Fast Fixes On Pictilisib Troubles

, 2002). A number of earlier studies used physical models to explain the formation of compact nucleoids that occupy only a fraction of the entire bacterial cytoplasm. A statistical mechanical model used the osmotic effects of myriad small proteins to explain the apparent phase separation (Odijk, 1998). A recent experimental study of free bacterial nucleoids confined in a microfluidic channel showed that crowding by added polyethylene glycine chains (PEG) led to reversible, first-order ��coil-to-globule�� collapse of the nucleoids (Pelletier et al., 2012). This study augmented the earlier statistical model to include the entropic spring nature of the nucleoids. A very recent coarse-grained simulation showed that small, spherical crowding agents can induce compaction of a DNA polymer, modeled as a freely jointed chain (Shendruk et al., 2015). We have found that a simple physical model using Monte Carlo simulations of DNA and ribosome spatial distributions in a confining cytoplasmic space enhances our understanding of the observed ribosome-ARAF nucleoid segregation (Mondal et al., 2011). In the model, entropic and excluded volume effects cause strong segregation of the unperturbed nucleoid from 70S-polysomes. The biochemical state of ribosomes (70S-polysomes vs. free 30S and 50S subunits) plays an essential role in ribosome-nucleoid segregation. When the model 70S-polysomes are converted to 30S and 50S subunits, the components mix quite thoroughly with the DNA and the nucleoid expands (Bakshi et al., 2014a). This suggests that the fraction of 70S-polysomes vs. 30S and 50S subunits strongly affects the relative compactness of the nucleoid. Based on these new experimental and computational results, we are developing a comprehensive model of the spatial organization within the E. coli cytoplasm and how it may work to optimize cell growth. Our present view encompasses a variety of inter-related phenomena: (1) In rapidly growing cells, most translation occurs in the ribosome-rich regions, not within the nucleoids. (2) Yet there is direct evidence of co-transcriptional translation (Miller et al., 1970), and this is important for protecting nascent mRNA from degradation and for efficient transcription. Evidently most or all transcription is co-translational, but only ?10�C15% of translation is co-transcriptional. (3) Therefore 30S and 50S subunits must be able to penetrate the nucleoid where they initiate co-transcriptional translation (Sanamrad et al., 2014). This picture implies a circulation of 30S and 50S subunits between the nucleoids and the ribosome-rich regions. (4) Transertion expands the nucleoids beyond their relaxed, highly compacted state (Woldringh, 2002). The evidence suggests that transertion plays an essential role, enabling 30S and 50S subunits to move into the nucleoids where they initiate co-transcriptional translation and form nascent 70S-polysomes.