Modelling microbial processes (phyto- and bacterioplankton) in the Schelde estuary

Since about 10 years, studies have been conducted at the University of Brussels in modelling the microbiological processes affecting biogenic substances in the Schelde estuary and its watershed.The first model, a one dimensional redox model, simulated the longitudinal distribution of oxygen, nitrate, iron and manganese in relation to the observed bacterial heterotrophic activity. A model allowing calculation of bacterial activity from data on organic discharge was coupled to this model. It was completed by a model of phytoplanktonic development within the estuary. Finally, an idealized model of the hydrographical network, based on Horton analysis, is being established in order to calculate the quality of the water at the downward boundary of the estuary.Together, all these sub-models form a general model of the ecological working of the Schelde estuary, able to predict at least the general trends of the redox state, the organic carbon, mineral nitrogen, and chlorophyll-a concentrations as a function of distance to the sea, from the knowledge of geomorphological and meteorological data, along with informations concerning the distribution of anthropogenic discharges. This model therefore provides a powerfull tool for the rational management of the Schelde estuary.Research Associate of the Belgian National Scientific Research Funds.     

Quantum processes in evolution of regulation of living system (mathematical modelling)

We have developed an imitation model of the appearance of regulation of physiological functions of protocell at the initial stages of evolution of living system. It is based on suggestion of the appearance of signal function in spontaneously formed products of partial hydrolysis of the protocell polypeptides, based on which there appear the regulatory molecules--quanta of regulation. For construction of the model, the mathematical apparatus of final automats and of genetic algorithm is used. The model has demonstrated the positive role of involvement of regulatory peptides in the system of regulation of protocell functions to provide its viability under the changing envelopment conditions.     

Modelling of processes in enzyme electrodes

The modelling of processes in enzyme electrodes and the comparison of experimental data to such models allows us to establish the rate limiting steps in the transduction of the analyte concentration into a sensor response and to determine the relevant mass transport and enzyme kinetic rates. These are of importance in the design and optimisation of enzyme electrodes.     

Morphogenetic processes and seasonal changes in the anatomic and histological organization of the Barents Sea sponge Halichondria panicea (Pallas)

As a result of histological investigations of seasonal dynamics in the anatomical-tissue organization of the litoral sponge Halichondria panicea (Pallas), morphogenetical processes during different periods of its life cycle are described in detail. Correlations between different phases of sexual reproduction and conditions of anatomical and tissue organization in the maternal organism are stated. It is noted that tissue reduction of the definitive sponge Halichondria panicea during autumn--winter season is a natural phenomenon, regularly repeating in the life of the litoral sponge investigated, as a result of the maternal organism's "exhaustion" in the period of sexual embryogenesis.     

Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems

One of the main issues in Systems Biology is to deal with semantic data integration. Previously, we examined the requirements for a reference conceptual model to guide semantic integration based on the systemic principles. In the present paper, we examine the usefulness of the Unified Modelling Language (UML) to describe and specify biological systems and processes. This makes unambiguous representations of biological systems, which would be suitable for translation into mathematical and computational formalisms, enabling analysis, simulation and prediction of these systems behaviours.     

Tissue inhibitor of metalloproteinases 4 (TIMP4) is involved in inflammatory processes of human cardiovascular pathology

Tissue inhibitors of matrix metalloproteinases (TIMPs) comprise a family of four members, of which TIMP4 is characterized by being primarily restricted to cardiovascular structures. We demonstrate with immunohistochemical analysis of healthy human tissue that TIMP4 is present in medial smooth muscle cells and adventitial capillaries of arteries as well as in cardiomyocytes. Animal studies have suggested a role for TIMP4 in several inflammatory diseases and cardiovascular pathologies. We therefore examined whether TIMP4 is involved in human inflammatory cardiovascular disorders, specifically atherosclerosis, giant cell arteritis and chronic rejection of heart allografts. TIMP4 was most clearly visible in cardiovascular tissue areas populated by abundant inflammatory cells, mainly macrophages and CD3+ T cells. Using western blotting and immunocytochemistry, human blood derived lymphocytes, monocytes/macrophages and mast cells were shown to produce TIMP4. In advanced atherosclerotic lesions, TIMP4 was detected around necrotic lipid cores, whereas TIMP3 and caspase 3 resided within and around the core regions, indicating different roles for TIMP3 and TIMP4 in inflammation-induced apoptosis and in matrix turnover. In conclusion, the data demonstrate upregulation of TIMP4 in human cardiovascular disorders exhibiting inflammation, suggesting its future use as a novel systemic marker for vascular inflammation.     

Evolutionary processes in the genusCapsella (Brassicaceae)

Capsella comprises diploid (C. grandiflora andC. rubella) and tetraploid taxa. It is argued that the tetraploidC. bursa-pastoris is of intraspecific origin despite disomic inheritance and fixed heterozygosity. It is of considerable age as evidenced by the fossil record and molecular data. Gene duplication by polyploidization and a mixed mating system provided the genetic flexibility for greatest colonizing success. Pronounced variation patterns at a micro- and macrogeographic scale are observed inC. bursa-pastoris for many characters including life history traits, leaf morphology and allozymes. This variation pattern can be explained by several components comprising phylogenetic age, random processes, ecotypic variation and colonization history. The adaptive strategy ofC. bursa-pastoris cannot be assigned to either ecotypic differentiation or phenotypic plasticity alone. It depends on the trait under study.Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

Modelling tendon excursions and moment arms of the finger flexors: anatomic fidelity versus function

A detailed musculoskeletal model of the human hand is needed to investigate the pathomechanics of tendon disorders and carpal tunnel syndrome. The purpose of this study was to develop a biomechanical model with realistic flexor tendon excursions and moment arms. An existing upper extremity model served as a starting point, which included programmed movement of the index finger. Movement capabilities were added for the other fingers. Metacarpophalangeal articulations were modelled as universal joints to simulate flexion/extension and abduction/adduction while interphalangeal articulations used hinges to represent flexion. Flexor tendon paths were modelled using two approaches. The first method constrained tendons with control points, representing annular pulleys. The second technique used wrap objects at the joints as tendon constraints. Both control point and joint wrap models were iteratively adjusted to coincide with tendon excursions and moment arms from a anthropometric regression model using inputs for a 50th percentile male. Tendon excursions from the joint wrap method best matched the regression model even though anatomic features of the tendon paths were not preserved (absolute differences: mean<0.33 mm, peak<0.74 mm). The joint wrap model also produced similar moment arms to the regression (absolute differences: mean<0.63 mm, peak<1.58 mm). When a scaling algorithm was used to test anthropometrics, the scaled joint wrap models better matched the regression than the scaled control point models. Detailed patient-specific anatomical data will improve model outcomes for clinical use; however, population studies may benefit from simplified geometry, especially with anthropometric scaling.     

Modelling of processes in nerve fibres at the interface of physiology and mathematics

Biomechanics and Modeling in Mechanobiology - The in silico simulations are widely used in contemporary systems biology including the analysis of nerve pulse propagation. As known from numerous...     

Shaping processes in drying drops of serum in norm and pathology

The results of physical and mathematical simulation of the drying process for colloid liquids under different initial conditions were considered. It was shown that the concentration and stability of a colloid solution play an important role in the shaping of drying drops. Possible mechanisms of the formation of morphological differences in dried drops of serum in healthy and ill people are discussed.     

Modelling the occurrence of rainbow lorikeets (Trichoglossus haematodus) in Melbourne

Abstract Over the previous three decades, the rainbow lorikeet (Trichoglossus haematodus Family Psittacidae) has increased in urbanized areas of Australia. To help understand the nature of this increase, we investigated the influence of road density, tree cover and season on the occurrence of the rainbow lorikeet in the Melbourne region. Bayesian logistic regression was used to construct models to predict the occurrence of rainbow lorikeets, using Birds Australia atlas data at 207 2‐ha sites. The results demonstrate a strong relationship between tree cover and urbanization and the distribution of the species. The best model incorporated quadratic terms for road density and tree cover, and interaction terms, as well as season as a categorical variable. Probability of occurrence of rainbow lorikeets was highest at medium tree cover (40% to 70% of the site covered) and medium road density (9% to 12% of the surrounding area covered by roads). There was a close correspondence between the predictions of the model and new observations from bird surveys conducted at randomly selected field sites. The increased abundance of the species in urban areas has occurred despite a paucity of hollows that would act as suitable nesting sites, suggesting that only a small proportion of the population is breeding in these areas.     

Modelling the effect of directional spatial ecological processes at different scales

Understanding the effects of disturbance and secondary succession on spatio-temporal patterns in the abundance of species is stymied by a lack of long-term demographic data, especially in response to infrequent and high intensity disturbances, such as hurricanes. Moreover, resistance and resilience to hurricane-induced disturbance may be mediated by legacies of previous land use, although such interactive effects are poorly understood, especially in tropical environments. We address these central issues in disturbance ecology by analyzing an extensive dataset, spanning the impacts of Hurricanes Hugo and Georges, on the abundance of a Neotropical walking stick, Lamponius portoricensis, in tabonuco rainforest of Puerto Rico during the wet and dry seasons from 1991 to 2007. By synthesizing data from two proximate sites in tabonuco forest, we show that resistance to Hurricane Hugo (97% reduction in abundance) was much less than resistance to Hurricane Georges (21% reduction in abundance). Based on a powerful statistical approach (generalized linear mixed-effects models with Poisson error terms), we documented that the temporal trajectories of abundance during secondary succession (i.e., patterns of resilience) differed between hurricanes and among historical land use categories, but that the effects of hurricanes and land use histories were independent of each other. These complex results likely arise because of differences in the intensities of the two hurricanes with respect to microclimatic effects (temperature and moisture) in the forest understory, as well as to time-lags in the response of L. portoricensis to changes in the abundance and distribution of preferred food plants (Piper) in post-hurricane environments.     

Tree diseases and landscape processes: the challenge of landscape pathology

Forest pathology inherently involves a landscape perspective, because tree pathogens propagate according to heterogeneous spatial patterns of flow and isolation. Landscape pathology is a field that is now emerging from the transdisciplinary cooperation of forest pathologists with landscape ecologists. Here, we review recent broad-scale assessments of tree disease risk, investigations of site and host preferences for several root rot pathogens, and regional historical analyses of pathogen outbreak in plantations. Crucial topics include fragmentation effects on pathogen spread and geophysical features that predispose forest patches to disease expression. Recent methodological developments facilitate the spatially explicit analysis of reciprocal coarse-scale relationships among hosts and pathogens. Landscape pathology studies fill a significant research gap in the context of our understanding of sustainable forest management, the introduction of exotic organisms and how climate change might affect the spread of disease.     

Habitat suitability modelling for mayflies (Ephemeroptera) in Flanders (Belgium)

Logistic regressions, artificial neural networks, support vector machines, random forests and classification trees were used to predict habitat suitability for mayflies on basis of physical–chemical water characteristics, dominant land use type and structural parameters. As a case-study, the dataset of Flanders was used, which consisted of 4289 samples containing mayflies (presences) and 3315 samples from waters where mayflies were never encountered (absences). For all techniques, data were randomly divided in a training set (two thirds) and a test set (one third). Models were calibrated using a tenfold cross-validation on the training set and subsequently validated using the test set. All techniques delivered good models that were able to discriminate sites with and without mayflies and performance (expressed as percent correctly classified instances and kappa-statistics) was in all cases similar for the training and the test set. Artificial neural networks and random forests performed slightly better compared to the other techniques. Samples with mayflies contained significantly more oxygen, a better developed river structure, higher values for sinuosity and steeper slopes, while samples without mayflies had significantly higher values for ammonium, nitrite, Kjeldahl nitrogen, total phosphorous, orthophosphate, biological and chemical oxygen demand, pH and conductivity. Also land use differed significantly, with mayflies usually present in forests but absent in industrial areas. The prevalence of mayflies gradually increased during the nineties from about 20 to 40%, which corresponded with an improvement of the chemical water quality. During the last decade, however, water quality did not further improve and as a result, mayflies prevalence did not continue to increase. Based on the planned measures, an ensemble forecast using the five mentioned modelling techniques predicted that mayflies prevalence will increase to 46% by 2015 and to 72% by 2027. To meet the requirements of the European Water Framework Directive, which states that all surface waters should obtain a good ecological quality, extra efforts will be needed to decrease nutrient concentrations and to improve habitat quality.