Connectomics

Connectomics is the production and study of connectomes: comprehensive maps of connections within an organism's nervous system, typically its brain or eye. Because these structures are extremely complex, methods within this field use a high-throughput application of neural imaging and histological techniques in order to increase the speed, efficiency, and resolution of maps of the multitude of neural connections in a nervous system. While the principal focus of such a project is the brain, any neural connections could theoretically be mapped by connectomics, including, for example, neuromuscular junctions.[1]

Tools

One of the main tools used for connectomics research at the macroscale level is diffusion MRI.[2] The main tool for connectomics research at the microscale level is chemical brain preservation followed by 3D electron microscopy,[3] used for neural circuit reconstruction. To see one of the first micro-connectomes at full-resolution, visit the Open Connectome Project, which is hosting several connectome datasets, including the 12TB dataset from Bock et al. (2011).

Model systems

Aside from the human brain, some of the model systems used for connectomics research are the mouse,[4] the fruit fly,[5] the nematode C. elegans,[6][7] and the barn owl.[8]

Applications

By comparing diseased connectome and healthy connectomes, we should gain insight into certain psychopathologies, such as neuropathic pain, and potential therapies for them. Generally, the field of neuroscience would benefit from standardization and raw data. For example, connectome maps can be used to inform computational models of whole-brain dynamics.[9] Current neural networks mostly rely on probabilistic representations of connectivity patterns.[10] Connectograms (circular diagrams of connectomics) have been used in traumatic brain injury cases to document the extent of damage to neural networks.[11][12]

Criticism

The use of the word -omics to describe this system has been criticized.[13][14] The coinage of the word is seen in two sources, in an article by Olaf Sporns[15] and a PhD thesis by Patric Hagmann.[16]

Others have criticized attempts towards a microscale connectome, arguing that we don't have enough knowledge about where to look for insights, or that it cannot be completed within a realistic time frame.[17]

Comparison to genomics

The human genome project initially faced many of the above criticisms, but was nevertheless completed ahead of schedule and has led to many advances in genetics. Some have argued that analogies can be made between genomics and connectomics, and therefore we should be at least slightly more optimistic about the prospects in connectomics.[18]

See also

References

  1. ↑ Boonstra, Tjeerd W.; Danna-Dos-Santos, Alessander; Hong-Bo, Xie.; Roerdink, Melvyn; Stins, John F.; Breakspear, Michael (2015). "Muscle networks: Connectivity analysis of EMG activity during postural control". Scientific Reports. 5: 17830. doi:10.1038/srep17830. PMC 4669476Freely accessible. PMID 26634293.
  2. ↑ Wedeen, V.J.; Wang, R.P.; Schmahmann, J.D.; Benner, T.; Tseng, W.Y.I.; Dai, G.; Pandya, D.N.; Hagmann, P.; et al. (2008). "Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers". NeuroImage. 41 (4): 1267–77. doi:10.1016/j.neuroimage.2008.03.036. PMID 18495497.
  3. ↑ Anderson, JR; Jones, BW; Watt, CB; Shaw, MV; Yang, JH; Demill, D; Lauritzen, JS; Lin, Y; et al. (2011). "Exploring the retinal connectome". Molecular vision. 17: 355–79. PMC 3036568Freely accessible. PMID 21311605.
  4. ↑ Bock, Davi D.; Lee, Wei-Chung Allen; Kerlin, Aaron M.; Andermann, Mark L.; Hood, Greg; Wetzel, Arthur W.; Yurgenson, Sergey; Soucy, Edward R.; et al. (2011). "Network anatomy and in vivo physiology of visual cortical neurons". Nature. 471 (7337): 177–82. doi:10.1038/nature09802. PMC 3095821Freely accessible. PMID 21390124.
  5. ↑ Chklovskii, Dmitri B; Vitaladevuni, Shiv; Scheffer, Louis K (2010). "Semi-automated reconstruction of neural circuits using electron microscopy". Current Opinion in Neurobiology. 20 (5): 667–75. doi:10.1016/j.conb.2010.08.002. PMID 20833533.
  6. ↑ Chen, B. L.; Hall, D. H.; Chklovskii, D. B. (2006). "Wiring optimization can relate neuronal structure and function". Proceedings of the National Academy of Sciences. 103 (12): 4723–8. doi:10.1073/pnas.0506806103.
  7. ↑ Perez-Escudero, A.; Rivera-Alba, M.; De Polavieja, G. G. (2009). "Structure of deviations from optimality in biological systems". Proceedings of the National Academy of Sciences. 106 (48): 20544–9. doi:10.1073/pnas.0905336106.
  8. ↑ Pena, JL; Debello, WM (2010). "Auditory processing, plasticity, and learning in the barn owl". ILAR journal. 51 (4): 338–52. PMC 3102523Freely accessible. PMID 21131711.
  9. ↑ http://www.scholarpedia.org/article/Connectome[][]
  10. ↑ Nordlie, Eilen; Gewaltig, Marc-Oliver; Plesser, Hans Ekkehard (2009). Friston, Karl J., ed. "Towards Reproducible Descriptions of Neuronal Network Models". PLoS Computational Biology. 5 (8): e1000456. doi:10.1371/journal.pcbi.1000456. PMC 2713426Freely accessible. PMID 19662159.
  11. ↑ Van Horn, John D.; Irimia, A.; Torgerson, C.M.; Chambers, M.C.; Kikinis, R.; Toga, A.W. (2012). "Mapping connectivity damage in the case of Phineas Gage". PLoS ONE. 7 (5): e37454. doi:10.1371/journal.pone.0037454. PMC 3353935Freely accessible. PMID 22616011.
  12. ↑ Irimia, Andrei; Chambers, M.C.; Torgerson, C.M.; Filippou, M.; Hovda, D.A.; Alger, J.R.; Gerig, G.; Toga, A.W.; Vespa, P.M.; Kikinis, R.; Van Horn, J.D. (6 February 2012). "Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury". Frontiers in Neurotrauma. 3: 10. doi:10.3389/fneur.2012.00010. PMC 3275792Freely accessible. PMID 22363313.
  13. ↑ "Bad omics word of the day: connectome" Kaboodle.nescent.org. January 31, 2010
  14. ↑ Talk:Connectome. Scholarpedia.org.
  15. ↑ Sporns, Olaf; Tononi, Giulio; Kötter, Rolf (2005). "The Human Connectome: A Structural Description of the Human Brain". PLoS Computational Biology. 1 (4): e42. doi:10.1371/journal.pcbi.0010042. PMC 1239902Freely accessible. PMID 16201007.
  16. ↑ Hagmann, Patric (April 21, 2005). "From Diffusion MRI to Brain Connectomics" (PDF). École Polytechnique Fédérale de Lausanne. Ph.D. Thesis. pp. 1, 107.
  17. ↑ Vance, Ashlee (27 December 2010). "Seeking the Connectome, a Mental Map, Slice by Slice". The New York Times.
  18. ↑ Lichtman, J; Sanes, J (2008). "Ome sweet ome: what can the genome tell us about the connectome?". Current Opinion in Neurobiology. 18 (3): 346–53. doi:10.1016/j.conb.2008.08.010. PMC 2735215Freely accessible. PMID 18801435.

Further reading

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