Dataset Information

Adams2012 - Locke2006 Circadian Rhythm model refined with Input Signal Light Function

ABSTRACT: As per BIO0000000089.xml but including a functional light.

SUBMITTER: Vijayalakshmi Chelliah

PROVIDER: BIOMD0000000476 | BioModels | 2007-02-20

REPOSITORIES: BioModels

ACCESS DATA

Publications

The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models.

Adams R R RR Tsorman N N Stratford K K Akman O E OE Gilmore S S Juty N N Le Novère N N Millar A J AJ Millar A J AJ

Journal of biological rhythms 20120801 4

Time-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodi ...[more]

PMID: 22855577

Similar Datasets

Project description:We utilized the Nematostella vectensis to quantify gene expression differences and loss during light:dark cycling and immediately after light cue removal through comparisons of 136 transcriptomes Organismal responses to light:dark cycles can result from two general processes: (i) direct response to light or (ii) a free-running rhythm (i.e., a circadian clock). Previous research in cnidarians has shown that candidate circadian clock genes have rhythmic expression in the presence of diel lighting, but these oscillations appear to be lost quickly after removal of the light cue. Here, we measure whole-organism gene expression changes in 136 transcriptomes of the sea anemone Nematostella vectensis, entrained to a light:dark environment and immediately following light cue removal to distinguish two broadly defined responses in cnidarians: light entrainment and circadian regulation. Direct light exposure resulted in significant differences in expression for hundreds of genes, including more than 200 genes with rhythmic, 24-hour periodicity. Removal of the lighting cue resulted in the loss of significant expression for 80% of these genes after one day, including most of the hypothesized cnidarian circadian genes. Further, 70% of these candidate genes were phase shifted. Most surprisingly, thousands of genes, some of which are involved in oxidative stress, DNA damage response, and chromatin modification, had significant differences in expression in the 24 hours following light removal, suggesting that loss of the entraining cue may induce a cellular stress response. Together, our findings suggest that a majority of genes with significant differences in expression for anemones cultured under diel lighting are largely driven by the primary photoresponse rather than a circadian clock when measured at the whole animal level. These results provide context for the evolution of cnidarian circadian biology and help to disassociate two commonly confounded factors driving oscillating phenotypes.

Dataset Information

Adams2012 - Locke2006 Circadian Rhythm model refined with Input Signal Light Function

Publications

The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure