Three-Dimensional Numerical Simulations of Biofilm Dynamics with Quorum Sensing in a Flow Cell

We develop a multiphasic hydrodynamic theory for biofilms taking into account interactions among various bacterial phenotypes, extracellular polymeric substance (EPS), quorum sensing (QS) molecules, solvent, and antibiotics. In the model, bacteria are classified into down-regulated QS, up-regulated QS, and non-QS cells based on their QS ability. The model is first benchmarked against an experiment yielding an excellent fit to experimental measurements on the concentration of QS molecules and the cell density during biofilm development. It is then applied to study development of heterogeneous structures in biofilms due to interactions of QS regulation, hydrodynamics, and antimicrobial treatment. Our 3D numerical simulations have confirmed that (i). QS is beneficial for biofilm development in a long run by building a robust EPS population to protect the biofilm; (ii). biofilms located upstream can induce QS downstream when the colonies are close enough spatially; (iii). QS induction may not be fully operational and can even be compromised in strong laminar flows; (v). the hydrodynamic stress alters the biofilm morphology. Through further numerical investigations, our model suggests that (i). QS-regulated EPS production contributes to the structural formation of heterogeneous biofilms; (ii) QS down-regulated cells tend to grow at the surface of the biofilm while QS up-regulated ones tend to grow in the bulk; (iii) when nutrient supply is sufficient, QS induction might be more effective upstream than downstream; (iv) QS may be of little benefit in a short timescale in term of fighting against invading strain/species; (v) the material properties of biomass (bacteria and EPS) have strong impact on the dilution of QS molecules under strong shear flow. In addition, with this modeling framework, hydrodynamic details and rheological quantities associated with biofilm formation under QS regulation can be resolved.     

Moving from Complaints to Action: Oppositional Consciousness and Collective Action in a Political Community

This article analyzes the process of youth political activism and development by drawing on ethnographic research on Asian and Pacific Islander youth activists. Young people revealed that collective action begins with a critical analysis of their lived experiences with inequalities. Their actions also involved oppositional consciousness that was nurtured in social justice-oriented community organizations. Tracking youth's successful efforts for school reform, I show how oppositional consciousness is realized and what activism looks like in practice.  [youth activism, oppositional consciousness, social–educational change, Asian and Pacific Islanders]     

Complex Dynamics Based on a Quorum: Decision-Making Process by Cockroaches in a Patchy Environment

In the absence of complex communication and a global knowledge of the environment, cockroaches are able to assess the availability of resources and to reach a consensual decision: the group aggregates in a single resting site. We show that the aggregation dynamics and the collective shelter selection of cockroaches are influenced by their social context as, unlike single individuals, groups of cockroaches are more likely to respond to environmental heterogeneities. The decision of individuals to stay under a shelter relies on the modulation of their resting time, according to the perception of two local cues: (1) the shelters luminosity and (2) the number of congeners. This study on the cockroach species Periplaneta americana highlights a shelter-selection mechanism based on an amplification process resulting from the interactions between congeners. This mechanism leads to complex spatiotemporal aggregation dynamics characterized by transient bimodality, bifurcation patterns (shelter selection) and the existence of a quorum size in the settlement behaviour of the cockroaches. Finally, we discuss the generic aspect for other gregarious species of the collective decision-making process demonstrated for cockroaches.     

Quorum Sensing Signaling Molecules Involved in the Production of Violacein by Pseudoalteromonas

The production of violacein by Pseudoalteromonas sp. 520P1 has many features of quorum sensing. Signaling molecules were extracted from bacterial culture and subsequently identified as N-(3-oxooctanoyl)-homoserine lactone and N-tetradecanoyl-homoserine lactone. The former but not the latter induced the production of violacein in strain 520P1. We conclude that N-(3-oxooctanoyl)-homoserine lactone is a signaling molecule involved in the production of violacein.     

Adenylyl Cyclase Signaling Mechanism of Relaxin Action

In connection with our discovery of the adenylyl cyclase signaling mechanism (ACSM) of action of some peptides belonging to the insulin superfamily, a possibility of its involvement in action of another insulin superfamily peptide, relaxin, was studied. It was shown for the first time that human relaxin-2 (10^–12–10^–8 M) activated adenylyl cyclase (AC) in a dose-dependent manner. The maximal peptide effect was revealed at a concentration of 10^–8 M. Under condition of the hormonal action the basal enzyme activity increased by +310% in human myometrium, by +117%, in rat skeletal muscles, and by +49%, in foot smooth muscles of the bivalve mollusc Anodonta cygnea. Insulin and mammalian insulin-like growth factor-I (IGF-I) also produced the AC activating effect in these muscles. The order of efficiency of these peptides, based on their ability to induce the maximal AC stimulating effect, was as follows: relaxin > IGF-I > insulin (human myometrium); IGF-I > relaxin > insulin (rat skeletal muscle); insulin-like peptide of Anodonta (ILPA) > IGF-I > insulin > relaxin (molluscan muscle). The relaxin activating effect on AC was potentiated by a guanine nucleotide, the non-hydrolyzed analog of GTP, guanylylimidodiphosphate (Gpp[NH]p), which indicates participation of G_s-protein in realization of this effect. This effect was inhibited by a tyrosine kinase selective blocker, tyrphostin 47, and a phosphatidylinositol-3-kinase (PI-3-K) selective blocker, wortmannin. Thus, for the first time, participation of ACSM in the relaxin action has been established. This mechanism, as suggested at the present time state of its study, includes the following signal pathway: receptor-tyrosine kinase PI-3-K G_s-protein AC.     

Dynamics of Notch Activity in a Model of Interacting Signaling Pathways

Networks of interacting signaling pathways are formulated with systems of reaction-diffusion (RD) equations. We show that weak interactions between signaling pathways have negligible effects on formation of spatial patterns of signaling molecules. In particular, a weak interaction between Retinoic Acid (RA) and Notch signaling pathways does not change dynamics of Notch activity in the spatial domain. Conversely, large interactions of signaling pathways can influence effects of each signaling pathway. When the RD system is largely perturbed by RA-Notch interactions, new spatial patterns of Notch activity are obtained. Moreover, analysis of the perturbed Homogeneous System (HS) indicates that the system admits bifurcating periodic orbits near a Hopf bifurcation point. Starting from a neighborhood of the Hopf bifurcation, oscillatory standing waves of Notch activity are numerically observed. This is of particular interest since recent laboratory experiments confirm oscillatory dynamics of Notch activity.     

Collective Action in Action: Prosocial Behavior in and out of the Laboratory

ABSTRACT  Experiments have become a popular method to study altruism and cooperation in laboratory and, more recently, in field settings. However, few studies have examined whether behavior in experiments tells us anything about behavior in the "real world." To investigate the external validity of several common experimental economics games, we compare game behavior with prosocial behavior among Tsimane forager-horticulturalists of lowland Bolivia. We find that food-sharing patterns, social visitation, beer production and consumption, labor participation, and contributions to a feast are not robustly correlated with levels of giving in the economics games. Payoff structure and socioecological context may be more important in predicting prosocial behavior in a wide variety of domains than stable personality traits. We argue that future experimental methods should be tailored to specific research questions, show reduced anonymity, and incorporate repeat measures under a variety of conditions to inform and redirect ethnographic study and build scientific theory. [Keywords: altruism, cooperation, experimental economics, Tsimane]     

Collective Action and Social Capital of Wildlife Management Associations

Abstract: In areas with dense landownership patterns, management of white-tailed deer (Odocoileus virginianus) depends upon collective decision making of landowners and hunters. To resolve conflicts associated with this commons dilemma, wildlife management associations (WMAs) have become a popular mechanism for coordinating wildlife management decisions in private land states, especially in Texas, USA. Social capital, represented by metrics such as trust, reciprocity, and community involvement, has been identified as an important determinant of the success of collaborative institutional arrangements. To determine the influence of social capital on the effectiveness of WMAs, we address 2 research questions: 1) do WMAs exhibit elements of social capital, and 2) what landowner characteristics affect elements of social capital within WMAs? We used a mail survey questionnaire to determine the effect of various factors on the activities and management practices in 4 WMAs in 2 regions in Texas: the Lower Post Oak Savannah (LPOS) and the Central Post Oak Savannah (CPOS). The LPOS landowners were members of larger associations, had generally acquired their land more recently, held more frequent meetings, and tended to have longer association membership than CPOS landowners, yet they exhibited lower social capital. The CPOS landowners owned significantly larger properties, and were predominantly absentee wealthy males that considered relaxation and hunting more important land uses than property ownership for a place to live. The smaller group size of the CPOS associations may be the most important factor in building and maintaining social capital. Intra-association trust, a primary measure of social capital, was positively influenced by the longevity of property ownership, the number of association meetings, the percentage of males in the association, and other factors. Conversely, negative influences on trust included absentee ownership and the proportion of woodland habitat present in each WMA. We suggest that deer are a common-pool resource whose populations are dependent upon collective action by stakeholders. Social capital building within landowner associations could facilitate the sustainable harvest of quality deer and possibly lead to cooperative management of other common-pool natural resources.     

Collective Bacterial Dynamics Revealed Using a Three-Dimensional Population-Scale Defocused Particle Tracking Technique

An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria.     

Social Influence and the Collective Dynamics of Opinion Formation

Social influence is the process by which individuals adapt their opinion, revise their beliefs, or change their behavior as a result of social interactions with other people. In our strongly interconnected society, social influence plays a prominent role in many self-organized phenomena such as herding in cultural markets, the spread of ideas and innovations, and the amplification of fears during epidemics. Yet, the mechanisms of opinion formation remain poorly understood, and existing physics-based models lack systematic empirical validation. Here, we report two controlled experiments showing how participants answering factual questions revise their initial judgments after being exposed to the opinion and confidence level of others. Based on the observation of 59 experimental subjects exposed to peer-opinion for 15 different items, we draw an influence map that describes the strength of peer influence during interactions. A simple process model derived from our observations demonstrates how opinions in a group of interacting people can converge or split over repeated interactions. In particular, we identify two major attractors of opinion: (i) the expert effect, induced by the presence of a highly confident individual in the group, and (ii) the majority effect, caused by the presence of a critical mass of laypeople sharing similar opinions. Additional simulations reveal the existence of a tipping point at which one attractor will dominate over the other, driving collective opinion in a given direction. These findings have implications for understanding the mechanisms of public opinion formation and managing conflicting situations in which self-confident and better informed minorities challenge the views of a large uninformed majority.     

Molecular Dynamics Simulation of Collective Motions in Binary Liquids

Collective dynamic properties of different kind of binary liquid mixtures have been investigated by molecular dynamics simulation. The study includes both the longitudinal and the transverse current spectra in simple liquid alloys, 1:1 molten salts and liquid binary mixtures of neutral particles with an ionic-like structure. These systems were chosen as representative of binary liquids with different static structures in order to analyse the effects of structural ordering on the mechanisms of dynamic collective properties. The effect of the mass asymmetry between the two species in the mixture has been also discussed from the results for two different mass ratios for each kind of structure. Two length scales have been considered. On the one hand, the hydrodynamic scale (low wave numbers), where the modes for the partial currents of the two species are characterised by very close frequencies. On the other hand, the molecular scale (higher wave numbers), where the characteristic frequencies for the two species show noticeable differences. Vibrational concentration current modes (optic modes) have been found in neutral mixtures though their influence is rather weak, being the collective dynamic properties of this kind of systems dominated by the mass current modes (acoustic modes). On the contrary, in mixtures of charged particles such as molten salts the contribution of the concentration (charge) currents to the collective dynamics is important and optic modes can be characterised by a well-defined frequency for a wide range of wave numbers. It has been observed that heavy particles have a more relevant role on the mass current correlations whereas light particles play a dominant role on the concentration current correlations. The overall results for the three kinds of liquid mixtures analysed in this paper show that both the longitudinal and transverse current spectra are little dependent on the static structure of the system whereas marked differences are revealed when the particles in the system are either neutral or carry an electric charge.     

Phosphorylation Site Dynamics of Early T-cell Receptor Signaling

In adaptive immune responses, T-cell receptor (TCR) signaling impacts multiple cellular processes and results in T-cell differentiation, proliferation, and cytokine production. Although individual protein–protein interactions and phosphorylation events have been studied extensively, we lack a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites with central roles in TCR signaling. The model was used to generate predictions suggesting unexpected roles for the phosphatase PTPN6 (SHP-1) and shortcut recruitment of the actin regulator WAS. Predictions were validated experimentally. This integration of proteomics and modeling illustrates a novel, generalizable framework for solidifying quantitative understanding of a signaling network and for elucidating missing links.     

Structural Dynamics of Glutamate Signaling Systems by smFRET

Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for investigating the structural dynamics of biological macromolecules. smFRET reveals the conformational landscape and dynamic changes of proteins by building on the static structures found using cryo-electron microscopy, x-ray crystallography, and other methods. Combining smFRET with static structures allows for a direct correlation between dynamic conformation and function. Here, we discuss the different experimental setups, fluorescence detection schemes, and data analysis strategies that enable the study of structural dynamics of glutamate signaling across various timescales. We illustrate the versatility of smFRET by highlighting studies of a wide range of questions, including the mechanism of activation and transport, the role of intrinsically disordered segments, and allostery and cooperativity between subunits in biological systems responsible for glutamate signaling.     

Opinion Formation and the Collective Dynamics of Risk Perception

The formation of collective opinion is a complex phenomenon that results from the combined effects of mass media exposure and social influence between individuals. The present work introduces a model of opinion formation specifically designed to address risk judgments, such as attitudes towards climate change, terrorist threats, or children vaccination. The model assumes that people collect risk information from the media environment and exchange them locally with other individuals. Even though individuals are initially exposed to the same sample of information, the model predicts the emergence of opinion polarization and clustering. In particular, numerical simulations highlight two crucial factors that determine the collective outcome: the propensity of individuals to search for independent information, and the strength of social influence. This work provides a quantitative framework to anticipate and manage how the public responds to a given risk, and could help understanding the systemic amplification of fears and worries, or the underestimation of real dangers.     

Individual-Based Model for Quorum Sensing with Background Flow

Quorum sensing is a wide-spread mode of cell–cell communication among bacteria in which cells release a signalling substance at a low rate. The concentration of this substance allows the bacteria to gain information about population size or spatial confinement. We consider a model for \(N\) cells which communicate with each other via a signalling substance in a diffusive medium with a background flow. The model consists of an initial boundary value problem for a parabolic PDE describing the exterior concentration \(u\) of the signalling substance, coupled with \(N\) ODEs for the masses \(a_i\) of the substance within each cell. The cells are balls of radius \(R\) in \(\mathbb {R} ^3\) , and under some scaling assumptions we formally derive an effective system of \(N\) ODEs describing the behaviour of the cells. The reduced system is then used to study the effect of flow on communication in general, and in particular for a number of geometric configurations.     

Dynamics of Insulin Action on Mammary Epithelium

WE have found that, without entering its target cells, insulin elicits biological effects by impinging on the cell membrane. Furthermore, prolonged contact between hormone and mammary cell membrane is not necessary; transient contact through collisions suffices to produce a biological response.     

Extended Anti-inflammatory Action of a Degradation-resistant Mutant of Cell-penetrating Suppressor of Cytokine Signaling 3

Suppressor of cytokine signaling 3 (SOCS3) regulates the proinflammatory cytokine signaling mediated by the JAK/STAT signaling pathway. SOCS3 is rapidly induced and then targeted to the ubiquitin-proteasome pathway via a mechanism that requires the C-terminal SOCS box. Due to its rapid turnover, the intracellular stores of SOCS3 seem insufficient to control acute or protracted inflammatory diseases. Previously, we developed an intracellular protein therapy that uses a recombinant cell-penetrating form of SOCS3 (CP-SOCS3) to inhibit the JAK/STAT pathway and prevent cytokine-mediated lethal inflammation and apoptosis of the liver (Jo, D., Liu, D., Yao, S., Collins, R. D., and Hawiger, J. (2005) Nat. Med. 11, 892–898). The potent anti-inflammatory and cytoprotective activity of CP-SOCS3 prompted us to analyze its intracellular turnover, as compared with that of endogenous SOCS3 protein induced in macrophages by the proinflammatory agonists, interferon-γ and lipopolysaccharide. We found that the half-life (t½) of endogenous SOCS3 is 0.7 h in activated macrophages, compared with a t½ of 6.2 h for recombinant CP-SOCS3. Deletion of the SOCS box in CP-SOCS3 renders it more resistant to proteasomal degradation, extending its t½ to 29 h. Consequently, this SOCS box-deleted form of CP-SOCS3 displays persistent inhibitory activity for 24 h toward interferon-γ- and lipopolysaccharide-induced cytokine and chemokine production. Compared with the wild-type suppressor, this gain-of-function CP-SOCS3 mutant provides a longer acting inhibitor of cytokine signaling, a feature that offers a clear advantage for the intracellular delivery of proteins to treat acute or protracted inflammatory diseases.