ABSTRACT
Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.
Subject(s)
DNA Footprinting/methods , Escherichia coli Proteins/genetics , Escherichia coli/growth & development , Genome, Bacterial , Aerobiosis , Amino Acids/biosynthesis , Culture Media , DNA Transposable Elements , Escherichia coli/genetics , Escherichia coli Proteins/metabolism , Evolution, Molecular , Gene Expression Regulation, Bacterial , Genes, Essential , Mutagenesis, Insertional , PhylogenyABSTRACT
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated biochemical networks lacks quantitative support. Here, we show that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law. Within Escherichia coli, the uncovered hierarchical modularity closely overlaps with known metabolic functions. The identified network architecture may be generic to system-level cellular organization.
Subject(s)
Metabolism , Models, Biological , Escherichia coli/metabolism , Systems TheoryABSTRACT
We report on a series of measurements aimed to characterize the development and the dynamics of the rhythmic applause in concert halls. Our results demonstrate that while this process shares many characteristics of other systems that are known to synchronize, it also has features that are unexpected and unaccounted for in many other systems. In particular, we find that the mechanism lying at the heart of the synchronization process is the period doubling of the clapping rhythm. The characteristic interplay between synchronized and unsynchronized regimes during the applause is the result of a frustration in the system. All results are understandable in the framework of the Kuramoto model.
Subject(s)
Models, Theoretical , Social Behavior , Sound , Acoustic Stimulation , Computer Simulation , Humans , Physical Phenomena , PhysicsABSTRACT
The one-dimensional Ising model is analytically studied in a spatially periodic and oscillatory external magnetic field using the transfer-matrix method. For low enough magnetic field intensities the correlation between the external magnetic field and the response in magnetization presents a maximum for a given temperature. The phenomenon can be interpreted as a resonance phenomenon induced by the stochastic heat bath. This "spatial stochastic resonance" is realized in the equilibrium state and not as a dynamical response to the external time-periodic driving.