Evolution of biological regulation networks under complex environmental constraints.

This work investigates the influence of environmental inducers on the organization of cell regulation networks, using a connectionist approach. Protein interactions are modeled by an asymmetrical recurrent network, the units of which take continuous values. In contrast to classical models, we explicitly introduce a genome to encode the architecture of the system. This feature enables us to introduce an evolution model, in which a genetic algorithm that mimics the effects of evolution on proteins mutual interactions is used. We assume an efficient system to respond to persistent environmental stimuli, independently of their amplitude. Results are presented that show a structuration of the network with the emergence of specialized hierarchal structures. These structures seem to drive the system at the edge of chaos, so that it can present adapted responses to significant environmental changes.

Detection of compositional constraints in nucleic acid sequences using neural networks.

We describe in this paper a neural network method for the detection of compositional constraints in introns and exons. The first part of the algorithm (learning phase) consisted in presenting examples of intron and exon sequences to the network and in modifying its connections using the back-propagation algorithm. Previous connectionist methods achieved the learning of exons and introns using the latter as negative examples to the former. However, we chose to learn introns and exons jointly, using junk DNA as a common counter-example. In a second part (generalization phase), we tested the neural networks in the search for exons and introns in the human globin cluster. Their performances were also checked on the classification of unknown examples. As with the previous approaches, this technique discriminates introns and exons: values of the correlation coefficients are respectively 0.50 and 0.64 for the best achieved network. Moreover, using junk DNA sequences in the learning phase allows one to detect constrained regions inside the intron and the exon sequences (i.e. sequences that differ, by their nucleic acid compositions, from junk DNA). The application of our approach could be useful in the study of the internal organization of these sequences.

Computer analysis of two-dimensional electrophoresis gels as a tool in cell biology: study of the protein expression of human keratinocytes from normal to tumor cells.

The usefulness of computer analysis of two-dimensional electrophoresis gels has been investigated on the example of human keratinocytes transformation. For this purpose, the protein expression of various keratinocytes strains from normal to tumor cells has been analysed by two-dimensional electrophoresis. The resulting gels have been submitted to computer analysis, including various data analysis techniques allowing to select spots on the gels or to classify the gels themselves. The latter techniques appeared very useful, since they demonstrated that the major transition in words of variation of the protein expression lies at the normal cell/transformed cell transition rather than at the transformed cell/tumorigenic cell transition.

Striking differences in cellular catalase activity between two DNA repair-deficient diseases: xeroderma pigmentosum and trichothiodystrophy.

Xeroderma pigmentosum (XP) and trichothiodystrophy (TTD) are two recessively transmitted human diseases characterized by DNA repair deficiency. While XP is associated with a very high incidence of cancer on skin exposed to sunlight, TTD is not a cancer-prone disease. Therefore, unrepaired UV-induced DNA lesions do not appear to be enough to give rise to tumors. In order to understand the differences between these two syndromes, we measured catalase activity in cellular extracts, UV irradiated or not, and quantified H2O2 production following in vitro UV irradiation. We confirmed on 21 different XP diploid fibroblast lines that catalase activity was decreased on average by a factor of five as compared to controls, while XP heterozygote lines exhibited intermediary responses. All seven TTD lines we tested were deficient in UV-induced lesion repair and exhibited a high level of catalase activity. However, molecular analysis of catalase transcription showed no difference between normal, XP and TTD cell lines. This was confirmed by Western blots where the amount of catalase subunits was identical in all cell lines studied. Finally, UV irradiation induces five and three times more H2O2 production in XP lines compared with TTD or controls respectively. These striking differences between TTD and XP indicate that UV light, directly or indirectly, together with defective oxidative metabolism may increase the initiation and/or the progression steps in the XP environment compared to TTD. This may partly explain the different tumoral phenotype observed between the two diseases.

Stage transitions in B-lymphocyte differentiation correlate with limited variations in nuclear proteins.

Total nuclear proteins extracted from cell lines representing various stages of differentiation of mouse B lymphocytes were studied by computer analysis of two-dimensional gels. Of the 1438 spots present on the gels, 55 varied significantly in intensity during differentiation. The variations occurred most often in steps correlating with those classically defined for B-cell differentiation. Seventeen spots were not detectable in at least one of the stages (qualitative variations) and could represent switching on or off of genes coding for nuclear proteins. Detailed analysis of the 55 variable spots showed that they fall into small sets characterized by similar expression profiles, which argues for a combinatorial, multistep control mechanism of gene expression. In addition, analysis of the expression of all the nuclear proteins resolved on the gels clearly differentiated B-lineage cells from myeloid cells and suggested that the most important transition in B-cell differentiation occurs between the resting B cell and plasmocyte stages.

Catalase-associated abnormalities and H2O2 increase in pre-neoplastic and neoplastic lesions of the human lower female genital tract and their near adjacent epithelia.

We report that an internal and non-UV-dependent type of neoplasia, the human cervical intraepithelial neoplasia (SIL), is also deficient in catalase activity, like the UV-induced tumors in the autosomal recessive human epithelial disease, xeroderma pigmentosum (XP). Whether or not the lesions are papillomavirus (HPV) positive in the different categories of preneoplastic and neoplastic extracts, the following parameters are affected: i), catalase activity level; ii), kinetic profile of catalase activity; iii), H2O2 increase. Mathematical treatment of these parameters (CONSTEL-Program), unambiguously distinguishes between normal and pathological cases. Such analyses make it possible to grade the pathological samples into 4 classes, depending on their deviance from normality. These classes may be correlated with the gradual steps in the process of malignant transformation defined by histological and clinical diagnosis. We found conformity between catalase activity and histological analyses in 66 biopsies, out of a total of 100 biopsies (35 patients). Moreover, 23 patients presenting decreased catalase activities in 31 biopsies showed disease progression after 3 to 6 months contrary to surgery histological data. We show that ATP synthesis in the presence of catalase and H2O2 (further aspect of catalase function), may occur in neoplastic extracts at much lower concentrations of H2O2 than in normal extracts. Thus, the catalase abnormality seems to be a good tool to study pre-neoplastic to neoplastic evolution of lesions and their adjacent tissues of the lower female genital tract; furthermore, i) it provides an earlier, more powerful means of detecting micro-SIL in progression to squamous cell carcinoma, than combined clinical and histological examinations; ii) model for investigating drugs such as in situ H2O2 scavengers or agents increasing glutathione peroxidase activity (GSH).

Improvement and simplification of low-background silver staining of proteins by using sodium dithionite.

High sensitivity and low background, the attractive characteristics of the procedure of Blum et al., Electrophoresis 1987, 8, 93-99, for silver staining of proteins in polyacrylamide gels have been improved by sensitizing the gels with sodium dithionite instead of sodium thiosulfate and by equilibration in water after fixation and prior to sensitization. These modifications decrease the background and allow for a longer development period, which in turn increases sensitivity and color contrast. In addition, the colors of the spots are shifted toward colder tones when compared with the original method.

Specific modulation by ethanol of the protein synthesis pattern in the C2 rat hepatoma cell line.

The effect of ethanol on protein synthesis in the C2 rat hepatoma cell line was analyzed by two-dimensional gel electrophoresis after the labeling with [35S]methionine of cells that were untreated or had been treated with 180 mM ethanol. In this cell line, this concentration of ethanol is known to induce gamma-glutamyl transpeptidase, a marker of alcoholism in man (Barouki et al., Hepatology 1983; 3: 323-329). In the present work we demonstrate that ethanol, besides causing a slight decrease in overall protein synthesis (less than 25%), primarily regulates the expression of two unique proteins among 1500 labeled products that were analyzed: one of these was induced and did not correspond to gamma-glutamyl transpeptidase, and one was repressed after 20 h of ethanol treatment. We conclude that the set of hepatic proteins altered by ethanol is likely to be very limited in number, which reflects the specificity of alcohol action on protein synthesis in the C2 cell line.

Two-dimensional electrophoresis computerized processing.

This paper describes various methods suitable for implementation of two-dimensional processing software. The different steps leading to a complete processing are described, from the digitalization of the image to the processing of the resulting data. The characteristics of a convenient digitalization system are discussed. The different software devoted to spot detection is reviewed with respect to the presence or otherwise of a spot model and its characteristics. The major techniques for gel matching are compared as are designs for database structures suitable for tabulation of measurements. Finally, the need for a sophisticated system of data processing is stressed and its main requirements are described.

Deficiency in the catalase activity of xeroderma pigmentosum cell and simian virus 40-transformed human cell extracts.

It has been previously shown that skin biopsies isolated from various xeroderma pigmentosum (XP) patients present a permanent decline in catalase activity from the onset of the disease to the tumor formation. We report here that cultured XP cell strains are also markedly deficient in the catalase activity with about only 25% of the activity measured in normal human cells. No direct correlation between catalatic activity and excision repair ability has been found, since a XP variant line is as deficient as an XP-C strain. The exact cause of the catalase deficiency is still unknown but could be due to the synthesis of a modified enzyme or to an abnormal regulation leading to a limited enzyme synthesis. Furthermore, simian virus 40 transformation of normal and radiosensitive cells (XP, ataxia telangiectasia) provokes a decrease in catalase activity of about 80% compared to the control derivatives. Mathematical analysis performed on our data shows a clearcut distinction between XP and normal cells while some of the XP heterozygote cells exhibit an intermediate behavior. Although most of the XP syndrome could be explained by the impairment in the excision repair ability, the decrease in catalase activity leading to a probable increase in intracellular H2O2 concentration and/or to a higher sensitivity to any oxygen-activated species could represent an additive effect in inducing the carcinogenic process.

Changes in nuclear proteins induced by heat shock in Drosophila culture cells.

Nuclear proteins of normal and heat-shocked Drosophila cells were analysed by two-dimensional electrophoresis. The computerized processing of the gels allowed us to detect 6 proteins strongly induced by the heat treatment, but which were different from the usually described heat-shock proteins. The possible role of these proteins in genetic regulation is discussed, as is the value of this type of approach for the study of other genetic regulation phenomena.

Poly A (+) mRNA metabolism in wing imaginal discs during normal development and diapause in Pieris brassicae.

Poly A (+)mRNA synthesis was analyzed during the nymphal stage and the diapause in the wing discs of the Lepidopteran Pieris brassicae. The main events of differentiation, i.e. scale formation, adult cuticle elaboration and pigment deposition, occurred during the period studied. We only detected one phase of synthesis for poly A (+)mRNA molecules, 48-72 hours after the nymphal moult. This synthesis was found to be related to that of late proteins at 120-140 hours. Examination of mRNA metabolism in discs treated with cordycepin (3' dA) showed a decline in mRNA stability. This decline corresponded to a turn-over phase followed by a period of stabilization which preceded mRNA translation. In diapausing animals, poly A (+)mRNA metabolism was unexpectedly high, and many messengers were synthesized and rapidly destroyed. These messengers were found to be slightly heavier than the mRNAs produced during normal development, suggesting a blocking at some step in their maturation. We developed a mathematical model for mRNA metabolism which enabled us to calculate the effects of synthesis and degradation on the quantity of mRNAs, from the poly A (+)mRNA concentration and the turnover time in the mRNA pool. In addition determination phases associated with embryological events and terminal differentiation are clearly distinguished. This feature offers opportunities to investigate the commitment events which take place during the end of the larval stage and the beginning of the nymphal stage.

RNA metabolism during a developmental process. Modeling by Boolean functions and automata theory.

This work describes a model for simulation of rRNA and polyA(+)mRNA evolution during a developmental process - the wing disc differentiation of an Insect, Pieris Brassicae. The model was constructed in two sections: --a logical section built around a logical network of genetic regulations for RNA synthesis and degradation. We postulated the existence of clock pulses, which act as specific stages of development on parameters determining the accumulation and disappearance of the different RNA classes. A simple model was thus able to account for the complex variations of the studied macromolecules during the differentiation phase. --an analogical section, to account for and calculate the accumulation of terminal gene products. This part of the model was based on essential features of the automata theory. In addition, the relations between clock pulses, biological rhythms and their alteration during diapause are discussed. Diapause and emergence from diapause were included in the above model for RNA metabolism. This model enabled us to compute the time at which particular events take place and the stages of synthesis of the main RNA classes. We evaluated the synthesis and degradation rates of these different classes of molecules. These rates are closely related to those reported by other authors in several differentiation systems. Our model seems applicable to any developmental process in which RNA synthesis exhibits noticeable variations. Although such an approach has seldom been used to interpret macromolecular expressions, its application in the present case allowed us to obtain by a simple computation, complex information on the genetic and biochemical features of RNA molecule regulation.

Characterization and purification of messenger RNAs containing poly A in insect imaginal disks.

The presence of a fragment of polyA resistant to both T1 and p ribonucleases in mRNAs extracted from wing imaginal disks of an insect, Pieris brassicae, is reported. Its length was approximatively 150 nucleotides. PolyU sepharose affinity chromatography was subsequently used for purification of these polyA(+)mRNA molecules. Analyses on sucrose gradients showed a good recovery of poly(+)molecules characterized by their size (20-100 S) and a polydisperse pattern. These mRNAlike species represent 2-3 per cent of the total radioactivity incorporated into RNA in 3 hours of labeling. Sequential extractions were carried out to provide cytoplasmic RNA rich fractions (4 degrees C) and nuclear rich fractions (45 degrees C). When assayed for the presence of polyA(+)RNA, molecules extracted by these two sequential methods were found to be very similar in their polyA content.