Enhancement of the stability of genetic switches by overlapping upstream regulatory domains

We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterised by a well defined lifetime which grows sub-exponentially with the number of copies of the most-expressed transcription factor, in the regime accessible by our numerical simulations. The stability can be markedly enhanced by a suitable choice of overlap between the upstream regulatory domains. Our results suggest that robustness against biochemical noise can provide a selection pressure that drives operons, that regulate each other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX

A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters and is particularly well-suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation and demonstrate the utility of the method via illustrative examples.Comment: v4: 12 pages, 5 figures, final accepted version. Error found and fixed in Appendi

The JJ Shuttle and In-Game Defensive Basketball Performance for Collegiate Male Players

Agility is widely considered an important skill related fitness component in the game of basketball. Players are tasked to execute successful and efficient accelerations, sprints, abrupt stops, quick changes of direction, varying vertical jumps, and many times a combination of these motor skills. Agility can greatly impact the skills required for an athlete to excel on the court. The purpose of this study was to investigate how the agility of basketball players affected their in-game performance during regular season conference contests. The subjects (N = 10) in this study were members of a collegiate men’s basketball team. Agility of the subjects were measured using the JJ Shuttle which produces four segment times and a total time. These five shuttle times were compared for correlation to their in-game performance during regular season conference play. Performance measures of interest were steals, blocks, and defensive rebounds. A Pearson Correlation was conducted between the JJ Shuttle time segments and total time and the steals, blocks, and defensive rebounds of each player. There was a positive correlation between the duration of Segment 3 of the JJ Shuttle and the number of blocks (r = 0.65, p \u3c 0.05). The results of this study suggest the agility of male collegiate basketball players, as measured by the JJ Shuttle, does not have a strong correlation and is a poor predictor of the in-game performance of steals, blocks, and defensive rebounds. It is suggested that future studies increase the sample size and expand the subject parameters to determine a more holistic representation of this relationship

Spider webs, stable isotopes and molecular gut content analysis: Multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders

1.Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival.2.We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web-building and the other actively hunting, which co-occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both: (a) among species within a clade, indicating food resource partitioning, and (b) between the two clades, corresponding to their differences in foraging strategy.3.To assess niches of the spider species, we measure: (a) web architecture, the structure of the hunting tool, and (b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring (c) stable isotope signatures of carbon and nitrogen in the spiders\u27 tissues, and (d) gut content of spiders based on metabarcoding data.4.We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web-building species, as well as significant isotopic differences between web-builders and active hunters. Gut content data also show interspecific and inter-clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature.5.Our results reveal trophic niche partitioning among species within each clade, as well as between the web-building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders\u27 tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha

On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models

This paper presents an on-the-fly uniformization technique for the analysis of time-inhomogeneous Markov population models. This technique is applicable to models with infinite state spaces and unbounded rates, which are, for instance, encountered in the realm of biochemical reaction networks. To deal with the infinite state space, we dynamically maintain a finite subset of the states where most of the probability mass is located. This approach yields an underapproximation of the original, infinite system. We present experimental results to show the applicability of our technique

Error threshold in finite populations

A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage disequilibrium at the population level is neglected. In particular, for the single-sharp-peak replication landscape we investigate the dependence of the error threshold on the population size and find that the replication accuracy at threshold increases linearly with the reciprocal of the population size for sufficiently large populations. Furthermore, in the deterministic limit our formulation yields the exact steady-state of the quasispecies model, indicating then the population composition is a random combination of the molecules.Comment: 14 pages and 4 figure

Lack of self-averaging in neutral evolution of proteins

We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in sequence space which share two universal features for all of the examined proteins. First, the number of neutral mutations fluctuates broadly from one sequence to another, leading to a non-Poissonian substitution process. Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process.Comment: 4 pages, 2 figure

Thermal noise in half infinite mirrors with non-uniform loss: a slab of excess loss in a half infinite mirror

We calculate the thermal noise in half-infinite mirrors containing a layer of arbitrary thickness and depth made of excessively lossy material but with the same elastic material properties as the substrate. For the special case of a thin lossy layer on the surface of the mirror, the excess noise scales as the ratio of the coating loss to the substrate loss and as the ratio of the coating thickness to the laser beam spot size. Assuming a silica substrate with a loss function of 3x10-8 the coating loss must be less than 3x10-5 for a 6 cm spot size and a 7 micrometers thick coating to avoid increasing the spectral density of displacement noise by more than 10%. A similar number is obtained for sapphire test masses.Comment: Passed LSC (internal) review. Submitted to Phys. Rev. D. (5/2001) Replacement: Minor typo in Eq. 17 correcte

The interplay of intrinsic and extrinsic bounded noises in genetic networks

After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a genetic network. The influence of intrinsic and extrinsic noises on genetic networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: $(i)$ the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, $(ii)$ a model of enzymatic futile cycle and $(iii)$ a genetic toggle switch. In $(ii)$ and $(iii)$ we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possibile functional role of bounded noises

A jump-growth model for predator-prey dynamics: derivation and application to marine ecosystems

This paper investigates the dynamics of biomass in a marine ecosystem. A stochastic process is defined in which organisms undergo jumps in body size as they catch and eat smaller organisms. Using a systematic expansion of the master equation, we derive a deterministic equation for the macroscopic dynamics, which we call the deterministic jump-growth equation, and a linear Fokker-Planck equation for the stochastic fluctuations. The McKendrick--von Foerster equation, used in previous studies, is shown to be a first-order approximation, appropriate in equilibrium systems where predators are much larger than their prey. The model has a power-law steady state consistent with the approximate constancy of mass density in logarithmic intervals of body mass often observed in marine ecosystems. The behaviours of the stochastic process, the deterministic jump-growth equation and the McKendrick--von Foerster equation are compared using numerical methods. The numerical analysis shows two classes of attractors: steady states and travelling waves.Comment: 27 pages, 4 figures. Final version as published. Only minor change