Predictive coding: a fresh view of inhibition in the retina

Interneurons exhibiting centre--surround antagonism within their receptive fields are commonly found in peripheral visual pathways. We propose that this organization enables the visual system to encode spatial detail in a manner that minimizes the deleterious effects of intrinsic noise, by exploiting the spatial correlation that exists within natural scenes. The antagonistic surround takes a weighted mean of the signals in neighbouring receptors to generate a statistical prediction of the signal at the centre. The predicted value is subtracted from the actual centre signal, thus minimizing the range of outputs transmitted by the centre. In this way the entire dynamic range of the interneuron can be devoted to encoding a small range of intensities, thus rendering fine detail detectable against intrinsic noise injected at later stages in processing. This predictive encoding scheme also reduces spatial redundancy, thereby enabling the array of interneurons to transmit a larger number of distinguishable images, taking into account the expected structure of the visual world. The profile of the required inhibitory field is derived from statistical estimation theory. This profile depends strongly upon the signal: noise ratio and weakly upon the extent of lateral spatial correlation. The receptive fields that are quantitatively predicted by the theory resemble those of X-type retinal ganglion cells and show that the inhibitory surround should become weaker and more diffuse at low intensities. The latter property is unequivocally demonstrated in the first-order interneurons of the fly's compound eye. The theory is extended to the time domain to account for the phasic responses of fly interneurons. These comparisons suggest that, in the early stages of processing, the visual system is concerned primarily with coding the visual image to protect against subsequent intrinsic noise, rather than with reconstructing the scene or extracting specific features from it. The treatment emphasizes that a neuron's dynamic range should be matched to both its receptive field and the statistical properties of the visual pattern expected within this field. Finally, the analysis is synthetic because it is an extension of the background suppression hypothesis (Barlow & Levick 1976), satisfies the redundancy reduction hypothesis (Barlow 1961 a, b) and is equivalent to deblurring under certain conditions (Ratliff 1965).     

Synaptic limitations to contrast coding in the retina of the blowfly Calliphora

We investigate the effects of synaptic transmission on early visual processing by examining the passage of signals from photoreceptors to second order neurons (LMCS). We concentrate on the roles played by three properties of synaptic transmission: (1) the shape of the characteristic curve, relating pre- and postsynaptic signal amplitudes, (2) the dynamics of synaptic transmission and (3) the noise introduced during transmission. The characteristic curve is sigmoidal and follows a simple model of synaptic transmission (Appendix) in which transmitter release rises exponentially with presynaptic potential. According to this model a presynaptic depolarization of 1.50-1.86 mV produces an e-fold increase in postsynaptic conductance. The characteristic curve generates a sigmoidal relation between postsynaptic (LMC) response amplitude and stimulus contrast. The shape and slope of the characteristic curve is unaffected by the state of light adaptation. Retinal antagonism adjusts the characteristic curve to keep it centred on the mean level of receptor response generated by the background. Thus the photoreceptor synapses operate in the mid-region of the curve, where the slope or gain is highest and equals approximately 6. The dynamics of transmission of a signal from photoreceptor to second-order neuron approximates to the sum of two processes with exponential time courses. A momentary receptor depolarization generates a postsynaptic hyperpolarization of time constant 0.5-1.0 ms, followed by a slower and weaker depolarization. Light adaptation increases the relative amplitude of the depolarizing process and reduces its time constant from 80 ms to 1.5 ms. The hyperpolarizing process is too rapid to bandlimit receptor signals. The noise introduced during the passage of the signal from receptor to second-order neuron is measured by comparing signal:noise ratios and noise power spectra in the two cell types. Under daylight conditions from 50 to 70% of the total noise power is generated by events associated with the transmission of photoreceptor signals and the generation of LMC responses. According to the exponential model of transmitter release, the effects of synaptic noise are minimized when synaptic gain is maximized. Moreover, both retinal antagonism and the sigmoidal shape of the characteristic curve promote synaptic gain. We conclude that retinal antagonism and nonlinear synaptic amplification act in concert to protect receptor signals from contamination by synaptic noise. This action may explain the widespread occurrence of these processes in early visual processing.     

The potential utility of postnatalskeletal developmental patterns in squamate phylogenetics

Postnatal patterns of skeletal development, includingthe sequence of appearance of ossification centres and the distributionof sesamoids, appear to be highly conserved species-level phenomenain squamates. As such, they are a potential source of charactersfor phylogenetic inquiry. These patterns, from 21 species representing14 crown squamate clades, form the basis for two analyses. In thefirst, the sequence of postnatal skeletal events is coded as charactersusing the sequence unit approach. This analysis reveals that thesequence of postnatal skeletal events might be useful for determiningrelationships at or above the level of crown clades, but not amongthem. The second analysis utilizes discrete data from postnatalskeletal development, such as the presence/absence of sesamoidsand the number of secondary centres in epiphyseal cartilages. Thesediscrete data appear capable of recovering the deeper divergenceswithin Squamata, but evolve too slowly to be informative at thelevel of crown clades. Thus, patterns of postnatal skeletal developmenthave the potential to help illuminate relationships throughout thesquamate tree. Further progress in this area will require the examinationof additional squamate species, the exploration of alternative codingschemes for developmental sequences, and comparable postnatal datafor Sphenodon .  © 2002 The Linnean Societyof London, Zoological Journal of the Linnean Society, 2002, 136 ,277−313.     

Membrane potential clamping in horizontal cells of the fish retina

The membrane potential of horizontal cells of the retina was clamped by uniform polarization of the layer of these cells by a current passed through extracellular electrodes. The volt-ampere characteristic curve of the synaptic membrane of the horizontal cells in some cases had segments with negative slope. With a sharp change in the level of voltage clamping the time taken for the resistance of the membrane to change was under 20 msec. Comparison of responses to photic stimulation recorded with and without voltage clamping showed that participation of the nonsynaptic membrane in the generation of responses to photic stimulation can affect their shape substantially.Institute of Problems in Information Transmission, Academy of Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 9, No. 4, pp. 402–407, July–August, 1977.     

Trichromacy, opponent colours coding and optimum colour information transmission in the retina

This paper presents a systematic analysis of the role of opponent type processing in colour vision and the relation between opponent type colour transformations and the initial three colour mechanisms. It is shown that efficient information transmission is achieved by a transformation of the initial three colour mechanisms into an achromatic and two opponent chromatic channels. The derivation of the transformation is dependent solely on criteria from information theory. Thus it provides a logical rationale reconciling opponent type processing as an optimal necessary step after the initial three colour mechanisms, unifying respectively the Hering and Young-Helmholtz approaches to colour vision. The effects of chromatic adaptation on the spectral response of the achromatic and two chromatic channels are discussed from the point of view of information theory. It is argued that adaptation serves as a dynamic readjustment of these responses, necessary to meet criteria of efficient colour information transmission. The results are confronted with empirical observations to test the principles of the theory and the relation to other theories is discussed. Within the same framework the issue of trichromacy is discussed. It is argued that a broad class of typical colour spectra can effectively be represented by three significant degrees of freedom that make up a trichromatic system.     

Evaluating the protein coding potential of exonized transposable element sequences

Background  

Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons.     

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii

We have identified 141 novel palindromic repetitive elements in the genome of euryarchaeon Methanocaldococcus jannaschii. The total length of these elements is 14.3kb, which corresponds to 0.9% of the total genomic sequence and 6.3% of all extragenic regions. The elements can be divided into three groups (MJRE1-3) based on the sequence similarity. The low sequence identity within each of the groups suggests rather old origin of these elements in M. jannaschii. Three MJRE2 elements were located within the protein coding regions without disrupting the coding potential of the host genes, indicating that insertion of repeats might be a widespread mechanism to enhance sequence diversity in coding regions.     

The bionic retina: a small molecule with big potential for visual restoration

In this issue of Neuron, Polosukhina et?al. (2012) intravitreally deliver the light-activatable molecule acrylamide-azobenzene-quaternary ammonium (AAQ) to the eyes of mice with end-stage retinal degeneration. Results show that, with the appropriate illumination, AAQ restores light sensitivity and visual behavior.     

The functions of acetylcholine in the rabbit retina

Rabbit retinas were incubated in vitro under conditions known to maintain their physiological function. The acetylcholine stores of the cholinergic amacrine cells were labelled by incubation in the presence of [3H]choline. The tissue was then mounted in a fast-flow superfusion chamber, and the release of [3H]acetylcholine under various conditions was measured by liquid cation exchange or high-voltage electrophoresis. When the retina was stimulated by flashing light, the rate of appearance of radioactive acetylcholine in the superfusate increased, with a latency shorter than the resolution of the system. The rate of release of acetylcholine remained elevated as long as the light was flashing, and returned rapidly to baseline when the light was extinguished. A one minute stimulation with steady light caused a burst of acetylcholine release following stimulus onset and a second, smaller, burst following stimulus cessation. In the presence of 2-amino-4-phosphonobutyrate (APB), an agent known to eliminate selectively the transmission of ON responses to the proximal retina, steady light caused acetylcholine release only at stimulus cessation. Other retinas were labelled with [3H]choline, then incubated for 10-80 min in the presence of flashing light (to promote acetylcholine release) and either control medium or medium containing 100 micron APB (to prevent release from cells activated by stimulus onset). These retinas were quick-frozen, freeze-dried and radioautographed on dry emulsion. In retinas incubated under control conditions [3H]acetylcholine was initially present within two bands within the inner plexiform layer. The two bands became fainter together as the tissue's [3H]acetylcholine was released. APB selectively retarded the depletion of [3H]acetylcholine from the band nearest the ganglion cell layer. We conclude that the displaced cholinergic amacrine cells release acetylcholine at the transient when light appears, and the conventionally placed cholinergic amacrine cells release acetylcholine at the transient when light is extinguished. The retinal ganglion cells that receive a light-driven cholinergic input are distinguished from those that do not by a great sensitivity to slow stimulus motion. It is proposed that the dense plexus of cholinergic dendrites and the transient nature of acetylcholine release combine to create the local subunit that enables detection of motion within regions smaller than those ganglion cells' receptive fields.     

The global average DNA base composition of coding regions may be determined by the electron-ion interaction potential

It is shown how one can understand the frequencies of occurrence of nucleotides in coding DNA sequences on the basis of electron-ion interaction potential.     

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes

We suggest an annotation strategy for genes encoded by retroviruses and transposable elements (RETRA genes) based on a set of marker protein domains. Usually RETRA genes are masked in vertebrate genomes prior to the application of automated gene prediction pipelines under the assumption that they provide no selective advantage to the host. Yet, we show that about 1000 genes in four vertebrate gene sets analyzed contain at least one RETRA gene marker domain. Using the conservation of genomic neighborhood (synteny), we were able to discriminate between RETRA genes with putative functionality in the vertebrates and those that probably function only in the context of mobile elements. We identified 35 such genes in human, along with their corresponding mouse and rat orthologs; which included almost all known human genes with similarity to mobile elements. The results also imply that the vast majority of the remaining RETRA genes in current gene sets are unlikely to encode vertebrate functions. To automatically annotate RETRA genes in other vertebrate genomes, we provide as a tool a set of marker protein domains and a manually refined list of domesticated or ancestral RETRA genes for rescuing genes with vertebrate functions.     

The coding of temperature in the Drosophila brain

Thermosensation is an indispensable sensory modality. Here, we study temperature coding in Drosophila, and show that temperature is represented by a spatial map of activity in the brain. First, we identify TRP channels that function in the fly antenna to mediate the detection of cold stimuli. Next, we identify the hot-sensing neurons and show that hot and cold antennal receptors project onto distinct, but adjacent glomeruli in the Proximal-Antennal-Protocerebrum (PAP) forming a thermotopic map in the brain. We use two-photon imaging to reveal the functional segregation of hot and cold responses in the PAP, and show that silencing the hot- or cold-sensing neurons produces animals with distinct and discrete deficits in their behavioral responses to thermal stimuli. Together, these results demonstrate that dedicated populations of cells orchestrate behavioral responses to different temperature stimuli, and reveal a labeled-line logic for the coding of temperature information in the brain.