Long-lived Giant Number Fluctuations in a Swarming Granular Nematic

Coherently moving flocks of birds, beasts or bacteria are examples of living matter with spontaneous orientational order. How do these systems differ from thermal equilibrium systems with such liquid-crystalline order? Working with a fluidized monolayer of macroscopic rods in the nematic liquid crystalline phase, we find giant number fluctuations consistent with a standard deviation growing linearly with the mean, in contrast to any situation where the Central Limit Theorem applies. These fluctuations are long-lived, decaying only as a logarithmic function of time. This shows that flocking, coherent motion and large-scale inhomogeneity can appear in a system in which particles do not communicate except by contact.Comment: This is the author's version of the work. It is posted here by permission of the AAAS. The definitive version is to appear in SCIENC

Active contractility in actomyosin networks

Contractile forces are essential for many developmental processes involving cell shape change and tissue deformation. Recent experiments on reconstituted actomyosin networks, the major component of the contractile machinery, have shown that active contractility occurs above a threshold motor concentration and within a window of crosslink concentration. We present a microscopic dynamic model that incorporates two essential aspects of actomyosin self-organization: the asymmetric load response of individual actin filaments and the correlated motor-driven events mimicking myosin-induced filament sliding. Using computer simulations we examine how the concentration and susceptibility of motors contribute to their collective behavior and interplay with the network connectivity to regulate macroscopic contractility. Our model is shown to capture the formation and dynamics of contractile structures and agree with the observed dependence of active contractility on microscopic parameters including the contractility onset. Cooperative action of load-resisting motors in a force-percolating structure integrates local contraction/buckling events into a global contractile state via an active coarsening process, in contrast to the flow transition driven by uncorrelated kicks of susceptible motors.Comment: 15 pages, 4 main figures, 4 supplementary figure

Elastic properties of grafted microtubules

We use single-particle tracking to study the elastic properties of single microtubules grafted to a substrate. Thermal fluctuations of the free microtubule's end are recorded, in order to measure position distribution functions from which we calculate the persistence length of microtubules with contour lengths between 2.6 and 48 micrometers. We find the persistence length to vary by more than a factor of 20 over the total range of contour lengths. Our results support the hypothesis that shearing between protofilaments contributes significantly to the mechanics of microtubules.Comment: 9 pages, 3 figure

Frozen steady states in active systems

Even simple active systems can show a plethora of intriguing phenomena and often we find complexity were we would have expected simplicity. One striking example is the occurrence of a quiescent or absorbing state with frozen fluctuations that at first sight seems to be impossible for active matter driven by the incessant input of energy. While such states were reported for externally driven systems through macroscopic shear or agitation, the investigation of frozen active states in inherently active systems like cytoskeletal suspensions or active gels is still at large. Using high density motility assay experiments, we demonstrate that frozen steady states can arise in active systems if active transport is coupled to growth processes. The experiments are complemented by agent-based simulations which identify the coupling between self-organization, growth and mechanical properties to be responsible for the pattern formation process

Diffusion on networked systems is a question of time or structure

Network science investigates the architecture of complex systems to understand their functional and dynamical properties. Structural patterns such as communities shape diffusive processes on networks. However, these results hold under the strong assumption that networks are static entities where temporal aspects can be neglected. Here we propose a generalized formalism for linear dynamics on complex networks, able to incorporate statistical properties of the timings at which events occur. We show that the diffusion dynamics is affected by the network community structure and by the temporal properties of waiting times between events. We identify the main mechanism—network structure, burstiness or fat tails of waiting times—determining the relaxation times of stochastic processes on temporal networks, in the absence of temporal–structure correlations. We identify situations when fine-scale structure can be discarded from the description of the dynamics or, conversely, when a fully detailed model is required due to temporal heterogeneities

Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries

The nuclear topography of splicing snRNPs, mRNA transcripts and chromosome domains in various mammalian cell types are described. The visualization of splicing snRNPs, defined by the Sm antigen, and coiled bodies, revealed distinctly different distribution patterns in these cell types. Heat shock experiments confirmed that the distribution patterns also depend on physiological parameters. Using a combination of fluorescencein situ hybridization and immunodetection protocols, individual chromosome domains were visualized simultaneously with the Sm antigen or the transcript of an integrated human papilloma virus genome. Three-dimensional analysis of fluorescence-stained target regions was performed by confocal laser scanning microscopy. RNA transcripts and components of the splicing machinery were found to be generally excluded from the interior of the territories occupied by the individual chromosomes. Based on these findings we present a model for the functional compartmentalization of the cell nucleus. According to this model the space between chromosome domains, including the surface areas of these domains, defines a three-dimensional network-like compartment, termed the interchromosome domain (ICD) compartment, in which transcription and splicing of mRNA occurs

Connecting Network Properties of Rapidly Disseminating Epizoonotics

To effectively control the geographical dissemination of infectious diseases, their properties need to be determined. To test that rapid microbial dispersal requires not only susceptible hosts but also a pre-existing, connecting network, we explored constructs meant to reveal the network properties associated with disease spread, which included the road structure.Using geo-temporal data collected from epizoonotics in which all hosts were susceptible (mammals infected by Foot-and-mouth disease virus, Uruguay, 2001; birds infected by Avian Influenza virus H5N1, Nigeria, 2006), two models were compared: 1) 'connectivity', a model that integrated bio-physical concepts (the agent's transmission cycle, road topology) into indicators designed to measure networks ('nodes' or infected sites with short- and long-range links), and 2) 'contacts', which focused on infected individuals but did not assess connectivity.THE CONNECTIVITY MODEL SHOWED FIVE NETWORK PROPERTIES: 1) spatial aggregation of cases (disease clusters), 2) links among similar 'nodes' (assortativity), 3) simultaneous activation of similar nodes (synchronicity), 4) disease flows moving from highly to poorly connected nodes (directionality), and 5) a few nodes accounting for most cases (a "20:80" pattern). In both epizoonotics, 1) not all primary cases were connected but at least one primary case was connected, 2) highly connected, small areas (nodes) accounted for most cases, 3) several classes of nodes were distinguished, and 4) the contact model, which assumed all primary cases were identical, captured half the number of cases identified by the connectivity model. When assessed together, the synchronicity and directionality properties explained when and where an infectious disease spreads.Geo-temporal constructs of Network Theory's nodes and links were retrospectively validated in rapidly disseminating infectious diseases. They distinguished classes of cases, nodes, and networks, generating information usable to revise theory and optimize control measures. Prospective studies that consider pre-outbreak predictors, such as connecting networks, are recommended

Poly-β-hydroxybutyrate administration during early life: effects on performance, immunity and microbial community of European sea bass yolk-sac larvae

The reliable production of marine fish larvae is one of the major bottlenecks in aquaculture due to high mortalities mainly caused by infectious diseases. To evaluate if the compound poly-β-hydroxybutyrate (PHB) might be a suitable immunoprophylactic measure in fish larviculture, its capacity to improve immunity and performance in European sea bass (Dicentrarchus labrax) yolk-sac larvae was explored. PHB was applied from mouth opening onwards to stimulate the developing larval immune system at the earliest possible point in time. Larval survival, growth, microbiota composition, gene expression profiles and disease resistance were assessed. PHB administration improved larval survival and, furthermore, altered the larva-associated microbiota composition. The bacterial challenge test using pathogenic Vibrio anguillarum revealed that the larval disease resistance was not influenced by PHB. The expression profiles of 26 genes involved e.g. in the immune response showed that PHB affected the expression of the antimicrobial peptides ferritin (fer) and dicentracin (dic), however, the response to PHB was inconsistent and weaker than previously demonstrated for sea bass post-larvae. Hence, the present study highlights the need for more research focusing on the immunostimulation of different early developmental stages for gaining a more comprehensive picture and advancing a sustainable production of high quality fry

Time varying networks and the weakness of strong ties

In most social and information systems the activity of agents generates rapidly evolving time-varying networks. The temporal variation in networks' connectivity patterns and the ongoing dynamic processes are usually coupled in ways that still challenge our mathematical or computational modelling. Here we analyse a mobile call dataset and find a simple statistical law that characterize the temporal evolution of users' egocentric networks. We encode this observation in a reinforcement process defining a time-varying network model that exhibits the emergence of strong and weak ties. We study the effect of time-varying and heterogeneous interactions on the classic rumour spreading model in both synthetic, and real-world networks. We observe that strong ties severely inhibit information diffusion by confining the spreading process among agents with recurrent communication patterns. This provides the counterintuitive evidence that strong ties may have a negative role in the spreading of information across networks

Changes in the geographical distribution of plant species and climatic variables on the West Cornwall peninsula (South West UK)

Recent climate change has had a major impact on biodiversity and has altered the geographical distribution of vascular plant species. This trend is visible globally; however, more local and regional scale research is needed to improve understanding of the patterns of change and to develop appropriate conservation strategies that can minimise cultural, health, and economic losses at finer scales. Here we describe a method to manually geo-reference botanical records from a historical herbarium to track changes in the geographical distributions of plant species in West Cornwall (South West England) using both historical (pre-1900) and contemporary (post-1900) distribution records. We also assess the use of Ellenberg and climate indicator values as markers of responses to climate and environmental change. Using these techniques we detect a loss in 19 plant species, with 6 species losing more than 50% of their previous range. Statistical analysis showed that Ellenberg (light, moisture, nitrogen) and climate indicator values (mean January temperature, mean July temperature and mean precipitation) could be used as environmental change indicators. Significantly higher percentages of area lost were detected in species with lower January temperatures, July temperatures, light, and nitrogen values, as well as higher annual precipitation and moisture values. This study highlights the importance of historical records in examining the changes in plant species’ geographical distributions. We present a method for manual geo-referencing of such records, and demonstrate how using Ellenberg and climate indicator values as environmental and climate change indicators can contribute towards directing appropriate conservation strategies