Team:Heidelberg/Modeling network
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== Introduction == | == Introduction == | ||
- | The research field of [[Team:Heidelberg/Eucaryopedia#Regulation of transcription in eukaryotic organisms|regulation of gene expression in eukaryotes]] is a field of biological research growing rapidly [ref aus GertzNature2009: 1 und 2 | + | The research field of [[Team:Heidelberg/Eucaryopedia#Regulation of transcription in eukaryotic organisms|regulation of gene expression in eukaryotes]] is a field of biological research growing rapidly [[Team:Heidelberg/Modeling_network#References|[1,2]]ref aus GertzNature2009: 1 und 2. Hereby the interaction of DNA with certain proteins known as transcription factors (TFs) plays an essential role for the complex mechanism of transcriptional activation [GertzNature, TRAPpaper]. One strong focus of synthetic biology aims at the reconstruction of such gene regulatory networks []. To act within the scope of synthetic biology’s duties, the iGEM Team Heidelberg 09 claims that any synthetic promoter can be constructed by using our two methods for the construction of synthetic promoters. However, the only efficient way to construct systems of high complexity (such as computers or airplanes) is simulating these systems on the computer prior to construction [7]. In our case, this strongly emphasizes the necessity of HEARTBEAT (Heidelberg Artificial Transcription Factor Binding Site Engineering and Assembly Tool) which comprises data analysis (data analysis (HEARTBEAT-DB), user interface (?, schöneres Wort) (HEARTBEAT-GUI) and network modeling (HEARTBEAT fuzzy network (FN)). |
Revision as of 23:55, 17 October 2009
HEARTBEAT Fuzzy ModelingIntroductionThe research field of regulation of gene expression in eukaryotes is a field of biological research growing rapidly [1,2ref aus GertzNature2009: 1 und 2. Hereby the interaction of DNA with certain proteins known as transcription factors (TFs) plays an essential role for the complex mechanism of transcriptional activation [GertzNature, TRAPpaper]. One strong focus of synthetic biology aims at the reconstruction of such gene regulatory networks []. To act within the scope of synthetic biology’s duties, the iGEM Team Heidelberg 09 claims that any synthetic promoter can be constructed by using our two methods for the construction of synthetic promoters. However, the only efficient way to construct systems of high complexity (such as computers or airplanes) is simulating these systems on the computer prior to construction [7]. In our case, this strongly emphasizes the necessity of HEARTBEAT (Heidelberg Artificial Transcription Factor Binding Site Engineering and Assembly Tool) which comprises data analysis (data analysis (HEARTBEAT-DB), user interface (?, schöneres Wort) (HEARTBEAT-GUI) and network modeling (HEARTBEAT fuzzy network (FN)).
Background / MotivationThe need for standardized measurements of promoter activity in vivo has been widely accepted across the synthetic biology community [1]. Only if a part is well characterized initially, function of an engineered device or system can be predicted reliably. Most work of synthetic biology has focused on bacteria, especially Escherichia Coli, as a model system. Novel tasks in synthetic biology, especially for medical applications, will require synthetic biology of mammalian cells. Mammalian systems are the most complex biological systems, and therefore, little work has been done in the field of mammalian synthetic biology, leaving a huge potential for future research. [[Image:HD09_formula1.png|thumb|left|294px|Box 1: Calculation of PoPs, where γM is the mRNA degradation rate, a is the GFP maturation rate, γi is the degradation rate of immature GFP, ρ is the tranlation rate of immature GFP from mRNA and n is the number of copies of promoter per cell. References[1] Kelly, JR et al in Journal of Biological Engineering 3 (2009): "Measuring the activity of BioBrick promoters using an in vivo reference standard" |