Contribution of cell and molecular biology and genetics to plant protection

Plants resist to the majority of their potential aggressors by opposing physical and chemical barriers: cell walls, secondary metabolites.... Phenomena of specific recognition between a plant variety and a pathovar induce on the one hand, a local (hypersensitive) reaction that tends to limit pathogen growth and, on the other hand, a cascade of signals that allows the activation of a non-specific general (systemic) resistance. The contribution of genetics to the fight against pathogens depends on the natural variability that comes from the co-evolution between plants and their aggressors. Many plant varieties resistant to one or several pathogens have been obtained and are cultivated. The use of biotechnology will facilitate the rapid generation of new, resistant cultivars and cultivars with multiple resistances. New methods in order to increase the efficiency and the durability of resistance are envisaged.     

Theory of degenerate coding and informational parameters of protein coding genes

The theory of degenerate coding is presented in a way enabling further application to molecular biology. There are two kinds of redundancy of a degenerate code. The first is due to the excess in codon length and the second to the code degeneracy. If the code is asymmetrically degenerate, the second kind of redundancy can be profitable for control of error rate. This control can be performed just by selective synonymous codon usage. Utilisation of the genetic code is partially influenced by this theoretical possibility. In particular the degree of error protectivity is well correlated with deviation from equiprobability in synonymous codon usage. The biological significance of this fact is discussed.     

Nucleotidic cofactors and the origin of the genetic code

In this article it is suggested that the first coding system started from specific interactions between the nucleotide part of nucleotidic cofactors and enzymes. These interactions generated a first primitive code of four words of one letter each for the four primittive amino acids (phenylalanine, lysine, glycine and proline); when the triplet code (which allowed the integration of 20 amino acids into proteins) progressively appeared, it must have been modulated by the existence of this first coding system.     

Statistical analysis of oligonucleotide microarray data

Microchip arrays have become one of the most rapidly growing techniques for monitoring gene expression at the genomic level and thereby gaining valuable insight about various important biological mechanisms. Examples of such mechanisms are: identifying disease-causing genes, genes involved in the regulation of some aspect of the cell cycle, etc. In this article, we discuss the problem of estimating gene expression based on a proper statistical model. More precisely, we show how the model introduced by Li and Wong can be used in its full bivariate generality to provide a new measure of gene expression from high-density oligonucleotide arrays. We also present a second gene expression index based on a new way of reducing the model into a simpler univariate model. In both cases, the gene expression indices are shown to be unbiased and to have lower variance than the established ones. Moreover, we present a bootstrap method aiming at providing non-parametric confidence intervals for the expression index.     

Genetic susceptibility to ageing-associated diseases

The constant and rapid increase of life expectancy in western countries is associated with a major ageing of our populations. In these conditions, we can expect an epidemic progression of most chronic diseases, especially cardiovascular, neurodegenerative and metabolic disorders, the main causes of death in the world. The global burden of these diseases will have a dramatic impact on the health and on the socio-economical context of our societies. From a global point of view, the occurrence and progression of these multifactorial diseases rely upon the nature and intensity of the environmental determinants we are exposed to all life long, but also to our individual genetic susceptibility. Through the determination of this higher susceptibility to an environmental risk factor and the understanding of its mechanisms of action, prevention and management efforts will be better focused. In such multifactorial affections, the development and the transmission of the disease do not follow the simple laws of monogenic Mendelian models. The complexity of this transmission is associated with the influence, at various degrees, of several genes and of a close interaction between this particular genetic susceptibility and environmental risk factors. With the recent development of automated and high throughput molecular biology techniques and their use in epidemiological studies, gene expression regulation and post genomic studies, the determination of sub-groups facing a higher individual genetic susceptibility has begun. This determination will offer new clues for a better-targeted disease management.     

Multiplicative genetic effects in scrapie disease susceptibility

Despite experimental evidence that scrapie is an infectious disease of sheep, variations of the occurrence of the natural disease suggest an influence of host genetic factors. It has been established that the genetic polymorphism of the prion protein (PrP) gene is correlated to the incidence of scrapie and to the survival time: five polymorphisms have been described by variations at amino-acid codons 136, 154 and 171. In this paper we study the effect on scrapie susceptibility of the pairing of the five allelic variants known to exist: we show that scrapie susceptibility is given by the produce of the elementary allelic factors. This first well-documented evidence of a multiplicative property of genetic risk factors could give hints on the underlying mechanisms of prion-induced neurodegenerative diseases.     

Hardware (DNA) circuits

A scheme is presented whereby a new genetic control circuit can be introduced into an organism, permitting the experimenter to turn the expression of a given gene (or set of genes) on or off at will. The proposed scheme involves a positive feedback loop--here, a positive regulator, the CII protein of phage lambda, with its structural gene engineered so as to require CII for its expression. This feedback loop creates the possibility of two stable steady states, with gene cII ON or OFF. Genes added downstream of cII and lacking a promoter will follow the same expression as cII. Two additional circuits allow the experimenter to switch at will between the ON and OFF states.     

AFLP analysis of the genetic diversity of Meloidogyne chitwoodi and M. fallax, major agricultural pests

M. chitwoodi and M. fallax populations are clustered and separated from the other species studied. The genetic diversity observed for M. incognita, M. arenaria, M. javanica, M. hapla, and M. mayaguensis correlates well with the previously validated species. Two main groups can be identified within the M. chitwoodi/M. fallax cluster, the first group comprises only M. chitwoodi populations whereas the second group is made of M. chitwoodi and M. fallax populations. Moreover, M. chitwoodi displays a higher genetic diversity than M. fallax and is characterised by the presence of several clusters.     

Demographic and genetic structures of white sea bream populations (Diplodus sargus, Linnaeus, 1758) inside and outside a Mediterranean marine reserve

We studied the white sea bream (Diplodus sargus), a protandrous hermaphroditic fish, in two protected and unprotected areas in southwestern France. We observed a significant difference in the demographic structure between the two areas. Females were present in two different age distributions inside and outside the marine reserve with younger females outside. This suggests plasticity in the age of sexual inversion in the case of an exploited population. Genetic differentiation was weak and apparent at only one locus of 26 surveyed (FST = 0.007, p = 0.04). Our data suggest that gene flow between the two areas is important, or the separation between the two sites is recent. Our data on the white sea bream show that fishes inside and outside the marine reserve are very similar genetically, which means that the 'reserve effect' is truly a demographic one, not the result of genetic differences.     

Management of disease resistance diversity of cultivars of a species in single fields: controlling epidemics

The use of a diversity of resistance genes limits the development of polycyclic epidemics caused by airborne pathogens and reduces the risk that resistance be overcome by virulent races. Diversity can be easily achieved by growing mixtures of cultivars with different resistance genes and homogeneous agronomic traits. The mechanisms by which disease is reduced in cultivar mixtures include the loss of inoculum due to the presence of resistant plants between susceptible ones and resistance induced by avirulent pathogens. The complementary effects of individual mixture components reacting to disease pressure and to abiotic stresses result in greater yield stability compared with pure stands. The quality of products from mixtures is at least equal to that obtained with pure stands. This type of resistance management is applicable to both annual and perennial crops.     

Search for promoter sites of prokaryotic DNA using learning techniques

Using learning techniques previously described in this journal, we have built an expert system able to point to the start DNA point of a sequence and therefore to recognize a promoter. However, to build this system, we have focused on the TATA box and its environment. We have used this expert system to look for new promoters and also to construct new promoters. The results obtained are discussed.     

Évolution de la composition génétique et du pouvoir infectieux du Baculovirus deMamestra brassicae L. au cours de 25 multiplications successives sur les larves de la Noctuelle du Chou

BioControl - L'évolution du Baculovirus deMamestra brassicae origine France a été suivie au cours de passages successifs sur des chenilles du chou infectéesper os au stade...     

Bio-array images processing and genetic networks modelling

The new tools available for gene expression studies are essentially the bio-array methods using a large variety of physical detectors (isotopes, fluorescent markers, ultrasounds...). Here we present first rapidly an image-processing method independent of the detector type, dealing with the noise and with the peaks overlapping, the peaks revealing the detector activity (isotopic in the presented example), correlated with the gene expression. After this primary step of bio-array image processing, we can extract information about causal influence (activation or inhibition) a gene can exert on other genes, leading to clusters of genes co-expression in which we extract an interaction matrix M and an associated interaction graph G explaining the genetic regulatory dynamics correlated to the studied tissue function. We give two examples of such interaction matrices and graphs (the flowering genetic regulatory network of Arabidopsis thaliana and the lytic/lysogenic operon of the phage Mu) and after some theoretical rigorous results recently obtained concerning the asymptotic states generated by the genetic networks having a given interaction matrix and reciprocally concerning the minimal (in the sense of having a minimal number of non-zero coefficients) matrices having given stationary stable states.     

A simple framework to describe the regulation of gene expression in prokaryotes

Based on the bimolecular mass action law and the derived mass conservation laws, we propose a mathematical framework in order to describe the regulation of gene expression in prokaryotes. It is shown that the derived models have all the qualitative properties of the activation and inhibition regulatory mechanisms observed in experiments. The basic construction considers genes as templates for protein production, where regulation processes result from activators or repressors connecting to DNA binding sites. All the parameters in the models have a straightforward biological meaning. After describing the general properties of the basic mechanisms of positive and negative gene regulation, we apply this framework to the self-regulation of the trp operon and to the genetic switch involved in the regulation of the lac operon. One of the consequences of this approach is the existence of conserved quantities depending on the initial conditions that tune bifurcations of fixed points. This leads naturally to a simple explanation of threshold effects as observed in some experiments.     

Établissement d'une nouvelle lignée cellulaire (IAFEs-1) a partir d'ovarioles d'Euxoa scandens [Lep.: Noctuidae]

Résumé Une nouvelle lignée cellulaire stable (IAFEs-1) des ovarioles de chrysalides du lepidoptèreEuxoa scandens Riley a été obtenue. La forme prédominante des cellules est sphérique et le doublement de la population cellulaire s'effectue en 18 et 24 h en utilisant respectivement 20 et 10% de sérum de veau foetal. Cette lignée est sensible à divers virus des polyédroses nucléaires et cytoplasmiques.

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Summary A new continuous cell line designated IAFEs-1 was obtained from ovaries ofEuxoa scandens Riley in order to study the replication and the productionin vitro of viruses infecting this cutworm. Predominant cell morphology is spherical and cell population doubling time is 18 and 24 h using respectively 20 and 10% fetal calf serum. Susceptiblity of the cell line to several nuclear and cytoplasmic polyhedrosis viruses is demonstrated.

     

Genetic regulation networks: circuits,regulons and attractors

We deal in this paper with the concept of genetic regulation network. The genes expression observed through the bio-array imaging allows the geneticist to obtain the intergenic interaction matrix W of the network. The interaction graph G associated to W presents in general interesting features like connected components, gardens of Eden, positive and negative circuits (or loops), and minimal components having 1 positive and 1 negative loop called regulons. Depending on parameters values like the connectivity coefficient K(W) and the mean inhibition weight I(W), the genetic regulation network can present several dynamical behaviours (fixed configuration, limit cycle of configurations) called attractors, when the observation time increases. We give some examples of such genetic regulation networks and analyse their dynamical properties and their biological consequences.     

Heterozygosity and selective value: the case of the marine fish,Diplodus sargus (Linné, 1758)

A total of 842 white sea bream (Diplodus sargus), sampled in Banyuls-sur-Mer, were analysed to test 'genotype-phenotype' relationship for various characters related to the fitness. The results show significant differences (MLH and FIS) for the age according to the sex between females carrying out and not carrying out sexual inversion. This suggests an overdominance for old females and a genetic sex determination. The individuals laying very early during the period of reproduction are also differentiated from the individuals reproducing later in the season. These results suggest either a stable calendar of laying in time separating the individuals genetically reproducing precociously from the others and this by differential selection and/or genetic drift either a Wahlund effect among cohorts.     

Cell culture models of transmissible spongiform encephalopathies

Cell cultures represent versatile and useful experimental models of transmissible spongiform encephalopathies. These models include chronically prion infected cell lines, as well as cultures expressing variable amounts of wild-type, mutated or chimeric prion proteins. These cultures have been widely used to investigate the biology of both the normal and the pathological isoform of the prion protein. They have also contributed to the comprehension of the pathogenic processes occurring in transmissible spongiform encephalopathies and in the development of new therapeutic approaches of these diseases.