Finite element simulations of the active stress in the imaginal disc of the Drosophila Melanogaster

During the larval stages of development, the imaginal disc of Drosphila Melanogaster is composed by a monolayer of epithelial cells, which undergo a strain actively produced by the cells themselves. The well-organized collective contraction produces a stress field that seemingly has a double morphogenetic role: it orchestrates the cellular organization towards the macroscopic shape emergence while simultaneously providing a local information on the organ size. Here we perform numerical simulations of such a mechanical control on morphogenesis at a continuum level, using a three-dimensional finite model that accounts for the active cell contraction. The numerical model is able to reproduce the (few) known qualitative characteristics of the tensional patterns within the imaginal disc of the fruit fly. The computed stress components slightly deviate from planarity, thus confirming the previous theoretical assumptions of a nonlinear elastic analytical model, and enforcing the hypothesis that the spatial variation of the mechanical stress may act as a size regulating signal that locally scales with the global dimension of the domain.     

Docking of a Series of Peptide-Based Interleukin-1β Converting Enzyme Inhibitors with Aspartyl Hemiacetals, α-((2,6-Dichlorobenzoyl)oxy)methyl and (Acyloxy)methyl Ketone Moieties

The enzyme-binding mode of a series of interleukin-1 converting enzyme (ICE) inhibitors has been analysed on the basis of the crystal structure of the complex between hICE and tetrapeptide aldehyde. The conformation of these ligands were explored by performing molecular dynamics simulations at 100 ps. The conformation adopted by these inhibitors was very similar to and could be superimposable onto the regions of crystal structure. The active and the low energy conformers were docked either by grid or manually into the binding site. The analysis of the resulting model indicated that O-benzylacyl group of aspartyl hemiacetals interact with Cys285 and the large substituents: semicarbazone, 2,6-bis(trifluoromethyl) benzoate, other leaving groups of (acyloxy)methyl and -((2,6-dichlorobenzoyl)oxy)methyl ketone series of P1 site protrude from the surface of Cys285 and interact with Val338, which is located below the binding pocket. The hydrogen bonding interaction between -NH of semicarbazone and Cys285 seems to have significant role. The total potential energy including intermolecular interaction energy, consisting of van der Waals and electrostatic energies were calculated. The resulting model is qualitatively consistent with the reported experimental data and can be useful for the design of more potent inhibitors of ICE.Electronic Supplementary Material available.     

A re-appraisal of the diversity of the methanogens associated with the rumen ciliates

The diversity of methanogenic archaea associated with different species of ciliated protozoa in the rumen was analysed. Partial fragments of archaeal SSU rRNA genes were amplified from DNA isolated from single cells from the rumen protozoal species Metadinium medium, Entodinium furca, Ophryoscolex caudatus and Diplodinium dentatum. Sequence analysis of these fragments indicated that although all of the new isolates clustered with sequences previously described for methanogens, there was a difference in the relative distribution of sequences detected here as compared to that of previous work. In addition, many of the novel sequences, although clearly of archaeal origin have relatively low identity to the sequences in database which are most closely related to them.     

Establishment of microscale vegetation pattern in maritime chaparral after fire

We quantified microscale pattern in vegetation and seed assemblages along a 24 m transect before and for two years following a controlled burn in chamise (Adenostoma fasciculatum) chaparral in central coastal California. Our objective was to document scale-dependent correlation between pre-burn seed assemblages, pre-burn canopy cover, microtopography, soil temperatures during burning, post-burn seed assemblages and post-burn vegetation. Scale-dependent correlations among pre- and post-burn seed densities, maximum soil temperatures during burning, microtopography and post-burn vegetation were measured based on two-term local covariance analysis.Seed distribution varied among species prior to fire, with seeds of some annual species concentrated in gap areas. Maximum soil temperatures during burning ranged from less than 50 °C to 225 °C, and were generally lowest in gaps in the pre-burn canopy. These gaps were associated with local topographic depressions. After burning, readily germinable seeds were concentrated in or near gaps in the pre-burn canopy. Germination of different species was variously enhanced, diminished or unchanged by the passage of fire. Post-burn vegetation was very patchy, with some areas nearly devoid of seedlings and other areas, especially pre-burn canopy gaps, supporting numerous seedlings. Seedling recruitment patterns in the second year were generally highly correlated with patterns in pre-burn seed banks and first year vegetation. Although many species exhibited similar recruitment patterns, several different mechanisms may have been responsible for the origin of those patterns.     

Three-dimensional pore space quantification of apple tissue using X-ray computed microtomography

The microstructure and the connectivity of the pore space are important variables for better understanding of the complex gas transport phenomena that occur in plant tissues. In this study, we present an experimental procedure for image acquisition and image processing to quantitatively characterize in 3D the pore space of apple tissues (Malus domestica Borkh.) for two cultivars (Jonagold and Braeburn) taken from the fleshy part of the cortex using X-ray computer microtomography. Preliminary sensitivity analyses were performed to determine the effect of the resolution and the volume size (REV, representative elementary volume analysis) on the computed porosity of apple samples. For comparison among cultivars, geometrical properties such as porosity, specific surface area, number of disconnected pore volumes and their distribution parameters were extracted and analyzed in triplicate based on the 3D skeletonization of the pore space (medial axis analysis). The results showed that microtomography provides a resolution at the micrometer level to quantitatively analyze and characterize the 3D topology of the pore space in apple tissue. The computed porosity was confirmed to be highly dependent of the resolution used, and the minimum REV of the cortical flesh of apple fruit was estimated to be 1.3 mm³. Comparisons among the two cultivars using a resolution of 8.5 μm with a minimum REV cube showed that in spite of the complexity and variability of the pore space network observed in Jonagold and Braeburn apples, the extracted parameters from the medial axis were significantly different (P-value < 0.05). Medial axis parameters showed potential to differentiate the microstructure between the two evaluated apple cultivars.