The use of high energy laser-plasma sources in soft X-ray contact microscopy of living biological samples

In this paper the results of an experiment on soft X-ray contact microscopy using a laser-plasma source are presented. A resolution of 50 nm has been achieved imaging pig sperm cells, while other specimens, such as algae and yeast cells, showed internal details, proving the technique to be a powerful tool for biological investigations. Original biological information has been obtained and the conditions for optimal image formation have been studied. Received 5 June 2002 Published online 24 September 2002 RID="a" ID="a"e-mail: batani@mib.infn.it     

Structure factor of a lamellar smectic phase with inclusions

Motivated by numerous X-ray scattering studies of lamellar phases with membrane proteins, amphiphilic peptides, polymers, or other inclusions, we have determined the modifications of the classical Caillé law for a smectic phase as a function of the nature and concentration of inclusions added to it. Besides a fundamental interest on the behavior of fluctuating systems with inclusions, a precise characterization of the action of a given protein on a lipid membrane (anchoring, swelling, stiffening ...) is of direct biological interest and could be probed by way of X-ray measurements. As a first step we consider three different couplings involving local pinching (or swelling), stiffening or curvature of the membrane. In the first two cases we predict that independent inclusions induce a simple renormalization of the bending and compression moduli of the smectic phase. The X-ray experiments may also be used to probe correlations between inclusions. Finally we show that asymmetric coupling (such as a local curvature of the membrane) results in a modification of the usual Caillé law. Received 10 March 2000 and Received in final form 30 August 2000     

Response of boolean networks to perturbations

We evaluate the probability that a Boolean network returns to an attractor after perturbing h nodes. We find that the return probability as function of h can display a variety of different behaviours, which yields insights into the state-space structure. In addition to performing computer simulations, we derive analytical results for several types of Boolean networks, in particular for Random Boolean Networks. We also apply our method to networks that have been evolved for robustness to small perturbations, and to a biological example.     

High reproduction rate versus sexual fidelity

We introduce fidelity into the bit-string Penna model for biological ageing and study the advantage of this fidelity when it produces a higher survival probability of the offspring due to paternal care. We attribute a lower reproduction rate to the faithful males but a higher death probability to the offspring of non-faithful males that abandon the pups to mate other females. The fidelity state of the father is transmitted to the male offspring (with or without error). We show that nature may prefer a lower reproduction rate to warrant the survival of the offspring already born. Received 18 February 1999     

Network robustness to targeted attacks. The interplay of expansibility and degree distribution

We study the property of certain complex networks of being both sparse and highly connected, which is known as “good expansion” (GE). A network has GE properties if every subset S of nodes (up to 50% of the nodes) has a neighborhood that is larger than some “expansion factor” φ multiplied by the number of nodes in S. Using a graph spectral method we introduce here a new parameter measuring the good expansion character of a network. By means of this parameter we are able to classify 51 real-world complex networks — technological, biological, informational, biological and social — as GENs or non-GENs. Combining GE properties and node degree distribution (DD) we classify these complex networks in four different groups, which have different resilience to intentional attacks against their nodes. The simultaneous existence of GE properties and uniform degree distribution contribute significantly to the robustness in complex networks. These features appear solely in 14% of the 51 real-world networks studied here. At the other extreme we find that ∼40% of all networks are very vulnerable to targeted attacks. They lack GE properties, display skewed DD — exponential or power-law — and their topologies are changed more dramatically by targeted attacks directed at bottlenecks than by the removal of network hubs.     

The Penna model for biological ageing on a lattice: spatial consequences of child-care

We introduce a square lattice into the Penna bit-string model for biological ageing and study the evolution of the spatial distribution of the population considering different strategies of child-care. Two of the strategies are related to the movements of a whole family on the lattice: in one case the mother cannot move if she has any child younger than a given age, and in the other case if she moves, she brings these young children with her. A stronger condition has also been added to the second case, considering that young children die with a higher probability if their mothers die, this probability decreasing with age. We show that a highly non uniform occupation can be obtained when child-care is considered, even for an uniform initial occupation per site. We also compare the standard survival rate of the model with that obtained when the spacial lattice is considered (without any kind of child-care). Received 30 October 1998 and Received in final form 27 November 1998     

Monte Carlo simulations of parapatric speciation

Parapatric speciation is studied using an individual-based model with sexual reproduction. We combine the theory of mutation accumulation for biological ageing with an environmental selection pressure that varies according to the individuals geographical positions and phenotypic traits. Fluctuations and genetic diversity of large populations are crucial ingredients to model the features of evolutionary branching and are intrinsic properties of the model. Its implementation on a spatial lattice gives interesting insights into the population dynamics of speciation on a geographical landscape and the disruptive selection that leads to the divergence of phenotypes. Our results suggest that assortative mating is not an obligatory ingredient to obtain speciation in large populations at low gene flow.     

Boerdijk-Coxeter helix and biological helices

Helices and dense packing of spherical objects are two closely related problems. For instance, the Boerdijk-Coxeter helix, which is obtained as a linear packing of regular tetrahedra, is a very efficient solution to some close-packing problems. The shapes of biological helices result from various kinds of interaction forces, including steric repulsion. Thus, the search for a maximum density can lead to structures related to the Boerdijk-Coxeter helix. Examples are presented for the -helix structure in proteins and for the structure of the protein collagen, but there are other examples of helical packings at different scales in biology. Models based on packing efficiency related to the Boerdijk-Coxeter helix, explain, mainly from topological arguments, why the number of amino acids per turn is close to 3.6 in -helices and 2.7 in collagen. Received 26 November 1998 and Received in final form 12 April 1999     

Oscillatory Activities in Regulatory Biological Networks and Hopf Bifurcation

Exploiting the nonlinear dynamics in the negative feedback loop, we propose a statistical signal-response model to describe the different oscillatory behaviour in a biological network motif. By choosing the delay as a bifurcation parameter, we discuss the existence of Hopf bifurcation and the stability of the periodic solutions of model equations with the centre manifold theorem and the normal form theory. It is shown that a periodic solution is born in a Hopf bifurcation beyond a critical time delay, and thus the bifurcation phenomenon may be important to elucidate the mechanism of oscillatory activities in regulatory biological networks.     

Instabilities in population dynamics

Biologists have long known that the smaller the population, the more susceptible it is to extinction from various causes. Biologists define minimum viable population size (MVP), which is the critical population size, below which the population has a very small chance to survive. There are several theoretical models for predicting the probability that a small population will become extinct. But these models either embody unrealistic assumptions or lead to currently unresolved mathematical problems. In other popular models of population dynamics, like the logistic model, MVP does not exist. In this paper we find the existence of such a critical concentration in a simple model of evolution. We solve this model by a mean field theory and show, in one and two dimensions, the existence of the critical adaptation and concentration below which a population dies out. We also show that, like in the logistic model, above the critical value a population reaches its carrying capacity. Moreover, in the two-dimensional case we find - the so common in biological models - periodic solutions and their biffurcations. Received 15 February 2000     

Transfection and imaging of diamond nanocrystals as scattering optical labels

We report on the first demonstration of nanodiamond (ND) as a scattering optical label in a biological environment. NDs were efficiently transfected into cells using cationic liposomes, and imaged using differential interference and Hoffman modulation ‘space’ contrast microscopy techniques. We have shown that 55 nm NDs are biologically inert and produce a bright signal compared to the cell background. ND as a scattering label presents the possibility for extended biological imaging with relatively little thermal or biochemical perturbations due to the optical transparency and biologically inert nature of diamond.     

Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein

Eosinophil Cationic Protein (ECP) is a member of RNase A superfamily which carries out the obligatory catalytic role of cleaving RNA. It is involved in a variety of biological functions. Molecular dynamics simulations followed by essential dynamics analysis on this protein are carried out with the goal of gaining insights into the dynamical properties at atomic level. The top essential modes contribute to subspaces and to the transition phase. Further, the sidechain-sidechain/sidechain-mainchain hydrogen bond clusters are analyzed in the top modes, and compared with those of crystal structure. The role of residues identified by these methods is discussed in the context of concerted motion, structure and stability of the protein. Received 16 January 2002 Published online 13 September 2002     

Duplication： a Mechanism Producing Disassortative Mixing Networks in Biology

Assortative/disassortative mixing is an important topological property of a network. A network is called assortative mixing if the nodes in the network tend to connect to their connectivity peers, or disassortative mixing if nodes with low degrees are more likely to connect with high-degree nodes. We have known that biological networks such as protein-protein interaction networks （PPI）, gene regulatory networks, and metabolic networks tend to be disassortative. On the other hand, in biological evolution, duplication and divergence are two fundamental processes. In order to make the relationship between the property of disassortative mixing and the two basic biological principles clear and to study the cause of the disassortative mixing property in biological networks, we present a random duplication model and an anti-preference duplication model. Our results show that disassortative mixing networks can be obtained by both kinds of models from uncorrelated initial networks. Moreover, with the growth of the network size, the disassortative mixing property becomes more obvious.     

Pattern formation in reaction diffusion systems: a Galerkin model

Reaction diffusion systems are extremely useful for studying pattern formation in biological systems. We carry out a Lorenz like few mode truncation of a reaction diffusion system and show that it not only gives the same qualitative behaviour as the more complicated systems but also indicates of the existence of a Hopf-bifurcation in the turing region. Received 10 May 2000 and Received in final form 14 March 2001     

Quantum optical coherence tomography of a biological sample

Quantum optical coherence tomography (QOCT) makes use of an entangled-photon light source to carry out dispersion-immune axial optical sectioning. We present the first experimental QOCT images of a biological sample: an onion-skin tissue coated with gold nanoparticles. 3D images are presented in the form of 2D sections of different orientations. In the context of quantum information, this represents the first experiment in which a quantum-entangled entity interacts with a biological specimen, generating a collection of quantum interferograms, from which an image is constructed.     

Inclusions induced phase separation in mixed lipid film

The effect of rigid inclusions on the phase behavior of a film containing a mixture of lipid molecules is investigated. In the proposed model, the inclusion-induced deformation of the film, and the resulting energy cost are strongly dependent upon the spontaneous curvature of the mixed film. The spontaneous curvature is in turn strongly influenced by the composition of film. This coupling between the film composition and the energy per inclusion leads to a lateral modulation of the composition, which follows the local curvature of the membrane. In particular, it is shown that inclusions may induce a global phase separation in a film which would otherwise be homogeneously mixed. The mixed film is then composed of patches of different average composition, separated by the inclusions. This process may be of relevance to explain some aspects of lipid-protein association in biological membranes. Received 8 April 1999 and Received in final form 4 October 1999     

Chaos out of internal noise in the collective dynamics of diffusively coupled cells

We study the transition from stochasticity to determinism in calcium oscillations via diffusive coupling of individual cells that are modeled by stochastic simulations of the governing reaction-diffusion equations. As expected, the stochastic solutions gradually converge to their deterministic limit as the number of coupled cells increases. Remarkably however, although the strict deterministic limit dictates a fully periodic behavior, the stochastic solution remains chaotic even for large numbers of coupled cells if the system is set close to an inherently chaotic regime. On the other hand, the lack of proximity to a chaotic regime leads to an expected convergence to the fully periodic behavior, thus suggesting that near-chaotic states are presently a crucial predisposition for the observation of noise-induced chaos. Our results suggest that chaos may exist in real biological systems due to intrinsic fluctuations and uncertainties characterizing their functioning on small scales.