Theoretical Biology Forum最新文献

Description: Classical Molecular Dynamics (MD) simulations can provide insights at the nanoscopic scale into protein dynamics. Currently, simulations of large proteins and complexes can be routinely carried out in the ns-μs time regime. Clustering of MD trajectories is often performed to identify selective conformations and to compare simulation and experimental data coming from different sources on closely related systems. However, clustering techniques are usually applied without a careful validation of results and benchmark studies involving the application of different algorithms to MD data often deal with relatively small peptides instead of average or large proteins; finally clustering is often applied as a means to analyze refined data and also as a way to simplify further analysis of trajectories. Herein, we propose a strategy to classify MD data while carefully benchmarking the performance of clustering algorithms and internal validation criteria for such methods. We demonstrate the method on two showcase systems with different features, and compare the classification of trajectories in real and PCA space. We posit that the prototype procedure adopted here could be highly fruitful in clustering large trajectories of multiple systems or that resulting especially from enhanced sampling techniques like replica exchange simulations.

Incipit: It may sound as a truism but it may be necessary to recall that science is not made by instruments, or by well equipped laboratories, but by the unique personalities that use them. As a consequence their intellect, their emotional experiences and their physical ability, cannot be separated from their achievements - being they minor or profound.

Description: I reflect on my fifty-year history as a philosopher of biology, showing how it has taken me from rather narrow analytic studies, through the history of ideas, and now on to issues to do with science and religion. I argue that moral concerns were and still are a major motivation behind what I do and write.

Description: In this essay the researcher modeled contagious cholera illness by geometrical dynamic methods in two forms, seasonal variables and without seasonal variables. In modeling the illness without seasonal variables geometric points and dynamical results are acquired. Disease free equilibrium of this model is considered. The model which is made by seasonal variables is a complicated model from geometrical point of view. So it is considered numerically. The numerical results are given in six figures and the figures are studied biologically.

Description: Cancer may be the most important global public health problem. The effort of understanding carcinogenesis has been accelerating over the last years on account of its high incidence and impact on the lives of individuals' affected. There are a number of theories of carcinogenesis and these theories may be used to justify various alternative cancer treatments. The small variations in cancer mortality observed during the previous years indicate that the clinical applications of these theories have been very limited. In this article, we tried to explain carcinogenesis based on complex adaptive system (CAS) theory.

The probability of fixation of a mutant that causes assortative mating according to the 'mass action model' has been studied. A gene of this kind represents one of the simplest hypothetical mechanisms of prezygotic isolation. Computer analysis by Monte Carlo simulations revealed that the fixation of the mutant is very unlikely unless the population is very small in size and/or the degree of partial assortative mating is very low. The introduction into the biological model of pleiotropic effects of the gene on fitness (viability) can facilitate the process of fixation (even to a very large extent in the case of strong selection in favor of the mutant allele). The most interesting situation, from the point of view of a possible role of the mutant in triggering a process of allopatric speciation, occurs when the effect of assortative mating on gene frequency prevails over the effect of differential viability. In these cases, the probability of fixation of the mutant and the consequent establishment of partial prezygotic isolation shows a pattern similar to that described in literature for the simple case of postzygotic isolating mechanism constituted by a Mendelian factor (gene locus or chromosomal variant) with negative heterosis and selective advantage of the 'new' homozygote over the ancestral homozygote.

Every nucleated cell can produce and respond to cytokines, extracellular proteic/glycoproteic mediators that constitute a complex, interconnected, and flexible signaling network, addressed to modulate cell behavior and homeostasis through the interaction with high-affinity surface receptors. These messenger molecules, whose main characteristics are potency, pleiotropism, and redundancy, primarily act in autocrine, paracrine, and juxtacrine way, but can also display systemic activity in endocrine-like modality. They are generally classified according to their cellular sources, three-dimensional structure, or biological functions. Among cytokines, interleukins (ILs) represent a fascinating and multifunctional group of immunomodulators that primarily mediate the leukocyte cross-talk (hence the name), and mainly regulate the immune cell proliferation, differentiation, growth, survival, activation, and functions. Up to 38 ILs have been so far identified, numbered according to the order of discovery, and grouped in different subsets, based on distinguishing structural/functional features. Due to their crucial role in regulating inflammation and immune response, ILs are known to be involved in the pathogenesis of human inflammatory/autoimmune diseases. Therefore, they have increasingly attracted great interest as effective or promising therapeutic targets. The biology and functions of the hitherto identified human ILs are reviewed and discussed: herein, ILs from IL-20 to IL-38 are presented.

Recently, the venues of exposure to nanoparticles have increased significantly owing to their increased deliberate production. In this study the interaction of fullerenes with DNA was analyzed along with various factors affecting this interaction like mol. wt. of fullerenes (C20 to C180), the form of DNA i.e., A, B and Z, and sequences of DNA, and was compared with the DNA binding of CNTs. Increase in the molecular weight of the fullerene showed increase in the binding score with A & B-form of DNA, but no regular affect was seen on binding with Z-form of DNA. Although the binding of all fullerenes was best with A form. While CNTs bind with all forms of DNA, but best scores were with B form, which were comparable with those of fullerene C80 and C84 with A form. The interaction of both fullerenes and CNTs were not affected by the sequence of DNA. The number of interacting base pairs increased from 1 base-pair to 4, as the molecular size of fullerene increases in all A & B-and Z form of DNA. Whereas CNTs interact with 5 bases in A and B form, and 3 bases in Z form. The groove where binding occurs depended on the form of DNA. Smaller (< C48) fullerenes bind in minor groove of B-DNA, and larger fullerenes bind in major groove. While in A form of DNA, fullerenes of all sizes bind in major groove. The binding was random and not size dependent in Z form of DNA. Whereas, CNTs bind to major groove of DNA in a parallel fashion in A and B form of DNA, and in minor groove attached perpendicularly in Z form.

An elementary but correct concept of plant life has come to us in writings of Theophrastus who divided the plant life in its three basic stages: generation, sprouting, growth. This image of plants remained practically unchanged until the seventeenth-century, when the scientific method based on experimentation was introduced by Bacon. The invention of the microscope and the change of the traditional alchemy for an embryonic chemistry allowed some penetrating minds to look upon plants as highly complex living structures, to which had to correspond some specific functions. The observations and deductions of Mariotte, Malpighi, Grew and Ray revealed that the plant was operating as a real factory that, with the contribution of sunrays, changed inert matter in the components of plant structure and that these transformations could give an account for its concept of life. The subsequent work of Hales supported the concept of plant life as a materialistic processes planned by a divine architect. With Hales began a new phase of research, which reached its full development from the nineteenth century.