On the structural complexity of a protein

The determination of the configuration of a protein in three-dimensional (3D) space constitutes one of the major challenges in molecular biology research today. A method consists in choosing a protein structure from a database that minimizes an energy function. First, we model the problem in terms of dynamic programming and show that the determination of the order in which the variables must be considered to minimize the time complexity is an NP-hard problem. Second, we propose a new decomposition algorithm of the threading problem that is based on the connectivity of the graph induced by the 3D structure of a protein. Our decomposition could be used to solve the threading problem. The goal in this paper is to evaluate the intrinsic complexity of 3D structure, which can be viewed as information that may be incorporated into a solution method. It provides two indexes of complexity (time and space) and determines in polynomial time complex components of the 3D structure of a protein.     

IGF-I binding in primary culture of muscle cells of rainbow trout: changes during in vitro development

To characterize and study the variations of IGF-I binding during the development of trout muscle cells, in vitro experiments were conducted using myocyte cultures, and IGF-I binding assays were performed in three stages of cell development: mononuclear cells (day 1), small myotubes (day 4), and large myotubes (day 10). Binding experiments were done by incubating cells with IGF-I for 12 h at 4 degrees C. Specific IGF-I binding increased with the concentration of labeled IGF-I and reached a plateau at 32 pM. The displacement of cold human and trout IGF-I showed a very similar curve (EC(50) = 1.19 +/- 0.05 and 0.95 +/- 0.05 nM, respectively). IGF binding proteins did not interfere significantly because displacement of labeled IGF-I by either cold trout recombinant IGF-I or Des (1-3) IGF-I resulted in similar curves. Insulin did not displace labeled IGF-I even at very high concentrations (>1 microM), which indicates the specificity of IGF-I binding. The amount of receptor (R(0)) increased from 253 +/- 51 fmol/mg DNA on day 1 to 766 +/- 107 fmol/mg DNA on day 10. However, the affinity (K(d)) of IGF-I receptors did not change significantly during this development (from 1.29 +/- 0.19 to 0.79 +/- 0.13 nM). On the basis of our results, we conclude that rainbow trout muscle cells in culture express specific IGF-I receptors, which increase their number with development from mononuclear cells to large myotubes.     

Evaluation in rhesus macaques of Tat and rev-targeted immunization as a preventive vaccine against mucosal challenge with SHIV-BX08

Recent evidence suggests that a CD8-mediated cytotoxic T-cell response against the regulatory proteins of human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV) may control infection after pathogenic virus challenge. Here, we evaluated whether vaccination with Tat or Tat and Rev could significantly reduce viral load in nonhuman primates. Rhesus macaques were primed with Semliki forest Virus (SFV) expressing HIV-1 tat (SFV-tat) and HIV-1 rev (SFV-rev) and boosted with modified vaccinia virus Ankara (MVA) expressing tat and rev. A second group of monkey was primed with SFV-tat only and boosted with MVA-tat. A third group received a tat and rev DNA/MVA prime-boost vaccine regimen. Monitoring of anti-Tat and anti-Rev antibody responses or antigen-specific IFN-gamma production, as measured by enzyme-linked immunospot assays revealed no clear differences between the three groups. These results suggest that priming with either DNA or SFV seemed to be equivalent, but the additive or synergistic effect of a rev vaccine could not be clearly established. The animals were challenged by the rectal route 9 weeks after the last booster immunization, using 10 MID(50) of a SHIV-BX08 stock. Postchallenge follow-up of the monkeys included testing seroconversion to Gag and Env antigens, measuring virus infectivity in PBMC by cocultivation with noninfected human cells, and monitoring of plasma viral load. None of the animals was protected from infection as assessed by PCR, but peak viremia was reduced more than 200-fold compared to sham controls in one third (6/18) of vaccinated macaques, whatever the vaccine regimen they received. Interestingly, among these six protected animals four did not seroconvert. Altogether, these results clearly indicated that the addition of early HIV proteins like Tat and Rev in a multicomponent preventive vaccine including structural proteins like Env or Gag may be beneficial in preventive vaccinal strategies.     

Microstructural characterization of annulus fibrosus by ultrasonography: a feasibility study with an in vivo and in vitro approach

The main function of the intervertebral disc is biomechanical function, since it must resist repetitive high loadings, while giving the spine its flexibility and protecting the spinal cord from over-straining. It partially owes its mechanical characteristics to the lamellar architecture of its outer layer, the annulus fibrosus. Today, no non-invasive means exist to characterize annulus lamellar structure in vivo. The aim of this work was to test the feasibility of imaging annulus fibrosus microstructure in vivo with ultrasonography. Twenty-nine healthy adolescents were included. Ultrasonographies of L3–L4 disc were acquired with a frontal approach. Annulus fibrosus was segmented in the images to measure the thickness of the lamellae. To validate lamellar appearance in ultrasonographies, multimodality images of two cow tail discs were compared: ultrasonography, magnetic resonance and optical microscopy. In vivo average lamellar thickness was 229.7 ± 91.5 μm, and it correlated with patient body mass index and age. Lamellar appearance in the three imaging modalities in vitro was consistent. Lamellar measurement uncertainty was 7%, with good agreement between two operators. Feasibility of ultrasonography for the analysis of lumbar annulus fibrosus structure was confirmed. Further work should aim at validating measurement reliability, and to assess the relevance of the method to characterize annulus alterations, for instance in disc degeneration or scoliosis.

     

The self-organization of speech sounds

The speech code is a vehicle of language: it defines a set of forms used by a community to carry information. Such a code is necessary to support the linguistic interactions that allow humans to communicate. How then may a speech code be formed prior to the existence of linguistic interactions? Moreover, the human speech code is discrete and compositional, shared by all the individuals of a community but different across communities, and phoneme inventories are characterized by statistical regularities. How can a speech code with these properties form? We try to approach these questions in the paper, using the "methodology of the artificial". We build a society of artificial agents, and detail a mechanism that shows the formation of a discrete speech code without pre-supposing the existence of linguistic capacities or of coordinated interactions. The mechanism is based on a low-level model of sensory-motor interactions. We show that the integration of certain very simple and non-language-specific neural devices leads to the formation of a speech code that has properties similar to the human speech code. This result relies on the self-organizing properties of a generic coupling between perception and production within agents, and on the interactions between agents. The artificial system helps us to develop better intuitions on how speech might have appeared, by showing how self-organization might have helped natural selection to find speech.     

Social facilitation of long-lasting memory is mediated by CO2 in Drosophila

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A two-stage ultrafiltration process for separating multiple components of Tetraselmis suecica after cell disruption

A two-stage ultrafiltration process was applied to the aqueous phase of Tetraselmis suecica after breaking its cell wall by high-pressure homogenization. Microscopic observation revealed that the cells were completely disrupted from 600 bar and cell fragmentation of the cells was also noticeable after 800 bar. In addition, the highest concentration of all the molecules of interest in the aqueous phase was observed at 1,000 bar and a temperature of 46 °C while preserving the integrity of the molecules of interest in the downstream process. After centrifugation, the aqueous phase was submitted to ultrafiltration through two consecutive membranes of different molecular weight cutoffs. Complete retention of starch was possible with a 100-kDa membrane and separation of sugars from proteins with a 10-kDa membrane on the remaining mixture. After testing the process with model solutions, the transmembrane pressure selected was 2.07 bar, which succeeded in retaining starch and pigments during the first part of the process, and proteins during the second part. A linear correlation between the permeate flux rate and the pressure was observed in both parts of the process.