A deformation gradient decomposition method for the analysis of the mechanics of morphogenesis

A new finite element model is proposed for the analysis of the mechanical aspects of morphogenesis and tested on the biologically well studied gastrulation phenomenon, in particular ventral furrow invagination of the Drosophila melanogaster embryo. A set of mechanisms are introduced in the numerical model, which lead to the observed deformed shapes. We split the total deformation into two parts: an imposed active deformation, and an elastic deformation superimposed onto the latter. The active deformation simulates the effects of apical constriction and apico-basal elongation. These mechanisms are associated with known gene expressions and so in this way we attempt to bridge the well explored signalling pathways, and their associated phenotypes in a mechanical model. While the former have been studied in depth, much less can be said about the forces they produce and the mechanisms involved. From the numerical results, we are able to test different plausible mechanical hypotheses that generate the necessary folding observed in the invagination process. In particular, we conclude that only certain ratios between both modes (apical constriction and apico-basal elongation) can successfully reproduce the invagination process. The model also supports the idea that this invagination requires the contribution of several mechanisms, and that their redundancy provides the necessary robustness.     

Predicting the external formation of a bone fracture callus: an optimisation approach

The formation of a fracture callus in vivo tends to form in a structurally efficient manner distributing tissues where mechanical stimulus persists. Therefore, it is proposed that the formation of a fracture callus can be modelled in silico by way of an optimisation algorithm. This was tested by generating a finite element model of a transversal bone fracture embedded in a large tissue domain which was subjected to axial, bending and torsional loads. It was found that the relative fragment motion induced a compressive strain field in the early callus tissue which could be utilised to simulate the formation of external callus structures through an iterative optimisation process of tissue maintenance and removal. The phenomenological results showed a high level of congruence with in vivo healing patterns found in the literature. Consequently, the proposed strategy shows potential as a means of predicting spatial bone healing phenomena for pre-clinical testing.     

Community analysis of methanogenic archaea within a riparian flooding gradient

Anoxic soils in river floodplains (or riparian soils) are a source of methane emission. However, little is known about the ecology and community structure of archaeal methanogenic microbes, which are a crucial component of methane flux in those habitats. We studied the archaeal community in the vertical profile of four different sites along the River Waal in the Netherlands. These sites differ in their annual flooding regime ranging from never or seldom to permanently flooded. The archaeal community structure has been characterized by terminal restriction fragment length polymorphism (T-RFLP) and comparative sequence analysis of the archaeal SSU rRNA gene and the mcrA gene. The latter gene codes for the alpha-subunit of methyl-coenzyme M reductase. Additionally, the potential methanogenic activity was determined by incubation of soil slurries under anoxic conditions. The community composition differed only slightly with the depth of the soil (0-20 cm). However, the diversity of archaeal SSU rRNA genes increased with the frequency of flooding. Terminal restriction fragment length polymorphism analysis of mcrA gene amplicons confirmed the results concerning methanogenic archaea. In the never and rarely flooded soils, crenarchaeotal sequences were the dominant group. In the frequently and permanently flooded soils, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae and the uncultured Rice Clusters IV and VI (Crenarchaeota) were detectable independently from duration of anoxic conditions. Methanosaetaceae, on the other hand, were only found in the permanently and frequently flooded soils under conditions where concentrations of acetate were < 30 microM. The results indicate that methanogens as well as other archaea occupy characteristic niches according to the flooding conditions in the field. Methanosaetaceae, in particular, seem to be adapted (or proliferate at) to low acetate concentrations.     

Development of a pH gradient within a biofilm is dependent upon the limiting nutrient

Monospecies Citrobacter sp. biofilms were grown in a laminar flow cell using a carbon-limiting medium. Microelectrode measurements showed no change in pH between the bulk fluid and biofilm when the flow cell was supplied with the carbon-limiting medium under static or flowing conditions. When the biofilm was supplied with a phosphate-limiting medium the biofilm became more acidic than the bulk fluid and developed a gradient within. The implications for metals-bioremediation processes are discussed.     

Optical aspect of deformation analysis in the bone-denture complex

The aim of this study was to register and measure any deformation of mandible models under load. The method for full field measurement of strain is done by using the ARAMIS three-dimensional image correlation system. The system uses two digital cameras that provide a synchronized stereo view of the specimen and the results show the complete strain field during the tests. The biggest deformation values were just under the working force of the biggest intensity 500 N, and for the region of the lower second premolar the deformation is 625 microm. The following study is presented that highlight the use of stereometric measuring system for modern research. It is shown that this measuring methodology can capture the trends of the experiments.     

Fine structural localization of acid phosphomonoesterase in the osteoblasts and osteocytes of fracture callus

Summary The fine structural localization of acid phosphatase was studied in osteoblasts and osteocytes of fracture callus in the rat using glutaraldehyde-fixed EDTA-decalcified, dimethylsulfoxide-treated tissues incubated in a modified Gomori lead salt medium. The results showed that enzyme was not only localized in conventional lysosomes but also in Golgi cisternae, Golgi associated vesicles, and — in the case of osteoblasts — GERL-like regions. The Golgi regions were large and abundant in osteoblasts and small and inconspicuous in osteocytes while lysosomes were of approximately equal size in the two cell types but appeared to be more concentrated in osteocytes. The results were discussed in relation to the possible role of lysosomes and lysosomal enzymes in osteocytic osteolysis and the functional diversity of the Golgi apparatus in osteogenic cells.     

Relative influence of shredders and fungi on leaf litter decomposition along a river altitudinal gradient

We compared autumn decomposition rates of European alder leaves at four sites along the Lasset–Hers River system, southern France, to test whether changes in litter decomposition rates from upstream (1,300 m elevation) to downstream (690 m) could be attributed to temperature-driven differences in microbial growth, shredder activity, or composition of the shredder community. Alder leaves lost 75–87% of original mass in 57 days, of which 46–67% could be attributed to microbial metabolism and 8–29% to shredder activity, with no trend along the river. Mass loss rates in both fine-mesh (excluding shredders) and coarse-mesh (including shredders) bags were faster at warm, downstream sites (mean daily temperature 7–8°C) than upstream (mean 1–2°C), but the difference disappeared when rates were expressed in heat units to remove the temperature effect. Mycelial biomass did not correlate with mass loss rates. Faster mass loss rates upstream, after temperature correction, evidently arise from more efficient shredding by Nemourid stoneflies than by the Leuctra-dominated assemblage downstream. The influence of water temperature on decomposition rate is therefore expressed both directly, through microbial metabolism, and indirectly, through the structure of shredder communities. These influences are evident even in cold water where temperature variation is small.     

Histochemical and biochemical studies on the localization and activity of lysosomal enzymes in fracture callus

Summary Quantitative biochemical studies on the activities of four lysosomal hydrolases during different stages of fracture healing in the rat were performed, and the results obtained were integrated with those of histochemical observations relating to changes in the localization of acid phosphatase in the same tissue.The findings showed presence of all the four lysosomal enzymes assayed in the callus; during early callus formation the enzyme activities calculated on a DNA basis increased up to about 12 days after the fracture. The enzyme activities appeared to be roughly reflected histochemically by the acid phosphatase staining. The increasing activity during early callus formation seemed to depend on the presence of numerous macrophage-like cells in the tissue containing many large lysosomes. A decrease in enzyme activity was found after day 12. Comparison with the histochemical and ultrastructural findings suggested that this decrease was due to a reduction in the number of macrophage-like cells and a concomitant increase in osteogenic cells with a lower enzyme content.     

induction of heat shock response and acquisition of thermotolerance in callus cultures of Gerbera jamesonii

Summary The heat shock (HS) response in callus cultures of the ornamental plant Gerbera jamesonii H. Bolus var. hybrida was analyzed. A HS at 35° C or 40° C for 4 h induced (a) the synthesis of several heat shock proteins (HSPs), especially in the small molecular weight range and some spots corresponding to HSP70 components, and (b) an increase in the steady state levels of some specific mRNAs. At the nonstressing temperature (26° C), a sustainable level of translation for HSP70 was indeed carried out, as confirmed by immunological analysis with a monoclonal antibody against cotton HSP70. The steady state levels of mRNAs measured before and after a HS by Northern hybridization showed an increase with the heterologous probes HSP17.4, HSP17.6, and HSP21, whereas the probes HSC70 and HSP70 did not show any difference between the levels of control and HS-mRNAs. A pretreatment at 35° C, which induced a set of HSPs in the callus cultures, decreased the cell damage upon exposure to a temperature of 45° C as determined either with a regrowth test or by the tetrazolium reduction assay. Typically, as with the whole plants, callus of Gerbera jamesonii possessed the ability to respond to HS both by inducing HSPs and by developing an acquired thermotolerance.     

Soil C and N dynamics within a precipitation gradient in Mediterranean eucalypt plantations

Soil C and N dynamics were evaluated in five eucalypt plantations within a precipitation gradient (500–2,000 mm) in Portugal. Soil physical and chemical properties, total and labile (particulate organic matter, hydrolyzable, hot water soluble and microbial) soil C and N pools, and C and N mineralization were measured to characterize the C and N dynamics and their controlling factors within this gradient. Contents of total and labile soil organic C and N were positively correlated with the mean annual precipitation. A similar relationship was observed for net N mineralization (anaerobic and long-term aerobic incubation), gross N mineralization (¹⁵N isotope dilution technique) and C mineralization. In contrast, rates of C and N mineralization (per unit of C and N) were higher in the driest sites due to their higher proportion of particulate organic matter C. Net and gross N mineralization were strongly correlated and showed similar controlling factors (mean annual precipitation, total and labile C and N and extractable P contents), suggesting that net N mineralization during long-term aerobic incubation reflects gross N transformations. Although, gross NO₃–N production and gross NO₃–N immobilization were observed in all sites, net nitrification in the drier sites was not observed in the first weeks of the study. Our results suggest that, under Mediterranean conditions, mean annual precipitation is the major factor determining the C and N dynamics in soils with Eucalyptus plantations.     

Radiation-induced decomposition of the purine bases within DNA and related model compounds

This survey focuses on recent developments in the radiation chemistry of purine bases in nucleic acids and related model compounds. Both direct and indirect effects of ionizing radiation are investigated with special emphasis on the structural characterization of the final decomposition products of nucleic acid components. Available assays for monitoring radiation-induced base lesions are critically reviewed.     

Variability of polar scurvygrass Cochlearia groenlandica individual traits along a seabird influenced gradient across Spitsbergen tundra

In the resource-limited Arctic environment, vegetation developing near seabird colonies is exceptionally luxuriant. Nevertheless, there are very few detailed quantitative studies of any specific plant species responses to ornithogenic manuring. Therefore, we studied variability of polar scurvygrass Cochlearia groe nlandica individual biomass and leaf width along a seabird influenced gradient determining environmental conditions for vegetation in south-west Spitsbergen. We found seabird colony effect being a paramount factor responsible for augmented growth of C. groenlandica. The species predominated close to the colony and reached the highest mean values of individual biomass (1.4 g) and leaf width (26.6 mm) 10 m below the colony. Its abundance and size declined towards the coast. Both C. groenlandica individual traits significantly decreased with distance from the colony, soil water and organic matter content and increased with guano deposition, soil δ ¹⁵N, conductivity, acidity and nitrate, phosphate and potassium ion content. Our study supports the hypothesis that seabirds have fundamental importance for vegetation growth in poor Arctic environment. Highly plastic species such as C. groenlandica may be a useful instrument in detecting habitat condition changes, for instance resulting from climate change.