1,092 research outputs found
Host-Parasite Co-evolution and Optimal Mutation Rates for Semi-conservative Quasispecies
In this paper, we extend a model of host-parasite co-evolution to incorporate
the semi-conservative nature of DNA replication for both the host and the
parasite. We find that the optimal mutation rate for the semi-conservative and
conservative hosts converge for realistic genome lengths, thus maintaining the
admirable agreement between theory and experiment found previously for the
conservative model and justifying the conservative approximation in some cases.
We demonstrate that, while the optimal mutation rate for a conservative and
semi-conservative parasite interacting with a given immune system is similar to
that of a conservative parasite, the properties away from this optimum differ
significantly. We suspect that this difference, coupled with the requirement
that a parasite optimize survival in a range of viable hosts, may help explain
why semi-conservative viruses are known to have significantly lower mutation
rates than their conservative counterparts
Equivalence testing using existing reference data: An example with genetically modified and conventional crops in animal feeding studies
An equivalence testing method is described to assess the safety of regulated products using relevant data obtained in historical studies with assumedly safe reference products. The method is illustrated using data from a series of animal feeding studies with genetically modified and reference maize varieties. Several criteria for quantifying equivalence are discussed, and study-corrected distribution-wise equivalence is selected as being appropriate for the example case study. An equivalence test is proposed based on a high probability of declaring equivalence in a simplified situation, where there is no between-group variation, where the historical and current studies have the same residual variance, and where the current study is assumed to have a sample size as set by a regulator. The method makes use of generalized fiducial inference methods to integrate uncertainties from both the historical and the current data
Modeling the interactions of biomatter and biofluid
The internal motions of biomatter immersed in biofluid are investigated. The
interactions between the fragments of biomatter and its surrounding biofluid
are modeled using field theory. In the model, the biomatter is coupled to the
gauge field representing the biofluid. It is shown that at non-relativistic
limit various equation of motions, from the well-known Sine-Gordon equation to
the simultaneous nonlinear equations, can be reproduced within a single
framework.Comment: 10 pages, 3 figure
Computational models for inferring biochemical networks
Biochemical networks are of great practical importance. The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects, which contributed to a vast amount of biological information. The construction of biochemical systems (systems of chemical reactions), which include both topology and kinetic constants of the chemical reactions, is NP-hard and is a well-studied system biology problem. In this paper, we propose a hybrid architecture, which combines genetic programming and simulated annealing in order to generate and optimize both the topology (the network) and the reaction rates of a biochemical system. Simulations and analysis of an artificial model and three real models (two models and the noisy version of one of them) show promising results for the proposed method.The Romanian National Authority for Scientific Research, CNDI–UEFISCDI,
Project No. PN-II-PT-PCCA-2011-3.2-0917
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