Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo

This article presents a statistical method for detecting recombination in DNA sequence alignments, which is based on combining two probabilistic graphical models: (1) a taxon graph (phylogenetic tree) representing the relationship between the taxa, and (2) a site graph (hidden Markov model) representing interactions between different sites in the DNA sequence alignments. We adopt a Bayesian approach and sample the parameters of the model from the posterior distribution with Markov chain Monte Carlo, using a Metropolis-Hastings and Gibbs-within-Gibbs scheme. The proposed method is tested on various synthetic and real-world DNA sequence alignments, and we compare its performance with the established detection methods RECPARS, PLATO, and TOPAL, as well as with two alternative parameter estimation schemes.

Inter-simple sequence repeat and aggressiveness analyses revealed high genetic diversity, recombination and long-range dispersal in Fusarium culmorum

Inter-simple sequence repeat (ISSR) analysis and aggressiveness assays were used to investigate genetic variability within a global collection of Fusarium culmorum isolates. A set of four ISSR primers were tested, of which three primers amplified a total of 37 bands out of which 30 (81%) were polymorphic. The intraspecific diversity was high, ranging from four to 28 different ISSR genotypes for F. culmorum depending on the primer. The combined analysis of ISSR data revealed 59 different genotypes clustered into seven distinct clades amongst 75 isolates of F. culmorum examined. All the isolates were assayed to test their aggressiveness on a winter wheat cv. 'Armada'. A significant quantitative variation for aggressiveness was found among the isolates. The ISSR and aggressiveness variation existed on a macro- as well as micro-geographical scale. The data suggested a long-range dispersal of F. culmorum and indicated that this fungus may have been introduced into Canada from Europe. In addition to the high level of intraspecific diversity observed in F. culmorum, the index of multilocus association calculated using ISSR data indicated that reproduction in F. culmorum cannot be exclusively clonal and recombination is likely to occur.

Improving baculovirus recombination

Recombinant baculoviruses have established themselves as a favoured technology for the high-level expression of recombinant proteins. The construction of recombinant viruses, however, is a time consuming step that restricts consideration of the technology for high throughput developments. Here we use a targeted gene knockout technology to inactivate an essential viral gene that lies adjacent to the locus used for recombination. Viral DNA prepared from the knockout fails to initiate an infection unless rescued by recombination with a baculovirus transfer vector. Modified viral DNA allows 100% recombinant virus formation, obviates the need for further virus purification and offers an efficient means of mass parallel recombinant formation.

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype–phenotype mapping.

Asset recombination in international partnerships as a source of improved innovation capabilities in China

Purpose This paper examines how multinational enterprises (MNEs) and local partners, including suppliers, customers, and competitors in China, improve their innovation capabilities through collaboration. We analyse this collaboration as a three-way interaction between the ownership-specific (O) advantages or firm-specific assets (FSAs) of the MNE subsidiary, the FSAs of the local partner, and the location-specific assets of the host location. Design/methodology/approach Our propositions are examined through a survey of 320 firms, supplemented with 30 in-depth case studies, based in mainland China. Findings We find that the recombination of asset-type (Oa) FSAs and transaction-type (Ot) FSAs from both partners leads to new innovation-related ownership advantages, or ‘recombinant advantages’. Ot FSAs, in the form of access to local suppliers, customers or government networks are particularly important for reducing the liability of foreignness for MNEs. Originality/value The study reveals important patterns of reciprocal transfer, sharing, and integration for different asset categories (tacit, codified) and different forms of FSA and explicitly links these to different innovation performance outcomes. The paper reports on these findings, making an empirical contribution in an important context (China-based partnerships). We also contribute to conceptual developments, connecting various kinds of FSA, tacit and codifiable assets and ‘recombinant advantages’. Limited conceptual, methodological, and empirical contributions are made in linking asset integration with (measurable) innovation performance outcomes in international partnerships.

The Recombination Protein RAD52 Cooperates with the Excision Repair Protein OGG1 for the Repair of Oxidative Lesions in Mammalian Cells

Oxidized bases are common types of DNA modifications. Their accumulation in the genome is linked to aging and degenerative diseases. These modifications are commonly repaired by the base excision repair (BER) pathway. Oxoguanine DNA glycosylase (OGG1) initiates BER of oxidized purine bases. A small number of protein interactions have been identified for OGG1, while very few appear to have functional consequences. We report here that OGG1 interacts with the recombination protein RAD52 in vitro and in vivo. This interaction has reciprocal functional consequences as OGG1 inhibits RAD52 catalytic activities and RAD52 stimulates OGG1 incision activity, likely increasing its turnover rate. RAD52 colocalizes with OGG1 after oxidative stress to cultured cells, but not after the direct induction of double-strand breaks by ionizing radiation. Human cells depleted of RAD52 via small interfering RNA knockdown, and mouse cells lacking the protein via gene knockout showed increased sensitivity to oxidative stress. Moreover, cells depleted of RAD52 show higher accumulation of oxidized bases in their genome than cells with normal levels of RAD52. Our results indicate that RAD52 cooperates with OGG1 to repair oxidative DNA damage and enhances the cellular resistance to oxidative stress. Our observations suggest a coordinated action between these proteins that may be relevant when oxidative lesions positioned close to strand breaks impose a hindrance to RAD52 catalytic activities.

Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies

Paracoccidioides brasiliensis is the etiologic agent of paracoccidioidomycosis, a disease confined to Latin America and of marked importance in the endemic areas due to its frequency and severity. This species is considered to be clonal according to mycological criteria and has been shown to vary in virulence. To characterize natural genetic variation and reproductive mode in this fungus, we analyzed P. brasiliensis phylogenetically in search of cryptic species and possible recombination using concordance and nondiscordance of gene genealogies with respect to phylogenies of eight regions in five nuclear loci. Our data indicate that this fungus consists of at least three distinct, previously unrecognized species: S1 (species 1 with 38 isolates), PS2 (phylogenetic species 2 with six isolates), and PS3 (phylogenetic species 3 with 21 isolates). Genealogies of four of the regions studied strongly supported the PS2 clade, composed of five Brazilian and one Venezuelan isolate. The second clade, PS3, composed solely of 21 Colombian isolates, was strongly supported by the alpha-tubulin genealogy. The remaining 38 individuals formed S1. Two of the three lineages of P. brasiliensis, S1 and PS2, are sympatric across their range, suggesting barriers to gene flow other than geographic isolation. Our study provides the first evidence for possible sexual reproduction in P. brasiliensis S1, but does not rule it out in the other two species.

Three-boson recombination at ultralow temperatures

The effects of trimer continuum resonances are considered in the three-body recombination rate of a Bose system at finite energies for large and negative two-body scattering lengths (a). The thermal average of the rate allows to apply our formula to Bose gases at ultra-low temperatures. We found a good quantitative description of the experimental three-body recombination length of cesium atoms to deeply bound molecules up to 500 nK. Consistent with the experimental data, the increase of the temperature moves the resonance peak of the three-body recombination rate to lower values of vertical bar a vertical bar exhibiting a saturation behavior. (C) 2006 Elsevier B.V. All rights reserved.

Reading, equivalence, and recombination of units: A replication with students with different learning histories

First graders, preschoolers, special education students, and adults received a reading program in which they learned to match printed to dictated words and to construct (copy) printed words. The students not only learned to match the training words but also learned to read them. In addition, most of the students learned to read new words that involved recombinations of the syllables of the training words. The results replicate and extend the generality of a prior analysis of a reading program based on stimulus equivalence and recombination of units.

Recombination nodules in coleopteran species: Palembus dermestoides(Tenebrionidae) and Epicauta atomaria (Meloidae)

This work describes the first report about the occurrence of recombination nodules (RNs) in spread pachytene cells of two species of Coleoptera: Palembus dermestoides (Tenebrionidae) and Epicauta atomaria (Meloidae). The RNs were observed in preparations contrasted with phosphotungstic acid. Considering RN morphology and its occurrence in pachytene bivalents (one per autosome bivalent) these structures were interpreted to be late RNs. P. dermestoides and E. atolraria have 2n = 20 chromosomes including an Xyp sex determination system. In spite of most frequently subtelocentric morphology observed in the autosomes of both species, the occurrence of RNs is limited only to the synaptonemal complex (SC) structure of the long arms. These findings are in agreement with those obtained using light microscopy analysis in which only one chiasma or terminalization event is observed per autosomal bivalent in early or late metaphase I cells. The RNs have the same average width of the SC of each analyzed species, a circular shape, strong electron density, and are observed mainly between the lateral elements of the SC. The RNs of P. dermestoides and E. atomaria have approximately the same average size (width), 180 +/- 20 nm and 160 +/- 80 nm, respectively. The absence of RNs in the short arms and its occurrence in the long arms are discussed considering the short arm pericentromeric and pro-centric heterochromatin. Copyright (C) 2003 S. Karger AG, Basel