Protein secondary structure assignment through Voronoï tessellation

We present a new automatic algorithm, named VoTAP (Vo ronoï T essellation A ssignment P rocedure), which assigns secondary structures of a polypeptide chain using the list of α‐carbon coordinates. This program uses three‐dimensional Voronoï tessellation. This geometrical tool associates with each amino acid a Voronoï polyhedron, the faces of which unambiguously define contacts between residues. Thanks to the face area, for the contacts close together along the primary structure (low‐order contacts) a distinction is made between strong and normal ones. This new definition yields new contact matrices, which are analyzed and used to assign secondary structures. This assignment is performed in two stages. The first one uses contacts between residues close together along the primary structure and is based on data collected on a bank of 282 well‐refined nonredundant structures. In this bank, associations were made between the prints defined by these low‐order contacts and the assignments performed by different automatic methods. The second step focuses on the strand assignment and uses contacts between distant residues. Comparison with several other automatic assignment methods are presented, and the influence of resolution on the assignment is investigated. Proteins 2004. © 2004 Wiley‐Liss, Inc.     

Recent contributions of electronic circular dichroism to the investigation of oligopeptide conformations

Recent applications in our laboratories of electronic circular dichroism to the study of peptide secondary structures and their changes under external stimuli are briefly reviewed. More specifically, this article deals with: 1). characterization of a novel peptide conformation; 2). origin of amino acid homo-chirality on Earth; 3). bend and helical peptides as spacers; and 4). transfer and propagation of chirality in peptides.     

Aquatic snails, passive hosts of Mycobacterium ulcerans

Accumulative indirect evidence of the epidemiology of Mycobacterium ulcerans infections causing chronic skin ulcers (i.e., Buruli ulcer disease) suggests that the development of this pathogen and its transmission to humans are related predominantly to aquatic environments. We report that snails could transitorily harbor M. ulcerans without offering favorable conditions for its growth and replication. A novel intermediate link in the transmission chain of M. ulcerans becomes likely with predator aquatic insects in addition to phytophage insects. Water bugs, such as Naucoris cimicoides, a potential vector of M. ulcerans, were shown to be infected specifically by this bacterium after feeding on snails experimentally exposed to M. ulcerans.     

Reproduction of Mothocya epimerica (Crustacea: Isopoda: Cymothoidae), parasitic on the sand smelt Atherina boyeri (Osteichthyes: Atherinidae) in Greek lagoons

The reproduction and growth pattern of Mothocya epimerica (Crustacea: Isopoda: Cymothoidae), a protandrous hermaphroditic gill parasite of Atherina boyeri (Osteichthyes: Atherinidae), were investigated in the Mesolongi and Etolikon lagoons. The parasite shows an extensive reproductive period. Gravid females were found between April and November, and juveniles between May and December. M. epimerica grew allometrically (slopes of the total weight-total length regressions were >3). Females were significantly heavier than males. The relationship between number of eggs or mancas larvae (F) and total length (TL) was investigated in gravid female parasites in which the marsupium was still closed; the relationship was clearly curvilinear: F = 0.128TL3.18. The number of eggs or mancas larvae held in the marsupia of females increased proportionally with female length, varying from 39 in an isopod of 6.3 mm length to 158 in one of 8.5 mm length. The average number of eggs or mancas larvae was 76.70 +/- 27.8.     

A model for non-viral gene delivery: through syndecan adhesion molecules and powered by actin

BACKGROUND: Cell transfection requires cationic DNA complexes and heparan sulfate proteoglycans (HSPGs) at the cell surface. Syndecans are transmembrane HSPGs that are ubiquitously expressed on adherent cells. Their polyanionic heparan sulfate moieties are bound at the distal end of their ectodomain, thus facilitating interaction with large cationic particles. METHODS: We propose a model for cell entry involving syndecans as receptors for the DNA complexes by comparing transfection with bacteria uptake and using drug inhibition experiments along with confocal microscopy. RESULTS: When combined with results from the literature, our data suggest the following sequence of events: after initial particle binding, gradual electrostatic zippering of the plasma membrane onto the particle is sustained by lateral diffusion of syndecan molecules that cluster into cholesterol-rich rafts. Clustering in turn triggers PKC activity and linker protein-mediated actin binding to the cytoplasmic tail of the syndecans. Resulting tension fibers and a growing network of cortical actin may then pull the particle into the cell. CONCLUSIONS: Diversion of integrin- and syndecan-mediated cell adhesion processes for particle engulfment appears to be widely exploited by animals (chylomicrons), by pathogens (bacteria, viruses) and, as suggested here, by non-viral vectors.     

Absence of accessory subunit in the DNA polymerase gamma purified from yeast mitochondria

In yeast and animals, replication of the mitochondrial genome is carried out by the DNA polymerase gamma. In mammals this polymerase is composed of a catalytic and an accessory subunit. Yeast DNA polymerase gamma was purified over 6600-fold from mitochondria. The catalytic polypeptide of this enzyme was identified as a 135-kDa protein by a photochemical crosslinking procedure and its native molecular weight was estimated between 120 and 140 kDa by gel filtration and glycerol gradient sedimentation. These results indicate that yeast DNA polymerase gamma contains only one subunit and thus has a different quaternary structure from its counterpart in animals.     

A polyclonal antibody directed against syringylpropane epitopes of native lignins

With a view to visualizing the ultrastructural distribution of syringyl lignins in secondary plant cell walls, a polyclonal antibody raised from a synthetic DHP polymer consisting only of syringyl propane units was prepared. To test the reactivity of the antiserum, a mini-dot-blot immunoassay reducing the amounts of substrates and antiserum was developed. A characteristic attribute of the S-antiserum appears to be its specific recognition of sequences of three or more consecutive syringyl units. On ultra-thin sections of model plants of Arabidopsis thaliana, Populus and tobacco, the antiserum allowed us to demonstrate a higher concentration of syringyl epitopes in fibres than in vessels. Variations in the distribution pattern of these epitopes between the three plants examined suggest that the synthesis of syringyl lignins in angiosperms depends on the species.     

Social induction of maturation and sex determination in a coral reef fish

Labile maturation and sex determination should be advantageous where the probability of finding a mating partner is unpredictable. Here we tested the hypothesis that the presence of a potential mating partner induces maturation and sex determination in a coral-dwelling fish, Gobiodon erythrospilus. In natural populations at Lizard Island (Great Barrier Reef), single individuals were less likely to be mature than paired individuals and they matured at a larger size, indicating plasticity in the timing of maturation. By manipulating group structure we demonstrated that both the timing of maturation and the sex of maturing individuals are socially controlled. Single juveniles did not mature, but maturation was rapidly induced by the presence of an adult partner. In addition, sex determination was found to be labile, with juveniles maturing into the opposite sex of the partner encountered. To our knowledge, this is the first experimental demonstration of social induction of maturation in conjunction with labile sex determination at maturation in vertebrates. This flexibility enables individuals to maximize their reproductive success in an environment where the timing of mate acquisition and the sex of their future partner are unpredictable.     

EFA6, exchange factor for ARF6, regulates the actin cytoskeleton and associated tight junction in response to E-cadherin engagement

We addressed the role of EFA6, exchange factor for ARF6, during the development of epithelial cell polarity in Madin-Darby canine kidney cells. EFA6 is located primarily at the apical pole of polarized cells, including the plasma membrane. After calcium-triggered E-cadherin-mediated cell adhesion, EFA6 is recruited to a Triton X-100-insoluble fraction and its protein level is increased concomitantly to the accelerated formation of a functional tight junction (TJ). The expression of EFA6 results in the selective retention at the cell surface of the TJ protein occludin. This effect is due to EFA6 capacities to promote selectively the stability of the apical actin ring onto which the TJ is anchored, resulting in the exclusion of TJ proteins from endocytosis. Finally, our data suggest that EFA6 effects are achieved by the coordinate action of both its exchange activity and its actin remodeling C-terminal domain. We conclude that EFA6 is a signaling molecule that responds to E-cadherin engagement and is involved in TJ formation and stability.