Editorial: Computational modelling of cell &; tissue processes &; function

Computational modelling of whole biological systems from cells to organs is gaining momentum in cell biology and disease studies. This pathway is essential for the derivation of explanatory frameworks that will facilitate the development of a predictive capacity for estimating outcomes or risk associated with particular disease processes and therapeutic or stressful treatments. This article introduces a series of invited papers covering a hierarchy of issues and modelling problems, ranging from crucial conceptual considerations of the validity of cellular modelling through to multi-scale modelling up to organ level. The challenges and approaches in cellular modelling are described, including the potential of in silico modelling applications for receptor–ligand interactions in cell signalling, simulated organ dysfunction (i.e., heart), human and environmental toxicity and the progress of the IUPS Physiome Project. A major challenge now facing biologists is how to translate the wealth of reductionist detail about cells and tissues into a real understanding of how these systems function and are perturbed in disease processes. In biomedicine, simulation models of biological systems now contain sufficient detail, not only to reconstruct normal functions, but also, to reconstruct major disease states. More widely, simulation modelling will aid the targeting of current knowledge gaps and how to fill them; and also provide a research tool for selecting critical factors from multiple simulated experiments for real experimental design. The envisaged longer-term end- product is the creation of simulation models for predicting drug interactions and harmful side-effects; and their use in therapeutic and environmental health risk management. Finally, we take a speculative look at possible future scenarios in cellular modelling, where it is envisioned that integrative biology will move from being largely qualitative and instead become a highly quantitative, computer-intensive discipline.     

Evolutionary convergences and parallelisms: &;their theoretical differences and the difficulty &;of discriminating them in a practical &;phylogenetic context

The importance of evolutionary parallelisms and their differences from evolutionary convergences have been historically underappreciated, as recently noticed in Gould's last book `The structure of evolutionary history'. In that book, Gould make an effort to distinguish and to reinterpret these concepts in the light of the new discoveries of the last decades on developmental biology and genetics, presenting the elegant metaphor of `Pharaonic bricks versus Corinthian columns'. In this paper I will briefly discuss these concepts, and will argue that, despite the advances that have been made to define them in theory, it is rather hard to differentiate them in a practical phylogenetic context. In order to do so, I will provide some few examples from my own empirical studies on the last years of one of the most morphologically and taxonomically diverse groups of Vertebrates, the catfishes.     

Signaling Functions of Free Radicals Superoxide &; Nitric Oxide under Physiological &; Pathological Conditions

Superoxide and nitric oxide are ubiquitous physiological free radicals that are responsible for many pathological disorders. Both radicals by themselves are relatively harmless but are the precursors of many toxic species such as peroxy and hydroxyl radicals, hydrogen peroxide, and peroxynitrite. However, it has been shown now that both superoxide and nitric oxide are also able to perform important signaling functions in physiological and pathophysiological processes. Wrongly named “superoxide,” the radical anion of dioxygen is not a super-oxidant but the strong super-nucleophile, an efficient catalyst of heterogenic nucleophilic reaction. Due to this, superoxide plays an important role in many enzymatic processes such as the phosphorylation and activation of numerous protein kinases. On the other hand, superoxide inhibits the activation of phosphatases, the enzymes catalyzed by dephosphorylation of protein kinases. We suggest that superoxide catalyzes these enzymatic processes as a result of its nucleophilic properties. Another important physiological function of superoxide and nitric oxide is their competition for the interaction with mitochondrial cytochrome c oxidase. Disturbance of superoxide/nitric oxide balance leads to the dysfunction of mitochondria and the enhancement of apoptosis and oxidative stress, which are primary causes of various pathological disorders and aging. In conclusion, interplay between superoxide and nitric oxide, one of major factors of aging development, is considered.     

Global diversity of cumaceans &; tanaidaceans (Crustacea: Cumacea &; Tanaidacea) in freshwater

Cumacea and Tanaidacea are marginal groups in continental waters. Although many euryhaline species from both groups are found in estuaries and coastal lagoons, most occur only temporarily in non-marine habitats, appearing unable to form stable populations there. A total of 21 genuinely non-marine cumaceans are known, mostly concentrated in the Ponto-Caspian region, and only four tanaids have been reported from non-marine environments. Most non-marine cumaceans (19 species) belong in the Pseudocumatidae and appear restricted to the Caspian Sea (with salinity up to 13‰) and its peripheral fluvial basins, including the northern, lower salinity zones of the Black Sea (Sea of Azov). There are nine Ponto-Caspian genera, all endemic to the region. Only two other taxa (in the family Nannastacidae) occur in areas free of any marine–water influence, in river basins in North and South America. Both seem able to survive in waters of raised salinity of the lower reaches of these fluvial systems; but neither has been recorded in full salinity marine environments. The only non-marine tanaidacean thus far known lives in a slightly brackish inland spring in Northern Australia. The genus includes a second species, from a brackish-water lake at the Bismarck Archipelago, tentatively included here as non-marine also. Two additional species of tanaidaceans have been reported from non-marine habitats but both also occur in the sea. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

Synchrony &; chaos in patchy ecosystems

The apparent synchronisation of spatially discrete populations is a well documented phenomenon. However, it is not clear what the governing mechanisms are for this synchrony, and whether they are robust over a range of environmental conditions and patch specific population dynamic behaviours. In this paper, we explore two (possibly interacting) modes of coupling, and investigate their theoretically discernible, and perhaps even experimentally measurable, signatures. To aid us in this investigation we employ a planktonic example system, with direct application to plankton patchiness. Furthermore, we address the role of chaos in complex spatio-temporal dynamics; we find that chaos associated with funnel attractors can play a distinguished role, over dynamics less sensitive to small variations, in being more susceptible to generalised synchronisation (such as phase synchronisation) in the presence of small local parameter variation. This is in contrast to the case for coupled systems with identical dynamics, and suggests that non-identically coupled systems are more vulnerable to global extinction events when exhibiting funnel-type chaotic dynamics.     

Global diversity of spelaeogriphaceans & thermosbaenaceans (Crustacea; Spelaeogriphacea & Thermosbaenacea) in freshwater

Spelaeogriphaceans and thermosbaenaceans are two orders of eyeless, unpigmented peracarid crustaceans represented by very few species from subterranean waters. Spelaeogriphaceans occur only in continental waters, either running or still, in limestone or sandstone caves, or in calcrete aquifers. The four species known are limnic except one occurring in slightly brackish water loosely associated with an endorheic basin. The Thermosbaenacea are primarily marine, with only 18 species recorded in limnic conditions or in brackish inland waters whose salinity does not derive from dilution of seawater. They occur in limestone caves, the interstitial medium associated to alluvial deposits, or in thermo-mineral springs. Spelaeogriphaceans are found on the southern continents, in ancient cratons not affected by sea transgressions at least since the Early Cretaceous, when Gondwana started to break-up. The former integration of these terranes into Gondwana suggests that the penetration of spelaeogriphaceans in continental waters took place previous to the fragmentation of this super continent (starting ca. 140 Ma), and that their current distribution pattern was driven by continental drift. The distribution of the Thermosbaenacea matches precisely the area covered by the ancient Tethys Sea or its coastlines. They are most probably relicts of a once widespread shallow-water marine Tethyan fauna stranded in interstitial or crevicular groundwater during marine regressions. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

Sporulation in saprotrophic and clinical strains of <Emphasis Type="Italic">Aspergillus sydowii</Emphasis> (Bain. &; Sart.) Thom &; Church under various environmental conditions

Molecular genetic characteristics and capacity for sporulation under different levels of temperature and humidity were compared for three saprotrophic and four clinical strains of A. sydowii. Analysis of the ITS and D1/D2 loci of these A. sydowii strains revealed two clades, each including both the clinical and saprotrophic strains. The differences in sporulation in the saprotrophic and clinical strains of the potentially pathogenic microscopic fungus A. sydowii under different environmental conditions were demonstrated. In the clinical A. sydowii strains, the level of spore formation was generally higher, especially at humidity levels of 0.90 and 0.95 a_w and 20–25°C. The level of spore formation for the clinical strains inoculated into sterile soil was several times higher than for the saprotrophic ones. On the contrary, nonsterile soils (sod-podzolic and urban soils) exhibited a fungistatic effect against A. sydowii populations.