposon expression is responsive to environmental signals, and many transposons are activated by various cellular stresses. TEs can confer local gene regulation by acting as enhancers and can also confer global gene regulation through their non-coding RNAs. Thus, transposable elements can act as stress-responsive regulators that control host gene expression in cis and trans.

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.

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.

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.

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.

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

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.

Evolution of heliobacteria: implications for photosynthetic reaction center complexes

NASA Technical Reports Server (NTRS)

Vermaas, W. F.; Blankenship, R. E. (Principal Investigator)

1994-01-01

The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein show rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to the core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.

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.

Biogeography predicts macro‐evolutionary patterning of gestural display complexity in a passerine family

PubMed Central

Miles, Meredith C.; Cheng, Samantha; Fuxjager, Matthew J.

2017-01-01

Gestural displays are incorporated into the signaling repertoire of numerous animal species. These displays range from complex signals that involve impressive and challenging maneuvers, to simpler displays or no gesture at all. The factors that drive this evolution remain largely unclear, and we therefore investigate this issue in New World blackbirds by testing how factors related to a species’ geographical distribution and social mating system predict macro‐evolutionary patterns of display elaboration. We report that species inhabiting temperate regions produce more complex displays than species living in tropical regions, and we attribute this to (i) ecological factors that increase the competitiveness of the social environment in temperate regions, and (ii) different evolutionary and geological contexts under which species in temperate and tropical regions evolved. Meanwhile, we find no evidence that social mating system predicts species differences in display complexity, which is consistent with the idea that gestural displays evolve independently of social mating system. Together, these results offer some of the first insight into the role played by geographic factors and evolutionary context in the evolution of the remarkable physical displays of birds and other vertebrates. PMID:28240772

The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa.

PubMed

Davis, P L; Rambaut, A; Bourhy, H; Holmes, E C

2007-01-01

Two variants of rabies virus (RABV) currently circulate in southern Africa: canid RABV, mainly associated with dogs, jackals, and bat-eared foxes, and mongoose RABV. To investigate the evolutionary dynamics of these variants, we performed coalescent-based analyses of the G-L inter-genic region, allowing for rate variation among viral lineages through the use of a relaxed molecular clock. This revealed that mongoose RABV is evolving more slowly than canid RABV, with mean evolutionary rates of 0.826 and 1.676 x 10(-3) nucleotide substitutions per site, per year, respectively. Additionally, mongoose RABV exhibits older genetic diversity than canid RABV, with common ancestors dating to 73 and 30 years, respectively, and while mongoose RABV has experienced exponential population growth over its evolutionary history in Africa, populations of canid RABV have maintained a constant size. Hence, despite circulating in the same geographic region, these two variants of RABV exhibit striking differences in evolutionary dynamics which are likely to reflect differences in their underlying ecology.

Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome.

PubMed

Rizzon, Carène; Marais, Gabriel; Gouy, Manolo; Biémont, Christian

2002-03-01

We analyzed the distribution of 54 families of transposable elements (TEs; transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of Drosophila melanogaster, using data from the sequenced genome. The density of LTR and non-LTR retrotransposons (RNA-based elements) was high in regions with low recombination rates, but there was no clear tendency to parallel the recombination rate. However, the density of transposons (DNA-based elements) was significantly negatively correlated with recombination rate. The accumulation of TEs in regions of reduced recombination rate is compatible with selection acting against TEs, as selection is expected to be weaker in regions with lower recombination. The differences in the relationship between recombination rate and TE density that exist between chromosome arms suggest that TE distribution depends on specific characteristics of the chromosomes (chromatin structure, distribution of other sequences), the TEs themselves (transposition mechanism), and the species (reproductive system, effective population size, etc.), that have differing influences on the effect of natural selection acting against the TE insertions.

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 hotspots in the Mojave Desert

USGS Publications Warehouse

Vandergast, Amy G.; Inman, Richard D.; Barr, Kelly R.; Nussear, Kenneth E.; Esque, Todd C.; Hathaway, Stacie A.; Wood, Dustin A.; Medica, Philip A.; Breinholt, Jesse W.; Stephen, Catherine L.; Gottscho, Andrew D.; Marks, Sharyn B.; Jennings, W. Bryan; Fisher, Robert N.

2013-01-01

Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

[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.

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

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.

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

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.

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.

Biogeography predicts macro-evolutionary patterning of gestural display complexity in a passerine family.

PubMed

Miles, Meredith C; Cheng, Samantha; Fuxjager, Matthew J

2017-05-01

Gestural displays are incorporated into the signaling repertoire of numerous animal species. These displays range from complex signals that involve impressive and challenging maneuvers, to simpler displays or no gesture at all. The factors that drive this evolution remain largely unclear, and we therefore investigate this issue in New World blackbirds by testing how factors related to a species' geographical distribution and social mating system predict macro-evolutionary patterns of display elaboration. We report that species inhabiting temperate regions produce more complex displays than species living in tropical regions, and we attribute this to (i) ecological factors that increase the competitiveness of the social environment in temperate regions, and (ii) different evolutionary and geological contexts under which species in temperate and tropical regions evolved. Meanwhile, we find no evidence that social mating system predicts species differences in display complexity, which is consistent with the idea that gestural displays evolve independently of social mating system. Together, these results offer some of the first insight into the role played by geographic factors and evolutionary context in the evolution of the remarkable physical displays of birds and other vertebrates. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Evolution of high-mass star-forming regions .

NASA Astrophysics Data System (ADS)

Giannetti, A.; Leurini, S.; Wyrowski, F.; Urquhart, J.; König, C.; Csengeri, T.; Güsten, R.; Menten, K. M.

Observational identification of a coherent evolutionary sequence for high-mass star-forming regions is still missing. We use the progressive heating of the gas caused by the feedback of high-mass young stellar objects to prove the statistical validity of the most common schemes used to observationally define an evolutionary sequence for high-mass clumps, and identify which physical process dominates in the different phases. From the spectroscopic follow-ups carried out towards the TOP100 sample between 84 and 365 km s^-1 giga hertz, we selected several multiplets of CH3CN, CH3CCH, and CH3OH lines to derive the physical properties of the gas in the clumps along the evolutionary sequence. We demonstrate that the evolutionary sequence is statistically valid, and we define intervals in L/M separating the compression, collapse and accretion, and disruption phases. The first hot cores and ZAMS stars appear at L/M≈10usk {L_ȯ}msun-1

Ecological and evolutionary drivers of the elevational gradient of diversity.

PubMed

Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón

2018-05-02

Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.

Evolutionary paths of streptococcal and staphylococcal superantigens

PubMed Central

2012-01-01

Background Streptococcus pyogenes (GAS) harbors several superantigens (SAgs) in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE), the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and staphylococcal SAgs. PMID:22900646

Relationship between the column density distribution and evolutionary class of molecular clouds as viewed by ATLASGAL

NASA Astrophysics Data System (ADS)

Abreu-Vicente, J.; Kainulainen, J.; Stutz, A.; Henning, Th.; Beuther, H.

2015-09-01

We present the first study of the relationship between the column density distribution of molecular clouds within nearby Galactic spiral arms and their evolutionary status as measured from their stellar content. We analyze a sample of 195 molecular clouds located at distances below 5.5 kpc, identified from the ATLASGAL 870 μm data. We define three evolutionary classes within this sample: starless clumps, star-forming clouds with associated young stellar objects, and clouds associated with H ii regions. We find that the N(H2) probability density functions (N-PDFs) of these three classes of objects are clearly different: the N-PDFs of starless clumps are narrowest and close to log-normal in shape, while star-forming clouds and H ii regions exhibit a power-law shape over a wide range of column densities and log-normal-like components only at low column densities. We use the N-PDFs to estimate the evolutionary time-scales of the three classes of objects based on a simple analytic model from literature. Finally, we show that the integral of the N-PDFs, the dense gas mass fraction, depends on the total mass of the regions as measured by ATLASGAL: more massive clouds contain greater relative amounts of dense gas across all evolutionary classes. Appendices are available in electronic form at http://www.aanda.org

On the early emergence of reverse transcription: theoretical basis and experimental evidence

NASA Technical Reports Server (NTRS)

Lazcano, A.; Valverde, V.; Hernandez, G.; Gariglio, P.; Fox, G. E.; Oro, J.

1992-01-01

Reverse transcriptase (RT) was first discovered as an essential catalyst in the biological cycle of retroviruses. However, in the past years evidence has accumulated showing that RTs are involved in a surprisingly large number of RNA-mediated transpositional events that include both viral and nonviral genetic entities. Although it is probable that some RT-bearing genetic elements like the different types of AIDS viruses and the mammalian LINE family have arisen in recent geological times, the possibility that reverse transcription first took place in the early Archean is supported by (1) the hypothesis that RNA preceded DNA as cellular genetic material; (2) the existence of homologous regions of the subunit tau of the E. coli DNA polymerase III with the simian immunodeficiency virus RT, the hepatitis B virus RT, and the beta' subunit of the E. coli RNA polymerase (McHenry et al. 1988); (3) the presence of several conserved motifs, including a 14-amino-acid segment that consists of an Asp-Asp pair flanked by hydrophobic amino acids, which are found in all RTs and in most cellular and viral RNA polymerases. However, whether extant RTs descend from the primitive polymerase involved in the RNA-to-DNA transition remains unproven. Substrate specificity of the AMV and HIV-1 RTs can be modified in the presence of Mn2+, a cation which allows them to add ribonucleotides to an oligo (dG) primer in a template-dependent reaction. This change in specificity is comparable to that observed under similar conditions in other nucleic acid polymerases. This experimentally induced change in RT substrate specificity may explain previous observations on the misincorporation of ribonucleotides by the Maloney murine sarcoma virus RT in the minus and plus DNA of this retrovirus (Chen and Temin 1980). Our results also suggest that HIV-infected macrophages and T-cell cells may contain mixed polynucleotides containing both ribo- and deoxyribonucleotides. The evolutionary significance of these changes in substrate specificities of nucleic acid polymerases is also discussed.

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

Reexamining the P-Element Invasion of Drosophila melanogaster Through the Lens of piRNA Silencing

PubMed Central

Kelleher, Erin S.

2016-01-01

Transposable elements (TEs) are both important drivers of genome evolution and genetic parasites with potentially dramatic consequences for host fitness. The recent explosion of research on regulatory RNAs reveals that small RNA-mediated silencing is a conserved genetic mechanism through which hosts repress TE activity. The invasion of the Drosophila melanogaster genome by P elements, which happened on a historical timescale, represents an incomparable opportunity to understand how small RNA-mediated silencing of TEs evolves. Repression of P-element transposition emerged almost concurrently with its invasion. Recent studies suggest that this repression is implemented in part, and perhaps predominantly, by the Piwi-interacting RNA (piRNA) pathway, a small RNA-mediated silencing pathway that regulates TE activity in many metazoan germlines. In this review, I consider the P-element invasion from both a molecular and evolutionary genetic perspective, reconciling classic studies of P-element regulation with the new mechanistic framework provided by the piRNA pathway. I further explore the utility of the P-element invasion as an exemplar of the evolution of piRNA-mediated silencing. In light of the highly-conserved role for piRNAs in regulating TEs, discoveries from this system have taxonomically broad implications for the evolution of repression. PMID:27516614

The topology of evolutionary novelty and innovation in macroevolution

PubMed Central

2017-01-01

Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arising by accessing previously inaccessible or difficult to reach regions of a space. Here I discuss the nature of evolutionary novelty and innovation within the context of evolutionary spaces, and argue that the primacy of search as a conceptual metaphor ignores the generation of new spaces as well as other changes that have played important evolutionary roles. This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’. PMID:29061895

Interpreting Mammalian Evolution using Fugu Genome Comparisons

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

Stubbs, L; Ovcharenko, I; Loots, G G

2004-04-02

Comparative sequence analysis of the human and the pufferfish Fugu rubripes (fugu) genomes has revealed several novel functional coding and noncoding regions in the human genome. In particular, the fugu genome has been extremely valuable for identifying transcriptional regulatory elements in human loci harboring unusually high levels of evolutionary conservation to rodent genomes. In such regions, the large evolutionary distance between human and fishes provides an additional filter through which functional noncoding elements can be detected with high efficiency.

Evolutionary history of the ABCB2 genomic region in teleosts

USGS Publications Warehouse

Palti, Y.; Rodriguez, M.F.; Gahr, S.A.; Hansen, J.D.

2007-01-01

Gene duplication, silencing and translocation have all been implicated in shaping the unique genomic architecture of the teleost MH regions. Previously, we demonstrated that trout possess five unlinked regions encoding MH genes. One of these regions harbors ABCB2 which in all other vertebrate classes is found in the MHC class II region. In this study, we sequenced a BAC contig for the trout ABCB2 region. Analysis of this region revealed the presence of genes homologous to those located in the human class II (ABCB2, BRD2, ??DAA), extended class II (RGL2, PHF1, SYGP1) and class III (PBX2, Notch-L) regions. The organization and syntenic relationships of this region were then compared to similar regions in humans, Tetraodon and zebrafish to learn more about the evolutionary history of this region. Our analysis indicates that this region was generated during the teleost-specific duplication event while also providing insight about potential MH paralogous regions in teleosts. ?? 2006 Elsevier Ltd. All rights reserved.

Characterization of the human lineage-specific pericentric inversion that distinguishes human chromosome 1 from the homologous chromosomes of the great apes.

PubMed

Szamalek, Justyna M; Goidts, Violaine; Cooper, David N; Hameister, Horst; Kehrer-Sawatzki, Hildegard

2006-08-01

The human and chimpanzee genomes are distinguishable in terms of ten gross karyotypic differences including nine pericentric inversions and a chromosomal fusion. Seven of these large pericentric inversions are chimpanzee-specific whereas two of them, involving human chromosomes 1 and 18, were fixed in the human lineage after the divergence of humans and chimpanzees. We have performed detailed molecular and computational characterization of the breakpoint regions of the human-specific inversion of chromosome 1. FISH analysis and sequence comparisons together revealed that the pericentromeric region of HSA 1 contains numerous segmental duplications that display a high degree of sequence similarity between both chromosomal arms. Detailed analysis of these regions has allowed us to refine the p-arm breakpoint region to a 154.2 kb interval at 1p11.2 and the q-arm breakpoint region to a 562.6 kb interval at 1q21.1. Both breakpoint regions contain human-specific segmental duplications arranged in inverted orientation. We therefore propose that the pericentric inversion of HSA 1 was mediated by intra-chromosomal non-homologous recombination between these highly homologous segmental duplications that had themselves arisen only recently in the human lineage by duplicative transposition.

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.

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.

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.

Nup124p Is a Nuclear Pore Factor of Schizosaccharomyces pombe That Is Important for Nuclear Import and Activity of Retrotransposon Tf1

PubMed Central

Balasundaram, David; Benedik, Michael J.; Morphew, Mary; Dang, Van-Dinh; Levin, Henry L.

1999-01-01

The long terminal repeat (LTR)-containing retrotransposon Tf1 propagates within the fission yeast Schizosaccharomyces pombe as the result of several mechanisms that are typical of both retrotransposons and retroviruses. To identify host factors that contribute to the transposition process, we mutagenized cultures of S. pombe and screened them for strains that were unable to support Tf1 transposition. One such strain contained a mutation in a gene we named nup124. The product of this gene contains 11 FXFG repeats and is a component of the nuclear pore complex. In addition to the reduced levels of Tf1 transposition, the nup124-1 allele caused a significant reduction in the nuclear localization of Tf1 Gag. Surprisingly, the mutation in nup124-1 did not cause any reduction in the growth rate, the nuclear localization of specific nuclear localization signal-containing proteins, or the cytoplasmic localization of poly(A) mRNA. A two-hybrid analysis and an in vitro precipitation assay both identified an interaction between Tf1 Gag and the N terminus of Nup124p. These results provide evidence for an unusual mechanism of nuclear import that relies on a direct interaction between a nuclear pore factor and Tf1 Gag. PMID:10409764

Nup124p is a nuclear pore factor of Schizosaccharomyces pombe that is important for nuclear import and activity of retrotransposon Tf1.

PubMed

Balasundaram, D; Benedik, M J; Morphew, M; Dang, V D; Levin, H L

1999-08-01

The long terminal repeat (LTR)-containing retrotransposon Tf1 propagates within the fission yeast Schizosaccharomyces pombe as the result of several mechanisms that are typical of both retrotransposons and retroviruses. To identify host factors that contribute to the transposition process, we mutagenized cultures of S. pombe and screened them for strains that were unable to support Tf1 transposition. One such strain contained a mutation in a gene we named nup124. The product of this gene contains 11 FXFG repeats and is a component of the nuclear pore complex. In addition to the reduced levels of Tf1 transposition, the nup124-1 allele caused a significant reduction in the nuclear localization of Tf1 Gag. Surprisingly, the mutation in nup124-1 did not cause any reduction in the growth rate, the nuclear localization of specific nuclear localization signal-containing proteins, or the cytoplasmic localization of poly(A) mRNA. A two-hybrid analysis and an in vitro precipitation assay both identified an interaction between Tf1 Gag and the N terminus of Nup124p. These results provide evidence for an unusual mechanism of nuclear import that relies on a direct interaction between a nuclear pore factor and Tf1 Gag.

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.

The dynamic genome: transposons and environmental adaptation in the nervous system.

PubMed

Lapp, Hannah E; Hunter, Richard G

2016-02-01

Classically thought as genomic clutter, the functional significance of transposable elements (TEs) has only recently become a focus of attention in neuroscience. Increasingly, studies have demonstrated that the brain seems to have more retrotransposition and TE transcription relative to other somatic tissues, suggesting a unique role for TEs in the central nervous system. TE expression and transposition also appear to vary by brain region and change in response to environmental stimuli such as stress. TEs appear to serve a number of adaptive roles in the nervous system. The regulation of TE expression by steroid, epigenetic and other mechanisms in interplay with the environment represents a significant and novel avenue to understanding both normal brain function and disease.

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.

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.

[Decubitus ulcer in the calcaneus region: rapid development, difficult recovery].

PubMed

Fugazza, G; Bona, F

1996-03-01

Heel pressure sores frequently arise in patients kept in bed for a long time independently of their primary disease. In account of this event the authors completed a study concerning possible mutual relations between heel pressure sores and primary disease of the patients; to validate the pharmacological treatment in less severe sores and the surgical resolution in more serious cutaneous lesions. In the last 3 years (1992-1995) at the Rehabilitation Centre of Montescano the authors have treated 39 patients suffering from 63 different severe cutaneous lesions: from phlycten to deep necrosis. The therapeutic plane utilized pharmacological treatment for 1st, 2nd, 3rd degree pressure sores, and surgical treatment for 4th degree. Pharmacological treatment included: enzymatic drugs, bactericidal and bacteriostatic medicines and cicatrizing substances. Different healing times were related to different pressure sore severity. Surgical treatment consisted of transposition of flap into wound defect. This system caused considerable reduction in resolution times. The authors noticed how easily pressure sores arise in the heel region, and how difficultly they heal. This is probably connected with particular anatomical and vascular characteristics of this region.

Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

PubMed Central

2011-01-01

Background Several susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open interesting questions on the evolutionary forces shaping the frequency of these alleles in human populations. We aimed at testing the hypothesis whereby balancing selection has shaped the frequency of opposite risk alleles. Results Since balancing selection signatures are expected to extend over short genomic portions, we focused our analyses on 11 regions carrying putative functional polymorphisms that may represent the disease variants (and the selection targets). No exceptional nucleotide diversity was observed for ZSCAN23, HLA-DMB, VARS2, PTPN22, BAT3, C6orf47, and IL10; summary statistics were consistent with evolutionary neutrality for these gene regions. Conversely, CDSN/PSORS1C1, TRIM10/TRIM40, BTNL2, and TAP2 showed extremely high nucleotide diversity and most tests rejected neutrality, suggesting the action of balancing selection. For TAP2 and BTNL2 these signatures are not secondary to linkage disequilibrium with HLA class II genes. Nonetheless, with the exception of variants in TRIM40 and CDSN, our data suggest that opposite risk SNPs are not selection targets but rather have accumulated as neutral variants. Conclusion Data herein indicate that balancing selection is common within the extended MHC region and involves several non-HLA loci. Yet, the evolutionary history of most SNPs with an opposite effect for autoimmune diseases is consistent with evolutionary neutrality. We suggest that variants with an opposite effect on autoimmune diseases should not be considered a distinct class of disease alleles from the evolutionary perspective and, in a few cases, the opposite effect on distinct diseases may derive from complex haplotype structures in regions with high genetic diversity. PMID:21682861

The adaptation of polar fishes to climatic changes: Structure, function and phylogeny of haemoglobin.

PubMed

Verde, Cinzia; Giordano, Daniela; di Prisco, Guido

2008-01-01

In the Antarctic, fishes of dominant suborder Notothenioidei have evolved in a unique thermal scenario. Phylogenetically related taxa of the suborder live in a wide range of latitudes, in Antarctic, sub-Antarctic and temperate oceans. Consequently, they offer a remarkable opportunity to study the physiological and biochemical characters gained and, conversely, lost during their evolutionary history. The evolutionary perspective has also been pursued by comparative studies of some features of the heme protein devoted to O(2) transport in fish living in the other polar region, the Arctic. The two polar regions differ by age and isolation. Fish living in each habitat have undergone regional constraints and fit into different evolutionary histories. The aim of this contribution is to survey the current knowledge of molecular structure, functional features, phylogeny and adaptations of the haemoglobins of fish thriving in the Antarctic, sub-Antarctic and Arctic regions (with some excursions in the temperate latitudes), in search of insights into the convergent processes evolved in response to cooling. Current climate change may disturb adaptation, calling for strategies aimed at neutralising threats to biodiversity.

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

Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions.

PubMed

Huang, He; Sarai, Akinori

2012-12-01

The evolvability of proteins is not only restricted by functional and structural importance, but also by other factors such as gene duplication, protein stability, and an organism's robustness. Recently, intrinsically disordered proteins (IDPs)/regions (IDRs) have been suggested to play a role in facilitating protein evolution. However, the mechanisms by which this occurs remain largely unknown. To address this, we have systematically analyzed the relationship between the evolvability, stability, and function of IDPs/IDRs. Evolutionary analysis shows that more recently emerged IDRs have higher evolutionary rates with more functional constraints relaxed (or experiencing more positive selection), and that this may have caused accelerated evolution in the flanking regions and in the whole protein. A systematic analysis of observed stability changes due to single amino acid mutations in IDRs and ordered regions shows that while most mutations induce a destabilizing effect in proteins, mutations in IDRs cause smaller stability changes than in ordered regions. The weaker impact of mutations in IDRs on protein stability may have advantages for protein evolvability in the gain of new functions. Interestingly, however, an analysis of functional motifs in the PROSITE and ELM databases showed that motifs in IDRs are more conserved, characterized by smaller entropy and lower evolutionary rate, than in ordered regions. This apparently opposing evolutionary effect may be partly due to the flexible nature of motifs in IDRs, which require some key amino acid residues to engage in tighter interactions with other molecules. Our study suggests that the unique conformational and thermodynamic characteristics of IDPs/IDRs play an important role in the evolvability of proteins to gain new functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

Imaging congenital heart disease in adults

PubMed Central

Kilner, P J

2011-01-01

Transthoracic echocardiography is the first-line modality for cardiovascular imaging in adults with congenital heart disease (ACHD). The windows of access that are possible with transthoracic echocardiography are, however, rarely adequate for all regions of interest. The choice of further imaging depends on the clinical questions that remain to be addressed. The strengths of MRI include comprehensive access and coverage, providing imaging of all parts of the right ventricle, the pulmonary arteries, pulmonary veins and aorta. Cine images and velocity maps are acquired in specifically aligned planes, with stacks of cines or dynamic contrast angiography providing more comprehensive coverage. Tissues can be characterised if necessary, and MRI provides relatively accurate measurements of biventricular function and volume flow. These parameters are important in the assessment and follow-up of adults after repairs for tetralogy of Fallot or transposition of the great arteries and after Fontan operations. The superior spatial resolution and rapid acquisition of CT are invaluable in selected situations, including the visualisation of anomalous coronary or aortopulmonary collateral arteries, the assessment of luminal patency after stenting and imaging in patients with pacemakers. Ionising radiation is, however, a concern in younger patients who may need repeated investigation. Adults with relatively complex conditions should ideally be imaged in a specialist ACHD centre, where dedicated echocardiographic and cardiovascular MRI services are a necessary facility. General radiologists should be aware of the nature and pathophysiology of congenital heart disease, and should be alert for previously undiagnosed cases presenting in adulthood, including cases of atrial septal defect, aortic coarctation, patent ductus arteriosus, double-chambered right ventricle and congenitally corrected transposition. PMID:22723533

Mariner and the ITm Superfamily of Transposons.

PubMed

Tellier, Michael; Bouuaert, Corentin Claeys; Chalmers, Ronald

2015-04-01

The IS630-Tc1-mariner (ITm) family of transposons is one of the most widespread in nature. The phylogenetic distribution of its members shows that they do not persist for long in a given lineage, but rely on frequent horizontal transfer to new hosts. Although they are primarily selfish genomic-parasites, ITm transposons contribute to the evolution of their hosts because they generate variation and contribute protein domains and regulatory regions. Here we review the molecular mechanism of ITm transposition and its regulation. We focus mostly on the mariner elements, which are understood in the greatest detail owing to in vitro reconstitution and structural analysis. Nevertheless, the most important characteristics are probably shared across the grouping. Members of the ITm family are mobilized by a cut-and-paste mechanism and integrate at 5'-TA dinucleotide target sites. The elements encode a single transposase protein with an N-terminal DNA-binding domain and a C-terminal catalytic domain. The phosphoryl-transferase reactions during the DNA-strand breaking and joining reactions are performed by the two metal-ion mechanism. The metal ions are coordinated by three or four acidic amino acid residues located within an RNase H-like structural fold. Although all of the strand breaking and joining events at a given transposon end are performed by a single molecule of transposase, the reaction is coordinated by close communication between transpososome components. During transpososome assembly, transposase dimers compete for free transposon ends. This helps to protect the host by dampening an otherwise exponential increase in the rate of transposition as the copy number increases.

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.

Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back.

PubMed

Koonin, Eugene V; Makarova, Kira S

2017-10-01

The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-CRISPR-associated proteins (Cas) systems of bacterial and archaeal adaptive immunity show multifaceted evolutionary relationships with at least five classes of mobile genetic elements (MGE). First, the adaptation module of CRISPR-Cas that is responsible for the formation of the immune memory apparently evolved from a Casposon, a self-synthesizing transposon that employs the Cas1 protein as the integrase and might have brought additional cas genes to the emerging immunity loci. Second, a large subset of type III CRISPR-Cas systems recruited a reverse transcriptase from a Group II intron, providing for spacer acquisition from RNA. Third, effector nucleases of Class 2 CRISPR-Cas systems that are responsible for the recognition and cleavage of the target DNA were derived from transposon-encoded TnpB nucleases, most likely, on several independent occasions. Fourth, accessory nucleases in some variants of types I and III toxin and type VI effectors RNases appear to be ultimately derived from toxin nucleases of microbial toxin-antitoxin modules. Fifth, the opposite direction of evolution is manifested in the recruitment of CRISPR-Cas systems by a distinct family of Tn7-like transposons that probably exploit the capacity of CRISPR-Cas to recognize unique DNA sites to facilitate transposition as well as by bacteriophages that employ them to cope with host defense. Additionally, individual Cas proteins, such as the Cas4 nuclease, were recruited by bacteriophages and transposons. The two-sided evolutionary connection between CRISPR-Cas and MGE fits the "guns for hire" paradigm whereby homologous enzymatic machineries, in particular nucleases, are shuttled between MGE and defense systems and are used alternately as means of offense or defense. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

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

Cis-regulatory Evolution of Chalcone-Synthase Expression in the Genus Arabidopsis

PubMed Central

de Meaux, Juliette; Pop, A.; Mitchell-Olds, T.

2006-01-01

The contribution of cis-regulation to adaptive evolutionary change is believed to be essential, yet little is known about the evolutionary rules that govern regulatory sequences. Here, we characterize the short-term evolutionary dynamics of a cis-regulatory region within and among two closely related species, A. lyrata and A. halleri, and compare our findings to A. thaliana. We focused on the cis-regulatory region of chalcone synthase (CHS), a key enzyme involved in the synthesis of plant secondary metabolites. We observed patterns of nucleotide diversity that differ among species but do not depart from neutral expectations. Using intra- and interspecific F1 progeny, we have evaluated functional cis-regulatory variation in response to light and herbivory, environmental cues, which are known to induce CHS expression. We find that substantial cis-regulatory variation segregates within and among populations as well as between species, some of which results from interspecific genetic introgression. We further demonstrate that, in A. thaliana, CHS cis-regulation in response to herbivory is greater than in A. lyrata or A. halleri. Our work indicates that the evolutionary dynamics of a cis-regulatory region is characterized by pervasive functional variation, achieved mostly by modification of response modules to one but not all environmental cues. Our study did not detect the footprint of selection on this variation. PMID:17028316

Different evolutionary stages in massive star formation. Centimeter continuum and H2O maser emission with ATCA

NASA Astrophysics Data System (ADS)

Sánchez-Monge, Á.; Beltrán, M. T.; Cesaroni, R.; Fontani, F.; Brand, J.; Molinari, S.; Testi, L.; Burton, M.

2013-02-01

Aims: We present Australia Telescope Compact Array (ATCA) observations of the H2O maser line and radio continuum at 18.0 GHz and 22.8 GHz toward a sample of 192 massive star-forming regions containing several clumps already imaged at 1.2 mm. The main aim of this study is to investigate the water maser and centimeter continuum emission (that likely traces thermal free-free emission) in sources at different evolutionary stages, using evolutionary classifications previously published. Methods: We used the recently comissioned Compact Array Broadband Backend (CABB) at ATCA that obtains images with ~20'' resolution in the 1.3 cm continuum and H2O maser emission in all targets. For the evolutionary analysis of the sources we used millimeter continuum emission from the literature and the infrared emission from the MSX Point Source Catalog. Results: We detect centimeter continuum emission in 88% of the observed fields with a typical rms noise level of 0.45 mJy beam-1. Most of the fields show a single radio continuum source, while in 20% of them we identify multiple components. A total of 214 cm continuum sources have been identified, that likely trace optically thin H ii regions, with physical parameters typical of both extended and compact H ii regions. Water maser emission was detected in 41% of the regions, resulting in a total of 85 distinct components. The low angular (~20'') and spectral (~14 km s-1) resolutions do not allow a proper analysis of the water maser emission, but suffice to investigate its association with the continuum sources. We have also studied the detection rate of H ii regions in the two types of IRAS sources defined in the literature on the basis of the IRAS colors: High and Low. No significant differences are found, with high detection rates (>90%) for both High and Low sources. Conclusions: We classify the millimeter and infrared sources in our fields in three evolutionary stages following the scheme presented previously: (Type 1) millimeter-only sources, (Type 2) millimeter plus infrared sources, (Type 3) infrared-only sources. We find that H ii regions are mainly associated with Type 2 and Type 3 objects, confirming that these are more evolved than Type 1 sources. The H ii regions associated with Type 3 sources are slightly less dense and larger in size than those associated with Type 2 sources, as expected if the H ii region expands as it evolves, and Type 3 objects are older than Type 2 objects. The maser emission is mostly found to be associated with Type 1 and Type 2 sources, with a higher detection rate toward Type 2, consistent with the results of the literature. Finally, our results on H ii region and H2O maser association with different evolutionary types confirm the evolutionary classification proposed previously. Appendices are available in electronic form at http://www.aanda.orgTables 3-5, 7-9 are only, and Table 1 is also available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/550/A21

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.

piggyBac transposons expressing full-length human dystrophin enable genetic correction of dystrophic mesoangioblasts

PubMed Central

Loperfido, Mariana; Jarmin, Susan; Dastidar, Sumitava; Di Matteo, Mario; Perini, Ilaria; Moore, Marc; Nair, Nisha; Samara-Kuko, Ermira; Athanasopoulos, Takis; Tedesco, Francesco Saverio; Dickson, George; Sampaolesi, Maurilio; VandenDriessche, Thierry; Chuah, Marinee K.

2016-01-01

Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disorder caused by the absence of dystrophin. We developed a novel gene therapy approach based on the use of the piggyBac (PB) transposon system to deliver the coding DNA sequence (CDS) of either full-length human dystrophin (DYS: 11.1 kb) or truncated microdystrophins (MD1: 3.6 kb; MD2: 4 kb). PB transposons encoding microdystrophins were transfected in C2C12 myoblasts, yielding 65±2% MD1 and 66±2% MD2 expression in differentiated multinucleated myotubes. A hyperactive PB (hyPB) transposase was then deployed to enable transposition of the large-size PB transposon (17 kb) encoding the full-length DYS and green fluorescence protein (GFP). Stable GFP expression attaining 78±3% could be achieved in the C2C12 myoblasts that had undergone transposition. Western blot analysis demonstrated expression of the full-length human DYS protein in myotubes. Subsequently, dystrophic mesoangioblasts from a Golden Retriever muscular dystrophy dog were transfected with the large-size PB transposon resulting in 50±5% GFP-expressing cells after stable transposition. This was consistent with correction of the differentiated dystrophic mesoangioblasts following expression of full-length human DYS. These results pave the way toward a novel non-viral gene therapy approach for DMD using PB transposons underscoring their potential to deliver large therapeutic genes. PMID:26682797

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

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.

Evolutionary rescue of a parasite population by mutation rate evolution.

PubMed

Greenspoon, Philip B; Mideo, Nicole

2017-10-01

The risk of antibiotic resistance evolution in parasites is a major problem for public health. Identifying factors which promote antibiotic resistance evolution is thus a priority in evolutionary medicine. The rate at which new mutations enter the parasite population is one important predictor; however, mutation rate is not necessarily a fixed quantity, as is often assumed, but can itself evolve. Here we explore the possible impacts of mutation rate evolution on the fate of a disease circulating in a host population, which is being treated with drugs, the use of which varies over time. Using an evolutionary rescue framework, we find that mutation rate evolution provides a dramatic increase in the probability that a parasite population survives treatment in only a limited region, while providing little or no advantage in other regions. Both epidemiological features, such as the virulence of infection, and population genetic parameters, such as recombination rate, play important roles in determining the probability of evolutionary rescue and whether mutation rate evolution enhances the probability of evolutionary rescue or not. While efforts to curtail mutation rate evolution in parasites may be worthwhile under some circumstances, our results suggest that this need not always be the case. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolution, the loss of diversity and the role of trade-offs.

PubMed

Best, Alex; Bowers, Roger; White, Andy

2015-06-01

We investigate how the loss of previously evolved diversity in host resistance to disease is dependent on the complexity of the underlying evolutionary trade-off. Working within the adaptive dynamics framework, using graphical tools (pairwise invasion plots, PIPs; trait evolution plots, TEPs) and algebraic analysis we consider polynomial trade-offs of increasing degree. Our focus is on the evolutionary trajectory of the dimorphic population after it has been attracted to an evolutionary branching point. We show that for sufficiently complex trade-offs (here, polynomials of degree three or higher) the resulting invasion boundaries can form closed 'oval' areas of invadability and strategy coexistence. If no attracting singular strategies exist within this region, then the population is destined to evolve outside of the region of coexistence, resulting in the loss of one strain. In particular, the loss of diversity in this model always occurs in such a way that the remaining strain is not attracted back to the branching point but to an extreme of the trade-off, meaning the diversity is lost forever. We also show similar results for a non-polynomial but complex trade-off, and for a different eco-evolutionary model. Our work further highlights the importance of trade-offs to evolutionary behaviour. Copyright © 2015 Elsevier Inc. All rights reserved.

Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

PubMed

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Evolutionary Relationship and Structural Characterization of the EPF/EPFL Gene Family

PubMed Central

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes. PMID:23755192

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 ...

Mapping of within-species segregation distortion in Drosophila persimilis and hybrid sterility between D. persimilis and D. pseudoobscura.

PubMed

McDermott, S R; Noor, M A F

2012-10-01

In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids that may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL maps for segregation distortion and hybrid sterility in crosses between D. persimilis and D. pseudoobscura. The maps localize regions along the XR contributing to both phenotypes, and they indicate one region of overlap between the two maps. This overlap could provide preliminary evidence for an association between segregation distortion within species and hybrid sterility, but the localizations are currently too broad to have confidence in this conclusion. This work is a first step towards possibly supporting a genetic conflict model of speciation in this system. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

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.

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

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.

Physical properties of high-mass star-forming clumps in different evolutionary stages from the Bolocam Galactic Plane Survey

NASA Astrophysics Data System (ADS)

Svoboda, Brian; Shirley, Yancy; Rosolowsky, Erik; Dunham, Miranda; Ellsworth-Bowers, Timothy; Ginsburg, Adam

2013-07-01

High mass stars play a key role in the physical and chemical evolution of the interstellar medium, yet the evolutionary sequence for high mass star forming regions is poorly understood. Recent Galactic plane surveys are providing the first systematic view of high-mass star-forming regions in all evolutionary phases across the Milky Way. We present observations of the 22.23 GHz H2O maser transition J(Ka,Kc) = 6(1,6)→5(2,3) transition toward 1398 clumps identified in the Bolocam Galactic Plane Survey using the 100m Green Bank Telescope (GBT). We detect 392 H2O masers, 279 (71%) newly discovered. We show that H2O masers can identify the presence of protostars which were not previously identified by Spitzer/MSX Galactic plane IR surveys: 25% of IR-dark clumps have an H2O maser. We compare the physical properties of the clumps in the Bolocam Galactic Plane Survey (BGPS) with observations of diagnostics of star formation activity: 8 and 24 um YSO candidates, H2O and CH3OH masers, shocked H2, EGOs, and UCHII regions. We identify a sub-sample of 400 clumps with no star formation indicators representing the largest and most robust sample of pre-protocluster candidates from an unbiased survey to date. The different evolutionary stages show strong separations in HCO+ linewidth and integrated intensity, surface mass density, and kinetic temperature. Monte Carlo techniques are applied to distance probability distribution functions (DPDFs) in order to marginalize over the kinematic distance ambiguity and calculate the distribution of derived quantities for clumps in different evolutionary stages. Surface area and dust mass show weak separations above > 2 pc^2 and > 3x10^3 solar masses. An observed breakdown occurs in the size-linewidth relationship with no differentiation by evolutionary stage. Future work includes adding evolutionary indicators (MIPSGAL, HiGal, MMB) and expanding DPDF priors (HI self-absorption, Galactic structure) for more well-resolved KDAs.

A Bright Future for Evolutionary Methods in Drug Design.

PubMed

Le, Tu C; Winkler, David A

2015-08-01

Most medicinal chemists understand that chemical space is extremely large, essentially infinite. Although high-throughput experimental methods allow exploration of drug-like space more rapidly, they are still insufficient to fully exploit the opportunities that such large chemical space offers. Evolutionary methods can synergistically blend automated synthesis and characterization methods with computational design to identify promising regions of chemical space more efficiently. We describe how evolutionary methods are implemented, and provide examples of published drug development research in which these methods have generated molecules with increased efficacy. We anticipate that evolutionary methods will play an important role in future drug discovery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nucleotide variability at its limit? Insights into the number and evolutionary dynamics of the sex-determining specificities of the honey bee Apis mellifera.

PubMed

Lechner, Sarah; Ferretti, Luca; Schöning, Caspar; Kinuthia, Wanja; Willemsen, David; Hasselmann, Martin

2014-02-01

Deciphering the evolutionary processes driving nucleotide variation in multiallelic genes is limited by the number of genetic systems in which such genes occur. The complementary sex determiner (csd) gene in the honey bee Apis mellifera is an informative example for studying allelic diversity and the underlying evolutionary forces in a well-described model of balancing selection. Acting as the primary signal of sex determination, diploid individuals heterozygous for csd develop into females, whereas csd homozygotes are diploid males that have zero fitness. Examining 77 of the functional heterozygous csd allele pairs, we established a combinatorical criteria that provide insights into the minimum number of amino acid differences among those pairs. Given a data set of 244 csd sequences, we show that the total number of csd alleles found in A. mellifera ranges from 53 (locally) to 87 (worldwide), which is much higher than was previously reported (20). Using a coupon-collector model, we extrapolate the presence of in total 116-145 csd alleles worldwide. The hypervariable region (HVR) is of particular importance in determining csd allele specificity, and we provide for this region evidence of high evolutionary rate for length differences exceeding those of microsatellites. The proportion of amino acids driven by positive selection and the rate of nonsynonymous substitutions in the HVR-flanking regions reach values close to 1 but differ with respect to the HVR length. Using a model of csd coalescence, we identified the high originating rate of csd specificities as a major evolutionary force, leading to an origin of a novel csd allele every 400,000 years. The csd polymorphism frequencies in natural populations indicate an excess of new mutations, whereas signs of ancestral transspecies polymorphism can still be detected. This study provides a comprehensive view of the enormous diversity and the evolutionary forces shaping a multiallelic gene.

Nucleotide Variability at Its Limit? Insights into the Number and Evolutionary Dynamics of the Sex-Determining Specificities of the Honey Bee Apis mellifera

PubMed Central

Lechner, Sarah; Ferretti, Luca; Schöning, Caspar; Kinuthia, Wanja; Willemsen, David; Hasselmann, Martin

2014-01-01

Deciphering the evolutionary processes driving nucleotide variation in multiallelic genes is limited by the number of genetic systems in which such genes occur. The complementary sex determiner (csd) gene in the honey bee Apis mellifera is an informative example for studying allelic diversity and the underlying evolutionary forces in a well-described model of balancing selection. Acting as the primary signal of sex determination, diploid individuals heterozygous for csd develop into females, whereas csd homozygotes are diploid males that have zero fitness. Examining 77 of the functional heterozygous csd allele pairs, we established a combinatorical criteria that provide insights into the minimum number of amino acid differences among those pairs. Given a data set of 244 csd sequences, we show that the total number of csd alleles found in A. mellifera ranges from 53 (locally) to 87 (worldwide), which is much higher than was previously reported (20). Using a coupon-collector model, we extrapolate the presence of in total 116–145 csd alleles worldwide. The hypervariable region (HVR) is of particular importance in determining csd allele specificity, and we provide for this region evidence of high evolutionary rate for length differences exceeding those of microsatellites. The proportion of amino acids driven by positive selection and the rate of nonsynonymous substitutions in the HVR-flanking regions reach values close to 1 but differ with respect to the HVR length. Using a model of csd coalescence, we identified the high originating rate of csd specificities as a major evolutionary force, leading to an origin of a novel csd allele every 400,000 years. The csd polymorphism frequencies in natural populations indicate an excess of new mutations, whereas signs of ancestral transspecies polymorphism can still be detected. This study provides a comprehensive view of the enormous diversity and the evolutionary forces shaping a multiallelic gene. PMID:24170493

JCoDA: a tool for detecting evolutionary selection.

PubMed

Steinway, Steven N; Dannenfelser, Ruth; Laucius, Christopher D; Hayes, James E; Nayak, Sudhir

2010-05-27

The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda.

JCoDA: a tool for detecting evolutionary selection

PubMed Central

2010-01-01

Background The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. Results JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. Conclusions JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda. PMID:20507581

A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice

PubMed Central

White, Michael A.; Ikeda, Akihiro; Payseur, Bret A.

2012-01-01

The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located just ~700 kb from the distal end of the X chromosome, whereas the boundary is found at a more proximal position in Mus spretus, a species that diverged from house mice 2–4 million years ago. Here, we use a combination of genetic and physical mapping to document a pronounced shift in the PAR boundary in a second house mouse subspecies, Mus musculus castaneus (represented by the CAST/EiJ strain), ~430 kb proximal of the M. m. domesticus boundary. We demonstrate molecular evolutionary consequences of this shift, including a marked lineage-specific increase in sequence divergence within Mid1, a gene that resides entirely within the M. m. castaneus PAR but straddles the boundary in other subspecies. Our results extend observations of structural divergence in the PAR to closely related subspecies, pointing to major evolutionary changes in this functionally important genomic region over a short time period. PMID:22763584

A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice.

PubMed

White, Michael A; Ikeda, Akihiro; Payseur, Bret A

2012-08-01

The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located just ~700 kb from the distal end of the X chromosome, whereas the boundary is found at a more proximal position in Mus spretus, a species that diverged from house mice 2-4 million years ago. In this study we used a combination of genetic and physical mapping to document a pronounced shift in the PAR boundary in a second house mouse subspecies, Mus musculus castaneus (represented by the CAST/EiJ strain), ~430 kb proximal of the M. m. domesticus boundary. We demonstrate molecular evolutionary consequences of this shift, including a marked lineage-specific increase in sequence divergence within Mid1, a gene that resides entirely within the M. m. castaneus PAR but straddles the boundary in other subspecies. Our results extend observations of structural divergence in the PAR to closely related subspecies, pointing to major evolutionary changes in this functionally important genomic region over a short time period.

Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion

PubMed Central

Wu, Chung-Shien; Chaw, Shu-Miaw

2015-01-01

In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes. PMID:26116919

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 ...

[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) .

[What's new in instrumental dermatology?].

PubMed

Amici, J-M

2014-12-01

This "What's new in instrumental dermatology" focuses on cutaneous oncologic surgery, base on a review of the 2012-2014 literature. First, the ability of dermatologists to make a good "oncologic reading of tumors" is the key of radical surgical treatment. Advantages and disadvantages of the biopsy are discussed. Then, the second message is the management of anticoagulants, that should not be interrupted for skin surgery. Despite recommendations, this practice is not followed in 40% of cases; this point is critical because bleeding complications are minor compared to potential morbidity of thrombotic events when stopping these medications. Regarding infection, nasal carriage of Staphylococcus aureus is identified as a risk factor for wound infection. A preoperative shower with chlorhexidine and mupirocin topical decolonization of nostril reduces this risk. Surgical techniques are trying to reach minimalism, by reducing undermining and scarring. On the trunk, using deep slow resorbable sutures improve scarring. In addition using adhesive sutures (strip) reduce the wideness of scar. On the face, the lower third of the nose is the most challenging because of the free edges, which are deformable. In this location bilobed or trilobed transposition flap offer the advantage of remaining in the nasal aesthetic unit and not disturbing the free edges of the nasal orifices. Regarding scarring, early hypertrophic scar is now well defined and linked with transposition flaps of the nasal region. An early treatment with intralesional corticosteroid injection appears to be effective. Finally, the biological mechanism of the effectiveness of compression in the prevention and treatment of dystrophic scar is now clear. The mechanotransduction explain how a mechanical stress of the skin activates biological cell pathways, which regulate the quality of collagen synthesis and the arrangement of skin fibrosis. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Current evidence for effectiveness of interventions for cubital tunnel syndrome, radial tunnel syndrome, instability, or bursitis of the elbow: a systematic review.

PubMed

Rinkel, Willem D; Schreuders, Ton A R; Koes, Bart W; Huisstede, Bionka M A

2013-12-01

To provide an evidence-based overview of the effectiveness of interventions for 4 nontraumatic painful disorders sharing the anatomic region of the elbow: cubital tunnel syndrome, radial tunnel syndrome, elbow instability, and olecranon bursitis. The Cochrane Library, PubMed, Embase, PEDro, and CINAHL were searched to identify relevant reviews and randomized clinical trials (RCTs). Two reviewers independently extracted data and assessed the quality of the methodology. A best-evidence synthesis was used to summarize the results. One systematic review and 6 RCTs were included. For the surgical treatment of cubital tunnel syndrome (1 review, 3 RCTs), comparing simple decompression with anterior ulnar nerve transposition, no evidence was found in favor of either one of these. Limited evidence was found in favor of medial epicondylectomy versus anterior transposition and for early postoperative therapy versus immobilization. No evidence was found for the effect of local steroid injection in addition to splinting. No RCTs were found for radial tunnel syndrome. For olecranon bursitis (1 RCT), limited evidence for effectiveness was found for methylprednisolone acetate injection plus naproxen. Concerning elbow instability, including 2 RCTs, one showed that nonsurgical treatment resulted in similar results compared with surgery, whereas the other found limited evidence for the effectiveness in favor of early mobilization versus 3 weeks of immobilization after surgery. In this review no, or at best, limited evidence was found for the effectiveness of nonsurgical and surgical interventions to treat painful cubital tunnel syndrome, radial tunnel syndrome, elbow instability, or olecranon bursitis. Well-designed and well-conducted RCTs are clearly needed in this field.

Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region

PubMed Central

Jiang, Zhi J; Castoe, Todd A; Austin, Christopher C; Burbrink, Frank T; Herron, Matthew D; McGuire, Jimmy A; Parkinson, Christopher L; Pollock, David D

2007-01-01

Background The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence. Results We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs. Conclusion Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria. PMID:17655768

The Spectral Energy Distribution of the Earliest Phases of Massive Star Formation from the Spizter and Herschel Archives

NASA Astrophysics Data System (ADS)

Klein, Randolf; Looney, Leslie; Henning, Thomas; Chakrabarti, Sukanya; Shenoy, Sachin

2015-08-01

Infrared Dark Clouds (IRDCs) are very good candidates for the earliest phases of massive star formation, but can only be found in regions with high infrared background. We have searched for early phases among cold and massive (M>100M⊙) cloud cores by selecting cores from millimeter continuum surveys (Faundez et al. 2004, Sridharan et al. 2005, Klein et al. 2005, Beltran et al. 2006) without associations at short wavelengths. We compared the millimeter continuum peak positions with IR and radio catalogs (2MASS, MSX, IRAS, and NVSS) and excluded cores that had sources associated with the cores' peaks. We compiled a list of 173 cores in over 117 regions that are candidates for very early phases of Massive Star Formation (MSF). Now with the Spitzer and Herschel archives, these cores can be characterized further. The GLIMPSE and MIPSGAL programs alone covered 86 of these regions. The Herschel Archive adds even longer wavelengths. We are compiling this data set to construct the complete spectral energy distribution (SED) in the mid- and far-infrared with good spatial resolution and broad spectral coverage. This allow us to disentangle the complex regions and model the SED of the deeply embedded protostars/clusters.We will be presenting the IR properties of all cores and their embedded source, attempt a characterization, and order the cores in an evolutionary sequence. The resulting properties can be compared to e.g. IRDCs, a class of objects suggested to be the earliest stages of MSF. With the relative large number of cores, we can try to answer questions like: How homogeneous or diverse are our regions in terms of their evolutionary stage? Where do our embedded sources fit in the evolutionary sequence of IRDCs, hot molecular cores, ultra-compact HII regions, etc? How is the MSF shaping the environment and vice versa? Can we extrapolate to the initial conditions of MSF using our evolutionary sequence?

The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics.

PubMed

Brusatte, S L; Sakamoto, M; Montanari, S; Harcourt Smith, W E H

2012-02-01

Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions.

PubMed

Vieira-da-Silva, Ana; Louzada, Sandra; Adega, Filomena; Chaves, Raquel

2015-01-01

Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes. © 2015 S. Karger AG, Basel.

Site Specific Probable Maximum Precipitation Estimates and Professional Judgement

NASA Astrophysics Data System (ADS)

Hayes, B. D.; Kao, S. C.; Kanney, J. F.; Quinlan, K. R.; DeNeale, S. T.

2015-12-01

State and federal regulatory authorities currently rely upon the US National Weather Service Hydrometeorological Reports (HMRs) to determine probable maximum precipitation (PMP) estimates (i.e., rainfall depths and durations) for estimating flooding hazards for relatively broad regions in the US. PMP estimates for the contributing watersheds upstream of vulnerable facilities are used to estimate riverine flooding hazards while site-specific estimates for small water sheds are appropriate for individual facilities such as nuclear power plants. The HMRs are often criticized due to their limitations on basin size, questionable applicability in regions affected by orographic effects, their lack of consist methods, and generally by their age. HMR-51 for generalized PMP estimates for the United States east of the 105th meridian, was published in 1978 and is sometimes perceived as overly conservative. The US Nuclear Regulatory Commission (NRC), is currently reviewing several flood hazard evaluation reports that rely on site specific PMP estimates that have been commercially developed. As such, NRC has recently investigated key areas of expert judgement via a generic audit and one in-depth site specific review as they relate to identifying and quantifying actual and potential storm moisture sources, determining storm transposition limits, and adjusting available moisture during storm transposition. Though much of the approach reviewed was considered a logical extension of HMRs, two key points of expert judgement stood out for further in-depth review. The first relates primarily to small storms and the use of a heuristic for storm representative dew point adjustment developed for the Electric Power Research Institute by North American Weather Consultants in 1993 in order to harmonize historic storms for which only 12 hour dew point data was available with more recent storms in a single database. The second issue relates to the use of climatological averages for spatially interpolating 100-year dew point values rather than a more gauge-based approach. Site specific reviews demonstrated that both issues had potential for lowering the PMP estimate significantly by affecting the in-place and transposed moisture maximization value and, in turn, the final controlling storm for a given basin size and PMP estimate.

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 ...

Predicting loss of evolutionary history: Where are we?

PubMed

Veron, Simon; Davies, T Jonathan; Cadotte, Marc W; Clergeau, Philippe; Pavoine, Sandrine

2017-02-01

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides. © 2015 Cambridge Philosophical Society.

Evolutionary lag times and recent origin of the biota of an ancient desert (Atacama-Sechura).

PubMed

Guerrero, Pablo C; Rosas, Marcelo; Arroyo, Mary T K; Wiens, John J

2013-07-09

The assembly of regional biotas and organismal responses to anthropogenic climate change both depend on the capacity of organisms to adapt to novel ecological conditions. Here we demonstrate the concept of evolutionary lag time, the time between when a climatic regime or habitat develops in a region and when it is colonized by a given clade. We analyzed the time of colonization of four clades (three plant genera and one lizard genus) into the Atacama-Sechura Desert of South America, one of Earth's driest and oldest deserts. We reconstructed time-calibrated phylogenies for each clade and analyzed the timing of shifts in climatic distributions and biogeography and compared these estimates to independent geological estimates of the time of origin of these deserts. Chaetanthera and Malesherbia (plants) and Liolaemus (animal) invaded arid regions of the Atacama-Sechura Desert in the last 10 million years, some 20 million years after the initial onset of aridity in the region. There are also major lag times between when these clades colonized the region and when they invaded arid habitats within the region (typically 4-14 million years). Similarly, hyperarid climates developed ∼8 million years ago, but the most diverse plant clade in these habitats (Nolana) only colonized them ∼2 million years ago. Similar evolutionary lag times may occur in other organisms and habitats, but these results are important in suggesting that many lineages may require very long time scales to adapt to modern desertification and climatic change.

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.

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.

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.

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.

piggyBac transposons expressing full-length human dystrophin enable genetic correction of dystrophic mesoangioblasts.

PubMed

Loperfido, Mariana; Jarmin, Susan; Dastidar, Sumitava; Di Matteo, Mario; Perini, Ilaria; Moore, Marc; Nair, Nisha; Samara-Kuko, Ermira; Athanasopoulos, Takis; Tedesco, Francesco Saverio; Dickson, George; Sampaolesi, Maurilio; VandenDriessche, Thierry; Chuah, Marinee K

2016-01-29

Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disorder caused by the absence of dystrophin. We developed a novel gene therapy approach based on the use of the piggyBac (PB) transposon system to deliver the coding DNA sequence (CDS) of either full-length human dystrophin (DYS: 11.1 kb) or truncated microdystrophins (MD1: 3.6 kb; MD2: 4 kb). PB transposons encoding microdystrophins were transfected in C2C12 myoblasts, yielding 65±2% MD1 and 66±2% MD2 expression in differentiated multinucleated myotubes. A hyperactive PB (hyPB) transposase was then deployed to enable transposition of the large-size PB transposon (17 kb) encoding the full-length DYS and green fluorescence protein (GFP). Stable GFP expression attaining 78±3% could be achieved in the C2C12 myoblasts that had undergone transposition. Western blot analysis demonstrated expression of the full-length human DYS protein in myotubes. Subsequently, dystrophic mesoangioblasts from a Golden Retriever muscular dystrophy dog were transfected with the large-size PB transposon resulting in 50±5% GFP-expressing cells after stable transposition. This was consistent with correction of the differentiated dystrophic mesoangioblasts following expression of full-length human DYS. These results pave the way toward a novel non-viral gene therapy approach for DMD using PB transposons underscoring their potential to deliver large therapeutic genes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

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

Fifty years of the European medicines regulatory network: reflections for strengthening intra-regional cooperation in the Region of the Americas.

PubMed

Allchurch, Martin Harvey; Barbano, Dirceu Brás Aparecido; Pinheiro, Marie-Hélène; Lazdin-Helds, Janis

2016-05-01

This report considers how the experience of the European regulatory system might be applied to help strengthen the regulatory systems for medicines in the Region of the Americas. The work of the European Medicines Agencies (EMA) is carried out through its scientific committees, composed of members from European Economic Area countries. A robust legal framework allows EMA to coordinate resources from Member States' competent authorities, including, for example, assisting candidate countries as they prepare to join the European Union (EU). Capacity-building programs help countries adjust their regulatory systems ahead of full participation in the European medicines regulatory network. These programs facilitate adoption of common technical requirements, identify areas where action might be needed to ensure the smooth transposition of EU pharmaceutical law into national legislation, and prepare candidate countries for participation in EMA committees and the European regulatory network. The methodology of these programs could be of potential interest to the Pan American Health Organization (PAHO), the Regional Office of the World Health Organization for the Americas. Given resolutions adopted by the World Health Assembly and the PAHO Directing Council, there is a strong indication that the countries of the Region of the Americas wish to assemble a system that uses the existing regulatory capacity of some countries to strengthen local regulatory capacities in others.

Evolutionary history of a keystone pollinator parallels the biome occupancy of angiosperms in the Greater Cape Floristic Region.

PubMed

de Jager, Marinus L; Ellis, Allan G

2017-02-01

The Greater Cape Floristic Region (GCFR) in South Africa has been extensively investigated for its phenomenal angiosperm diversity. A key emergent pattern is the occurrence of older plant lineages in the southern Fynbos biome and younger lineages in the northern Succulent Karoo biome. We know practically nothing, however, about the evolutionary history of the animals that pollinate this often highly-specialized flora. In this study, we explore the evolutionary history of an important GCFR fly pollinator, Megapalpus capensis, and ask whether it exhibits broadly congruent genetic structuring and timing of diversification to flowering plants within these biomes. We find that the oldest M. capensis lineages originated in Fynbos during the Miocene, while younger Succulent Karoo lineages diverged in the Pliocene and correspond to the proposed age of this recent biome. A strong signature of population expansion is also recovered for flies in this arid biome, consistent with recent colonization. Our first investigation into the evolutionary history of GCFR pollinators thus supports a recent origin of the SK biome, as inferred from angiosperm phylogenies, and suggests that plants and pollinators may have co-diverged within this remarkable area. Copyright © 2016 Elsevier Inc. All rights reserved.

Co-evolutionary data mining for fuzzy rules: automatic fitness function creation phase space, and experiments

NASA Astrophysics Data System (ADS)

Smith, James F., III; Blank, Joseph A.

2003-03-01

An approach is being explored that involves embedding a fuzzy logic based resource manager in an electronic game environment. Game agents can function under their own autonomous logic or human control. This approach automates the data mining problem. The game automatically creates a cleansed database reflecting the domain expert's knowledge, it calls a data mining function, a genetic algorithm, for data mining of the data base as required and allows easy evaluation of the information extracted. The co-evolutionary fitness functions, chromosomes and stopping criteria for ending the game are discussed. Genetic algorithm and genetic program based data mining procedures are discussed that automatically discover new fuzzy rules and strategies. The strategy tree concept and its relationship to co-evolutionary data mining are examined as well as the associated phase space representation of fuzzy concepts. The overlap of fuzzy concepts in phase space reduces the effective strategies available to adversaries. Co-evolutionary data mining alters the geometric properties of the overlap region known as the admissible region of phase space significantly enhancing the performance of the resource manager. Procedures for validation of the information data mined are discussed and significant experimental results provided.

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

PubMed Central

Longo, Mark S; Carone, Dawn M; Green, Eric D; O'Neill, Michael J; O'Neill, Rachel J

2009-01-01

Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials and eutherians that may have predisposed these genomic regions to large-scale chromosomal instability. PMID:19630942

Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion.

PubMed

Wu, Chung-Shien; Chaw, Shu-Miaw

2015-06-27

In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

THE HCN/HNC ABUNDANCE RATIO TOWARD DIFFERENT EVOLUTIONARY PHASES OF MASSIVE STAR FORMATION

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

Jin, Mihwa; Lee, Jeong-Eun; Kim, Kee-Tae, E-mail: mihwajin.sf@gmail.com, E-mail: jeongeun.lee@khu.ac.kr, E-mail: ktkim@kasi.re.kr

2015-07-20

Using the H{sup 13}CN and HN{sup 13}C J = 1–0 line observations, the abundance ratio of HCN/HNC has been estimated for different evolutionary stages of massive star formation: infrared dark clouds (IRDCs), high-mass protostellar objects (HMPOs), and ultracompact H ii regions (UCH iis). IRDCs were divided into “quiescent IRDC cores (qIRDCc)” and “active IRDC cores (aIRDCc),” depending on star formation activity. The HCN/HNC ratio is known to be higher at active and high temperature regions related to ongoing star formation, compared to cold and quiescent regions. Our observations toward 8 qIRDCc, 16 aIRDCc, 23 HMPOs, and 31 UCH iis showmore » consistent results; the ratio is 0.97 (±0.10), 2.65 (±0.88), 4.17 (±1.03), and 8.96 (±3.32) in these respective evolutionary stages, increasing from qIRDCc to UCH iis. The change of the HCN/HNC abundance ratio, therefore, seems directly associated with the evolutionary stages of star formation, which have different temperatures. One suggested explanation for this trend is the conversion of HNC to HCN, which occurs effectively at higher temperatures. To test the explanation, we performed a simple chemical model calculation. In order to fit the observed results, the energy barrier of the conversion must be much lower than the value provided by theoretical calculations.« less

Sequence similarities and evolutionary relationships of microbial, plant and animal alpha-amylases.

PubMed

Janecek, S

1994-09-01

Amino acid sequence comparison of 37 alpha-amylases from microbial, plant and animal sources was performed to identify their mutual sequence similarities in addition to the five already described conserved regions. These sequence regions were examined from structure/function and evolutionary perspectives. An unrooted evolutionary tree of alpha-amylases was constructed on a subset of 55 residues from the alignment of sequence similarities along with conserved regions. The most important new information extracted from the tree was as follows: (a) the close evolutionary relationship of Alteromonas haloplanctis alpha-amylase (thermolabile enzyme from an antarctic psychrotroph) with the already known group of homologous alpha-amylases from streptomycetes, Thermomonospora curvata, insects and mammals, and (b) the remarkable 40.1% identity between starch-saccharifying Bacillus subtilis alpha-amylase and the enzyme from the ruminal bacterium Butyrivibrio fibrisolvens, an alpha-amylase with an unusually large polypeptide chain (943 residues in the mature enzyme). Due to a very high degree of similarity, the whole amino acid sequences of three groups of alpha-amylases, namely (a) fungi and yeasts, (b) plants, and (c) A. haloplanctis, streptomycetes, T. curvata, insects and mammals, were aligned independently and their unrooted distance trees were calculated using these alignments. Possible rooting of the trees was also discussed. Based on the knowledge of the location of the five disulfide bonds in the structure of pig pancreatic alpha-amylase, the possible disulfide bridges were established for each of these groups of homologous alpha-amylases.

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.

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

Computationally mapping sequence space to understand evolutionary protein engineering.

PubMed

Armstrong, Kathryn A; Tidor, Bruce

2008-01-01

Evolutionary protein engineering has been dramatically successful, producing a wide variety of new proteins with altered stability, binding affinity, and enzymatic activity. However, the success of such procedures is often unreliable, and the impact of the choice of protein, engineering goal, and evolutionary procedure is not well understood. We have created a framework for understanding aspects of the protein engineering process by computationally mapping regions of feasible sequence space for three small proteins using structure-based design protocols. We then tested the ability of different evolutionary search strategies to explore these sequence spaces. The results point to a non-intuitive relationship between the error-prone PCR mutation rate and the number of rounds of replication. The evolutionary relationships among feasible sequences reveal hub-like sequences that serve as particularly fruitful starting sequences for evolutionary search. Moreover, genetic recombination procedures were examined, and tradeoffs relating sequence diversity and search efficiency were identified. This framework allows us to consider the impact of protein structure on the allowed sequence space and therefore on the challenges that each protein presents to error-prone PCR and genetic recombination procedures.

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

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.

A Panchromatic View of Star-Forming Regions in the Magellanic Clouds: Characterizing Physical and Evolutionary Parameters of 1,000 Young Stellar Objects

NASA Astrophysics Data System (ADS)

Carlson, Lynn R.

2010-01-01

I discuss newly discovered Young Stellar Objects (YSOs) in several star-forming regions in the Magellanic Clouds. I exploit the synergy between infrared photometry from the Spitzer SAGE (Surveying the Agents of Galaxy Evolution) legacy programs, near-infrared and optical photometry from ground-based surveys, and HST imaging to characterize young stellar populations. This reveals a variety of Main Sequence Stars and Proto-Stars over a wide range of evolutionary stages. Through SED fitting, I characterize the youngest, embedded, infrared-bright YSOs. Complementary color-Magnitude analysis and isochrone fitting of optical data allows a statistical description of more evolved, unembedded stellar and protostellar populations within these same regions. I examine the early evolution of Magellanic star clusters, including propagating and triggered star formation, and take a step toward characterizing evolutionary timescales for YSOs. In this talk, I present an overview of the project and exemplify the analysis by focusing on NGC 602 in the SMC and Henize 206 in the LMC as examples. The SAGE Project is supported by NASA/Spitzer grant 1275598 and NASA NAG5-12595.

Evolution Under Environmental Stress at Macro- and Microscales

PubMed Central

Nevo, Eviatar

2011-01-01

Environmental stress has played a major role in the evolution of living organisms (Hoffman AA, Parsons PA. 1991. Evolutionary genetics and environmental stress. Oxford: Oxford University Press; Parsons PA. 2005. Environments and evolution: interactions between stress, resource inadequacy, and energetic efficiency. Biol Rev Camb Philos Soc. 80:589–610). This is reflected by the massive and background extinctions in evolutionary time (Nevo E. 1995a. Evolution and extinction. Encyclopedia of Environmental Biology. New York: Academic Press, Inc. 1:717–745). The interaction between organism and environment is central in evolution. Extinction ensues when organisms fail to change and adapt to the constantly altering abiotic and biotic stressful environmental changes as documented in the fossil record. Extreme environmental stress causes extinction but also leads to evolutionary change and the origination of new species adapted to new environments. I will discuss a few of these global, regional, and local stresses based primarily on my own research programs. These examples will include the 1) global regional and local experiment of subterranean mammals; 2) regional experiment of fungal life in the Dead Sea; 3) evolution of wild cereals; 4) “Evolution Canyon”; 5) human brain evolution, and 6) global warming. PMID:21979157

Evolution under environmental stress at macro- and microscales.

PubMed

Nevo, Eviatar

2011-01-01

Environmental stress has played a major role in the evolution of living organisms (Hoffman AA, Parsons PA. 1991. Evolutionary genetics and environmental stress. Oxford: Oxford University Press; Parsons PA. 2005. Environments and evolution: interactions between stress, resource inadequacy, and energetic efficiency. Biol Rev Camb Philos Soc. 80:589-610). This is reflected by the massive and background extinctions in evolutionary time (Nevo E. 1995a. Evolution and extinction. Encyclopedia of Environmental Biology. New York: Academic Press, Inc. 1:717-745). The interaction between organism and environment is central in evolution. Extinction ensues when organisms fail to change and adapt to the constantly altering abiotic and biotic stressful environmental changes as documented in the fossil record. Extreme environmental stress causes extinction but also leads to evolutionary change and the origination of new species adapted to new environments. I will discuss a few of these global, regional, and local stresses based primarily on my own research programs. These examples will include the 1) global regional and local experiment of subterranean mammals; 2) regional experiment of fungal life in the Dead Sea; 3) evolution of wild cereals; 4) "Evolution Canyon"; 5) human brain evolution, and 6) global warming.

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.

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.

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.

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical Society of America.

In vitro evaluation of physiological spiral anastomoses for the arterial switch operation in simple transposition of the great arteries: a first step towards a surgical alternative?

PubMed

Sievers, Hans-Hinrich; Scharfschwerdt, Michael; Putman, Léon M

2015-08-01

The currently most frequently used technique for the arterial switch operation (ASO) in simple transposition of the great arteries (TGA) includes the transposition of the pulmonary artery anterior to the ascending aorta. This arterial arrangement is less anatomical, and although the initial results are excellent, some long-term data are indicating a certain risk of morbidity, encouraging the search for more physiological techniques. As a first step, we studied the feasibility of anatomical spiral anastomoses of the great vessels in vitro. A TGA model was constructed to simulate the different spatial positions of the great arteries followed by ASO with physiological spiral connections of the great arteries. It was possible to perform a physiological spiral connection of the great arteries without tension or torsion when the roots of the great vessels were arranged anterior-posterior and with up to 35° rotation of the aortic root to the right around the pulmonary root. With further rotation of the aorta, patch plasties were required for pulmonary artery elongation. The maximal width of the patch was 5 mm. In this TGA model, it was possible to perform tension- and torsion-free arterial anastomoses for ASO without artificial material, when the aortic root was positioned from 0° up to 35° to the right of the pulmonary root. Evaluation of coronary transfer is the next step. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

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.

One WEEE, many species: lessons from the European experience.

PubMed

Deepali Sinha Khetriwal; Widmer, Rolf; Kuehr, Ruediger; Huisman, Jaco

2011-09-01

Electrical and electronic equipment (EEE) pervades modern lifestyles, but its quick obsolescence is resulting in huge quantities of EEE to be disposed of. This fast-growing waste stream has been recognized for its hazard potential. The European Union's (EU) Waste Electrical and Electronic Equipment (WEEE) Directive was essentially in response to the toxicity of e-waste - to ensure that it was collected and treated in an environmentally sound manner. Since then, the WEEE Directive has expanded its aims to include recovery of valuable resources as a means to reduce raw material extraction. With these objectives in mind, the Directive sets a common minimum legislative framework for all EU member states. However, the transposition of the Directive into national legislations has meant many differences in actual implementation models. There are 27 national transpositions of the Directive with different definitions, provisions and agreements. Each legislation reflects national situations, whether they are geographical considerations, legislative history, the influence of lobby groups and other national priorities. Although this diversity in legislations has meant massive problems in compliance and enforcement, it provides an opportunity to get an insight into the possible operational models of e-waste legislation. Building on the study by the United Nations University commissioned by the European Commission as part of its 2008 Review of the WEEE Directive, the paper identifies some key features of the Directive as well as legislative and operational differences in transposition and implementation in the various members states. The paper discusses the successes and challenges of the Directive and concludes with lessons learnt from the European experience.

Assessing Working Memory in Mild Cognitive Impairment with Serial Order Recall.

PubMed

Emrani, Sheina; Libon, David J; Lamar, Melissa; Price, Catherine C; Jefferson, Angela L; Gifford, Katherine A; Hohman, Timothy J; Nation, Daniel A; Delano-Wood, Lisa; Jak, Amy; Bangen, Katherine J; Bondi, Mark W; Brickman, Adam M; Manly, Jennifer; Swenson, Rodney; Au, Rhoda

2018-01-01

Working memory (WM) is often assessed with serial order tests such as repeating digits backward. In prior dementia research using the Backward Digit Span Test (BDT), only aggregate test performance was examined. The current research tallied primacy/recency effects, out-of-sequence transposition errors, perseverations, and omissions to assess WM deficits in patients with mild cognitive impairment (MCI). Memory clinic patients (n = 66) were classified into three groups: single domain amnestic MCI (aMCI), combined mixed domain/dysexecutive MCI (mixed/dys MCI), and non-MCI where patients did not meet criteria for MCI. Serial order/WM ability was assessed by asking participants to repeat 7 trials of five digits backwards. Serial order position accuracy, transposition errors, perseverations, and omission errors were tallied. A 3 (group)×5 (serial position) repeated measures ANOVA yielded a significant group×trial interaction. Follow-up analyses found attenuation of the recency effect for mixed/dys MCI patients. Mixed/dys MCI patients scored lower than non-MCI patients for serial position 3 (p < 0.003) serial position 4 (p < 0.002); and lower than both group for serial position 5 (recency; p < 0.002). Mixed/dys MCI patients also produced more transposition errors than both groups (p < 0.010); and more omissions (p < 0.020), and perseverations errors (p < 0.018) than non-MCI patients. The attenuation of a recency effect using serial order parameters obtained from the BDT may provide a useful operational definition as well as additional diagnostic information regarding working memory deficits in MCI.

Left Ventricular Retraining and Late Arterial Switch for D-Transposition of the Great Arteries.

PubMed

Watanabe, Naruhito; Mainwaring, Richard D; Carrillo, Sergio A; Lui, George K; Reddy, V Mohan; Hanley, Frank L

2015-05-01

For many decades, patients with d-transposition of the great arteries underwent an atrial switch procedure. Although many of these patients have continued to do well, a subset experience profound right ventricular failure. Some may be candidates for left ventricular (LV) retraining and late arterial switch. The purpose of this study was to review our experience with LV retraining and late arterial switch. This was a retrospective review of 32 patients with d-transposition. Thirty patients underwent a previous atrial switch and subsequently experienced right ventricular failure, whereas 2 presented late (8 months and 6 years) without previous intervention. The median age at the time of enrollment in this program was 15 years. Seven patients proceeded directly to late arterial switch owing to systemic LV pressures. The remaining 25 underwent a pulmonary artery band for LV retraining. Twenty of the 32 (63%) patients enrolled in this program were able to undergo a late arterial switch. There were 2 operative mortalities (10%). Two additional patients survived surgery but died in the early outpatient time period. There has been no late mortality after the arterial switch with a median follow-up of 5 years. Twelve patients underwent one or more pulmonary artery band procedures without evidence of effective LV retraining. There have been 2 early and 3 late (42%) deaths in this subgroup. The outcomes after arterial switch are encouraging and suggest that LV retraining and late arterial switch provide a viable option for this complex group of patients. Copyright © 2015 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Effect of Orthographic Processes on Letter Identity and Letter-Position Encoding in Dyslexic Children

PubMed Central

Reilhac, Caroline; Jucla, Mélanie; Iannuzzi, Stéphanie; Valdois, Sylviane; Démonet, Jean-François

2012-01-01

The ability to identify letters and encode their position is a crucial step of the word recognition process. However and despite their word identification problem, the ability of dyslexic children to encode letter identity and letter-position within strings was not systematically investigated. This study aimed at filling this gap and further explored how letter identity and letter-position encoding is modulated by letter context in developmental dyslexia. For this purpose, a letter-string comparison task was administered to French dyslexic children and two chronological age (CA) and reading age (RA)-matched control groups. Children had to judge whether two successively and briefly presented four-letter strings were identical or different. Letter-position and letter identity were manipulated through the transposition (e.g., RTGM vs. RMGT) or substitution of two letters (e.g., TSHF vs. TGHD). Non-words, pseudo-words, and words were used as stimuli to investigate sub-lexical and lexical effects on letter encoding. Dyslexic children showed both substitution and transposition detection problems relative to CA-controls. A substitution advantage over transpositions was only found for words in dyslexic children whereas it extended to pseudo-words in RA-controls and to all type of items in CA-controls. Letters were better identified in the dyslexic group when belonging to orthographically familiar strings. Letter-position encoding was very impaired in dyslexic children who did not show any word context effect in contrast to CA-controls. Overall, the current findings point to a strong letter identity and letter-position encoding disorder in developmental dyslexia. PMID:22661961

Evolution of Dengue Virus Type 3 Genotype III in Venezuela: Diversification, Rates and Population Dynamics

PubMed Central

2010-01-01

Background Dengue virus (DENV) is a member of the genus Flavivirus of the family Flaviviridae. DENV are comprised of four distinct serotypes (DENV-1 through DENV-4) and each serotype can be divided in different genotypes. Currently, there is a dramatic emergence of DENV-3 genotype III in Latin America. Nevertheless, we still have an incomplete understanding of the evolutionary forces underlying the evolution of this genotype in this region of the world. In order to gain insight into the degree of genetic variability, rates and patterns of evolution of this genotype in Venezuela and the South American region, phylogenetic analysis, based on a large number (n = 119) of envelope gene sequences from DENV-3 genotype III strains isolated in Venezuela from 2001 to 2008, were performed. Results Phylogenetic analysis revealed an in situ evolution of DENV-3 genotype III following its introduction in the Latin American region, where three different genetic clusters (A to C) can be observed among the DENV-3 genotype III strains circulating in this region. Bayesian coalescent inference analyses revealed an evolutionary rate of 8.48 × 10-4 substitutions/site/year (s/s/y) for strains of cluster A, composed entirely of strains isolated in Venezuela. Amino acid substitution at position 329 of domain III of the E protein (A→V) was found in almost all E proteins from Cluster A strains. Conclusions A significant evolutionary change between DENV-3 genotype III strains that circulated in the initial years of the introduction in the continent and strains isolated in the Latin American region in recent years was observed. The presence of DENV-3 genotype III strains belonging to different clusters was observed in Venezuela, revealing several introduction events into this country. The evolutionary rate found for Cluster A strains circulating in Venezuela is similar to the others previously established for this genotype in other regions of the world. This suggests a lack of correlation among DENV genotype III substitution rate and ecological pattern of virus spread. PMID:21087501

Evolutionary signals of selection on cognition from the great tit genome and methylome

PubMed Central

Laine, Veronika N.; Gossmann, Toni I.; Schachtschneider, Kyle M.; Garroway, Colin J.; Madsen, Ole; Verhoeven, Koen J. F.; de Jager, Victor; Megens, Hendrik-Jan; Warren, Wesley C.; Minx, Patrick; Crooijmans, Richard P. M. A.; Corcoran, Pádraic; Adriaensen, Frank; Belda, Eduardo; Bushuev, Andrey; Cichon, Mariusz; Charmantier, Anne; Dingemanse, Niels; Doligez, Blandine; Eeva, Tapio; Erikstad, Kjell Einar; Fedorov, Slava; Hau, Michaela; Hille, Sabine; Hinde, Camilla; Kempenaers, Bart; Kerimov, Anvar; Krist, Milos; Mand, Raivo; Matthysen, Erik; Nager, Reudi; Norte, Claudia; Orell, Markku; Richner, Heinz; Slagsvold, Tore; Tilgar, Vallo; Tinbergen, Joost; Torok, Janos; Tschirren, Barbara; Yuta, Tera; Sheldon, Ben C.; Slate, Jon; Zeng, Kai; van Oers, Kees; Visser, Marcel E.; Groenen, Martien A. M.

2016-01-01

For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species. PMID:26805030

Deciding to Cooperate in Northern Ghana: Trust as an Evolutionary Constraint Across Cultural Diversity.

PubMed

Acedo-Carmona, Cristina; Gomila, Antoni

2015-11-27

The upper-east and northern regions of Ghana offers a unique opportunity to study the influence of evolutionary social dynamics in making cooperation possible, despite cultural differences. These regions are occupied by several distinct ethnic groups, in interaction, such as the Kussasi, Mamprusi, Bimoba, Konkomba, and Fulani. We will report our fieldwork related to how cooperation takes places there, both within each group and among people from the different groups. Methods included personal networks of cooperation (ego networks), interviews and analysis of group contexts. The most important result is that, while each ethnic group may differ in terms of family and clan structure, a similar pattern can be found in all of them, of cooperation structured around small groups of trust-based close relationships. The study suggests that habitual decisions about cooperation are not strategic or self-interested, but instead are based on unconscious processes sustained by the emotional bonds of trust. These kind of emotional bonds are claimed to be relevant from an evolutionary point of view.

The scope and strength of sex-specific selection in genome evolution.

PubMed

Wright, A E; Mank, J E

2013-09-01

Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Molecular evolutionary rates are not correlated with temperature and latitude in Squamata: an exception to the metabolic theory of ecology?

PubMed

Rolland, Jonathan; Loiseau, Oriane; Romiguier, Jonathan; Salamin, Nicolas

2016-05-20

The metabolic theory of ecology stipulates that molecular evolutionary rates should correlate with temperature and latitude in ectothermic organisms. Previous studies have shown that most groups of vertebrates, such as amphibians, turtles and even endothermic mammals, have higher molecular evolutionary rates in regions where temperature is high. However, the association between molecular evolutionary rates and temperature or latitude has never been tested in Squamata. We used a large dataset including the spatial distributions and environmental variables for 1,651 species of Squamata and compared the contrast of the rates of molecular evolution with the contrast of temperature and latitude between sister species. Using major axis regressions and a new algorithm to choose independent sister species pairs, we found that temperature and absolute latitude were not associated with molecular evolutionary rates. This absence of association in such a diverse ectothermic group questions the mechanisms explaining current pattern of species diversity in Squamata and challenges the presupposed universality of the metabolic theory of ecology.

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.

Should patients with esophageal atresia be submitted to esophageal substitution before they start walking?

PubMed

Tannuri, U; Tannuri, A C A

2011-01-01

Esophagocoloplasty and gastric transposition are two major methods for esophageal substitution in children with esophageal atresia, and there is broad agreement that these operations should not be performed before the children start walking. However, there are some reported advantages of performing such operations in the first months of life or in the neonatal period. In this study, we compared our experience with esophageal substitution procedures performed in walking children with esophageal atresia, with the outcomes of children who had the operation before the third month of life reported in the literature. The purpose of this study was to establish if we have to wait until the children start walking before indicating the esophageal replacement procedure. From February 1978 to October 2009, 129 children with esophageal atresia underwent esophageal replacement in our hospital (99 colonic interpositions and 30 gastric transpositions). The records of these patients were reviewed for data regarding demographics, complications (leaks, graft failures, strictures, and graft torsion), and mortality and compared with those reported in the two main articles on esophageal replacement in the neonatal period or in patients less than 3 months of age. The main complication of our casuistic was cervical anastomosis leakage, which sealed spontaneously in all except in four patients. One patient of the esophagocoloplasty group developed graft necrosis and three patients in the gastric transposition group had gastric outlet obstruction, secondary to axial torsion of the stomach placed in the retrosternal space. The long-term outcome of the patients in both groups was considered good to excellent in terms of normal weight gain, absence of dysphagia, and other gastrointestinal symptoms. The comparisons of the main complications and mortality rates in walking children with esophageal substitutions performed in the first months of life showed that the incidences of cervical anastomotic leaks and graft failures were similar, but mortality rate in the first few months of life was significantly greater than that observed in our group of patients (P= 0.001). Based on the comparison of our results with those of published series, we conclude that the recommendation of performing esophagocoloplasty or total gastric transposition in children with esophageal atresia after they start walking is still valid. © 2010 Copyright the Authors. Journal compilation © 2010, Wiley Periodicals, Inc. and the International Society for Diseases of the Esophagus.

Lineage-specific evolutionary rate in plants: Contributions of a screening for Cereus (Cactaceae).

PubMed

Romeiro-Brito, Monique; Moraes, Evandro M; Taylor, Nigel P; Zappi, Daniela C; Franco, Fernando F

2016-01-01

Predictable chloroplast DNA (cpDNA) sequences have been listed for the shallowest taxonomic studies in plants. We investigated whether plastid regions that vary between closely allied species could be applied for intraspecific studies and compared the variation of these plastid segments with two nuclear regions. We screened 16 plastid and two nuclear intronic regions for species of the genus Cereus (Cactaceae) at three hierarchical levels (species from different clades, species of the same clade, and allopatric populations). Ten plastid regions presented interspecific variation, and six of them showed variation at the intraspecific level. The two nuclear regions showed both inter- and intraspecific variation, and in general they showed higher levels of variability in almost all hierarchical levels than the plastid segments. Our data suggest no correspondence between variation of plastid regions at the interspecific and intraspecific level, probably due to lineage-specific variation in cpDNA, which appears to have less effect in nuclear data. Despite the heterogeneity in evolutionary rates of cpDNA, we highlight three plastid segments that may be considered in initial screenings in plant phylogeographic studies.

Deciphering evolutionary strata on plant sex chromosomes and fungal mating-type chromosomes through compositional segmentation.

PubMed

Pandey, Ravi S; Azad, Rajeev K

2016-03-01

Sex chromosomes have evolved from a pair of homologous autosomes which differentiated into sex determination systems, such as XY or ZW system, as a consequence of successive recombination suppression between the gametologous chromosomes. Identifying the regions of recombination suppression, namely, the "evolutionary strata", is central to understanding the history and dynamics of sex chromosome evolution. Evolution of sex chromosomes as a consequence of serial recombination suppressions is well-studied for mammals and birds, but not for plants, although 48 dioecious plants have already been reported. Only two plants Silene latifolia and papaya have been studied until now for the presence of evolutionary strata on their X chromosomes, made possible by the sequencing of sex-linked genes on both the X and Y chromosomes, which is a requirement of all current methods that determine stratum structure based on the comparison of gametologous sex chromosomes. To circumvent this limitation and detect strata even if only the sequence of sex chromosome in the homogametic sex (i.e. X or Z chromosome) is available, we have developed an integrated segmentation and clustering method. In application to gene sequences on the papaya X chromosome and protein-coding sequences on the S. latifolia X chromosome, our method could decipher all known evolutionary strata, as reported by previous studies. Our method, after validating on known strata on the papaya and S. latifolia X chromosome, was applied to the chromosome 19 of Populus trichocarpa, an incipient sex chromosome, deciphering two, yet unknown, evolutionary strata. In addition, we applied this approach to the recently sequenced sex chromosome V of the brown alga Ectocarpus sp. that has a haploid sex determination system (UV system) recovering the sex determining and pseudoautosomal regions, and then to the mating-type chromosomes of an anther-smut fungus Microbotryum lychnidis-dioicae predicting five strata in the non-recombining region of both the chromosomes.

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes

PubMed Central

2017-01-01

Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity. PMID:28796803

Recombinant transfer in the basic genome of E. coli

DOE PAGES

Dixit, Purushottam; Studier, F. William; Pang, Tin Yau; ...

2015-07-07

An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly betweenmore » genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kbp. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. As a result, most recombinant transfers seem likely to be due to generalized transduction by co-evolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.« less

Recombinant transfer in the basic genome of E. coli

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

Dixit, Purushottam; Studier, F. William; Pang, Tin Yau

An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly betweenmore » genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kbp. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. As a result, most recombinant transfers seem likely to be due to generalized transduction by co-evolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.« less

Long Distance Dispersal of Zooplankton Endemic to Isolated Mountaintops - an Example of an Ecological Process Operating on an Evolutionary Time Scale

PubMed Central

Vanschoenwinkel, Bram; Mergeay, Joachim; Pinceel, Tom; Waterkeyn, Aline; Vandewaerde, Hanne; Seaman, Maitland; Brendonck, Luc

2011-01-01

Recent findings suggest a convergence of time scales between ecological and evolutionary processes which is usually explained in terms of rapid micro evolution resulting in evolution on ecological time scales. A similar convergence, however, can also emerge when slow ecological processes take place on evolutionary time scales. A good example of such a slow ecological process is the colonization of remote aquatic habitats by passively dispersed zooplankton. Using variation at the protein coding mitochondrial COI gene, we investigated the balance between mutation and migration as drivers of genetic diversity in two Branchipodopsis fairy shrimp species (Crustacea, Anostraca) endemic to remote temporary rock pool clusters at the summit of isolated mountaintops in central South Africa. We showed that both species colonized the region almost simultaneously c. 0.8 My ago, but exhibit contrasting patterns of regional genetic diversity and demographic history. The haplotype network of the common B. cf. wolfi showed clear evidence of 11 long distance dispersal events (up to 140 km) with five haplotypes that are shared among distant inselbergs, as well as some more spatially isolated derivates. Similar patterns were not observed for B. drakensbergensis presumably since this rarer species experienced a genetic bottleneck. We conclude that the observed genetic patterns reflect rare historic colonization events rather than frequent ongoing gene flow. Moreover, the high regional haplotype diversity combined with a high degree of haplotype endemicity indicates that evolutionary- (mutation) and ecological (migration) processes in this system operate on similar time scales. PMID:22102865

Pathological findings in dicephalus dipus dibrachius: implications for mechanisms in two pairs of lateral conjoined twins.

PubMed

Itoh, K; Imai, Y; Obayashi, C; Hayashi, Y; Hanioka, K; Itoh, H

1993-06-01

The anatomical and pathological features of two pairs of dicephalic conjoined twins (case 1 and 2) are described. Both twins showed duplicitas lateralis representing diprosopus dipus dibrachius. There were two complete heads on two necks, one thorax, one abdomen and externally normal two arms and two legs. Case 1 showed dicephalus with anencephaly, two vertebral columns and two spinal cords, which converged from the thoracic region distally. The esophagus, stomachs and partial small intestines were duplicated, which fused at yolk sac (with Meckel's diverticulum). The heart was incompletely fused. The lungs and trachea were doubled. Two spinal cords were fused from the thoracic region caudally and showed myelomeningocele and Arnold-Chiari malformation in case 2. Two larynxes and two thracheas connected with the incompletely fused three lobes of lungs. The conjoined lungs were hypoplastic. The heart was single, showing ventral septal defect, transposition of great arteries, two cuspid aortic valves and preductal aortic coarctation. The duplicated esophagi were conjoined in Y-shape and single stomach, duodenum, intestine and colon were found. There were pairs of kidneys, adrenal glands and ureters and single female genitalia in both cases. These findings indicate that the craniocaudal paleoaxes were separated in the cranial region and converted or fused under the thoracic region like a Y-shape. Further development defects and deformations might be important factors to form malformations in these case.

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

Turnover of Sex Chromosomes in the Stickleback Fishes (Gasterosteidae)

PubMed Central

Ross, Joseph A.; Urton, James R.; Boland, Jessica; Shapiro, Michael D.; Peichel, Catherine L.

2009-01-01

Diverse sex-chromosome systems are found in vertebrates, particularly in teleost fishes, where different systems can be found in closely related species. Several mechanisms have been proposed for the rapid turnover of sex chromosomes, including the transposition of an existing sex-determination gene, the appearance of a new sex-determination gene on an autosome, and fusions between sex chromosomes and autosomes. To better understand these evolutionary transitions, a detailed comparison of sex chromosomes between closely related species is essential. Here, we used genetic mapping and molecular cytogenetics to characterize the sex-chromosome systems of multiple stickleback species (Gasterosteidae). Previously, we demonstrated that male threespine stickleback fish (Gasterosteus aculeatus) have a heteromorphic XY pair corresponding to linkage group (LG) 19. In this study, we found that the ninespine stickleback (Pungitius pungitius) has a heteromorphic XY pair corresponding to LG12. In black-spotted stickleback (G. wheatlandi) males, one copy of LG12 has fused to the LG19-derived Y chromosome, giving rise to an X1X2Y sex-determination system. In contrast, neither LG12 nor LG19 is linked to sex in two other species: the brook stickleback (Culaea inconstans) and the fourspine stickleback (Apeltes quadracus). However, we confirmed the existence of a previously reported heteromorphic ZW sex-chromosome pair in the fourspine stickleback. The sex-chromosome diversity that we have uncovered in sticklebacks provides a rich comparative resource for understanding the mechanisms that underlie the rapid turnover of sex-chromosome systems. PMID:19229325

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

Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria

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

Zhou Fengfeng; Tran Thao; Xu Ying

2008-01-25

Miniature inverted-repeat transposable elements (MITEs) were first identified in plants and exerted extensive proliferations throughout eukaryotic and archaeal genomes. But very few MITEs have been characterized in bacteria. We identified a novel MITE, called Nezha, in cyanobacteria Anabaena variabilis ATCC 29413 and Nostoc sp. PCC 7120. Nezha, like most previously known MITEs in other organisms, is small in size, non-coding, carrying TIR and DR signals, and of potential to form a stable RNA secondary structure, and it tends to insert into A+T-rich regions. Recent transpositions of Nezha were observed in A. variabilis ATCC 29413 and Nostoc sp. PCC 7120, respectively.more » Nezha might have proliferated recently with aid from the transposase encoded by ISNpu3-like elements. A possible horizontal transfer event of Nezha from cyanobacteria to Polaromonas JS666 is also observed.« less

Evolution of brain region volumes during artificial selection for relative brain size.

PubMed

Kotrschal, Alexander; Zeng, Hong-Li; van der Bijl, Wouter; Öhman-Mägi, Caroline; Kotrschal, Kurt; Pelckmans, Kristiaan; Kolm, Niclas

2017-12-01

The vertebrate brain shows an extremely conserved layout across taxa. Still, the relative sizes of separate brain regions vary markedly between species. One interesting pattern is that larger brains seem associated with increased relative sizes only of certain brain regions, for instance telencephalon and cerebellum. Till now, the evolutionary association between separate brain regions and overall brain size is based on comparative evidence and remains experimentally untested. Here, we test the evolutionary response of brain regions to directional selection on brain size in guppies (Poecilia reticulata) selected for large and small relative brain size. In these animals, artificial selection led to a fast response in relative brain size, while body size remained unchanged. We use microcomputer tomography to investigate how the volumes of 11 main brain regions respond to selection for larger versus smaller brains. We found no differences in relative brain region volumes between large- and small-brained animals and only minor sex-specific variation. Also, selection did not change allometric scaling between brain and brain region sizes. Our results suggest that brain regions respond similarly to strong directional selection on relative brain size, which indicates that brain anatomy variation in contemporary species most likely stem from direct selection on key regions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Understanding Pressure: Didactical Transpositions and Pupils' Conceptions.

ERIC Educational Resources Information Center

Kariotogloy, Petros; And Others

1990-01-01

Described are features of a theoretical model for fluid pressure. Analyzes six introductory physics textbooks based on an introduction and meaning of the pressure concept; characteristics of pressure; and liquid as a pressure transmitter. Presents three models of pupils' conceptions. (YP)

Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundary

USDA-ARS?s Scientific Manuscript database

Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation...

LINEs Contribute to the Origins of Middle Bodies of SINEs besides 3′ Tails

PubMed Central

2018-01-01

Abstract Short interspersed elements (SINEs), which are nonautonomous transposable elements, require the transposition machinery of long interspersed elements (LINEs) to mobilize. SINEs are composed of two or more independently originating parts. The 5′ region is called the “head” and is derived mainly from small RNAs, and the 3′ region (“tail”) originates from the 3′ region of LINEs and is responsible for being recognized by counterpart LINE proteins. The origin of the middle “body” of SINEs is enigmatic, although significant sequence similarities among SINEs from very diverse species have been observed. Here, a systematic analysis of the similarities among SINEs and LINEs deposited on Repbase, a comprehensive database of eukaryotic repeat sequences was performed. Three primary findings are described: 1) The 5′ regions of only two clades of LINEs, RTE and Vingi, were revealed to have contributed to the middle parts of SINEs; 2) The linkage of the 5′ and 3′ parts of LINEs can be lost due to occasional tail exchange of SINEs; and 3) The previously proposed Ceph-domain was revealed to be a fusion of a CORE-domain and a 5′ part of RTE clade of LINE. Based on these findings, a hypothesis that the 5′ parts of bipartite nonautonomous LINEs, which possess only the 5′ and 3′ regions of the original LINEs, can contribute to the undefined middle part of SINEs is proposed. PMID:29325122

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.

Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain.

PubMed

Moreno, I M; Malpica, J M; Díaz-Pendón, J A; Moriones, E; Fraile, A; García-Arenal, F

2004-01-05

The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection.

Evolutionary Characteristics of Missing Proteins: Insights into the Evolution of Human Chromosomes Related to Missing-Protein-Encoding Genes.

PubMed

Xu, Aishi; Li, Guang; Yang, Dong; Wu, Songfeng; Ouyang, Hongsheng; Xu, Ping; He, Fuchu

2015-12-04

Although the "missing protein" is a temporary concept in C-HPP, the biological information for their "missing" could be an important clue in evolutionary studies. Here we classified missing-protein-encoding genes into two groups, the genes encoding PE2 proteins (with transcript evidence) and the genes encoding PE3/4 proteins (with no transcript evidence). These missing-protein-encoding genes distribute unevenly among different chromosomes, chromosomal regions, or gene clusters. In the view of evolutionary features, PE3/4 genes tend to be young, spreading at the nonhomology chromosomal regions and evolving at higher rates. Interestingly, there is a higher proportion of singletons in PE3/4 genes than the proportion of singletons in all genes (background) and OTCSGs (organ, tissue, cell type-specific genes). More importantly, most of the paralogous PE3/4 genes belong to the newly duplicated members of the paralogous gene groups, which mainly contribute to special biological functions, such as "smell perception". These functions are heavily restricted into specific type of cells, tissues, or specific developmental stages, acting as the new functional requirements that facilitated the emergence of the missing-protein-encoding genes during evolution. In addition, the criteria for the extremely special physical-chemical proteins were first set up based on the properties of PE2 proteins, and the evolutionary characteristics of those proteins were explored. Overall, the evolutionary analyses of missing-protein-encoding genes are expected to be highly instructive for proteomics and functional studies in the future.

Global loss of avian evolutionary uniqueness in urban areas.

PubMed

Ibáñez-Álamo, Juan Diego; Rubio, Enrique; Benedetti, Yanina; Morelli, Federico

2017-08-01

Urbanization, one of the most important anthropogenic impacts on Earth, is rapidly expanding worldwide. This expansion of urban land-covered areas is known to significantly reduce different components of biodiversity. However, the global evidence for this effect is mainly focused on a single diversity measure (species richness) with a few local or regional studies also supporting reductions in functional diversity. We have used birds, an important ecological group that has been used as surrogate for other animals, to investigate the hypothesis that urbanization reduces the global taxonomical and/or evolutionary diversity. We have also explored whether there is evidence supporting that urban bird communities are evolutionarily homogenized worldwide in comparison with nonurban ones by means of using evolutionary distinctiveness (how unique are the species) of bird communities. To our knowledge, this is the first attempt to quantify the effect of urbanization in more than one single diversity measure as well as the first time to look for associations between urbanization and phylogenetic diversity at a large spatial scale. Our findings show a strong and globally consistent reduction in taxonomic diversity in urban areas, which is also synchronized with the evolutionary homogenization of urban bird communities. Despite our general patterns, we found some regional differences in the intensity of the effect of cities on bird species richness or evolutionary distinctiveness, suggesting that conservation efforts should be adapted locally. Our findings might be useful for conservationists and policymakers to minimize the impact of urban development on Earth's biodiversity and help design more realistic conservation strategies. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Evolutionary mechanisms shaping the genetic population structure of coastal fish: insight from populations of Coilia nasus in Northwestern Pacific.

PubMed

Gao, Tianxiang; Wan, Zhenzhen; Song, Na; Zhang, Xiumei; Han, Zhiqiang

2014-12-01

A number of evolutionary mechanisms have been suggested for generating significant genetic structuring among marine fish populations in Northwestern Pacific. We used mtDNA control region to assess the factors in shaping the genetic structure of Japanese grenadier anchovy, Coilia nasus, an anadromous and estuarine coastal species, in Northwestern Pacific. Sixty seven individuals from four locations in Northwestern Pacific were sequenced for mitochondrial control region, detecting 61 haplotypes. The length of amplified control region varied from 677 to 754 bp. This length variability was due to the presence of varying numbers of a 38-bp tandemly repeated sequence. Two distinct lineages were detected, which might have diverged during Pleistocene low sea levels. There were strong differences in the geographical distribution of the two lineages. Analyses of molecular variance and the population statistic ΦST revealed significant genetic structure between China and Ariake Bay populations. Based on the frequency distribution of tandem repeat units, significant genetic differentiation was also detected between China and Ariake Bay populations. Isolation by distance seems to be the main factor driving present genetic structuring of C. nasus populations, indicating coastal dispersal pattern in this coastal species. Such an evolutionary process agrees well with some of the biological features characterizing this species.

Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.

PubMed

Ruan, Jiangxing; Cheng, Jian; Zhang, Tongcun; Jiang, Huifeng

2017-01-01

Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.

Mathematical Modelling as a Professional Task

ERIC Educational Resources Information Center

Frejd, Peter; Bergsten, Christer

2016-01-01

Educational research literature on mathematical modelling is extensive. However, not much attention has been paid to empirical investigations of its scholarly knowledge from the perspective of didactic transposition processes. This paper reports from an interview study of mathematical modelling activities involving nine professional model…

Evolutionary genomics and HIV restriction factors.

PubMed

Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio

2015-03-01

To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

PubMed

Vierstra, Jeff; Rynes, Eric; Sandstrom, Richard; Zhang, Miaohua; Canfield, Theresa; Hansen, R Scott; Stehling-Sun, Sandra; Sabo, Peter J; Byron, Rachel; Humbert, Richard; Thurman, Robert E; Johnson, Audra K; Vong, Shinny; Lee, Kristen; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Giste, Erika; Haugen, Eric; Dunn, Douglas; Wilken, Matthew S; Josefowicz, Steven; Samstein, Robert; Chang, Kai-Hsin; Eichler, Evan E; De Bruijn, Marella; Reh, Thomas A; Skoultchi, Arthur; Rudensky, Alexander; Orkin, Stuart H; Papayannopoulou, Thalia; Treuting, Piper M; Selleri, Licia; Kaul, Rajinder; Groudine, Mark; Bender, M A; Stamatoyannopoulos, John A

2014-11-21

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes. Copyright © 2014, American Association for the Advancement of Science.

Incorporating evolutionary processes into population viability models.

PubMed

Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

2015-06-01

We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

Arctic biodiversity: Increasing richness accompanies shrinking refugia for a cold-associated tundra fauna

USGS Publications Warehouse

Hope, Andrew G.; Waltari, Eric; Malaney, Jason L.; Payer, David C.; Cook, J.A.; Talbot, Sandra L.

2015-01-01

As ancestral biodiversity responded dynamically to late-Quaternary climate changes, so are extant organisms responding to the warming trajectory of the Anthropocene. Ecological predictive modeling, statistical hypothesis tests, and genetic signatures of demographic change can provide a powerful integrated toolset for investigating these biodiversity responses to climate change, and relative resiliency across different communities. Within the biotic province of Beringia, we analyzed specimen localities and DNA sequences from 28 mammal species associated with boreal forest and Arctic tundra biomes to assess both historical distributional and evolutionary responses and then forecasted future changes based on statistical assessments of past and present trajectories, and quantified distributional and demographic changes in relation to major management regions within the study area. We addressed three sets of hypotheses associated with aspects of methodological, biological, and socio-political importance by asking (1) what is the consistency among implications of predicted changes based on the results of both ecological and evolutionary analyses; (2) what are the ecological and evolutionary implications of climate change considering either total regional diversity or distinct communities associated with major biomes; and (3) are there differences in management implications across regions? Our results indicate increasing Arctic richness through time that highlights a potential state shift across the Arctic landscape. However, within distinct ecological communities, we found a predicted decline in the range and effective population size of tundra species into several discrete refugial areas. Consistency in results based on a combination of both ecological and evolutionary approaches demonstrates increased statistical confidence by applying cross-discipline comparative analyses to conservation of biodiversity, particularly considering variable management regimes that seek to balance sustainable ecosystems with other anthropogenic values. Refugial areas for cold-adapted taxa appear to be persistent across both warm and cold climate phases and although fragmented, constitute vital regions for persistence of Arctic mammals.

Geomagnetic Navigation of Autonomous Underwater Vehicle Based on Multi-objective Evolutionary Algorithm.

PubMed

Li, Hong; Liu, Mingyong; Zhang, Feihu

2017-01-01

This paper presents a multi-objective evolutionary algorithm of bio-inspired geomagnetic navigation for Autonomous Underwater Vehicle (AUV). Inspired by the biological navigation behavior, the solution was proposed without using a priori information, simply by magnetotaxis searching. However, the existence of the geomagnetic anomalies has significant influence on the geomagnetic navigation system, which often disrupts the distribution of the geomagnetic field. An extreme value region may easily appear in abnormal regions, which makes AUV lost in the navigation phase. This paper proposes an improved bio-inspired algorithm with behavior constraints, for sake of making AUV escape from the abnormal region. First, the navigation problem is considered as the optimization problem. Second, the environmental monitoring operator is introduced, to determine whether the algorithm falls into the geomagnetic anomaly region. Then, the behavior constraint operator is employed to get out of the abnormal region. Finally, the termination condition is triggered. Compared to the state-of- the-art, the proposed approach effectively overcomes the disturbance of the geomagnetic abnormal. The simulation result demonstrates the reliability and feasibility of the proposed approach in complex environments.

Geomagnetic Navigation of Autonomous Underwater Vehicle Based on Multi-objective Evolutionary Algorithm

PubMed Central

Li, Hong; Liu, Mingyong; Zhang, Feihu

2017-01-01

This paper presents a multi-objective evolutionary algorithm of bio-inspired geomagnetic navigation for Autonomous Underwater Vehicle (AUV). Inspired by the biological navigation behavior, the solution was proposed without using a priori information, simply by magnetotaxis searching. However, the existence of the geomagnetic anomalies has significant influence on the geomagnetic navigation system, which often disrupts the distribution of the geomagnetic field. An extreme value region may easily appear in abnormal regions, which makes AUV lost in the navigation phase. This paper proposes an improved bio-inspired algorithm with behavior constraints, for sake of making AUV escape from the abnormal region. First, the navigation problem is considered as the optimization problem. Second, the environmental monitoring operator is introduced, to determine whether the algorithm falls into the geomagnetic anomaly region. Then, the behavior constraint operator is employed to get out of the abnormal region. Finally, the termination condition is triggered. Compared to the state-of- the-art, the proposed approach effectively overcomes the disturbance of the geomagnetic abnormal. The simulation result demonstrates the reliability and feasibility of the proposed approach in complex environments. PMID:28747884

Implant and clinical characteristics for pediatric and congenital heart patients in the national cardiovascular data registry implantable cardioverter defibrillator registry.

PubMed

Jordan, Christopher P; Freedenberg, Vicki; Wang, Yongfei; Curtis, Jeptha P; Gleva, Marye J; Berul, Charles I

2014-12-01

In 2010, the National Cardiovascular Data Registry enhanced pediatric, nonatherosclerotic structural heart disease and congenital heart disease (CHD) data collection. This report characterizes CHD and pediatric patients undergoing implantable cardioverter defibrillator implantation. In this article, we report implantable cardioverter defibrillator procedures (April 2010 to December 2012) in the registry for 2 cohorts: (1) all patients with CHD (atrial septal defect, ventricular septal defect, tetralogy of Fallot, Ebstein anomaly, transposition of the great vessels, and common ventricle) and (2) patients <21 years. We evaluated indications and characteristics to include transvenous and nontransvenous lead implants, CHD type, and New York Heart Association class. There were 3139 CHD procedures, 1601 for patients <21 years and 126 for CHD <21 years. Implantable cardioverter defibrillator indications for patients with CHD were primary prevention in 1943 (61.9%) and secondary prevention in 1107 (35.2%). Pediatric patients had 935 (58.4%) primary prevention and 588 (36.7%) secondary prevention devices. Primary prevention had higher New York Heart Association class. Nontransvenous age (35.9 ± 23.2 versus 40.1 ± 24.6 years; P=0.05) and nontransvenous height (167.1 ± 18.9 cm; range, 53-193 cm versus 170.4 ± 13.1 cm; range, 61-203 cm; P<0.01) were lower than for transvenous patients. CHD and pediatrics had similar rates of transvenous (97%) and nontransvenous (3%) leads and did not differ from the overall registry. Transposition of the great vessels and common ventricle had higher rates of nontransvenous leads. Primary prevention exceeds secondary prevention for CHD and pediatrics. Nontransvenous lead patients were younger, with higher rates of transposition of the great vessels and common ventricle patients compared with transvenous lead patients. © 2014 American Heart Association, Inc.

Coronary Events and Anatomy After Arterial Switch Operation for Transposition of the Great Arteries: Detection by 16-Row Multislice Computed Tomography Angiography in Pediatric Patients

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

Oztunc, Funda, E-mail: foztunc@yahoo.com; Baris, Safa, E-mail: safabaris@hotmail.co; Adaletli, Ibrahim, E-mail: iadaletli@yahoo.com

2009-03-15

The purpose of this study was to evaluate the feasibility of multislice computed tomographic (MSCT) angiography as a noninvasive method for detecting ostial, proximal, and middle segment coronary stenosis or occlusion and anatomy in patients with transposition of the great arteries who had undergone arterial switch operation (ASO). Sixteen-detector-row MSCT angiography was performed in 16 patients treated with ASO for transposition of the great arteries. The median age was 10.3 years (range, 6.2-16.3 years). Sixteen-detector-row MSCT angiography was performed in 16 patients who had undergone ASO. CT imaging was performed in the craniocaudal direction from 2 cm above the carinamore » up to the heart basis. Noninvasive assessment of coronary artery stenosis and anatomy were investigated by MSCT angiography. Two patients were excluded from the study because of artifacts. Of 14 evaluated patients, 1 patient had ostial stenosis (7.1%). A coronary artery anatomy variant was present in six patients: left main artery (LMA) and right coronary artery (RCA) originating from the right sinus as a single orifice (n = 2); left circumflex artery (LCX) originating from the RCA (n = 1); LMA and RCA, after branching to the LCX, originating separately from the right sinus (n = 1); and LMA (n = 1) and left anterior descending artery (LADA; n = 1) originating directly from the right sinus. Intramural bridging in the LAD (n = 2) was detected. Five patients were normal. In conclusion, MSCT angiography, as a noninvasive, feasible technique for assessing coronary stenosis or occlusion and anatomy, can be used in the follow-up of patients who have undergone ASO.« less

Factors Influencing Outcomes after Ulnar Nerve Stability-Based Surgery for Cubital Tunnel Syndrome: A Prospective Cohort Study

PubMed Central

Kang, Ho Jung; Oh, Won Taek; Koh, Il Hyun; Kim, Sungmin

2016-01-01

Purpose Simple decompression of the ulnar nerve has outcomes similar to anterior transposition for cubital tunnel syndrome; however, there is no consensus on the proper technique for patients with an unstable ulnar nerve. We hypothesized that 1) simple decompression or anterior ulnar nerve transposition, depending on nerve stability, would be effective for cubital tunnel syndrome and that 2) there would be determining factors of the clinical outcome at two years. Materials and Methods Forty-one patients with cubital tunnel syndrome underwent simple decompression (n=30) or anterior transposition (n=11) according to an assessment of intra-operative ulnar nerve stability. Clinical outcome was assessed using grip and pinch strength, two-point discrimination, the mean of the disabilities of arm, shoulder, and hand (DASH) survey, and the modified Bishop Scale. Results Preoperatively, two patients were rated as mild, another 20 as moderate, and the remaining 19 as severe according to the Dellon Scale. At 2 years after operation, mean grip/pinch strength increased significantly from 19.4/3.2 kg to 31.1/4.1 kg, respectively. Two-point discrimination improved from 6.0 mm to 3.2 mm. The DASH score improved from 31.0 to 14.5. All but one patient scored good or excellent according to the modified Bishop Scale. Correlations were found between the DASH score at two years and age, pre-operative grip strength, and two-point discrimination. Conclusion An ulnar nerve stability-based approach to surgery selection for cubital tunnel syndrome was effective based on 2-year follow-up data. Older age, worse preoperative grip strength, and worse two-point discrimination were associated with worse outcomes at 2 years. PMID:26847300

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

Potential pitfalls and methods of improving in utero diagnosis of transposition of the great arteries, including the baby bird's beak image.

PubMed

McGahan, John P; Moon-Grady, Anita J; Pahwa, Anokh; Towner, Dena; Rhee-Morris, Laila; Gerscovich, Eugenio O; Fogata, Maria

2007-11-01

The goal of this study was to analyze our recent experience with fetuses with transposition of the great arteries (TGA) to identify potential pitfalls and possible methods to better detect conotruncal anomalies such as TGA. We analyzed all nonreferral obstetric ultrasound examinations in which we performed basic, targeted, or formal fetal echocardiography with a newborn diagnosis of TGA. Nine neonates had TGA. Five of these cases were diagnosed prenatally, and 4 of these had complex congenital heart abnormalities. In these 4 cases, there were abnormalities in the cardiac axis (n = 3), abnormal valves or ventricular size (n = 2), and ventricular septal defects (n = 3) that were detected on the 4-chamber view of the heart. In all cases that were not detected prenatally, both prospective and retrospective reviews of the 4-chamber heart appeared normal. The prospective analyses of the outflow tracts were all interpreted as normal, whereas the retrospective review showed subtle abnormalities such as the "baby bird's beak" image. In review of these cases, there was failure to show the "crisscross" relationship of the outflow tracts. In 1 case, 5 short axis views of the heart, retrospectively showed the artery originating from the left ventricle and bifurcated, representing the pulmonary artery. Transposition of the great arteries may be associated with complex cardiac disease that could be detected on the 4-chamber view of the heart. When the 4-chamber view is normal, it is important to identify the crisscross relationship of the outflow tracts. If this is not done, it is important to document that the pulmonary artery bifurcates and originates from the right ventricle. Five short axis views of the heart may be helpful to detect conotruncal abnormalities.

Persistent institutional difficulties in surgery for transposition of the great arteries in guatemala: analysis with the aristotle basic and comprehensive scores.

PubMed

Leon-Wyss, Juan; Lo Rito, Mauro; Barnoya, Joaquin; Castañeda, Aldo R

2011-07-01

Background. Neonates with complex congenital cardiac lesions are largely inadequately managed in Guatemala. Methods. Between 1997 and 2009, 79 patients who underwent operations for transposition of the great arteries were identified; 51 (63.3%) had an arterial switch operation (ASO) and 28 (36%) an atrial switch operation (ATSO). The Aristotle Basic Complexity score (ABC score) and the Aristotle Comprehensive Complexity score (ACC score) have been used to aid in the evaluation of quality of care associated with pediatric cardiac surgery by adjusting for operative complexity. Results. In-hospital mortality was 47% for the ASO and 25% for the ATSO group; 36.7% were beyond 1 month of age and many exhibited increased preoperative risk factors. The mean ABC score was 9.75 ± 0.89 and the ACC score was 12.12 ± 2.7, with a mean 2.36-point increase (P < .05). Comparing survivors and nonsurvivors with both scores, significant differences were identified (ABC: P < .04 and ACC: P < .02). Conclusion. During this 13-year period, a low volume of surgery for transposition of the great arteries (TGA) was performed at our institution with a relatively high surgical mortality. Many patients with TGA in Guatemala are either never referred for surgery or referred late. Strategies to improve outcomes for neonates with TGA in Guatemala must include increases in early diagnosis countrywide and prompt referral to our unit. Based on the larger number of neonates with TGA that would be referred to our center, we anticipate that this strategy should substantially improve surgical outcomes and favor overall team-related skills.

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 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

Transvenous Lead Extraction in Adults With Congenital Heart Disease: Insights From a 20-Year Single-Center Experience.

PubMed

Gourraud, Jean-Baptiste; Chaix, Marie-A; Shohoudi, Azadeh; Pagé, Pierre; Dubuc, Marc; Thibault, Bernard; Poirier, Nancy C; Dore, Annie; Marcotte, François; Mongeon, François-Pierre; Asgar, Anita W; Ibrahim, Réda; Khairy, Paul; Mondésert, Blandine

2018-02-01

Safety and feasibility data on transvenous lead extraction (TLE) in the challenging population of adults with congenital heart disease (A-CHD) are limited. Herein, we report the results of TLE in A-CHD during a 20-year period. All consecutive TLE procedures in A-CHD were included in a monocentric prospective registry from 1996. A total of 121 leads were extracted in 49 A-CHD (median age, 38 years; 51% men) during 71 TLE procedures. Twenty-four (49%) patients had transposition of the great arteries. Main indications for extraction were infection in 34 (48%) and lead failure in 22 (31%). A laser sheath was required for 56 (46%) leads and a femoral approach for 10 (8%). Complete TLE was achieved for 111 leads (92%). In multivariable analysis, lead duration (odds ratio, 1.02; 95% confidence interval, 1.00-1.04; P <0.01) and number of previous cardiac surgeries (odds ratio, 2.65; 95% confidence interval, 1.52-4.67; P <0.01) were predictive of TLE failure. No perioperative death or pericardial effusion was observed. Subpulmonary atrioventricular valve regurgitation increased in 8 patients (5 with transposition of the great arteries) and was independently associated with an implantable cardioverter defibrillator lead (odds ratio, 9.69; 95% confidence interval, 1.31-71.64; P =0.03) and valvular vegetation (odds ratio, 7.29; 95% confidence interval, 1.32-40.51; P =0.02). After a median of 54 (19-134) months of follow-up after the first TLE, 3 deaths occurred independently from lead management. Despite complex anatomic issues, TLE can be achieved successfully in most A-CHD using advanced extraction techniques. Subpulmonary atrioventricular valve regurgitation is a prevalent complication, particularly in patients with transposition of the great arteries. © 2018 American Heart Association, Inc.

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

Water pollutant fingerprinting tracks recent industrial transfer from coastal to inland China: A case study

PubMed Central

Zheng, Weiwei; Wang, Xia; Tian, Dajun; Jiang, Songhui; Andersen, Melvin E.; He, Genhsjeng; Crabbe, M. James C.; Zheng, Yuxin; Zhong, Yang; Qu, Weidong

2013-01-01

In recent years, China’s developed regions have transferred industries to undeveloped regions. Large numbers of unlicensed or unregistered enterprises are widespread in these undeveloped regions and they are subject to minimal regulation. Current methods for tracing industrial transfers in these areas, based on enterprise registration information or economic surveys, do not work. We have developed an analytical framework combining water fingerprinting and evolutionary analysis to trace the pollution transfer features between water sources. We collected samples in Eastern China (industrial export) and Central China (industrial acceptance) separately from two water systems. Based on the water pollutant fingerprints and evolutionary trees, we traced the pollution transfer associated with industrial transfer between the two areas. The results are consistent with four episodes of industrial transfers over the past decade. Our results also show likely types of the transferred industries - electronics, plastics, and biomedicines - that contribute to the water pollution transfer. PMID:23301152

Anisotropic invasion and its consequences in two-strategy evolutionary games on a square lattice

NASA Astrophysics Data System (ADS)

Szabó, György; Varga, Levente; Szabó, Mátyás

2016-11-01

We have studied invasion processes in two-strategy evolutionary games on a square lattice for imitation rule when the players interact with their nearest neighbors. Monte Carlo simulations are performed for systems where the pair interactions are composed of a unit strength coordination game when varying the strengths of the self-dependent and cross-dependent components at a fixed noise level. The visualization of strategy distributions has clearly indicated that circular homogeneous domains evolve into squares with an orientation dependent on the composition. This phenomenon is related to the anisotropy of invasion velocities along the interfaces separating the two homogeneous regions. The quantified invasion velocities indicate the existence of a parameter region in which the invasions are opposite for the horizontal (or vertical) and the tilted interfaces. In this parameter region faceted islands of both strategies shrink and the system evolves from a random initial state into the homogeneous state that first percolated.

Water pollutant fingerprinting tracks recent industrial transfer from coastal to inland China: A case study

NASA Astrophysics Data System (ADS)

Zheng, Weiwei; Wang, Xia; Tian, Dajun; Jiang, Songhui; Andersen, Melvin E.; He, Genhsjeng; Crabbe, M. James C.; Zheng, Yuxin; Zhong, Yang; Qu, Weidong

2013-01-01

In recent years, China's developed regions have transferred industries to undeveloped regions. Large numbers of unlicensed or unregistered enterprises are widespread in these undeveloped regions and they are subject to minimal regulation. Current methods for tracing industrial transfers in these areas, based on enterprise registration information or economic surveys, do not work. We have developed an analytical framework combining water fingerprinting and evolutionary analysis to trace the pollution transfer features between water sources. We collected samples in Eastern China (industrial export) and Central China (industrial acceptance) separately from two water systems. Based on the water pollutant fingerprints and evolutionary trees, we traced the pollution transfer associated with industrial transfer between the two areas. The results are consistent with four episodes of industrial transfers over the past decade. Our results also show likely types of the transferred industries - electronics, plastics, and biomedicines - that contribute to the water pollution transfer.

Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies

PubMed Central

Majeský, Ľuboš; Schwarzacher, Trude; Gornall, Richard; Heslop-Harrison, Pat

2017-01-01

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems. PMID:28182646

Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies.

PubMed

M Salih, Rubar Hussein; Majeský, Ľuboš; Schwarzacher, Trude; Gornall, Richard; Heslop-Harrison, Pat

2017-01-01

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

Genetic adaptation as a biological buffer against climate change: potential and limitations.

PubMed

De Meester, Luc; Stoks, Robby; Brans, Kristien I

2017-11-23

Climate change profoundly impacts ecosystems and their biota, resulting in range shifts, novel interactions, food web alterations, changed intensities of host-parasite interactions, and extinctions. An increasing number of studies documented evolutionary changes in, amongst others, phenology and thermal tolerance. In this opinion paper, we argue that, while evolutionary responses have the potential to provide a buffer against extinctions or range shifts, a number of constraints and complexities blur this simple prediction. First, there are limits to evolutionary potential both in terms of genetic variation and demographic effects, and these limits differ strongly among taxa and populations. Secondly, there can be costs associated with genetic adaptation, such as a reduced evolutionary potential towards other (human-induced) environmental stressors or direct fitness costs due to trade-offs. Third, the differential capacity of taxa to genetically respond to climate change results in novel interactions because different organism groups respond to a different degree with local compared to regional (cf. dispersal and range shift) responses. These complexities result in additional changes in the selection pressures on populations. We conclude that evolution can provide an initial buffer against climate change for some taxa and populations, but does not guarantee their survival. It does not necessarily result in reduced extinction risks across the range of taxa in a region or continent. Yet, considering evolution is crucial, as it is likely to strongly change how biota will respond to climate change and will impact which taxa will be the winners or losers at the local, metacommunity, and regional scales. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

PubMed

Galián, José A; Rosato, Marcela; Rosselló, Josep A

2014-03-01

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.