Functional Analysis of Spontaneous Cell Movement under Different Physiological Conditions

Cells can show not only spontaneous movement but also tactic responses to environmental signals. Since the former can be regarded as the basis to realize the latter, playing essential roles in various cellular functions, it is important to investigate spontaneous movement quantitatively at different physiological conditions in relation to cellular physiological functions. For that purpose, we observed a series of spontaneous movements by Dictyostelium cells at different developmental periods by using a single cell tracking system. Using statistical analysis of these traced data, we found that cells showed complex dynamics with anomalous diffusion and that their velocity distribution had power-law tails in all conditions. Furthermore, as development proceeded, average velocity and persistency of the movement increased and as too did the exponential behavior in the velocity distribution. Based on these results, we succeeded in applying a generalized Langevin model to the experimental data. With this model, we discuss the relation of spontaneous cell movement to cellular physiological function and its relevance to behavioral strategies for cell survival.Comment: Accepted to PLoS ON

Random Topologies and the emergence of cooperation: the role of short-cuts

We study in detail the role of short-cuts in promoting the emergence of cooperation in a network of agents playing the Prisoner's Dilemma Game (PDG). We introduce a model whose topology interpolates between the one-dimensional euclidean lattice (a ring) and the complete graph by changing the value of one parameter (the probability p to add a link between two nodes not already connected in the euclidean configuration). We show that there is a region of values of p in which cooperation is largely enhanced, whilst for smaller values of p only a few cooperators are present in the final state, and for p \rightarrow 1- cooperation is totally suppressed. We present analytical arguments that provide a very plausible interpretation of the simulation results, thus unveiling the mechanism by which short-cuts contribute to promote (or suppress) cooperation

Aggregation Patterns in Stressed Bacteria

We study the formation of spot patterns seen in a variety of bacterial species when the bacteria are subjected to oxidative stress due to hazardous byproducts of respiration. Our approach consists of coupling the cell density field to a chemoattractant concentration as well as to nutrient and waste fields. The latter serves as a triggering field for emission of chemoattractant. Important elements in the proposed model include the propagation of a front of motile bacteria radially outward form an initial site, a Turing instability of the uniformly dense state and a reduction of motility for cells sufficiently far behind the front. The wide variety of patterns seen in the experiments is explained as being due the variation of the details of the initiation of the chemoattractant emission as well as the transition to a non-motile phase.Comment: 4 pages, REVTeX with 4 postscript figures (uuencoded) Figures 1a and 1b are available from the authors; paper submitted to PRL

Novel type of phase transition in a system of self-driven particles

A simple model with a novel type of dynamics is introduced in order to investigate the emergence of self-ordered motion in systems of particles with biologically motivated interaction. In our model particles are driven with a constant absolute velocity and at each time step assume the average direction of motion of the particles in their neighborhood with some random perturbation ($\eta$) added. We present numerical evidence that this model results in a kinetic phase transition from no transport (zero average velocity, $| {\bf v}_a | =0$) to finite net transport through spontaneous symmetry breaking of the rotational symmetry. The transition is continuous since $| {\bf v}_a |$ is found to scale as $(\eta_c-\eta)^\beta$ with $\beta\simeq 0.45$

Template coexistence in prebiotic vesicle models

The coexistence of distinct templates is a common feature of the diverse proposals advanced to resolve the information crisis of prebiotic evolution. However, achieving robust template coexistence turned out to be such a difficult demand that only a class of models, the so-called package models, seems to have met it so far. Here we apply Wright's Island formulation of group selection to study the conditions for the coexistence of two distinct template types confined in packages (vesicles) of finite capacity. In particular, we show how selection acting at the level of the vesicles can neutralize the pressures towards the fixation of any one of the template types (random drift) and of the type with higher replication rate (deterministic competition). We give emphasis to the role of the distinct generation times of templates and vesicles as yet another obstacle to coexistence.Comment: 7 pages, 8 figure

20 questions on Adaptive Dynamics

Abstract Adaptive Dynamics is an approach to studying evolutionary change when fitness is density or frequency dependent. Modern papers identifying themselves as using this approach first appeared in the 1990s, and have greatly increased up to the present. However, because of the rather technical nature of many of the papers, the approach is not widely known or understood by evolutionary biologists. In this review we aim to remedy this situation by outlining the methodology and then examining its strengths and weaknesses. We carry this out by posing and answering 20 key questions on Adaptive Dynamics. We conclude that Adaptive Dynamics provides a set of useful approximations for studying various evolutionary questions. However, as with any approximate method, conclusions based on Adaptive Dynamics are valid only under some restrictions that we discuss

Group selection models in prebiotic evolution

The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it The Evolution of Populations and Communities}, Benjamin/Cumings, Menlo Park, 1980) is a mean-field approach in which the actual environment that a particular individual experiences is replaced by an {\it average} environment. That formalism is further developed so as to avoid the mean-field approximation and then applied to the problem of enzyme production in the prebiotic context, where the enzyme producer molecules play the altruists role while the molecules that benefit from the catalyst without paying its production cost play the non-altruists role. The effects of synergism (i.e., division of labor) as well as of mutations are also considered and the results of the equilibrium analysis are summarized in phase diagrams showing the regions of the space of parameters where the altruistic, non-altruistic and the coexistence regimes are stable. In general, those regions are delimitated by discontinuous transition lines which end at critical points.Comment: 22 pages, 10 figure

Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)

BACKGROUND: Garlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not been the subject of either classical breeding or genetic studies. However, recent achievements in fertility restoration in a number of genotypes have led to flowering and seed production, thus enabling genetic studies and breeding in garlic. RESULTS: A transcriptome catalogue of fertile garlic was produced from multiplexed gene libraries, using RNA collected from various plant organs, including inflorescences and flowers. Over 32 million 250-bp paired-end reads were assembled into an extensive transcriptome of 240,000 contigs. An abundant transcriptome assembled separately from 102,000 highly expressed contigs was annotated and analyzed for gene ontology and metabolic pathways. Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers. Analysis of the enriched biological processes and molecular functions revealed characteristic patterns for stress response, flower development and photosynthetic activity. Orthologues of key flowering genes were differentially expressed, not only in reproductive tissues, but also in leaves and bulbs, suggesting their role in flower-signal transduction and the bulbing process. More than 100 variants and isoforms of enzymes involved in organosulfur metabolism were differentially expressed and had organ-specific patterns. In addition to plant genes, viral RNA of at least four garlic viruses was detected, mostly in the roots and cloves, whereas only 1–4% of the reads were found in the foliage leaves. CONCLUSIONS: The de novo transcriptome of fertile garlic represents a new resource for research and breeding of this important crop, as well as for the development of effective molecular markers for useful traits, including fertility and seed production, resistance to pests and neutraceutical characteristics. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1212-2) contains supplementary material, which is available to authorized users

Sex differences in mathematics and reading achievement are inversely related: within- and across-nation assessment of 10 years of PISA data

We analyzed one decade of data collected by the Programme for International Student Assessment (PISA), including the mathematics and reading performance of nearly 1.5 million 15 year olds in 75 countries. Across nations, boys scored higher than girls in mathematics, but lower than girls in reading. The sex difference in reading was three times as large as in mathematics. There was considerable variation in the extent of the sex differences between nations. There are countries without a sex difference in mathematics performance, and in some countries girls scored higher than boys. Boys scored lower in reading in all nations in all four PISA assessments (2000, 2003, 2006, 2009). Contrary to several previous studies, we found no evidence that the sex differences were related to nations’ gender equality indicators. Further, paradoxically, sex differences in mathematics were consistently and strongly inversely correlated with sex differences in reading: Countries with a smaller sex difference in mathematics had a larger sex difference in reading and vice versa. We demonstrate that this was not merely a between-nation, but also a within-nation effect. This effect is related to relative changes in these sex differences across the performance continuum: We did not find a sex difference in mathematics among the lowest performing students, but this is where the sex difference in reading was largest. In contrast, the sex difference in mathematics was largest among the higher performing students, and this is where the sex difference in reading was smallest. The implication is that if policy makers decide that changes in these sex differences are desired, different approaches will be needed to achieve this for reading and mathematics. Interventions that focus on high-achieving girls in mathematics and on low achieving boys in reading are likely to yield the strongest educational benefits