Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assembly
The primacy and power of RNA in governing many processes of life has begun to be more fully appreciated in both the discovery and inventive sciences. A variety of RNA interactions regulate gene expression, and structural self-assembly underlies many of these processes. The understanding sparked by these discoveries has inspired and informed the engineering of novel RNA structures, control elements, and genetic circuits in cells. Many of these engineered systems are built up fundamentally from RNA-RNA interactions, often combining modular, rational design with functional selection and screening. It is therefore useful to review the particular class of RNA-based regulatory mechanisms that rely on RNA self-assembly either through homomeric (self-self) or heteromeric (self-nonself) RNA-RNA interactions. Structures and sequence elements within individual RNAs create a basis for the pairing interactions, and in some instances can even lead to the formation of RNA polymers. Example systems of dimers, multimers, and polymers are reviewed in this article in the context of natural systems, wherein the function and impact of self-assemblies are understood. Following this, a brief overview is presented of specific engineered RNA self-assembly systems implemented , with lessons learned from both discovery and engineering approaches to RNA-RNA self-assembly.
Neuronal spike-train responses in the presence of threshold noise
The variability of neuronal firing has been an intense topic of study for many years. From a modelling perspective it has often been studied in conductance based spiking models with the use of additive or multiplicative noise terms to represent channel fluctuations or the stochastic nature of neurotransmitter release. Here we propose an alternative approach using a simple leaky integrate-and-fire model with a noisy threshold. Initially, we develop a mathematical treatment of the neuronal response to periodic forcing using tools from linear response theory and use this to highlight how a noisy threshold can enhance downstream signal reconstruction. We further develop a more general framework for understanding the responses to large amplitude forcing based on a calculation of first passage times. This is ideally suited to understanding stochastic mode-locking, for which we numerically determine the Arnol'd tongue structure. An examination of data from regularly firing stellate neurons within the ventral cochlear nucleus, responding to sinusoidally amplitude modulated pure tones, shows tongue structures consistent with these predictions and highlights that stochastic, as opposed to deterministic, mode-locking is utilised at the level of the single stellate cell to faithfully encode periodic stimuli.
How the pine seeds attach to/detach from the pine cone scale?
One of the primary purposes of pine cones is the protection and distant dispersal of pine seeds. Pine cones open and release their embedded seeds on dry and windy days for long-distance dispersal. In this study, how the pine seed attach to/ detach from the pine cone scale for efficient seed dispersal were experimentally investigated by using X-ray micro-imaging technique. The cone and seeds adhere to one another in the presence of water, which could be explained by the surface tension and the contact angle hysteresis. Otherwise, without water, the waterproof seed wing surface permits rapid drying for detach and dispersion. On the other hand, during wildfires, pine cones open their seed racks and detach the pine seeds from pine cones for rapid seed dispersal. Due to these structural advantages, pine seeds are released safely and efficiently on adjust condition. These advantageous structure could be mimicked in practical applications.
