Engineered protein switches for exogenous control of gene expression

There is an ongoing need in the synthetic biology community for novel ways to regulate gene expression. Protein switches, which sense biological inputs and respond with functional outputs, represent one way to meet this need. Despite the fact that there is already a large pool of transcription factors and signaling proteins available, the pool of existing switches lacks the substrate specificities and activities required for certain applications. Therefore, a large number of techniques have been applied to engineer switches with novel properties. Here we discuss some of these techniques by broadly organizing them into three approaches. We show how novel switches can be created through mutagenesis, domain swapping, or domain insertion. We then briefly discuss their use as biosensors and in complex genetic circuits.

Stability and Control of Chaplygin Beanies Coupled to a Platform Through Nonholonomic Constraints

Many multi-agent systems in nature are comprised of agents that interact with, and respond to, the dynamics of their environment. In this paper, we approach the study of such agent environment interactions through the study of passively compliant vehicles coupled to their environment via simple nonholonomic constraints. We first consider a single passively compliant Chaplygin beanie atop a platform having translational compliance, introduce the reduced equations for the system using the notion of nonholonomic momentum, and provide proof for its stability under arbitrary deformations of the elastic element modeling its compliance. We then direct our focus to results concerning the frequency response and control of passive Chaplygin beanies under actuation of the platform, discuss rich dynamical features arising from periodic actuation, and develop rules by which control can be exerted to collect and disperse multiple passive vehicles. We then discuss how the latter of these results clarifies the extent to which stable behavior can be excited in the system through exogenous control.

How Does Active Participation Affect Consensus: Adaptive Network Model of Opinion Dynamics and Influence Maximizing Rewiring

In this paper we study the impact of active participation, or deliberately seeking out other agents with an aim of convincing them, on the dynamics of consensus formation. For this purpose, we propose an adaptive network model in which two processes shape opinion dynamics at interwoven time-scales as follows: (i) agents adapt their opinions subject to influence from social network neighbours who hold opinions within a tolerance interval δ and (ii) agents rewire network connections with an aim of maximizing their own influence on overall system opinion. We study this system both in an endogenous setting, in which all agents are subject to influence and also attempt to maximize influence, and in a setting of exogenous control, in which external agents not subject to influence adaptively attempt to maximize their influence. In both settings we find three regimes of stationary opinion configurations: (i) for low δ a regime of two evenly balanced radicalized opinion clusters at the extremes of the opinion space, (ii) for intermediate δ a ’winner-takes-most’ regime of two unevenly sized radicalized opinion clusters, and (iii) for large δ a regime in which very low spread compromise consensus states can be reached. Comparing to adaptive processes of random and deliberately spread-reducing rewiring, we demonstrate that in regime (iii) competitive influence maximization can achieve near-minimal opinion spread within near-optimal times. Further, we also show that competitive influence maximizing rewiring can reduce the impact of small influential minorities on consensus states.

Nucleic Acids-Based Nanotechnology

Nanobiotechnology is emerging as a valuable field that integrates research from science and technology to create novel nanodevices and nanostructures with various applications in modern nanotechnology. Applications of nanobiotechnology are employed in biomedical and pharmaceutical research, biosensoring, nanofluidics, self-assembly of nanostructures, nanopharmaceutics, molecular computing, and others. It has been proven that nucleic acids are a very suitable medium for self-assembly of diverse nanostructures and catalytic nanodevices for various applications. In this chapter, the authors discuss various applications of nucleic-based nanotechnology. The areas discussed here include building nanostructures using DNA oligonucleodite, self-assembly of integrated RNA-based nanodevices for molecular computing and diagnostics, antibacterial drug discovery, exogenous control of gene expression, and gene silencing.

Humans are sensitive to attention control when predicting others’ actions

Studies of social perception report acute human sensitivity to where another’s attention is aimed. Here we ask whether humans are also sensitive to how the other’s attention is deployed. Observers viewed videos of actors reaching to targets without knowing that those actors were sometimes choosing to reach to one of the targets (endogenous control) and sometimes being directed to reach to one of the targets (exogenous control). Experiments 1 and 2 showed that observers could respond more rapidly when actors chose where to reach, yet were at chance when guessing whether the reach was chosen or directed. This implicit sensitivity to attention control held when either actor’s faces or limbs were masked (experiment 3) and when only the earliest actor’s movements were visible (experiment 4). Individual differences in sensitivity to choice correlated with an independent measure of social aptitude. We conclude that humans are sensitive to attention control through an implicit kinematic process linked to empathy. The findings support the hypothesis that social cognition involves the predictive modeling of others’ attentional states.