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.     

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.     

A flexible method to align large numbers of biological sequences

Summary A method for the alignment of two or more biological sequences is described. The method is a direct extension of the method of Taylor (1987) incorporating a consensus sequence approach and allows considerable freedom in the control of the clustering of the sequences. At one extreme this is equivalent to the earlier method (Taylor 1987), whereas at the other, the clustering approaches the binary method of Feng and Doolittle (1987). Such freedom allows the program to be adapted to particular problems, which has the important advantage of resulting in considerable savings in computer time, allowing very large problems to be tackled. Besides a detailed analysis of the alignment of the cytochrome c superfamily, the clustering and alignment of the PIR sequence data bank (3500 sequences approx.) is described.     

Hierarchical clustering based upon contextual alignment of proteins: a different way to approach phylogeny

We perform a computational study using a new approach to the analysis of protein sequences. The contextual alignment model, proposed recently by Gambin et al. (2002), is based on the assumption that, while constructing an alignment, the score of a substitution of one residue by another depends on the surrounding residues. The contextual alignment scores calculated in this model were used to hierarchical clustering of several protein families from the database of Clusters of Orthologous Groups (COG). The clustering has been also constructed based on the standard approach. The comparative analysis shows that the contextual model results in more consistent clustering trees. The difference, although small, is with no exception in favour of the contextual model. The consistency of the family of trees is measured by several consensus and agreement methods, as well as by the inter-tree distance approach.     

An exact parallel algorithm to compare very long biological sequences in clusters of workstations

Biological Sequence Comparison is one of the most important operations in Computational Biology since it is used to determine how similar two sequences are. Smith and Waterman proposed an exact algorithm (SW), based on dynamic programming, that is able to obtain the best local alignment between two sequences in quadratic time and space. In order to compare long biological sequences, SW is rarely used since the computation time and the amount of memory required becomes prohibitive. For this reason, heuristic methods like BLAST are widely used. Although faster, these heuristic methods do not guarantee that the best result will be produced. In this paper, we propose an exact parallel variant of the SW algorithm that obtains the best local alignments in quadratic time and reduced space. The results obtained in two clusters (8-machine and 16-machine) for DNA sequences longer than 32 KBP (kilo base-pairs) were very close to linear and, in some cases, superlinear. For very long DNA sequences (1.6 MBP), we were able to reduce execution time from 12.25 hours to 1.54 hours, in our 8-machine cluster. As far as we know, this is the first time 1.6 MBP sequences are compared with an exact SW variant. In this case, 30240 best local alignments were obtained.

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.     

A sequence from drosophila DNA cross-hybridizing with a mouse class I H-2 Gene: absence of relevant nucleic acid or amino acid sequence homology

Following serological data (1) showing cross-reactivity of drosophila surface antigens with anti-H-2 and mouse beta 2-microglobulin (beta 2-m) antisera, we have looked for homologous sequences in the drosophila genome by low stringency hybridization with mouse H-2 and beta 2-m probes. A 240 bp drosophila DNA segment cross-hybridizing with a H-2 probe, was isolated and sequenced. No homology at the nucleotide or amino acid levels was found with the mouse probe which was used, except for a perfectly matching 16-mer containing 11 G-C, which might be responsible for the cross-hybridization. Therefore, our present data do not support the existence of class I H-2 and/or beta 2-m related gene sequences in the drosophila genome.     

Radioactive analogs of neurotensin. I. Solid phase synthesis and biological characterization of Trp 11-neurotensin, a precursor of an iodized ligand

In order to generate highly labelled neurotensin analogues, synthesis has been performed of two types of precursors, one for iodination and one for tritiation. Iodination of native neurotensin occurs on both tyrosines in position 3 and 11 and thus affects greatly its binding capacities. In this article, synthesis and chemical characterization of [Trp11]-neurotensin are described which can be iodinated without loss of activity. Synthesis was by solid phase procedure on an experimental support, Pab-resin, alpha-(4-chloromethylphenylacetamido)-benzyl copoly (styrene 1 per cent divinylbenzene). After esterification of Boc-Leu by its cesium salt on the Pab-resin, each amino acid was incorporated by a double coupling with dicyclohexylcarbodiimide on a Beckman 990 synthesizer. The trifunctionnal amino acids were protected as follows : Tyr as the 2,6-dichlorobenzyl ether, Glu as benzyl ester, Lys by the benzyloxycarbonyl group, Arg by the tosyl group, and Trp by the formyl group. Boc-Asn was incorporated by the HOBt procedure. The cleavage of peptide-resin bond and the removal of lateral chain protecting groups was realized by hydrofluoric acid with 10 per cent anisol for 1 h at 0 degrees C. The peptide obtained was then treated by NH4HCO3 1 M, pH 9, for 24 h for the removal of tryptophan formyl protecting group. Purification of the crude peptide on Bio-Gel P2 followed by ion exchange chromatography on carboxymethylcellulose (CM 52) and a final desalting on Bio-Gel P2 proved very efficient in removing several shorter contaminants.(ABSTRACT TRUNCATED AT 250 WORDS)     

Ostracoda as bioindicators of anthropogenic impact in salt lakes,saltpans, and a lagoon: A case study from the Gulf of Saros coast (NE Aegean Sea), Turkey

The study area consists of wetlands and semi-wetlands (saltpan and salt lakes) that are separated from the Gulf of Saros in the northeastern Aegean Sea by a littoral cordon. Twenty-four samples were collected from the Enez Salt Lake; Dalyan, Enez Gala, Kuvalak, Isik, and Tasalti Lakes; Vakif and Erikli Saltpans; and Karagol Lagoon. The overall distribution of the sediment sizes reveals that they consist predominantly of mud and sand and a mixture of mud, sand, and gravel. The average proportion of gravel size particles is 8.36%. Feldspar and mica are abundant in sand and gravel-sized materials. Ecological conditions of these coastal areas were assessed on the basis of ostracod assemblages that can be considered as useful bioindicators and depend on water depth, temperature, and salinity. In this context, the effects of physical and chemical properties of the environment, geochemistry of the sediment, and anthropogenic impact on the meiofauna, in particular ostracoda, was here evaluated. Cyprideis torosa Jones, a cosmopolitan species of ostracoda, was found in salt lakes. Other species of ostracoda were shown to be affected by environmental conditions. The toxicity of some heavy metals in the saltpans, salt lakes, and hypersaline lagoons was evaluated. Lake Dalyan and Erikli Saltpan display high toxicity for Cu and Cd levels. The distribution of hydrocarbon pollution of terrestrial origin was determined.     

High ecomorphological diversity among Early Cretaceous frogs from a large subtropical wetland of Iberia

Anurans are extremely diverse amphibians with a unique Bauplan, whose origin, early ecomorphological diversification, and adaptive significance remain elusive. Their early fossil record is improving at an accelerated pace worldwide, but its contribution to these issues is still wanting. Here we explore ecomorphological diversity among Early Cretaceous (Barremian) frogs that inhabited a large subtropical wetland from Iberia by inferring locomotor abilities with a phylogenetic flexible discriminant analysis on data from limb proportions, which strongly correlate with locomotion. The results show a remarkable diversity among these frogs when compared with the extant diversity from this region and from tropical and subtropical wetland assemblages worldwide, encompassing miniature to medium-size jumpers and dedicated swimmers with more extreme proportions than extant ‘archeobatrachians,’ but also more generalized jumping and/or swimming forms. This agrees with the inferred wetland paleoenvironment and the hypothesis regarding early frogs as small poor jumpers or swimmers that evolved their peculiar Bauplan in aquatic environments.     

Eimeria tenella: cloning of a novel Eimeria tenella cDNA encoding a protein related to rhomboid family from F2 hybrid strain

A novel cDNA sequence with an open reading frame of 774 bp from Eimeria tenella F2 hybrid strain (ETRH01) was isolated from a lambda cDNA library with a monoclonal antibody against sporozoite. Analysis of the genomic sequence suggests that this is an intronless gene. The deduced protein sequence has 257 amino acids with a calculated molecular weight of 28.349 kDa and an isoelectric point of 8.56. Sequence analysis revealed seven transmembrane domains and a rhomboid domain within the protein. RT-PCR result indicates that this gene was expressed in all of the five E. tenella isolates analyzed. To further study the role of this novel gene in the life cycle of E. tenella, ETRH01 was successfully expressed using pET28b(+) expression system.