356 research outputs found
The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers
This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information’s (NCBI’s) Entrez system. The NLB collects these links from each resource and passes them to the NCBI which incorporates them into its Entrez LinkOut service. In this way, an Entrez user looking at a specific Entrez entry can LinkOut directly to related neuroscience information. The information stored in the NLB can also be utilized in other ways. A second approach, which is operational on a pilot basis, is for the NLB Web server to create dynamically its own Web page of LinkOut links for each NCBI identifier in the NLB database. This approach can allow other resources (in addition to the NCBI Entrez) to LinkOut to related neuroscience information. The paper describes the current NLB system and discusses certain design issues that arose during its implementation
The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience
With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience’s Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line
Morphology of Dbx1 respiratory neurons in the preBotzinger complex and reticular formation of neonatal mice
The relationship between neuron morphology and function is a perennial issue in neuroscience. Information about synaptic integration, network connectivity, and the specific roles of neuronal subpopulations can be obtained through morphological analysis of key neurons within a microcircuit. Here we present morphologies of two classes of brainstem respiratory neurons. First, interneurons derived from Dbx1-expressing precursors (Dbx1 neurons) in the preBotzinger complex (preBotC) of the ventral medulla that generate the rhythm for inspiratory breathing movements. Second, Dbx1 neurons of the intermediate reticular formation that influence the motor pattern of pharyngeal and lingual movements during the inspiratory phase of the breathing cycle. We describe the image acquisition and subsequent digitization of morphologies of respiratory Dbx1 neurons from the preBotC and the intermediate reticular formation that were first recorded in vitro. These data can be analyzed comparatively to examine how morphology influences the roles of Dbx1 preBotC and Dbx1 reticular interneurons in respiration and can also be utilized to create morphologically accurate compartmental models for simulation and modeling of respiratory circuits
3D-printer visualization of neuron models
Neurons come in a wide variety of shapes and sizes. In a quest to understand this neuronal diversity, researchers have three-dimensionally traced tens of thousands of neurons; many of these tracings are freely available through online repositories like NeuroMorpho.Org and ModelDB. Tracings can be visualized on the computer screen, used for statistical analysis of the properties of different cell types, used to simulate neuronal behavior, and more. We introduce the use of 3D printing as a technique for visualizing traced morphologies. Our method for generating printable versions of a cell or group of cells is to expand dendrite and axon diameters and then to transform the wireframe tracing into a 3D object with a neuronal surface generating algorithm like Constructive Tessellated Neuronal Geometry (CTNG). We show that 3D printed cells can be readily examined, manipulated, and compared with other neurons to gain insight into both the biology and the reconstruction process. We share our printable models in a new database, 3DModelDB, and encourage others to do the same with cells that they generate using our code or other methods. To provide additional context, 3DModelDB provides a simulatable version of each cell, links to papers that use or describe it, and links to associated entries in other databases
Neuroanatomical and Morphological Properties of Neurons that Generate Inspiratory Related Breathing Rhythm and Influence Respiratory Motor Pattern in Mice
The relationship between neuron morphology and function is a perennial issue in neuroscience. Information about synaptic integration, network connectivity, and the specific roles of neuronal subpopulations can be obtained through morphological analysis of key neurons within any given microcircuit. Breathing is essential behavior for humans and all mammals, yet the neural microcircuit that governs respiration is not completely understood. The respiratory neural microcircuit resides within the ventral respiratory column located in the medulla. Within the respiratory column, the site of respiratory rhythm generation is the bilaterally distributed preBötzinger complex (preBötC). Rhythm-generating neurons in the preBötC are derived from a single genetic line, i.e., precursor cells expressing the transcription factor Developing brain homeobox-1 (Dbx1). An analysis of over 40 dendritic morphological features of rhythmogenic Dbx1 preBötC neurons and putatively premotor Dbx1 neurons in the intermediate reticular formation, revealed these two populations are similar except reticular neurons have a larger dendritic diameter, which may contribute to a greater passive transmembrane conductance. Both populations showed commissural axon projections and reticular formation neurons show premotor-like projections to the XII motor nucleus. These morphological data provide additional evidence supporting bilateral synchronization the preBötC through Dbx1 neurons, and demonstrate that Dbx1 preBötC neuron connectivity includes recurrent interconnections. On the molecular level, the ion channels that mediate rhythm-generating whole-cell ion currents have not been not identified, and were investigated using principally an anatomical approach. The nonspecific cation current, ICAN, underlies robust inspiratory drive potentials in the preBötC and the persistent sodium current, INaP may play a role in the production of robust bursts when respiration is challenged in such cases as anoxia or hypoxia. The leading candidate for ion channels that contribute to ICAN belong to the transient membrane receptor (Trp) ion channel superfamily and the leading ion channel candidate for INaP is Nav1.6. I determined the presence of Trpc3 ion channels and Nav1.6 ion channels on Dbx1 preBötC neurons (as well as their expression in neighboring non-Dbx1 preBötC neurons). Finally, breathing behavior involves periodic sighs, which are slower than normal eupneic breathing but critical for lung function. I examined receptor expression for bomebsin-like peptides neuromedin B (NMB) and gastrin releasing peptide (GRP), which are important for sigh behavior. I show that NMB and GRP receptors are expressed in Dbx1 preBötC neurons and are not expressed by glia in the preBötC, as posited by some because of the low frequency of sigh breaths. These advances in morphological and anatomical knowledge can be used to design targeted in vitro and in vivo experiments to further explore their role in respiratory rhythm and pattern generation
Design and implementation of multi-signal and time-varying neural reconstructions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.Several efficient procedures exist to digitally trace neuronal structure from light microscopy, and mature community resources have emerged to store, share, and analyze these datasets. In contrast, the quantification of intracellular distributions and morphological dynamics is not yet standardized. Current widespread descriptions of neuron morphology are static and inadequate for subcellular characterizations. We introduce a new file format to represent multichannel information as well as an open-source Vaa3D plugin to acquire this type of data. Next we define a novel data structure to capture morphological dynamics, and demonstrate its application to different time-lapse experiments. Importantly, we designed both innovations as judicious extensions of the classic SWC format, thus ensuring full back-compatibility with popular visualization and modeling tools. We then deploy the combined multichannel/time-varying reconstruction system on developing neurons in live Drosophila larvae by digitally tracing fluorescently labeled cytoskeletal components along with overall dendritic morphology as they changed over time. This same design is also suitable for quantifying dendritic calcium dynamics and tracking arbor-wide movement of any subcellular substrate of interest.Peer reviewe
1st INCF Workshop on Global Portal Services for Neuroscience
The goal of this meeting was to map out existing portal services for neuroscience, identify their features and future plans, and outline opportunities for synergistic developments. The workshop discussed alternative formats of future global and integrated portal services
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