Gene Expression Model

We're working on models of gene expression using Netlogo.

Our second model, the lac operon, is our best so far. We've also built a Logical Promoter that simulates logical gates. Our first Gene Expression Model just demonstrated a proof of concept.

At the BioQUEST workshop, we brainstormed some GeneExpressionModelUses.

I'm planning a GeneExpressionLab for Intro Biology.

Here are some of the learning goals we're defining for the instructional unit:

Central Dogma

DNA -> RNA -> Protein

Genes have a promoter that can include enhancers and silencers

Signals can be transcription factors

Products of genes can be transcription factors

One gene can turn on a cascade of other genes

Negative and positive feedback loops.

Competetive inhibition as a transcription mechanism.

RP suggestions / additions / complications

Transcription factors are combinatorial. For transcription to occur, the proper combination of factors must be present.

External signals can alter concentrations/presence of transcription factors

External signals make use of signal transduction to activate key transcription factors (genes).

Just as some genes encode transcription factors that affect the expression of other genes, some genes encode signals, receptors or signal transduction molecules that affect the expression of other genes.

Different cell types express different sets of genes.

A cell's gene expression pattern is set by many factors including signals received, receptors, signal transduction pathways, transcription factors and chromatin structure....

Signal transduction is complex and combinatorial.

RNA processing is essential to gene expression.

Alternative RNA processing can lead to related proteins with different properties. Some splice variants can be inhibitory while others are stimulatory.

Some gene regulation occurs at the level of chromatin structure. - whole regions of the genome can be activated or repressed this way.

some regulation of protein production might occur at the level of mRNA translation, eg, there may be a large number of mRNA molecules relative to a smaller number of Ribosomes (eg, enzymes in pancreas).

For each Binding of a transcription factor to a gene, how many transcripts (and proteins) are made?

Can one model a transcription cascade that causes morphologic changes in development?

Are there any well worked out experimental model systems that one can use (ie a scientific publication) that can be used to re-inforce that this in silico model reflects truth.