Self-organization in biological systems

Biological systems are considered that are capable of dynamic self-organization, i.e., spontaneous emergence of spatio-temporal order with the formation of various spatio-temporal patterns. A cell is involved in the organization of ontogenesis of all stages. Embryonic cells exhibit coordinated social behavior and generate ordered morphological patterns displaying variability and equifinality of development. Physical and topological patterns are essential for biological systems as an imperative that restricts and directs biological morphogenesis. Biological self-organization is directed and fixed by natural selection during which selection of the most sustainable, flexible, modular systems capable of adaptive self-organization occurs.     

Receptor uptake arrays for vitamin B12, siderophores,and glycans shape bacterial communities

Molecular variants of vitamin B₁₂, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B₁₂ and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B₁₂, siderophores, and glycans.     

A computational system for simulating and analyzing arrays of biological and artificial chemical sensors

We have designed an approach for modeling olfactory pathways by which one can explore how the properties of individual receptors affect the information coding capacity of an entire system. The effect of receptor tuning breadth on system performance was explored explicitly. We presented model sensory arrays with sets of stimuli randomly and uniformly distributed in an "olfactory space". Arrays of uniformly sized model receptors responding to 25-35% of the stimuli gave the best performance as measured by the ability to capture the most information about the stimulus set. Arrays of variably sized model receptors that were both more broadly and more narrowly tuned than this optimum could, however, perform better than uniform arrays. This method and the results obtained using it suggest a framework for considering the growing body of evidence on the functional properties of individual olfactory receptor and relay neurons from a systems coding perspective.     

Contributions of electric fish to the understanding of sensory processing by reafferent systems.

Sensory systems must solve the inverse problem of determining environmental events based on patterns of neural activity in the central nervous system that are affected by those environmental events. Different environmental events can give rise to indistinguishable patterns of neural activity, so that there will often, perhaps even always, be multiple solutions to a sensory inverse problem. Imaging strategies and brain organization confine these multiple solutions within a bounded set. Three different active strategies may be employed by animals to constrain the number of solutions to the sensory inverse problem: active generation of the energy (carrier) that stimulates receptors; reorientation of the point of view; and control of signal conditioning before transduction (pre-receptor mechanisms). This paper describes how these strategies are used in sensory-motor systems, using electric fish as a paradigmatic example. Carrier generation and receptor tuning to the carrier improve signal to noise ratio. Receptor tuning to different frequency bands of the carrier spectrum allows a sensory system to evaluate different kinds of carrier modulations and to extract the different features of objects in the environment. Pre-receptor mechanisms condition the signals, optimizing their detection at a foveal region where the sensory resolution is maximum. Active orientation of the sensory surface redirects the fovea to explore in detail the source of interesting signals. Sensory input generated by these active exploration mechanisms ('reafference') has two components: one, necessary, derived from the self-generated actions and another, contingent, consisting of the information obtained from the external world. Extracting environmental information ('exafference') requires that the self generated afference be subtracted from the sensory inflow. Such subtraction is often associated with the generation and storage of expectations about sensory inputs. It can be concluded that an animal's perceptual world and its ability to transform the world are inextricably linked. Understanding sensory systems must, therefore, always require understanding the organization of motor behavior.     

Multimodal sensory integration in the strike-feeding behaviour of predatory fishes

The search for useful model systems for the study of sensory processing in vertebrate nervous systems has resulted in many neuroethological studies investigating the roles played by a single sensory modality in a given behaviour. However, behaviours relying solely upon information from one sensory modality are relatively rare. Animals behaving in a complex, three-dimensional environment receive a large amount of information from external and internal receptor arrays. Clearly, the integration of sensory afference arising from different modalities into a coherent 'gestalt' of the world is essential to the behaviours of most animals. In the last several years our laboratory team has examined the roles played by the visual and lateral line sensory systems in organizing the feeding behaviour of two species of predatory teleost fishes, the largemouth bass, Micropterus salmoides, and the muskellunge, Esox masquinongy. The free-field feeding behaviours of these fishes were studied quantitatively in intact animals and compared to animals in which the lateral line and visual systems had been selectively suppressed. All groups of animals continued to feed successfully, but significant differences were observed between each experimental group, providing strong clues as to the relative role played by each sensory system in the organization of the behaviour. Furthermore, significant differences exist between the two species. The differences in behaviour resulting when an animal is deprived of a given sensory modality reflect the nature of central integrative sensory processes, and these behavioural studies provide a foundation for further neuroanatomical and physiological studies of sensory integration in the vertebrate central nervous system.     

A Rho GTPase Signal Treadmill Backs a Contractile Array

Contractile arrays of actin filaments (F-actin) and myosin-2 power diverse biological processes. Contractile array formation is stimulated by the Rho GTPases Rho and Cdc42; after assembly, array movement is thought to result from contraction itself. Contractile array movement and GTPase activity were analyzed during cellular wound repair, in which arrays close in association with zones of Rho and Cdc42 activity. Remarkably, contraction suppression prevents translocation of F-actin and myosin-2 without preventing array or zone closure. Closure is driven by an underlying "signal treadmill" in which the GTPases are preferentially activated at the leading edges and preferentially lost from the trailing edges of their zones. Treadmill organization requires myosin-2-powered contraction and F-actin turnover. Thus, directional gradients in Rho GTPase turnover impart directional information to contractile arrays, and proper functioning of these gradients is dependent on both contraction and F-actin turnover. VIDEO ABSTRACT:     

Signal acquisition and analysis for cortical control of neuroprosthetics

Work in cortically controlled neuroprosthetic systems has concentrated on decoding natural behaviors from neural activity, with the idea that if the behavior could be fully decoded it could be duplicated using an artificial system. Initial estimates from this approach suggested that a high-fidelity signal comprised of many hundreds of neurons would be required to control a neuroprosthetic system successfully. However, recent studies are showing hints that these systems can be controlled effectively using only a few tens of neurons. Attempting to decode the pre-existing relationship between neural activity and natural behavior is not nearly as important as choosing a decoding scheme that can be more readily deployed and trained to generate the desired actions of the artificial system. These artificial systems need not resemble or behave similarly to any natural biological system. Effective matching of discrete and continuous neural command signals to appropriately configured device functions will enable effective control of both natural and abstract artificial systems using compatible thought processes.     

3-phosphoinositides modulate cyclic nucleotide signaling in olfactory receptor neurons

Phosphatidylinositol 3-kinase (PI3K)-dependent phosphoinositide signaling has been implicated in diverse cellular systems coupled to receptors for many different ligands, but the extent to which it functions in sensory transduction is yet to be determined. We now report that blocking PI3K activity increases odorant-evoked, cyclic nucleotide-dependent elevation of [Ca(2+)](i) in acutely dissociated rat olfactory receptor neurons and does so in an odorant-specific manner. These findings imply that 3-phosphoinositide signaling acts in vertebrate olfactory transduction to inhibit cyclic nucleotide-dependent excitation of the cells and that the interaction of the two signaling pathways is important in odorant coding, indicating that 3-phosphoinositide signaling can play a role in sensory transduction.     

Emerging principles of molecular signal processing by mitral/tufted cells in the olfactory bulb

The olfactory system shares many principles of functional organization with other sensory systems, but differs in that the sensory input is in the form of molecular information carried in odor molecules. Current studies are providing new insights into how this information is processed. In analogy with the spatial receptive fields of visual neurons, the molecular receptive range of olfactory cells is defined as the range of odor molecules that will affect the firing of that cell. Olfactory receptor molecules belong to a large gene family; it is hypothesized that individual receptor molecule may have relatively broad molecular receptive ranges, and that an individual receptor cell need therefore express only one or a few different types of receptors to cover a broad range. Mitral/tufted cells have narrower molecular receptive ranges, comprising molecules with related structures (odotopes). This is believed to reflect processing through the olfactory glomeruli, each glomerulus acting as a convergence center for related inputs. Varying overlapping specificities of receptor cells, glomeruli and mitral/tufted cells appear to provide the basis for discrimination of odor molecules, in analogy with discrimination of color in the visual systems.     

Biomimetic nanopores: learning from and about nature

Through recent advances in nanotechnology and molecular engineering, biomimetics - the development of synthetic systems that imitate biological structures and processes - is now emerging at the nanoscale. In this review, we explore biomimetic nanopores and nanochannels. Biological systems are full of nano-scale channels and pores that inspire us to devise artificial pores that demonstrate molecular selectivity or other functional advantages. Moreover, with a biomimetic approach, we can also study biological pores, through bottom-up engineering approaches whereby constituent components can be investigated outside the complex cellular environment.     

Signal transduction: receptor clusters as information processing arrays

The organization of transmembrane receptors into higher-order arrays occurs in cells as different as bacteria, lymphocytes and neurons. What are the implications of receptor clustering for short-term and long-term signaling processes that occur in response to ligand binding?     

Adaptation Dynamics in Densely Clustered Chemoreceptors

In many sensory systems, transmembrane receptors are spatially organized in large clusters. Such arrangement may facilitate signal amplification and the integration of multiple stimuli. However, this organization likely also affects the kinetics of signaling since the cytoplasmic enzymes that modulate the activity of the receptors must localize to the cluster prior to receptor modification. Here we examine how these spatial considerations shape signaling dynamics at rest and in response to stimuli. As a model system, we use the chemotaxis pathway of Escherichia coli, a canonical system for the study of how organisms sense, respond, and adapt to environmental stimuli. In bacterial chemotaxis, adaptation is mediated by two enzymes that localize to the clustered receptors and modulate their activity through methylation-demethylation. Using a novel stochastic simulation, we show that distributive receptor methylation is necessary for successful adaptation to stimulus and also leads to large fluctuations in receptor activity in the steady state. These fluctuations arise from noise in the number of localized enzymes combined with saturated modification kinetics between the localized enzymes and the receptor substrate. An analytical model explains how saturated enzyme kinetics and large fluctuations can coexist with an adapted state robust to variation in the expression levels of the pathway constituents, a key requirement to ensure the functionality of individual cells within a population. This contrasts with the well-mixed covalent modification system studied by Goldbeter and Koshland in which mean activity becomes ultrasensitive to protein abundances when the enzymes operate at saturation. Large fluctuations in receptor activity have been quantified experimentally and may benefit the cell by enhancing its ability to explore empty environments and track shallow nutrient gradients. Here we clarify the mechanistic relationship of these large fluctuations to well-studied aspects of the chemotaxis system, precise adaptation and functional robustness.     

Optimal Control of Transitions between Nonequilibrium Steady States

Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have an interest in optimizing such transitions. Using the Hatano-Sasa Y-value, we extend a recently developed geometrical framework for determining optimal protocols so that it can be applied to systems driven from nonequilibrium steady states. We calculate and numerically verify optimal protocols for a colloidal particle dragged through solution by a translating optical trap with two controllable parameters. We offer experimental predictions, specifically that optimal protocols are significantly less costly than naive ones. Optimal protocols similar to these may ultimately point to design principles for biological energy transduction systems and guide the design of artificial molecular machines.     

Constraining the connectivity of neuronal networks cultured on microelectrode arrays with microfluidic techniques: a step towards neuron-based functional chips

In vitro culture of small neuronal networks with pre-defined topological features is particularly desirable when the electrical activity of such assemblies can be monitored for long periods of time. Indeed, it is hoped that such networks, with pre-determined connectivity, will provide unique insights into the structure/function relationship of biological neural networks and their properties of self-organization. However, the experimental techniques that have been developed so far for that purpose have either failed to provide very long-term pattern definition and retention, or they have not shown potential for integration into more complex microfluidic devices. To address this problem, three-dimensional microfluidic systems in poly(dimethylsiloxane) (PDMS) were fabricated and used in conjunction with both custom-made and commercially available planar microelectrode arrays (pMEAs). Various types of primary neuronal cell cultures were established inside these systems. Extracellular electrical signals were successfully recorded from all types of cells placed inside the patterns, and this bioelectrical activity was present for several weeks. The advantage of this approach is that it can be further integrated with microfluidic devices and pMEAs to yield, for example, complex neuron-based biosensors or chips for pharmacological screening.     

Left/right,up/down: the role of endogenous electrical fields as directional signals in development,repair and invasion

A fundamental aspect of biological systems is their spatial organization. In development, regeneration and repair, directional signals are necessary for the proper placement of the components of the organism. Likewise, pathogens that invade other organisms rely on directional signals to target vulnerable areas. It is widely understood that chemical gradients are important directional signals in living systems. Less well recognized are electrical fields, which can also provide directional information. Small, steady electrical fields can directly guide cell movement and growth and can generate chemical gradients of charged macromolecules against the leveling action of diffusion. At the site of a lesion in an ion-transporting epithelium, for example, a substantial electrical field is instantly generated and may extend over many cell diameters. There are numerous other situations in which relatively long-range electrical fields have been shown to exist naturally. Recently, there has been substantial progress in identifying specific processes that are controlled, to some extent, by these endogenous electrical fields. This review highlights these recent data and discusses possible mechanisms by which the fields might affect biological processes.     

Noninactivation of thyrotropin by cultured porcine thyroid cells.

Freshly isolated porcine thyroid cells were cultured in the presence of highly purified porcine thyrotropin. Cells associate into follicles between the second and tenth day of culture and later form a monolayer. The biological and immunological activity of thyrotropin was measured daily in the media. Thyrotropin concentration and biological activity remained unchanged from the onset of the culture up to day 14. Limiting factors influencing thyroglobulin biosynthesis do not appear before day 13. The loss of follicular organization at day 10 cannot be explained by thyrotropin degradation in the medium. Considering the number of receptors per cell and the half life of the thyrotropin . receptor complex in the two dissociation compartments previously demonstrated, it appears in terms of both biological activity and affinity for the receptors that the thyrotropin molecules released from the first compartment do not differ from native molecules. It can be calculated that at least 31% of the molecules released from the second compartment are not inactivated. Thus, it is probable that the catabolism of thyrotropin on the receptor, or near the receptor site, does not play an important role in the regulation of thyroid cell function in vitro.