Use of a crop model ensemble to quantify CO2 stimulation of water-stressed and well-watered crops

Increased atmospheric concentrations of carbon dioxide (CO2) will benefit the yield of most crops. Two free air CO2 enrichment (FACE) meta-analyses have shown increases in yield of between 0 and 73% for C3 crops. Despite this large range, few crop modelling studies quantify the uncertainty inherent in the parameterisation of crop growth and development. We present a novel perturbed-parameter method of crop model simulation, which uses some constraints from observations, that does this. The model used is the groundnut (i.e. peanut; Arachis hypogaea L.) version of the general large-area model for annual crops (GLAM). The conclusions are of relevance to C3 crops in general. The increases in yield simulated by GLAM for doubled CO2 were between 16 and 62%. The difference in mean percentage increase between well-watered and water-stressed simulations was 6.8. These results were compared to FACE and controlled environment studies, and to sensitivity tests on two other crop models of differing levels of complexity: CROPGRO, and the groundnut model of Hammer et al. [Hammer, G.L., Sinclair, T.R., Boote, K.J., Wright, G.C., Meinke, H., Bell, M.J., 1995. A peanut simulation model. I. Model development and testing. Agron. J. 87, 1085-1093]. The relationship between CO2 and water stress in the experiments and in the models was examined. From a physiological perspective, water-stressed crops are expected to show greater CO2 stimulation than well-watered crops. This expectation has been cited in literature. However, this result is not seen consistently in either the FACE studies or in the crop models. In contrast, leaf-level models of assimilation do consistently show this result. An analysis of the evidence from these models and from the data suggests that scale (canopy versus leaf), model calibration, and model complexity are factors in determining the sign and magnitude of the interaction between CO2 and water stress. We conclude from our study that the statement that 'water-stressed crops show greater CO2 stimulation than well-watered crops' cannot be held to be universally true. We also conclude, preliminarily, that the relationship between water stress and assimilation varies with scale. Accordingly, we provide some suggestions on how studies of a similar nature, using crop models of a range of complexity, could contribute further to understanding the roles of model calibration, model complexity and scale. (C) 2008 Elsevier B.V. All rights reserved.

Dietary supplements of whole linseed and vitamin E to increase levels of alpha-linolenic acid and vitamin E in bovine milk

The potential to increase the concentrations of n-3 polyunsaturated fatty acids (PUFAs) in milk fat was investigated by studying the effects of feeding a xylose-treated, whole cracked linseed supplement ( rich in alpha-linolenic acid) to dairy cows. Also the effect of increasing the dietary intake of vitamin E on the vitamin E status of milk was investigated. The effect of pasteurisation on milk fatty acid composition was also examined. Using a 3 x 2 factorial design, a total of 60 Holstein dairy cows were fed a total mixed ration based on grass silage supplemented with one of three levels of whole cracked linseed (78, 142 or 209 g . kg(-1) diet dry matter (DM); designated LL, ML or HL, respectively) in combination with one of two levels of additional dietary vitamin E intake ( 6 or 12 g vitamin E . animal(-1) . day(-1); designated LE or HE, respectively). Increasing lipid supplementation reduced (P < 0.01) diet DM intake and milk yield, and increased (P < 0.001) the overall content of oleic, vaccenic, alpha-linolenic and conjugated linoleic acids, and total PUFAs and monounsaturated fatty acids (MUFA). Myristic and palmitic acids in milk fat were reduced ( P < 0.001) through increased lipid supplementation. While α-linolenic acid concentrations were substantially increased this acid only accounted for 0.02 of total fatty acids in milk at the highest level of supplementation (630 g α-linolenic acid &BULL; animal(-1) &BULL; day(-1) for HL). Conjugated linoleic acid concentrations in milk fat were almost doubled by increasing the level of lipid supplementation (8.9, 10.4 and 16.1 g &BULL; kg(-1) fatty acids for LL, ML and HL, respectively). Although milk vitamin E contents were generally increased there was no benefit (P > 0.05) of increasing vitamin E intake from 6 to 12 g . animal(-1) . day(-1). The fatty acid composition of milk was generally not affected by pasteurisation.

Splanchnic metabolism of dairy cows during the transition from late gestation through early lactation

Blood flow and net nutrient fluxes for portal-drained viscera (PDV) and liver ( total splanchnic tissues) were measured at 19 and 9 d prepartum and at 11, 21, 33, and 83 d in milk ( DIM) in 5 multiparous Holstein-Friesian cows. Cows were fed a grass silage-based gestation ration initially and a corn silage-based lactation ration peripartum and postpartum. Meals were fed at 8-h intervals and hourly (n = 8) measures of splanchnic metabolism were started before ( 0730 h and 0830 h) feeding at 0830 h. Dry matter intakes (DMI) at 19 and 9 d prepartum were not different. Metabolism changes measured from 19 to 9 d prepartum were lower arterial insulin and acetate, higher arterial nonesterified fatty acids and increased net liver removal of glycerol. After calving, PDV and liver blood flow and oxygen consumption more than doubled as DMI and milk yield increased, but 85 and 93% of the respective increases in PDV and liver blood flow at 83 DIM had occurred by 11 DIM. Therefore, factors additional to DMI must also contribute to increased blood flow in early lactation. Most postpartum changes in net PDV and liver metabolism could be attributed to increases in DMI and digestion or increased milk yield and tissue energy loss. Glucose release was increasingly greater than calculated requirements as DIM increased, presumably as tissue energy balance increased. Potential contributions of lactate, alanine, and glycerol to liver glucose synthesis were greatest at 11 DIM but decreased by 83 DIM. Excluding alanine, there was no evidence of an increased contribution of amino acids to liver glucose synthesis is required in early lactation. Increased net liver removal of propionate (69%), lactate (20%), alanine (8%), and glycerol (4%) can account for increased liver glucose release in transition cows from 9 d before to 11 d after calving.

Rates of production of acetate, propionate, and butyrate in the rumen of lactating dairy cows given normal and low-roughage diets

Five lactating dairy cows with a permanent cannula in the rumen were given ( kg DM/d) a normal diet (7.8 concentrates, 5.1 hay) or a low-roughage (LR) diet (11.5 concentrates, 1.2 hay) in two meals daily in a two-period crossover design. Milk fat (g/kg) was severely reduced on diet LR. To measure rates of production of individual volatile fatty acids (VFA) in the rumen, 0.5 mCi 1-C-14-acetic acid, 2-C-14-propionic acid, or 1-C-14-n-butyric acid were infused into the rumen for 22 h at intervals of 2 to 6 d; rumen samples were taken over the last 12 h. To measure rumen volume, we infused Cr-EDTA into the rumen continuously, and polyethylene glycol was injected 2 h before the morning feed. Results were very variable, so volumes measured by rumen emptying were used instead. Net production of propionic acid more than doubled on LR, but acetate and butyrate production was only numerically lower. Net production rates pooled across both diets were significantly related to concentrations for each VFA. Molar proportions of net production were only slightly higher than molar proportions of concentrations for acetate and propionate but were lower for butyrate. The net energy value (MJ/d) of production of the three VFA increased from 89.5 on normal to 109.1 on LR, equivalent to 55 and 64% of digestible energy, respectively. Fully interchanging, three-pool models of VFA C fluxes are presented. It is concluded that net production rates of VFA can be measured in non-steady states without the need to measure rumen volumes.

Recent advances in the application of in vitro systems to plant improvement

The horticultural industry was instrumental in the early development and exploitation of genetic techniques over a century ago. This review will describe recent advances in a range of in vitro methods and their application to plant breeding, with especial emphasis on horticultural crops. These methods include improvements in the efficiency of haploid breeding techniques in many fruit and vegetable species using either microspore-derived or ovule-derived plants. Significant molecular information is now available to supplement these essentially empirical approaches and this may enable the more predictable application of these technologies in previously intransigent crops. Similarly there are now improved techniques for isolation of somatic hybrids, by application of either in vitro fertilisation or the culture of excised ovules from interspecific crosses. In addition to examples taken from the traditional scientific literature, emphasis will also be given to the use of patent databases as a valuable source of information on recent novel technologies developed in the commercial world.

A functional genomics approach reveals novel quantitative trait loci associated with platelet signalling pathways

Platelet response to activation varies widely between individuals but shows interindividual consistency and strong heritability. The genetic basis of this variation has not been properly explored. We therefore systematically measured the effect on function of sequence variation in 97 candidate genes in the collagen and adenosine-diphosphate (ADP) signaling pathways. Resequencing of the genes in 48 European DNA samples nearly doubled the number of known single nucleotide polymorphisms (SNPs) and informed the selection of 1327 SNPs for genotyping in 500 healthy Northern European subjects with known platelet responses to collagen-related peptide (CRP-XL) and ADP. This identified 17 novel associations with platelet function (P < .005) accounting for approximately 46% of the variation in response. Further investigations with platelets of known genotype explored the mechanisms behind some of the associations. SNPs in PEAR1 associated with increased platelet response to CRP-XL and increased PEAR1 protein expression after platelet degranulation. The minor allele of a 3' untranslated region (UTR) SNP (rs2769668) in VAV3 was associated with higher protein expression (P = .03) and increased P-selectin exposure after ADP activation (P = .004). Furthermore the minor allele of the intronic SNP rs17786144 in ITPR1 modified Ca2+ levels after activation with ADP (P < .004). These data provide novel insights into key hubs within platelet signaling networks.

Longevity, early emergence and body size in a pollinating fig wasp - implications for stability in a fig-pollinator mutualism

1. Fig trees (Ficus) are pollinated only by agaonid wasps, whose larvae also gall fig ovules. Each ovule develops into either a seed (when pollinated) or a wasp (when an egg is also laid inside) but not both. 2. Ovipositing wasps (foundresses) favour ovules near the centre of the enclosed inflorescence (syconium or 'fig'), leaving ovules near the outer wall to develop into seeds. This spatial stratification of wasps and seeds ensures reproduction in both partners, and thereby enables mutualism persistence. However, the mechanism(s) responsible remain(s) unknown. 3. Theory shows that foundresses will search for increasingly rare inner ovules and ignore outer ovules, as long as ovipositing in outer ovules is sufficiently slow and/or if inner ovules confer greater fitness to wasps. The fig-pollinator mutualism can therefore be stabilized by strong time constraints on foundresses and by offspring fitness gradients over variation in ovule position. 4. Female fig wasps cannot leave their galls without male assistance. We found that females in outer ovules were unlikely to be released. Inner ovules thus have added value to foundresses, because their female offspring are more likely to mate and disperse. 5. For those offspring that did emerge, gall position (inner/outer) and body size did not influence the order in which female pollinators exited syconia, nor did early emerging wasps enjoy increased life spans. 6. We also found that the life spans of female wasps nearly doubled when given access to moisture. We suggest that conflict resolution in the fig-pollinator mutualism may thus be influenced by tropical seasonality, because wasps may be less able to over-exploit ovules in dry periods due to time constraints.

Hemokinins and endokinins

The mammalian tachykinins are a family of peptides that, until recently, has included substance P (SP), neurokinin A and neurokinin B. Since, the discovery of a third preprotachykinin gene (TAC4), the number of tachykinins has more than doubled to reveal several species-divergent peptides. This group includes hemokinin-1 (HK-1) in mouse and rat, endokinin-1 (EK-1) in rabbit, and EKA, EKB, human HK-1 (hHK-1) and hHK(4-11) in humans. Each exhibits a remarkable selectivity and potency for the tachykinin NK1 receptor similar to SP. Their peripheral expression has led to the proposal that they are the endogenous peripheral SP-like endocrine/paracrine agonists where SP is not expressed. Moreover, their strong cross-reactivity with a specific SP antibody leads us to question many of the proposed locations and roles of SP in the periphery. Additionally, three orphan tachykinin gene-related peptides are identified on TAC4, in rabbit, EK-2 and in humans, EKC and EKD.

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.

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.

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.