Interface focus: a theme supplement of Journal of the Royal Society interface (Interface Focus )

Description

  • Impact factor
    2.21
  • 5-year impact
    2.21
  • Cited half-life
    1.10
  • Immediacy index
    1.67
  • Eigenfactor
    0.00
  • Article influence
    0.70
  • ISSN
    2042-8901

Publications in this journal

  • Interface focus: a theme supplement of Journal of the Royal Society interface 04/2014; 4(3):20140027.
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    ABSTRACT: Although Turing's reaction-diffusion model (RD model) has been gradually accepted among biologists, application of the model is still limited. Accumulated experimental studies have shown that the morphogen gradient model can explain most patterning phenomena in embryogenesis. These experiments have been performed only in a few model animals. Therefore, it is not clear whether the discovered principle of the mechanism is generally applicable. The wing venation pattern of Drosophila melanogaster is largely determined by the morphogen gradient mechanism. We found that the gradient model cannot be applied to some other species. In the Hemiptera insect Orosanga japonicus, each individual has a unique pattern. Veins of O. japonicus extend radially from the proximal region and bifurcate to add the veins in the distal region. Interestingly, the bifurcation points are almost random and the vein number at the wing edge differs with wing size. However, the spacing between the veins is maintained evenly. Computer simulation of the RD model showed these properties do not fit the morphogen gradient model, but perfectly fit the RD model. This result suggests that the RD model may explain phenomena to which the morphogen gradient mechanism is currently believed to apply.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):451-6.
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    ABSTRACT: The application of mathematical models in biology and medicine has a long history. From the sparse number of papers in the first half of the twentieth century with a few scientists working in the field it has become vast with thousands of active researchers. We give a brief, and far from definitive history, of how some parts of the field have developed and how the type of research has changed. We describe in more detail just two examples of specific models which are directly related to real biological problems, namely animal coat patterns and the growth and image enhancement of glioblastoma brain tumours.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):397-406.
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    ABSTRACT: In his seminal 1952 paper, 'The Chemical Basis of Morphogenesis', Alan Turing lays down a milestone in the application of theoretical approaches to understand complex biological processes. His deceptively simple demonstration that a system of reacting and diffusing chemicals could, under certain conditions, generate spatial patterning out of homogeneity provided an elegant solution to the problem of how one of nature's most intricate events occurs: the emergence of structure and form in the developing embryo. The molecular revolution that has taken place during the six decades following this landmark publication has now placed this generation of theoreticians and biologists in an excellent position to rigorously test the theory and, encouragingly, a number of systems have emerged that appear to conform to some of Turing's fundamental ideas. In this paper, we describe the history and more recent integration between experiment and theory in one of the key models for understanding pattern formation: the emergence of feathers and hair in the skins of birds and mammals.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):433-50.
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    ABSTRACT: The paper reviews two computing models by DNA self-assembly whose proof of principal have recently been experimentally confirmed. The first model incorporates DNA nano-devices and triple crossover DNA molecules to algorithmically arrange non-DNA species. This is achieved by simulating a finite-state automaton with output where golden nanoparticles are assembled to read-out the result. In the second model, a complex DNA molecule representing a graph emerges as a solution of a computational problem. This supports the idea that in molecular self-assembly computing, it may be necessary to develop the notion of shape processing besides the classical approach through symbol processing.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):504-11.
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    ABSTRACT: In his pioneering work, Alan Turing showed that de novo pattern formation is possible if two substances interact that differ in their diffusion range. Since then, we have shown that pattern formation is possible if, and only if, a self-enhancing reaction is coupled with an antagonistic process of longer range. Knowing this crucial condition has enabled us to include nonlinear interactions, which are required to design molecularly realistic interactions. Different reaction schemes and their relation to Turing's proposal are discussed and compared with more recent observations on the molecular-genetic level. The antagonistic reaction may be accomplished by an inhibitor that is produced in the activated region or by a depletion of a component that is used up during the self-enhancing reaction. The autocatalysis may be realized by an inhibition of an inhibition. Activating molecules can be processed into molecules that have an inhibiting function; patterning of the Wnt pathway is proposed to depend on such a mechanism. Three-component systems, as discussed in Turing's paper, are shown to play a major role in the generation of highly dynamic patterns that never reach a stable state.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):407-16.
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    ABSTRACT: Pattern formation in development is a complex process which involves spatially distributed signals called morphogens that influence gene expression and thus the phenotypic identity of cells. Usually different cell types are spatially segregated, and the boundary between them may be determined by a threshold value of some state variable. The question arises as to how sensitive the location of such a boundary is to variations in properties, such as parameter values, that characterize the system. Here, we analyse both deterministic and stochastic reaction-diffusion models of pattern formation with a view towards understanding how the signalling scheme used for patterning affects the variability of boundary determination between cell types in a developing tissue.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):465-86.
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    ABSTRACT: One of the fundamental questions in developmental biology is how the vast range of pattern and structure we observe in nature emerges from an almost uniformly homogeneous fertilized egg. In particular, the mechanisms by which biological systems maintain robustness, despite being subject to numerous sources of noise, are shrouded in mystery. Postulating plausible theoretical models of biological heterogeneity is not only difficult, but it is also further complicated by the problem of generating robustness, i.e. once we can generate a pattern, how do we ensure that this pattern is consistently reproducible in the face of perturbations to the domain, reaction time scale, boundary conditions and so forth. In this paper, not only do we review the basic properties of Turing's theory, we highlight the successes and pitfalls of using it as a model for biological systems, and discuss emerging developments in the area.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):487-96.
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    ABSTRACT: We study the potential for molecule recycling in chemical reaction systems and their DNA strand displacement realizations. Recycling happens when a product of one reaction is a reactant in a later reaction. Recycling has the benefits of reducing consumption, or waste, of molecules and of avoiding fuel depletion. We present a binary counter that recycles molecules efficiently while incurring just a moderate slowdown compared with alternative counters that do not recycle strands. This counter is an n-bit binary reflecting Gray code counter that advances through 2(n) states. In the strand displacement realization of this counter, the waste-total number of nucleotides of the DNA strands consumed-is polynomial in n, the number of bits of the counter, while the waste of alternative counters grows exponentially in n. We also show that our n-bit counter fails to work correctly when many (Θ(n)) copies of the species that represent the bits of the counter are present initially. The proof applies more generally to show that in chemical reaction systems where all but one reactant of each reaction are catalysts, computations longer than a polynomial function of the size of the system are not possible when there are polynomially many copies of the system present.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):512-21.
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    ABSTRACT: We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may 'compute' synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):497-503.
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    ABSTRACT: Recent advances in the spectroscopy of biomolecules have highlighted the possibility of quantum coherence playing an active role in biological energy transport. The revelation that quantum coherence can survive in the hot and wet environment of biology has generated a lively debate across both the physics and biology communities. In particular, it remains unclear to what extent non-trivial quantum effects are used in biology and what advantage, if any, they afford. We propose an analogue quantum simulator, based on currently available techniques in ultra-cold atom physics, to study a model of energy and electron transport based on the Holstein Hamiltonian. By simulating the salient aspects of a biological system in a tunable laboratory set-up, we hope to gain insight into the validity of several theoretical models of biological quantum transport in a variety of relevant parameter regimes.
    Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):522-8.
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    ABSTRACT: Genes store heritable information, but actual gene expression often depends on many so-called epigenetic factors, both physical and chemical, external to DNA. Epigenetic changes can be both reversible and heritable. The genome is associated with a physical object (DNA) with a specific location, whereas the epigenome is a global, systemic, entity. Furthermore, genomic information is tied to specific coded molecular sequences stored in DNA. Although epigenomic information can be associated with certain non-DNA molecular sequences, it is mostly not. Therefore, there does not seem to be a stored 'epigenetic programme' in the information-theoretic sense. Instead, epigenomic control is-to a large extent-an emergent self-organizing phenomenon, and the real-time operation of the epigenetic 'project' lies in the realm of nonlinear bifurcations, interlocking feedback loops, distributed networks, top-down causation and other concepts familiar from the complex systems theory. Lying at the heart of vital eukaryotic processes are chromatin structure, organization and dynamics. Epigenetics provides striking examples of how bottom-up genetic and top-down epigenetic causation intermingle. The fundamental question then arises of how causal efficacy should be attributed to biological information. A proposal is made to implement explicit downward causation by coupling information directly to the dynamics of chromatin, thus permitting the coevolution of dynamical laws and states, and opening up a new sector of dynamical systems theory that promises to display rich self-organizing and self-complexifying behaviour.
    Interface focus: a theme supplement of Journal of the Royal Society interface 02/2012; 2(1):42-8.