Fractal analysis of the root architecture of Gliricidia sepium for the spatial prediction of root branching,size and mass: model development and evaluation in agroforestry

Based on fractal and pipe model assumptions, a static three-dimensional model of the Gliricidia sepium root system was developed, in order to provide a basis for the prediction of root branching, size and mass in an alley cropping system. The model was built from observations about the topology, branching rules, link length and diameter, and root orientation, provided by in situ and extracted root systems. Evaluation tests were carried out at the plant level and at the field level. These tests principally concerned coefficients α and q –- the proportionality factor α between total cross-sectional area of a root before and after branching, and allocation parameter q that defines the partitioning of biomass between the new links after a branching event –- that could be considered as key variables of this fractal approach. Although independent of root diameter, these coefficients showed a certain variability that may affect the precision of the predictions. When calibrated, however, the model provided suitable predictions of root dry matter, total root length and root diameter at the plant level. At the field level, the simulation of 2D root maps was accurate for root distribution patterns, but the number of simulated root dots was underestimated in the surface layers. Hence recommendations were made to improve the model with regard to α and q. This static approach appeared to be well suited to study the root system of adult trees. Compared with explicit models, the main advantage of the fractal approach is its plasticity and ease of use. This revised version was published online in June 2006 with corrections to the Cover Date.     

Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale

A comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. Thirty-four r-protein families are represented in all domains but 33 families are specific to Archaea and Eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to Archaea and Eukaryotes. With only one specific r-protein, the archaeal ribosome appears to be a small-scale model of the eukaryotic one in terms of protein composition. However, the mechanism of evolution of the protein component of the ribosome appears dramatically different in Archaea. In Bacteria and Eucarya, a restricted number of ribosomal genes can be lost with a bias toward losses in intracellular pathogens. In Archaea, losses implicate 15% of the ribosomal genes revealing an unexpected plasticity of the translation apparatus and the pattern of gene losses indicates a progressive elimination of ribosomal genes in the course of archaeal evolution. This first documented case of reductive evolution at the domain scale provides a new framework for discussing the shape of the universal tree of life and the selective forces directing the evolution of prokaryotes.     

Sphingomyelin content conditions insertion of daunorubicin within phosphatidylcholine monolayers

Cell death induced by the chemotherapeutic drug daunorubicin (DNR) implicates an apoptotic pathway originating at the plasma membrane and characterized by sphingomyelin (SM) hydrolysis and ceramide generation. The mechanisms by which such a drug (hypothetically passively diffusing across a structural membrane) can trigger SM hydrolysis is unknown, but raises the question of the precise interaction between DNR and membrane lipid constituents. In this initial study, using alternative current polarography together with voltammetry, we report that after a first step of adsorption, insertion of DNR within a condensed phosphatidylcholine monolayer was significantly facilitated by SM content.     

Community ecology of the terrestrial small mammals of Zakouma National Park,Chad

The terrestrial small mammal community of the Zakouma National Park (Chad) was assessed by live trapping in various habitats during the dry season. Nearly 3000 trap-nights yielded 505 captures of nine rodent and two shrew species, making up a representative small mammal community for the Sudanian savanna biotic zone. Murine rodents of the genusMastomys dominated, withM. erythroleucus andM. cf.kollmannspergeri occuring at similar abundances. The former was widespread and especially abundant in habitats with high tree cover. The latter was more localized, predominantly in annually flooded habitats characterized by a clay-rich soil, often withAcacia seyal as the main vegetation. Population structure differed between the two species, suggesting distinct reproductive strategies possibly linked with habitat preferences: theM. erythroleucus population comprised mainly young, immature individuals, whereasM. cf.kollmannspergeri was represented by older individuals, a significant fraction of which had already reproduced.Taterillus congicus andTatera kempi (gerbilline rodents), together withLemniscomys zebra, were mainly found in more open habitats with sand-rich soils.Arvicanthis niloticus, Acomys cf.johannis, Mus mattheyi andXerus erythropus were the other rodents captured, whereas shrews were represented byCrocidura fulvastra andSuncus sp.     

Whole-exome sequencing identifies mutations in GPR179 leading to autosomal-recessive complete congenital stationary night blindness

Congenital stationary night blindness (CSNB) is a heterogeneous retinal disorder characterized by visual impairment under low light conditions. This disorder is due to a signal transmission defect from rod photoreceptors to adjacent bipolar cells in the retina. Two forms can be distinguished clinically, complete CSNB (cCSNB) or incomplete CSNB; the two forms are distinguished on the basis of the affected signaling pathway. Mutations in NYX, GRM6, and TRPM1, expressed in the outer plexiform layer (OPL) lead to disruption of the ON-bipolar cell response and have been seen in patients with cCSNB. Whole-exome sequencing in cCSNB patients lacking mutations in the known genes led to the identification of a homozygous missense mutation (c.1807C>T [p.His603Tyr]) in one consanguineous autosomal-recessive cCSNB family and a homozygous frameshift mutation in GPR179 (c.278delC [p.Pro93Glnfs^∗57]) in a simplex male cCSNB patient. Additional screening with Sanger sequencing of 40 patients identified three other cCSNB patients harboring additional allelic mutations in GPR179. Although, immunhistological studies revealed Gpr179 in the OPL in wild-type mouse retina, Gpr179 did not colocalize with specific ON-bipolar markers. Interestingly, Gpr179 was highly concentrated in horizontal cells and Müller cell endfeet. The involvement of these cells in cCSNB and the specific function of GPR179 remain to be elucidated.     

Comparative anatomy of rabbit and human achilles tendons with magnetic resonance and ultrasound imaging

We sought to describe the comparative anatomy of the Achilles tendon in rabbits and humans by using macroscopic observation, magnetic resonance imaging, and ultrasonography. The calcaneus-Achilles tendon-gastrocnemius-soleus complexes from 18 New Zealand white rabbits underwent ultrasound (US) and magnetic resonance (MR) imaging and gross anatomic sectioning; these results were compared with those from a cadaveric gastrocnemius-soleus-Achilles tendon-calcaneus specimen from a 68-y-old human male. The medial and lateral gastrocnemius muscle tendons merged 5.2 +/- 0.6 mm proximal to the calcaneal insertion macroscopically, at 93% of their course, different from the gastrocnemius human tendons, which merged at 23% of their overall course. The rabbit flexor digitorum superficialis tendon, corresponding to the flexor digitorum longus tendon in human and comparable in size with the gastrocnemius tendons, was located medial and anterior to the medial gastrocnemius tendon proximally and rotated dorsally and laterally to run posterior to the Achilles tendon-calcaneus insertion. In humans, the flexor digitorum longus tendon tracks posteriorly to the medial malleolus. The soleus muscle and tendon are negligible in the rabbit; these particular comparative anatomic features in the rabbit were confirmed on the MR images. Therefore the rabbit Achilles tendon shows distinctive gross anatomical and MR imaging features that must be considered when using the rabbit as a research model, especially for mechanical testing, or when generalizing results from rabbits to humans.     

Biosynthese des ramifications en C-24 des phytosterols de Physarum polycephalum et d'Ochromonas danica

The side chain C-24 alkylation mechanism of phytosterols of Physarum polycephalum and Ochromonas danica, cultured in a nutrient medium containing methionine-CD₃, has been studied. Depending on species, five or four deuterium atoms were incorporated respectively in C-24 ethyl phytosterols. No relation could be established between the stereochemistry of C-24 and the alkylation mechanism at this position.     

Interaction of human gamma-carboxyglutamic acid domainless prothrombin with phospholipids

The conversion of prothrombin into thrombin occurs at the surface of stimulated platelets. In order to see the influence of gamma-carboxyglutamic acid in the interaction of prothrombin with phospholipid, we investigated the direct interaction of the peptide 1-41 and prothrombin (des 1-44) with phospholipid monolayers of various compositions. Adsorption of the labeled proteins was determined by surface radioactivity measurements. Penetration of the proteins into the lipid layers was inferred from capacitance variation of the monolayer, measured by a.c. polarography. Prothrombin (des 1-44) was found both to adsorb and to penetrate the lipid monolayers, in the presence and in the absence of Ca++. The effects are higher on 100% PS than on 25% PS. This protein was also found to increase the permeability of vesicles containing 25% PS to T1+ ions, in the presence and in the absence of Ca++. Comparison with prothrombin shows that Gla residues are clearly involved in the interaction at 25% PS; nevertheless, the peptide 1-41 does not penetrate. A model of interaction of prothrombin with phospholipid, including both adsorption of prothrombin by Gla residues and its penetration by another domain, is proposed.     

Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism

ABSTRACT: BACKGROUND: Membrane trafficking involves the complex regulation of proteins and lipids intracellular localization and is required for metabolic uptake, cell growth and development. Different trafficking pathways passing through the endosomes are coordinated by the ENTH/ANTH/VHS adaptor protein superfamily. The endosomes are crucial for eukaryotes since the acquisition of the endomembrane system was a central process in eukaryogenesis. RESULTS: Our in silico analysis of this ENTH/ANTH/VHS superfamily, consisting of proteins gathered from 84 complete genomes representative of the different eukaryotic taxa, revealed that genomic distribution of this superfamily allows to discriminate Fungi and Metazoa from Plantae and Protists. Next, in a four way genome wide comparison, we showed that this discriminative feature is observed not only for other membrane trafficking effectors, but also for proteins involved in metabolism and in cytokinesis, suggesting that metabolism, cytokinesis and intracellular trafficking pathways co-evolved. Moreover, some of the proteins identified were implicated in multiple functions, in either trafficking and metabolism or trafficking and cytokinesis, suggesting that membrane trafficking is central to this co-evolution process. CONCLUSION: Our study suggests that membrane trafficking and compartmentalization were not only key features for the emergence of eukaryotic cells but also drove the separation of the eukaryotes in the different taxa.