Search results for "Modeling and Simulation"
showing 10 items of 1561 documents
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species.
2018
International audience; Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast …
Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis.
2020
The bacterial and fungal community involved in ambrosia beetle fungiculture remains poorly studied compared to the famous fungus-farming ants and termites. Here we studied microbial community dynamics of laboratory nests, adults, and brood during the life cycle of the sugarcane shot hole borer, Xyleborus affinis. We identified a total of 40 fungal and 428 bacterial operational taxonomic units (OTUs), from which only five fungi (a Raffaelea fungus and four ascomycete yeasts) and four bacterial genera (Stenotrophomonas, Enterobacter, Burkholderia, and Ochrobactrum) can be considered the core community playing the most relevant symbiotic role. Both the fungal and bacterial populations varied s…
Molecular signatures of silencing suppression degeneracy from a complex RNA virus
2021
As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA sil…
Energy intake functions and energy budgets of ectotherms and endotherms derived from their ontogenetic growth in body mass and timing of sexual matur…
2017
Abstract Ectothermic and endothermic vertebrates differ not only in their source of body temperature (environment vs. metabolism), but also in growth patterns, in timing of sexual maturation within life, and energy intake functions. Here, we present a mathematical model applicable to ectothermic and endothermic vertebrates. It is designed to test whether differences in the timing of sexual maturation within an animal's life (age at which sexual maturity is reached vs. longevity) together with its ontogenetic gain in body mass (growth curve) can predict the energy intake throughout the animal's life (food intake curve) and can explain differences in energy partitioning (between growth, repro…
Plankton Tracker: A novel integrated system to investigate the dynamic sinking behavior in phytoplankton
2020
Abstract Phytoplankton sinking is an important property that can determine community composition, affecting nutrient and light absorption in the photic zone, and influencing biogeochemical cycling via material loss to the deep ocean. To date, the difficulty in exploring the sinking processes is partly due to methodological limitations in measuring phytoplankton sinking rate. However, in the last decade, works have illustrated various methods based on some non-invasive and low perturbing approaches (laser scanner, video-microscopy, fluorescence spectroscopy). In this study, we review the methods for sinking rate estimation and describe the Plankton Tracker, a novel integrated system to inves…
Coupling agent-based with equation-based models to study spatially explicit megapopulation dynamics
2018
International audience; The incorporation of the spatial heterogeneity of real landscapes into population dynamics remains extremely difficult. We propose combining equation-based modelling (EBM) and agent-based modelling (ABM) to overcome the difficulties classically encountered. ABM facilitates the description of entities that act according to specific rules evolving on various scales. However, a large number of entities may lead to computational difficulties (e.g., for populations of small mammals, such as voles, that can exceed millions of individuals). Here, EBM handles age-structured population growth, and ABM represents the spreading of voles on large scales. Simulations applied to t…
Identifying small pelagic Mediterranean fish schools from acoustic and environmental data using optimized artificial neural networks
2019
Abstract The Common Fisheries Policy of the European Union aims to exploit fish stocks at a level of Maximum Sustainable Yield by 2020 at the latest. At the Mediterranean level, the General Fisheries Commission for the Mediterranean (GFCM) has highlighted the importance of reversing the observed declining trend of fish stocks. In this complex context, it is important to obtain reliable biomass estimates to support scientifically sound advice for sustainable management of marine resources. This paper presents a machine learning methodology for the classification of pelagic species schools from acoustic and environmental data. In particular, the methodology was tuned for the recognition of an…
Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
2008
The rate of mutation is central to evolution. Mutations are required for adaptation, yet most mutations with phenotypic effects are deleterious. As a consequence, the mutation rate that maximizes adaptation will be some intermediate value. Here, we used digital organisms to investigate the ability of natural selection to adjust and optimize mutation rates. We assessed the optimal mutation rate by empirically determining what mutation rate produced the highest rate of adaptation. Then, we allowed mutation rates to evolve, and we evaluated the proximity to the optimum. Although we chose conditions favorable for mutation rate optimization, the evolved rates were invariably far below the optimu…
Integrated membrane bioreactors modelling: A review on new comprehensive modelling framework
2021
International audience; Integrated Membrane Bioreactor (MBR) models, combination of biological and physical models, have been representing powerful tools for the accomplishment of high environmental sustainability. This paper, produced by the International Water Association (IWA) Task Group on Membrane Modelling and Control, reviews the state-of-the-art, identifying gaps for future researches, and proposes a new integrated MBR modelling framework. In particular, the framework aims to guide researchers and managers in pursuing good performances of MBRs in terms of effluent quality, operating costs (such as membrane fouling, energy consumption due to aeration) and mitigation of greenhouse gas…
Exploring the development of scientific research on Marine Protected Areas: From conservation to global ocean sustainability
2021
Abstract Marine Protected Areas (MPAs) are playing a central role in the achievement of ocean sustainability and, since 2000, their global coverage has increased over ten times. The success of MPAs, and therefore the delivery of their potential outcomes for human well-being and global sustainability, requires multi-disciplinary, holistic, and comprehensive approaches for its achievement. In this study, the global scientific literature on MPAs was quantitatively reviewed through bibliometrics approaches, investigating patterns and trends in its development over time. In particular, bibliometric network and citation burst analyses of keywords were performed using VOSviewer and CiteSpace softw…