Statistics and geometry of orientation selectivity in primary visual cortex

Orientation maps are a prominent feature of the primary visual cortex of higher mammals. In macaques and cats, for example, preferred orientations of neurons are organized in a specific pattern, where cells with similar selectivity are clustered in iso-orientation domains. However, the map is not always continuous, and there are pinwheel-like singularities around which all orientations are arranged in an orderly fashion. Although subject of intense investigation for half a century now, it is still not entirely clear how these maps emerge and what function they might serve. Here, we suggest a new model of orientation selectivity that combines the geometry and statistics of clustered thalamocortical afferents to explain the emergence of orientation maps. We show that the model can generate spatial patterns of orientation selectivity closely resembling the maps found in cats or monkeys. Without any additional assumptions, we further show that the pattern of ocular dominance columns is inherently connected to the spatial pattern of orientation.     

Functional organization of adult motor cortex is dependent upon continued protein synthesis

The functional organization of adult cerebral cortex is characterized by the presence of highly ordered sensory and motor maps. Despite their archetypical organization, the maps maintain the capacity to rapidly reorganize, suggesting that the neural circuitry underlying cortical representations is inherently plastic. Here we show that the circuitry supporting motor maps is dependent upon continued protein synthesis. Injections of two different protein synthesis inhibitors into adult rat forelimb motor cortex caused an immediate and enduring loss of movement representations. The disappearance of the motor map was accompanied by a significant reduction in synapse number, synapse size, and cortical field potentials and caused skilled forelimb movement impairments. Further, motor skill training led to a reappearance of movement representations. We propose that the circuitry of adult motor cortex is perpetually labile and requires continued protein synthesis in order to maintain its functional organization.     

Functional connectivity models for decoding of spatial representations from hippocampal CA1 recordings

Hippocampus stores spatial representations, or maps, which are recalled each time a subject is placed in the corresponding environment. Across different environments of similar geometry, these representations show strong orthogonality in CA3 of hippocampus, whereas in the CA1 subfield a considerable overlap between the maps can be seen. The lower orthogonality decreases reliability of various decoders developed in an attempt to identify which of the stored maps is active at the moment. Especially, the problem with decoding emerges with a need to analyze data at high temporal resolution. Here, we introduce a functional-connectivity-based decoder, which accounts for the pairwise correlations between the spiking activities of neurons in each map and does not require any positional information, i.e. any knowledge about place fields. We first show, on recordings of hippocampal activity in constant environmental conditions, that our decoder outperforms existing decoding methods in CA1. Our decoder is then applied to data from teleportation experiments, in which an instantaneous switch between the environment identity triggers a recall of the corresponding spatial representation . We test the sensitivity of our approach on the transition dynamics between the respective memory states (maps). We find that the rate of spontaneous state shifts (flickering) after a teleportation event is increased not only within the first few seconds as already reported, but this instability is sustained across much longer (> 1 min.) periods.     

3D electron microscopy of the interaction of kinesin with tubulin

We have studied the structure of microtubules decorated with kinesin motor domains in different nucleotide states by 3D electron microscopy. Having docked the atomic coordinates of both dimeric ADP.kinesin and tubulin heterodimer into a map of kinesin dimers bound to microtubules in the presence of ADP, we try to predict which regions of the proteins interact in the weakly binding state. When either the presence of 5'-adenylyimidodiphosphate (AMP-PNP) or an absence of nucleotides puts motor domains into a strongly-bound state, the 3D maps show changes in the motor domains which modify their interaction with beta-tubulin. The maps also show differences in beta-tubulin conformation compared with undecorated microtubules or those decorated with weakly-bound motors. Strongly-bound ncd appears to produce an identical change.     

Topographic motor projections in the limb imposed by LIM homeodomain protein regulation of ephrin-A:EphA interactions

The formation of topographic neural maps relies on the coordinate assignment of neuronal cell body position and axonal trajectory. The projection of motor neurons of the lateral motor column (LMC) along the dorsoventral axis of the limb mesenchyme constitutes a simple topographic map that is organized in a binary manner. We show that LIM homeodomain proteins establish motor neuron topography by coordinating the mediolateral settling position of motor neurons within the LMC with the dorsoventral selection of axon pathways in the limb. These topographic projections are established, in part, through LIM homeodomain protein control of EphA receptors and ephrin-A ligands in motor neurons and limb mesenchymal cells.     

Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein, Ncd

Molecular motors undergo conformational changes to produce force and move along cytoskeletal filaments. Structural changes have been detected in kinesin motors; however, further changes are expected because previous crystal structures are in the same or closely related conformations. We report here a 2.5 A crystal structure of the minus-end kinesin, Ncd, with the coiled-coil stalk/neck and one head rotated by approximately 75 degrees relative to the other head. The two heads are asymmetrically positioned with respect to the stalk and show asymmetry of nucleotide state: one head is fully occupied, but the other is unstably bound to ADP. Unlike previous structures, our new atomic model can be fit into cryoelectron microscopy density maps of the motor attached to microtubules, where it appears to resemble a one-head-bound motor with the stalk rotated towards the minus end. Interactions between neck and motor core residues, observed in the head that moves with the stalk, are disrupted in the other head, permitting rotation of the stalk/neck. The rotation could represent a force-producing stroke that directs the motor to the minus end.     

Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor

Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.     

Brain maps on the go: functional imaging during motor challenge in animals

Brain mapping in the freely moving animal is useful for studying motor circuits, not only because it avoids the potential confound of sedation or restraints, but because activated brain states may serve to accentuate differences that only manifest partially while a subject is in the resting state. Perfusion or metabolic mapping using autoradiography allows one to examine changes in brain function at the circuit level across the entire brain with a spatial resolution (100 μ) appropriate for the rat or mouse brain, and a temporal resolution (seconds–minutes) sufficient for capturing acute brain changes. Here we summarize the application of these methods to the functional brain mapping of behaviors involving locomotion of small animals, methods for the three-dimensional reconstruction of the brain from autoradiographic sections, voxel based analysis of the whole brain, and generation of maps of the flattened rat cortex. Application of these methods in animal models promises utility in improving our understanding of motor function in the normal brain, and of the effects of neuropathology and treatment interventions such as exercise have on the reorganization of motor circuits.     

A central back-coupling hypothesis on the organization of motor synergies: a physical metaphor and a neural model

We offer a hypothesis on the organization of multi-effector motor synergies and illustrate it with the task of force production with a set of fingers. A physical metaphor, a leaking bucket, is analyzed to demonstrate that an inanimate structure can show apparent error compensation among its elements. A neural model is developed using tunable back-coupling loops as means of assuring error compensation in a task-specific way. The model demonstrates non-trivial features of multi-finger interaction such as delayed emergence of force stabilizing synergies and simultaneous stabilization of the total force and total moment produced by the fingers. The hypothesis suggests that neurophysiological structures involving short-latency feedback may play a central role in the formation of motor synergies.     

KIF14 Binds Tightly to Microtubules and Adopts a Rigor-Like Conformation

The mitotic kinesin motor protein KIF14 is essential for cytokinesis during cell division and has been implicated in cerebral development and a variety of human cancers. Here we show that the mouse KIF14 motor domain binds tightly to microtubules and does not display typical nucleotide-dependent changes in this affinity. It also has robust ATPase activity but very slow motility. A crystal structure of the ADP-bound form of the KIF14 motor domain reveals a dramatically opened ATP-binding pocket, as if ready to exchange its bound ADP for Mg·ATP. In this state, the central β-sheet is twisted ~ 10° beyond the maximal amount observed in other kinesins. This configuration has only been seen in the nucleotide-free states of myosins—known as the “rigor-like” state. Fitting of this atomic model to electron density maps from cryo-electron microscopy indicates a distinct binding configuration of the motor domain to microtubules. We postulate that these properties of KIF14 are well suited for stabilizing midbody microtubules during cytokinesis.     

All-atom structural investigation of kinesin-microtubule complex constrained by high-quality cryo-electron-microscopy maps

In this study, we have performed a comprehensive structural investigation of three major biochemical states of a kinesin complexed with microtubule under the constraint of high-quality cryo-electron-microscopy (EM) maps. In addition to the ADP and ATP state which were captured by X-ray crystallography, we have also modeled the nucleotide-free or APO state for which no crystal structure is available. We have combined flexible fitting of EM maps with regular molecular dynamics simulations, hydrogen-bond analysis, and free energy calculation. Our APO-state models feature a subdomain rotation involving loop L2 and α6 helix of kinesin, and local structural changes in active site similar to a related motor protein, myosin. We have identified a list of hydrogen bonds involving key residues in the active site and the binding interface between kinesin and microtubule. Some of these hydrogen bonds may play an important role in coupling microtubule binding to ATPase activities in kinesin. We have validated our models by calculating the binding free energy between kinesin and microtubule, which quantitatively accounts for the observation of strong binding in the APO and ATP state and weak binding in the ADP state. This study will offer promising targets for future mutational and functional studies to investigate the mechanism of kinesin motors.     

Astrocytic production of nerve growth factor in motor neuron apoptosis: implications for amyotrophic lateral sclerosis

Reactive astrocytes frequently surround degenerating motor neurons in patients and transgenic animal models of amyotrophic lateral sclerosis (ALS). We report here that reactive astrocytes in the ventral spinal cord of transgenic ALS-mutant G93A superoxide dismutase (SOD) mice expressed nerve growth factor (NGF) in regions where degenerating motor neurons expressed p75 neurotrophin receptor (p75(NTR)) and were immunoreactive for nitrotyrosine. Cultured spinal cord astrocytes incubated with lipopolysaccharide (LPS) or peroxynitrite became reactive and accumulated NGF in the culture medium. Reactive astrocytes caused apoptosis of embryonic rat motor neurons plated on the top of the monolayer. Such motor neuron apoptosis could be prevented when either NGF or p75(NTR) was inhibited with blocking antibodies. In addition, nitric oxide synthase inhibitors were also protective. Exogenous NGF stimulated motor neuron apoptosis only in the presence of a low steady state concentration of nitric oxide. NGF induced apoptosis in motor neurons from p75(NTR +/+) mouse embryos but had no effect in p75(NTR -/-) knockout embryos. Culture media from reactive astrocytes as well as spinal cord lysates from symptomatic G93A SOD mice-stimulated motor neuron apoptosis, but only when incubated with exogenous nitric oxide. This effect was prevented by either NGF or p75(NTR) blocking-antibodies suggesting that it might be mediated by NGF and/or its precursor forms. Our findings show that NGF secreted by reactive astrocytes induce the death of p75-expressing motor neurons by a mechanism involving nitric oxide and peroxynitrite formation. Thus, reactive astrocytes might contribute to the progressive motor neuron degeneration characterizing ALS.     

Modeling shape and topology of low-resolution density maps of biological macromolecules

In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory.     

Long-range information and physicality constraints improve predicted protein contact maps

Protein topology representations such as residue contact maps are an important intermediate step towards ab initio prediction of protein structure, but the problem of predicting reliable contact maps is far from solved. One of the main pitfalls of existing contact map predictors is that they generally predict unphysical maps, i.e. maps that cannot be embedded into three-dimensional structures or, at best, violate a number of basic constraints observed in real protein structures, such as the maximum number of contacts for a residue. Here, we focus on the problem of learning to predict more "physical" contact maps. We do so by first predicting contact maps through a traditional system (XXStout), and then filtering these maps by an ensemble of artificial neural networks. The filter is provided as input not only the bare predicted map, but also a number of global or long-range features extracted from it. In a rigorous cross-validation test, we show that the filter greatly improves the predicted maps it is input. CASP7 results, on which we report here, corroborate this finding. Importantly, since the approach we present here is fully modular, it may be beneficial to any other ab initio contact map predictor.     

Structural analysis of the ZEN-4/CeMKLP1 motor domain and its interaction with microtubules

The centralspindlin complex is required for the assembly and maintenance of the central spindle during late anaphase and the completion of cytokinesis. It is composed of two copies each of the kinesin-like protein ZEN-4, a Caenorhabditis elegans MKLP-1 (Kinesin-6 family), and the RhoGAP CYK-4. By using cryo-electron microscopy and helical 3D reconstruction, we are investigating the structural features of the interactions between monomeric and dimeric motor domain constructs of ZEN-4 and microtubules. We have calculated helically averaged 3D maps of microtubules decorated with ZEN-4 motor domain in the presence of AMP-PNP, ADP, ADP-AlF(4)(-), and nucleotide-free conditions. We used statistical difference mapping to compare these maps among each other and to related maps obtained from microtubules decorated with a well-characterized Kinesin-1 motor domain from Neurospora crassa. Thereby, we found distinct structural features in microtubule-ZEN-4 complexes that may directly relate to the functional properties of ZEN-4 and centralspindlin. Furthermore, we investigated the location, structure, and function of a highly conserved extension of approximately 50 residues unique to the Kinesin-6 subfamily, located in the motor core loop6/beta4 region.     

Neuropilar Projections of the Anterior Gastric Receptor Neuron in the Stomatogastric Ganglion of the Jonah Crab,Cancer Borealis

Sensory neurons provide important feedback to pattern-generating motor systems. In the crustacean stomatogastric nervous system (STNS), feedback from the anterior gastric receptor (AGR), a muscle receptor neuron, shapes the activity of motor circuits in the stomatogastric ganglion (STG) via polysynaptic pathways involving anterior ganglia. The AGR soma is located in the dorsal ventricular nerve posterior to the STG and it has been thought that its axon passes through the STG without making contacts. Using high-resolution confocal microscopy with dye-filled neurons, we show here that AGR from the crab Cancer borealis also has local projections within the STG and that these projections form candidate contact sites with STG motor neurons or with descending input fibers from other ganglia. We develop and exploit a new masking method that allows us to potentially separate presynaptic and postsynaptic staining of synaptic markers. The AGR processes in the STG show diversity in shape, number of branches and branching structure. The number of AGR projections in the STG ranges from one to three simple to multiply branched processes. The projections come in close contact with gastric motor neurons and descending neurons and may also be electrically coupled to other neurons of the STNS. Thus, in addition to well described long-loop pathways, it is possible that AGR is involved in integration and pattern regulation directly in the STG.     

Analysis of the hotfoot (ho) locus by creation of an insertional mutation in a transgenic mouse.

Hotfoot (ho) mutation is a recessive trait in mice, characterized by motor disorder and male sterility, that maps to chromosome 6. We have identified a transgenic mouse pedigree with a similar trait. Using genetic and molecular approaches, we have demonstrated that the foreign DNA element is located in or near the ho locus. This new allele, designated hoJwg and presumably created by insertional mutagenesis, should make it possible to clone the ho gene. Male infertility in hoJwg male homozygotes was determined to be due to inability of sperm to penetrate the zona pellucida. This was demonstrated by rescuing mutant males by a new technique of gamete micromanipulation, zona pellucida drilling. These findings show that zona drilling is useful both for analysis and preservation of animals with reduced male fertility.     

Comparable ecological dynamics underlie early cancer invasion and species dispersal, involving self-organizing processes

Occupancy of new habitats through dispersion is a central process in nature. In particular, long-distance dispersal is involved in the spread of species and epidemics, although it has not been previously related with cancer invasion, a process that involves cell spreading to tissues far away from the primary tumour.Using simulations and real data we show that the early spread of cancer cells is similar to the species individuals spread and we suggest that both processes are represented by a common spatio-temporal signature of long-distance dispersal and subsequent local proliferation. This signature is characterized by a particular fractal geometry of the boundaries of patches generated, and a power-law scaled, disrupted patch size distribution. In contrast, invasions involving only dispersal but not subsequent proliferation (“physiological invasions”) like trophoblast cells invasion during normal human placentation did not show the patch size power-law pattern. Our results are consistent under different temporal and spatial scales, and under different resolution levels of analysis.We conclude that the scaling properties are a hallmark and a direct result of long-distance dispersal and proliferation, and that they could reflect homologous ecological processes of population self-organization during cancer and species spread. Our results are significant for the detection of processes involving long-range dispersal and proliferation like cancer local invasion and metastasis, biological invasions and epidemics, and for the formulation of new cancer therapeutical approaches.