Impact of environmental inputs on reverse-engineering approach to network structures.

BACKGROUND: Uncovering complex network structures from a biological system is one of the main topic in system biology. The network structures can be inferred by the dynamical Bayesian network or Granger causality, but neither techniques have seriously taken into account the impact of environmental inputs. RESULTS: With considerations of natural rhythmic dynamics of biological data, we propose a system biology approach to reveal the impact of environmental inputs on network structures. We first represent the environmental inputs by a harmonic oscillator and combine them with Granger causality to identify environmental inputs and then uncover the causal network structures. We also generalize it to multiple harmonic oscillators to represent various exogenous influences. This system approach is extensively tested with toy models and successfully applied to a real biological network of microarray data of the flowering genes of the model plant Arabidopsis Thaliana. The aim is to identify those genes that are directly affected by the presence of the sunlight and uncover the interactive network structures associating with flowering metabolism. CONCLUSION: We demonstrate that environmental inputs are crucial for correctly inferring network structures. Harmonic causal method is proved to be a powerful technique to detect environment inputs and uncover network structures, especially when the biological data exhibit periodic oscillations.

Induction of synchronous oscillatory activity in the rat lateral amygdala in vitro is dependent on gap junction activity.

Synchronized and rhythmic activity within the amygdala is thought to play a pivotal role in the generation of fear- and anxiety-related behaviour. The aim here was to determine the validity of the in vitro amygdala slice preparation to investigate the generation of rhythmic activity similar to that observed in vivo. Extracellular population activity recorded from the lateral nucleus of the amygdala in vitro showed significant enhancement of activity within the theta-band frequency (3-9 Hz) in the presence of kainic acid (100 nm; n=18). Alterations in the patterns of oscillatory activity within the gamma frequency band (20-40 Hz) were observed in the presence of (RS)-3,5-dihydroxyphenylglycine (10 microm; n=7) or carbachol (50 microm; n=5). Theta frequency oscillatory activity was blocked in the presence of the gap junction blocker carbenoxolone (100 mm), whereas gamma frequency oscillatory activity showed increased variability in the dominant frequency of rhythmic activity. The results suggest that the neuronal circuitry of the amygdala in vitro is capable of generating and sustaining rhythmic activity and that intercellular communication via gap junctions may play a role in the synchronization of population activity underlying this oscillatory activity.