Entropy involved in fidelity of DNA replication

Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorporation of the nucleotides. The copied strand is, to first order of approximation, a state of independent and non-indentically distributed random variables for which the nucleotide that is incorporated by the polymerase at each step is dictated by the template strand, and to second order of approximation, a state of non-uniformly distributed random variables with nearest-neighbor interactions for which the recognition of secondary structure by the polymerase in the resultant double-stranded polymer determines the entropy of the replicated strand. Two incorporation mechanisms arise naturally and their biological meanings are explained. It is known that replication occurs far from equilibrium and therefore the Shannon entropy here derived represents an upper bound for replication to take place. Likewise, this entropy sets a universal lower bound for the copying fidelity in replication.Comment: 25 pages, 5 figure

The Rate of Information Transfer of Naturalistic Stimulation by Graded Potentials

We present a method to measure the rate of information transfer for any continuous signals of finite duration without assumptions. After testing the method with simulated responses, we measure the encoding performance of Calliphora photoreceptors. We find that especially for naturalistic stimulation the responses are nonlinear and noise is nonadditive, and show that adaptation mechanisms affect signal and noise differentially depending on the time scale, structure, and speed of the stimulus. Different signaling strategies for short- and long-term and dim and bright light are found for this graded system when stimulated with naturalistic light changes

Brain activity at 70-80 Hz changes during olfactory stimulation protocols in Drosophila

Oscillatory and synchronized activities in the mammalian brain have been correlated with the execution of complex cognitive tasks. Similar oscillations have been observed in local field potentials (LFPs) in flies, in this case correlated with different attentional states. To further test the significance of these oscillations we recorded LFPs from the brain of Drosophila melanogaster as it responded to the presentation of olfactory stimuli. We find that responses in the 70-80 Hz range increase during olfactory stimulation. Recurrent stimulation specifically decreased the power of LFPs in this frequency range. Delivery of electric shocks before olfactory stimulation modulated LFPs in the 70-80 Hz range by evoking a transient increase. These results suggest that these signals are a simple neuronal correlate of higher-order olfactory processing in flies. © 2010 Prieto-Godino, de Polavieja.Peer Reviewe