A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model.
Relating structure and function of neuronal circuits is a challenging problem. It requires demonstrating how dynamical patterns of spiking activity lead to functions like cognitive behaviour and identifying the neurons and connections that lead to appropriate activity of a circuit. We apply a "...
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089461&type=printable |
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| author | Roman Borisyuk Abul Kalam Al Azad Deborah Conte Alan Roberts Stephen R Soffe |
| author_facet | Roman Borisyuk Abul Kalam Al Azad Deborah Conte Alan Roberts Stephen R Soffe |
| author_sort | Roman Borisyuk |
| collection | DOAJ |
| description | Relating structure and function of neuronal circuits is a challenging problem. It requires demonstrating how dynamical patterns of spiking activity lead to functions like cognitive behaviour and identifying the neurons and connections that lead to appropriate activity of a circuit. We apply a "developmental approach" to define the connectome of a simple nervous system, where connections between neurons are not prescribed but appear as a result of neuron growth. A gradient based mathematical model of two-dimensional axon growth from rows of undifferentiated neurons is derived for the different types of neurons in the brainstem and spinal cord of young tadpoles of the frog Xenopus. Model parameters define a two-dimensional CNS growth environment with three gradient cues and the specific responsiveness of the axons of each neuron type to these cues. The model is described by a nonlinear system of three difference equations; it includes a random variable, and takes specific neuron characteristics into account. Anatomical measurements are first used to position cell bodies in rows and define axon origins. Then a generalization procedure allows information on the axons of individual neurons from small anatomical datasets to be used to generate larger artificial datasets. To specify parameters in the axon growth model we use a stochastic optimization procedure, derive a cost function and find the optimal parameters for each type of neuron. Our biologically realistic model of axon growth starts from axon outgrowth from the cell body and generates multiple axons for each different neuron type with statistical properties matching those of real axons. We illustrate how the axon growth model works for neurons with axons which grow to the same and the opposite side of the CNS. We then show how, by adding a simple specification for dendrite morphology, our model "developmental approach" allows us to generate biologically-realistic connectomes. |
| format | Article |
| id | doaj-art-7585edcbbd9744b3b8f35bd87d8cc137 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-7585edcbbd9744b3b8f35bd87d8cc1372025-08-20T03:11:55ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0192e8946110.1371/journal.pone.0089461A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model.Roman BorisyukAbul Kalam Al AzadDeborah ConteAlan RobertsStephen R SoffeRelating structure and function of neuronal circuits is a challenging problem. It requires demonstrating how dynamical patterns of spiking activity lead to functions like cognitive behaviour and identifying the neurons and connections that lead to appropriate activity of a circuit. We apply a "developmental approach" to define the connectome of a simple nervous system, where connections between neurons are not prescribed but appear as a result of neuron growth. A gradient based mathematical model of two-dimensional axon growth from rows of undifferentiated neurons is derived for the different types of neurons in the brainstem and spinal cord of young tadpoles of the frog Xenopus. Model parameters define a two-dimensional CNS growth environment with three gradient cues and the specific responsiveness of the axons of each neuron type to these cues. The model is described by a nonlinear system of three difference equations; it includes a random variable, and takes specific neuron characteristics into account. Anatomical measurements are first used to position cell bodies in rows and define axon origins. Then a generalization procedure allows information on the axons of individual neurons from small anatomical datasets to be used to generate larger artificial datasets. To specify parameters in the axon growth model we use a stochastic optimization procedure, derive a cost function and find the optimal parameters for each type of neuron. Our biologically realistic model of axon growth starts from axon outgrowth from the cell body and generates multiple axons for each different neuron type with statistical properties matching those of real axons. We illustrate how the axon growth model works for neurons with axons which grow to the same and the opposite side of the CNS. We then show how, by adding a simple specification for dendrite morphology, our model "developmental approach" allows us to generate biologically-realistic connectomes.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089461&type=printable |
| spellingShingle | Roman Borisyuk Abul Kalam Al Azad Deborah Conte Alan Roberts Stephen R Soffe A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. PLoS ONE |
| title | A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. |
| title_full | A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. |
| title_fullStr | A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. |
| title_full_unstemmed | A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. |
| title_short | A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. |
| title_sort | developmental approach to predicting neuronal connectivity from small biological datasets a gradient based neuron growth model |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089461&type=printable |
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