Mode de formation des inclusions lamellaires dans le poumon embryonnaire de poulet

Résumé Les pneumocytes granuleux, qui constituent l'un des principaux types cellulaires de l'épithélium pulmonaire, sont caractérisés par la présence de volumineuses inclusions osmiophiles lamellaires.Nous avons étudié l'apparition et l'origine de ces inclusions dans l'épithélium du poumon embryonnaire de Poulet, en l'examinant à différents stades du développement.Les premières inclusions lamellaires apparaissent dans le poumon de l'embryon de 16 jours. A ce stade, quelques lamelles concentriques entourent une zône centrale amorphe étendue; la périphérie des inclusions contient toujours de petites structures granulaires. Les jours suivants le nombre de cellules contenant des inclusions lamellaires augmente rapidement; en même temps, les lamelles deviennent plus nombreuses. A 19 jours, les inclusions lamellaires ont un aspect semblable à celui qu'elles ont dans les poumons d'animaux adultes.Dès l'apparition des ébauches pulmonaires, à 2 1/2 jours d'incubation, les cellules épithéliales contiennent des inclusions typiques: les inclusions granulaires. Ces organites sont caractérisés par un centre granulaire, qu'entouré un système membranaire. Ce système, simple chez le jeune embryon, évolue ensuite en se compliquant; chez l'embryon de 16 jours, il s'enroule en plusieurs couches autour de la masse centrale. Au moment où les premières inclusions lamellaires apparaissent, le nombre des inclusions granulaires augmente rapidement; on les trouve souvent étroitement associées à des vacuoles lipidiques.L'analyse des relations entre inclusions lamellaires, inclusions granulaires et vacuoles lipidiques suggère que l'inclusion lamellaire résulte de la collaboration entre une vacuole lipidique et plusieurs inclusions granulaires.

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Differentiation of lamellar inclusions in the chick embryonic lung

Summary The granular pneumocytes, one of the main cellular types of the lung epithelium, are characterized by the presence of large osmiophilic lamellar inclusions. The appearance and origin of these inclusions has been studied in the epithelium of chick embryonic lung at different developmental stages.Lamellar inclusions are first seen in the lung of 16 day old embryos. At this stage, few concentric lamellae surround a large amorphous center; the periphery of the inclusions always contains small granular structures. In the following days, the number of cells containing these lamellar inclusions increases rapidly, while their lamellae progressively become more numerous. In 19 day old embryos, the lamellar inclusions are similar to those in the lungs of adult animals.From the earliest formation of the bronchial primordia, their epithelial cells contain a number of typical granular inclusions. These organelles are characterized by a granular center, enclosed in a membranous system. This structure becomes more complex as the embryo develops; in the 16 day old embryo, the multilayered membranous system coils around the granular center. At the time when lamellar inclusions first appear, granular inclusions increase rapidly in number and are often found in close association with lipidic vacuoles.The relationships between lamellar inclusions, granular inclusions and lipidic vacuoles are discussed. The evidence suggests that a lamellar inclusion arises from the cooperation of several granular inclusions and a lipidic vacuole.

     

Glutathione-coated cadmium-sulfide crystallites in Candida glabrata

Cadmium-sulfide crystallites form in the yeast Candida glabrata cultured in the presence of cadmium salts. The particles function to sequester and detoxify intracellular cadmium ions. The crystallites are peptide-coated, but the coating peptide varies with the nutrient conditions of the growth medium. When cultured in rich nutrient broth the yeast forms intracellular CdS particles coated with a mixture of glutathione and the gamma-glutamylcysteine dipeptide. In contrast, cultures in synthetic minimal medium yield particles coated with polymerized gamma EC peptides of general structure (gamma-Glu-Cys)n-Gly. Glutathione/gamma-glutamylcysteine particles exhibit properties analogous to quantum, semiconductor-type crystallites. The optical properties are dependent on particle size, and irradiation results in photoluminescence and photoreduction not observed in bulk CdS mineral. Aerobic irradiation leads to particle decomposition presumably via oxidation of the sulfide ions within the crystallite.     

Metal thiolate coordination in the E7 proteins of human papilloma virus 16 and cottontail rabbit papilloma virus as expressed in Escherichia coli.

The oncogenic E7 proteins of human papilloma virus (HPV 16) and of cottontail rabbit papilloma virus (CRPV) have been purified from an expression system in Escherichia coli. The proteins as purified from E. coli contain one tightly bound Zn(II) ion per molecule. The metal site shows facile exchange with either Cd(II) or Cu(I). The HPV 16 E7 maximally bound one Cd(II) or two Cu(I) ions, while the CRPV E7 bound two Cd(II) or three Cu(I) ions. The Cd(II) and Cu(I) E7 molecules exhibited optical transitions in the ultraviolet suggestive of metal:thiolate coordination. E7 proteins from HPV 16 and CRPV contain 7 and 8 cysteines/molecule, respectively. Reaction of the E7 proteins with the sulfhydryl reagent, dithiodipyridine, revealed that all the cysteinyl sulfurs are present in the reduced thiol state. Cu(I)-E7 molecules are luminescent with maximal emission at 570 nm. The observed emission at room temperature is indicative of metal coordination within a compact protein environment shielded from solvent interactions. The emission maxima occurs at the same wavelength (570 nm) as Cu(I)-cysteinyl sulfur clusters in Cu(I)-metallothioneins. The single Zn(II) atom in each protein can be removed from E7 in the presence of EDTA. The resulting apoE7 molecules remain soluble and can be partially reconstituted with Cd(II) to regain the ultraviolet charge transfer transitions.     

Comparison of pathways of copper metabolism in aorta and liver. A functional test of metallothionein.

Soluble fractions from chick liver and aorta were examined for copper-binding proteins. In liver a zinc-binding thionein appeared to be the major binding protein for copper. Aortic tissue contained only traces of this thionein protein. Unlike liver, moderate amounts of soluble copper in aorta showed no association with macromolecules. Chicks fed on copper-deficient diets for 8 days had one-third the liver copper concentrations of controls. Aortic copper concentration was decreased only slightly, but the activity of lysyl oxidase, a copper-dependent enzyme in aorta, was decreased significantly. Treating the deficient chicks with CuSO4 (1 mg/kg) restored liver copper rapidly. The increase correlated with the binding of copper to a 10 000-mol.wt. component in the soluble fraction. Aortic copper concentrations responded much less to the CuSO4 treatment, but lysyl oxidase activity was again measurable in the tissue. Radioactive isotopes of copper bound almost exclusively to the 10 000-mol.wt. component in liver and to components of mol.wt. 30 000 or above in aorta. Hardly any of the administered radioactivity appeared with the 10 000-mol.wt. components in aorta, and none was found with unbound copper. The 30 000-mol.wt. components in aorta showed superoxide dismutase activity that was sensitive to NaCN. They also showed the highest specific activity of copper of any other aorta component. A clear distinction was seen between the metabolism of copper in liver and aortic tissues. Whereas a copper thionein, metallothionein, was a major component in the liver pathway, it is doubtful that this protein plays a major role in the intracellular metabolism of copper in aortic tissue.     

The Enterococcus hirae copper chaperone CopZ delivers copper(I) to the CopY repressor

Expression of the cop operon which effects copper homeostasis in Enterococcus hirae is controlled by the copper responsive repressor CopY. Purified Zn(II)CopY binds to a synthetic cop promoter fragment in vitro. Here we show that the 8 kDa protein CopZ acts as a copper chaperone by specifically delivering copper(I) to Zn(II)CopY and releasing CopY from the DNA. As shown by gel filtration and luminescence spectroscopy, two copper(I) are thereby quantitatively transferred from Cu(I)CopZ to Zn(II)CopY, with displacement of the zinc(II) and transfer of copper from a non-luminescent, exposed, binding site in CopZ to a luminescent, solvent shielded, binding site in CopY.     

Système sémantiquement interopérable de sélection semi-automatique des patients éligibles aux essais thérapeutiques en cancérologie

Automatic Selection of clinical Trial based on Eligibility Criteria (ASTEC) project is to automate, so as to make it systematic, the search of cancer clinical trials, by reusing the patient data contained into an oncologic electronic health record. ASTEC project tackles two major scientific challenges for medical informatics: 1) the syntactic and semantic interoperability between information systems. The oncologic electronic medical records and the recruitment decision system must be interoperable. The ASTEC project proposes a framework of syntactico-semantic interoperability based on international standards. Generic methods of mediation and reasoning based on ontologies are developed to match data from the electronic medical records to the inclusion/exclusion criteria of clinical trials; 2) a decision support system for recruitment. We have developed inference methods on the electronic medical records adapted to the data structure as well as the eligibility criteria. this paper, we present and justify our choices, concerning the medical process in oncology and the scientific and technical aspects. Furthermore the system will be evaluated in real time. The aim is to demonstrate a significative improvement of the prescreening rate of patient.     

Copper transfer from the Cu(I) chaperone, CopZ, to the repressor, Zn(II)CopY: metal coordination environments and protein interactions

Extracellular copper regulates the DNA binding activity of the CopY repressor of Enterococcus hirae and thereby controls expression of the copper homeostatic genes encoded by the cop operon. CopY has a CxCxxxxCxC metal binding motif. CopZ, a copper chaperone belonging to a family of metallochaperones characterized by a MxCxxC metal binding motif, transfers copper to CopY. The copper binding stoichiometries of CopZ and CopY were determined by in vitro metal reconstitutions. The stoichiometries were found to be one copper(I) per CopZ and two copper(I) per CopY monomer. X-ray absorption studies suggested a mixture of two- and three-coordinate copper in Cu(I)CopZ, but a purely three-coordinate copper coordination with a Cu-Cu interaction for Cu(I)2CopY. The latter coordination is consistent with the formation of a compact binuclear Cu(I)-thiolate core in the CxCxxxxCxC binding motif of CopY. Displacement of zinc, by copper, from CopY was monitored with 2,4-pyridylazoresorcinol. Two copper(I) ions were required to release the single zinc(II) ion bound per CopY monomer. The specificity of copper transfer between CopZ and CopY was dependent on electrostatic interactions. Relative copper binding affinities of the proteins were investigated using the chelator, diethyldithiocarbamic acid (DDC). These data suggest that CopY has a higher affinity for copper than CopZ. However, this affinity difference is not the sole factor in the copper exchange; a charge-based interaction between the two proteins is required for the transfer reaction to proceed. Gain-of-function mutation of a CopZ homologue demonstrated the necessity of four lysine residues on the chaperone for the interaction with CopY. Taken together, these results suggest a mechanism for copper exchange between CopZ and CopY.     

The genome‐scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond

Brown algae (stramenopiles) are key players in intertidal ecosystems, and represent a source of biomass with several industrial applications. Ectocarpus siliculosus is a model to study the biology of these organisms. Its genome has been sequenced and a number of post‐genomic tools have been implemented. Based on this knowledge, we report the reconstruction and analysis of a genome‐scale metabolic network for E. siliculosus, EctoGEM ( http://ectogem.irisa.fr ). This atlas of metabolic pathways consists of 1866 reactions and 2020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling and manual refinement. The capability of the network to produce biomass was validated by flux balance analysis. EctoGEM enabled the reannotation of 56 genes within the E. siliculosus genome, and shed light on the evolution of metabolic processes. For example, E. siliculosus has the potential to produce phenylalanine and tyrosine from prephenate and arogenate, but does not possess a phenylalanine hydroxylase, as is found in other stramenopiles. It also possesses the complete eukaryote molybdenum co‐factor biosynthesis pathway, as well as a second molybdopterin synthase that was most likely acquired via horizontal gene transfer from cyanobacteria by a common ancestor of stramenopiles. EctoGEM represents an evolving community resource to gain deeper understanding of the biology of brown algae and the diversification of physiological processes. The integrative computational method applied for its reconstruction will be valuable to set up similar approaches for other organisms distant from biological benchmark models.     

Semantic Particularity Measure for Functional Characterization of Gene Sets Using Gene Ontology

Background

Genetic and genomic data analyses are outputting large sets of genes. Functional comparison of these gene sets is a key part of the analysis, as it identifies their shared functions, and the functions that distinguish each set. The Gene Ontology (GO) initiative provides a unified reference for analyzing the genes molecular functions, biological processes and cellular components. Numerous semantic similarity measures have been developed to systematically quantify the weight of the GO terms shared by two genes. We studied how gene set comparisons can be improved by considering gene set particularity in addition to gene set similarity.

Results

We propose a new approach to compute gene set particularities based on the information conveyed by GO terms. A GO term informativeness can be computed using either its information content based on the term frequency in a corpus, or a function of the term''s distance to the root. We defined the semantic particularity of a set of GO terms Sg1 compared to another set of GO terms Sg2. We combined our particularity measure with a similarity measure to compare gene sets. We demonstrated that the combination of semantic similarity and semantic particularity measures was able to identify genes with particular functions from among similar genes. This differentiation was not recognized using only a semantic similarity measure.

Conclusion

Semantic particularity should be used in conjunction with semantic similarity to perform functional analysis of GO-annotated gene sets. The principle is generalizable to other ontologies.