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    ABSTRACT: Non-coding transcripts play an important role in gene expression regulation in all species, including budding and fission yeast. Such regulatory transcripts include intergenic ncRNA (non-coding RNA), 5' and 3' UTRs, introns and antisense transcripts. In the present review, we discuss advantages and limitations of recently developed sequencing techniques, such as ESTs, DNA microarrays, RNA-Seq (RNA sequencing), DRS (direct RNA sequencing) and TIF-Seq (transcript isoform sequencing). We provide an overview of methods applied in yeast and how each of them has contributed to our knowledge of gene expression regulation and transcription.
    Biochemical Society Transactions 12/2013; 41(6):1654-1659.
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    ABSTRACT: Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).
    RNA 10/2013;
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    ABSTRACT: Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. It is therefore necessary to segment observed tracks into swimming and reorientation phases to extract useful statistics. We present novel robust analysis tools to discern these two phases in tracks. Our methods comprise a simple and effective protocol for removing spurious tracks from tracking datasets, followed by analysis based on a two-state hidden Markov model, taking advantage of the availability of mutant strains that exhibit swimming-only or reorientating-only motion to generate an empirical prior distribution. Using simulated tracks with varying levels of added noise, we validate our methods and compare them with an existing heuristic method. To our knowledge this is the first example of a systematic assessment of analysis methods in this field. The new methods are substantially more robust to noise and introduce less systematic bias than the heuristic method. We apply our methods to tracks obtained from the bacterial species Rhodobacter sphaeroides and Escherichia coli. Our results demonstrate that R. sphaeroides exhibits persistence over the course of a tumbling event, which is a novel result with important implications in the study of this and similar species.
    PLoS Computational Biology 10/2013; 9(10):e1003276.
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    ABSTRACT: Turing morphogen models have been extensively explored in the context of large-scale self-organization in multicellular biological systems. However, reconciling the detailed biology of morphogen dynamics, while accounting for time delays associated with gene expression, reveals aberrant behaviours that are not consistent with early developmental self-organization, especially the requirement for exquisite temporal control. Attempts to reconcile the interpretation of Turing's ideas with an increasing understanding of the mechanisms driving zebrafish pigmentation suggests that one should reconsider Turing's model in terms of pigment cells rather than morphogens (Nakamasu et al., 2009, PNAS, 106, 8429-8434; Yamaguchi et al., 2007, PNAS, 104, 4790-4793). Here the dynamics of pigment cells is subject to response delays implicit in the cell cycle and apoptosis. Hence we explore simulations of fish skin patterning, focussing on the dynamical influence of gene expression delays in morphogen-based Turing models and response delays for cell-based Turing models. We find that reconciling the mechanisms driving the behaviour of Turing systems with observations of fish skin patterning remains a fundamental challenge.
    Mathematical Medicine and Biology 10/2013;
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    ABSTRACT: A 2D model is developed for fluid flow, mass transport and cell distribution in a hollow fibre membrane bioreactor. The geometry of the modelling region is simplified by excluding the exit ports at either end and focusing on the upper half of the central section of the bioreactor. Cells are seeded on a porous scaffold throughout the extracapillary space (ECS), and fluid pumped through the bioreactor via the lumen inlet and/or exit ports. In the fibre lumen and porous fibre wall, flow is described using Stokes and Darcy governing equations, respectively, while in the ECS porous mixture theory is used to model the cells, culture medium and scaffold. Reaction-advection-diffusion equations govern the concentration of a solute of interest in each region. The governing equations are reduced by exploiting the small aspect ratio of the bioreactor. This yields a coupled system for the cell volume fraction, solute concentration and ECS water pressure which is solved numerically for a variety of experimentally relevant case studies. The model is used to identify different regimes of cell behaviour, and results indicate how the flow rate can be controlled experimentally to generate a uniform cell distribution under regimes relevant to nutrient- and/or chemotactic-driven behaviours.
    Mathematical Medicine and Biology 09/2013;
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    ABSTRACT: We consider the solution of left preconditioned linear systems P−1Cx=P−1cP−1Cx=P−1c, where P,C∈Cn×nP,C∈Cn×n are non-Hermitian, c∈Cnc∈Cn, and CC, PP, and P−1CP−1C are diagonalisable with spectra symmetric about the real line. We prove that, when PP and CC are self-adjoint with respect to the same Hermitian sesquilinear form, the convergence of a minimum residual method in a particular nonstandard inner product applied to the preconditioned linear system is bounded by a term that depends only on the spectrum of P−1CP−1C. The inner product is related to the spectral decomposition of PP. When PP is self-adjoint with respect to a nearby Hermitian sesquilinear form to CC, the convergence of a minimum residual method in this nonstandard inner product applied to the preconditioned linear system is bounded by a term involving the eigenvalues of P−1CP−1C and a constant factor. The size of this factor is related to the nearness of the Hermitian sesquilinear forms. Numerical experiments indicate that for certain matrices eigenvalue-dependent convergence is observed both for the nonstandard method and for standard GMRES.
    Journal of Computational and Applied Mathematics 09/2013; 249:57–68.
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    ABSTRACT: A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is bistable is considered. A general analytical approximation is derived for the stationary probability density and the mean switching time between metastable states, which includes the pre exponential factor. The results are illustrated with a model of gene expression that displays bistable switching. In this model, the external state represents the number of protein molecules produced by a hypothetical gene. Once produced, a protein is eventually degraded. The internal state represents the activated or unactivated state of the gene; in the activated state the gene produces protein more rapidly than the unactivated state. The gene is activated by a dimer of the protein it produces so that the activation rate depends on the current protein level. This is a well studied model, and several model reductions and diffusion approximation methods are available to analyze its behavior. However, it is unclear if these methods accurately approximate long-time metastable behavior (i.e., mean switching time between metastable states of the bistable system). Diffusion approximations are generally known to fail in this regard.
    Journal of Mathematical Biology 09/2013;
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    ABSTRACT: Blebs are cellular protrusions that are used by cells for multiple purposes including locomotion. A mechanical model for the problem of pressure-driven blebs based on force and moment balances of an axisymmetric shell model is proposed. The formation of a bleb is initiated by weakening the shell over a small region, and the deformation of the cellular membrane from the cortex is obtained during inflation. However, simply weakening the shell leads to an area increase of more than 4 %, which is physically unrealistic. Thus, the model is extended to include a reconfiguration process that allows large blebs to form with small increases in area. It is observed that both geometric and biomechanical constraints are important in this process. In particular, it is shown that although blebs are driven by a pressure difference across the cellular membrane, it is not the limiting factor in determining bleb size.
    Biomechanics and Modeling in Mechanobiology 07/2013;
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    ABSTRACT: Extensive studies have explored the dynamics of the ocular surface fluid, though theoretical investigations are typically limited to the use of the lubrication approximation, which is not guaranteed to be uniformly valid a-priori throughout the tear meniscus. However, resolving tear film behaviour within the meniscus and especially its apices is required to characterise the flow dynamics where the tear film is especially thin, and thus most susceptible to evaporatively induced hyperosmolarity and subsequent epithelial damage. Hence, we have explored the accuracy of the standard lubrication approximation for the tear film by explicit comparisons with the 2D Navier-Stokes model, considering both stationary and moving eyelids. Our results demonstrate that the lubrication model is qualitatively accurate except in the vicinity of the eyelids. In particular, and in contrast to lubrication theory, the solution of the full Navier-Stokes equations predict a distinct absence of fluid flow, and thus convective mixing in the region adjacent to the tear film contact line. These observations not only support emergent hypotheses concerning the formation of Marx's line, a region of epithelial cell staining adjacent to the contact line on the eyelid, but also enhance our understanding of the pathophysiological consequences of the flow profile near the tear film contact line.
    Bulletin of Mathematical Biology 07/2013;
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    ABSTRACT: The study of reaction-diffusion processes is much more complicated on general curved surfaces than on standard Cartesian coordinate spaces. Here we show how to formulate and solve systems of reaction-diffusion equations on surfaces in an extremely simple way, using only the standard Cartesian form of differential operators, and a discrete unorganized point set to represent the surface. Our method decouples surface geometry from the underlying differential operators. As a consequence, it becomes possible to formulate and solve rather general reaction-diffusion equations on general surfaces without having to consider the complexities of differential geometry or sophisticated numerical analysis. To illustrate the generality of the method, computations for surface diffusion, pattern formation, excitable media, and bulk-surface coupling are provided for a variety of complex point cloud surfaces.
    Proceedings of the National Academy of Sciences 05/2013;
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