Identification of Faba bean genetic loci associated with quantitative resistance to the fungus Botrytis fabae, causal agent of chocolate spot.

Introduction: Chocolate spot, caused by the ascomycete fungus Botrytis fabae, is a devastating foliar disease and a major constraint on the quality and yield of faba beans (Vicia faba). The use of fungicides is the primary strategy for controlling the disease. However, high levels of partial genetic resistance have been identified and can be exploited to mitigate the disease. Methods: The partially resistant V. faba cultivar Maris Bead and susceptible Egyptian accession ig70726 were crossed, and a genetic mapping population of 184 individuals was genotyped in the F2 generation and screened for resistance to B. fabae infection in the F3, F5, and F6 generations in a series of field experiments. A high-density linkage map of V. faba containing 3897 DArT markers spanning 1713.7 cM was constructed. Results: Multiple candidate quantitative trait loci (QTLs) in 11 separate regions of the V. faba genome were identified; some on chromosomes 2, 3, and 6 overlapped with loci previously linked to resistance to Ascochyta leaf and pod blight caused by the necrotrophic fungus Ascochyta fabae. A transcriptomics experiment was conducted at 18 h post-inoculation in seedlings of both parents of the mapping population, identifying several differentially expressed transcripts potentially involved in early stage defence against B. fabae, including cell-wall associated protein kinases, NLR genes, and genes involved in metabolism and response to reactive oxygen species. Discussion: This study identified several novel candidate QTLs in the V. faba genome that contribute to partial resistance to chocolate spot, but differences between growing seasons highlighted the importance of multi-year phenotyping experiments when searching for candidate QTLs for partial resistance.

A brief note on substantial sub-daily arsenic variability in pumping drinking-water wells in New Hampshire.

Large variations in redox-related water parameters, like pH and dissolved oxygen (DO), have been documented in New Hampshire (United States) drinking-water wells over the course of a few hours under pumping conditions. These findings suggest that comparable sub-daily variability in dissolved concentrations of redox-reactive and toxic arsenic (As) also may occur, representing a potentially critical public-health data gap and a fundamental challenge for long-term As-trends monitoring. To test this hypothesis, discrete groundwater As samples were collected approximately hourly during one day in May and again in August 2019 from three New Hampshire drinking-water wells (2 public-supply, 1 private) under active pumping conditions. Collected samples were assessed by laboratory analysis (total As [AsTot], As(III), As(V)) and by field analysis (AsTot) using a novel integrated biosensor system. Laboratory analysis revealed sub-daily variability (range) in AsTot concentrations equivalent to 16 % - 36 % of that observed in the antecedent 3-year bimonthly trend monitoring. Thus, the results indicated that, along with previously demonstrated seasonality effects, the timing and duration of pumping are important considerations when assessing trends in drinking-water As exposures and concomitant risks. Results also illustrated the utility of the field sensor for monitoring and management of AsTot exposures in near-real-time.

Environmental STEM Study of the Oxidation Mechanism for Iron and Iron Carbide Nanoparticles.

The oxidation of solution-synthesized iron (Fe) and iron carbide (Fe2C) nanoparticles was studied in an environmental scanning transmission electron microscope (ESTEM) at elevated temperatures under oxygen gas. The nanoparticles studied had a native oxide shell present, that formed after synthesis, an ~3 nm iron oxide (FexOy) shell for the Fe nanoparticles and ~2 nm for the Fe2C nanoparticles, with small void areas seen in several places between the core and shell for the Fe and an ~0.8 nm space between the core and shell for the Fe2C. The iron nanoparticles oxidized asymmetrically, with voids on the borders between the Fe core and FexOy shell increasing in size until the void coalesced, and finally the Fe core disappeared. In comparison, the oxidation of the Fe2C progressed symmetrically, with the core shrinking in the center and the outer oxide shell growing until the iron carbide had fully disappeared. Small bridges of iron oxide formed during oxidation, indicating that the Fe transitioned to the oxide shell surface across the channels, while leaving the carbon behind in the hollow core. The carbon in the carbide is hypothesized to suppress the formation of larger crystallites of iron oxide during oxidation, and alter the diffusion rates of the Fe and O during the reaction, which explains the lower sensitivity to oxidation of the Fe2C nanoparticles.

Defect-assisted electronic metal-support interactions: tuning the interplay between Ru nanoparticles and CuO supports for pH-neutral oxygen evolution.

Electronic metal-support interactions (EMSIs) comprise an area of intense study, the manipulation of which is of paramount importance in the improvement of heterogeneous metal nanoparticle (NP) supported catalysts. EMSI is the transfer of charge from the support to NP, enabling more effective adsorption and interaction of reactants during catalysis. Ru NPs on CuO supports show different levels of EMSI (via charge transfer) depending on their crystal structure, with multiple twinned NPs showing greater potential for EMSI. We use magnetron-assisted gas phase aggregation for the synthesis of batches of Ru NPs with different populations of single crystal and multiple twinned nanoparticles, which were deposited on CuO nanowires (NWs). The surface charging of the Ru-CuO catalysts was investigated by Kelvin probe force microscopy (KPFM) and X-ray photoelectron spectroscopy (XPS). By doubling the population of multiple twinned NPs, the surface potential of the Ru-CuO catalysts increases roughly 4 times, coinciding with a similar increase in the amount of Ru4+. Therefore, tuning the amount of EMSI in a catalyst is possible through changing the population of multiple twinned Ru NPs in the catalyst. Increasing the amount of multiple twin NPs resulted in improved activity in the oxygen evolution reaction (a roughly 2.5 times decrease in the overpotentials when the population of multiple twinned NPs is increased) and better catalyst stability. This improvement is attributed to the fact that the multiple twin NPs maintained a metallic character under oxidation conditions (unlike single crystal NPs) due to the EMSI between the NP and support.

Chromosome analysis in a case of a plutonium contaminated wound.

Chromosome analysis of peripheral blood lymphocytes was undertaken over a 10 year period following an intake of plutonium through a hand wound. Frequencies of cells with unstable complex aberrations remained high throughout this time, probably reflecting direct exposure of lymphocytes as they passed plutonium which had transferred to regional lymph nodes. Analysis at the final sampling time also revealed cells with stable aberrations at a much higher frequency relative to the number of unstable cells than expected from direct exposure, and is therefore most likely to be reflecting exposure to lymphocyte precursor cells from plutonium that has become deposited on bone surfaces.

Visualizing the Cu/Cu2(O) Interface Transition in Nanoparticles with Environmental Scanning Transmission Electron Microscopy.

Understanding the oxidation and reduction mechanisms of catalytically active transition metal nanoparticles is important to improve their application in a variety of chemical processes. In nanocatalysis the nanoparticles can undergo oxidation or reduction in situ, and thus the redox species are not what are observed before and after reactions. We have used the novel environmental scanning transmission electron microscope (ESTEM) with 0.1 nm resolution in systematic studies of complex dynamic oxidation and reduction mechanisms of copper nanoparticles. The oxidation of copper has previously been reported to be dependent on its crystallography and its interaction with the substrate. By following the dynamic oxidation process in situ in real time with high-angle annular dark-field imaging in the ESTEM, we use conditions ideal to track the oxidation front as it progresses across a copper nanoparticle by following the changes in the atomic number (Z) contrast with time. The oxidation occurs via the nucleation of the oxide phase (Cu2O) from one area of the nanoparticle which then progresses unidirectionally across the particle, with the Cu-to-Cu2O interface having a relationship of Cu{111}//Cu2O{111}. The oxidation kinetics are related to the temperature and oxygen pressure. When the process is reversed in hydrogen, the reduction process is observed to be similar to the oxidation, with the same crystallographic relationship between the two phases. The dynamic observations provide unique insights into redox mechanisms which are important to understanding and controlling the oxidation and reduction of copper-based nanoparticles.

A New Cytogenetic Biodosimetry Image Repository for the Dicentric Assay.

The BioDoseNet was founded by the World Health Organization as a global network of biodosimetry laboratories for building biodosimetry laboratory capacities in countries. The newly established BioDoseNet image repository is a databank of ~25 000 electronically captured images of metaphases from the dicentric assay, which have been previously analysed by international experts. The detailed scoring results and dose estimations have, in most cases, already been published. The compilation of these images into one image repository provides a valuable tool for training and research purposes in biological dosimetry. No special software is needed to view and score the image galleries. For those new to the dicentric assay, the BioDoseNet Image Repository provides an introduction to and training for the dicentric assay. It is an excellent instrument for intra-laboratory training purposes or inter-comparisons between laboratories, as recommended by the International Organization for Standardisation standards. In the event of a radiation accident, the repository can also increase the surge capacity and reduce the turnaround time for dose estimations. Finally, it provides a mechanism for the discussion of scoring discrepancies in difficult cases.

Internet-based media coverage on dengue in Sri Lanka between 2007 and 2015.

BACKGROUND: Internet-based media coverage to explore the extent of awareness of a disease and perceived severity of an outbreak at a national level can be used for early outbreak detection. Dengue has emerged as a major public health problem in Sri Lanka since 2009. OBJECTIVE: To compare Internet references to dengue in Sri Lana with references to other diseases (malaria and influenza) in Sri Lanka and to compare Internet references to dengue in Sri Lanka with notified cases of dengue in Sri Lanka. DESIGN: We examined Internet-based news media articles on dengue queried from HealthMap for Sri Lanka, for the period January 2007 to November 2015. For comparative purposes, we compared hits on dengue with hits on influenza and malaria. RESULTS: There were 565 hits on dengue between 2007 and 2015, with a rapid rise in 2009 and followed by a rising trend ever since. These hits were highly correlated with the national epidemiological trend of dengue. The volume of digital media coverage of dengue was much higher than of influenza and malaria. CONCLUSIONS: Dengue in Sri Lanka is receiving increasing media attention. Our findings underpin previous claims that digital media reports reflect national epidemiological trends, both in annual trends and inter-annual seasonal variation, thus acting as proxy biosurveillance to provide early warning and situation awareness of emerging infectious diseases.

Verification by the FISH translocation assay of historic doses to Mayak workers from external gamma radiation.

The aim of this study was to apply the fluorescence in situ hybridization (FISH) translocation assay in combination with chromosome painting of peripheral blood lymphocytes for retrospective biological dosimetry of Mayak nuclear power plant workers exposed chronically to external gamma radiation. These data were compared with physical dose estimates based on monitoring with badge dosimeters throughout each person's working life. Chromosome translocation yields for 94 workers of the Mayak production association were measured in three laboratories: Southern Urals Biophysics Institute, Leiden University Medical Center and the former Health Protection Agency of the UK (hereinafter Public Health England). The results of the study demonstrated that the FISH-based translocation assay in workers with prolonged (chronic) occupational gamma-ray exposure was a reliable biological dosimeter even many years after radiation exposure. Cytogenetic estimates of red bone marrow doses from external gamma rays were reasonably consistent with dose measurements based on film badge readings successfully validated in dosimetry system "Doses-2005" by FISH, within the bounds of the associated uncertainties.

The NuA4 complex promotes translesion synthesis (TLS)-mediated DNA damage tolerance.

Lesions in DNA can block replication fork progression, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, the DNA damage tolerance (DDT) pathway becomes engaged, allowing the replisome to bypass a lesion and complete S phase. Chromatin remodeling complexes have been implicated in the DDT pathways, and here we identify the NuA4 remodeler, which is a histone acetyltransferase, to function on the translesion synthesis (TLS) branch of DDT. Genetic analyses in Saccharomyces cerevisiae showed synergistic sensitivity to MMS when NuA4 alleles, esa1-L254P and yng2Δ, were combined with the error-free bypass mutant ubc13Δ. The loss of viability was less pronounced when NuA4 complex mutants were disrupted in combination with error-prone/TLS factors, such as rev3Δ, suggesting an epistatic relationship between NuA4 and error-prone bypass. Consistent with cellular viability measurements, replication profiles after exposure to MMS indicated that small regions of unreplicated DNA or damage were present to a greater extent in esa1-L254P/ubc13Δ mutants, which persist beyond the completion of bulk replication compared to esa1-L254P/rev3Δ. The critical role of NuA4 in error-prone bypass is functional even after the bulk of replication is complete. Underscoring this observation, when Yng2 expression is restricted specifically to G2/M of the cell cycle, viability and TLS-dependent mutagenesis rates were restored. Lastly, disruption of HTZ1, which is a target of NuA4, also resulted in mutagenic rates of reversion on level with esa1-L254P and yng2Δ mutants, indicating that the histone variant H2A.Z functions in vivo on the TLS branch of DDT.

What radiation dose does the FISH translocation assay measure in cases of incorporated radionuclides for the Southern Urals populations?

The fluorescence in situ hybridisation (FISH) technique is now well established for retrospective dosimetry in cases of external radiation exposure that occurred many years ago. However, the question remains as to whether FISH provides valid estimates of cumulative red bone marrow radiation doses in cases of incorporation of radionuclides or combined external and internal exposures. This question has arisen in connection with the interpretation of results of dose assessments for epidemiological studies of plutonium workers at the Russian Mayak plant and of members of the public exposed to strontium radioisotopes and external radiation as a result of discharges from Mayak to the Techa River. Exposures to penetrating external radiation result in fairly uniform irradiation of body tissues, and hence similar doses to all tissues, for which FISH dosimetry can provide a reliable measure of this whole body dose. However, intakes of radionuclides into the body by inhalation or ingestion may result in retention in specific organs and tissues, so that the distribution of dose is highly heterogeneous. For radionuclides emitting short-range radiations (e.g. alpha particles), this heterogeneity can apply to dose delivery within tissues and between cells within tissues. In this paper, an attempt is made to address the question of what FISH measures in such circumstances by considering evidence regarding the origin and lifetime dynamics of lymphocyte subsets in the human body in relation to the localised delivery of dose from the internal emitters (90)Sr and (239)Pu, which are of particular interest for the Southern Urals Mayak and Techa River populations, and for which most evidence is available in these populations. It is concluded that the FISH translocation assay can be usefully applied for detecting internal and combined external gamma and internal doses from internally deposited (90)Sr, albeit with fairly large uncertainties. The same may be true of (239)Pu, as well as other radionuclides, although much work remains to be done to establish dose-response relationships.

Review of Bayesian statistical analysis methods for cytogenetic radiation biodosimetry, with a practical example.

Classical methods of assessing the uncertainty associated with radiation doses estimated using cytogenetic techniques are now extremely well defined. However, several authors have suggested that a Bayesian approach to uncertainty estimation may be more suitable for cytogenetic data, which are inherently stochastic in nature. The Bayesian analysis framework focuses on identification of probability distributions (for yield of aberrations or estimated dose), which also means that uncertainty is an intrinsic part of the analysis, rather than an 'afterthought'. In this paper Bayesian, as well as some more advanced classical, data analysis methods for radiation cytogenetics are reviewed that have been proposed in the literature. A practical overview of Bayesian cytogenetic dose estimation is also presented, with worked examples from the literature.

CytoBayesJ: software tools for Bayesian analysis of cytogenetic radiation dosimetry data.

A number of authors have suggested that a Bayesian approach may be most appropriate for analysis of cytogenetic radiation dosimetry data. In the Bayesian framework, probability of an event is described in terms of previous expectations and uncertainty. Previously existing, or prior, information is used in combination with experimental results to infer probabilities or the likelihood that a hypothesis is true. It has been shown that the Bayesian approach increases both the accuracy and quality assurance of radiation dose estimates. New software entitled CytoBayesJ has been developed with the aim of bringing Bayesian analysis to cytogenetic biodosimetry laboratory practice. CytoBayesJ takes a number of Bayesian or 'Bayesian like' methods that have been proposed in the literature and presents them to the user in the form of simple user-friendly tools, including testing for the most appropriate model for distribution of chromosome aberrations and calculations of posterior probability distributions. The individual tools are described in detail and relevant examples of the use of the methods and the corresponding CytoBayesJ software tools are given. In this way, the suitability of the Bayesian approach to biological radiation dosimetry is highlighted and its wider application encouraged by providing a user-friendly software interface and manual in English and Russian.

A comparison of six statistical distributions for analysis of chromosome aberration data for radiation biodosimetry.

The Poisson distribution is the most widely recognised and commonly used distribution for cytogenetic radiation biodosimetry. However, it is recognised that, due to the complexity of radiation exposure cases, other distributions may be more properly applied. Here, the Poisson, gamma, negative binomial, beta, Neyman type-A and Hermite distributions are compared in terms of their applicability to 'real-life' radiation exposure situations. The identification of the most appropriate statistical model in each particular exposure situation more correctly characterises data. The results show that for acute, homogeneous (whole-body) exposures, the Poisson distribution can still give a good fit to the data. For localised partial-body exposures, the Neyman type-A model was found to be the most robust. Overall, no single distribution was found to be universally appropriate. A distribution-specific method of analysis of cytogenetic data is therefore recommended. Such an approach may lead potentially to more accurate biological dose estimates.

Isolation of human mitotic protein phosphatase complexes: identification of a complex between protein phosphatase 1 and the RNA helicase Ddx21.

Metazoan mitosis requires remodelling of sub-cellular structures to ensure proper division of cellular and genetic material. Faults often lead to genomic instability, cell cycle arrests and disease onset. These key structural changes are under tight spatial-temporal and post-translational control, with crucial roles for reversible protein phosphorylation. The phosphoprotein phosphatases PP1 and PP2A are paramount for the timely execution of mitotic entry and exit but their interaction partners and substrates are still largely unresolved. High throughput, mass-spectrometry based studies have limited sensitivity for the detection of low-abundance and transient complexes, a typical feature of many protein phosphatase complexes. Moreover, the limited timeframe during which mitosis takes place reduces the likelihood of identifying mitotic phosphatase complexes in asynchronous cells. Hence, numerous mitotic protein phosphatase complexes still await identification. Here we present a strategy to enrich and identify serine/threonine protein phosphatase complexes at the mitotic spindle. We thus identified a nucleolar RNA helicase, Ddx21/Gu, as a novel, direct PP1 interactor. Furthermore, our results place PP1 within the toposome, a Topoisomerase II alpha (TOPOIIα) containing complex with a key role in mitotic chromatin regulation and cell cycle progression, possibly via regulated protein phosphorylation. This study provides a strategy for the identification of further mitotic PP1 partners and the unravelling of PP1 functions during mitosis.

Limitations associated with analysis of cytogenetic data for biological dosimetry.

The scientific literature concerning cytogenetic biodosimetry has been reviewed to identify the range of scenarios of radiation exposure where biodosimetry has been carried out. Limitations in the existing standardized statistical methodology have been identified and categorized, and the reasons for these limitations have been explored. Statistical problems generally occur due to either low numbers of aberrations leading to large uncertainties or deviations in aberration-per-cell distributions leading to over- or under-dispersion with respect to the Poisson model. A number of difficulties also stem from limitations of the classical statistical methodology, which requires that chromosome aberration yields be considered as something "fixed" and thus provides a deterministic estimate of radiation dose and associated confidence limits (because an assignment of a probability to an event is based solely on the observed frequency of occurrence of the event). Therefore, it is suggested that solutions to the listed problems should be based in the Bayesian framework. This will allow the investigator to take a probabilistic approach to analysis of cytogenetic data, which can be considered highly appropriate for biological dose estimation.

Synopsis of partial-body radiation diagnostic biomarkers and medical management of radiation injury workshop.

Radiation exposures from accidents, nuclear detonations or terrorist incidents are unlikely to be homogeneous; however, current biodosimetric approaches are developed and validated primarily in whole-body irradiation models. A workshop was held at the Armed Forces Radiobiology Research Institute in May 2008 to draw attention to the need for partial-body biodosimetry, to discuss current knowledge, and to identify the gaps to be filled. A panel of international experts and the workshop attendees discussed the requirements and concepts for a path forward. This report addresses eight key areas identified by the Workshop Program Committee for future focus: (1) improved cytogenetics, (2) clinical signs and symptoms, (3) cutaneous bioindicators, (4) organ-specific biomarkers, (5) biophysical markers of dose, (6) integrated diagnostic approaches, (7) confounding factors, and (8) requirements for post-event medical follow-up. For each area, the status, advantages and limitations of existing approaches and suggestions for new directions are presented.

Dose estimation software for radiation biodosimetry.

Cytogenetic analysis of chromosome damage in blood lymphocytes is widely used for radiation biodosimetry. Mathematical and statistical analysis is extremely important for accurate assessment of the data and results, and there are a number of classical statistical methods which are routinely employed. However, the large number of different mathematical techniques, the dependence of the models on certain statistical principles, and the complexity of some of the methods can lead to errors in data analysis and thus misinterpretation of results. Cytogenetic dose estimation software has been developed to address these problems by simplifying mathematical and statistical analysis of the cytogenetic data. "Dose Estimate" is a collection of mathematical and statistical methods based on the cytogenetic methods that are used for biodosimetry at the Health Protection Agency and elsewhere in the radiation cytogenetics community. Details of the biological and mathematical tools incorporated into the software are presented. Preliminary testing has been carried out, and the results demonstrate the accuracy and usefulness of the software in its current form. Proposals for improving the software through implementation of recently published Bayesian analysis techniques for cytogenetics are also outlined. An evaluation copy of the software is available on request from the authors.

WHO 1st consultation on the development of a global biodosimetry laboratories network for radiation emergencies (BioDoseNet).

The World Health Organization (WHO) held a consultation meeting at WHO Headquarters, Geneva, Switzerland, December 17-18, 2007, to develop the framework for a global biodosimetry network. The WHO network is envisioned to enable dose assessment using multiple methods [cytogenetics, electron paramagnetic resonance (EPR), radionuclide bioassays, etc.]; however, the initial discussion focused on the cytogenetic bioassay (i.e., metaphase-spread dicentric assay). Few regional cytogenetic biodosimetry networks have been established so far. The roles and resources available from United Nations (UN) agencies that provide international cooperation in biological dosimetry after radiological emergencies were reviewed. In addition, extensive reliance on the use of the relevant International Standards Organization (ISO) standards was emphasized. The results of a WHO survey of global cytogenetic biological dosimetry capability were reported, and while the survey indicates robust global capability, there was also a clear lack of global leadership and coordination. The expert group, which had a concentrated focus on cytogenetic biodosimetry, formulated the general scope and concept of operations for the development of a WHO global biodosimetry laboratory network for radiation emergencies (BioDoseNet). Follow-on meetings are planned to further develop technical details for this network.