Multiple-locus sequence typing analysis of Bacillus thuringiensis recovered from the phylloplane of clover (Trifolium hybridum) in vegetative form

The chromosomal genotype, as judged by multi locus sequence typing, and the episomal genotype, as judged by plasmid profile and cry gene content, were analyzed for a collection of strains of Bacillus thuringiensis. These had been recovered in vegetative form over a period of several months from the leaves of a small plot of clover (Trifolium hybridum). A clonal population structure was indicated, although greater variation in sequence types (STs) was discovered than in previous collections of B. cereus/B. thuringiensis. Isolates taken at the same time had quite different genotypes, whereas those of identical genotypes were recovered at different times. The profiles of plasmid content and cry genes generally bore no relation to each other nor to the STs. Evidently, although relatively little recombination was occurring in the seven chromosomal genes analyzed, a great deal of conjugal transfer, and perhaps recombination, was occurring involving plasmids. A clinical diarrheal isolate of B. cereus and the commercial biopesticide strain HD-1 of B. thuringiensis, both included as out-groups, were found to have very similar STs. This further emphasizes the role of episomal elements in the characteristics and differentiation of these two species.

Chloroplast microsatellites: new tools for studies in plant ecology and systematics

The nonrecombinant, uniparentally inherited nature of organelle genomes
makes them useful tools for evolutionary studies. However, in plants, detecting
useful polymorphism at the population level is often difficult because of the
low level of substitutions in the chloroplast genome, and because of the slow
substitution rates and intramolecular recombination of mtDNA. Chloroplast
microsatellites represent potentially useful markers to circumvent this problem
and, to date, studies have demonstrated high levels of intraspecific variability.
Here,we discuss the use of these markers in ecological and evolutionary
studies of plants, as well as highlighting some of the potential problems
associated with such use.

Electron-impact ionization of hydrogen-like iron ions

Electron-impact ionization cross sections have been determined for hydrogen like iron ions at selected electron energies between 1.45 and 4.3 times the threshold energy. The cross sections were obtained by measuring the equilibrium ionization balance in an electron beam ion trap. This ionization balance is obtained from x-ray measurements of radiative recombination into the K-shell of hydrogen-like and bare iron ions. The measured cross sections are compared with distorted-wave calculations and several semiempirical formulations.

Numerical simulation of the charge balance in an EBIT

The electron beam ions traps (EBITs) are widely used to study highly charged ions (HCIs). In an EBIT, a high energy electron beam collides with atoms and ions to generate HCIs in the trap region. It is important to study the physics in the trap. The atomic processes, such as electron impact ionisation (EI), radiative recombination (RR), dielectronic recombination (DR) and charge exchange (CX), occur in the trap and numerical simulation can give some parameters for design, predict the composition and describe charge state evolution in an EBIT [Phys. Rev. A 43 (199 1) 4861]. We are presently developing a new code, which additionally includes a description of the overlaps between the ion clouds of the various charge-states. It has been written so that it can simulate experiments where various machine parameters (e.g. beam energy and current) can vary throughout the simulation and will be able to use cross- sections either based on scaling laws or derived from atomic structure calculations. An object-oriented method is used in developing the new software, which is an efficient way to organize and write code. (C) 2003 Elsevier Science B.V. All rights reserved.

High harmonic generation by halogen anions and noble gas atoms in a laser field

A comparative study of high harmonic generation (HHG) by atoms and ions with active p-electrons is carried out in the theoretical framework of the rescattering mechanism. The substate with m(l) = 0, i.e. zero orbital momentum projection along the electric vector of a linearly polarized laser wave, is found to give the major contribution to the HHG rate. Our calculations for HHG by an H atom in an excited 2p-state demonstrate that the rate for recombination into a final state with a different value of m(l) (= +/- 1), is higher for lower harmonic orders N, while for higher N (beyond the plateau domain) the difference vanishes. For species with closed electron shells, the m(l)-changing transitions are forbidden by the Pauli exclusion principle. We report absolute HHG rates for halogen ions and noble gas atoms at various intensities. These results demonstrate that the Coulomb binding potential of the atoms considerably enhances both the ionization and recombination steps in the rescattering process. However, the weak binding energy of the anions allows lower orders of HHG to be efficiently produced at relatively low intensities, from which we conclude that observation of HHG by an anion is experimentally feasible.

The UMIST Database for Astrochemistry 2006

We present a new version of the UMIST Database for Astrochemistry, the fourth such version to be released to the public. The current version contains some 4573 binary gas-phase reactions, an increase of 10% from the previous (1999) version, among 420 species, of which 23 are new to the database. Major updates have been made to ion-neutral reactions, neutral-neutral reactions, particularly at low temperature, and dissociative recombination reactions. We have included for the first time the interstellar chemistry of fluorine. In addition to the usual database, we have also released a reaction set in which the effects of dipole-enhanced ion-neutral rate coefficients are included. These two reactions sets have been used in a dark cloud model and the results of these models are presented and discussed briefly. The database and associated software are available on the World Wide Web at www.udfa.net. Tables 1, 2, 4 and 9 are only available in electronic form at http://www.aanda.org

Deletion of complement factor H-related genes CFHR1 and CFHR3 is associated with atypical hemolytic uremic syndrome.

Atypical hemolytic uremic syndrome (aHUS) is associated with defective complement regulation. Disease-associated mutations have been described in the genes encoding the complement regulators complement factor H, membrane cofactor protein, factor B, and factor I. In this study, we show in two independent cohorts of aHUS patients that deletion of two closely related genes, complement factor H-related 1 (CFHR1) and complement factor H-related 3 (CFHR3), increases the risk of aHUS. Amplification analysis and sequencing of genomic DNA of three affected individuals revealed a chromosomal deletion of approximately 84 kb in the RCA gene cluster, resulting in loss of the genes coding for CFHR1 and CFHR3, but leaving the genomic structure of factor H intact. The CFHR1 and CFHR3 genes are flanked by long homologous repeats with long interspersed nuclear elements (retrotransposons) and we suggest that nonallelic homologous recombination between these repeats results in the loss of the two genes. Impaired protection of erythrocytes from complement activation is observed in the serum of aHUS patients deficient in CFHR1 and CFHR3, thus suggesting a regulatory role for CFHR1 and CFHR3 in complement activation. The identification of CFHR1/CFHR3 deficiency in aHUS patients may lead to the design of new diagnostic approaches, such as enhanced testing for these genes.

Suppressing mitotic catastrophe: identifying mcs3 in Schizosaccharomyces pombe

In Schizosaccharomyces pombe (fission yeast), the transition from G2 phase of the cell cycle to mitosis is under strict regulation. The activation of Cdc2, a cyclin dependent serine/threonine protein kinase, is the critical control step in this process. The Cdc2/Cyclin-B (Cdc13) complex is regulated by Wee1 tyrosine kinase and Cdc25 tyrosine phosphatase, which work antagonistically to control progression into mitosis. Hyperactivation of the Cdc2/Cdc13 complex by phosphorylation results in premature mitosis, and as a consequence leads to genome instability. This is referred to as mitotic catastrophe, a lethal phenotype associated with chromosomal segregation abnormalities including chromosome breakage. Six mitotic catastrophe loci were found, five of which have been characterized and identified as various activators and repressors of the core mitotic control. The locus for mcs3 remains unknown. I used tetrad analysis in this study to determine the linkage distance between three genes suspected of flanking the region in which mcs3 is located. Linkage distances obtained in this study confirm that the SPBC428.10 and met17, as well as SPBC428.10 and wpl1 are tightly linked, suggesting this is an area of low recombination. Further linkage analysis should be conducted to determine the precise location of mcs3-12.

Optical Thomson scatter from laser-ablated plumes

We have obtained density and temperature informations on an expanding KrF laser-ablated magnesium plume via optical Thomson scatter with a frequency doubled Nd:YAG laser. The electron temperature was found to decay with the expected Te t-1 dependence. However, we have found the electron density to have a time dependence ne t-4.95 which can be explained by strong recombination processes. We also observed atomic Raman satellites originating from transitions between the different angular momentum levels of the metastable 3P0 term in Mg I.

Two-electron QED contributions to the ground-state binding energy in He-like Kr34+ ions

The two-electron QED contributions to the ground-state binding energy of Kr34+ ions have been determined in two independent experiments performed with electron beam ion traps (EBIT) in Heidelberg (HD) and Tokyo (BT, Belfast-Tokyo collaboration). X rays arising from radiative recombination (RR) of free electrons to the ground state of initially bare Kr36+ and hydrogenlike Kr35+ ions were observed as a function of the interacting electron energy. The K edge absorption by thin Eu and W foils provided fixed photon energy references used to measure the difference in binding energy Delta E-2e between the H- and He-like Kr ions (Kr35+ and Kr34+, respectively). The two values agree well, yielding a final result of Delta E-2e=641.8 +/- 1.7 eV, confirming recent results of rigorous QED calculations. This accuracy is just of the order required to access screened radiative QED contributions.

Detection and localisation of protein-protein interactions in Saccharomyces cerevisiae using a split-GFP method

An alternative method for monitoring protein-protein interactions in Saccharomyces cerevisiae has been developed. It relies on the ability of two fragments of enhanced green fluorescent protein (EGFP) to reassemble and fluoresce when fused to interacting proteins. Since this fluorescence can be detected in living cells, simultaneous detection and localisation of interacting pairs is possible. DNA sequences encoding N- and C-terminal EGFP fragments flanked by sequences from the genes of interest were transformed into S. cerevisicie JPY5 cells and homologous recombination into the genome verified by PCR. The system was evaluated by testing known interacting proteins: labelling of the phosphofructokinase subunits, Pfk1p and Pfk2p, with N- and C-terminal EGFP fragments, respectively, resulted in green fluorescence in the cytoplasm. The system works in other cellular compartments: labelling of Idh1p and Idh2p, (mitochondrial matrix), Sdh3p and Sdh4p (mitochondrial membrane) and Pap2p and Mtr4p (nucleus) all resulted in fluorescence in the appropriate cellular compartment. (c) 2008 Elsevier Inc. All rights reserved.

A transposase-independent mechanism gives rise to precise excision of IS256 from insertion sites in Staphylococcus epidermidis.

The mobile element IS256 causes phase variation of biofilm formation in Staphylococcus epidermidis by insertion and precise excision from the icaADBC operon. Precise excision, i.e., removal of the target site duplications (TSDs) and restoration of the original DNA sequence, occurs rarely but independently of functional transposase. Instead, the integrity of the TSDs is crucial for precise excision. Excision increased significantly when the TSDs were brought into closer spatial proximity, suggesting that excision is a host-driven process that might involve most likely illegitimate recombination.

Comparison between fluid simulations and experiments in inductively coupled argon/chlorine plasmas

Comparisons of 2D fluid simulations with experimental measurements of Ar/Cl-2 plasmas in a low-pressure inductively coupled reactor are reported. Simulations show that the wall recombination coefficient of Cl atom (gamma) is a crucial parameter of the model and that neutral densities are very sensitive to its variations. The best agreement between model and experiment is obtained for gamma = 0.02, which is much lower than the value predicted for stainless steel walls (gamma = 0.6). This is consistent with reactor wall contaminations classically observed in such discharges. The electron density, negative ion fraction and Cl atom density have been investigated under various conditions of chlorine and argon concentrations, gas pressure and applied rf input power. The plasma electronegativity decreases with rf power and increases with chlorine concentration. At high pressure, the power absorption and distribution of charged particles become more localized below the quartz window. Although the experimental trends are well reproduced by the simulations, the calculated charged particle densities are systematically overestimated by a factor of 3-5. The reasons for this discrepancy are discussed in the paper.

Deficiencies of double-strand break repair factors and effects on mutagenesis in directly gamma-irradiated and medium-mediated bystander human lymphoblastoid cells

Using RNA interference techniques to knock down key proteins in two major double-strand break (DSB) repair pathways (DNA-PKcs for nonhomologous end joining, NHEJ, and Rad54 for homologous recombination, HR), we investigated the influence of DSB repair factors on radiation mutagenesis at the autosomal thymidine kinase (TK) locus both in directly irradiated cells and in unirradiated bystander cells. We also examined the role of p53 (TP53) in these processes by using cells of three human lymphoblastoid cell lines from the same donor but with differing p53 status (TK6 is p53 wild-type, NH32 is p53 null, and WTK1 is p53 mutant). Our results indicated that p53 status did not affect either the production of radiation bystander mutagenic signals or the response to these signals. In directly irradiated cells, knockdown of DNA-PKcs led to an increased mutant fraction in WTK1 cells and decreased mutant fractions in TK6 and NH32 cells. In contrast, knockdown of DNA-PKcs led to increased mutagenesis in bystander cells regardless of p53 status. In directly irradiated cells, knockdown of Rad54 led to increased induced mutant fractions in WTK1 and NH32 cells, but the knockdown did not affect mutagenesis in p53 wild-type TK6 cells. In all cell lines, Rad54 knockdown had no effect on the magnitude of bystander mutagenesis. Studies with extracellular catalase confirmed the involvement of H2O2 in bystander signaling. Our results demonstrate that DSB repair factors have different roles in mediating mutagenesis in irradiated and bystander cells. (C) 2008 by Radiation Research Society.

Histone H2AX phosphorylation as a molecular pharmacological marker for DNA interstrand crosslink cancer chemotherapy

The aims of this study were to investigate mechanisms of action involved in H2AX phosphorylation by DNA interstrand crosslinking (ICL) agents and determine whether gamma H2AX could be a suitable pharmacological marker for identifying potential ICL cellular chemosensitivity. In normal human fibroblasts, after treatment with nitrogen mustard (HN2) or cisplatin, the peak gamma H2AX response was detected 2-3 h after the peak of DNA ICLs measured using the comet assay, a validated method for detecting ICLs in vitro or in clinical samples. Detection of gamma H2AX foci by immunofluorescence microscopy could be routinely detected with 6-10 times lower concentrations of both drugs compared to detection of ICLs using the comet assay. A major pathway for repairing DNA ICLs is the initial unhooking of the ICL by the ERCC1-XPF endonuclease followed by homologous recombination. HN2 or cisplatin-induced gamma H2AX foci persisted significantly longer in both, ERCC1 or XRCC3 (homologous recombination) defective Chinese hamster cells that are highly sensitive to cell killing by ICL agents compared to wild type or ionising radiation sensitive XRCC5 cells. An advantage of using gamma H2AX immunofluorescence over the comet assay is that it appears to detect ICL chemosensitivity in both ERCC1 and HR defective cells. With HN2 and cisplatin, gamma H2AX foci also persisted in chemosensitive human ovarian cancer cells (A2780) compared to chemoresistant (A2780cisR) cells. These results show that gamma H2AX can act as a highly sensitive and general marker of DNA damage induced by HN2 or cisplatin and shows promise for predicting potential cellular chemosensitivity to ICL agents. (c) 2008 Elsevier Inc. All rights reserved.