Modelling of signal transduction in yeast – sensitivity and model analysis

Experimental research has revealed components and mechanisms of cellular stress sensing and adaptation. In addition, mathematical modelling has proven to foster the understanding of some basic principles of signal transduction and signal processing as well as of sensitivity and robustness of information perception and cellular response. Here we review some modelling principles, results and open questions exemplified for a model organism, the yeast Saccharomyces cerevisiae

The plant phenological online database (PPODB): An online database for long-term phenological data

We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de

The plant phenological online database (PPODB): An online database for long-term phenological data

We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de

A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast

Cells must be able to process multiple information in parallel and, moreover, they must also be able to combine this information in order to trigger the appropriate response. This is achieved by wiring signalling pathways such that they can interact with each other, a phenomenon often called crosstalk. In this study, we employ mathematical modelling techniques to analyse dynamic mechanisms and measures of crosstalk. We present a dynamic mathematical model that compiles current knowledge about the wiring of the pheromone pathway and the filamentous growth pathway in yeast. We consider the main dynamic features and the interconnections between the two pathways in order to study dynamic crosstalk between these two pathways in haploid cells. We introduce two new measures of dynamic crosstalk, the intrinsic specificity and the extrinsic specificity. These two measures incorporate the combined signal of several stimuli being present simultaneously and seem to be more stable than previous measures. When both pathways are responsive and stimulated, the model predicts that (a) the filamentous growth pathway amplifies the response of the pheromone pathway, and (b) the pheromone pathway inhibits the response of filamentous growth pathway in terms of mitogen activated protein kinase activity and transcriptional activity, respectively. Among several mechanisms we identified leakage of activated Ste11 as the most influential source of crosstalk. Moreover, we propose new experiments and predict their outcomes in order to test hypotheses about the mechanisms of crosstalk between the two pathways. Studying signals that are transmitted in parallel gives us new insights about how pathways and signals interact in a dynamical way, e.g., whether they amplify, inhibit, delay or accelerate each other

Phenology of the alfalfa weevil (Coleoptera: Curculionidae) in alfalfa grown for seed in southern Alberta

An algorithm to forecast occurrence of four life-stage categories of the alfalfa weevil, Hypera postica (Gyllenhal), was derived from data collected in fields of seed alfalfa, Medicago sativa (L.) in southern Alberta. The algorithm assumes a linear developmental response to mean daily temperatures above a threshold of 10C. Overwintering adults were active after the accumulation of 100 degree-days above 10C (DD10), and were scarce by 250-300 DD10. Early larvae (instars 1 + 2) were found beginning at 120 DD10 and their numbers peaked at 200 DD10. Late larvae (instars 3 + 4) were present beginning at 160 DD10 and their numbers peaked at 350 DD10. New generation adults appeared after 500 DD10. In southern Alberta, alfalfa seed production is frequently combined with honey production. This algorithm enables producers to forecast the occurrence of the most damaging stage of alfalfa weevils which may require control with insecticides; the advance notice enables optimal timing of treatment and also allows apiarists to minimize pesticide mortality by moving or confining their bees.Key words: Thermal units; degree days; simulation; phenolog

Nuclear fusion and renewable energy forms: Are they compatible?

Nuclear fusion can be considered as a base-load power plant technology: High investment costs and limited operational flexibility require continuous operation. Wind and solar, on the other hand, as the putative main pillars of a future renewable energy system, are intermittent power sources. The resulting variations that occur on many different time scales require at first sight a rather flexible back-up system to balance this stochastic behavior. Fusion would appear not to be well suited for this task. The situation changes, however, if a large-scale renewable energy system is envisaged based on a transnational, or even transcontinental power grid. The present paper discusses a possible European power system in the year 2050 and beyond. A high percentage share of renewable energies and a strong power grid spanning the whole of Europe and involving neighboring countries, in particular those in North Africa, are assumed. The linear programming model URBS is used to describe the power system. The model optimizes the overall system costs and simulates power plant operation with an hourly resolution for one whole year. The geographical resolution is at least at the country level. The renewable technologies are modeled first on a more local level and then summed together at the country or regional level. The results indicate that the smoothing effects of the large-scale power grid transform the intermittent renewable supply, which is then more compatible with base-load power plants such as fusion reactors

Low-emissivity impact craters on Venus

An analysis of 144 impact craters on Venus has shown that 11 of these have floors with average emissivities lower than 0.8. The remaining craters have emissivities between 0.8 and 0.9, independent of the specific backscatter cross section of the crater floors. These 144 impact craters were chosen from a possible 164 craters with diameters greater than 30 km as identified by researchers for 89 percent of the surface of Venus. We have only looked at craters below 6053.5 km altitude because a mineralogical change causes high reflectivity/low emissivity above the altitude. We have also excluded all craters with diameters smaller than 30 km because the emissivity footprint at periapsis is 16 x 24 km and becomes larger at the poles

The wetting state of water on a rose petal

The rose petal features surface structures that offer unique wetting properties. A water droplet placed on a rose petal forms a high contact angle but exhibits significant contact angle hysteresis, such that relatively large droplets remain stuck to the surface when it is tilted. Understanding this distinctive ‘parahydrophobic’ wetting behavior can provide insight into the design of highly nonwetting, yet highly adhesive, synthetic surfaces. Surface features of the rose petal are characterized via focused ion beam scanning electron microscopy, which reveals microscale papillae that are partially covered with nanoscale striae. The wetting state of water on a rose petal is directly visualized using confocal microscopy. This experimental evidence confirms the microscale wetting behavior on the papillae, but cannot resolve the wetting behavior on the nanoscale striae. To infer the wetting state on the striae, an energyminimization- based model is developed and the results from the model are compared to the experimental evidence. In combination, the experimental findings and the model results reveal the wetting state of water on the hierarchical surface structure and explain the macroscopic wetting behavior of the rose petal

Tempo and mode of early gene loss in endosymbiotic bacteria from insects

BACKGROUND: Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts. RESULTS: Our results demonstrate that genes lost in the early stages of symbiosis were on average less selectively constrained than genes conserved in any of the extant symbiotic strains studied. These results also extend to more recent events of gene losses (i.e. among Buchnera strains) that still tend to concentrate on genes with low adaptive bias in E. coli and high evolutionary rates both in free-living and in symbiotic lineages. In addition, we analyzed the physical organization of gene losses for early steps of symbiosis acquisition under the hypothesis of a common origin of different symbioses. In contrast with previous findings we show that gene losses mostly occurred through loss of rather small blocks and mostly in syntenic regions between at least one of the symbionts and present-day E. coli. CONCLUSION: At both ancient and recent stages of symbiosis evolution, gene loss was at least partially influenced by selection, highly conserved genes being retained more readily than lowly conserved genes: although losses might result from drift due to the bottlenecking of endosymbiontic populations, we demonstrated that purifying selection also acted by retaining genes of greater selective importance

Effect of burning alfalfa stubble for insect pest control on seed yield

Burning alfalfa (Medicago sativa (L.) stubble in the spring has been shown to be effective in reducing some insect pest populations. A study was conducted to detennine the long-tenn effect of this practice on seed yield. Plots were established at Lethbridge, Alberta, and burned in the spring or fall at various heights of plant growth from 1983 to 1989, with one half of each plot treated annually with insecticides when the pest insects were in their most vulnerable stage. Yields from burned treatments were not significantly different from unburned ones for the years 1983 to 1986, and 1988. In 1987, treatments burned in the fall had significantly higher yields than other treatments. Burning at 15-20 cm of growth significantly reduced yield compared to burning before spring growth. In 1989, yields from plots burned at 15-20 cm of growth were significantly lower than those burned every fall or spring. Insecticide treated plots had significantly higher yields in all years except 1983. Burning in the fall, or in the spring before growth, increased gross economic returns, but insecticide treatment gave the highest returns