Biomedical subjects

Vincent Torre

Publications and source records attributed to Vincent Torre.

At least 19 recordsLinked to original sources

PubMed2007

Origin of functional diversity among tetrameric voltage-gated channels.

The aim of the present work is to relate functional differences of voltage-gated K(+) (K(v)), hyperpolarization-activated cyclic nucleotide-gated (HCN), and cyclic nucleotide gated (CNG) channels to differences in their amino acid sequences. By means of combined bioinformatic sequence analyses and homology modelling, we suggest that: (1) CNG channels are less voltage-dependent than K(v) channels since the charge of their voltage sensor, the S4 helix, is lower than that of K(v) channels and because of the presence of a conserved proline in the S4-S5 linker, which is quite likely to uncouple S4 from S5 and S6. (2) In HCN channels, S4 features a higher net positive charge with respect to K(v) channels and an extensive network of hydrophobic residues, which is quite likely to provide a tight coupling among S4 and the neighboring helices. We suggest insights on the gating of HCN channels and the reasons why they open with membrane hyperpolarization and with a significantly longer time constant with respect to other channels.

Amino Acid Motifs↗

PubMed2006

Embryonic stem cell-derived neurons form functional networks in vitro.

Embryonic stem (ES) cells provide a flexible and unlimited source for a variety of neuronal types. Because mature neurons establish neuronal networks very easily, we tested whether ES-derived neurons are capable of generating functional networks and whether these networks, generated in vitro, are capable of processing information. Single-cell electrophysiology with pharmacological antagonists demonstrated the presence of both excitatory and inhibitory synaptic connections. Extracellular recording with planar multielectrode arrays showed that spontaneous bursts of electrical activity are present in ES-derived networks with properties remarkably similar to those of hippocampal neurons. When stimulated with extracellular electrodes, ES-derived neurons fired action potentials, and the evoked electrical activity spread throughout the culture. A statistical analysis indicated that ES-derived networks discriminated between stimuli of different intensity at a single trial level, a key feature for an efficient information processing. Thus, ES-derived neurons provide a novel in vitro strategy to create functional networks with defined computational properties.

6-Cyano-7-nitroquinoxaline-2,3-dione↗

PubMed2006

Locking CNGA1 channels in the open and closed state.

With the aim of understanding the relation between structure and gating of CNGA1 channels from bovine rod, an extensive cysteine scanning mutagenesis was performed. Each residue from Phe-375 to Val-424 was mutated into a cysteine one at a time and the modification caused by various sulfhydryl reagents was analyzed. The addition of the mild oxidizing agent copper phenanthroline (CuP) in the open (presence of 1 mM cGMP) or closed state locked the channel in the respective states. A subsequent treatment with the reducing agent DTT restored normal gating fully in the open state and partially in the closed state. This action of CuP was not observed when F380 was mutated into a cysteine in the cysteine-free CNGA1 channel and in the double mutant C314S&F380C. These observations suggest that these effects are mediated by the formation of a disulfide bond (S-S) between F380C and the endogenous Cys-314 in the S5 segment. It can be rationalized by supposing that during gating the S6 segment rotates anticlockwise-when viewed from the extracellular side-by approximately 30 degrees .

Animals↗

PubMed2006

A versatile segmentation procedure.

In this paper, a new method for the segmentation of natural images is proposed. Original images g(x, y) are first regularized by using a self-adaptive implementation of the Mumford-Shah functional so that the two parameters alpha and gamma controlling the smoothness and fidelity, automatically adapt to the local scale and contrast of g(x, y). From the regularized image u(x, y) which is piecewise smooth, it is possible to obtain a piecewise constant image sN(x, y) representing a segmentation of the original image g(x, y). Indeed, sN(X, y) is the union of N closed regions, having a constant grey level, preserving thin bars and trihedral junctions present in the original image g(x, y). If the number N of closed regions is too high, closed regions can be merged by minimizing a functional which depends on a parameter n. When n is set equal to 1, a coarse segmentation is obtained with a few tens of distinct regions. With larger values of n, finer segmentations are obtained with about a hundred distinct regions. Therefore, by selecting the value of n it is possible to obtain segmentations at different resolutions. The proposed method for image segmentation was evaluated in two cases where a ground truth segmentation is available. The proposed procedure for image segmentation is rather versatile and depends on only one parameter n and seems suitable for higher level processing, such as categorization, recognition, and scene understanding.

Algorithms↗

PubMed2005

Calcium dynamics and compartmentalization in leech neurons.

Calcium dynamics in leech neurons were studied using a fast CCD camera. Fluorescence changes (DeltaF/F) of the membrane impermeable calcium indicator Oregon Green were measured. The dye was pressure injected into the soma of neurons under investigation. DeltaF/F caused by a single action potential (AP) in mechanosensory neurons had approximately the same amplitude and time course in the soma and in distal processes. By contrast, in other neurons such as the Anterior Pagoda neuron, the Annulus Erector motoneuron, the L motoneuron, and other motoneurons, APs evoked by passing depolarizing current in the soma produced much larger fluorescence changes in distal processes than in the soma. When APs were evoked by stimulating one distal axon through the root, DeltaF/F was large in all distal processes but very small in the soma. Our results show a clear compartmentalization of calcium dynamics in most leech neurons in which the soma does not give propagating action potentials. In such cells, the soma, while not excitable, can affect information processing by modulating the sites of origin and conduction of AP propagation in distal excitable processes.

Action Potentials↗

PubMed2005

Structural basis of gating of CNG channels.

Cyclic nucleotide-gated (CNG) ion channels, underlying sensory transduction in vertebrate photoreceptors and olfactory sensory neurons, require cyclic nucleotides to open. Here, we present structural models of the tetrameric CNG channel pore from bovine rod in both open and closed states, as obtained by combining homology modeling-based techniques, experimentally derived spatial constraints and structural patterns present in the PDB database. Gating is initiated by an anticlockwise rotation of the N-terminal region of the C-linker, which is then, transmitted through the S6 transmembrane helices to the P-helix, and in turn from this to the pore lumen, which opens up from 2 to 5A thus allowing for ion permeation. The approach, here presented, is expected to provide a general methodology for model ion channels and their gating when structural templates are available and an extensive electrophysiological analysis has been performed.

Amino Acid Sequence↗

PubMed2005

Statistics of decision making in the leech.

Animals continuously decide among different behaviors, but, even in invertebrates, the mechanisms underlying choice and decision are unknown. In this article, leech spontaneous behavior was tracked and quantified for up to 12 h. We obtained a statistical characterization, in space and time domains, of the decision processes underlying selection of behavior in the leech. We found that the spatial distribution of leech position in a uniform environment is isotropic (the same in all directions), but this isotropy is broken in the presence of localized external stimuli. In the time domain, transitions among behaviors can be described by a Markov process, the structure of which (allowed states and transitions) is highly conserved across individuals. Finally, a wide range of recurrent, deterministic motifs was identified in the apparently irregular and unstructured exploratory behavior. These results provide a rigorous description of the inner dynamics that control the spontaneous and continuous flow of behavioral decisions in the leech.

Animals↗

PubMed2005

Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.

The NMR high-resolution structure of calmodulin complexed with a fragment of the olfactory cyclic-nucleotide gated channel is described. This structure shows features that are unique for this complex, including an active role of the linker connecting the N- and C-lobes of calmodulin upon binding of the peptide. Such linker is not only involved in the formation of an hydrophobic pocket to accommodate a bulky peptide residue, but it also provides a positively charged region complementary to a negative charge of the target. This complex of calmodulin with a target not belonging to the kinase family was used to test the residual dipolar coupling (RDC) approach for the determination of calmodulin binding modes to peptides. Although the complex here characterized belongs to the (1--14) family, high Q values were obtained with all the 1:1 complexes for which crystalline structures are available. Reduction of the RDC data set used for the correlation analysis to structured regions of the complex allowed a clear identification of the binding mode. Excluded regions comprise calcium binding loops and loops connecting the EF-hand motifs.

Amino Acid Motifs↗

PubMed2005

Toward the neurocomputer: image processing and pattern recognition with neuronal cultures.

Information processing in the nervous system is based on parallel computation, adaptation and learning. These features cannot be easily implemented on conventional silicon devices. In order to obtain a better insight of how neurons process information, we have explored the possibility of using biological neurons as parallel and adaptable computing elements for image processing and pattern recognition. Commercially available multielectrode arrays (MEAs) were used to record and stimulate the electrical activity from neuronal cultures. By mapping digital images, i.e., arrays of pixels, into the stimulation of neuronal cultures, a low and bandpass filtering of images could be quickly and easily obtained. Responses to specific spatial patterns of stimulation were potentiated by an appropriate training (tetanization). Learning allowed pattern recognition and extraction of spatial features in processed images. Therefore, neurocomputers, (i.e., hybrid devices containing man-made elements and natural neurons) seem feasible and may become a new generation of computing devices, to be developed by a synergy of Neuroscience and Material Science.

Animals↗

PubMed2005

Statistical properties of information processing in neuronal networks.

Information processing and coding were analysed in dissociated hippocampal cultures, grown on multielectrode arrays. Multisite stimulation was used to activate different neurons and pathways of the network. The neural activity was binned into firing rates and the variability of the firing of individual neurons and of the whole population was analysed. In individual neurons, the timing of the first action potential (AP) was rather precise from trial to trial, whereas the timing of later APs was much more variable. Pooling APs in an ensemble of neurons reduced the variability of the response and allowed stimuli varying in intensity to be distinguished reliably in a single trial. A similar decrease of variability was observed pooling the first evoked APs in an ensemble of neurons. The size of the neuronal pool (approximately 50-100 neurons) and the time bin (approximately 20 ms) necessary to provide reproducible responses are remarkably similar to those obtained in in vivo preparations and in small nervous systems. Blockage of excitatory synaptic pathways mediated by NMDA receptors improved the mutual information between the evoked response and stimulus properties. When inhibitory GABAergic pathways were blocked by bicuculline the opposite effect was obtained. These results show how ensemble averages and an appropriate balance between inhibition and excitation allow neuronal networks to process information in a fast and reliable way.

Action Potentials↗

PubMed2004

Quantitative characterization and classification of leech behavior.

This paper describes an automatic system for the analysis and classification of leech behavior. Three colored beads were attached to the dorsal side of a free moving or pinned leech, and color CCD camera images were taken of the animal. The leech was restrained to moving in a small tank or petri dish, where the water level can be varied. An automatic system based on color processing tracked the colored beads over time, allowing real-time monitoring of the leech motion for several hours. At the end of each experimental session, six time series (2 for each bead) describing the leech body motion were obtained. A statistical analysis based on the speed and frequency content of bead motion indicated the existence of several stereotypical patterns of motion, corresponding to different leech behaviors. The identified patterns corresponded to swimming, pseudo-swimming, crawling, exploratory behavior, stationary states, abrupt movements, and combinations of these behaviors. The automatic characterization of leech behavior demonstrated here represents an important step toward understanding leech behavior and its properties. This method can be used to characterize the behavior of other invertebrates and also for some small vertebrates.

Animals↗

PubMed2004

Dynamics and reproducibility of a moderately complex sensory-motor response in the medicinal leech.

Local bending, a motor response caused by mechanical stimulation of the leech skin, has been shown to be remarkably reproducible, in its initial phase, despite the highly variable firing of motoneurons sustaining it. In this work, the reproducibility of local bending was further analyzed by monitoring it over a longer period of time and by using more intact preparations, in which muscle activation in an entire body segment was studied. Our experiments showed that local bending is a moderately complex motor response, composed of a sequence of four different phases, which were consistently identified in all leeches. During each phase, longitudinal and circular muscles in specific areas of the body segment acted synergistically, being co-activated or co-inhibited depending on their position relative to the stimulation site. Onset and duration of the first phase were reproducible across different trials and different animals as a result of the massive co-activation of excitatory motoneurons sustaining it. The other phases were produced by the inhibition of excitatory and activation of inhibitory motoneurons, and also by the intrinsic relaxation dynamics of leech muscles. As a consequence, their duration and relative timing was variable across different preparations, whereas their order of appearance was conserved. These results suggest that, during local bending, the leech neuromuscular system 1) operates a reduction of its available degrees of freedom, by simultaneously recruiting groups of otherwise antagonistic muscles and large populations of motoneurons; and 2) ensures reliability and effectiveness of this escape reflex, by guaranteeing the reproducibility of its crucial initial phase.

Animals↗

PubMed2004

Histidine 518 in the S6-CNBD linker controls pH dependence and gating of HCN channel from sea-urchin sperm.

Sperm motility is a tightly regulated process. One of the crucial factors determining the swimming of the sea-urchin sperm is an elevation of intracellular pH (pH(i)). The possibility that its hyperpolarisation-activated cyclic nucleotide-gated channel (SpHCN) is modulated directly by pH is addressed here. Site-directed mutagenesis showed that histidine 518 from the linker connecting the S6 helix with the cyclic nucleotide binding domain is responsible for the pH modulation of current kinetics and voltage dependence of activation. The effect of mutating histidine 518 to serine (H518S) on the time constant of activation was maximal at pH 6.4: 180+/-20 ms in the wild-type (wt) but only 56+/-10 ms in the H518S mutant channel. Furthermore, histidine 518 accounted for 31% of the shift in the voltage of half activation ( V(1/2)) in wt following a pH change from 6.4 to 8.4. The mutation H518S also shifted V(1/2) by 19 mV at pH 7.4 (-50.2+/-0.2 and -69+/-2 mV for H518S and wt, respectively). This indicates that histidine 518 couples voltage sensing to gating. The wt and H518S channels had a different affinity for cyclic adenosine monophosphate (cAMP) (IC(50) 1.0+/-0.02 and 2.5+/-0.06 microM, respectively). Changes in pH(i) also modulated channel selectivity.

Amino Acid Sequence↗

PubMed2004

Edge detection revisited.

The present manuscript aims at solving four problems of edge detection: the simultaneous detection of all step edges from a fine to a coarse scale; the detection of thin bars with a width of very few pixels; the detection of trihedral junctions; the development of an algorithm with image-independent parameters. The proposed solution of these problems combines an extensive spatial filtering with classical methods of computer vision and newly developed algorithms. Step edges are computed by extracting local maxima from the energy summed over a large bank of directional odd filters with a different scale. Thin roof edges are computed by considering maxima of the energy summed over narrow odd and even filters along the direction providing maximal response. Junctions are precisely detected and recovered using the output of directional filters. The proposed algorithm has a threshold for the minimum contrast of detected edges: for the large number of tested images this threshold was fixed equal to three times the standard deviation of the noise present in usual acquisition system (estimated to be between 1 and 1.3 gray levels out of 256), therefore, the proposed scheme is in fact parameter free. This scheme for edge detection performs better than the classical Canny edge detector in two quantitative comparisons: the recovery of the original image from the edge map and the structure from motion task. As the Canny detector in previous comparisons was shown to be the best or among the best detectors, the proposed scheme represents a significant improvement over previous approaches.

Algorithms↗

PubMed2003

Molecular modeling studies on CNG channel from bovine retinal rod: a structural model of the cyclic nucleotide-binding domain.

A dimeric model of the cyclic nucleotide-binding domain of the all-alpha homomeric cyclic nucleotide-gated channel from bovine retinal rod is constructed. The model, based on the structure of the fairly homologous catabolite gene activator protein (Weber and Steitz, J Mol Biol 1987;198:311-326), is obtained by use of comparative modeling and molecular dynamics simulations. Our model provides a structural basis for the experimentally measured difference in activity between cAMP and cGMP, as well as the different solvent accessibilities of GLY597 in the complex with cGMP, with cAMP and in the protein in free state. In addition, it provides support for the rearrangement of the domain C helix on ligand binding and releasing proposed by Matulef et al. (Neuron 1999;24:443-452).

Animals↗

PubMed2003

Two distinct calcium-calmodulin interactions with N-terminal regions of the olfactory and rod cyclic nucleotide-gated channels characterized by NMR spectroscopy.

The interactions of calcium-calmodulin with two fragments of the N-terminal domains of the olfactory alpha-subunit and rod beta-subunit cyclic nucleotide-gated channels have been investigated using nuclear magnetic resonance spectroscopy. The results indicate that in the two cases both the N-terminal and the C-terminal calmodulin lobes are involved in the interaction. The olfactory cyclic nucleotide-gated channel segment forms a 1:1 complex with calmodulin, whereas the rod fragment forms a 2:1 complex. The correlation times of the two complexes, as estimated by (15)N relaxation studies, are compatible with the observed stoichiometries. These results indicate differences in the mode of action by which calmodulin modulates the activity of both channels, and suggest either that the rod channel is modulated through a simultaneous interaction of two beta-subunits with calmodulin or that other regions of the N-terminus are necessarily implicated in the binding.

Amino Acid Sequence↗

PubMed2002

Highly variable spike trains underlie reproducible sensorimotor responses in the medicinal leech.

The nervous system of the leech is a particularly suitable model to investigate neural coding of sensorimotor responses because it allows both observation of behavior and the simultaneous measurement of a large fraction of its underlying neuronal activity. In this study, we used a combination of multielectrode recordings, videomicroscopy, and computation of the optical flow to investigate the reproducibility of the motor response caused by local mechanical stimulation of the leech skin. We analyzed variability at different levels of processing: mechanosensory neurons, motoneurons, muscle activation, and behavior. Spike trains in mechanosensory neurons were very reproducible, unlike those in motoneurons. The motor response, however, was reproducible because of two distinct biophysical mechanisms. First, leech muscles contract slowly and therefore are poorly sensitive to the jitter of motoneuron spikes. Second, the motor response results from the coactivation of a population of motoneurons firing in a statistically independent way, which reduces the variability of the population firing. These data show that reproducible spike trains are not required to sustain reproducible behaviors and illustrate how the nervous system can cope with unreliable components to produce reliable action.

Action Potentials↗

PubMed2002

Using optical flow to characterize sensory-motor interactions in a segment of the medicinal leech.

Activation of motoneurons innervating leech muscles causes the appearance of a two-dimensional vector field of deformations on the skin surface that can be fully characterized using a new technique (Zoccolan et al., 2001) based on the computation of the optical flow, the two-dimensional vector field describing the point displacements on the skin. These vector fields are characterized by their origin (i.e., the singular point) and by four elementary components that combine linearly: expansion (or compression), rotation, longitudinal shear, and oblique shear. All motoneurons can be classified and recognized according to the components of the deformations they elicit: longitudinal motoneurons give rise almost exclusively to longitudinal negative shear, whereas circular motoneurons give rise to both positive longitudinal shear and significant negative expansion. Oblique motoneurons induce strong oblique shear, in addition to longitudinal shear and negative expansion. Vector fields induced by the contraction of longitudinal, circular, and oblique fibers superimpose linearly. Skin deformations can therefore be attributed rather reliably to the contraction of distinct longitudinal, circular, and oblique muscle fibers. We compared the deformation patterns produced by touching the skin with those produced by intracellular stimulation of P, T, and N cells: vector fields resulting from the activation of P cells were almost identical to those produced by mechanical stimulation. Therefore, motor responses triggered by light or moderate touch are almost entirely mediated by excitation of P cells, with minor contributions from T and N cells.

Action Potentials↗