Mapping quantitative trait loci for flag leave senescence as a yield determinant in winter wheat under optimal and drought stressed environments

The timing of flag leaf senescence (FLS) is an important determinant of yield under stress and optimal environments. A doubled haploid population derived from crossing the photo period-sensitive variety Beaver,with the photo period-insensitive variety Soissons, varied significantly for this trait, measured as the percent green flag leaf area remaining at 14 days and 35 days after anthesis. This trait also showed a significantly positive correlation with yield under variable environmental regimes. QTL analysis based on a genetic map derived from 48 doubled haploid lines using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers, revealed the genetic control of this trait. The coincidence of QTL for senescence on chromosomes 2B and 2D under drought-stressed and optimal environments, respectively, indicate a complex genetic mechanism of this trait involving the re-mobilisation of resources from the source to the sink during senescence.

Demographic models and the management of endangered species: a case study of the critically endangered Seychelles magpie robin

1. Demographic models are assuming an important role in management decisions for endangered species. Elasticity analysis and scope for management analysis are two such applications. Elasticity analysis determines the vital rates that have the greatest impact on population growth. Scope for management analysis examines the effects that feasible management might have on vital rates and population growth. Both methods target management in an attempt to maximize population growth. 2. The Seychelles magpie robin Copsychus sechellarum is a critically endangered island endemic, the population of which underwent significant growth in the early 1990s following the implementation of a recovery programme. We examined how the formal use of elasticity and scope for management analyses might have shaped management in the recovery programme, and assessed their effectiveness by comparison with the actual population growth achieved. 3. The magpie robin population doubled from about 25 birds in 1990 to more than 50 by 1995. A simple two-stage demographic model showed that this growth was driven primarily by a significant increase in the annual survival probability of first-year birds and an increase in the birth rate. Neither the annual survival probability of adults nor the probability of a female breeding at age 1 changed significantly over time. 4. Elasticity analysis showed that the annual survival probability of adults had the greatest impact on population growth. There was some scope to use management to increase survival, but because survival rates were already high (> 0.9) this had a negligible effect on population growth. Scope for management analysis showed that significant population growth could have been achieved by targeting management measures at the birth rate and survival probability of first-year birds, although predicted growth rates were lower than those achieved by the recovery programme when all management measures were in place (i.e. 1992-95). 5. Synthesis and applications. We argue that scope for management analysis can provide a useful basis for management but will inevitably be limited to some extent by a lack of data, as our study shows. This means that identifying perceived ecological problems and designing management to alleviate them must be an important component of endangered species management. The corollary of this is that it will not be possible or wise to consider only management options for which there is a demonstrable ecological benefit. Given these constraints, we see little role for elasticity analysis because, when data are available, a scope for management analysis will always be of greater practical value and, when data are lacking, precautionary management demands that as many perceived ecological problems as possible are tackled.

Effects of genotype and environment on free amino acid levels in wheat grain: implications for acrylamide formation during processing

Acrylamide forms from free asparagine and reducing sugars during cooking, with asparagine concentration being the key parameter determining the formation in foods produced from wheat flour. In this study free amino acid concentrations were measured in the grain of varieties Spark and Rialto and four doubled haploid lines from a Spark x Rialto mapping population. The parental and doubled haploid lines had differing levels of total free amino acids and free asparagine in the grain, with one line consistently being lower than either parent for both of these factors. Sulfur deprivation led to huge increases in the concentrations of free asparagine and glutamine, and canonical variate analysis showed clear separation of the grain samples as a result of treatment (environment, E) and genotype (G) and provided evidence of G x E interactions. Low grain sulfur and high free asparagine concentration were closely associated with increased risk of acrylamide formation. G, E, and G x E effects were also evident in grain from six varieties of wheat grown at field locations around the United Kingdom in 2006 and 2007. The data indicate that progress in reducing the risk of acrylamide formation in processed wheat products could be made immediately through the selection and cultivation of low grain asparagme varieties and that further genetically driven improvements should be achievable. However, genotypes that are selected should also be tested under a range of environmental conditions.

Effects of reduced height (Rht) and photoperiod insensitivity (Ppd) alleles on yield of wheat in contrasting production systems

Near isogenic lines (NILs) varying for reduced height (Rht) and photoperiod insensitivity (Ppd-D1) alleles in a cv. Mercia background (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht8c+Ppd-D1a, Rht-D1c, Rht12) were compared for interception of photosynthetically active radiation (PAR), radiation use efficiency (RUE), above-ground biomass (AGB), harvest index (HI), height, weed prevalence, lodging and grain yield, at one field site but within contrasting (‘organic’ v ‘conventional’) rotational and agronomic contexts, in each of three years. In the final year, further NILs (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-B1b+Rht-D1b, Rht-D1b+Rht-B1c) in Maris Huntsman and Maris Widgeon backgrounds were added together with 64 lines of a doubled haploid (DH) population [Savannah (Rht-D1b) × Renesansa (Rht-8c+Ppd-D1a)]. There were highly significant genotype × system interactions for grain yield, mostly because differences were greater in the conventional system than in the organic system. Quadratic fits of NIL grain yield against height were appropriate for both systems when all NILs and years were included. Extreme dwarfing was associated with reduced PAR, RUE, AGB, HI, and increased weed prevalence. Intermediate dwarfing was often associated with improved HI in the conventional system, but not in the organic system. Heights in excess of the optimum for yield were associated particularly with reduced HI and, in the conventional system, lodging. There was no statistical evidence that optimum height for grain yield varied with system although fits peaked at 85cm and 96cm in the conventional and organic systems, respectively. Amongst the DH lines, the marker for Ppd-D1a was associated with earlier flowering, and just in the conventional system also with reduced PAR, AGB and grain yield. The marker for Rht-D1b was associated with reduced height, and again just in the conventional system, with increased HI and grain yield. The marker for Rht8c reduced height, and in the conventional system only, increased HI. When using the System × DH line means as observations grain yield was associated with height and early vegetative growth in the organic system, but not in the conventional system. In the conventional system, PAR interception after anthesis correlated with yield. Savannah was the highest yielding line in the conventional system, producing significantly more grain than several lines that out yielded it in the organic system.

Mechanisms of femtosecond laser-induced refractive index modification of poly(methyl methacrylate)

The mechanisms of refractive index change in poly(methyl methacrylate) by frequency doubled femtosecond laser pulses are investigated. It is demonstrated that positive refractive index modificaton can be caused by a combination of depolymerization and crosslinking.

A human volunteer study to assess the impact of confectionery sweeteners on the gut microbiota composition.

Sweeteners are being sourced to lower the energetic value of confectionery including chocolates. Some, especially non-digestible carbohydrates, may possess other benefits for human health upon their fermentation by the colonic microbiota. The present study assessed non-digestible carbohydrate sweeteners, selected for use in low-energy chocolates, for their ability to beneficially modulate faecal bacterial profiles in human volunteers. Forty volunteers consumed a test chocolate (low-energy or experimental chocolate) containing 22·8 g of maltitol (MTL), MTL and polydextrose (PDX), or MTL and resistant starch for fourteen consecutive days. The dose of the test chocolates was doubled every 2 weeks over a 6-week period. Numbers of faecal bifidobacteria significantly increased with all the three test treatments. Chocolate containing the PDX blend also significantly increased faecal lactobacilli (P = 0·00 001) after the 6 weeks. The PDX blend also showed significant increases in faecal propionate and butyrate (P = 0·002 and 0·006, respectively). All the test chocolates were well tolerated with no significant change in bowel habit or intestinal symptoms even at a daily dose of 45·6 g of non-digestible carbohydrate sweetener. This is of importance not only for giving manufacturers a sugar replacement that can reduce energetic content, but also for providing a well-tolerated means of delivering high levels of non-digestible carbohydrates into the colon, bringing about improvements in the biomarkers of gut health.

Northern Hemisphere extratropical cyclones in a warming climate in the HiGEM high-resolution climate model

Changes to the Northern Hemisphere winter (December, January and February) extratropical storm tracks and cyclones in a warming climate are investigated. Two idealised climate change experiments with HiGEM1.1, a doubled CO2 and a quadrupled CO2 experiment, are compared against a present day control run. An objective feature tracking method is used and a focus given to regional changes. The climatology of extratropical storm tracks from the control run is shown to be in good agreement with ERA-40, while the frequency distribution of cyclone intensity also compares well. In both simulations the mean climate changes are generally consistent with the simulations of the IPCC AR4 models, with a strongly enhanced surface warming at the winter pole and the reduced lower tropospheric warming over the North Atlantic Ocean associated with the slowdown of the Meridional Overturning Circulation. The circulation changes in the North Atlantic are different between the two idealised simulations with different CO2 forcings. In the North Atlantic the storm tracks are influenced by the slowdown of the MOC, the enhanced surface polar warming, and the enhanced upper tropical troposphere warming, giving a north eastward shift of the storm tracks in the 2XCO2 experiment, but no shift in the 4XCO2 experiment. Over the Pacific, in the 2XCO2 experiment, changes in the mean climate are associated with local temperature changes, while in the 4XCO2 experiment the changes in the Pacific are impacted by the weakened tropical circulation. The storm track changes are consistent with the shifts in the zonal wind. Total cyclone numbers are found to decrease over the Northern Hemisphere with increasing CO2 forcing. Changes in cyclone intensity are found using 850hPa vorticity, mean sea level pressure, and 850hPa winds. The intensity of the Northern Hemisphere cyclones is found to decrease relative to the control.

Reduced height alleles (Rht) and Hagberg falling number of wheat

Near isogenic lines varying for alleles for reduced height (Rht) and photoperiod insensitivity (Ppd-D1) in cv. Mercia (2005/6 to 2010/11; rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht8c+Ppd-D1a, Rht-D1c, Rht12) and cvs Maris Huntsman and Maris Widgeon (2007/8 to 2010/11; rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-B1b+Rht-D1b, Rht-D1b+Rht-B1c) were compared at one field site, but within different systems (‘organic’, O, 2005/6 to 2007/8 v ‘intensive’, I, 2005/6 to 2010/11). Further experiments at the site (2006/7 to 2008/9) compared 64 lines of a doubled haploid (DH) population [Savannah (Rht-D1b) × Renesansa (Rht-8c+Ppd-D1a)]. Gibberellin (GA) insensitive dwarfing alleles (Rht-B1b; Rht-B1c; Rht-D1b; Rht-D1c) could reduce α-amylase activity and/or increase Hagberg falling number (HFN) but effects depended greatly on system, background and season. Only Rht-B1c increased grain dormancy despite producing plants taller than Rht-D1c. The GA-sensitive Rht8c+Ppd-D1a in Mercia was associated with reduced HFN but analysis of the DH population suggested this was more closely linked with Ppd-D1a, rather than Rht8c. The severe GA-sensitive dwarfing allele Rht12 was associated with reduced HFN. Instability in HFN over season tended to increase with degree of dwarfing. There was a negative association between mean grain weight and HFN that was in addition to effects of Rht and Ppd-D1 allele.

Improvement of the GenTHREADER method for genomic fold recognition

Motivation: In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins. Results: The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method.

Fine-root turnover rates of European forests revisited: an analysis of data from sequential coring and ingrowth cores

Background and Aims Forest trees directly contribute to carbon cycling in forest soils through the turnover of their fine roots. In this study we aimed to calculate root turnover rates of common European forest tree species and to compare them with most frequently published values. Methods We compiled available European data and applied various turnover rate calculation methods to the resulting database. We used Decision Matrix and Maximum-Minimum formula as suggested in the literature. Results Mean turnover rates obtained by the combination of sequential coring and Decision Matrix were 0.86 yr−1 for Fagus sylvatica and 0.88 yr−1 for Picea abies when maximum biomass data were used for the calculation, and 1.11 yr−1 for both species when mean biomass data were used. Using mean biomass rather than maximum resulted in about 30 % higher values of root turnover. Using the Decision Matrix to calculate turnover rate doubled the rates when compared to the Maximum-Minimum formula. The Decision Matrix, however, makes use of more input information than the Maximum-Minimum formula. Conclusions We propose that calculations using the Decision Matrix with mean biomass give the most reliable estimates of root turnover rates in European forests and should preferentially be used in models and C reporting.

Effect of mountain breeze in ventilating the city under calm and neutral atmospheric environment: Interaction of airflow structures and ventilation efficiency

Many modern cities locate in the mountainous areas, like Hong Kong, Phoenix City and Los Angles. It is confirmed in the literature that the mountain wind system developed by differential heating or cooling can be very beneficial in ventilating the city nearby and alleviating the UHI effect. However, the direct interaction of mountain wind with the natural-convection circulation due to heated urban surfaces has not been studied, to our best knowledge. This kind of unique interaction of two kinds of airflow structures under calm and neutral atmospheric environment is investigated in this paper by CFD approach. A physical model comprising a simple mountain and three long building blocks (forming two street canyons) is firstly developed. Different airflow structures are identified within the conditions of different mountain-building height ratios (R=Hm/Hb) by varying building height but fixing mountain height. It is found that the higher ventilation rate in the street canyons is expected in the cases of smaller mountain-building ratios, indicating the stronger natural convection due to increasing heated building surfaces. However, there is the highest air change rate (ACH) in the lowest-building-height case and most of the air is advective into the street canyon through the top open area, highlighting the important role played by the mountain wind. In terms of the ventilation efficiency, it is shown that the smallest R case enjoys the best air change efficiency followed by the highest R case, while the worst ventilative street canyons occur at the middle R case. In the end, a gap across the streets is introduced in the modeling. The existence of the gap can greatly channel the mountain wind and distribute the air into streets nearby. Thus the ACH can be doubled and air quality can be significantly improved.

Origin of regional climate differences: role of boundary conditions and model formulation in two GCMs

Model differences in projections of extratropical regional climate change due to increasing greenhouse gases are investigated using two atmospheric general circulation models (AGCMs): ECHAM4 (Max Planck Institute, version 4) and CCM3 (National Center for Atmospheric Research Community Climate Model version 3). Sea-surface temperature (SST) fields calculated from observations and coupled versions of the two models are used to force each AGCM in experiments based on time-slice methodology. Results from the forced AGCMs are then compared to coupled model results from the Coupled Model Intercomparison Project 2 (CMIP2) database. The time-slice methodology is verified by showing that the response of each model to doubled CO2 and SST forcing from the CMIP2 experiments is consistent with the results of the coupled GCMs. The differences in the responses of the models are attributed to (1) the different tropical SST warmings in the coupled simulations and (2) the different atmospheric model responses to the same tropical SST warmings. Both are found to have important contributions to differences in implied Northern Hemisphere (NH) winter extratropical regional 500 mb height and tropical precipitation climate changes. Forced teleconnection patterns from tropical SST differences are primarily responsible for sensitivity differences in the extratropical North Pacific, but have relatively little impact on the North Atlantic. There are also significant differences in the extratropical response of the models to the same tropical SST anomalies due to differences in numerical and physical parameterizations. Differences due to parameterizations dominate in the North Atlantic. Differences in the control climates of the two coupled models from the current climate, in particular for the coupled model containing CCM3, are also demonstrated to be important in leading to differences in extratropical regional sensitivity.

Will greenhouse gas-induced warming over the next 50 years lead to higher frequency and greater intensity of hurricanes?

The use of a high resolution atmospheric model at T106 resolution, for studying the influence of greenhouse warming on tropical storm climatology, is investigated. The same method for identifying the storms has been used as in a previous study by Bengtsson et al. The sea surface temperature anomalies have been taken from a previous transient climate change experiment, obtained with a low resolution ocean-atmosphere coupled model. The global distribution of the storms, at the time when the CO2 concentration in the atmosphere had doubled, agrees in geographical position and seasonal variability with that of the present climate, but the number of storms is significantly reduced, particularly at the Southern Hemisphere. The main reason to this, appear to be connected to changes in the large scale circulation, such as a weaker Hadley circulation and stronger upper air westerlies. The low level vorticity in the hurricane genesis regions is generally reduced compared to the present climate, while the vertical tropospheric wind shear is somewhat increased. Most tropical storm regions indicate reduced surface windspeeds and a slightly weaker hydrological cycle.

A Possible Change in Mass Balance of Greenland and Antarctic Ice Sheets in the Coming Century

A high-resolution GCM is found to simulate precipitation and surface energy balance of high latitudes with high accuracy. This opens new possibilities to investigate the future mass balance of polar glaciers and its effect on sea level. The surface mass balance of the Greenland and the Antarctic ice sheets is simulated using the ECHAM3 GCM with TI06 horizontal resolution. With this model, two 5-year integrations for the present and doubled carbon dioxide conditions based on the boundary conditions provided by the ECHAM1/T21 transient experiment have been conducted. A comparison of the two experiments over Greenland and Antarctica shows to what extent the effect of climate change on the mass balance on the two largest glaciers of the world can differ. On Greenland one sees a slight decrease in accumulation and a substantial increase in melt, while on Antarctica a large increase in accumulation without melt is projected. Translating the mass balances into terms of sea-level equivalent. the Greenland discharge causes a sea level rise of 1.1 mm yr−1, while the accumulation on Antarctica tends to lower it by 0.9 mm yr−1. The change in the combined mass balance of the two continents is almost zero. The sea level change of the next century can be affected more effectively by the thermal expansion of seawater and the mass balance of smaller glaciers outside of Greenland and Antarctica.

Synoptic scale disturbances of the Indian Summer Monsoon as simulated in a high resolution climate model

Hamburg atmospheric general circulation model ECHAM3 at T106 resolution (1.125' lat.Aon.) has considerable skill in reproducing the observed seasonal reversal of mean sea level pressure, the location of the summer heat low as well as the position of the monsoon trough over the Indian subcontinent. The present-day climate and its seasonal cycle are realistically simulated by the model over this region. The model simulates the structure, intensity, frequency, movement and lifetime of monsoon depressions remarkably well. The number of monsoon depressions/storms simulated by the model in a year ranged from 5 to 12 with an average frequency of 8.4 yr-', not significantly different from the observed climatology. The model also simulates the interannual variability in the formation of depressions over the north Bay of Bengal during the summer monsoon season. In the warmer atmosphere under doubled CO2 conditions, the number of monsoon depressions/cyclonic storms forming in Indian seas in a year ranged from 5 to 11 with an average frequency of 7.6 yr-', not significantly different from those inferred in the control run of the model. However, under doubled CO2 conditions, fewer depressions formed in the month of June. Neither the lowest central pressure nor the maximum wind speed changes appreciably in monsoon depressions identified under simulated enhanced greenhouse conditions. The analysis suggests there will be no significant changes in the number and intensity of monsoon depressions in a warmer atmosphere.