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Design, Surface Treatment, Cellular Plating, and Culturing of Modular Neuronal Networks Composed of Functionally Inter-connected Circuits

Design, Surface Treatment, Cellular Plating, and Culturing of Modular Neuronal Networks Composed of Functionally Inter-connected Circuits

Published on: April 15, 2015

Evolutionary design principles and functional characteristics based on kingdom-specific network motifs.

Tae-Hwan Kim¹, Junil Kim, Pat Heslop-Harrison

¹Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.

Bioinformatics (Oxford, England)

|November 16, 2010

Summary

Biological networks share significant two-node feedback motifs across species. Motif enrichment varies by kingdom, reflecting evolutionary design principles and species-specific behaviors.

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Area of Science:

Systems biology
Network science
Comparative genomics

Background:

Biological networks exhibit non-randomly abundant network motifs across scales.
Large directed protein networks are defined in diverse species.
Comparing network motifs across kingdoms can reveal fundamental biological principles.

Purpose of the Study:

To compare two- and three-node network motifs across plants (Arabidopsis thaliana), fungi (Saccharomyces cerevisiae), and animals (Homo sapiens).
To investigate the enrichment patterns of different types of two-node feedback motifs.

Main Methods:

Analysis of significantly observed two- and three-node network motifs.
Comparative analysis across three kingdoms: plants, fungi, and animals.
Examination of feedback interaction signs (positive-positive, negative-negative, positive-negative).

Main Results:

'Two-node feedback' is the most significant motif in all three species studied.
Positive-negative (PN) feedback is enriched in Arabidopsis thaliana.
Negative-negative (NN) feedback is enriched in Saccharomyces cerevisiae.
Positive-positive (PP) and negative-negative (NN) feedbacks are enriched in Homo sapiens.

Conclusions:

Enrichment of specific network motifs reflects evolutionary design principles selected by species-specific behaviors.
Motif amplification arises from dynamical and topological properties, indicating species function and behavior.
Network motif analysis provides signatures of organismal behavior and function.