Methionyl-tRNA synthetase from E. coli: direct evidence for exchange of protomers in the dimeric enzyme by using deuteration and small-angle neutron scattering

Direct demonstration of the reversible dissociation of native dimeric methionyl-tRNA synthetase from E. coli has been obtained using small angle neutron scattering and deuterated enzyme. Structural parameters of the fully deuterated dimer are very similar to the hydrogenated one. Analysis of the variations of the intensity and of the radius of gyration of a stoichiometric mixture of the two types of dimer (hydrogenated and deuterated), as a function of D2O content in the solvent, enabled us to characterize an hybrid dimer, having both hydrogenated and deuterated protomers. By separating the contribution of each protomer to the scattering, the radius of gyration of the protomer in situ and the distance between the centers of mass of each protomer in the dimer are determined.     

Status of the so-called African pygmy elephant (Loxodonta pumilio (NOACK 1906)): phylogeny of cytochrome b and mitochondrial control region sequences

Among the African elephants, it has been unanimously acknowledged that the forest elephants (cyclotis form) are peculiar, so that they have been elevated to the specific rank. The development of molecular analyses of extant Loxodonta has only focused on two forms yet: the savannah form (africana) and the forest form (cyclotis), disregarding the so-called pygmy elephants (pumilio or fransseni) the systematic status of which has been debated since their discovery. Therefore, we have sampled nine dwarfed-labelled specimens in collection and eight specimens of typical forest elephants that we compared to three savannah elephants and two Asian elephants. Because of the degraded nature of the nuclear DNA content in bone samples of old specimens, we assayed mitochondrial markers; 1961 bp of the mitochondrial genome were sequenced (over a continuous range spanning the cytochrome b gene, tRNA Thr, tRNA Pro, hypervariable region 1 and central conserved region of the control region). Pumilio and cyclotis are not sister-taxa: the phylogenetic analyses rather account for the inclusion of the so-called pygmy elephants within a monophyletic group of forest elephants sensu lato. The internal structure of this clade reveals to depend on isolation and remoteness between populations, characteristics that may have been extensively influenced by climatic variations during the Quaternary period. We conclude that the specific taxon Loxodonta pumilio (or Loxodonta fransseni) should be abandoned.     

A hierarchical matrix model to assess the impact of habitat fragmentation on population dynamics: an elasticity analysis

To better understand the role of habitat quality and boundaries on population dynamics at the landscape scale, we develop a model combining a spatially implicit approach, a spatial population Leslie-type model and an implicit model of habitat fragmentation. An original approach of elasticity permits to identify which types of element and boundary influence the most population viability according to the wood fragmentation degree. The studied species is a corridor forest insect sensitive to fragmentation (Abax parallelepipedus, Coleoptera, Carabidae). We show that a single large patch of wood is better than several small patches for the population viability.     

A simple framework to describe the regulation of gene expression in prokaryotes

Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mathematical framework in order to describe the regulation of gene expression in prokaryotes. It is shown that the derived models have all the qualitative properties of the activation and inhibition regulatory mechanisms observed in experiments. The basic construction considers genes as templates for protein production, where regulation processes result from activators or repressors connecting to DNA binding sites. All the parameters in the models have a straightforward biological meaning. After describing the general properties of the basic mechanisms of positive and negative gene regulation, we apply this framework to the self-regulation of the trp operon and to the genetic switch involved in the regulation of the lac operon. One of the consequences of this approach is the existence of conserved quantities depending on the initial conditions that tune bifurcations of fixed points. This leads naturally to a simple explanation of threshold effects as observed in some experiments.     

Kinetic studies of the reaction mechanism of rat liver phosphoglycerate kinase in the direction of ADP utilization

The kinetic properties of rat liver phosphoglycerate kinase were investigated in the forward direction of the reaction (utilization of ADP). The kinetic studies were performed in an assay system using combined hexokinase/glucose-6-phosphate dehydrogenase as an ATP trap. The Km values for Mg ADP1- and 1,3-diphospho-D-glycerate were approximately 0.11 and 0.006 mM, respectively. Reciprocal plots of 1/v versus 1/ (Mg ADP1-) at different fixed concentrations of 1,3-diphospho-D-glycerate and 1/v versus 1/ (1,3-diphospho-D-glycerate) at different fixed concentrations of Mg ADP1- were apparently parallel. However, product inhibition studies (3-phospho-D-glycerate), dead-end inhibition studies (2,3-diphospho-D-glycerate), and adenosine and AMP inhibition patterns yielded results consistent with a rapid equilibrium random mechanism in which the binding of one substrate greatly decreases the affinity of the enzyme for the second substrate. Existence of two sites for 3-phospho-D-glycerate is suggested.     

Finite element analysis of the cranium: Validity,sensitivity and future directions

Finite element analysis (FEA) is increasingly applied in skeletal biomechanical research in general, and in fossil studies in particular. Underlying such studies is the principle that FEA provides results that approximate reality. This paper provides further understanding of the reliability of FEA by presenting a validation study in which the deformations experienced by a real cadaveric human cranium are compared to those of an FE model of that cranium under equivalent simulated loading. Furthermore, model sensitivity to simplifications in segmentation and material properties is also assessed. Our results show that absolute deformations are not accurately predicted, but the distribution of the regions of relatively high and low strains, and so the modes of global deformation, are reasonably approximated.     

Pigmentation pattern formation in butterflies: experiments and models

Butterfly pigmentation patterns are one of the most spectacular and vivid examples of pattern formation in biology. They have attracted much attention from experimentalists and theoreticians, who have tried to understand the underlying genetic, chemical and physical processes that lead to patterning. In this paper, we present a brief review of this field by first considering the generation of the localised, eyespot, patterns and then the formation of more globally controlled patterns. We present some new results applied to pattern formation on the wing of the mimetic butterfly Papilio dardanus.     

Overproduction of the membrane-bound components of the histidine permease from Salmonella typhimurium: identification of the M protein

The periplasmic histidine permease of Salmonella typhimurium is composed of a soluble histidine-binding protein and three membrane-bound components. These latter are produced in very small amounts and only two, the Q and the P protein, have been previously identified. This paper describes the construction of a plasmid carrying the hisQ, hisM, and hisP genes under the control of the lambda PL promoter, thus allowing great overproduction of those gene products. The M protein has been identified in such overproducing strains and its nature confirmed by constructing in vitro hisM deletions within the plasmid. With these results the identification of all components of the histidine permease has been completed.     

The tight junctions of rabbit choroid plexus and ciliary body epithelia. A comparative study using the double replica freeze-fracture technique

The spatial arrangement of tight junctions in choroid plexus and ciliary body rabbit epithelia has been determined by studying freeze-fracture complementary replicas. In the choroid plexus epithelium, the interruptions of the junctional P-face fibrils were measured to be 14% of their total length. In the ciliary body epithelium, where the fibrils were found to be more fragmented than in the choroid plexus, the P-face fibril interruptions accounted for 12 % of the total length of the zonulae occludentes sealing the non-pigmented cells and 30% in the focal linear tight junctions connecting the non-pigmented and pigmented cells at their apices. In both epithelia, the interruptions of the ridges are precisely complemented by particles or short bars of similar length found in the E-face furrows. Consequently, it is possible to conclude that the junctional fibrils are continuous in these two epithelia. For the zonulae occludentes, this continuity appears to be inconsistent with the ‘leaky’ properties of these epithelia shown by some physiological investigations.     

Electrophoretic characterization of the protein and glycoprotein content of purified Kurloff cell cytosol

Proteins and glycoproteins from Kurloff cells (KC) were analyzed by SDS-polyacrylamide electrophoresis, isoelectric focusing, and two-dimensional electrophoresis, and major cytosolic glycoproteins of Mr 30,000-35,000 and pHi 5.7-6.7 were characterized. After incubation with radiolabeled amino acids (L-35S) methionine and L-(U14C) leucine) and gel autoradiography, all the proteins seemed to be labeled. D-(U14C) glucosamine-labeled proteins and periodic-acid-Schiff(PAS)-positive proteins focalized at the same pH. These data suggest that the major glycoprotein are synthesized by the KC themselves and that the PAS-positive Kurloff body has an endogenous origin. Whereas estrogens increase the KC number, 10(-6) M estradiol had no effect on the KC protein electrophoretic pattern and protein biosynthesis, in agreement with the lack of estradiol receptor in the KC cytosol.