Coulon A.,University Claude Bernard Lyon 1 |
Coulon A.,INSA Lyon |
Coulon A.,Rhone Alpes Complex Systems Institute IXXI |
Gandrillon O.,University Claude Bernard Lyon 1 |
And 3 more authors.
BMC Systems Biology | Year: 2010
Background: Gene promoters can be in various epigenetic states and undergo interactions with many molecules in a highly transient, probabilistic and combinatorial way, resulting in a complex global dynamics as observed experimentally. However, models of stochastic gene expression commonly consider promoter activity as a two-state on/off system. We consider here a model of single-gene stochastic expression that can represent arbitrary prokaryotic or eukaryotic promoters, based on the combinatorial interplay between molecules and epigenetic factors, including energy-dependent remodeling and enzymatic activities.Results: We show that, considering the mere molecular interplay at the promoter, a single-gene can demonstrate an elaborate spontaneous stochastic activity (eg. multi-periodic multi-relaxation dynamics), similar to what is known to occur at the gene-network level. Characterizing this generic model with indicators of dynamic and steady-state properties (including power spectra and distributions), we reveal the potential activity of any promoter and its influence on gene expression. In particular, we can reproduce, based on biologically relevant mechanisms, the strongly periodic patterns of promoter occupancy by transcription factors (TF) and chromatin remodeling as observed experimentally on eukaryotic promoters. Moreover, we link several of its characteristics to properties of the underlying biochemical system. The model can also be used to identify behaviors of interest (eg. stochasticity induced by high TF concentration) on minimal systems and to test their relevance in larger and more realistic systems. We finally show that TF concentrations can regulate many aspects of the stochastic activity with a considerable flexibility and complexity.Conclusions: This tight promoter-mediated control of stochasticity may constitute a powerful asset for the cell. Remarkably, a strongly periodic activity that demonstrates a complex TF concentration-dependent control is obtained when molecular interactions have typical characteristics observed on eukaryotic promoters (high mobility, functional redundancy, many alternate states/pathways). We also show that this regime results in a direct and indirect energetic cost. Finally, this model can constitute a framework for unifying various experimental approaches. Collectively, our results show that a gene - the basic building block of complex regulatory networks - can itself demonstrate a significantly complex behavior. © 2010 Coulon et al; licensee BioMed Central Ltd.
Baur A.H.,TU Berlin |
Thess M.,TU Berlin |
Thess M.,Rhone Alpes Complex Systems Institute IXXI |
Kleinschmit B.,TU Berlin |
And 2 more authors.
Journal of Urban Planning and Development | Year: 2014
As climate change mitigation becomes pervasive on all spatial scales, mitigation options related to urban spatial planning and behavioral change become increasingly important. Because transport energy consumption seems to scale inversely with population density, increased attention focuses on the role of urban form. This study specifically analyzes the importance of population density for the reduction of urban greenhouse gas emissions in Europe. For this, drivers of both carbon dioxide (CO2) emissions from transport (for 134 cities) and total urban greenhouse gas emissions (CO2eq emissions) of 62 cities across Europe are investigated. Results indicate that population density is not, per se, a strong determinant of greenhouse gas emissions in European cities. Crucially, the spatial scale of the analysis matters and national influences modulate CO2eq emissions in the analyzed urban areas. Results show that greenhouse gas emissions of European urbanites increase significantly with decreasing household sizes and increasing personal wealth. Although the results are bound by data quality, it is assumed that the relative similarity of European cities is also leading to a lesser degree of importance of population density with respect to climate change mitigation. The results further encourage more thorough analyses of the role of household size and personal wealth for effective mitigation of climate change, additional spatially explicit econometric studies, and detailed, city-specific causal models of urban areas. © 2013 American Society of Civil Engineers.
Bernard S.,Camille Jordan Institute |
Bernard S.,French Institute for Research in Computer Science and Automation |
Bernard S.,Rhone Alpes Complex Systems Institute IXXI
Acta Biotheoretica | Year: 2013
Biological processes span several scales in space, from the single molecules to organisms and ecosystems. Multiscale modelling approaches in biology are useful to take into account the complex interactions between different organisation levels in those systems. We review several single- and multiscale models, from the most simple to the complex ones, and discuss their properties from a multiscale point of view. Approaches based on master equations for stochastic processes, individual-based models, hybrid continuous-discrete models and structured PDE models are presented. © 2013 Springer Science+Business Media Dordrecht.