The Evolutionarily Dynamics of Aposematism: a Numerical Analysis of Co-Evolution in Finite Populations

The majority of species are under predatory risk in their natural habitat and targeted by predators as part of the food web. During the evolution of ecosystems, manifold mechanisms have emerged to avoid predation. So called secondary defences, which are used after a predator has initiated prey-catching behaviour, commonly involve the expression of toxins or deterrent substances which are not observable by the predator. Hence, the possession of such secondary defence in many prey species comes with a specific signal of that defence (aposematism). This paper builds on the ideas of existing models of such signalling behaviour, using a model of co-evolution and generalisation of aversive information and introduces a new methodology of numerical analysis for finite populations. This new methodology significantly improves the accessibility of previous models. In finite populations, investigating the co-evolution of defence and signalling requires an understanding of natural selection as well as an assessment of the effects of drift as an additional force acting on stability. The new methodology is able to reproduce the predicted solutions of preceding models and finds additional solutions involving negative correlation between signal strength and the extent of secondary defence. In addition, genetic drift extends the range of stable aposematic solutions through the introduction of a new pseudo-stability and gives new insights into the diversification of aposematic displays

The application of temporal difference learning in optimal diet models

An experience-based aversive learning model of foraging behaviour in uncertain environments is presented. We use Q-learning as a model-free implementation of Temporal difference learning motivated by growing evidence for neural correlates in natural reinforcement settings. The predator has the choice of including an aposematic prey in its diet or to forage on alternative food sources. We show how the predator's foraging behaviour and energy intake depend on toxicity of the defended prey and the presence of Batesian mimics. We introduce the precondition of exploration of the action space for successful aversion formation and show how it predicts foraging behaviour in the presence of conflicting rewards which is conditionally suboptimal in a fixed environment but allows better adaptation in changing environments

Networks for all

A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008

Network growth models and genetic regulatory networks

We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new links, allowing for the possibility that input and output links from a newly created node may have different probabilities of survival. We find some counterintuitive trends as parameters are varied, including the broadening of indegree distribution when the probability for retaining input links is decreased. We also find that both the scaling of transcription factors with genome size and the measured degree distributions for genes in yeast can be reproduced by the growth algorithm if and only if a special seed is used to initiate the process.Comment: 8 pages with 7 eps figures; uses revtex4. Added references, cleaner figure

TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation

<p>Abstract</p> <p>Background</p> <p>The re-replication inhibitor Geminin binds to several transcription factors including homeodomain proteins, and to members of the polycomb and the SWI/SNF complexes.</p> <p>Results</p> <p>Here we describe the TATA-binding protein-like factor-interacting protein (TIPT) isoform 2, as a strong binding partner of Geminin. TIPT2 is widely expressed in mouse embryonic and adult tissues, residing both in cyto- and nucleoplasma, and enriched in the nucleolus. Like Geminin, also TIPT2 interacts with several polycomb factors, with the general transcription factor TBP (TATA box binding protein), and with the related protein TBPL1 (TRF2). TIPT2 synergizes with geminin and TBP in the activation of TATA box-containing promoters, and with TBPL1 and geminin in the activation of the TATA-less NF1 promoter. Geminin and TIPT2 were detected in the chromatin near TBP/TBPL1 binding sites.</p> <p>Conclusion</p> <p>Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery.</p

Principles of assembly reveal a periodic table of protein complexes.

Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways. Most assembly transitions can be classified into three basic types, which can then be used to exhaustively enumerate a large set of possible quaternary structure topologies. These topologies, which include the vast majority of observed protein complex structures, enable a natural organization of protein complexes into a periodic table. On the basis of this table, we can accurately predict the expected frequencies of quaternary structure topologies, including those not yet observed. These results have important implications for quaternary structure prediction, modeling, and engineering.This work was supported by the Royal Society (S.E.A. and C.V.R.), the Human Frontier Science Program (J.A.M.), the Medical Research Council grant G1000819 (H.H. and C.V.R.) and the Lister Institute for Preventative Medicine (S.A.T.).This is the author accepted manuscript. The final version is available from AAAS via http://dx.doi.org/10.1126/science.aaa224

Bose-Einstein condensates in a double well: mean-field chaos and multi-particle entanglement

A recent publication [Phys. Rev. Lett. 100, 140408 (2008)] shows that there is a relation between mean-field chaos and multi-particle entanglement for BECs in a periodically shaken double well. 'Schrodinger-cat' like mesoscopic superpositions in phase-space occur for conditions for which the system displays mean-field chaos. In the present manuscript, more general highly-entangled states are investigated. Mean-field chaos accelerates the emergence of multi-particle entanglement; the boundaries of stable regions are particularly suited for entanglement generation.Comment: 5 Pages, 5 jpg-figures, to be published in the proceedings of the LPHYS0

Strong coupling expansion for the Bose-Hubbard and the Jaynes-Cummings lattice model

A strong coupling expansion, based on the Kato-Bloch perturbation theory, which has recently been proposed by Eckardt et al. [Phys. Rev. B 79, 195131] and Teichmann et al. [Phys. Rev. B 79, 224515] is implemented in order to study various aspects of the Bose-Hubbard and the Jaynes-Cummings lattice model. The approach, which allows to generate numerically all diagrams up to a desired order in the interaction strength is generalized for disordered systems and for the Jaynes-Cummings lattice model. Results for the Bose-Hubbard and the Jaynes-Cummings lattice model will be presented and compared with results from VCA and DMRG. Our focus will be on the Mott insulator to superfluid transition.Comment: 29 pages, 21 figure