title: Bio-Object, a stochastic simulator for post-transcriptional regulation.
abstract: BACKGROUND
  Recently, biologists learnt that the transport and degradation of transcribed mRNA and protein present critically important steps for the regulation of gene expression through extensive studies of RNA interference, none-sense mediated decay and ubiquitination. However, adequate consideration of these factors has not been done in the past in in silico analysis compared with transcriptional regulations.
  
  
  RESULTS
  We have developed a bio-system simulator 'Bio-Object' and assessed the contribution of numerous factors including movements, stability and interactions of both mRNAs and proteins in the virtual cell space to the Drosophila circadian rhythm. The oscillations of period (per), timeless (tim) and Drosophila Clock (dClk) mRNAs and proteins predicted by the simulations agreed with the observed data in Drosophila and were lost with the knock-out of either the per or the dClk gene as observed experimentally. Bio-Object predicts that (1) the stability of dClk mRNA, (2) the stability of dCLK and (3) the affinity of the PER-TIM complex are determinants of the circadian duration.
  
  
  BACKGROUND
  The source code is available for download from http://www.tmd.ac.jp/mri/mri-end/bio-object/download/
authors.affiliation: Department of Functional Genomics, Medical Research Institute, 1-5-45 Yushima, Tokyo 113-0034, Japan.
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Ohki
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Hagiwara
mesh_terms: D000465:Algorithms; D000818:Animals; D001683:Biological Clocks / Q000502:physiology; D002940:Circadian Rhythm / Q000502:physiology*; D003198:Computer Simulation; D004331:Drosophila melanogaster / Q000378:metabolism* / Q000502:physiology*; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D015233:Models, Statistical; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D013269:Stochastic Processes; D014157:Transcription Factors / Q000378:metabolism; D015533:Transcriptional Activation / Q000502:physiology*
chemical_list: D014157:Transcription Factors