Using multilayer network analysis to explore the temporal dynamics of collective behavior

Social organisms often show collective behaviors such as group foraging or movement.Collective behaviors can emerge from interactions between group members and may depend on the behavior of key individuals.When social interactions change over time,collective behaviors may change because these behaviors emerge from interactions among individuals.Despite the importance of,and growing interest in,the temporal dynamics of social interactions,it is not clear how to quantify changes in interactions over time or measure their stability.Furthermore,the temporal scale at which we should observe changes in social networks to detect biologically meaningful changes is not always apparent.Here we use multilayer network analysis to quantify temporal dynamics of social networks of the social spider Stegodyphus dumicola and determine how these dynamics relate to individual and group behaviors.We found that social interactions changed over time at a constant rate.Variation in both network structure and the identity of a keystone individual was not related to the mean or variance of the collective prey attack speed.Individuals that maintained a large and stable number of connections,despite changes in network structure,were the boldest individuals in the group.Therefore,social interactions and boldness are linked across time,but group collective behavior is not influenced by the stability of the social network.Our work demonstrates that dynamic social networks can be modeled in a multilayer framework.This approach may reveal biologically important temporal changes to social structure in other systems.     

The evolutionary dynamics of evolvability in a gene network model

Evolvability, the ability of populations to adapt, has recently emerged as a major unifying concept in biology. Although the study of evolvability offers new insights into many important biological questions, the conceptual bases of evolvability, and the mechanisms of its evolution, remain controversial. We used simulated evolution of a model of gene network dynamics to test the contentious hypothesis that natural selection can favour high evolvability, in particular in sexual populations. Our results conclusively demonstrate that fluctuating natural selection can increase the capacity of model gene networks to adapt to new environments. Detailed studies of the evolutionary dynamics of these networks establish a broad range of validity for this result and quantify the evolutionary forces responsible for changes in evolvability. Analysis of the genotype–phenotype map of these networks also reveals mechanisms connecting evolvability, genetic architecture and robustness. Our results suggest that the evolution of evolvability can have a pervasive influence on many aspects of organisms.     

我国粘虫周年区域动态规律的监测

【目的】探索我国粘虫Mythimnaseparata(Walker)种群周年北迁南回的动态规律。【方法】2014-2017年分别在全国16、25、24、23个省(市、区)17、28、27、26个县(市、区)设立了17、35、34、31台高空测报灯,系统观测了全年或主要发生期逐日蛾量。【结果】基本掌握了粘虫在我国全年各代发生区域、发生时间和发生数量,为全国区域预报提供了重要依据。【结论】我国华南江南、西南、长江中下游、黄淮、华北、东北和西北等区域是我国粘虫成虫发生区域,每年循环发生5个代次;30?N以南区域诱测到越冬粘虫,27?N及以南的观测点虫量较多,冬季未观测到区域间虫源交流;浙江象山、上海奉贤、江苏东台、山东长岛、河北滦县是粘虫北迁南回的主要路径;华南江南、长江中下游、黄淮、华北、东北等区域间观测到虫源交流,华北和东北地区2代、3代可进行虫源交流;东南亚国家或许为我国提供较多虫源,我国粘虫存在种群重建的可能,这有待于今后进行国际合作、深入研究。     

Using network properties to predict disease dynamics on human contact networks

Recent studies have increasingly turned to graph theory to model more realistic contact structures that characterize disease spread. Because of the computational demands of these methods, many researchers have sought to use measures of network structure to modify analytically tractable differential equation models. Several of these studies have focused on the degree distribution of the contact network as the basis for their modifications. We show that although degree distribution is sufficient to predict disease behaviour on very sparse or very dense human contact networks, for intermediate density networks we must include information on clustering and path length to accurately predict disease behaviour. Using these three metrics, we were able to explain more than 98 per cent of the variation in endemic disease levels in our stochastic simulations.     

Morphology and dynamics of protruding spirochete periplasmic flagella.

We recently characterized the three-dimensional shape of Treponema phagedenis periplasmic flagella (PFs). In the course of these studies, we observed protrusions on swimming cells that resembled PFs. Here we present a detailed characterization of the shape, structure, and motion of these protrusions. Although protrusion formation occurred primarily in wild-type cells during the stationary phase, a large fraction of exponential-phase cells of cell cylinder helicity mutants (greater than 90% of mutant T-52) had protrusions. These results suggest that cells bearing protrusions can still participate in cell division. T. phagedenis protrusions had the identical helix handedness, pitch, and diameter to those of purified PFs. Protrusions were not present on mutants unable to synthesize PFs, but were present in all motile revertants which regained PFs. These results, taken together with electron microscope observations, suggest that protrusions consist of PFs surrounded by an outer membrane sheath. To analyze protrusion movements, we held cells against a coverglass surface with optical tweezers and observed the motion of protrusions by video-enhanced differential interference contrast light microscopy. Protrusions were found to gyrate in both clockwise and counterclockwise directions, and direct evidence was obtained that protrusions rotate. Protrusions were also observed on Treponema denticola and Borrelia burgdorferi. These were also left-handed and had the same helix handedness, pitch, and diameter as purified PFs from their respective species. The PFs from T. denticola had a helix diameter of 0.26 microns and a helix pitch of 0.78 micron; PFs from B. burgdorferi had a helix diameter of 0.28 micron and a helix pitch of 1.48 microns. Protrusions from these spirochete species had similar structures and motion to those of T. phagedenis. Our results present direct evidence that PFs rotate and support previously proposed models of spirochete motility.     

Using large-scale perturbations in gene network reconstruction

Background  

Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative reconstruction method based on a discrete dynamical system model is used to study how microarray experiments involving modulated global perturbations can be designed to obtain reasonably accurate reconstructions. The method is tested on artificial gene networks with biologically realistic in/out degree characteristics.     

Orphan quality control shapes network dynamics and gene expression

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Function and dynamics of PKD2 in Chlamydomonas reinhardtii flagella

To analyze the function of ciliary polycystic kidney disease 2 (PKD2) and its relationship to intraflagellar transport (IFT), we cloned the gene encoding Chlamydomonas reinhardtii PKD2 (CrPKD2), a protein with the characteristics of PKD2 family members. Three forms of this protein (210, 120, and 90 kD) were detected in whole cells; the two smaller forms are cleavage products of the 210-kD protein and were the predominant forms in flagella. In cells expressing CrPKD2-GFP, about 10% of flagellar CrPKD2-GFP was observed moving in the flagellar membrane. When IFT was blocked, fluorescence recovery after photobleaching of flagellar CrPKD2-GFP was attenuated and CrPKD2 accumulated in the flagella. Flagellar CrPKD2 increased fourfold during gametogenesis, and several CrPKD2 RNA interference strains showed defects in flagella-dependent mating. These results suggest that the CrPKD2 cation channel is involved in coupling flagellar adhesion at the beginning of mating to the increase in flagellar calcium required for subsequent steps in mating.     

Epigenome dynamics: a quantitative genetics perspective

Classically, quantitative geneticists have envisioned DNA sequence variants as the only source of heritable phenotypes. This view should be revised in light of accumulating evidence for widespread epigenetic variation in natural and experimental populations. Here we argue that it is timely to consider novel experimental strategies and analysis models to capture the potentially dynamic interplay between chromatin and DNA sequence factors in complex traits.     

Human spermatozoa with large heads and multiple flagella: a quantitative ultrastructural study of 6 cases

Macrocephalic spermatozoa of six men were studied. In all cases, sperm concentration, proportion of live spermatozoa and sperm motility were very low. A range of ultrastructural abnormalities was found, essentially comprising a threefold increase in nuclear volume and acrosomal hyperdevelopment and malformation. There were on average 3.6 flagella for each sperm head found in the semen, some tails were separate from heads. The various defects appeared with great constancy in all of the six cases: this homogeneity indicated the existence of a defined semen profile whose most significant expression was sterility. In four of the cases large incidences of different flagellar abnormalities were also noted; whether these flagellar abnormalities are intrinsic to the above profile is not clear. Although the increase in nuclear volume suggests a disturbance in meiosis, its association with defective nuclear elongation would also indicate the existence of one or more anomalies of spermiogenesis. These results were discussed in relation to abnormalities already reported in other species either spontaneously in cases of mutations, or by experimental inhibition of microtubular structures.     

Human spermatozoa with large heads and multiple flagella: a quantitative ultrastructural study of 6 cases

Macrocephalic spermatozoa of six men were studied. In all cases, sperm concentration, proportion of live spermatozoa and sperm motility were very low. A range of ultrastructural abnormalities was found, essentially comprising a threefold increase in nuclear volume and acrosomal hyperdevelopment and malformation. There were on average 3.6 flagella for each sperm head found in the semen, some tails were separate from heads. The various defects appeared with great constancy in all of the six cases: this homogeneity indicated the existence of a defined semen profile whose most significant expression was sterility. In four of the cases large incidences of different flagellar abnormalities were also noted; whether these flagellar abnormalities are intrinsic to the above profile is not clear. Although the increase in nuclear volume suggests a disturbance in meiosis, its association with defective nuclear elongation would also indicate the existence of one or more anomalies of spermiogenesis. These results were discussed in relation to abnormalities already reported in other species either spontaneously in cases of mutations, or by experimental inhibition of microtubular structures.     

Model with asymptotically stable dynamics for Drosophila gap gene network

We consider a model of gap gene expression during the early development of Drosophila embryo. Parameter values in the model have been obtained by fitting to experimental patterns under an additional condition that the solution be asymptotically stable at large times. The patterns at the beginning of gastrulation in such solutions are very close to an actual attractor in the model. It is shown that such solutions are more robust to perturbations of concentrations and parameter values in the model.