Most biochemical and biophysical studies of the reaction mechanisms, kinetics, and thermodynamics of proteins and nucleic acids are carried out in vitro using dilute aqueous solutions of purified biopolymer constituents. However, the cytoplasm of both prokaryotic and eukaryotic cells contains a very high total concentration of proteins, nucleic acids, lipids, and supramolecular assemblies of these constituents. In Escherichia coli grown at moderate osmolality, the typical total mass density of protein and nucleic acid within the cytoplasm is ϳ220 mg/ml (5), distributed among the nucleoid, ribosomes, and a diverse collection of smaller proteins, tRNA, and mRNA (3). Taken together, these macromolecules occupy some 20 to 30% of the total cytoplasmic volume.In a crowded fluid, each molecule is excluded from much of the total volume by the presence of other biopolymers (11, 37). In thermodynamic terms, excluded volume decreases the translational entropy of each species, increases free energy, and, thus, increases the thermodynamic driving force to react or bind. These effects could be very large; the thermodynamic activity (the "effective concentration") of a typical globular protein could be Ͼ100 times higher in the E. coli cytoplasm than at the same concentration in an uncrowded solution (9). Crowding also dramatically affects diffusion (26), which is critical for normal cell function and growth (28). Excluded volume slows diffusion by making it less likely that a probe particle can find space in which to move without simultaneous, cooperative motion of several or many background particles (26).While the bacterial cytoplasm is often assumed to be a crowded aqueous solution (37), the physical state of the cytoplasm is uncertain. Particularly for the low water content induced by hyperosmotic stress, the cytoplasm might become a biopolymer meshwork comprising the nucleoid, associated proteins, nascent mRNA, ribosomes, polypeptide chains, and strongly associated water (13, 38). Such conditions are reminiscent of a polymeric hydrogel (1). Confinement within the pores of the meshwork would enhance protein binding equilibria and slow protein diffusion in a manner qualitatively similar to crowding.Strong effects of crowding and confinement in vitro have been observed for the tracer diffusion of globular proteins (26) and for the diffusion of tracer proteins in concentrated solutions of hydrophilic polymers (2, 8) and in hydrogels (1). The apparent diffusion coefficient decreases roughly exponentially with the macromolecular volume fraction , in agreement with a parametrized model called scaled particle theory (SPT) (14,26). Additional studies in vitro have shown crowding effects on protein folding (36) and association (24), on the thermodynamics of the protein-nucleic acid interactions critical to replication (27), on enzyme kinetics (25), and on the stability of protein oligomers such as F-actin (16, 20) and of fibrils such as ␤-amyloid (15).We know of no experimental studies of crowding/confinement effects on protein di...

As the ability to analyze individual cells in microbial populations expands, it is becoming apparent that isogenic microbial populations contain substantial cell-to-cell differences in physiological parameters such as growth rate, resistance to stress and regulatory circuit output. Subpopulations exist that are manyfold different in these parameters from the population average, and these differences arise by stochastic processes. Such differences can dramatically affect the response of cells to perturbations, especially stress, which in turn dictates overall population response. Defining the role of cell-to-cell heterogeneity in population behavior is important for understanding population-based research problems, including those involving infecting populations, normal flora and bacterial populations in water and soils. Emerging technological breakthroughs are poised to transform single-cell analysis and are critical for the next phase of insights into physiological heterogeneity in the near future. These include technologies for multiparameter analysis of live cells, with downstream processing and analysis.

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An NIR-emitting probe (λem~700 nm) with a large Stokes shift (Δλ≈234 nm) is synthesized by using excited-state intramolecular proton transfer (ESIPT). The phenolic proton, which controls ESIPT, acts as a switch to give strong fluorescence at pH≈5. The probe can selectively show lysosome organelles, therefore leading to a lysosome probe without exhibiting “an alkalinizing effect”.