Efferent organization of the cat pulvinar complex, with a note on bilateral claustrocortical and reticulocortical connections.
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Animals↗
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Results for “connectivity mapping”
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Notes on the application of radioactive amino acids for the tracing of neuronal connections.
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Animals↗
Functional connectivity and pain: how effectively connected is your brain?
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Brain↗
Perspectives on the estimation of effective connectivity from neuroimaging data.
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Brain↗
Development of interhemispheric cortical connections.
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Aging↗
Gramene, a tool for grass genomics.
Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.
Avena↗
Identification and molecular characterization of E-MAP-115, a novel microtubule-associated protein predominantly expressed in epithelial cells.
A novel microtubule-associated protein (MAP) of M(r) 115,000 has been identified by screening of a HeLa cell cDNA expression library with an anti-serum raised against microtubule-binding proteins from HeLa cells. Monoclonal and affinity-purified polyclonal antibodies were generated for the further characterization of this MAP. It is different from the microtubule-binding proteins of similar molecular weights, characterized so far, by its nucleotide-insensitive binding to microtubules and different sedimentation behavior. Since it is predominantly expressed in cells of epithelial origin (Caco-2, HeLa, MDCK), and rare (human skin, A72) or not detectable (Vero) in fibroblastic cells, we name it E-MAP-115 (epithelial MAP of 115 kD). In HeLa cells, E-MAP-115 is preferentially associated with subdomains or subsets of perinuclear microtubules. In Caco-2 cells, labeling for E-MAP-115 increases when they polarize and form blisters. The molecular characterization of E-MAP-115 reveals that it is a novel protein with no significant homologies to other known proteins. The secondary structure predicted from its sequence indicates two domains connected by a putative hinge region rich in proline and alanine (PAPA region). E-MAP-115 has two highly charged regions with predicted alpha-helical structure, one basic with a pI of 10.9 in the NH2-terminal domain and one neutral with a pI of 7.6 immediately following the PAPA region in the acidic COOH-terminal half of the molecule. A novel microtubule-binding site has been localized to the basic alpha-helical region in the NH2-terminal domain using in vitro microtubule-binding assays and expression of mutant polypeptides in vivo. Overexpression of this domain of E-MAP-115 by transfection of fibroblasts lacking significant levels of this protein with its cDNA renders microtubules stable to nocodazole. We conclude that E-MAP-115 is a microtubule-stabilizing protein that may play an important role during reorganization of microtubules during polarization and differentiation of epithelial cells.
Alanine↗
Gene induction by coagulation factor Xa is mediated by activation of protease-activated receptor 1.
Cell signaling by coagulation factor Xa (Xa) contributes to pro-inflammatory responses in vivo. This study characterizes the signaling mechanism of Xa in a HeLa cell line that expresses protease-activated receptor 1 (PAR-1) but not PAR-2, -3, or -4. Xa induced NF-kappaB in HeLa cells efficiently but with delayed kinetics compared to thrombin. This delay caused no difference in gene expression patterns, as determined by high-density microarray analysis. Both proteases prominently induced the angiogenesis-promoting gene Cyr61 and connective tissue growth factor. Inhibition of PAR-1 cleavage abolished MAP kinase phosphorylation and gene induction by Xa, demonstrating that Xa signals through PAR-1 and not through a novel member of the PAR family. Activation of cell surface prothrombin with the snake venom enzyme Ecarin also produced PAR-1-dependent signaling. However, though the response to Ecarin was completely blocked by the thrombin inhibitor hirudin, the response to Xa was not. This suggests that the Xa response is not mediated by locally generated thrombin. The concentration dependence of Xa for PAR-1 activation is consistent with previously characterized Xa-mediated PAR-2 signaling, suggesting that local concentration of Xa on the cell surface, rather than sequence-specific recognition of the PAR scissile bond, determines receptor cleavage. This study demonstrates that PAR-1 cleavage by Xa can elicit the same cellular response as thrombin, but mechanistic differences in receptor recognition may be crucial for specific roles for Xa in signaling during spatial or temporal separation from thrombin generation.
Antithrombins↗
Functional connectivity from CA3 to the ipsilateral and contralateral CA1 in the rat dorsal hippocampus.
Anatomical advances have led to a reappraisal of the organization of hippocampal circuitry. However, it is not clear whether the functional connectivity is fully determined by the anatomical connectivity or whether it is significantly modified by feed-forward inhibition and modulatory inputs. Therefore, we have mapped CA1 responses evoked by stimulation of ipsilateral and contralateral CA3 in vivo. Population spike amplitude and threshold were plotted to produce response maps. All CA3 subregions projected diffusely to ipsilateral CA1. However, a pattern of maximal response emerged. Caudal CA3 stimulation evoked the maximal responses septally, while rostral CA3 responses were maximal temporally. The ipsilateral CA3 response maps were compared with those produced by stimulation at the homotopic point in the contralateral CA3. The CA1 areas of maximal functional connectivity were the same implying that there is convergence of the input to CA1 from homotopic CA3 sites in the two hippocampi. Although a response in CA1 was evoked widely, our results suggest that the functional connectivity is ordered, within and between the dorsal hippocampi, and that it is consistent with the recent anatomical data. The present findings allow more precise study of the propagation of normal and abnormal neuronal activity, within and between the dorsal hippocampi. Information on the site and speed of propagation of neuronal activity would be necessary for the development of a physiologically realistic model of hippocampal computation.
Animals↗
Connections of the piriform cortex in homing pigeons (Columba livia) studied with fast blue and WGA-HRP.
The piriform cortex in homing pigeons receives a projection from the olfactory bulb and is necessary for the operation of those aspects of the navigational map based on olfactory stimuli in these animals. The afferent and efferent projections of the piriform cortex were studied using retrograde migration of wheat-germ agglutinin horseradish peroxidase (WGA-HRP) and Fast Blue, and anterograde migration of WGA-HRP. The piriform cortex was found to receive projections from, and send projections to, numerous regions and nuclei in the telencephalon, diencephalon and lower brainstem. A reciprocal connection with the parahippocampal region suggests that the piriform cortex and hippocampal formation may be part of a neural system that regulates navigational map learning. The piriform cortex also connects reciprocally with a large portion of the anterior telencephalon, including the cortex prepiriformis and hyperstriatum dorsale. In general, the pathway connections of the piriform cortex in homing pigeons are similar to those of the piriform cortex in mammals.
Animals↗
Role of intrinsic synaptic circuitry in collicular sensorimotor integration.
The superficial gray layer of the superior colliculus contains a map that represents the visual field, whereas the underlying intermediate gray layer contains a vector map of the saccades that shift the direction of gaze. These two maps are aligned so that a particular region of the visual field is represented directly above the neurons that orient the highest acuity area of the retina toward that region. Although it has been proposed that the transmission of information from the visuosensory to the motor map plays an important role in the generation of visually guided saccades, experiments have failed to demonstrate any functional linkage between the two layers. We examined synaptic transmission between these layers in vitro by stimulating the superficial layer while using whole-cell patch-clamp methods to measure the responses of intermediate layer neurons. Stimulation of superficial layer neurons evoked excitatory postsynaptic currents in premotor cells. This synaptic input was columnar in organization, indicating that the connections between the layers link corresponding regions of the visuosensory and motor maps. Excitatory postsynaptic currents were large enough to evoke action potentials and often occurred in clusters similar in duration to the bursts of action potentials that premotor cells use to command saccades. Our results indicate the presence of functional connections between the superficial and intermediate layers and show that such connections could play a significant role in the generation of visually guided saccades.
Action Potentials↗
Neutralizing epitopes on the extracellular interferon gamma receptor (IFNgammaR) alpha-chain characterized by homolog scanning mutagenesis and X-ray crystal structure of the A6 fab-IFNgammaR1-108 complex.
The extracellular interferon gamma receptor alpha-chain comprises two immunoglobulin-like domains, each with fibronectin type-III topology, which are responsible for binding interferon gamma at the cell surface. The epitopes on the human receptor recognized by three neutralizing antibodies, A6, gammaR38 and gammaR99, have been mapped by homolog scanning mutagenesis. In this way, a loop connecting beta-strands C and C' in the N-terminal domain was identified as a key component of the epitopes bound by A6 and gammaR38, whereas gammaR99 binds to the C-terminal domain in a region including strands A and B and part of the large C'E loop. The epitope for A6 was confirmed in a crystal structure of a complex between a recombinant N-terminal receptor domain and the Fab fragment from A6, determined by X-ray diffraction to 2.8 A resolution. The antibody-antigen interface buries 1662 A2 of protein surface, including 22 antibody residues from five complementarity determining regions, primarily through interactions with the CC' surface loop of the receptor. The floor of the antigen binding cavity is formed mainly by residues from CDR L3 and CDR H3 while a surrounding ridge is formed by residues from all other CDRs except L2. Many potential polar interactions, as well as 13 aromatic side-chains, four in VL, six in VH and three in the receptor, are situated at the interface. The surface of the receptor contacted by A6 overlaps to a large extent with that contacted by interferon-gamma, in the ligand-receptor complex. However, the conformation of this epitope is very different in the two complexes, demonstrating that conformational mobility in a surface loop on this cytokine receptor permits steric and electrostatic complementarity to two quite differently shaped binding sites.
Amino Acid Sequence↗
Functional connectivity between the superficial and deeper layers of the superior colliculus: an anatomical substrate for sensorimotor integration.
The superior colliculus (SC) transforms both visual and nonvisual sensory signals into motor commands that control orienting behavior. Although the afferent and efferent connections of this midbrain nucleus have been well characterized, little is know about the intrinsic circuitry involved in sensorimotor integration. Transmission of visual signals from the superficial (sSC) to the deeper layers (dSC) of the SC has been implicated in both the triggering of orienting movements and the activity-dependent processes that align maps of different sensory modalities during development. However, evidence for the synaptic connectivity appropriate for these functions is lacking. In this study, we used a variety of anatomical and physiological methods to examine the functional organization of the sSC-dSC pathway in juvenile and adult ferrets. Axonal tracing in adult ferrets showed that, as in other species, sSC neurons project topographically to the dSC, providing a route for the transmission of visual signals to the multisensory output layers of the SC. We found that sSC axons terminate on dSC neurons that stain prominently for the NR1 subunit of the NMDA receptor, a subpopulation of which were identified as tectoreticulospinal projection neurons. We also show that the sSC-dSC pathway is topographically organized and mediated by monosynaptic excitatory synapses even before eye opening in young ferrets, suggesting that visual signals routed via the sSC may influence the activity of dSC neurons before the emergence of their multisensory response properties. These findings indicate that superficial- to deep-layer projections provide spatially ordered visual signals, both during development and into adulthood, directly to SC neurons that are involved in coordinating sensory inputs with motor outputs.
Age Factors↗
Spatial reciprocity of connections between areas 17 and 18 in the cat.
We examined whether the interconnections between areas 17 and 18 are spatially reciprocal, i.e., whether a column of cells in area 17 receives from the same region of area 18 as it sends projections to, and vice versa. We addressed this question by making side by side injections of retrograde fluorescent tracers in area 18, calculating the convergence and divergence of the connections from area 17 to 18. We compared these values with previously reported values of divergence and convergence of the projections from area 18 to area 17. The results demonstrate that there is a good match between the convergence and divergence of the area 17 to area 18 connection and, respectively, the divergence and convergence of the reverse connection. We confirmed directly the spatial reciprocity by injecting simultaneously in area 17 a retrograde and an anterograde tracer and by analyzing quantitatively the density of anterograde and retrograde labeling across the surface of area 18. There was an excellent match between the density maps of retrogradely labeled cells and anterogradely labeled axon terminals in area 18. Connections between areas 17 and 18 therefore exhibit large degrees of convergence and divergence and are spatially reciprocal. Thus, a given column of cells within one of these two areas is reciprocally interconnected with a large region of the opposite area. Such an organization may provide the basis for synchronization of firing of neurons across these two areas, as revealed by cross-correlation studies.
Amidines↗
Neural representation of language: activation versus long-range connectivity.
Cognitive functions are thought to build on connectivity within large-scale neuronal networks, rather than on strictly localized processes. Yet, present understanding of neural mechanisms of language function, as derived from neuroimaging, is based on mapping brain areas that are more active during specific linguistic tasks than in control conditions. Connectivity can then be evaluated among those areas. However, network nodes should ideally be determined based on their correlated time series of activity. Recent developments in analysis methods now facilitate localization and characterization of functionally connected neural networks directly from real-time magnetoencephalography data. Analysis of long-range connectivity might clarify and expand the view provided by traditional neurophysiological and hemodynamic activation studies. Here, we use silent reading as the example process.
Brain↗
IXDB, an X chromosome integrated database.
The integrated X chromosome database (IXDB) is a repository for physical mapping data of the human X chromosome. Its current content is the result of a strict integration of data stemming from many different sources. The main features of IXDB include a flexible and extendible schema, a comfortable and fully cross-referenced WWW interface (http://ixdb.mpimg-berlin-dahlem.mpg.de ) and a graphical map viewer implemented in JAVA. The database stores objects used in physical mapping as well as the maps resulting from this work, but a strong emphasis is placed on recording experiments that connect objects together. This should greatly contribute to fulfilling one of the major goals of the database: to support the construction of an integrated physical, genetic, transcript and sequence map of the human X chromosome.
Chromosome Mapping↗
Plasticity of binocular visual connections in the frog, Xenopus laevis: reversibility of effects of early visual deprivation.
In frogs, each lobe of the midbrain optic tectum receives two spatially aligned maps of binocular visual space, one through each eye. The map from the contralateral eye is the product of direct retinal input to the tectum, while that from the ipsilateral eye is mediated by a commissural system of connections that relays binocular visual information from one tectal lobe to the other. In Xenopus laevis, dark-reared from early life, the visuotectal map through the ipsilateral eye exhibits significant signs of disorder indicating that the normal development of the underlying "intertectal" system involves experience-dependent processes. Here we investigate the potential of this system for recovery from such deprivation-induced disruption. Three groups of animals were first dark-reared from embryonic stages until 3 months, 12 months or 2 years after metamorphosis. These short-, medium- and long-term periods of visual deprivation are associated with a progressive disturbance of the intertectal system (Grant and Keating 1989b). The animals then experienced 12-18 months in a normal visual environment, before an electrophysiological mapping experiment was carried out to reveal the status of their intertectal system. Quantitative analyses of the visuotopic order in the ipsilateral visuotectal map and of its spatial alignment with the map derived from the contralateral eye revealed that these features were completely normal in all 3 experimental groups. It is concluded that defects present in the intertectal system of dark-reared Xenopus can be repaired by subsequent visual experience, and that the reparative capacity is not limited either by the animal's age or by the existing degree of prior disruption.
Animals↗
Demonstration of electrical and anatomic connections between Marshall bundles and left atrium in dogs: implications on the generation of P waves on surface electrocardiogram.
INTRODUCTION: The muscle bundles within the ligament of Marshall (LOM) are electrically active. The importance of these muscle bundles (Marshall bundle [MB]) to atrial activation and the generation of the ECG P wave is unclear. METHODS AND RESULTS: We used optical mapping techniques to study epicardial activation patterns in isolated perfused left atrium in four dogs. In another seven dogs, P waves were studied before and after in vivo radiofrequency (RF) ablation of the connection between coronary sinus (CS) and the LOM. Computerized mapping was performed before and after RF ablation. Optical mapping studies showed that CS pacing resulted in broad wavefronts propagating from the middle and distal LOM directly to the adjacent left atrium (LA). Serial sections showed direct connection between MB and LA near the orifice of the left superior pulmonary vein in two dogs. In vivo studies showed that MB potentials were recorded in three dogs. After ablation, the duration of P waves remained unchanged. In the other four dogs, MB potentials were not recorded. Computerized mapping showed that LA wavefronts propagated to the MB region via LA-MB connection and then excited the CS. After ablation, the activation of CS muscle sleeves is delayed, and P wave duration increased from 65.3 +/- 14.9 msec to 70.5 +/- 17.2 msec (P = 0.025). CONCLUSION: In about half of the normal dogs, MB provides an electrical conduit between LA free wall and CS. Severing MB alters the atrial activation and lengthens the P wave. MB contributes to generation of the P wave on surface ECG.
Animals↗