Simulation of mitochondrial metabolism using multi-agents system

Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or enzymatic complex build of several subunits). In our Mitochondria in Silico Project, MitoScop, we study the metabolism of the mitochondria, an intra-cellular organelle. Many ordinary differential equation models are available in the literature. They well fit experimental results on flux values inside the metabolic pathways, but many parameters are di$\pm$cult to transcribe with such models: localization of enzymes, rules about the reactions scheduler, etc Moreover, a model of a significant part of mitochondrial metabolism could become very complex and contain more than 50 equations. In this context, the multi-agents systems appear as an alternative to model the metabolic pathways. Firstly, we have looked after membrane design. The mitochondria is a particular case because the inner mitochondrial space, ie matricial space, is delimited by two membranes: the inner and the outer one. In addition to matricial enzymes, other enzymes are located inside the membranes or in the inter-membrane space. Analysis of mitochondrial metabolism must take into account this kind of architecture

Estimating landmarks on 2D images of beetle mandibles

Studying links between phenotype/genotype and agricultural practices is one of the main topics in agronomy research. Phenotypes can be characterized by informations like age, sex of animals/plants and more and more often with the help of image analysis of their morphology. From now, getting good quality of images for numerous individuals is easy but that leads to design automatic procedures to replace manual exploration of such amount of images. Several bottlenecks have been identified to analyze automatically images. One of them is segmentation of selected area and/or shapes, and another well-known one is setting automatically morphometric landmarks. Landmarks are points on the object which can be used to identify or to classify the objects. It exists a lot of methods to experiment landmarks setting, depending on the image contents. This work has been initiated by using the article of Palaniswamy et al. "Automatic identification of landmarks in digital images"[6]. They proposed a method based on calculus of a probabilistic Hough transform coupling to a template matching algorithm. They applied their method to the Drosophilia wings. In our study, we have gotten a set of 291 beetles . For each one 2D images of 5 different parts of their anatomy have been taken: mandibles left and right, head, pronotum and elytra. The first part of the project was to test how the Palaniswamy’s method could be used to analyze them. We have implemented all the required algorithms to compute positions of mandibles landmarks and compared the obtained results to landmarks which have been manually set by biologists. We will see that even positions automatically obtained are not fully precised, if we used centroid size to characterize mandibles, the size computed from automatic landmarks is closed to this one computed from the manual ones. Future works will focus on definition of a semi-landmarks procedure which would add some features as the measure of the curve between two landmarks

Towards landmarks prediction with Deep Network

International audienc

Confronting a spatialy explicit population model with biased random walk to agroecosystems complexity

Although a national strategy for the coexistence of GM and conventional/organic crops in Ireland has been published (McGill et al 2005) measures pertaining to the coexistence of GM and non-GM oilseed rape (OSR) crops was omitted pending the completion o

Understanding flying insect dispersion: Multiscale analyses of fragmented landscapes

International audienceA multiscale model was developed to simulate the rate of landing of a winged insect, the grain aphid, Sitobion avenae F. At a large scale (kilometric scale), it is convenient to use a deterministic model of their dispersion, based upon diffusion-advection-reaction partial derivative equations. At a small scale (hectometric scale), the process of site selection ('landing') is only partially understood, but is known to include the perception of field colour and landscape characteristics. Several hypotheses on aphids' behaviour were tested to simulate the rate of landing: the simulation was done by a cellular automata submodel under five different hypotheses on the precise organisation of the landing behaviour. We found a strong interaction between the effect of the proportion of wheat crops in the landscape and their spatial organisation. The spatial correlation between the places occupied by wheat crops appears crucial to determine the global rate of landing of the aerial insect stock. The shape of the response surface of landing rate against the proportion of surface occupied by wheat, and the spatial autocorrelation of wheat plots, appears very regular and relatively simple to model by ad hoc mathematical functions. Large scale simulations using the results of the small scale model in a diffusion-reaction equation solved numerically, showed that, on a real landscape extracted from a GIS on the whole Brittany region (western France), the spatial pattern of the aphid landing is sensitive to the hypothesis tested on their landing behaviour. This hierarchical modelling combining two different approaches at two different scales (mathematical deterministic equations on a large multi-kilometric scale, and partly stochastic cellular automata on a small hectometric scale), requires methods to validate its results in the field, in the framework of a decision support system. Such amultiscalemodel has a wide field of application including not only plant protection but also management and conservancy of animal species dispersing by flight

Simulation of mitochondrial metabolism using multi-agents system

International audienceMetabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or enzymatic complex build of several subunits). In our Mitochondria in Silico Project, MitoScop, we study the metabolism of the mitochondria, an intra-cellular organelle. Many ordinary differential equation models are available in the literature. They well fit experimental results on flux values inside the metabolic pathways, but many parameters are di±cult to transcribe with such models: localization of enzymes, rules about the reactions scheduler, etc Moreover, a model of a significant part of mitochondrial metabolism could become very complex and contain more than 50 equations. In this context, the multi-agents systems appear as an alternative to model the metabolic pathways. Firstly, we have looked after membrane design. The mitochondria is a particular case because the inner mitochondrial space, ie matricial space, is delimited by two membranes: the inner and the outer one. In addition to matricial enzymes, other enzymes are located inside the membranes or in the inter-membrane space. Analysis of mitochondrial metabolism must take into account this kind of architecture

Estimating landmarks on 2D images of beetle mandibles

Studying links between phenotype/genotype and agricultural practices is one of the main topics in agronomy research. Phenotypes can be characterized by informations like age, sex of animals/plants and more and more often with the help of image analysis of their morphology. From now, getting good quality of images for numerous individuals is easy but that leads to design automatic procedures to replace manual exploration of such amount of images. Several bottlenecks have been identified to analyze automatically images. One of them is segmentation of selected area and/or shapes, and another well-known one is setting automatically morphometric landmarks. Landmarks are points on the object which can be used to identify or to classify the objects. It exists a lot of methods to experiment landmarks setting, depending on the image contents. This work has been initiated by using the article of Palaniswamy et al. "Automatic identification of landmarks in digital images"[6]. They proposed a method based on calculus of a probabilistic Hough transform coupling to a template matching algorithm. They applied their method to the Drosophilia wings. In our study, we have gotten a set of 291 beetles . For each one 2D images of 5 different parts of their anatomy have been taken: mandibles left and right, head, pronotum and elytra. The first part of the project was to test how the Palaniswamy’s method could be used to analyze them. We have implemented all the required algorithms to compute positions of mandibles landmarks and compared the obtained results to landmarks which have been manually set by biologists. We will see that even positions automatically obtained are not fully precised, if we used centroid size to characterize mandibles, the size computed from automatic landmarks is closed to this one computed from the manual ones. Future works will focus on definition of a semi-landmarks procedure which would add some features as the measure of the curve between two landmarks

Relationship between the abundance of aphids and their natural enemies in crop fields and landscape composition.

International audienceWe investigated, over the course of two years, the importance of landscape context on the abundance of aphids and their natural carabid enemies, which may help to develop effective strategies for reduction of aphid outbreaks in agricultural landscapes. This was undertaken in 12 wheat fields and in 12 maize fields each year in an agricultural landscape in western France. Our study area was characterized by hedgerows surrounding arable ?elds and permanent grasslands. Some areas did not change much over a few decades, while ?eld enlargement and removal of hedges appeared in some places following agricultural intensi?cation,. The present paper aimed at examining if the landscape context around crop fields affected the abundance of aphids (either directly, or indirectly via their natural enemies) and if this effect depends on the landscape scale considered. We observed that the abundance of aphids in the field was associated with landscape composition at large scale (500 m and 800 m). There was a positive correlation between the abundance of the aphids and the proportion of woodland and grassland at these scales. There was a negative correlation between the abundance of carabids and the proportion of grassland and hedgerow around crop fields. The species richness of carabids was positively correlated with the proportion of hedgerows . We found that the proportion of grassy strips affect negatively the abundance of aphids in the wheat fields, and positively so in maize fields. Carabid abundance was positively correlated with the proportion of grassy strips at large scale in both types of cultures