Regulation of cell cycle and stress responses to hydrostatic pressure in fission yeast

We have investigated the cellular responses to hydrostatic pressure by using the fission yeast Schizosaccharomyces pombe as a model system. Exposure to sublethal levels of hydrostatic pressure resulted in G2 cell cycle delay. This delay resulted from Cdc2 tyrosine-15 (Y-15) phosphorylation, and it was abrogated by simultaneous disruption of the Cdc2 kinase regulators Cdc25 and Wee1. However, cell cycle delay was independent of the DNA damage, cytokinesis, and cell size checkpoints, suggesting a novel mechanism of Cdc2-Y15 phosphorylation in response to hydrostatic pressure. Spc1/Sty1 mitogen-activated protein (MAP) kinase, a conserved member of the eukaryotic stress-activated p38, mitogen-activated protein (MAP) kinase family, was rapidly activated after pressure stress, and it was required for cell cycle recovery under these conditions, in part through promoting polo kinase (Plo1) phosphorylation on serine 402. Moreover, the Spc1 MAP kinase pathway played a key role in maintaining cell viability under hydrostatic pressure stress through the bZip transcription factor, Atf1. Further analysis revealed that prestressing cells with heat increased barotolerance, suggesting adaptational cross-talk between these stress responses. These findings provide new insight into eukaryotic homeostasis after exposure to pressure stress.

Response of the North Atlantic storm track to climate change shaped by ocean–atmosphere coupling

A poleward shift of the mid-latitude storm tracks in response to anthropogenic greenhouse-gas forcing has been diagnosed in climate model simulations1, 2. Explanations of this effect have focused on atmospheric dynamics3, 4, 5, 6, 7. However, in contrast to storm tracks in other regions, the North Atlantic storm track responds by strengthening and extending farther east, in particular on its southern flank8. These adjustments are associated with an intensification and extension of the eddy-driven jet towards western Europe9 and are expected to have considerable societal impacts related to a rise in storminess in Europe10, 11, 12. Here, we apply a regression analysis to an ensemble of coupled climate model simulations to show that the coupling between ocean and atmosphere shapes the distinct storm-track response to greenhouse-gas forcing in the North Atlantic region. In the ensemble of simulations we analyse, at least half of the differences between the storm-track responses of different models are associated with uncertainties in ocean circulation changes. We compare the fully coupled simulations with both the associated slab model simulations and an ocean-forced experiment with one climate model to establish causality. We conclude that uncertainties in the response of the North Atlantic storm track to anthropogenic emissions could be reduced through tighter constraints on the future ocean circulation.

Heterozygosity and diversity analysis using mapped single nucelotide polymorphisms in a faba bean inbreeding programme

The aim of this study was to convert existing faba bean (Vicia faba L.) single nucleotide polymorphism (SNP) markers from cleaved amplification polymorphic sequences and SNaPshot® formats, which are expensive and time-consuming, to the more convenient KBiosciences competitive allele‐specific PCR (KASP) assay format. Out of 80 assays designed, 75 were validated, though a core set of 67 of the most robust markers is recommended for further use. The 67 best KASP SNP assays were used across two generations of single seed descent to detect unintended outcrossing and to track and quantify loss of heterozygosity, a capability that will significantly increase the efficiency and performance of pure line production and maintenance. This same set of assays was also used to examine genetic relationships between the 67 members of the partly inbred panel, and should prove useful for line identification and diversity studies in the future.

Analysis of frequency and intensity of European winter storm events from a multi-model perspective, at synoptic and regional scales

This study focuses on the analysis of winter (October-November-December-January-February-March; ONDJFM) storm events and their changes due to increased anthropogenic greenhouse gas concentrations over Europe. In order to assess uncertainties that are due to model formulation, 4 regional climate models (RCMs) with 5 high resolution experiments, and 4 global general circulation models (GCMs) are considered. Firstly, cyclone systems as synoptic scale processes in winter are investigated, as they are a principal cause of the occurrence of extreme, damage-causing wind speeds. This is achieved by use of an objective cyclone identification and tracking algorithm applied to GCMs. Secondly, changes in extreme near-surface wind speeds are analysed. Based on percentile thresholds, the studied extreme wind speed indices allow a consistent analysis over Europe that takes systematic deviations of the models into account. Relative changes in both intensity and frequency of extreme winds and their related uncertainties are assessed and related to changing patterns of extreme cyclones. A common feature of all investigated GCMs is a reduced track density over central Europe under climate change conditions, if all systems are considered. If only extreme (i.e. the strongest 5%) cyclones are taken into account, an increasing cyclone activity for western parts of central Europe is apparent; however, the climate change signal reveals a reduced spatial coherency when compared to all systems, which exposes partially contrary results. With respect to extreme wind speeds, significant positive changes in intensity and frequency are obtained over at least 3 and 20% of the European domain under study (35–72°N and 15°W–43°E), respectively. Location and extension of the affected areas (up to 60 and 50% of the domain for intensity and frequency, respectively), as well as levels of changes (up to +15 and +200% for intensity and frequency, respectively) are shown to be highly dependent on the driving GCM, whereas differences between RCMs when driven by the same GCM are relatively small.

A twenty-year independent record of sea surface temperature for climate from Along-track Scanning Radiometers

A new record of sea surface temperature (SST) for climate applications is described. This record provides independent corroboration of global variations estimated from SST measurements made in situ. Infrared imagery from Along-Track Scanning Radiometers (ATSRs) is used to create a 20 year time series of SST at 0.1° latitude-longitude resolution, in the ATSR Reprocessing for Climate (ARC) project. A very high degree of independence of in situ measurements is achieved via physics-based techniques. Skin SST and SST estimated for 20 cm depth are provided, with grid cell uncertainty estimates. Comparison with in situ data sets establishes that ARC SSTs generally have bias of order 0.1 K or smaller. The precision of the ARC SSTs is 0.14 K during 2003 to 2009, from three-way error analysis. Over the period 1994 to 2010, ARC SSTs are stable, with better than 95% confidence, to within 0.005 K yr−1(demonstrated for tropical regions). The data set appears useful for cleanly quantifying interannual variability in SST and major SST anomalies. The ARC SST global anomaly time series is compared to the in situ-based Hadley Centre SST data set version 3 (HadSST3). Within known uncertainties in bias adjustments applied to in situ measurements, the independent ARC record and HadSST3 present the same variations in global marine temperature since 1996. Since the in situ observing system evolved significantly in its mix of measurement platforms and techniques over this period, ARC SSTs provide an important corroboration that HadSST3 accurately represents recent variability and change in this essential climate variable.

A reprocessing for climate of sea surface temperature from the Along-Track Scanning Radiometers: a new retrieval scheme

We present a new coefficient-based retrieval scheme for estimation of sea surface temperature (SST) from the Along Track Scanning Radiometer (ATSR) instruments. The new coefficients are banded by total column water vapour (TCWV), obtained from numerical weather prediction analyses. TCWV banding reduces simulated regional retrieval biases to < 0.1 K compared to biases ~ 0.2 K for global coefficients. Further, detailed treatment of the instrumental viewing geometry reduces simulated view-angle related biases from ~ 0.1 K down to < 0.005 K for dual-view retrievals using channels at 11 and 12 μm. A novel analysis of trade-offs related to the assumed noise level when defining coefficients is undertaken, and we conclude that adding a small nominal level of noise (0.01 K) is optimal for our purposes. When applied to ATSR observations, some inter-algorithm biases appear as TCWV-related differences in SSTs estimated from different channel combinations. The final step in coefficient determination is to adjust the offset coefficient in each TCWV band to match results from a reference algorithm. This reference uses the dual-view observations of 3.7 and 11 μm. The adjustment is independent of in situ measurements, preserving independence of the retrievals. The choice of reference is partly motivated by uncertainty in the calibration of the 12 μm of Advanced ATSR. Lastly, we model the sensitivities of the new retrievals to changes to TCWV and changes in true SST, confirming that dual-view SSTs are most appropriate for climatological applications

A reprocessing for climate of sea surface temperature from the Along-Track Scanning Radiometers: basis in radiative transfer

We present new radiative transfer simulations to support determination of sea surface temperature (SST) from Along Track Scanning Radiometer (ATSR) imagery. The simulations are to be used within the ATSR Reprocessing for Climate project. The simulations are based on the “Reference Forward Model” line-by-line model linked with a sea surface emissivity model that accounts for wind speed and temperature, and with a discrete ordinates scattering model (DISORT). Input to the forward model is a revised atmospheric profile dataset, based on full resolution ERA-40, with a wider range of high-latitude profiles to address known retrieval biases in those regions. Analysis of the radiative impacts of atmospheric trace gases shows that geographical and temporal variation of N2O, CH4, HNO3, and CFC-11 and CFC-12 have effects of order 0.05, 0.2, 0.1 K on the 3.7, 11, 12 μm channels respectively. In addition several trace gases, neglected in previous studies, are included using fixed profiles contributing ~ 0.04 K to top-of-atmosphere BTs. Comparison against observations for ATSR2 and AATSR indicates that forward model biases have been reduced from 0.2 to 0.5 K for previous simulations to ~ 0.1 K.

An infrared desert dust index for the Along-Track Scanning Radiometers

A new aerosol index for the Along-Track Scanning Radiometers (ATSRs) is presented that provides a means to detect desert dust contamination in infrared SST retrievals. The ATSR Saharan dust index (ASDI) utilises only the thermal infrared channels and may therefore be applied consistently to the entire ATSR data record (1991 to present), for both day time and night time observations. The derivation of the ASDI is based on a principal component (PC) analysis (PCA) of two unique pairs of channel brightness temperature differences (BTDs). In 2-D space (i.e. BTD vs BTD), it is found that the loci of data unaffected by aerosol are confined to a single axis of variability. In contrast, the loci of aerosol-contaminated data fall off-axis, shifting in a direction that is approximately orthogonal to the clear-sky axis. The ASDI is therefore defined to be the second PC, where the first PC accounts for the clear-sky variability. The primary ASDI utilises the ATSR nadir and forward-view observations at 11 and 12 μm (ASDI2). A secondary, three-channel nadir-only ASDI (ASDI3) is also defined for situations where data from the forward view are not available. Empirical and theoretical analyses suggest that ASDI is well correlated with aerosol optical depth (AOD: correlation r is typically > 0.7) and provides an effective tool for detecting desert mineral dust. Overall, ASDI2 is found to be more effective than ASDI3, with the latter being sensitive only to very high dust loading. In addition, use of ASDI3 is confined to night time observations as it relies on data from the 3.7 μm channel, which is sensitive to reflected solar radiation. This highlights the benefits of having data from both a nadir- and a forward-view for this particular approach to aerosol detection.

Deriving a sea surface temperature record suitable for climate change research from the along-track scanning radiometers

We describe the approach to be adopted for a major new initiative to derive a homogeneous record of sea surface temperature for 1991–2007 from the observations of the series of three along-track scanning radiometers (ATSRs). This initiative is called (A)RC: (Advanced) ATSR Re-analysis for Climate. The main objectives are to reduce regional biases in retrieved sea surface temperature (SST) to less than 0.1 K for all global oceans, while creating a very homogenous record that is stable in time to within 0.05 K decade−1, with maximum independence of the record from existing analyses of SST used in climate change research. If these stringent targets are achieved, this record will enable significantly improved estimates of surface temperature trends and variability of sufficient quality to advance questions of climate change attribution, climate sensitivity and historical reconstruction of surface temperature changes. The approach includes development of new, consistent estimators for SST for each of the ATSRs, and detailed analysis of overlap periods. Novel aspects of the approach include generation of multiple versions of the record using alternative channel sets and cloud detection techniques, to assess for the first time the effect of such choices. There will be extensive effort in quality control, validation and analysis of the impact on climate SST data sets. Evidence for the plausibility of the 0.1 K target for systematic error is reviewed, as is the need for alternative cloud screening methods in this context.

High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes

Background: Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. Results: We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Conclusions: Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.

Process analysis of trauma-focused cognitive behavioural therapy for individuals with schizophrenia

Objective. Therapeutic alliance, modality, and ability to engage with the process of therapy have been the main focus of research into what makes psychotherapy successful. Individuals with complex trauma histories or schizophrenia are suggested to be more difficult to engage and may be less likely to benefit from therapy. This study aimed to track the in-session ‘process’ of working alliance and emotional processing of trauma memories for individuals with schizophrenia. Design. The study utilized session recordings from the treatment arm of an open randomized clinical trial investigating trauma-focused cognitive behavioural therapy (TF-CBT) for individuals with schizophrenia (N = 26). Method. Observer measures of working alliance, emotional processing, and affect arousal were rated at early and late phases of therapy. Correlation analysis was undertaken for process measures. Temporal analysis of expressed emotions was also reported. Results. Working alliance was established and maintained throughout the therapy; however, agreement on goals reduced at the late phase. The participants appeared to be able to engage in emotional processing, but not to the required level for successful cognitive restructuring. Conclusion. This study undertook novel exploration of process variables not usually explored in CBT. It is also the first study of process for TF-CBT with individuals with schizophrenia. This complex clinical sample showed no difficulty in engagement; however, they may not be able to fully undertake the cognitive–emotional demands of this type of therapy. Clinical and research implications and potential limitations of these methods are considered.

Impact of a Fram Strait cyclone on ice edge, drift, divergence, and concentration: Possibilities and limits of an observational analysis

This study aims at the determination of a Fram Strait cyclone track and of the cyclone’s impact on ice edge, drift, divergence, and concentration. A 24 h period on 13–14 March 2002 framed by two RADARSAT images is analyzed. Data are included from autonomous ice buoys, a research vessel, Special Sensor Microwave Imager (SSM/I) and QuikSCAT satellite, and the operational European Centre for Medium-Range Weather Forecasts (ECMWF) model. During this 24 h period the cyclone moved northward along the western ice edge in the Fram Strait, crossed the northern ice edge, made a left-turn loop with 150 km diameter over the sea ice, and returned to the northern ice edge. The ECMWF analysis places the cyclone track 100 km too far west over the sea ice, a deviation which is too large for representative sea ice simulations. On the east side of the northward moving cyclone, the ice edge was pushed northward by 55 km because of strong winds. On the rear side, the ice edge advanced toward the open water but by a smaller distance because of weaker winds there. The ice drift pattern as calculated from the ice buoys and the two RADARSAT images is cyclonically curved around the center of the cyclone loop. Ice drift divergence shows a spatial pattern with divergence in the loop center and a zone of convergence around. Ice concentration changes as retrieved from SSM/I data follow the divergence pattern such that sea ice concentration increased in areas of divergence and decreased in areas of convergence.