Spatio-temporal patterns in a mechanical model for mesenchymal morphogenesis

We present an in-depth study of spatio-temporal patterns in a simplified version of a mechanical model for pattern formation in mesenchymal morphogenesis. We briefly motivate the derivation of the model and show how to choose realistic boundary conditions to make the system well-posed. We firstly consider one-dimensional patterns and carry out a nonlinear perturbation analysis for the case where the uniform steady state is linearly unstable to a single mode. In two-dimensions, we show that if the displacement field in the model is represented as a sum of orthogonal parts, then the model can be decomposed into two sub-models, only one of which is capable of generating pattern. We thus focus on this particular sub-model. We present a nonlinear analysis of spatio-temporal patterns exhibited by the sub-model on a square domain and discuss mode interaction. Our analysis shows that when a two-dimensional mode number admits two or more degenerate mode pairs, the solution of the full nonlinear system of partial differential equations is a mixed mode solution in which all the degenerate mode pairs are represented in a frequency locked oscillation.     

Physico-chemical model of a protocell

A physico-chemical model of a self-maintaining unity or protocell is constructed on the basis of reaction and diffusion processes. The surface motion of the protocell is taken into account explicitly by a so-called Stefan condition, which leads to a nonlinear feedback to the reaction and diffusion processes. The spatio-temporal dynamics in the neighbourhood of the steady states is investigated in the framework of linear stability analysis with the use of an expansion in terms of spherical harmonicsY _l ^m . It is shown that modes with l2 become successively unstable with increasing nutrient supply. The leading instability with l=2 initiates a process of the nonlinear dynamics which is interpreted as the onset of division. A stabilizing effect of surface tension is also discussed.     

Detection of a root-associated group of Hyaloscyphaceae (Helotiales) species that commonly colonizes Fagaceae roots and description of three new species in genus Glutinomyces

We used a culture-dependent approach to investigate root-associated fungal communities in Fagaceae roots at four fagaceous species-dominant forests in Japan. In total 1029 isolates were collected and classified, based on colony morphological features and molecular information. Species of order Helotiales (Ascomycota) were dominantly isolated at all four sites, in which a globally-distributed putative endophytic group in Hyaloscyphaceae predominated. This group of fungi was morphologically and phylogenetically investigated using these isolates as well as additional isolates collected from 8 different sites in Japan. Among the Hyaloscyphaceae, Glutinomyces species were frequently detected, and three novel species, G. inflatus, G. vulgaris, and G. takaragaikensis spp. nov. were identified and described according to their morphology and genealogical concordance.     

Spatial and temporal density dependence regulates the condition of central Baltic Sea clupeids: compelling evidence using an extensive international acoustic survey

For the first time an international acoustic survey dataset covering three decades was used to investigate the factors shaping the spatial and temporal patterns in the condition of sprat and herring in the Baltic Proper. Generalized additive models showed that the spatial and temporal fluctuations in sprat density have been the main drivers of the spatio-temporal changes of both sprat and herring condition, evidencing intra- and inter-specific density dependence mediated by the size and distribution of the sprat population. Salinity was also an important predictor of herring condition, whereas temperature explained only a minor part of sprat model deviance. Herring density was an additional albeit weak significant predictor for herring condition, evidencing also intra-specific density dependence within the herring population. For both species, condition was high and similar in all areas of the Baltic Proper until the early 1990s, coincident with low sprat densities. Afterwards, a drop in condition occurred and a clear south–north pattern emerged. The drop in condition after the early 1990s was stronger in the northern areas, where sprat population increased the most. We suggest that the increase in sprat density in the northern areas, and the consequent spatial differentiation in clupeid condition, have been triggered by the almost total disappearance of the predator cod from the northern Baltic Proper. This study provides a step forward in understanding clupeid condition in the Baltic Sea, presenting evidence that density-dependent mechanisms also operate at the spatial scale within stock units. This stresses the importance of spatio-temporal considerations in the management of exploited fish.     

An analysis of fish‐habitat associations on disturbed coral reefs: chaetodontid fishes in New Caledonia

A concordance analysis was used to study the simultaneous influence of several environmental data sets on chaetodontid (butterflyfish) distributions. This multivariate and multitable method enabled the correlation of three types of benthic characteristics (mineral substratum, coverage of structural species and large echinoderms) with butterflyfish abundances in two bays of the urban centre of Nouméa (New Caledonia). The first concordance axis was related to a gradient in the coverage of branching corals. This disturbance gradient compared damaged reef areas dominated by long‐spined sea urchins to areas with an extensive coverage of branching corals. The abundance of corallivorous chaetodontids was related to this gradient, supporting the view of corals as a food and shelter source for these fishes. The second concordance axis was interpreted as a gradient of heterogeneity in the coverage of benthic life‐forms. The abundance of omnivorous chaetodontids was related to this gradient. Thus, the concordance axes defined two key components of habitat structure that were related to the entire fish community structure.     

The dendrogeomorphic spatio-temporal reconstruction of flow-like landslides activity in one of the most susceptible region of Central Europe (the Vsetínské vrchy Mts.)

Flow-like landslides are a dangerous landslide type. They often express gradual movement or seeming dormancy, but occasional reactivation can, in extreme cases, result in catastrophic events. To predict their future behaviour, knowledge of past spatio-temporal development and relationships with hydrometeorological triggers is crucial. Moreover, regional data are more robust than case studies. Dendrogeomorphic (tree-ring-based) methods are a very precise approach for reconstructing past landslide behaviour. Nevertheless, regional reconstructions are very rare, which is probably due to their time-consuming procedures. This paper presents the results of a regional tree-ring-based reconstruction of the spatio-temporal development of flow-like landslides in a selected region in the Outer Western Carpathians. Six selected landslides were studied via analysis of 614 increment cores that came from 307 disturbed trees. The reconstruction provided data for approximately 70 individual landslide reactivation phases that were distributed in 44 event years. Events with regional extension (at least half of the studied landslides were active) were detected in six years (1940, 1941, 1953, 1961, 1985, and 1997). Periods of increased (1950s, 1990s) as well as decreased (1940s, 1970s, 2010s) landslide activity were reconstructed. The use of tree-ring data enabled the construction of landslide probability maps. Based on this analysis, all studied landslides exhibit extremely high probabilities of reactivation during a temporal horizon of 100 years, but even over shorter periods (5 and 20 years), their probability of reactivation is very high. Finally, analysis of meteorological triggers suggests the positive effect of precipitation in May (and possibly in September) to activate landslides with regional extent. Extreme short-duration (1-day) precipitation events probably do not play a role in landslide triggering. Moreover, gradual increases in precipitation totals during periods of at least one-half year preceding the event years were detected.     

Spatio-temporal trends in gastric cancer mortality in Spain: 1975–2008

Aim of the study: There has been a downward trend in gastric cancer mortality worldwide. In Spain, a marked spatial aggregation of areas with excess mortality due to this cause has long been reported. This paper sought to analyse the evolution of gastric cancer mortality risk in Spanish provinces and explore the possible attenuation of the geographical pattern. Methods: We studied a series of gastric cancer mortality data by province, year of death, sex and age group using a conditional autoregressive (CAR) model that incorporated space, time and spatio-temporal interactions. Results: Gastric cancer mortality risk decreased in all Spanish provinces in both males and females. Overall, decreasing trends were more pronounced during the first years of the study period, largely due to a sharper fall in gastric cancer mortality risk among the older population. Recent decades have witnessed a slowing in the rate of decrease, especially among the younger age groups. In most areas, risk declined at a similar rate, thus serving to maintain interprovincial differences and the persistence of the geographical pattern, though with some differences. The north and northwest provinces were the areas with higher mortality risks in both sexes and age groups over the entire study period. Concluding statement: Despite the decline in gastric cancer mortality risk observed for the 50 Spanish provinces studied, geographical differences still persist in Spain, and the cluster of excess mortality in the north-west of the country remains in evidence.     

Phylogeographical patterns in the American Pacific Northwest: lessons from the arionid slug Prophysaon coeruleum

Some of the earliest studies of phylogenetic concordance involve native plants from the Pacific Northwest where many taxa showed clear genetic breaks between southern and northern populations. To test whether similar breaks also occur in invertebrate species with low dispersal capacities, genetic data from two mitochondrial genes are assembled for individuals of the arionid slug Prophysaon coeruleum throughout the species' range. Bayesian inference revealed three major clades and a total of eight subclades. It is argued that the demographic and genealogical past of P. coeruleum has resulted in a deep and shallow phylogeographical structure. The deep structure is at least 2.6-5.9 million years old and therefore clearly predates the Pleistocene period. Superimposed on this structure is a shallow structure that is most likely less than 2 million years old and probably the result of Pleistocene perturbations. Molecular analyses revealed that the three known colour traits in P. coeruleum do not represent monophyletic groups and that they do not match the patterns of genetic structure found. It is argued that the colour traits are perhaps a response to different levels of UV-radiation. The study adds to the increasing evidence that the phylogeographical structure of some taxa is more complex than previously thought. Moreover, it shows that genealogical concordance should not be deduced from phylogeographical patterns alone but should be based on an understanding of timing and causes of historical processes that lead to those patterns.     

Stochastic chemical kinetics

A review of the physical principles that are the ground of the stochastic formulation of chemical kinetics is presented along with a survey of the algorithms currently used to simulate it. This review covers the main literature of the last decade and focuses on the mathematical models describing the characteristics and the behavior of systems of chemical reactions at the nano- and micro-scale. Advantages and limitations of the models are also discussed in the light of the more and more frequent use of these models and algorithms in modeling and simulating biochemical and even biological processes.     

Speciation in Pyricularia inferred from multilocus phylogenetic analysis

Pyricularia isolates from various host plants were subjected to a multilocus phylogenetic analysis based on rDNA-ITS, actin, β-tubulin, and calmodulin loci. A combined gene tree resolved seven groups with 100 % BS support, suggesting that they are monophyletic groups supported concordantly by all four loci. By incorporating biological and morphological species criteria, each of the seven groups was considered to be a current species. However, phylogenetic relationships among these species were unresolved in the single-gene trees and in the combined tree. Furthermore, the transition from concordance to conflict occurred more than once in the combined gene tree. They were interpreted by assuming that Pyricularia has evolved through repeated species radiation. The transition point other than the current species limit was considered to be the limit of the former species.