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Register a new userThe long-tail distribution function of mutations in bacteria
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Authors
Augusto Gonzalez
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Levy flights in the space of mutations model time evolution of bacterial DNA. Parameters in the model are adjusted in order to fit observations coming from the Long Time Evolution Experiment with E. Coli.
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This thesis is aimed at studying mutations, understood as trajectories in the DNA configuration space. An evolutive model of mutations in terms of Levy flights is proposed. The parameters of the model are estimated by means of data from the Long-Term Evolution Experiment (LTEE) with {it E. Coli} bacteria. The results of simulations on competition of clones, mean fitness, etc are compared with experimental data. We discuss the qualitative analogy found between the bacterial mutator phenotype and the cancerous cells. The role of radiation as source of mutations is analyzed. We focus on the case of Radons decay in the lungs in breathing.
I compare two quantum-theoretical approaches to the phenomenon of adaptive mutations, termed here Q-cell and Q-genome. I use fluctuation trapping model as a general framework. I introduce notions of R-error and D-error and argue that the fluctuation trapping model has to employ a correlation between the R- and D- errors. Further, I compare how the two approaches can justify the R-D-error correlation, focusing on the advantages of the Q-cell approach. The positive role of environmentally induced decoherence (EID) on both steps of the adaptation process is emphasized. A starving bacterial cell is proposed to be in an einselected state. The intracellular dynamics in this state has a unitary character and I propose to interpret it as exponential growth in imaginary time, analogously to the commonly considered diffusion interpretation of the Schroedinger equation. Addition of a substrate leads to Wick rotation and a switch from imaginary time reproduction to a real time reproduction regime. Due to the variations at the genomic level (such as base tautomery), the starving cell has to be represented as a superposition of different components, all reproducing in imaginary time. Adidtion of a selective substrate, allowing only one of these components to amplify, will cause Wick rotation and amplification of this component, thus justifying the occurence of the R-D-error correlation. Further ramifications of the proposed ideas for evolutionary theory are discussed.
Some bacteria and archaea possess an immune system, based on the CRISPR-Cas mechanism, that confers adaptive immunity against phage. In such species, individual bacteria maintain a cassette of viral DNA elements called spacers as a memory of past infections. The typical cassette contains a few dozen spacers. Given that bacteria can have very large genomes, and since having more spacers should confer a better memory, it is puzzling that so little genetic space would be devoted by bacteria to their adaptive immune system. Here, we identify a fundamental trade-off between the size of the bacterial immune repertoire and effectiveness of response to a given threat, and show how this tradeoff imposes a limit on the optimal size of the CRISPR cassette.
Data from a long time evolution experiment with Escherichia Coli and from a large study on copy number variations in subjects with european ancestry are analyzed in order to argue that mutations can be described as Levy flights in the mutation space. These Levy flights have at least two components: random single-base substitutions and large DNA rearrangements. From the data, we get estimations for the time rates of both events and the size distribution function of large rearrangements.
Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might affect the diversity of these groups, we developed a novel stochastic network model for examining the co-evolution of these ecologies. In our approach, nodes represent whole species or strains of bacteria or phages, rather than individuals, with speciation and extinction modelled by duplication and removal of nodes. Phage-bacteria links represent host-parasite relationships and temperate-virulent phage links denote prophage-encoded resistance. The effect of horizontal transfer of genetic information between strains was also included in the dynamical rules. The observed networks evolved in a highly dynamic fashion but the ecosystems were prone to collapse (one or more entire groups going extinct). Diversity could be stably maintained in the model only if the probability of speciation was independent of the diversity. Such an effect could be achieved in real ecosystems if the speciation rate is primarily set by the availability of ecological niches.
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