From sparks to spikes: information processing in the electrosensory systems of fish

Recent work on electrosensory systems in fish has combined traditional neuroethological approaches with quantitative methods for characterizing neural coding. These studies have shed light on general issues in sensory processing, including how peripheral sensory receptors encode external stimuli and how these representations are transformed at subsequent stages of processing.     

Phase coding: spikes get a boost from local fields

The brain exhibits coherent, long-range oscillations, and it now appears that these oscillations play a substantial role in neural coding: they can boost the information contained in action potentials by as much as 50%.     

Spatiotemporal receptive fields: a dynamical model derived from cortical architectonics

We assume that the mammalian neocortex is built up out of some six layers which differ in their morphology and their external connections. Intrinsic connectivity is largely excitatory, leading to a considerable amount of positive feedback. The majority of cortical neurons can be divided into two main classes: the pyramidal cells, which are said to be excitatory, and local cells (most notably the non-spiny stellate cells), which are said to be inhibitory. The form of the dendritic and axonal arborizations of both groups is discussed in detail. This results in a simplified model of the cortex as a stack of six layers with mutual connections determined by the principles of fibre anatomy. This stack can be treated as a multi-input-multi-output system by means of the linear systems theory of homogeneous layers. The detailed equations for the simulation are derived in the Appendix. The results of the simulations show that the temporal and spatial behaviour of an excitation distribution cannot be treated separately. Further, they indicate specific processing in the different layers and some independence from details of wiring. Finally, the simulation results are applied to the theory of visual receptive fields. This yields some insight into the mechanisms possibly underlying hypercomplexity, putative nonlinearities, lateral inhibition, oscillating cell responses, and velocity-dependent tuning curves.     

From stress and strain to spikes: mechanotransduction in spider slit sensilla

This review focuses on the structure and function of a single mechanoreceptor organ in the cuticle of spiders. Knowledge emerging from the study of this organ promises to yield general principles that can be applied to mechanosensation in a wide range of animal systems. The lyriform slit sense organ on the antero-lateral leg patella of the spider Cupiennius salei is unusual in possessing large sensory neurons, whose cell bodies are close to the sites of sensory transduction, and accessible to intracellular recording during mechanotransduction. This situation, combined with recent technical developments, has made it possible to observe and experiment with all the major stages of mechanosensation. Important findings include the approximate size, number and ionic selectivity of the ion channels responsible for mechanotransduction, the types of voltage-activated ion channels responsible for action potential encoding, and the mechanisms controlling the dynamic properties of transduction and encoding. Most recently, a complex efferent system for peripheral modulation of mechanosensation has been discovered and partially characterized. Much remains to be learned about mechanosensation, but the lyriform slit sense organ system continues to offer important opportunities to advance our understanding of this crucial sense.     

Cone contributions to cat retinal ganglion cell receptive fields

Extracellular microelectrode recordings were made from ganglion cells of the intact, in situ eyes of adult common domestic cats. Three different photopic systems, with peak spectral sensitivities at 450, 500, and 556 nm, were observed. All ganglion cells received input from a cone system with a peak spectral sensitivity of 556 nm. The blue-sensitive cone system was observed in about one-half of the ganglion cells studied. In each case the 450-nm cone system contributed to only one functional type of response, either ON or OFF, in the same cell. The other two photopic systems most often contributed to both the ON and OFF responses of an individual ganglion cell. In four cases the 450-nm cone system mediated responses that were opponent to those of the other two photopic systems. The third photopic mechanism has a peak spectral sensitivity at 500 nm and contributed to most receptive field surrounds and many receptive field centers. It is distinguished from the rod system by the occurrence of a break in both dark-adaptation curves and increment-sensitivity curves. No apparent differences in receptive field cone contributions between brisk-sustained and brisk-transient cells were seen.     

Nanopore sensors: From hybrid to abiotic systems

This paper provides an overview of different nanostructured architectures utilised in electrochemical devices and their application in biosensing and bioelectronics. Emphasis is placed on the fabrication of nanostructured films based on a layer-by-layer (LBL) films approach. We discuss the theory and the mechanism of charge transfer in polyelectrolyte multilayer films (PEM), as well as between biomolecules and redox centres, for the development of more sensitive and selective biosensors. Further, this paper presents an overview of topics involving the interaction between nanostructured materials, including metallic nanoparticles and carbon materials, and their effects on the preservation of the activity of biological molecules immobilised on electrode surfaces. This paper also presents examples of biological molecules utilised in film fabrication, such as DNA, several kinds of proteins, and oligonucleotides, and of the role of molecular interaction in biosensing performance. Towards the utilisation of LBL films, examples of several architectures and different electrochemical approaches demonstrate the potential of nanostructured LBL films for several applications that include the diagnosis and monitoring of diseases. Our main aim in this review is to survey what can assist researchers by presenting various approaches currently used in the field of bioelectrochemistry utilising supramolecular architectures based on an LBL approach for application in electrochemical biosensing.     

Mapping information flow in sensorimotor networks

Biological organisms continuously select and sample information used by their neural structures for perception and action, and for creating coherent cognitive states guiding their autonomous behavior. Information processing, however, is not solely an internal function of the nervous system. Here we show, instead, how sensorimotor interaction and body morphology can induce statistical regularities and information structure in sensory inputs and within the neural control architecture, and how the flow of information between sensors, neural units, and effectors is actively shaped by the interaction with the environment. We analyze sensory and motor data collected from real and simulated robots and reveal the presence of information structure and directed information flow induced by dynamically coupled sensorimotor activity, including effects of motor outputs on sensory inputs. We find that information structure and information flow in sensorimotor networks (a) is spatially and temporally specific; (b) can be affected by learning, and (c) can be affected by changes in body morphology. Our results suggest a fundamental link between physical embeddedness and information, highlighting the effects of embodied interactions on internal (neural) information processing, and illuminating the role of various system components on the generation of behavior.     

The Alopex process: Visual receptive fields by response feedback

The determination of trigger features of single neurons in afferent pathways has been one of the central problems in sensory physiology. A novel method, called Alopex, has been developed, in which response feedback is used to construct visual patterns that optimize the responses. Data are presented which show the emergence of trigger features of cells monitored in frog visual tectum. The method is checked against results obtained by scanning the visual field with a small spot. Correlations between Alopex patterns and scan patterns are generally between 0.3 and 0.5 but may be as high as 0.9 when smoothing and/or averaging procedures are applied to the Alopex patterns. The dynamics of the Alopex process are discussed and details of the algorithms are presented. The series of experiments presented here has established the validity of the method and suggests that this approach should find wide application in receptive field studies. For that purpose data on the instrumentation and software are also presented.This research has been supported by the National Institutes of Health, under grant EY 01215     

From structure to disease: the evolving tale of aquaporin biology

Our understanding of the movement of water through cell membranes has been greatly advanced by the discovery of a family of water-specific, membrane-channel proteins - the aquaporins. These proteins are present in organisms at all levels of life, and their unique permeability characteristics and distribution in numerous tissues indicate diverse roles in the regulation of water homeostasis. The recognition of aquaporins has stimulated a reconsideration of membrane water permeability by investigators across a wide range of disciplines.     

BeingAliveLanguage: Visualizing soil information from a design perspective to enhance multidisciplinary communication

Soil forms the foundation for biotic and abiotic activities that shape landscapes over time. Effective communication and understanding of soil profiles, contents, and interactions with other systems such as vegetation and climate are crucial for multidisciplinary research and projects involving soil. A robust, comprehensible, and extendable visualization system is required to enhance communication across diverse disciplines, including landscape architecture, agronomy, and ecology.This paper introduces the BeingAliveLanguage, an innovative, extensible visualization system for soil-centric information within a multidisciplinary communication framework. The system employs a fractal-based visual language to effectively convey vital soil information to professionals in various fields engaged in architecture, landscape design, and urban planning projects. The corresponding software, developed as a plugin for the Rhino-Grasshopper CAD environment, allows users to automatically generate easily understandable soil-centered diagrams using a node-based programming language. Designed to enhance communication in landscape, geoscience, and agriculture-related fields, the system provides critical information to support the design and decision-making process. We showcase the system’s efficacy through two extensions and by utilizing the tool in multiple real-world projects.     

Spectro-temporal receptive fields of auditory neurons in the grassfrog

The nature of the stimulus-response relation for single auditory neurons is reflected in the properties of the Pre-Event Stimulus Ensemble: the ensemble of stimuli, preceding the occurrence of an action potential (neural event). This paper describes methods to analyse the spectro-temporal properties of this ensemble. These methods are based on the analytic signal representation of acoustic signals and functionals derived from it: the instantaneous amplitude and instantaneous frequency and the dynamic power spectrum. The procedures have been applied to a number of extra-cellular single unit recordings from the grassfrog, Rana temporatia L., recorded during presentation of an ensemble of tonal stimuli. The outcome of this analysis describes the spectro-temporal receptive field of the neuron under the present stimulus conditions. The procedure, based on the dynamic power spectrum is applicable to an arbitrary stimulus ensemble, thus allowing a comparison of the spectrotemporal receptive fields for different types of stimuli.     

Spectro-temporal receptive fields of auditory neurons in the grassfrog

The stimulus-event relation of single units in the auditory midbrain area, the torus semicircularis, of the anaesthetized grassfrog (Rana temporaria L.) during stimulation with a wide ensemble of natural stimuli, was analysed using first and second order statistical analysis techniques. The average stimulus preceding the occurrence of action potentials, in general, did not prove to give very informative results. The second order procedure consisted in the determination of the average dynamic power spectrum of the pre-event stimuli, following procedures as described elsewhere (Aertsen and Johannesma, 1980; Aertsen et al., 1980). The outcome of this analysis was filtered with the overall power spectrum of the complete stimulus ensemble in order to correct for its non-uniform spectral composition. The stimulus-filtered average pre-event dynamic spectrum gives a first indication of the spectro-temporal receptive field of a neuron under natural stimulus conditions. Results for a limited number of recordings are presented and, globally, compared to the outcome of an analogous analysis of experiments with tonal stimuli.     

Estimating receptive fields from responses to natural stimuli with asymmetric intensity distributions

The reasons for using natural stimuli to study sensory function are quickly mounting, as recent studies have revealed important differences in neural responses to natural and artificial stimuli. However, natural stimuli typically contain strong correlations and are spherically asymmetric (i.e. stimulus intensities are not symmetrically distributed around the mean), and these statistical complexities can bias receptive field (RF) estimates when standard techniques such as spike-triggered averaging or reverse correlation are used. While a number of approaches have been developed to explicitly correct the bias due to stimulus correlations, there is no complementary technique to correct the bias due to stimulus asymmetries. Here, we develop a method for RF estimation that corrects reverse correlation RF estimates for the spherical asymmetries present in natural stimuli. Using simulated neural responses, we demonstrate how stimulus asymmetries can bias reverse-correlation RF estimates (even for uncorrelated stimuli) and illustrate how this bias can be removed by explicit correction. We demonstrate the utility of the asymmetry correction method under experimental conditions by estimating RFs from the responses of retinal ganglion cells to natural stimuli and using these RFs to predict responses to novel stimuli.     

The linearity of emergent spectro-temporal receptive fields in a model of auditory cortex

The responses of cortical neurons are often characterized by measuring their spectro-temporal receptive fields (STRFs). The STRF of a cell can be thought of as a representation of its stimulus 'preference' but it is also a filter or 'kernel' that represents the best linear prediction of the response of that cell to any stimulus. A range of in vivo STRFs with varying properties have been reported in various species, although none in humans. Using a computational model it has been shown that responses of ensembles of artificial STRFs, derived from limited sets of formative stimuli, preserve information about utterance class and prosody as well as the identity and sex of the speaker in a model speech classification system. In this work we help to put this idea on a biologically plausible footing by developing a simple model thalamo-cortical system built of conductance based neurons and synapses some of which exhibit spike-time-dependent plasticity. We show that the neurons in such a model when exposed to formative stimuli develop STRFs with varying temporal properties exhibiting a range of heterotopic integration. These model neurons also, in common with neurons measured in vivo, exhibit a wide range of non-linearities; this deviation from linearity can be exposed by characterizing the difference between the measured response of each neuron to a stimulus, and the response predicted by the STRF estimated for that neuron. The proposed model, with its simple architecture, learning rule, and modest number of neurons (<1000), is suitable for implementation in neuromorphic analogue VLSI hardware and hence could form the basis of a developmental, real time, neuromorphic sound classification system.     

Structure of receptive fields of cat pulvinar neurons sensitive to photic stimulation

Receptive fields of 262 pulvinar neurons were studied. Receptive fields of 142 of these neurons were studied in detail with the aid of a stationary spot of light, flashing in different parts of the receptive field. Depending on responses to presentation of the stationary stimulus the neurons were divided into six groups. The first group included neurons with on—off responses to photic stimulation (44 of 142), the second group neurons with off responses only (42 of 142). In cells of the third group (19 of 142) an on response only was recorded in all structures of the receptive field tested. Neurons of the fourth group (eight of 142) had a receptive field of similar structure to that of the simple receptive fields of neurons in cortical area 17. The fifth group (10 of 142) included neurons with a receptive field of concentric structure, the sixth (19 of 142) consisted of neurons with receptive fields with multiple discharge centers. The structure of the receptive field of these neurons was mosaic, with an irregular distribution of exciting and "silent" zones. The mean response latency of the pulvinar neurons was 40–70 msec. Responses of neurons with shorter (20 msec) and longer (130–160 msec) latent periods also were recorded.L. A. Orbeli Institute of Physiology, Academy of Sciences of the Armenian SSR, Erevan. Translated from Neirofiziologiya, Vol. 11, No. 1, pp. 3–10, January–February, 1979.     

From nucleosome to chromosome: a dynamic organization of genetic information

Gene activity is controlled at different levels of chromatin organization, which involve genomic sequences, nucleosome structure, chromatin folding and chromosome arrangement. These levels are interconnected and influence each other. At the basic level nucleosomes generally occlude the DNA sequence from interacting with DNA-binding proteins. Evidently, nucleosome positioning is a major factor in gene control and chromatin organization. Understanding the biological rules that govern the deposition and removal of the nucleosomes to and from the chromatin fiber is the key to understanding gene regulation and chromatin organization. In this review we describe and discuss the relationship between the different levels of chromatin organization in plants and animals.