Computer search of calcium binding sites in a gene data bank: use of learning techniques to build an expert system

Using a learning set of 28 sequences able to bind calcium (each sequence is 12 residues long), we have built two filters by learning on this set. The first filter uses a pattern-matching technique and the second one takes into account the environment of amino-acids. These two filters have been used to find new calcium-binding proteins in a data bank. The results are discussed.     

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.     

Evolution and selection of reproduction

The examination of the official records from Artas, Isère (North Dauphiné, France), provides nearly continuous information from 1540 to 1900. These allowed us to study the twinning during this period, to specify its importance, its evolution, and its links with diverse other characteristics of reproduction. The number of twins per 1000 births is on a general average very close to 11. It seems to decrease during the last four centuries. However, the variability is very high from one year to another or one decade to another, including the composition of twins (identical or different sex), with the result that no statistical argument allows us to reject the null hypothesis. Numerous data have been collected that support a partially genetic determinism in twinning. The number of children in families with twins is clearly higher that in other families. Age of death of the mother of twins is higher than that of the mother of single births. With the result that 'gemellity', fecundity and longevity are related. On the other hand, the perinatal and infant death rate is much higher for twins than for single births, so that the percentage of 'useful' children is very low for twins. There is therefore, at the same time, selection and counter-selection. The momentary importance of either could explain the extent of variation of the 'gemellity' rate. The compensations, at short or long time, between the two processes could explain the roughly constant rate of 'gemellity' during the last four centuries.     

Extraction of symbolic determinants common to a family of biological sequences

A set of sequences can be defined by their common subsequences, and the length of these is a measure of the overall resemblance of the set. Each subsequence corresponds to a succession of symbols embedded in every sequence, following the same order but not necessarily contiguous. Determining the longest common subsequence (LCS) requires the exhaustive testing of all possible common subsequences, which sum up to about 2L, if L is the length of the shortest sequence. We present a polynomial algorithm (O(n X L4), where n is the number of sequences) for generating strings related to the LCS and constructed with the sequence alphabet and an indetermination symbol. Such strings are iteratively improved by deleting indetermination symbols and concomitantly introducing the greatest number of alphabet symbols. Processed accordingly, nucleic acid and protein sequences lead to key-words encompassing the salient positions of homologous chains, which can be used for aligning or classifying them, as well as for finding related sequences in data banks.     

Lutte biologique et intégrée en vergers de pommiers,poiriers et abricotiers

Résumé La lutte biologique contre les organismes nuisibles aux vergers évolue par étape vers une Protection intégrée. Dans cette optique, les recherches se développent en France sur les points suivants: effets indésirables des pesticides sur l'entomofaune auxiliaire, r?le d'abri-refuge pour l'entomofaune autochtone joué par l'environnement végétal des vergers, diversification des procédés de lutte, mise au point de méthodes plus sélectives, sélection de variétés résistantes ou moins sensibles aux attaques de plusieurs organismes nuisibles, amélioration des méthodes de surveillance des vergers pour la prévision des risques de dégats, lutte raisonnée contre les maladies cryptogamiques. La mise au point de programmes de lutte intégrée dépend essentiellement des possibilités de lutte disponibles contre les ennemis-clés. Dans les vergers de pommiers et de poiriers fran?ais, les ennemis-clés appartiennent à groupes d'arthropodes: Carpocapse (Cydia pomonella L.), Tordeuses de la pelure, Aphides, Psylle du poirier (Psylla pyri L.) Acariens phytophages et aussi à trois maladies fongiques: Tavelure du pommier (Venturia inaequalis Cke.) Wint., O?dium du pommier (Podosphaera leucotricha Ell. et Ev.), Tavelure du poirier (Venturia pirina (Bref.) Aderh. Les méthodes de lutte sélective sont passées en revue: régulateurs de croissance des insectes, lutte biologique par lachers de parasites et de prédateurs insecticide microbiologique, lutte par confusion avec les phéromones sexuelles. L'application de certaines d'entre elles dépend des possibilités de production industrielles d'agents biologique ou biotechnique. Les principaux éléments ayant contribué à une application pratique des programmes de lutte raisonnée et de lutte intégrée ont été: l'amélioration des connaissances biologiques et de la nuisibilité des organismes phytophages, ainsi que des méthodes de surveillance et de prévision permettant l'utilisation des seuils de tolérance économique l'aménagement de la lutte chimique contre le Carpocapse en vergers de pommiers, la démonstration de la bonne efficacité des prédateurs du Psylle du poirier, spécialement desAnthocoris. La lutte raisonnée, appliquée sur plusieurs milliers d'hectares de vergers de pommiers et de poiriers en France, a permis de réduire de plus de 50% le nombre de traitements avec un bon niveau économique de protection. Dans les vergers d'abricotiers, les maladies parasitaires, principalement l'Enroulement chlorotique causé par un mycoplasme, représentent les problèmes les plus importants. Des essais sont en cours pour parvenir à une lutte raisonnée contre la Petite mineuse (Anarsia lineatella Zell.) et le puceronHyalopterus pruni Geoffr. qui est l'agent de dissémination de la Sharka (maladie due à un virus de type I.L.A.R.).      

System analysis and nucleic acid sequence banks

The mass of published nucleic acid sequence data has required the design of several computerized data bases. We show that this activity is related to the methodology of System Analysis and that data bases are a means of modeling biological knowledge. As an example, the ACNUC data base we have created is presented.     

Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable

The most commonly accepted secondary structure models for 5S RNA differ for molecules of eubacterial origin, where the four-helix model of Fox and Woese is generally cited, and those of eukaryotic origin, where a fifth helix is assumed to exist. We have carefully aligned all available sequences from eukaryotes, eubacteria, chloroplasts, archaebacteria and plant mitochondria. We could thus derive a unified secondary structure model applicable to all 5S RNA sequences known to-date. It contains the five helices already present in the eukaryotic model, extended by additional segments that were not previously assumed to be universally present. One of the helices can be written in two equilibrium forms, which could reflect the existence of a flexible, dynamic structure. For the derivation of the model and the estimation of the free energies we followed a set of rules optimized to predict the tRNA cloverleaf. The stability of the unified model is higher than that of nearly all previously proposed sequence-specific and general models.     

Quaternary structure and proteolysis of the polynucleotide phosphorylase from C. perfringens]

This report describes structural studies on purified polynucleotide phosphorylase from C. perfringens. A method is described for the purification of the enzyme which yields a product equivalent in activity to the native polynucleotide phosphorylase from E. coli. These studies revealed a molecular heterogeneity arising from successive stages of proteolysis, to which this enzyme is especially sensitive; unusally, the enzyme is obtained as a mixture of variable proportions of the native and proteolysed forms. We found in all cases a trimeric basic structure composed of the native (alpha) or proteolysed (lapha) or proteolysed (alpha', alpha") catalytic sub-units, However, the enzyme is rather easily dissociated into its sub-units, a phenomenon which seems to accompany proteolysis (Table). Under the action of either endogenous proteases or trypsin, two enzymatic forms are obtained: their quaternary structures seem analogous, but they differ in their catalytic properties from each other and from the initial enzyme. With some care at each step of purification, the polynucleotide phosphorylase of E. coli can be obtained exclusively in its native form. The greater susceptibility to proteolysis of the enzyme from C. perfrigens and the relationship between such degradation and quaternary structure seem to be at the origin of the peculiar behavior of this polynucleotide phosphorylase.     

Complete nucleotide sequence of RNA 3 from alfalfa mosaic virus, strain S

We report the sequence of RNA 3 from strain S of Alfalfa mosaic virus (2,055 nucleotides). This RNA codes for a 32.4 kd protein (P3) and for the 24 kd coat protein (P4). The largest part of the sequence was established using RNA sequencing methods. The completion of the sequence in the region coding for P3 was achieved with cloned cDNA synthesized after priming at internal sites of RNA 3. Comparison of the RNA sequences coding P3 and P4 proteins in strain S with those reported in the literature for strain 425 revealed a higher amino acid substitution rate (3%) for P3 than for P4 (congruent to 1%) despite a similar average base substitution of 3-4% in these regions. In P3, two out of nine amino acid changes occur in hydrophilic regions. The amino acid changes in P4 do not modify the local hydrophilicity distribution. The intercistronic region displays a low degree of base substitution (2%) when compared with the untranslated 3'-end region (3.6%) or the 5'-end leader region (8%), the average substitution rate being 3.2%.     

PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM-LIKELIHOOD APPROACH

Restriction sites data can be analyzed by maximum likelihood to obtain estimates of phylogenies. The likelihood methods of Smouse and Li, who were able to compute likelihoods for up to four species under a simplified model of base change, can be extended numerically to deal with any number of species. The computational methods for doing so are outlined. The resulting algorithms are slow but take multiple gains and losses of restriction sites fully into account, unlike parsimony methods. They allow for the failure to observe potential sites that are absent from all species. Analysis of the five-species hominoid data of Ferris and coworkers confirms the pattern found by Smouse and Li with four species—that a chimpanzee-gorilla clade is favored, but not statistically significantly over other tree topologies. A large data set produced by computer simulation has also been analyzed to confirm that the method works properly. The methods used here do not allow for different rates of transitions and transversions. They can be extended to do so, but only at a cost of considerably slower computations. The present method is available in a computer program.     

Non-parametric statistics for nucleic acid sequence study

The use of non-parametric statistics for nucleic acid sequence studies is illustrated by some examples. This method is highly flexible and allows design of specific tests for detecting sequence structure. Tests devoted to local repetitivity, codon nearest neighbors, and dinucleotide avoidance are discussed in detail. An appendix indicates all computations required to use these tests.     

Immunological aging

Immune responses decline with age, as assessed by the increasing role of infections in elderly subjects. This decline is, however, very progressive, and usually only clear-cut after 80 years of age. Major difficulties have been encountered to delineate the cellular basis of this immunodeficiency, which is subtle and inconsistent, at the origin of contradictory reports. This is, however, an important challenge in view of the possible therapeutic perspectives of immunotherapy of aged subjects.