Statistical laws of protein motion in neuronal dendritic trees

  • Neurons are cells with a highly complex morphology; their dendritic arbor spans up to thousands of micrometers. This extended arbor poses a challenge for the logistics of neuronal processes: mRNA, proteins, and organelles have to be transported to dendrites, hundreds of micrometers away from the soma. This thesis aims to calculate the minimum number of proteins needed to populate the dendritic trees for different scenarios. In chapter 2, I analyzed the ability of different mechanisms to populate the dendritic arbor. I started from the solution of the diffusion equation in Sec. 2.1, then I included the contribution of active transport in Sec. 2.2 and showed how it could have either the effect of increasing the effective diffusion coefficient or of introducing a bias in the diffusion process. In Sec. 2.3 I studied the spatial distribution of locally synthesized protein, accordingly with actively and passively transported mRNA. In Sec. 2.5, I derived the boundary condition for branches showing a qualitatively different behavior of surface and cytoplasmic proteins induced by the medium’s dimensionality in which they diffuse. In chapter 3, I introduced the concept of protein requirement, defined as the minimum number of proteins that the neuron needs to produce to provide at least one protein to each micrometer of the dendritic arbor. In Sec. 3.1, I derived the protein requirement for diffusive proteins for somatic translation and constant translation in the dendritic arbor. In Sec. 3.2, I analyzed numerically the protein requirement in the case of actively transported protein synthesized in the soma, and, in Sec. 3.3, in the case of actively transported proteins synthesized in the dendritic arbor. In Sec. 3.4, I analyzed the protein requirement of protein synthesized in the dendrite accordingly with the distribution of mRNA described in Sec. 3.3 and 3.2. In Sec. 3.5, I derived the protein requirement for a single branch and purely diffusive proteins. In chapter 4, I analyzed the relation between the radii of the three afferent dendrites in a branch, their length, and the diffusion length of a protein. In Sec. 4.1 I derived the optimal ratio between the radii of the daughter dendrites that minimizes the protein requirement. In Sec. 4.3 I introduced the 3/2− Rall Rule and in Sec. 4.5 its generalization. Finally, I used those rules to estimate the fraction of proteins diffusing away from and toward the soma. In chapter 5, I analyzed the radii distribution for three categories of neurons: cultured hippocampal neurons in Sec. 5.1, stomatogastric ganglia neuron in Sec. 5.2, and 3DEM reconstructed prefrontal pyramidal neurons in Sec. 5.3. For each of these three classes, I analyzed the distribution of radii, Rall exponents, and the probability ratio. For most of them, I found that the probability of a protein diffusing away from the soma is higher for surface proteins than for cytoplasmic ones. I quantified this with a parameter called surface bias. In Chapter 6, I analyzed the fluorescent ratio imaged by our collaborators Anne-Sophie Hafner, for a surface protein, GFP::Nlg, and a soluble one, GFP, in cultured hippocampal neurons, and I compared the fluorescent ratio with the probability ratio obtained in 5.1, finding that they are in good agreement. In chapter 7, I compared the real dendritic morphologies imaged by one of our collaborators Ali Karimi with the optimal branching rule obtained in Sec. 4.1 and I calculated the cost for not having optimal branching radii. Finally, in Chapter 8, I used the knowledge of the branching statistics gathered in 5.3 to simulate the protein profile on three different classes of neurons: pyramidal neurons, granule neuron, and Purkinje neurons. I compared the protein profile for surface and cytoplasmic neurons for each morphology for two different values of the diffusion length: λ = 109µm and λ = 473µm, both for optimized radii and symmetrical radii. I showed how the radii optimization reduces the protein requirement of a factor 10 4 for pyramidal neurons.

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Author:Fabio Sartori
Place of publication:Frankfurt am Main
Referee:Tatjana Tchumatchenko, Jochen TrieschORCiD
Document Type:Doctoral Thesis
Date of Publication (online):2021/11/26
Year of first Publication:2021
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Granting Institution:Johann Wolfgang Goethe-Universität
Date of final exam:2021/09/20
Release Date:2021/12/08
Page Number:159
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 53 Physik / 530 Physik
Licence (German):License LogoDeutsches Urheberrecht