A model reduction method for biochemical reaction networks

Background: In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model. Results: We apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%. Conclusions: The method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of interest in a more coarse-grained yet realistic environment

Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes.

The data set supporting the results of this article is available in the Dryad repository, http://dx.doi.org/10.5061/dryad.6f4qs. Moustakas, A. and Evans, M. R. (2015) Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values.Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose

Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques

Inventory and Characterization of the Riparian Zone of the Current and Jacks Fork Rivers

The ecological, recreational, and economic value of the 134 mile (216 km) riparian corridor within the Ozark National Scenic Riverways (ONSR) is of great interest to land managers and conservationists. Recent interest in applying ecosystem management to forest systems has necessitated a fresh look at the tools and methods in use to assess existing patterns of plant community structure and diversity. The purpose and objective of the study described in this report was to initiate a series of vegetation studies that could be integrated with existing research and management infonnation on the riparian vegetation in the ONSR. Defining the compositional and spatial attributes of the riparian corridor were at the core of our research efforts. We used multivariate analysis and ordination techniques to characterize the composition and distribution of woody and herbaceous vegetation within the ONSR

The role of heterogeneity in spatial plant population dynamics

Ecological theory names interacting mechanisms that allow competing species to coexist in limited available space, some of them are perceive as antagonistic. Most prominent are niche differentiation, heterogeneity and neutrality (ecological equivalence). Species similarity is also influenced by two mechanisms: Habitat filtering selects for ecologically similar species, while niche differentiation reduces competitive pressure and thus prefers ecologically different species. The spatial arrangement of abiotic resources can determine the spatial pattern and competition framework for a pre-selected tree species ensemble. Spatial occurrence patterns of trees are formed by dispersal, growth and mortality which are influenced by the interacting abiotic and abiotic conditions. The relative impact of these mechanisms are underresearched in temperate forest trees, especially in Europe. We analysed a data set of a temperate old-growth forest with spatially explicit information about more than 15 000 individual trees of six tree species (90 % beech admixed with Ash, Hornbeam, Sycamore, Norway Maple, and Wych Elm) located in the central region of the Hainich National Park in central Germany. We tested space-related coexistence mechanisms under heterogeneous conditions. For this, we employed Point Pattern Analysis for testing several ecological hypotheses on inter- and intraspecific interactions of the species, varying from randomness to strict ecological niche. In order to identify the critical components of possible niches, we collected field data on the abiotic conditions such as the availability of water and light, and considered topography using a Digital Elevation Model. These field data were used for fitting suitability surfaces depending on tree species identity using spatial interpolation methods such as Kriging and Generalised Additive Models. We used Spatial Point Process Models to reconstruct the spatial distribution processes composed of purely biotic, abiotic or mixed covariates of the tree species. We found that spatial heterogeneity was important in all aspects we studied. Both, tree density and the distribution of the abiotic habitat components varied in space. Especially when species interacted with beech, abiotic heterogeneity played an important role: beech outcompeted the admixed species under most prevailing abiotic conditions. This way, beech influenced the spatial pattern of the six studied species by limiting available (niche) space via inter- and intraspecific competition. Here, Beech proved to be the superior competitor with no pronounced abiotic niche, but is mostly excluded from slopes. The remaining available niche space was often occupied by ecologically similar species, which formed typical associations in subregions of the study area less suitable for beech. We found spatial segregation between the three most abundant species Beech, Ash, and Hornbeam, coexistence by niches seem to be rather trait based rather than based on abiotic preferences. Habitat suitability and spatial distribution of Ash, Sycamore, and Norway Maple were more affected by the abiotic environmental condition than Beech, Hornbeam, and Elm. This indicates that the coexistence of rare species seems to be mediated by heterogeneity. Our study revealed that the difference in abiotic conditions, such as soil depth and plant-available water were relevant for habitat suitability at small spatial and temporal scales. When simulating the distribution pattern of the surveyed species, it became apparent that biotic interactions play an important part in shaping the scales at which aggregation or segregation happen in the abiotic environment. Beech and Sycamore both showed endogenous heterogeneity. For both species, point processes models incorporated several different interaction scales of intraspecific interaction. The interspecific interaction played only a minor role compared to the intraspecific one. All results together seem to underline that niche differentiation happens at the level of the individual allowing ecologically similar species to interact de facto neutrally within their niche space and thus, to coexist in presence of a strong competitor

The avian dawn chorus across Great Britain: using new technology to study breeding bird song

The avian dawn chorus is a period of high song output performed daily around sunrise during the breeding season. Singing at dawn is of such significance to birds that they remain motivated to do so amid the noise of numerous others. Yet, we still do not fully understand why the dawn chorus exists. Technological advances in recording equipment, data storage and sound analysis tools now enable collection and scrutiny of large acoustic datasets, encouraging research on sound-producing organisms and promoting ‘the soundscape’ as an indicator of ecosystem health. Using an unrivalled dataset of dawn chorus recordings collected during this thesis, I explore the chorus throughout Great Britain with the prospect of furthering our understanding and appreciation of this daily event. I first evaluate the performance of four automated signal recognition tools (‘recognisers’) when identifying the singing events of target species during the dawn chorus, and devise a new ensemble approach that improves detection of singing events significantly over each of the recognisers in isolation. I then examine daily variation in the timing and peak of the chorus across the country in response to minimum overnight temperature. I conclude that cooler temperatures result in later chorus onset and peak the following dawn, but that the magnitude of this effect is greater at higher latitude sites with cooler and less variable overnight temperature regimes. Next, I present evidence of competition for acoustic space during the dawn chorus between migratory and resident species possessing similar song traits, and infer that this may lead either to fine-scale temporal partitioning of song, such that each competitor maintains optimal output, or to one competitor yielding. Finally, I investigate day-to-day attenuation of song during the leaf-out period from budburst through to full-leaf in woodland trees, and establish the potential for climate-driven advances in leaf-out phenology to attenuate song if seasonal singing activity in birds has not advanced to the same degree. I find that gradual attenuation of sound through the leaf-out process is dependent on the height of the receiver, and surmise that current advances in leaf-out phenology are unlikely to have undue effect on song propagation. This project illustrates the advantage of applying new technology to ecological studies of complex acoustic environments, and highlights areas in need of improvement, which is essential if we are to comprehend and preserve our natural soundscapes

Biogeomorphology of Bedrock Fluvial Systems: Example from Shawnee Run, Kentucky, USA

The dynamic interactions between fluvial processes and vegetation vary in different environments and are uncertain in bedrock settings. Bedrock streams are much less studied than alluvial in all aspects, and in many respects act in qualitatively different ways. This research seeks to fill this lacuna by studying bedrock streams from a biogeomorphic perspective. The first part of this research aims to identify the impacts of woody vegetation that may be common to fluvial systems and rocky hillslopes in general, or that may be unique to bedrock channels. A review of the existing literature on biogeomorphology — mostly fluvial and rocky hillslope environments — was carried out, and field examples of biogeomorphic impacts (BGIs) associated with fluvial systems of six various bedrock environments were then examined to complement the review. This research shows that bedrock streams exhibit both shared and highly concentrated BGIs in relation to alluvial streams and bedrock hillslope environments. It shows that while no BGIs associated with bedrock streams are unique to the environment, the bioprotective function related to root-banks (when the root itself creates the stream bank) and the processes related to bioweathering and erosion are rarely addressed in alluvial fluvial literature, despite their importance in bedrock fluvial environments. The second part of the dissertation is largely grounded upon the important BGIs associated with bedrock fluvial environments identified in the first part. Drawing from ecological lexicon, this part introduces some biogeomorphic concepts, most importantly biogeomorphic keystone species and equivalents, with respect to different biotic impacts on surface processes and forms. Later, it explores these concepts by examining the general vs. species-specific BGIs of trees on a limestone bedrock-controlled stream, Shawnee Run, in central Kentucky. Results suggest that Platanus occidentalis plays a keystone role by promoting development of biogeomorphic pools in the study area. Further, some species play equivalent roles with respect to surface processes and landforms by promoting development of avulsion-associated islands and can be recognized as biogeomorphic equivalents. Finally, this dissertation also examines the relative importance of systematic up-to downstream vs. local scale variation explaining channel morphology and biogeomorphological phenomena in Shawnee Run. Results show that local scale variation − primarily attributable to the local scale structural controls, incision status and edaphic variation − largely explains channel morphology and vegetation patterns. These patterns may therefore be common in bedrock rivers strongly influenced by geological controls

Multi-level and hybrid modelling approaches for systems biology

During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The informa- tion collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the dif- ferent parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different sys- tem levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field

Physicochemical Influences on the Spawning and Rearing Habitat of Riverine Neosho Smallmouth Bass

Stream fishes are vulnerable to a range of natural and anthropogenic stressors. Information on fish movements and habitat use is essential to conserve and manage these populations, and is particularly limited for populations that occupy range boundaries and novel habitats. Neosho Smallmouth Bass Micropterus dolomieu velox occurs only in the southwestern Ozark Highlands ecoregion, where the riverscape is highly dissected by impoundments. I sought to broaden the knowledge of Neosho Smallmouth Bass (NSMB) ecology by evaluating movement patterns, nesting and rearing habitat use at multiple scales, and spawning phenology in relation to physicochemical conditions. Adult NSMB movements were greatest during the spring spawning period and were positively related to discharge and fish size, though I also observed considerable variability among individuals and streams. Tagged fish did not use the reservoir or associated interface habitats. I also documented nest "clustering" by NSMB in response to local habitat conditions; cluster presence was more likely in warmer streams with wide, shallow channels, and less likely in groundwater-gaining reaches. Nest abundance was greater in warmer streams and reaches with deeper pools. I observed spatiotemporal variation in the hatch timing and growth rate of age-0 NSMB in response to discharge and stream temperature conditions. I showed the importance of warmer streams and of deep pools in small streams for NSMB rearing. I also demonstrated the harm of July floods for first-year survival in these populations, and showed the importance of stream proximity (i.e., adjacency to larger streams) for mitigating this effect and modifying the habitat relationships of age-0 NSMB. Lastly, we observed juvenile NSMB movements were greater for larger individuals and with warmer water temperatures. Individual variation was high for both movement and microhabitat use. The variability in movement, habitat use, and response to physicochemical conditions among individuals and populations (i.e., in different streams) underscores the importance of maintaining habitat heterogeneity and streamflow sufficient to connect important habitats, especially in small streams. Protecting the inherent diversity of these populations is crucial for their persistence in a changing environment

New time-scale criteria for model simplification of bio-reaction systems

<p>Abstract</p> <p>Background</p> <p>Quasi-steady state approximation (QSSA) based on time-scale analysis is known to be an effective method for simplifying metabolic reaction system, but the conventional analysis becomes time-consuming and tedious when the system is large. Although there are automatic methods, they are based on eigenvalue calculations of the Jacobian matrix and on linear transformations, which have a high computation cost. A more efficient estimation approach is necessary for complex systems.</p> <p>Results</p> <p>This work derived new time-scale factor by focusing on the problem structure. By mathematically reasoning the balancing behavior of fast species, new time-scale criteria were derived with a simple expression that uses the Jacobian matrix directly. The algorithm requires no linear transformation or decomposition of the Jacobian matrix, which has been an essential part for previous automatic time-scaling methods. Furthermore, the proposed scale factor is estimated locally. Therefore, an iterative procedure was also developed to find the possible multiple boundary layers and to derive an appropriate reduced model.</p> <p>Conclusion</p> <p>By successive calculation of the newly derived time-scale criteria, it was possible to detect multiple boundary layers of full ordinary differential equation (ODE) models. Besides, the iterative procedure could derive the appropriate reduced differential algebraic equation (DAE) model with consistent initial values, which was tested with simple examples and a practical example.</p