Two-Ray Modeling of Recombination Effects in the Presence of a Phase Conjugation Array

This article describes by means of a simple model how signal recombination effects behave under the influence of phase conjugating retrodirective array (RDA) technology. A two-ray ground reflection model is used to predict the operational advantages of RDA technology in multipath rich environments. The simulation results show that advantageous signal recombination occurs due to automatic self-phasing. As the number of elements in the RDA increases, the fading effect normally observed due to out of phase multipath signal is mitigated to the extent that the system approaches that of one operating in a free space environment. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:1987–1989, 2013

Chromosome synapsis and recombination in simple and complex chromosomal heterozygotes of tuco-tuco (Ctenomys talarum: Rodentia: Ctenomyidae):Rodentia: Ctenomyidae)

The chromosomal speciation hypothesis suggests that irregularities in synapsis, recombination, and segregation in heterozygotes for chromosome rearrangements may restrict gene flow between karyotypically distinct populations and promote speciation. Ctenomys talarum is a South American subterranean rodent inhabiting the coastal regions of Argentina, whose populations polymorphic for Robertsonian and tandem translocations seem to have a very restricted gene flow. To test if chromosomal differences are involved in isolation among its populations, we examined chromosome pairing, recombination, and meiotic silencing of unsynapsed chromatin in male meiosis of simple and complex translocation heterozygotes using immunolocalization of the MLH1 marking mature recombination nodules and phosphorylated histone γH2A.X marking unrepaired double-strand breaks. We observed small asynaptic areas labeled by γH2A.X in pericentromeric regions of the chromosomes involved in the trivalents and quadrivalents. We also observed a decrease of recombination frequency and a distalization of the crossover distribution in the heterozygotes and metacentric homozygotes compared to acrocentric homozygotes. We suggest that the asynapsis of the pericentromeric regions are unlikely to induce germ cell death and decrease fertility of the heterozygotes; however, suppressed recombination in pericentromeric areas of the multivalents may reduce gene flow between chromosomally different populations of the Talas tuco-tuco.

Electron recombination, photoionization, and scattering via many-electron compound resonances

Highly excited eigenstates of atoms and ions with open f shell are chaotic superpositions of thousands, or even millions, of Hartree-Fock determinant states. The interaction between dielectronic and multielectronic configurations leads to the broadening of dielectronic recombination resonances and relative enhancement of photon emission due to opening of thousands of radiative decay channels. The radiative yield is close to 100% for electron energy <1 eV and rapidly decreases for higher energies due to opening of many autoionization channels. The same mechanism predicts suppression of photoionization and relative enhancement of the Raman scattering. Results of our calculations of the recombination rate are in agreement with the experimental data for W20+ and Au25+.

Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting

Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains capable of colonising the CF lung and the broader set of P. aeruginosa isolates found in natural environments. Here we report the results of a multilocus sequence typing (MLST)-based study designed to understand the genetic diversity and population structure of an extensive regional sample of P. aeruginosa isolates from South East Queensland, Australia. The analysis is based on 501 P. aeruginosa isolates obtained from environmental, animal and human (CF and non-CF) sources with particular emphasis on isolates from the Lower Brisbane River and isolates from CF patients obtained from the same geographical region. Overall, MLST identified 274 different sequence types, of which 53 were shared between one or more ecological settings. Our analysis revealed a limited association between genotype and environment and evidence of frequent recombination. We also found that genetic diversity of P. aeruginosa in Queensland, Australia was indistinguishable from that of the global P. aeruginosa population. Several CF strains were encountered frequently in multiple ecological settings; however, the most frequently encountered CF strains were confined to CF patients. Overall, our data confirm a non-clonal epidemic structure and indicate that most CF strains are a random sample of the broader P. aeruginosa population. The increased abundance of some CF strains in different geographical regions is a likely product of chance colonisation events followed by adaptation to the CF lung and horizontal transmission among patients.

Coherent and stochastic contributions of compound resonances in atomic processes: Electron recombination, photoionization, and scattering

In open-shell atoms and ions, processes such as photoionization, combination (Raman) scattering, electron scattering, and recombination are often mediated by many-electron compound resonances. We show that their interference (neglected in the independent-resonance approximation) leads to a coherent contribution, which determines the energy-averaged total cross sections of electron- and photon-induced reactions obtained using the optical theorem. In contrast, the partial cross sections (e.g., electron recombination or photon Raman scattering) are dominated by the stochastic contributions. Thus, the optical theorem provides a link between the stochastic and coherent contributions of the compound resonances. Similar conclusions are valid for reactions via compound states in molecules and nuclei.

Dielectronic recombination of W 35 +

Accurate data for dielectronic recombination (DR) of the ions of tungsten are of significant interest in the modelling of tungsten impurity transport and radiative power loss in current tokamaks and in ITER. However, the complexity of the atomic structure for many of these ions makes level-resolved DR calculations untenable on currently available computers, especially for open d- and f-subshell ions. The majority of DR data presently available for ITER modelling are based on an average-atom approximation. To improve upon these baseline calculations, we investigate the use of the configuration-average distorted-wave (CADW) method to calculate DR rate coefficients for complex open d-shell systems. The aim is to produce rate coefficients that are sufficiently accurate in terms of modelling, yet greatly reduced in term of computational complexity compared to level-resolved calculations. In this paper, we consider the DR of W 35 + . Initially, we carry out several large-scale level-resolved calculations for the DR associated with the 4d → 4f and 4p → 4d excitations in this ion, using both the level-resolved distorted-wave and Dirac R -matrix methods. These calculations allow us to test the validity of the CADW approach on these same excitations by comparing cross sections and rate coefficients. These comparisons demonstrate that the CADW method is relatively accurate in relation to these level-resolved methods for the temperature range for which W 35 + should exist in a collisionally ionized plasma. We then present results for CADW rate coefficients for both Δ n = 0 and Δ n = 1 excitations for this ion. This study indicates that it is now feasible to generate a much improved comprehensive set of DR data for the entire tungsten isonuclear sequence.

Contribution of near threshold states to recombination in plasmas

Resonance states in atoms or ions at low energies can control the rates of important plasma processes (e.g., dielectronic recombination). We examine the role of states at negative energies just below the ionization threshold of the recombined system and find that they can contribute as much, or more, to recombination as positive energy states. In plasmas, negative energy states can be populated by three body recombination, photorecombination, or continuum lowering. Properly including these negative energy states in a theoretical treatment of plasma processes can change the thermally averaged rate coefficients and, in some cases, removes much of the sensitivity to the energy of a state.

Electron-impact ionization and recombination of M -shell atomic ions in the argon isonuclear sequence

Electron-impact ionization and recombination cross sections and rate coefficients are calculated for M-shell Ar atomic ions using a configuration-average distorted-wave method. The electron-impact ionization calcula- tions are for all atomic ions in the Ar isonuclear sequence. Ionization contributions include both direct ioniza- tion and excitation-autoionization processes. Good agreement is found between theory and experimental crossed-beam measurements for moderately charged ion stages. Comparisons are made with previous theoret- ical calculations where possible.We also generate rate coefficients for neutral argon ionization, based on recent R-matrix with pseudostates calculations. Electron-impact dielectronic recombination is calculated for all M-shell ions of argon. For Ar6+ and Ar7+ the current theoretical results agree well with previous level-resolved distorted-wave calculations. In order to compare with published ionization balance results our dielectronic recombination data are combined with literature values for the higher ion stages and with recent radiative recombination data for all the ion stages. We find significant differences in our equilibrium fractional abun- dances for the M-shell ions, compared with literature values. We relate these differences to the underlying atomic data.

Dielectronic recombination of W20 + (4d104f8): Addressing the half-open f shell

A recent measurement of the dielectronic recombination (DR) of W20+ [Schippers et al., Phys.Rev.A 83, 012711 (2011)] found an exceptionally large contribution from near-threshold resonances (1 eV). This still affected the Maxwellian rate coefficient at much higher temperatures. The experimental result was found to be higher by a factor of 4 or more than that currently in use in the 100- to 300-eV range, which is of relevance for modeling magnetic fusion plasmas. We have carried out DR calculations with AUTOSTRUCTURE which include all significant single-electron promotions. Our intermediate-coupling (IC) results are more than a factor of 4 larger than our LS-coupling ones at 1 eV but still lie a factor of 3 below experiment here. If we assume complete (chaotic)mixing of near-threshold autoionizing states, then our results come into agreement (to within 20%)with experiment below 2 eV. Our total IC Maxwellian rate coefficients are 50%–30% smaller than those based on experiment over 100–300 eV.

Manipulation of adenovirus early region 1 rescue plasmids by homologous recombination in Saccharomyces cerevisiae

The manipulation of large (>10 kb) plasmid systems amplifies problems common to traditional cloning strategies. Unique or rare restriction enzyme recognition sequences are uncommon and very rarely located in opportunistic locations. Making site-specific deletions and insertions in larger plasmids consequently leads to multiple step cloning strategies that are often limited by time-consuming, low efficiency linker insertions or blunt-end cloning strategies. Manipulation ofthe adenovirus genome and the genomes ofother viruses as bacterial plasmids are systems that typify such situations. Recombinational cloning techniques based on homologous recombination in Saccharomyces cerevisiae that circumvent many ofthese common problems have been developed. However, these techniques are rarely realistic options for such large plasmid systems due to the above mentioned difficulties associated with the addition ofrequired yeast DNA replication, partitioning and selectable marker sequences. To determine ifrecombinational cloning techniques could be modified to simplify the manipulation of such a large plasmid system, a recombinational cloning system for the creation of human adenovirus EI-deletion rescue plasmids was developed. Here we report for the first time that the 1,456 bp TRP1/ARS fragment ofYRp7 is alone sufficient to foster successful recombinational cloning without additional partitioning sequences, using only slight modifications of existing protocols. In addition, we describe conditions for efficient recombinational cloning involving simultaneous deletion of large segments ofDNA (>4.2 kb) and insertion of donor fragment DNA using only a single non-unique restriction site. The discovery that recombinational cloning can foster large deletions has been used to develop a novel recombiliational cloillng technique, selectable inarker 'kilockouf" recombinational cloning, that uses deletion of a yeast selectable marker coupled with simultaneous negative and positive selection to reduce background transformants to undetectable levels. The modification of existing protocols as described in this report facilitates the use of recombinational cloning strategies that are otherwise difficult or impractical for use with large plasmid systems. Improvement of general recombinational cloning strategies and strategies specific to the manipulation ofthe adenovirus genome are considered in light of data presented herein.

Investigating the role of apoptosis regulator EndoG on exogenous DNA uptake, stability, replication and recombination

Endonuclease G (EndoG) is a well conserved mitochondrial nuclease with dual lethal and vital roles in the cell. It non-specifically cleaves endogenous DNA following apoptosis induction, but is also active in non-apoptotic cells for mitochondrial DNA (mtDNA) replication and may also be important for replication, repair and recombination of genomic DNA. The aim of our study was to examine whether EndoG exerts similar activities on exogenous DNA substrates such as plasmid DNA (pDNA) and viral DNA vectors, considering their importance in gene therapy applications. The effects of EndoG knockdown on pDNA stability and levels of encoded reporter gene expression were evaluated in the cervical carcinoma HeLa cells. Transfection of pDNA vectors encoding short-hairpin RNAs (shRNAs) reduced levels of EndoG mRNA and nuclease activity in HeLa cells. In physiological circumstances, EndoG knockdown did not have an effect on the stability of pDNA or the levels of encoded transgene expression as measured over a four day time-course. However, when endogenous expression of EndoG was induced by an extrinsic stimulus (a cationic liposome transfection reagent), targeting of EndoG by shRNA improved the perceived stability and transgene expression of pDNA vectors. Therefore, EndoG is not a mediator of exogenous DNA clearance, but in non-physiological circumstances it may non-specifically cleave intracellular DNA regardless of its origin. To investigate possible effects of EndoG on viral DNA vectors, we constructed and evaluated AdsiEndoG, a first generation adenovirus (Ad5 ΔE1) vector encoding a shRNA directed against EndoG mRNA, along with appropriate Ad5 ΔE1 controls. Infection of HeLa cells with AdsiEndoG at a multiplicity of infection (MOI) of 10 p.f.u./cell resulted in an early cell proliferation defect, absent from cells infected at equivalent MOI with control Ad5 ΔE1 vectors. Replication of Ad5 ΔE1 DNA was detected for all vectors, but AdsiEndoG DNA accumulated to levels that were 50 fold higher than initially, four days after infection, compared to 14 fold for the next highest control Ad5 ΔE1 vector. Deregulation of the cell cycle by EndoG depletion, which is characterized by an accumulation of cells in the G2/M transition, is the most likely reason for the observed cell proliferation defect. The enhanced replication of AdsiEndoG is consistent with this conclusion, as Ad5 ΔE1 DNA replication is intimately related to cell cycling and prolongation or delay in G2/M greatly enhances this process. Furthermore, infection of HeLa with AdsiEndoG at MOI of 50 p.f.u./cell resulted in an almost complete disappearance of viable, adherent tumour cells from culture, whereas almost a third of the cells were still adherent after infection with control Ad5 ΔE1 vectors, relative to the non-infected control. Therefore, targeting of EndoG by RNAi is a viable strategy for improving the oncolytic properties of first generation adenovirus vectors. In addition, AdsiEndoG-mediated knockdown of EndoG reduced homologous recombination between pDNA substrates in HeLa cells. The effect was modest but, nevertheless demonstrated that the proposed role of EndoG in homologous recombination of cellular DNA also extends to exogenous DNA substrates.

The role of Caulobacter crescentus XerC and XerD recombinases in site-specific recombination

XerC et XerD, deux recombinases impliquées dans la recombinaison site spécifique, résolvent les multimères d’ADN en monomères. Cette réaction se produit au niveau du site dif du chromosome, et nécessite le domaine C-terminale de la protéine de division cellulaire FtsK. Caulobacter crescentus est une bactérie aquatique de type Gram-négative qui se retrouve dans plusieurs environnements. Elle présente un cycle cellulaire asymétrique avec deux types de cellules distinctes. Cette propriété peut être utilisée pour synchroniser la croissance d’une population bactérienne pour permettre l’étude de l’expression de gènes à travers le temps et les liens entre le cycle cellulaire et le développement de la bactérie. La liaison à l’ADN et la capacité de former des complexes covalents (phosphotyrosyl) avec le site dif de C. crescentus (ccdif) ont été testé pour les recombinases de C. crescentus (ccXerC et ccXerD). Les deux recombinases ont eu une meilleure liaison au demi-site gauche de ccdif et sont incapable d’effectuer une liaison coopérative, contrairement à ce qui se produit au niveau du site dif de E. coli. La formation de complexes covalents a été testé en utilisant des «substrats suicides avec bris» marqués à la fluorescence ainsi que des protéines de fusion (marquées ou non à la fluorescence). Des complexes ADN-protéines résistants à la chaleur et au SDS ont été observé lors de la réaction de ccXerC et ccXerD de type sauvage avec ccdif, mais pas lors de la réaction de mutants avec le même ADN. Des complexes covalents phosphotyrosine sont formés de façon plus efficace sur les substrats suicides avec un bris au niveau du brin supérieur que ceux ayant un bris au niveau du brin inférieur. Dans les deux cas, c’est ccXerC qui est resté lié de façon covalente à l’ADN de ccdif.

Genomic variation in recombination patterns : implications for disease and cancer

Durant la méiose, il se produit des échanges réciproques entre fragments de chromosomes homologues par recombinaison génétique. Les chromosomes parentaux ainsi modifiés donnent naissance à des gamètes uniques. En redistribuant les mutations génétiques pour générer de nouvelles combinaisons, ce processus est à l’origine de la diversité haplotypique dans la population. Dans cette thèse, je présente des résultats décrivant l’implication de la recombinaison méiotique dans les maladies chez l’humain. Premièrement, l'analyse statistique de données de génotypage de familles québécoises démontre une importante hétérogénéité individuelle et sexe-spécifique des taux de recombinaisons. Pour la première fois chez l’humain, nous avons observé que le taux de recombinaison maternel diminue avec l'âge de la mère, un phénomène potentiellement impliqué dans la régulation du taux d’aneuploïdie associé à l’âge maternel. Ensuite, grâce à l’analyse de données de séquençage d’exomes de patients atteints de leucémie et de ceux de leurs parents, nous avons découvert une localisation anormale des évènements de recombinaison chez les enfants leucémiques. Le gène PRDM9, principal déterminant de la localisation des recombinaisons chez l’humain, présente des formes alléliques rares dans ces familles. Finalement, en utilisant un large spectre de variants génétiques identifiés dans les transcriptomes d’individus Canadiens Français, nous avons étudié et comparé le fardeau génétique présent dans les régions génomiques à haut et à faible taux de recombinaison. Le fardeau génétique est substantiellement plus élevé dans les régions à faible taux de recombinaison et nous démontrons qu’au niveau individuel, ce fardeau varie selon la population humaine. Grâce à l’utilisation de données génomiques de pointe pour étudier la recombinaison dans des cohortes populationnelles et médicales, ce travail démontre de quelle façon la recombinaison peut affecter la santé des individus.

Effet de la microstructure sur les propriétés excitoniques des polymères semi-conducteurs semi-cristallins

Les polymères semi-conducteurs semicristallins sont utilisés au sein de diodes électroluminescentes, transistors ou dispositifs photovoltaïques organiques. Ces matériaux peuvent être traités à partir de solutions ou directement à partir de leur état solide et forment des agrégats moléculaires dont la morphologie dicte en grande partie leurs propriétés optoélectroniques. Le poly(3-hexylthiophène) est un des polymères semi-conducteurs les plus étudiés. Lorsque le poids moléculaire (Mw) des chaînes est inférieur à 50 kg/mol, la microstructure est polycristalline et composée de chaînes formant des empilements-π. Lorsque Mw>50 kg/mol, la morphologie est semicristalline et composée de domaines cristallins imbriquées dans une matrice de chaînes amorphes. À partir de techniques de spectroscopie en continu et ultrarapide et appuyé de modèles théoriques, nous démontrons que la cohérence spatiale des excitons dans ce matériau est légèrement anisotrope et dépend de Mw. Ceci nous permet d’approfondir la compréhension de la relation intime entre le couplage inter et intramoléculaire sur la forme spectrale en absorption et photoluminescence. De plus, nous démontrons que les excitations photogénérées directement aux interfaces entre les domaines cristallins et les régions amorphes génèrent des paires de polarons liés qui se recombinent par effet tunnel sur des échelles de temps supérieures à 10ns. Le taux de photoluminescence à long temps de vie provenant de ces paires de charges dépend aussi de Mw et varie entre ∼10% et ∼40% pour les faibles et hauts poids moléculaires respectivement. Nous fournissons un modèle permettant d’expliquer le processus de photogénération des paires de polarons et nous élucidons le rôle de la microstructure sur la dynamique de séparation et recombinaison de ces espèces.