Searching for geometric molecular shape complementarity using bidimensional surface profiles

The study presented herein is a bidimensional approach to the complementarity of two molecular surfaces. From two chosen sections we have established a methodology of generating the optimal matching of two shapes. Our approach consists in describing two molecular surface sections by a shape vector (the angular profile), in finding their matching patterns by comparison of the two profiles, and in optimizing the relative locations of the two sections in two-dimensional space, using rotations and translations defined by geometric characteristics. The set of optimal configurations are successively displayed on a screen. Satisfying results have been obtained for the matching of the complex kallikreine Atrypsin pancreatic bovin 2. This efficient method could be used as a preprocessing for a tridimensional shape complementarity approach between two molecular surfaces.     

The Dynamics of a Fish Stock Exploited in Two Fishing Zones

This work presents a specific stock-effort dynamical model. The stocks correspond to two populations of fish moving and growing between two fishery zones. They are harvested by two different fleets. The effort represents the number of fishing boats of the two fleets that operate in the two fishing zones. The bioeconomical model is a set of four ODE's governing the fishing efforts and the stocks in the two fishing areas. Furthermore, the migration of the fish between the two patches is assumed to be faster than the growth of the harvested stock. The displacement of the fleets is also faster than the variation in the number of fishing boats resulting from the investment of the fishing income. So, there are two time scales: a fast one corresponding to the migration between the two patches, and a slow time scale corresponding to growth. We use aggregation methods that allow us to reduce the dimension of the model and to obtain an aggregated model for the total fishing effort and fish stock of the two fishing zones. The mathematical analysis of the model is shown. Under some conditions, we obtain a stable equilibrium, which is a desired situation, as it leads to a sustainable harvesting equilibrium, keeping the stock at exploitable densities.     

Aberrant valve formation in a centric diatom,Ditylum brightwellii

Summary Interphase cells of the centric diatom,Ditylum brightwellii (West) Grunow, were treated with a microtubule-inhibitor (amiprophosmethyl, 6×10^–7 M); the cells could proceed to divide, but the spindle apparatus in about 25% of the cells was displaced and their two sibling cells has either two nuclei or none. The cells with two nuclei formed a new valve with two labiate processes, instead of one as in normal cells. Most of the cells lacking a nucleus were unable to form a new valve, and of the 2% that did form new valves, all did so without dividing. The valves with two labiate processes were originally formed in two separate silica deposition vesicles (SDVs) and the two embryonic siliceous valves fused when these two expanding SDVs met. Accordingly, both the pattern of perforations and the shape of the marginal ridges on the new valve vary with the distance between the two initiation sites of the two SDVs. Implications of these observations in the evolution of valves in diatoms are discussed and a hypothesis on multiple origins of the valves is proposed.     

The cleavage initiation site establishes the posterior pole of the hydrozoan embryo

Summary When the first cleavage of the hydrozoan egg is reversibly suppressed, two cleavage furrows frequently form simultaneously at the time of the second cleavage. If these two cleavage initiation sites are far enough apart, each one specifies a site of gastrulation, and the embryo that forms develops into a two tailed planula larva. When two tailed planulae are induced to metamorphose, they form a polyp with two stalks and hydranths.     

Evidence for Retroviral Intramolecular Recombinations

As a consequence of being diploid, retroviruses have a high recombination rate. Naturally occurring retroviruses contain two repeat sequences (R regions) flanking either end of their RNA genomes, and recombination between these two R regions occurs at a high rate. We deduced that recombination may occur between two sequences within the same RNA molecule (intramolecular) as well as between sequences present within two separate RNA molecules (intermolecular). Intramolecular recombination would usually result in a deletion within the progeny provirus. In this report, we demonstrate that intramolecular recombination between two identical sequences occurred within a chimeric RNA vector. In addition, high rates of recombination between two identical sequences within the same RNA molecule resulted mostly from intramolecular recombination.     

Two chicken erythrocyte band 3 mRNAs are generated by alternative transcriptional initiation and differential RNA splicing.

The erythrocyte anion transport protein (band 3) mediates two distinct cellular functions: it provides plasma membrane attachment sites for the erythroid cytoskeletal network, and it also functions as the anion transporter between the erythrocyte cytoplasm and extracellular milieu. We previously showed that two chicken band 3 polypeptides are encoded by two different mRNAs with different translation initiation sites. Here we show that these two band 3 mRNAs are transcribed from two separate promoters within a single gene. In addition, the two pre-mRNAs are differentially spliced, leading to fusion with coding exons used in common in the two mRNAs. The chicken erythrocyte band 3 gene is therefore the first example of a gene that has two promoters within a single locus which function equally efficiently in one cell type at the same developmental stage.     

Domains in bovine serum amine oxidase

Analysis of the thermal unfolding of bovine serum amine oxidase by differential scanning calorimetry reveals for the dimeric protein a four domain structure consisting of two sets of domains. Each set contains two domains of similar size. The two smaller domains, in contrast with the larger ones, greatly differ in thermostability. Removal of copper changes the calorimetric pattern dramatically. The findings confirm that the metal cofactor plays a structural role. Since the enzyme contains two copper atoms and only one titratable carbonyl group, the calorimetric pattern suggests that the difference in thermostability of the two small domains might be due to the presence of a single organic cofactor.     

lac repressor forms loops with linear DNA carrying two suitably spaced lac operators.

Tetrameric lac repressor may bind to two lac operators on one DNA fragment and induce the intervening DNA to form a loop. Electron microscopy, non-denaturing polyacrylamide gel electrophoresis, and DNase I protection experiments were used to demonstrate such DNA loops, where the distance between the centres of symmetry of the two lac operators varies between 63 and 535 bp. Formation of a DNA loop is favoured by correct phasing of the two lac operators and a low concentration of both components of the reaction. When a large excess of lac repressor over DNA is used, a 'tandem' structure is observed, in which both lac operators are occupied independently by two repressor tetramers. When the concentrations of both lac repressor and lac operator are high, a 'sandwich' structure is observed, in which two DNA molecules are connected by two lac repressor tetramers in trans.     

Two complementary perspectives on inter-individual genetic distance

This paper examines population structure through the prism of pairwise genetic distances. Two complementary perspectives, framed as two simple questions, are explored: Q1: What is the probability that a random pair of individuals from the same local population is more genetically dissimilar than a random pair from two distinct populations? Q2: On average, how genetically different are two individuals from the same local population, in comparison with two individuals chosen from any two distinct populations? Models are developed to provide quantitative answers for the two questions, given allele frequencies across any number of markers from two diploid populations. The probability from Q1 is shown to drop to zero with increasing number of genetic markers even for very closely-related populations and rare alleles. The average genetic dissimilarity of two individuals from distinct populations diverges from the average dissimilarity of two individuals from the same population by a percentage dependent on estimates of population differentiation. This perspective also suggests a measure of population distance based on the intuitive notion of pairwise genetic distance, along with a simple method of estimation. Results from recent empirical research on inter-individual genetic distance in human populations are analyzed in the context of the theoretical framework.     

Comparative analysis of alternative statistical models for differentiation of herring stocks based on meristic characters

A basic stock assessment problem is the mixing and separation of herring populations in their specific areas. Within the transition zone between the North and the Baltic seas (Skagerrak, Kattegat, The Sound) a mixing of two herring populations ( Clupea harengus L.) temporarily takes place. One major component stems from the Baltic Sea (spring spawner), and the other from the North Sea (autumn spawner); each stock exhibits different meristic characteristics. In order to separate the two herring populations, 'pure' learning samples of meristic characters were created in 1995 as differential variables. Mainly gained during two research surveys at two geographically remote areas where a mixing of herring components was relatively unlikely, these learning samples were considered as representative for one or the other herring population. This paper compares the current (ICES) separation approach for herring stock assessment with two alternative methods wherein vertebra counts (vc) are used as meristic characters. The two proposed methods are (a) an inverted variance weighted linear model, and (b) a separation rule based on a quadratic discriminant analysis. The paper summarizes and discusses the results of predicting fractions of the two herring components derived from all three separation models. The underlying example data set stems from a 1991–97 routine Swedish survey in the transition zone. In comparison, the quadratic discriminant analysis separation model was identified as superior to the two other methods. Furthermore, the model suggests a higher degree of mixing of the two herring stocks in the transition area than was previously thought; inter-annual changes in the geographical distribution of the two populations are suggested as being less variable than previously assumed.     

Detection of the homology among proteins by immunochemical cross-reactivity between denatured antigens. Application to the threonine and methionine regulated aspartokinases-homoserine dehydrogenases from Escherichia coli K 12.

The two isofunctional enzymes aspartokinases-homoserine dehydrogenases I and II from Escherichia coli K 12 are compared using immunochemical techniques. The antibodies raised against one of these two proteins when in its native state can only recognize the homologous antigen, whether it is native or denatured. Contrarily, the antibodies raised against one of these two proteins when in its denatured state can recognize both the homologous and heterologous denatured antigens. The existence of this cross-reaction only between the two denatured aspartokinases-homoserine dehydrogenases suggests that these two enzymes have some similarity since such a reaction is not detected with several other denatured proteins. The regions involved in this similarity are buried inside the native proteins, and become exposed only upon denaturation. The same results, the existence of a cross-reaction between denatured species and none between the native ones, is obtained with proteolytic fragments derived from these two proteins and endowed with homoserine dehydrogenase activity. This resemblance between the two aspartokinases-homoserine dehydrogenases suggests that these proteins derive from a common ancestor. It is also proposed that such a cross-reaction between two denatured proteins is evidence for an homology between their amino acid sequences, and that the use of denatured proteins as both immunogens and antigens could be useful in detecting sequence homologies.     

Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase

Thymidine phosphorylase (TP) is a dual substrate enzyme with two domains. Each domain binds a substrate. In the crystal structure of Escherichia coli TP, the two domains are arranged so that the two substrate binding sites are too far away for the two substrates to directly react. Molecular dynamics simulations reveal a different structure of the enzyme in which the two domains have moved to place the two substrates in close contact. This structure has a root-mean-square deviation from the crystal structure of 4.1 A. Quantum mechanical calculations using this structure find that the reaction can proceed by a direct nucleophilic attack with a low barrier. This mechanism is not feasible in the crystal structure environment and is consistent with the mechanism observed for other N-glycosidic enzymes. Important catalytic roles are found for the three highly conserved residues His 85, Arg 171, and Lys 190.     

Catastrophic shifts in vertical distributions of phytoplankton The existence of a bifurcation set

A model of phytoplankton dynamics within a water column was analyzed with special consideration on the existence of a bifurcation set in the parameter space. We considered two resources, light and a limiting nutrient, for phytoplankton growth and assumed that the water column is separated into two layers by thermal and/or density stratification. It was shown that there exists a bifurcation set in the parameter space when the growth function meets several conditions that are general for growth functions of two essential resources. Specifically, these conditions include that a less abundant of the two resources limits the growth while the effect of the other is sufficiently small. Folded structure with two stable states separated by one unstable state appears in the catastrophe manifold when parameters move to a certain direction with a certain curvature from a point in the bifurcation set. These results suggest that occurrence of discontinuous transition between two alternative vertical patterns is possible nature of phytoplankton dynamics within a stratified water column.     

The chicken delta-crystallin gene family. Two genes of similar structure in close chromosomal approximation

delta-Crystallin is a major protein product of the differentiated chicken lens. We have isolated two, non-allelic delta-crystallin genes using a recombinant bacteriophage/chicken genomic DNA library. There appear to be only these two delta-crystallin genes in the haploid chicken genome. Southern hybridization and R-loop analyses indicate that the two genes are oriented on the chromosome with similar 5'-3' polarity. delta 1, arbitrarily designated as the directionally 5' of the two genes, is 6.7 kilobases in length, while delta 2 is 9.2 kilobases. The two delta-crystallin genes are about 4.2 kilobases apart. Structurally, both genes are arranged in a similar and characteristic pattern of 17 exons/16 introns, as judged by electron microscopy. The delta-crystallin gene locus represents a simple model for the study of structural co-evolution and/or functional co-expression of two related genes within a developmentally modulated region of the genome.     

Dual human immunodeficiency virus type 1 infection and recombination in a dually exposed transfusion recipient. The Transfusion Safety Study Group.

We studied a case in which a 2-month-old premature infant was concurrently transfused with packed erythrocytes from two different human immunodeficiency virus type 1 (HIV-1)-seropositive donors in late 1984. The two donors also each singly infected a second infant. Inspection of sequences from portions of the HIV-1 genomes in each of the two donors showed a close relationship to the strain in their respective singly exposed recipients. Inspection of sequences from the dually exposed recipient provided evidence of an individual simultaneously infected with two distinct HIV-1 strains, as well as recombination of the two strains in vivo.     

Characterization of peptide deformylase2 from B. cereus

Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, some bacteria including medically relevant pathogens possess two or more def-like genes. Here we have examined two PDFs from Bacillus cereus. The two share only 32% sequence identity and the crystal structures show overall similarity with PDF2 having a longer C-terminus. However, there are differences at the two active sites, and these differences appear to contribute to the activity difference seen between the two. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface.     

Determination of the primary structure of homologous proteins by sequence analysis of peptide mixtures

We propose a rapid method to determine the primary structure of a protein knowing the sequence of a homologous protein. The method consists in submitting both the reduced and alkylated proteins to an enzymatic or chemical hydrolysis and performing the sequence analysis of the peptide mixtures. The assessment of the unknown sequence and the degree of identity of the two proteins are reached by comparing the two sequence analyses. The sequences of all the possible peptides present in the two mixtures are reconstructed and the differences in the two sequences are determined. If necessary, the differences can be confirmed by performing a mass spectrometric analysis of the two mixtures. We used this procedure on two homologous proteins of known sequence to furnish an application example of the method.     

The New Dynamics of European Spaces since 1989

Since the collapse of the Soviet bloc, the term “Europe” has reached a new dimension. The fall of the Berlin Wall opened the East to the West and, in 1989, the European space moved up from two entities symbolically separated by a wall to one territorial unity. But we cannot say that this unity is a political one. This dichotomy is not based on two different political orientations, but on the adhesion or the non-adhesion to economic, political and especially moral principles. Thus two conceptions of the European space are competing. The term “Europe” has two major significations: firstly it refers to the European Union, and secondly to a Great Europe, including the states which have belonged to the former Soviet bloc. How can we define how this Great Europe perceived itself and what are its limits? The objective of this paper is to demonstrate that the two visions of the European space are under competition through two institutions. They convey two representations of this European space and imagine it in two perspectives. Therefore, the collapse of the Soviet bloc has altered in depth the perception of the European space and created a new dichotomy.     

Two independent gene systems controlling recombination in Schizophyllum commune

Summary Mating competence in the fungusSchizophyllum commune is controlled by two unlinked factors, each of which consists of two closely linked loci. The recombination frequencies between the loci of each factor were determined for a dikaryon and a group of back-crosses, at two meiotic temperatures. The results establish that the frequencies of recombination in the two regions are under genetic control. Although the two regions are similar in structure and function they are under separate recombination control.