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 hierarchical structures. These structures seem to drive the system at the edge of chaos, so that it can present adapted responses to significant environmental changes.     

Long timestep dynamics of peptides by the dynamics driver approach

Previous experience with the Langevin/implicit-Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high-frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13-residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small-time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time-dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all-atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full α_R-helix starting structure, and a high-temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA-generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two-state model for helix–coil transition. The good, near-Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley-Liss, Inc.     

A convenient method for the stereoselective preparation of 3-hydroxy-2-substituted propionaldehyde derivatives, C-terminal precursors for the synthesis of trans-alkene dipeptide isosteres

Summary (S)-3-hydroxy-2-substituted propionaldehyde dimethyl or diethyl acetals 3, which are versatile synthons in dipeptide isostere synthesis, were synthesized in 54–95% enantiomeric excess by reduction of (S,R)-acetalized acyloxazolidinones 7 with LiAlH₄.     

A new monoclonal antibody (3D3) generated with human respiratory mucins and directed against Lewis determinants

We have prepared a monoclonal antibody (MAb), 3D3, raised againstpurified human respiratory mucins. This antibody recognizedmucins and proteolytically derived glycopeptides. The epitoperecognized by the antibody was destroyed by -L-fucosidase, indicatingthat it was present on the carbohydrate moieties. Structuralspecificity was determined by adsorption on a variety of synthetic,insolubilized oligosaccharides. Several lines of evidence indicatethat the 3D3 MAb reacted strongly with the Lewis (Le^b) antigen,but also recognized Le^a and Le^y determinants. This antibodymight be useful to study mucin secretion. human bronchial mucins Lewis b     

Carbonic anhydrase in human platelets.

The carbonic anhydrase activity of human platelets was investigated by measuring the kinetics of CO2 hydration in supernatants of platelet lysates by using a pH stopped-flow apparatus. An average carbonic anhydrase concentration of 2.1 microM was determined for pellets of human platelets. Analysis of the kinetic properties of this carbonic anhydrase yielded a Km value of 1.0 mM, a catalytic-centre activity kcat. of 130000 s-1 and an inhibition constant Ki towards ethoxzolamide of 0.3 nM. From these values, CO2 hydration inside platelets is estimated to be accelerated by a factor of 2500. When platelet lysates were subjected to affinity chromatography, only the high-activity carbonic anhydrase II could be eluted from the affinity column, whereas the carbonic anhydrase isoenzyme I, which is known to occur in high concentrations in human erythrocytes, appeared to be absent.     

The genus Archidendron (Leguminosae – Mimosoideae)

An account is given of the morphology and the taxonomy of the Asian, Australian and Pacific genus Archidendron (Leguminosae – Mimosoideae). A new infrageneric classification based on morphological data is presented, the genus being subdivided in 8 series. The phylogeny of the genus is discussed, the base of discussion being all available morphological, palynological and wood–anatomical characters. The presence/absence of stipules, the length of the staminal tube compared with that of the corolla–tube, the sessile/stipitate ovary(–ies), the morphology of the pods and the wood–anatomy have been particularly useful in determining the evolutionary trends within the genus. Analyses of the geographical range of selected character states are presented. The data suggest a Central – W. Malesian origin of the genus. The series endemic to the E. Malesian – Australian area have probably evolved more recently. The pluricarpellate condition of the flowers in several species endemic to the E. Malesian and Australian area is considered to be a derived character state. The following new taxa are proposed: Ser. Calycinae Nielsen, ser. Ptenopae Nielsen, ser. Bellae Nielsen, Archidendron falcatum Nielsen, A. cockburnii Nielsen, A. sabahense Nielsen, A. fagifolium (Bl. ex Miq.) Nielsen var. borneense Nielsen, A. kunsrteri (Prain) Nielsen subsp. ashtonii Nielsen, A. ellipticum (Bl.) Nielsen subsp. cordifoliolatum Nielsen. New combinations are proposed in the Malesian species formerly referred to Abarema, Zygia and Morolobium by Kostermans. Keys to and an enumeration of the species are presented.     

Roche Susceptibility Test (RST) medium,a defined formulation for susceptibility testing: I. Nutrient interaction and optimization studies

Roche Susceptibility Test (RST) Medium represents the most completely optimized and convenient fully defined medium described. It requires no post-autoclaving supplementation with vitamins, supports good growth of all common aerobic and anaerobic pathogens and may be used as a broth or agar gel on which the swarming of Proteus spp. is virtually eliminated. The broth as a superior buffering capacity to most complex media and an osmolality and pH close to those of human serum. RST is highly satisfactory for the susceptibility testing of commonly used antibiotics and meets the requirements of the National Committe for Clinical Laboratory Standards of the U.S.A. in almost every respect.     

In situ detection and characterization of DNA polymerase activities in the nucleus of eukaryotic cells

We have developed a cytoenzymological method for localizing DNA polymerase activities in situ and for studying their responses to various chemical agents or environmental conditions. The incubation mixtures and the stimulatory or inhibitory agents added to these media were defined with reference to in vitro biochemical tests used to detect and to characterize DNA polymerases- or - found in eukaryotic cells. This method has already been used to study DNA polymerase activities during cell differentiation or cell senescence. Apart from two exceptions found with lower organisms, the nuclear DNA polymerase activity was always higher under conditions which favoured the in vitro expression of DNA polymerase- rather than DNA polymerase-. — In the various cell types studied, the cellular DNA polymerase activities were almost exclusively found in the nuclei. It is hoped that this methodology will be useful for obtaining more complete biochemical data on the intracellular localization of various DNA polymerases.