http://mol-biol4masters.masters.grkraj.org/html/Ribose_Nucleic_Acid2C-rRNA_Processing_in_Eukaryotes.htm

This image got me thinking - are specific nuclear pores associated with specific chromosomal territories? Could that be a mechanism of regulation? For example, if the ER were to cover a pore and restrict traffic through it, I imagine it would result in downregulation of expression of those genes associated with that pore. Or if the pore were to disappear, or a new pore were to appear - wouldn't this also affect the expression capability of the nearby genes? One aspect of this is that chromatin associated with the nuclear envelope is not active (heterochromatin).
I talked about this with David Goodsell, and he noted that diffusion is VERY fast - so simply putting an obstacle in front of a nuclear pore might not have much effect. But he thought the underlying idea was interesting. Perhaps nuclear pores, active chromatin domains, and the ER work together to create functionally significant microenvironments within the cell.

I was debating this morning whether or not to blog about a recent hypothesis. One aspect of science today is "being scooped". Scientists are secretive to prevent other people from stealing their ideas. Being the first to publish something leads to financial and political rewards. This is also why scientists often do not publish negative results, or cherry-pick results, or even worse, falsify results completely. I feel a conflict between wanting to share my ideas freely so that they can be developed as rapidly as possible, and a desire for money and status. I've decided to share my ideas freely. If some day my children are starving, I will ask my blog readers for help. It's a difficult world. This is where I've decided to make my stand.

I was just studying David Goodsell's paper Miniseries: Illustrating the Machinery of Life - Escherichia coli (http://onlinelibrary.wiley.com/doi/10.1002/bmb.20345/full - do yourself an enormous service and check it out!). I've reserved Thursdays for doing publication stuff - reading, writing, etc. I figured since David's paper is basically what I'm trying to do, I should get intimately familiar with it. Wow! I learned a lot! Especially interesting was the existence of SMC proteins (Structural Maintenance of Chromosomes). Right in the middle of his illustration was MukBEF, an enromous, star-like structure that I had never noticed before. Turns out these guys are important for condensing DNA. I had never even thought about this before! This is truly the great thing (one of the great things) about this work - it leads me to insights that I might never make without it. Thanks, David, for opening my eyes yet again!!! :)