Manipulating the sensitivity of signal-induced repression: quantification and consequences of altered brinker gradients.

Traditionally, the analysis of gene regulatory regions suffered from the caveat that it was restricted to artificial contexts (e.g. reporter constructs of limited size). With the advent of the BAC recombineering technique, genomic constructs can now be generated to test regulatory elements in their endogenous environment. The expression of the transcriptional repressor brinker (brk) is negatively regulated by Dpp signaling. Repression is mediated by small sequence motifs, the silencer elements (SEs), that are present in multiple copies in the regulatory region of brk. In this work, we manipulated the SEs in the brk locus. We precisely quantified the effects of the individual SEs on the Brk gradient in the wing disc by employing a 1D data extraction method, followed by the quantification of the data with reference to an internal control. We found that mutating the SEs results in an expansion of the brk expression domain. However, even after mutating all predicted SEs, repression could still be observed in regions of maximal Dpp levels. Thus, our data point to the presence of additional, low affinity binding sites in the brk locus.

Sensitivity loss by Corynespora cassiicola, isolated from soybean, to the fungicide carbendazim

Soybean target leaf spot, caused by the fungus Corynespora cassiicola, is controlled especially by leaf application of fungicides. In the last seasons, in the central-west region of Brazil, the disease chemical control efficiency has been low. This led to the hypothesis that the control failure could be due to the reduction or loss of the fungus sensitivity to fungicides. To clarify this fact, in vitro experiments were conducted to determine mycelial sensitivity of five C. cassiicola isolates to fungicides. Mycelial growth was assessed based on the growth of the mycelium on the culture medium, in Petri dishes. The medium potato-dextrose-agar was supplemented with the concentrations 0; 0.01; 0.1; 1; 10; 20 and 40 mg/L of the active ingredients carbendazim, cyproconazole, epoxiconazole, flutriafol and tebuconazole. The experiment was conducted and repeated twice in a controlled environment, temperature of 25±2ºC and photoperiod of 12 hours. Data on the percentage of mycelial inhibition were subjected to logarithmic regression analysis and the concentration that inhibits 50% of the mycelial growth (IC50) was calculated. Loss of sensitivity to carbendazim was observed for three fungal isolates, IC50 > 40 mg/L. Considering all five isolates, the IC50 for tebuconazole ranged from 1.89 to 2.80 mg/L, for epoxiconazol from 2.25 to 2.91, for cyproconazole from 9.21 to 20.32 mg/L, and for flutriafol from 0.77 to 2.18 mg/L. In the absence of information on the reference IC50 determined for wild isolates, the lowest values generated in our study can be used as standard to monitor the fungus sensitivity.

Learning Robot Environment through Simulation

Traditionally simulators have been used extensively in robotics to develop robotic systems without the need to build expensive hardware. However, simulators can be also be used as a “memory”for a robot. This allows the robot to try out actions in simulation before executing them for real. The key obstacle to this approach is an uncertainty of knowledge about the environment. The goal of the Master’s Thesis work was to develop a method, which allows updating the simulation model based on actual measurements to achieve a success of the planned task. OpenRAVE was chosen as an experimental simulation environment on planning,trial and update stages. Steepest Descent algorithm in conjunction with Golden Section search procedure form the principle part of optimization process. During experiments, the properties of the proposed method, such as sensitivity to different parameters, including gradient and error function, were examined. The limitations of the approach were established, based on analyzing the regions of convergence.

Analysis of heart rate control to assess thermal sensitivity responses in Brazilian toads

In anurans, changes in ambient temperature influence body temperature and, therefore, energy consumption. These changes ultimately affect energy supply and, consequently, heart rate (HR). Typically, anurans living in different thermal environments have different thermal sensitivities, and these cannot be distinguished by changes in HR. We hypothesized that Rhinella jimi (a toad from a xeric environment that lives in a wide range of temperatures) would have a lower thermal sensitivity regarding cardiac control than R. icterica (originally from a tropical forest environment with a more restricted range of ambient temperatures). Thermal sensitivity was assessed by comparing animals housed at 15° and 25°C. Cardiac control was estimated by heart rate variability (HRV) and heart rate complexity (HRC). Differences in HRV between the two temperatures were not significant (P=0.214 for R. icterica and P=0.328 for R. jimi), whereas HRC differences were. All specimens but one R. jimi had a lower HRC at 15°C (all P<0.01). These results indicate that R. jimi has a lower thermal sensitivity and that cardiac control is not completely dependent on the thermal environment because HRC was not consistently different between temperatures in all R. jimi specimens. This result indicates a lack of evolutive trade-offs among temperatures given that heart rate control at 25°C is potentially not a constraint to heart rate control at 15°C.

Prevalence and Antibiotic sensitivity of Escherichia coli in Extensive Brackish water Aquaculture Ponds

Prevalence and antibiotic resistance of Escherichia coli in the water and sediment samples of brackish water aquaculture ponds adjacent to Cochin backwaters was analysed. More than 50% of the water samples and more than 80% of sediment samples from all the sampling stations were tested positive for £. coli. Risk assessment of the E. coli strains was carried out using multiple antibiotic resistance (MAR) indexing. Majority of the strains were found to be multiple antibiotic resistant suggesting their origin from high risk sources of contamination such as human where antibiotics are frequently used. While none of the £. coli strains were resistant against amikacin, chloramphenicol, streptomycin and trimethoprim, considerable levels of resistance was encountered against ampicillin, erythromycin, penicillin G and vancomycin. High prevalence of £. coli in the water and sediment samples of this extensive brackish water ponds indicates high degree of faecal pollution of this environment. The high risk nature of the strains warrants efficient post harvest and processing measures to avoid health risk to consumers

Ensemble yield simulations: crop and climate uncertainties, sensitivity to temperature and genotypic adaptation to climate change

Estimates of the response of crops to climate change rarely quantify the uncertainty inherent in the simulation of both climate and crops. We present a crop simulation ensemble for a location in India, perturbing the response of both crop and climate under both baseline (12 720 simulations) and doubled-CO2 (171720 simulations) climates. Some simulations used parameter values representing genotypic adaptation to mean temperature change. Firstly, observed and simulated yields in the baseline climate were compared. Secondly, the response of yield to changes in mean temperature was examined and compared to that found in the literature. No consistent response to temperature change was found across studies. Thirdly, the relative contribution of uncertainty in crop and climate simulation to the total uncertainty in projected yield changes was examined. In simulations without genotypic adaptation, most of the uncertainty came from the climate model parameters. Comparison with the simulations with genotypic adaptation and with a previous study suggested that the relatively low crop parameter uncertainty derives from the observational constraints on the crop parameters used in this study. Fourthly, the simulations were used, together with an observed dataset and a simple analysis of crop cardinal temperatures and thermal time, to estimate the potential for adaptation using existing cultivars. The results suggest that the germplasm for complete adaptation of groundnut cultivation in western India to a doubled-CO2 environment may not exist. In conjunction with analyses of germplasm and local management

An integrated mathematical model to evaluate nutrient partition in dairy cattle between the animal and its environment

In the past decade, a number of mechanistic, dynamic simulation models of several components of the dairy production system have become available. However their use has been limited due to the detailed technical knowledge and special software required to run them, and the lack of compatibility between models in predicting various metabolic processes in the animal. The first objective of the current study was to integrate the dynamic models of [Brit. J. Nutr. 72 (1994) 679] on rumen function, [J. Anim. Sci. 79 (2001) 1584] on methane production, [J. Anim. Sci. 80 (2002) 2481 on N partition, and a new model of P partition. The second objective was to construct a decision support system to analyse nutrient partition between animal and environment. The integrated model combines key environmental pollutants such as N, P and methane within a nutrient-based feed evaluation system. The model was run under different scenarios and the sensitivity of various parameters analysed. A comparison of predictions from the integrated model with the original simulation models showed an improvement in N excretion since the integrated model uses the dynamic model of [Brit. J. Nutr. 72 (1994) 6791 to predict microbial N, which was not represented in detail in the original model. The integrated model can be used to investigate the degree to which production and environmental objectives are antagonistic, and it may help to explain and understand the complex mechanisms involved at the ruminal and metabolic levels. A part of the integrated model outputs were the forms of N and P in excreta and methane, which can be used as indices of environmental pollution. (C) 2004 Elsevier B.V All rights reserved.

A model of seed dormancy in wild oats (Avena fatua) for investigating genotype x environment interactions

Dormancy is an adaptive trait in seed populations that helps ensure that seed germination is distributed over time and occurs in environmental conditions suitable for seedling growth. Several genes.. associated with seed dormancy in various plant species, have been integrated into a hypothetical dormancy model for Avena fatua L. (wild oats). Generally, the synthesis of, and sensitivity to, abscisic acid (ABA) during imbibition determines whether genes similar to those during maturation are expressed leading to a maintenance of dormancy during extended imbibition. Alternatively, there may be a shift towards expression of genes associated with gibberellins leading to germination. Environmental factors during maturation, after-ripening and imbibition are likely to interact with the genotype to affect gene expression and hence whether or not a seed germinates. In spite of the difficulties of working on a hexaploid species, A. fatua was selected for study because of its worldwide importance as a weed. Dormant and non-dormant genotypes of this species were also available. Gene expression studies are being carried out on three A.fatua genotypes produced tinder different environmental conditions to investigate the role of specific genes in dormancy and genotype X environment interactions in relation to dormancy.

Measurement of mother-infant interactions and the home environment in a European setting: preliminary results from a cross-cultural study

Background Infant development is adversely affected in the context of postnatal depression. This relationship may be mediated by both the nature of early mother-infant interactions and the quality of the home environment. Aim To establish the usefulness of the Global Ratings Scales of Mother-Infant Interaction and the Infant-Toddler version of the Home Observation for the Measurement of the Environment (IT-HOME), and to test expected associations of the measures with characteristics of the social context and with major or minor depression. Method Both assessments were administered postnatally in four European centres; 144 mothers were assessed with the Global Ratings Scales and 114 with the IT-HOME. Affective disorder was assessed by means of the Structured Clinical Interview for DSM-IV Disorders. Results Analyses of mother-infant interaction indicated no main effect for depression but maternal sensitivity to infant behaviour was associated with better infant communication, especially for women who were not depressed. Poor overall emotional support also reduced sensitivity scores. Poor support was also related to poorer IT-HOME scores, but there was no effect of depression. Conclusions The Global Ratings Scales were effectively applied but there was less evidence of the usefulness of the IT-HOME. Declaration of interest None.

Modelling of the natural chlorine cycling in a coniferous stand: implications for chlorine-36 behaviour in a contaminated forest environment

Considered as one of the most available radionuclide in soileplant system, 36Cl is of potential concern for long-term management of radioactive wastes, due to its high mobility and its long half-life. To evaluate the risk of dispersion and accumulation of 36Cl in the biosphere as a consequence of a potential contamination, there is a need for an appropriate understanding of the chlorine cycling dynamics in the ecosystems. To date, a small number of studies have investigated the chlorine transfer in the ecosystem including the transformation of chloride to organic chlorine but, to our knowledge, none have modelled this cycle. In this study, a model involving inorganic as well as organic pools in soils has been developed and parameterised to describe the biogeochemical fate of chlorine in a pine forest. The model has been evaluated for stable chlorine by performing a range of sensitivity analyses and by comparing the simulated to the observed values. Finally a range of contamination scenarios, which differ in terms of external supply, exposure time and source, has been simulated to estimate the possible accumulation of 36Cl within the different compartments of the coniferous stand. The sensitivity study supports the relevancy of the model and its compartments, and has highlighted the chlorine transfers affecting the most the residence time of chlorine in the stand. Compared to observations, the model simulates realistic values for the chlorine content within the different forest compartments. For both atmospheric and underground contamination scenarios most of the chlorine can be found in its organic form in the soil. However, in case of an underground source, about two times less chlorine accumulates in the system and proportionally more chlorine leaves the system through drainage than through volatilisation.

The sensitivity of the tropical circulation and Maritime Continent precipitation to climate model resolution

The dependence of the annual mean tropical precipitation on horizontal resolution is investigated in the atmospheric version of the Hadley Centre General Environment Model (HadGEM1). Reducing the grid spacing from about 350 km to 110 km improves the precipitation distribution in most of the tropics. In particular, characteristic dry biases over South and Southeast Asia including the Maritime Continent as well as wet biases over the western tropical oceans are reduced. The annual-mean precipitation bias is reduced by about one third over the Maritime Continent and the neighbouring ocean basins associated with it via the Walker circulation. Sensitivity experiments show that much of the improvement with resolution in the Maritime Continent region is due to the specification of better resolved surface boundary conditions (land fraction, soil and vegetation parameters) at the higher resolution. It is shown that in particular the formulation of the coastal tiling scheme may cause resolution sensitivity of the mean simulated climate. The improvement in the tropical mean precipitation in this region is not primarily associated with the better representation of orography at the higher resolution, nor with changes in the eddy transport of moisture. Sizeable sensitivity to changes in the surface fields may be one of the reasons for the large variation of the mean tropical precipitation distribution seen across climate models.

Controls on inorganic nitrogen leaching from Finnish catchments assessed using a sensitivity and uncertainty analysis of the INCA-N model

The semi-distributed, dynamic INCA-N model was used to simulate the behaviour of dissolved inorganic nitrogen (DIN) in two Finnish research catchments. Parameter sensitivity and model structural uncertainty were analysed using generalized sensitivity analysis. The Mustajoki catchment is a forested upstream catchment, while the Savijoki catchment represents intensively cultivated lowlands. In general, there were more influential parameters in Savijoki than Mustajoki. Model results were sensitive to N-transformation rates, vegetation dynamics, and soil and river hydrology. Values of the sensitive parameters were based on long-term measurements covering both warm and cold years. The highest measured DIN concentrations fell between minimum and maximum values estimated during the uncertainty analysis. The lowest measured concentrations fell outside these bounds, suggesting that some retention processes may be missing from the current model structure. The lowest concentrations occurred mainly during low flow periods; so effects on total loads were small.

Temporal sensitivity of rice seed development from spikelet fertility to viable mature seed to extreme-temperature

Extreme temperature during reproductive development affects rice (Oryza sativa L.) yield and seed quality. A controlled-environment reciprocal-transfer experiment was designed where plants from two japonica cultivars were grown at 28/24 ⁰C and moved to 18/14 ⁰C and vice versa, or from 28/24 to 38/34 ⁰C and vice versa, for 7-d periods to determine the respective temporal pattern of sensitivity of spikelet fertility, yield, and seed viability to each temperature extreme. Spikelet fertility and seed yield per panicle were severely reduced by extreme temperature in the 14 d period prior to anthesis; and both cultivars were affected at 38/34 ⁰C while only cv. Gleva was affected at 18/14 ºC. The damage was greater the earlier the panicles were stressed within this period. Later-exserted panicles compensated only partly for yield loss. Seed viability was significantly reduced by 7-d exposure to 38/34 ⁰C or 18/14 ⁰C at 1 to 7 and 1 to 14 d after anthesis, respectively, in cv. Gleva. Cultivar Taipei 309 was not affected by 7 d exposure at 18/14 ⁰C; and no consistent temporal pattern of sensitivity was evident at 38/34 ⁰C. Hence, brief exposure to low or high temperature was most damaging to spikelet fertility and yield 14 to 7 d before anthesis, coinciding with microsporogenesis; and it was almost as damaging around anthesis. Seed viability was most vulnerable to low or high temperature in the 7 or 14 d after anthesis, when histodifferentiation occurs.