NDLI: Co-option and Irreducibility in Regulatory Networks for Cellular Pattern Development

Content Provider	IEEE Xplore Digital Library
Author	Dhanasekaran, R.A. Podgorski, G.J. Flann, N.S.
Copyright Year	2007
Description	Author affiliation: Dept. of Comput. Sci., Utah State Univ., Logan, UT (Dhanasekaran, R.A.)
Abstract	We used a computational approach to examine three questions at the intersection of developmental biology and evolution: 1) What is the space available for evolutionary exploration for genetic regulatory networks (GRNs) able to solve developmental patterning problems? 2) If different GRNs exist that can solve a particular pattern, are there differences between them that might lead to the selection of one over another? 3) What are the possibilities for co-opting GRN subcircuits or even entire GRNs evolved to solve one pattern for use in the solution of another pattern? We used a Monte Carlo strategy to search for simulated GRNs composed of nodes (proteins) and edges (regulatory interactions between proteins) capable of solving one of three striped cellular patterning problems. These GRNs were subjected to a knockout procedure akin to gene knock-outs in genetic research. Knockout was continued until all individual network components of the reduced GRN were shown to be essential for function. This GRN was termed irreducible. We found many different unique irreducible GRNs that were able to solve each patterning problem. Since any functional GRN must include an irreducible GRN as a core or subgraph, the space for evolutionary exploration of pattern-forming GRNs is large. Irreducible GRNs that solve a particular pattern differed widely in their robustness - the ability to solve a target pattern under different initial conditions. These differences may offer a target for selection to winnow out less robust GRNs from the set of GRNs found in nature. Finally, subgraph isomorphism analysis revealed great potential for co-option during evolution. Some irreducible GRNs appear in their entirety within larger GRNs that solve different patterning problems. At much higher frequency, subcycles are shared widely among irreducible GRNs, including those that solve different patterns. Irreducible GRNs may form the core elements of GRNs found in biological systems and provide insight into their evolution
Starting Page	179
Ending Page	186
File Size	9999122
Page Count	8
File Format	PDF
ISBN	142440701X
DOI	10.1109/ALIFE.2007.367794
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-04-01
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	GRN development self-organization Genetic regulatory network evolutionary dynamics subcircuit subgraph isomorphism Cellular networks Proteins Evolution (biology) cooption modularity Cells (biology) Biology computing Genetics Robustness Computer networks Space exploration pattern formation Computational biology
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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