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Gordon M Shepherd

Publications and source records attributed to Gordon M Shepherd.

35 records · Page 2Linked to original sources
PubMed2004

Informatics approaches to functional MRI odor mapping of the rodent olfactory bulb: OdorMapBuilder and OdorMapDB.

The present study applies informatics tools to aid and extend fMRI analysis of the coding mechanism of neural signals in the rodent olfactory system. Odor stimulation evokes unique spatial patterns of activity in the glomerular layer of the mammalian olfactory bulb (OB). An open-source software program, OdorMap-Builder, has been developed to process the high resolution anatomical and functional MRI images of the OB and to generate single two-dimensional flat maps, called odor maps, that describe the spatial activity patterns in the entire glomerular layer. Odor maps help identify the spatial activity patterns from the tremendous amount of fMRI data and they serve as ideal representation of space coding for the olfactory signals in the OB in response to a given odor stimulation. Based on the fMRI technology, OdorMapBuilder provides comparable odor maps on the intra-subject basis, a significant step towards the detailed analyses of the effects of odor types and/or concentrations. In addition, a new database, OdorMapDB, is developed to provide a repository for the generated odor maps. Web interfaces to the database are provided for the data entry, modification and retrieval. OdorMapDB is based on the EAV/CR (entity-attribute-value with classes and relationships) architecture and it is integrated with two other SenseLab olfactory databases: the olfactory receptor and odor databases. Both OdorMapBuilder and OdorMapDB should serve as useful tools and resources for the field and help facilitate experimental research in understanding the olfactory system and the mechanism for smell perception.

Animals↗
PubMed2004

Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation.

Citations play an important role in medical and scientific databases by indicating the authoritative source of the data. Manual citation entry is tedious and prone to errors. We describe a method and make available computer scripts which automate the process of citation entry. We use an open citation project PERL module (PARSER) for parsing citation data that is then used to retrieve PubMed records to supply the (validated) reference. Our PERL scripts are available via a link in the web references section of this article.

Databases, Bibliographic↗
PubMed2003

Odor maps of aldehydes and esters revealed by functional MRI in the glomerular layer of the mouse olfactory bulb.

Odorant identity is believed to be encoded in the olfactory bulb (OB) by glomerular activity patterns. It has not yet been possible to visualize and compare entire patterns for different odorants in the same animal because of technical limitations. For this purpose we used high-resolution functional MRI at 7 T, combined with glomerular-layer flat maps, to reveal responses to aliphatic homologues in the mouse OB. These odorants elicited reproducible patterns in the OB, with the medial and lateral regions containing the most intense signals. Unexpectedly, in view of the symmetrical projections of olfactory receptor neurons to medial and lateral glomeruli, the activity patterns in these regions were asymmetrical. The highly activated medial and lateral areas were shared by homologous members, generating a conserved "family signature" for a homologous series. The moderately active areas, including the dorsal region that has been extensively studied by optical imaging, were more sensitive to the length of the carbon chain, producing more subtle features of individual members and different changing trends among homologues. The global mapping with functional MRI not only extended previous studies but also revealed additional rules for representation of homologues in the OB. Insights into possible relations between the functional patterns, molecular projections, and odor perception may now be obtained based on the global from the olfactory epithelium to the OB glomerular activity patterns.

Aldehydes↗
PubMed2003

Olfactory signal transduction in the mouse septal organ.

The septal organ, a distinct chemosensory organ observed in the mammalian nose, is essentially a small island of olfactory neuroepithelium located bilaterally at the ventral base of the nasal septum. Virtually nothing is known about its physiological properties and function. To understand the nature of the sensory neurons in this area, we studied the mechanisms underlying olfactory signal transduction in these neurons. The majority of the sensory neurons in the septal organ express olfactory-specific G-protein and adenylyl cyclase type III, suggesting that the cAMP signaling pathway plays a critical role in the septal organ as in the main olfactory epithelium (MOE). This is further supported by patch-clamp recordings from individual dendritic knobs of the sensory neurons in the septal organ. Odorant responses can be mimicked by an adenylyl cyclase activator and a phosphodiesterase inhibitor, and these responses can be blocked by an adenylyl cyclase inhibitor. There is a small subset of cells in the septal organ expressing a cGMP-stimulated phosphodiesterase (phosphodiesterase 2), a marker for the guanylyl cyclase-D subtype sensory neurons identified in the MOE. The results indicate that the septal organ resembles the MOE in major olfactory signal transduction pathways, odorant response properties, and projection to the main olfactory bulb. Molecular and functional analysis of the septal organ, which constitutes approximately 1% of the olfactory epithelium, will provide new insights into the organization of the mammalian olfactory system and the unique function this enigmatic organ may serve.

Adenylyl Cyclases↗
PubMed2003

Text mining neuroscience journal articles to populate neuroscience databases.

We have developed a program NeuroText to populate the neuroscience databases in SenseLab (http://senselab.med.yale.edu/senselab) by mining the natural language text of neuroscience articles. NeuroText uses a two-step approach to identify relevant articles. The first step (pre-processing), aimed at 100% sensitivity, identifies abstracts containing database keywords. In the second step, potentially relevant abstracts identified in the first step are processed for specificity dictated by database architecture, and neuroscience, lexical and semantic contexts. NeuroText results were presented to the experts for validation using a dynamically generated interface that also allows expert-validated articles to be automatically deposited into the databases. Of the test set of 912 articles, 735 were rejected at the pre-processing step. For the remaining articles, the accuracy of predicting database-relevant articles was 85%. Twenty-two articles were erroneously identified. NeuroText deferred decisions on 29 articles to the expert. A comparison of NeuroText results versus the experts' analyses revealed that the program failed to correctly identify articles' relevance due to concepts that did not yet exist in the knowledgebase or due to vaguely presented information in the abstracts. NeuroText uses two "evolution" techniques (supervised and unsupervised) that play an important role in the continual improvement of the retrieval results. Software that uses the NeuroText approach can facilitate the creation of curated, special-interest, bibliography databases.

Abstracting and Indexing↗
PubMed2003

Creating knowledgebases to text-mine PUBMED articles using clustering techniques.

Knowledgebase-mediated text-mining approaches work best when processing the natural language of domain-specific text. To enhance the utility of our successfully tested program-NeuroText, and to extend its methodologies to other domains, we have designed clustering algorithms, which is the principal step in automatically creating a knowledgebase. Our algorithms are designed to improve the quality of clustering by parsing the test corpus to include semantic and syntactic parsing

Algorithms↗
PubMed2002

Emerging rules for the distributions of active dendritic conductances.

A key goal in neuroscience is to explain how the operations of a neuron emerge from sets of active channels with specific dendritic distributions. If general principles can be identified for these distributions, dendritic channels should reflect the computational role of a given cell type within its functional neural circuit. Here, we discuss insights from experimental and computational data on the distribution of voltage-gated channels in dendrites, and attempt to derive rules for how their interactions implement different dendritic functions. We propose that this type of analysis will be important for understanding behavioural processes in terms of single-neuron properties, and that it constitutes a step towards a 'functional proteomics' of nerve cells, which will be essential for defining neuronal phenotypes.

Animals↗
PubMed2002

Multiple modes of action potential initiation and propagation in mitral cell primary dendrite.

The mitral cell primary dendrite plays an important role in transmitting distal olfactory nerve input from olfactory glomerulus to the soma-axon initial segment. To understand how dendritic active properties are involved in this transmission, we have combined dual soma and dendritic patch recordings with computational modeling to analyze action-potential initiation and propagation in the primary dendrite. In response to depolarizing current injection or distal olfactory nerve input, fast Na(+) action potentials were recorded along the entire length of the primary dendritic trunk. With weak-to-moderate olfactory nerve input, an action potential was initiated near the soma and then back-propagated into the primary dendrite. As olfactory nerve input increased, the initiation site suddenly shifted to the distal primary dendrite. Multi-compartmental modeling indicated that this abrupt shift of the spike-initiation site reflected an independent thresholding mechanism in the distal dendrite. When strong olfactory nerve excitation was paired with strong inhibition to the mitral cell basal secondary dendrites, a small fast prepotential was recorded at the soma, which indicated that an action potential was initiated in the distal primary dendrite but failed to propagate to the soma. As the inhibition became weaker, a "double-spike" was often observed at the dendritic recording site, corresponding to a single action potential at the soma. Simulation demonstrated that, in the course of forward propagation of the first dendritic spike, the action potential suddenly jumps from the middle of the dendrite to the axonal spike-initiation site, leaving the proximal part of primary dendrite unexcited by this initial dendritic spike. As Na(+) conductances in the proximal dendrite are not activated, they become available to support the back-propagation of the evoked somatic action potential to produce the second dendritic spike. In summary, the balance of spatially distributed excitatory and inhibitory inputs can dynamically switch the mitral cell firing among four different modes: axo-somatic initiation with back-propagation, dendritic initiation either with no forward propagation, forward propagation alone, or forward propagation followed by back-propagation.

Action Potentials↗
PubMedDate not supplied

The role of distal dendritic gap junctions in synchronization of mitral cell axonal output.

One of the first and most important stages of odor processing occurs in the glomerular units of the olfactory bulb and most likely involves mitral cell synchronization. Using a detailed model constrained by a number of experimental findings, we show how the intercellular coupling mediated by intraglomerular gap junctions (GJs) in the tuft dendrites could play a major role in sychronization of mitral cell action potential output in spite of their distal dendritic location. The model suggests that the high input resistance and active properties of the fine tuft dendrites are instrumental in generating local spike synchronization and an efficient forward and backpropagation of action potentials between the tuft and the soma. The model also gives insight into the physiological significance of long primary dendrites in mitral cells, and provides evidence against the use of reduced single compartmental models to investigate network properties of cortical pyramidal neurons.

Animals↗
PubMedDate not supplied

ModelDB: A Database to Support Computational Neuroscience.

Wider dissemination and testing of computational models are crucial to the field of computational neuroscience. Databases are being developed to meet this need. ModelDB is a web-accessible database for convenient entry, retrieval, and running of published models on different platforms. This article provides a guide to entering a new model into ModelDB.

Animals↗