Dendritic and axonal morphologies play fundamental roles in physiological brain function and pathological dysfunction by affecting synaptic integration, spike train transmission, and circuit connectivity. Incorporating published experimental data into accurate, full-scale, and biologically plausible neural network simulations is important for quantitatively bridging the sub-cellular and systems-levels. We successfully designed, implemented, and freely distributed to the community computer software and databases to reconstruct, analyze, visualize, simulate, and share the 3D tree-like shape of neurons collected from any labeling and visualization techniques, animal species, brain regions, developmental stages, and experimental conditions. We imaged by light microscopy, digitally traced, and shared new data, and we provided our peers with the electronic means of freely doing the same. Moreover, we combined those data with computational models of membrane biophysics to investigate the neuronal structure-activity relationship with a special focus on the hippocampus and entorhinal cortex due to their central role in spatial representation and episodic memory. We additionally annotated a massive amount of cellular properties in an open-source web-based portal of neuron types in the rodent hippocampal formation. We now propose to expand this research approach with three specific aims. The first is to augment the power, scope, and usability of the NeuroMorpho.Org repository of digital tracings. We plan to more than double the number of shared reconstructions while enhancing the human- and machine-accessible utility by adding ?search similar? and summary reporting functionalities. Most importantly for long-term sustainability, we will dramatically modernize the information technology infrastructure of this resource to enable unsolicited submissions directly from authors, continuous agile releases, and community crowdsourcing.
The second aim i s to complete the Hippocampome.org knowledge base by adding synaptic information, including connection probabilities, physiology, and plasticity, and linking them to the existing morphological, physiological, and molecular properties of pre- and post-synaptic neurons. This will enable the implementation of a real-scale spiking neural network model to run predictive simulations of activity dynamics and computational functions.
The third aim i s to develop an innovative approach to classify neurons directly from network connectivity, validating it with the hippocampal circuit and deploying it on open-access high-throughput data from a popular model organism. Together, these three aims will allow us (and others) to test hypotheses relating neuronal morphology to molecular and developmental determinants on the one hand, and to functional circuits on the other. The focus of this application on structural plasticity is especially relevant to disabling neurological diseases prominently involving the hippocampal formation, including epilepsy and Alzheimer?s. Our proposed data-driven, biologically realistic network simulations may shed light on the role of specific neuron types and of their interactions in impairments of memory formation and retrieval.
Generation and Description of Neuronal Morphology & Connectivity Brain connectivity and the intricate tree-like shape of individual nerve cells underlie cognitive and physiological functions, and are dramatically altered in almost all known neurological disorders. Using state-of-the-art information technology, data mining, and computational modeling, this project will synthesize, analyze, and freely share a massive amount of quantitative information on neuronal morphology and on the synaptic properties of an exemplary neural system responsible for spatial representation and autobiographic memories. These developments will enable the creation of detailed, biologically plausible, full-scale, quantitatively predictive neural network models to investigate the circuit dynamics of learning and related impairments for the long-lasting benefit of scientific advancement and public health.
|Akram, Masood A; Nanda, Sumit; Maraver, Patricia et al. (2018) An open repository for single-cell reconstructions of the brain forest. Sci Data 5:180006|
|Nanda, Sumit; Chen, Hanbo; Das, Ravi et al. (2018) Design and implementation of multi-signal and time-varying neural reconstructions. Sci Data 5:170207|
|Hamilton, D J; White, C M; Rees, C L et al. (2017) Molecular fingerprinting of principal neurons in the rodent hippocampus: A neuroinformatics approach. J Pharm Biomed Anal 144:269-278|
|Rees, Christopher L; White, Charise M; Ascoli, Giorgio A (2017) Neurochemical Markers in the Mammalian Brain: Structure, Roles in Synaptic Communication, and Pharmacological Relevance. Curr Med Chem 24:3077-3103|
|Rees, Christopher L; Moradi, Keivan; Ascoli, Giorgio A (2017) Weighing the Evidence in Peters' Rule: Does Neuronal Morphology Predict Connectivity? Trends Neurosci 40:63-71|
|Das, Ravi; Bhattacharjee, Shatabdi; Patel, Atit A et al. (2017) Dendritic Cytoskeletal Architecture Is Modulated by Combinatorial Transcriptional Regulation in Drosophila melanogaster. Genetics 207:1401-1421|
|Ascoli, Giorgio A; Maraver, Patricia; Nanda, Sumit et al. (2017) Win-win data sharing in neuroscience. Nat Methods 14:112-116|
|Hamilton, D J; Wheeler, D W; White, C M et al. (2017) Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties. Brain Inform 4:1-12|
|Ascoli, Giorgio A (2016) On the Data-Driven Road from Neurology to Neuronomy. Neuroinformatics 14:251-2|
|Ascoli, Giorgio A; Wheeler, Diek W (2016) In search of a periodic table of the neurons: Axonal-dendritic circuitry as the organizing principle: Patterns of axons and dendrites within distinct anatomical parcels provide the blueprint for circuit-based neuronal classification. Bioessays 38:969-76|
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