Wood samples of 111 Vaccinieae specimens (Vaccinioideae, Ericaceae s.l.) representing 98 species and 26 genera are investigated with light microscopy and scanning electron microscopy. The wood... Show moreWood samples of 111 Vaccinieae specimens (Vaccinioideae, Ericaceae s.l.) representing 98 species and 26 genera are investigated with light microscopy and scanning electron microscopy. The wood structure of Vaccinieae delivers taxonomically important characters that can be used to define some subclades within the tribe. The wood of the large polyphyletic genus Vaccinium strongly resembles non-vaccinioid members of the family, which are characterized by bordered vessel-ray pits and relatively narrow (2- to 4-seriate) and low multiseriate rays (often less than 1000 m) with exclusively or mainly procumbent body ray cells. The East Malesian clade, Meso-American/Caribbean clade, and the Andean clade show a combination of wood anatomical features that is lacking in other representatives of the family. These features include scalariform vessel-ray pits with strongly reduced borders, a high portion of upright body ray cells, wide (4- to 14-seriate) and high multiseriate rays (often more than 3000 m), and prismatic crystals in chambered ray cells (although absent in Symphysia racemosa). The presence of secretory ducts in the primary xylem and in the pith tissue may represent a synapomorphy for the Andean clade. Furthermore, the presence of undivided axial parenchyma cells, usually ranging from 500 to 900 m, seems to be unique in the subfamily. Show less
An ensemble approach for force networks in static granular packings is developed. The framework is based on the separation of packing and force scales, together with an a priori flat measure in the... Show moreAn ensemble approach for force networks in static granular packings is developed. The framework is based on the separation of packing and force scales, together with an a priori flat measure in the force phase space under the constraints that the contact forces are repulsive and balance on every particle. In this paper we will give a general formulation of this force network ensemble, and derive the general expression for the force distribution P(f). For small regular packings these probability densities are obtained in closed form, while for larger packings we present a systematic numerical analysis. Since technically the problem can be written as a noninvertible matrix problem (where the matrix is determined by the contact geometry), we study what happens if we perturb the packing matrix or replace it by a random matrix. The resulting P(f)’s differ significantly from those of normal packings, which touches upon the deep question of how network statistics is related to the underlying network structure. Overall, the ensemble formulation opens up a different perspective on force networks that is analytically accessible, and which may find applications beyond granular matter. Show less
A comparative study of the thermal stability of wild type poplar plastocyanin and of a mutant form containing a disulfide bridge between residues 21 and 25 was performed using differential scanning... Show moreA comparative study of the thermal stability of wild type poplar plastocyanin and of a mutant form containing a disulfide bridge between residues 21 and 25 was performed using differential scanning calorimetry and optical spectroscopic techniques.For wild type plastocyanin the transition temperature, determined from the calorimetric profiles, is 62.7 degreesC at the scan rate of 60 degreesC/h, whereas for the mutant it is reduced to 58.0 degreesC. In both cases, the endothermic peak is followed by an exothermic one at higher temperatures.The unfolding process monitored by optical absorption at 596 nm also reveals a reduced thermal stability of the mutated plastocyanin compared to the wild type protein, with transition temperatures of 54.8 and 58.0 degreesC, respectively. For both proteins, the denaturation process was found to be irreversible and dependent on the scan rate preventing the thermodynamic analysis of the unfolding process.In parallel, small conformational changes between wild type and mutant plastocyanin emerge from fluorescence spectroscopy measurements. Here, a difference in the interaction of the two proteins between the microenvironment surrounding the fluorophores and the solvent was proposed.The destabilization observed in the disulfide containing mutant of plastocyanin suggests that the double mutation, Ile2lCys and Glu25Cys, introduces strain into the protein which offsets the stabilizing effect expected from the formation of a covalent crosslink. (C) 2004 Elsevier B.V. All rights reserved. Show less
Molecular dynamics (MD) simulations have been performed on quercetin 2,3 dioxygenase (2,3QD) to study the mobility and flexibility of the substrate cavity. 2,3QD is the only firmly established Cu... Show moreMolecular dynamics (MD) simulations have been performed on quercetin 2,3 dioxygenase (2,3QD) to study the mobility and flexibility of the substrate cavity. 2,3QD is the only firmly established Cu-containing dioxygenase known so far. It catalyses the breakage of the O-heterocycle of flavonols. The substrates occupy a shallow and overall hydrophobic cavity proximal to the metal centre of the homo-dimeric enzyme. The linker connecting the C-terminal and N-terminal domains in the monomer is partly disordered in the crystal structure and part of it forms a flexible lid at the entrance of the substrate cavity. This loop has been tentatively assigned a role in the enzyme mechanism: it helps lock the substrate into place. The dynamics of this loop has been investigated by MD simulation. The initial coordinates were taken from the crystal structure of 2,3QD in the presence of the substrate kaempferol (KMP). After equilibration and simulation over 7.2 ns the substrate was removed and another equilibration and simulation of 7.2 ns was performed. The results show that the structures of the free enzyme as well as of the enzyme-substrate complex are stable in MD simulation. The linker shows strongly enhanced mobility in the loop region that is close to the entrance to the substrate cavity (residues 154-169). Movement of the loop takes place on a timescale of 5-10 ns. To confirm the conclusions about the loop dynamics drawn from the 7.2 ns simulation, the simulation was extended with another 8 ns. When substrate binds into the cavity the loop orders remarkably, although mobility is retained by residues 155-158. Some regions of the loop (residues 154-160 and 164-176) move over a considerable distance and approach the substrate closely, reinforcing the idea that they lock the substrate in the substrate cavity The enthalpic component of the interaction of the loop with the protein and the KMP appears to favour the locking of the substrate. Two water molecules were found immobilised in the cavity, one of which exhibited rotation on the picosecond timescale. When the substrate is removed, the empty cavity fills up with water within 200 ps. (C) 2004 Elsevier Ltd. All rights reserved. Show less
