Molecular basis of the attenuated phenotype of human APOBEC3B DNA mutator enzyme

The human APOBEC3A and APOBEC3B genes (A3A and A3B) encode DNA mutator enzymes that deaminate cytidine and 5-methylcytidine residues in single-stranded DNA (ssDNA). They are important sources of mutations in many cancer genomes which show a preponderance of CG->TA transitions. Although both enzymes can hypermutate chromosomal DNA in an experimental setting, only A3A can induce double strand DNA breaks, even though the catalytic domains of A3B and A3A differ by only 9% at the protein level. Accordingly we sought the molecular basis underlying A3B attenuation through the generation of A3A-A3B chimeras and mutants. It transpires that the N-terminal domain facilitates A3B activity while a handful of substitutions in the catalytic C-terminal domain impacting ssDNA binding serve to attenuate A3B compared to A3A. Interestingly, functional attenuation is also observed for the rhesus monkey rhA3B enzyme compared to rhA3A indicating that this genotoxic dichotomy has been selected for and maintained for some 38 million years. Expression of all human ssDNA cytidine deaminase genes is absent in mature sperm indicating they contribute to somatic mutation and cancer but not human diversity.     

Reactivity of an Excess Electron with Monovalent Cations in Bulk Water by Mixed Quantum Classical Molecular Dynamics Simulations

A mixed quantum classical molecular dynamics (QCMD) simulation of the silver and sodium cations in presence of an excess electron is reported. The silver cation is shown to be reduced by the hydrated electron and to form a stable, highly polarized, neutral atom. On the contrary, the sodium cation is not reduced and a metastable contact ion pair is observed. The resulting absorption spectra of both species are compared with experiments and shown to be in good agreement. Furthermore, the free energy curve for the charge separation was calculated and rationalized in terms of a thermodynamic cycle. Finally, a direct, reactive, molecular dynamics trajectory provides some useful informations on the reduction mechanism.     

Biochemical and genetic properties of oligomeric structures: a general approach

The oligomers constituted by association of different subunits can exist under multiple forms. In the case of the genetically variable proteins, such a multiplicity leads to numerous questions (i) on the enumerations: what is the number of active forms when a given subunit can make the oligomer inactive, or when the subunits are encoded by s alleles; (ii) on the subunit effects on biochemical properties: how to estimate these effects, are they equal, are there interactions between subunits, etc. Theoretical methods for the study of such oligomeric structures are developed, which mainly rely on linear model techniques. Peculiar properties examined are Vmax and Km, but also the quantities of the various oligomers, which depend on their association law. This approach is extended to the oligomers composed of different sets of subunits, as are for example some enzymes. These aspects are discussed from numerous bibliographic examples, with special reference to molecular interactions (protein complementation or molecular heterosis). Otherwise the genetic application of this theoretical approach is presented: it is possible to consider a genotype as an oligomer of alleles, and thus to study their effects and their interactions, in the one-locus case as well as in the several-loci case. The relevance of this generalization is discussed in connection with two other concepts, the "sequence space" used in molecular evolution and the regression of the genotypic values on the number of alleles used in quantitative genetics.     

Seeking alternative stable states in a deep lake

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Regulation of Extracellular Matrix Synthesis by Shell Extracts from the Marine Bivalve <Emphasis Type="Italic">Pecten maximus</Emphasis> in Human Articular Chondrocytes— Application for Cartilage Engineering

The shells of the bivalve mollusks are organo-mineral structures predominantly composed of calcium carbonate, but also of a minor organic matrix, a mixture of proteins, glycoproteins, and polysaccharides. These proteins are involved in mineral deposition and, more generally, in the spatial organization of the shell crystallites in well-defined microstructures. In this work, we extracted different organic shell extracts (acid-soluble matrix, acid-insoluble matrix, water-soluble matrix, guanidine HCl/EDTA-extracted matrix, referred as ASM, AIM, WSM, and EDTAM, respectively) from the shell of the scallop Pecten maximus and studied their biological activities on human articular chondrocytes (HACs). We found that these extracts differentially modulate the biological activities of HACs, depending on the type of extraction and the concentration used. Furthermore, we showed that, unlike ASM and AIM, WSM promotes maintenance of the chondrocyte phenotype in monolayer culture. WSM increased the expression of chondrocyte-specific markers (aggrecan and type II collagen), without enhancing that of the main chondrocyte dedifferentiation marker (type I collagen). We also demonstrated that WSM could favor redifferentiation of chondrocyte in collagen sponge scaffold in hypoxia. Thus, this study suggests that the organic matrix of Pecten maximus, particularly WSM, may contain interesting molecules with chondrogenic effects. Our research emphasizes the potential use of WSM of Pecten maximus for cell therapy of cartilage.     

Modelling based method for pharmacokinetic hypotheses test

The aim of this work is to propose methods to test mechanism of synergy of toxic agents in bees. A synergy between prochloraz, an imidazole fungicide, and deltamethrin, a pyrethroid insecticide, was demonstrated experimentally. The hypothesis is that prochloraz modifies the penetration or the metabolism of deltamethrin. This hypothesis is tested using a pharmacokinetic box model. A previous experimental work showed that bee instantaneous mortalities were higher, from the time t ₁ to the time t ₂ after spraying, in groups sprayed with deltamethrin at dose D ₀ in the presence of prochloraz (+P) than in those sprayed with deltamethrin alone at a dose time as high (). We postulate that accrued mortality is proportional to the cumulated internal deltamethrin (ID ₂). ID ₂ of treatment (+P) had to be greater than ID ₂ of treatment () during the period from t ₁ to t ₂ so that the hypothesis would be consistent with the experimental data. The limit, for which the hypothesis is conceivable, is the ID ₂₍₎ = ID _2(+P ) curve. We study, in particular, the asymptotic behaviour of the limit curve when different parameters of the kinetic model tend to 0 or . These limits allow to verify quickly and easily whether a mechanism is conceivable or not As the limits are calculated with algebraic values, the test can be used for other synergies.     

The use of herbarium specimens in DNA phylogenetics: Evaluation and improvement

During the last few years we have been confronted with the need to use herbarium specimens in the molecular phylogeny studies, since it is generally difficult to obtain living material of some rare species. Ancient DNA has been sequenced, and there are also reports on successful DNA amplification from herbarium specimens. However, it is not easy to obtain amplified DNA from the first herbarium sample tested. In this paper, experiments are described about trials of DNA amplification from two to 151-year-old herbarium specimens of plant species we needed for our projects. Of the 17 herbarium samples tested only two allowed DNA amplification under standard DNA isolation conditions. Different types of PCR inhibiting activities were demonstrated in DNA extracts. In some of the extracts there was extremely low concentration of template with satisfactory quality. In some instances, PCR inhibiting activities were successfully removed by treating them either with insoluble polyvinylpyrrolidone or by adding bovine serum albumin (BSA) to the amplification mixture. However, some PCR-inhibiting activities were resistant to the treatments described above. When the concentration of template was very low, a second PCR amplification with internal primers was necessary to increase the amount of DNA for sequencing. Nevertheless, contamination of either DNA extract or amplification mixture were sometimes observed, and consequently precautions were taken to minimize them. Finally, successful amplification was obtained in eight samples out of the 17 examined.     

Radiation-induced carcinogenesis: Individual sensitivity and genomic instability

In spite of a well-known relationship between exposure to radiation and increased risk for cancer development, the biological mechanisms involved in radiation-induced carcinogenesis remain poorly documented. Various hypotheses are discussed in this paper. It appears that radiation cannot be directly responsible for the numerous genetic alterations of cancer cells. Most of them occur during tumor progression. Only one or a very limited number of them was induced by radiation many years before tumor growth. This long delay is a major difficulty for experimental research and raises many questions. Recently, it has been shown that a genomic instability occurs after many generations in cells descending from irradiated cells. This instability leads to multiple genetic alterations and, preferentially, affects some chromosome structures, particularly telomeres. This kind of telomeric instability - related to the shortening of telomeric DNA sequences - has also been observed in senescent cells as well as in non-senescent cells from patients predisposed to cancer, and this process may possibly also occur in the progeny of irradiated cells.Invited paper presented at the International Symposium on Heavy Ion Research: Space, Radiation Protection and Therapy, Sophia-Antipolis, France, 21–24 March 1994