Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation.

Many signaling systems execute adaptation under circumstances that require noise attenuation. Here, we identify an intrinsic trade-off existing between sensitivity and noise attenuation in the three-node networks. We demonstrate that although fine-tuning timescales in three-node adaptive networks can partially mediate this trade-off in this context, it prolongs adaptation time and imposes unrealistic parameter constraints. By contrast, four-node networks can effectively decouple adaptation and noise attenuation to achieve dual function without a trade-off, provided that these functions are executed sequentially. We illustrate ideas in seven biological examples, including Dictyostelium discoideum chemotaxis and the p53 signaling network and find that adaptive networks are often associated with a noise attenuation module. Our approach may be applicable to finding network design principles for other dual and multiple functions

Noise control and utility: From regulatory network to spatial patterning

Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how living systems deal with noise while performing desirable biological functions remains a major mystery. Regulatory network configurations, such as their topology and timescale, are shown to be critical in attenuating noise, and noise is also found to facilitate cell fate decision. Here we review major recent findings on noise attenuation through regulatory control, the benefit of noise via noise-induced cellular plasticity during developmental patterning, and summarize key principles underlying noise control

Evolutionary robotics and neuroscience

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Neuronal avalanches of a self-organized neural network with active-neuron-dominant structure

Neuronal avalanche is a spontaneous neuronal activity which obeys a power-law distribution of population event sizes with an exponent of -3/2. It has been observed in the superficial layers of cortex both \emph{in vivo} and \emph{in vitro}. In this paper we analyze the information transmission of a novel self-organized neural network with active-neuron-dominant structure. Neuronal avalanches can be observed in this network with appropriate input intensity. We find that the process of network learning via spike-timing dependent plasticity dramatically increases the complexity of network structure, which is finally self-organized to be active-neuron-dominant connectivity. Both the entropy of activity patterns and the complexity of their resulting post-synaptic inputs are maximized when the network dynamics are propagated as neuronal avalanches. This emergent topology is beneficial for information transmission with high efficiency and also could be responsible for the large information capacity of this network compared with alternative archetypal networks with different neural connectivity.Comment: Non-final version submitted to Chao

Plasma Membrane-Associated Restriction Factors and Their Counteraction by HIV-1 Accessory Proteins.

The plasma membrane is a site of conflict between host defenses and many viruses. One aspect of this conflict is the host's attempt to eliminate infected cells using innate and adaptive cell-mediated immune mechanisms that recognize features of the plasma membrane characteristic of viral infection. Another is the expression of plasma membrane-associated proteins, so-called restriction factors, which inhibit enveloped virions directly. HIV-1 encodes two countermeasures to these host defenses: The membrane-associated accessory proteins Vpu and Nef. In addition to inhibiting cell-mediated immune-surveillance, Vpu and Nef counteract membrane-associated restriction factors. These include BST-2, which traps newly formed virions at the plasma membrane unless counteracted by Vpu, and SERINC5, which decreases the infectivity of virions unless counteracted by Nef. Here we review key features of these two antiviral proteins, and we review Vpu and Nef, which deplete them from the plasma membrane by co-opting specific cellular proteins and pathways of membrane trafficking and protein-degradation. We also discuss other plasma membrane proteins modulated by HIV-1, particularly CD4, which, if not opposed in infected cells by Vpu and Nef, inhibits viral infectivity and increases the sensitivity of the viral envelope glycoprotein to host immunity

Short-Term Memory Through Persistent Activity: Evolution of Self-Stopping and Self-Sustaining Activity in Spiking Neural Networks

Memories in the brain are separated in two categories: short-term and long-term memories. Long-term memories remain for a lifetime, while short-term ones exist from a few milliseconds to a few minutes. Within short-term memory studies, there is debate about what neural structure could implement it. Indeed, mechanisms responsible for long-term memories appear inadequate for the task. Instead, it has been proposed that short-term memories could be sustained by the persistent activity of a group of neurons. In this work, we explore what topology could sustain short-term memories, not by designing a model from specific hypotheses, but through Darwinian evolution in order to obtain new insights into its implementation. We evolved 10 networks capable of retaining information for a fixed duration between 2 and 11s. Our main finding has been that the evolution naturally created two functional modules in the network: one which sustains the information containing primarily excitatory neurons, while the other, which is responsible for forgetting, was composed mainly of inhibitory neurons. This demonstrates how the balance between inhibition and excitation plays an important role in cognition.Comment: 28 page