Fluid Forces Enhance the Performance of an Aspirant Leader in Self-Organized Living Groups

In this paper, the performance of an individual aiming at guiding a self-organized group is numerically investigated. A collective behavioural model is adopted, accounting for the mutual repulsion, attraction and orientation experienced by the individuals. Moreover, these represent a set of solid particles which are supposed to be immersed in a fictitious viscous fluid. In particular, the lattice Boltzmann and Immersed boundary methods are used to predict the fluid dynamics, whereas the effect of the hydrodynamic forces on particles is accounted for by solving the equation of the solid motion through the time discontinuous Galerkin scheme. Numerical simulations are carried out by involving the individuals in a dichotomous process. On the one hand, an aspirant leader (AL) additional individual is added to the system. AL is forced to move along a prescribed direction which intersects the group. On the other hand, these tend to depart from an obstacle represented by a rotating lamina which is placed in the fluid domain. A numerical campaign is carried out by varying the fluid viscosity and, as a consequence, the hydrodynamic field. Moreover, scenarios characterized by different values of the size of the group are investigated. In order to estimate the AL''s performance, a proper parameter is introduced, depending on the number of individuals following AL. Present findings show that the sole collective behavioural equations are insufficient to predict the AL''s performance, since the motion is drastically affected by the presence of the surrounding fluid. With respect to the existing literature, the proposed numerical model is enriched by accounting for the presence of the encompassing fluid, thus computing the hydrodynamic forces arising when the individuals move.     

Global Genetic Response in a Cancer Cell: Self-Organized Coherent Expression Dynamics

Understanding the basic mechanism of the spatio-temporal self-control of genome-wide gene expression engaged with the complex epigenetic molecular assembly is one of major challenges in current biological science. In this study, the genome-wide dynamical profile of gene expression was analyzed for MCF-7 breast cancer cells induced by two distinct ErbB receptor ligands: epidermal growth factor (EGF) and heregulin (HRG), which drive cell proliferation and differentiation, respectively. We focused our attention to elucidate how global genetic responses emerge and to decipher what is an underlying principle for dynamic self-control of genome-wide gene expression. The whole mRNA expression was classified into about a hundred groups according to the root mean square fluctuation (rmsf). These expression groups showed characteristic time-dependent correlations, indicating the existence of collective behaviors on the ensemble of genes with respect to mRNA expression and also to temporal changes in expression. All-or-none responses were observed for HRG and EGF (biphasic statistics) at around 10–20 min. The emergence of time-dependent collective behaviors of expression occurred through bifurcation of a coherent expression state (CES). In the ensemble of mRNA expression, the self-organized CESs reveals distinct characteristic expression domains for biphasic statistics, which exhibits notably the presence of criticality in the expression profile as a route for genomic transition. In time-dependent changes in the expression domains, the dynamics of CES reveals that the temporal development of the characteristic domains is characterized as autonomous bistable switch, which exhibits dynamic criticality (the temporal development of criticality) in the genome-wide coherent expression dynamics. It is expected that elucidation of the biophysical origin for such critical behavior sheds light on the underlying mechanism of the control of whole genome.     

Dictyostelium discoideum CenB Is a Bona Fide Centrin Essential for Nuclear Architecture and Centrosome Stability

Centrins are a family of proteins within the calcium-binding EF-hand superfamily. In addition to their archetypical role at the microtubule organizing center (MTOC), centrins have acquired multiple functionalities throughout the course of evolution. For example, centrins have been linked to different nuclear activities, including mRNA export and DNA repair. Dictyostelium discoideum centrin B is a divergent member of the centrin family. At the amino acid level, DdCenB shows 51% identity with its closest relative and only paralog, DdCenA. Phylogenetic analysis revealed that DdCenB and DdCenA form a well-supported monophyletic and divergent group within the centrin family of proteins. Interestingly, fluorescently tagged versions of DdCenB were not found at the centrosome (in whole cells or in isolated centrosomes). Instead, DdCenB localized to the nuclei of interphase cells. This localization disappeared as the cells entered mitosis, although Dictyostelium cells undergo a closed mitosis in which the nuclear envelope (NE) does not break down. DdCenB knockout cells exhibited aberrant nuclear architecture, characterized by enlarged and deformed nuclei and loss of proper centrosome-nucleus anchoring (observed as NE protrusions). At the centrosome, loss of DdCenB resulted in defects in the organization and morphology of the MTOC and supernumerary centrosomes and centrosome-related bodies. The multiple defects that the loss of DdCenB generated at the centrosome can be explained by its atypical division cycle, transitioning into the NE as it divides at mitosis. On the basis of these findings, we propose that DdCenB is required at interphase to maintain proper nuclear architecture, and before delocalizing from the nucleus, DdCenB is part of the centrosome duplication machinery.Centrins (also known as caltractins) are small calcium-binding proteins of the EF-hand superfamily and are thought to have diversified by gene duplication (37). The first centrin was discovered in the unicellular green algae Tetraselmis striata more than 20 years ago (45). Since then, members of this family of proteins have been found in groups as diverse as yeasts, insects, plants, and humans, making these proteins essentially ubiquitous among eukaryotic cells (55). Furthermore, centrins have been included within the 347 “eukaryotic signature proteins” that are thought to be indispensable for the eukaryotic cell and share no similarities with prokaryotic proteins (21). Many lower eukaryotes have a single centrin gene (e.g., Saccharomyces cerevisiae and Chlamydomonas reinhardtii); however, up to three or four centrin paralogs have been found in higher eukaryotes (e.g., Xenopus laevis, Mus musculus, and Homo sapiens). Centrins have a high level of structural resemblance to calmodulin, exhibiting the characteristic two globular domains interconnected by a linker loop. Each globular domain in turn contains two helix-loop-helix motifs that, in calmodulins, bind calcium ions. However, in many centrins these motifs are slightly modified, and not all four of them have affinity for calcium in the normal range associated with signal transduction (33).Throughout the course of evolution, centrins have acquired multiple functionalities in addition to the archetypical role at the microtubule organizing center (MTOC). For example, the centrin of the flagellated green algae C. reinhardtii (CrCen) localizes to the basal bodies, to the fibers that interconnect the basal bodies and the nucleus, and to the axoneme. CrCen is required for normal basal body replication, segregation, and maturation (26). In addition, it plays an active role in the contraction of MTOC-related fibers (47, 57) and regulates the activity of the inner dynein arm in a calcium-regulated fashion (30).In the budding yeast Saccharomyces cerevisiae, centrin (ScCDC31) localizes primarily to a specialized region of the nuclear envelope (NE) called the half bridge (49), which is in close proximity to the MTOC (known as the spindle pole body [SPB]). Conditional mutants of ScCDC31 show cell cycle arrest and failure to duplicate the SPB (23, 49). CDC31 also binds the NEF2 complex and is required for efficient nucleotide excision repair. CDC31 mutants unable to bind to the complex showed an increased sensitivity to UV (1). In addition, CDC31 is involved in mRNA export through its interaction with SAC3 at the nuclear pore (11). Mammalian cells typically have four centrin paralogs; however, human cells express only three (HsCen1 to -3) and the fourth is a pseudogene (gene ID, 729338) (9, 13, 31, 36). All human centrins show partial localization at the centrioles, in a tissue-specific fashion (HsCen1) or ubiquitously (HsCen2 and -3) (29, 56). Knockdown of HsCen2 inhibits centriole duplication and induces cell division arrest in HeLa cells (46). Additionally, HsCen2 was shown to play a role similar to that of CDC31 in stimulating nucleotide excision repair by binding to xeroderma pigmentosum group C protein (38).The social amoeba Dictyostelium discoideum has emerged as a powerful model organism, in part because it is haploid, it is easy to propagate, and its genome has been recently completed (4, 8, 25). D. discoideum cells undergo a closed mitosis during which the NE remains intact. They also have multiple modes of cytokinesis (53), making them a very useful model for studying the cell division machinery. These cells lack basal bodies and have acentriolar centrosomes that are similar in their trilaminar core structure to yeast SPBs (17). However, D. discoideum interphase centrosomes are not embedded in the NE but are attached to it, and they are surrounded by a centrosomal corona analogous to the pericentriolar material of animal cell centrosomes (4). Centrosomal duplication in D. discoideum involves extensive structural changes and is synchronized with mitosis. It begins at early prophase, by increasing its size to about twice that of an interphase centrosome. At the prophase-prometaphase transition, the corona and the fibrous link to the nucleus are disassembled. This is followed by the insertion of the core into the NE. By metaphase, the two outer layers have come apart and migrated to opposite ends of the cell nucleus, where they organize the spindle. The anaphase-telophase transition marks the beginning of centrosomal maturation. The outer layers fold back into themselves, inducing the formation of a middle layer and a corona, and returning to the size of an interphase centrosome. Finally, the two maturing centrosomes transition out of the NE at the end of mitosis and reform the fibrous link that connects them to the NE (17, 52). It has recently been shown that the D. discoideum Sun1 protein is a key component of the fibrous link that bridges and anchors the centrosome to the cell nucleus (58). DdSun1 predominantly localizes to the nuclear membrane and links chromatin to other components of the fibrous link. Truncation or knockdown of DdSun1 promotes separation of the inner and outer NE membranes, inducing aberrant nuclear morphology and loss of the nucleus-centrosome connection (observed as protrusions of the outer NE membrane). Additionally, cells develop supernumerary centrosomes and aberrant spindles, leading to poor chromosome segregation. All this suggests that the centrosome-nucleus link is of extreme importance in maintaining the genetic stability of the cell.D. discoideum has two known centrin proteins, DdCenA (originally named DdCrp) and DdCenB. The initial characterization of DdCenA describes a very divergent centrin that localizes to the centrosomal corona and to the nucleus (5). The second centrin protein, known as DdCenB, was originally identified as a putative member of the centrin family based on sequence similarity by the Dictyostelium Genome Consortium and remained uncharacterized until now. In this work, we report the initial characterization of DdCenB, including molecular cloning, sequence analysis, cellular localization, and analysis of functional roles.     

Self-Organized Shape and Frontal Density of Fish Schools

Models of swarming (based on avoidance, alignment and attraction) produce patterns of behaviour also seen in schools of fish. However, the significance of such similarities has been questioned, because some model assumptions are unrealistic [e.g. speed in most models is constant with random error, the perception is global and the size of the schools that have been studied is small (up to 128 individuals)]. This criticism also applies to our former model, in which we demonstrated the emergence of two patterns of spatial organization, i.e. oblong school form and high frontal density, which are supposed to function as protection against predators. In our new model we respond to this criticism by making the following improvements: individuals have a preferred ‘cruise speed’ from which they can deviate in order to avoid others or to catch up with them. Their range of perception is inversely related to density, with which we take into account that high density limits the perception of others that are further away. Swarm sizes range from 10 to 2000 individuals. The model is three‐dimensional. Further, we show that the two spatial patterns (oblong shape and high frontal density) emerge by self‐organization as a side‐effect of coordination at two speeds (of two or four body lengths per second) for schools of sizes above 20. Our analysis of the model leads to the development of a new set of hypotheses. If empirical data confirm these hypotheses, then in a school of real fish these patterns may arise as a side‐effect of their coordination in the same way as in the model.     

Evolution of Self-Organized Task Specialization in Robot Swarms

Division of labor is ubiquitous in biological systems, as evidenced by various forms of complex task specialization observed in both animal societies and multicellular organisms. Although clearly adaptive, the way in which division of labor first evolved remains enigmatic, as it requires the simultaneous co-occurrence of several complex traits to achieve the required degree of coordination. Recently, evolutionary swarm robotics has emerged as an excellent test bed to study the evolution of coordinated group-level behavior. Here we use this framework for the first time to study the evolutionary origin of behavioral task specialization among groups of identical robots. The scenario we study involves an advanced form of division of labor, common in insect societies and known as “task partitioning”, whereby two sets of tasks have to be carried out in sequence by different individuals. Our results show that task partitioning is favored whenever the environment has features that, when exploited, reduce switching costs and increase the net efficiency of the group, and that an optimal mix of task specialists is achieved most readily when the behavioral repertoires aimed at carrying out the different subtasks are available as pre-adapted building blocks. Nevertheless, we also show for the first time that self-organized task specialization could be evolved entirely from scratch, starting only from basic, low-level behavioral primitives, using a nature-inspired evolutionary method known as Grammatical Evolution. Remarkably, division of labor was achieved merely by selecting on overall group performance, and without providing any prior information on how the global object retrieval task was best divided into smaller subtasks. We discuss the potential of our method for engineering adaptively behaving robot swarms and interpret our results in relation to the likely path that nature took to evolve complex sociality and task specialization.     

The Architecture and Chemical Stability of the Archaeal Sulfolobus Turreted Icosahedral Virus

Viruses utilize a diverse array of mechanisms to deliver their genomes into hosts. While great strides have been made in understanding the genome delivery of eukaryotic and prokaryotic viruses, little is known about archaeal virus genome delivery and the associated particle changes. The Sulfolobus turreted icosahedral virus (STIV) is a double-stranded DNA (dsDNA) archaeal virus that contains a host-derived membrane sandwiched between the genome and the proteinaceous capsid shell. Using cryo-electron microscopy (cryo-EM) and different biochemical treatments, we identified three viral morphologies that may correspond to biochemical disassembly states of STIV. One of these morphologies was subtly different from the previously published 27-Å-resolution electron density that was interpreted with the crystal structure of the major capsid protein (MCP). However, these particles could be analyzed at 12.5-Å resolution by cryo-EM. Comparing these two structures, we identified the location of multiple proteins forming the large turret-like appendages at the icosahedral vertices, observed heterogeneous glycosylation of the capsid shell, and identified mobile MCP C-terminal arms responsible for tethering and releasing the underlying viral membrane to and from the capsid shell. Collectively, our studies allow us to propose a fusogenic mechanism of genome delivery by STIV, in which the dismantled capsid shell allows for the fusion of the viral and host membranes and the internalization of the viral genome.Viruses are valuable biological tools for manipulating the cellular processes of their hosts, and they can also serve as model systems for describing macromolecular interactions through the analysis of their architecture. The Sulfolobus turreted icosahedral virus (STIV) is an archaeal virus that infects Sulfolobus solfataricus (phylum Crenarchaeota). STIV is a lytic virus that was isolated from an acidic hot spring (>80°C and pH of <3) in Yellowstone National Park (27). Hence, STIV is an important model for studying the biochemical requirements to sustain life in extreme physicochemical conditions and has the potential to become a tool for the biochemical and genetic manipulation of its host—much like bacteriophages lambda, P22, and phi29 have done for their respective hosts.Prior structural studies of STIV using cryo-electron microscopy (cryo-EM), X-ray crystallography, and proteomics have described large pentameric turret-like structures, with petal-like protrusions emanating from their central shafts (27). The T=31d capsid shell is composed of trimeric capsomers exhibiting pseudo-hexagonal symmetry, in which each of the three capsomer subunits donates two viral jelly rolls with its β-sheets normal to the capsid surface (15, 27). Capsomers surrounding the icosahedral 3-fold axes, and their neighboring subunits, make direct contact with the viral membrane via a highly basic C-terminal helix of each subunit (15, 23). Surrounding the base of the turrets are proteins that make contact with the capsid shell and a host-derived viral membrane (15). The viral membrane and the enclosed viral genome are referred to as the lipid core.The capsid architecture of STIV and the crystal structure of its major capsid protein (MCP) are strikingly similar to those of the bacteriophages PRD1, Bam35, and PM2, the alga virus PBCV-1, and the mammalian adenovirus. This similarity suggests that these viruses share an ancestral virus (2, 4, 7, 15, 25). Given the evolutionary relationship shared between STIV and PRD1, we postulated that the large turret-like vertices of STIV were used to inject the viral genome into the Sulfolobus host—a genome delivery mechanism employed by PRD1 (27).A recent report by Brumfield et al. (5) describes gross cellular ultrastructural changes induced in the Sulfolobus host during STIV infection and release. The authors identified distinct particles that appear to be assembly intermediates of STIV en route to maturation. From these intermediates the authors proposed a general mechanism of capsid assembly, in which MCP subunits and minor capsid proteins (mCPs) coassemble with the lipid membrane to form a lipid-enclosed protein vesicle. These vesicles are spherical and lack the double-stranded DNA (dsDNA) genome and turret-like appendages at the vertices.While these studies confirm an empty procapsid intermediate, the corresponding molecular mechanism associated with assembly and disassembly remains to be understood. Moreover, little is known about STIV or other archaeal virus genome delivery into the host. To obtain a better understanding of the molecular mechanism of STIV architecture and its role in genome delivery, we characterized three distinct morphologies of STIV particles using cryo-EM. An image reconstruction of one of these revealed the absence of a number of constituents decorating the STIV capsid. Hence, for simplicity, we refer to the previously reported image reconstruction (27) as “decorated” and the new image reconstruction reported here as “undecorated.” Reference-free two-dimensional (2D) class averages of the second identified morphology reveal a partially decorated STIV lipid core. The third identified morphology corresponds to the isolated STIV lipid core. Taken together, our analyses indicate that these morphologies correspond to different disassembly intermediates of STIV that can be isolated in vitro and help provide a picture of the STIV capsid architecture. Additionally, these morphologies allow us to propose an alternative possible mechanism of genome delivery.     

Living a Fast Life

The current research applied a mid-level evolutionary theory that has been successfully employed across numerous animal species—life history theory—in an attempt to understand the Dark Triad personality trait cluster (narcissism, psychopathy, and Machiavellianism). In Study 1 (N = 246), a measure of life history strategy was correlated with psychopathy, but unexpectedly with neither Machiavellianism nor narcissism. Study 2 (N = 321) replicated this overall pattern of results using longer, traditional measures of the Dark Triad traits and alternative, future-discounting indicators of life history strategy (a smaller-sooner, larger-later monetary dilemma and self-reported risk-taking behaviors). Additional findings suggested two sources of shared variance across the Dark Triad traits: confidence in predicting future outcomes and openness to short-term mating.     

Energy Confinement in Self-Organized Tokamak Plasma (without Transport Barriers)

Plasma Physics Reports - The phenomenon of improved energy confinement during radiative cooling at the plasma edge was studied experimentally in the T-10 tokamak. It was shown that the effect is...     

Importance of Reproducibility in Responsiveness Issues

In cohort studies, longitudinal changes in individuals are often studied. The sample size requirements are then directly related to the responsiveness of the measuring instrument/scale, which is defined as the ability to detect a clinically meaningful change over time. We demonstrate that whatever the index used to assess responsiveness (effect size, standardized response mean, Guyatt's index), it is enhanced by an increase in the intraclass correlation coefficient (ICC), which assesses the reproducibility of the measuring instrument/scale. Therefore, an improvement in reproducibility leads to an increase in responsiveness and thus an increase in power. In the special case of one observation per subject and time, we also prove that an increase in the ICC reduces the coefficient of variation of the estimators of the standardized response mean and of Guyatt's index. This result has also been observed for the effect size on an example. Such a result implies that the better the reproducibility, the lower the sample size requirements for confident statistical inference of responsiveness results.     

A Model of Speciation Preconditions in Terms of Percolation and Self-Organized Criticality Theories

Biophysics - Several models have been considered: those that describe mutation fixation in asexually or sexually reproducing species during speciation and are based on stochastic processes and a...