Computational neurogenetic modelling: a pathway to new discoveries in genetic neuroscience.
The paper presents a methodology for using computational neurogenetic modelling (CNGM) to bring new original insights into how genes influence the dynamics of brain neural networks. CNGM is a novel computational approach to brain neural network modelling that integrates dynamic gene networks with artificial neural network model (ANN). Interaction of genes in neurons affects the dynamics of the whole ANN model through neuronal parameters, which are no longer constant but change as a function of gene expression. Through optimization of interactions within the internal gene regulatory network (GRN), initial gene/protein expression values and ANN parameters, particular target states of the neural network behaviour can be achieved, and statistics about gene interactions can be extracted. In such a way, we have obtained an abstract GRN that contains predictions about particular gene interactions in neurons for subunit genes of AMPA, GABAA and NMDA neuro-receptors. The extent of sequence conservation for 20 subunit proteins of all these receptors was analysed using standard bioinformatics multiple alignment procedures. We have observed abundance of conserved residues but the most interesting observation has been the consistent conservation of phenylalanine (F at position 269) and leucine (L at position 353) in all 20 proteins with no mutations. We hypothesise that these regions can be the basis for mutual interactions. Existing knowledge on evolutionary linkage of their protein families and analysis at molecular level indicate that the expression of these individual subunits should be coordinated, which provides the biological justification for our optimized GRN.
Benuskova
Lubica
L
Knowledge Engineering & Discovery Research Institute, Auckland University of Technology, Ronald Trotter Building, 581-585 Great South Road, Penrose, Auckland, New Zealand. lbenusko@aut.ac.nz
Jain
Vishal
V
Wysoski
Simei G
SG
Kasabov
Nikola K
NK
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008433:Mathematics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D009488:Neurosciences; D016415:Sequence Alignment