98 results found
Jones NS, Hadjipantelis PZ, Moriarty J, et al., 2013, Function-valued traits in evolution, Interface, Vol: 10, Pages: 1-8, ISSN: 1742-5662
Many biological characteristics of evolutionary interest are not scalar variables but continuous functions. Given a dataset of function-valued traits generated by evolution, we develop a practical, statistical approach to infer ancestral function-valued traits, and estimate the generative evolutionary process. We do this by combining dimension reduction and phylogenetic Gaussian process regression, a non-parametric procedure that explicitly accounts for known phylogenetic relationships. We test the performance of methods on simulated, function-valued data generated from a stochastic evolutionary model. The methods are applied assuming that only the phylogeny, and the function-valued traits of taxa at its tips are known. Our method is robust and applicable to a wide range of function-valued data, and also offers a phylogenetically aware method for estimating the autocorrelation of function-valued traits.
Little MA, Jones NS, 2013, Signal processing for molecular and cellular biological physics: an emerging field, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 371, ISSN: 1364-503X
Jones NS, Maccarone TJ, 2013, Inference for the physical sciences Introduction, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 371, ISSN: 1364-503X
Jones NS, Moriarty J, 2013, Evolutionary inference for function-valued traits: Gaussian process regression on phylogenies, JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 10, ISSN: 1742-5689
Lewis ACF, Jones NS, Porter MA, et al., 2012, What Evidence Is There for the Homology of Protein-Protein Interactions?, PLOS COMPUTATIONAL BIOLOGY, Vol: 8
Johnston IG, Gaal B, Neves RPD, et al., 2012, Mitochondrial Variability as a Source of Extrinsic Cellular Noise, PLoS Comput Biol, Vol: 8
<title>Author Summary</title> <p>Cellular variability has been found to play a major role in diverse and important phenomena, including stem cell differentiation and drug resistance, but the sources of this variability have yet to be satisfactorily explained. We propose a mechanism, supported by a substantial number of recent and new experiments, by which cell-to-cell differences in both the number and functionality of mitochondria – the organelles responsible for energy production in eukaryotes – leads to variability in transcription rate between cells and may hence be a significant source of cellular noise in many downstream processes. We illustrate the downstream effect of mitochondrial variability through simulated studies of protein expression and stem cell differentiation, and suggest possible experimental approaches to further elucidate this mechanism.</p>
Schwarzlander M, Logan DC, Johnston IG, et al., 2012, Pulsing of Membrane Potential in Individual Mitochondria: A Stress-Induced Mechanism to Regulate Respiratory Bioenergetics in Arabidopsis, The Plant Cell, Vol: 24, Pages: 1188-1201
Mitochondrial ATP synthesis is driven by a membrane potential across the inner mitochondrial membrane; this potential is generated by the proton-pumping electron transport chain. A balance between proton pumping and dissipation of the proton gradient by ATP-synthase is critical to avoid formation of excessive reactive oxygen species due to overreduction of the electron transport chain. Here, we report a mechanism that regulates bioenergetic balance in individual mitochondria: a transient partial depolarization of the inner membrane. Single mitochondria in living Arabidopsis thaliana root cells undergo sporadic rapid cycles of partial dissipation and restoration of membrane potential, as observed by real-time monitoring of the fluorescence of the lipophilic cationic dye tetramethyl rhodamine methyl ester. Pulsing is induced in tissues challenged by high temperature, H2O2, or cadmium. Pulses were coincident with a pronounced transient alkalinization of the matrix and are therefore not caused by uncoupling protein or by the opening of a nonspecific channel, which would lead to matrix acidification. Instead, a pulse is the result of Ca2+ influx, which was observed coincident with pulsing; moreover, inhibitors of calcium transport reduced pulsing. We propose a role for pulsing as a transient uncoupling mechanism to counteract mitochondrial dysfunction and reactive oxygen species production.
Aston JAD, Buck D, Coleman J, et al., 2012, Phylogenetic inference for function-valued traits: speech sound evolution, Trends Ecol Evol, Vol: 27, Pages: 160-166, ISSN: 0169-5347
Phylogenetic models have recently been proposed for data that are best represented as a mathematical function (i.e. function valued). Such methods can be used to model the change over time in function-based descriptions of various data of interest to evolutionary biologists, including the sound of speech. This approach to phylogenetic inference and analysis is challenging, both in terms of modeling the phylogenetics of functions and in engaging with previously existing evidence for character-state change. Nevertheless, it is both a real and exciting prospect. Our approach could provide those interested in investigating a greater range of evolutionary processes with the ability to use statistical hypothesis-testing procedures and to create estimates of the states of function-valued characteristics (e.g. speech sounds) at earlier historical times.
Little MA, Jones NS, 2011, Generalized methods and solvers for noise removal from piecewise constant signals. II. New methods, PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 467, Pages: 3115-3140, ISSN: 1364-5021
Little MA, Jones NS, 2011, Generalized methods and solvers for noise removal from piecewise constant signals. I. Background theory, PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 467, Pages: 3088-3114, ISSN: 1364-5021
Fenn DJ, Porter MA, Williams S, et al., 2011, Temporal evolution of financial-market correlations, PRE, Vol: 84
Little MA, Steel BC, Bai F, et al., 2011, Steps and Bumps: Precision Extraction of Discrete States of Molecular Machines, BIOPHYSICAL JOURNAL, Vol: 101, Pages: 477-485, ISSN: 0006-3495
das Neves RP, Jones NS, Andreu L, et al., 2010, Connecting variability in global transcription rate to mitochondrial variability, PLOS Biology, Vol: 8, ISSN: 1545-7885
Populations of genetically identical eukaryotic cells show significant cell-to-cell variability in gene expression. However, welack a good understanding of the origins of this variation. We have found marked cell-to-cell variability in average cellularrates of transcription. We also found marked cell-to-cell variability in the amount of cellular mitochondrial mass. Weundertook fusion studies that suggested that variability in transcription rate depends on small diffusible factors. Followingthis, in vitro studies showed that transcription rate has a sensitive dependence on [ATP] but not on the concentration ofother nucleotide triphosphates (NTPs). Further experiments that perturbed populations by changing nutrient levels andavailable [ATP] suggested this connection holds in vivo. We found evidence that cells with higher mitochondrial mass, orhigher total membrane potential, have a faster rate of transcription per unit volume of nuclear material. We also foundevidence that transcription rate variability is substantially modulated by the presence of anti- or prooxidants. Daughterstudies showed that a cause of variability in mitochondrial content is apparently stochastic segregation of mitochondria atdivision. We conclude by noting that daughters that stochastically inherit a lower mitochondrial mass than their sisters haverelatively longer cell cycles. Our findings reveal a link between variability in energy metabolism and variability intranscription rate.
Cord-forming fungi form extensive networks that continuously adapt to maintain an efficient transport system. As osmotically driven water uptake is often distal from the tips, and aqueous fluids are incompressible, we propose that growth induces mass flows across the mycelium, whether or not there are intrahyphal concentration gradients. We imaged the temporal evolution of networks formed by Phanerochaete velutina, and at each stage calculated the unique set of currents that account for the observed changes in cord volume, while minimizing the work required to overcome viscous drag. Predicted speeds were in reasonable agreement with experimental data, and the pressure gradients needed to produce these flows are small. Furthermore, cords that were predicted to carry fast-moving or large currents were significantly more likely to increase in size than cords with slow-moving or small currents. The incompressibility of the fluids within fungi means there is a rapid global response to local fluid movements. Hence velocity of fluid flow is a local signal that conveys quasi-global information about the role of a cord within the mycelium. We suggest that fluid incompressibility and the coupling of growth and mass flow are critical physical features that enable the development of efficient, adaptive biological transport networks.
Lewis ACF, Jones NS, Porter MA, et al., 2010, The function of communities in protein interaction networks at multiple scales, BMC Systems Biology
Agarwal S, Deane CM, Porter MA, et al., 2010, Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks, PLOS Computational Biology, Vol: 6, ISSN: 1553-734X
The idea of “date” and “party” hubs has been influential in the study of protein–protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here, we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. However, we find significant correlations between interaction centrality and the functional similarity of the interacting proteins. We suggest that thinking in terms of a date/party dichotomy for hubs in protein interaction networks is not meaningful, and it might be more useful to conceive of roles for protein-protein interactions rather than for individual proteins.
Xue Q, Jones NS, Leake MC, 2010, A GENERAL APPROACH FOR SEGMENTING ELONGATED AND STUBBY BIOLOGICAL OBJECTS: EXTENDING A CHORD LENGTH TRANSFORM WITH THE RADON TRANSFORM, 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Publisher: IEEE, Pages: 161-164, ISSN: 1945-7928
Ecology Letters (2010) 13: 891–899 Abstract Food web structure plays an important role when determining robustness to cascading secondary extinctions. However, existing food web models do not take into account likely changes in trophic interactions (‘rewiring’) following species loss. We investigated structural dynamics in 12 empirically documented food webs by simulating primary species loss using three realistic removal criteria, and measured robustness in terms of subsequent secondary extinctions. In our model, novel trophic interactions can be established between predators and food items not previously consumed following the loss of competing predator species. By considering the increase in robustness conferred through rewiring, we identify a new category of species – overlap species – which promote robustness as shown by comparing simulations incorporating structural dynamics to those with static topologies. The fraction of overlap species in a food web is highly correlated with this increase in robustness; whereas species richness and connectance are uncorrelated with increased robustness. Our findings underline the importance of compensatory mechanisms that may buffer ecosystems against environmental change, and highlight the likely role of particular species that are expected to facilitate this buffering.
Little MA, Jones NS, 2010, Sparse Bayesian step-filtering for high-throughput analysis of molecular machine dynamics, Acoustics Speech and Signal Processing (ICASSP), 2010 IEEE International Conference on, Pages: 4162-4165, ISSN: 1520-6149
Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-like motion of these machines with time series from novel experimental assays has recently become possible. These time series are corrupted by molecular and experimental noise that requires removal, but classical signal processing is of limited use for recovering such step-like dynamics. This paper reports simple, novel Bayesian filters that are robust to step-like dynamics in noise, and introduce an L<sub>1</sub>-regularized, global filter whose sparse solution can be rapidly obtained by standard convex optimization methods. We show these techniques outperforming classical filters on simulated time series in terms of their ability to accurately recover the underlying step dynamics. To show the techniques in action, we extract step-like speed transitions from Rhodobacter sphaeroides flagellar motor time series.
Fenn DJ, Porter MA, McDonald M, et al., 2009, Dynamic communities in multichannel data: An application to the foreign exchange market during the 2007--2008 credit crisis, Chaos, Vol: 19, Pages: 033119-8
Smith DMD, Onnela J, Jones NS, 2009, Master-equation analysis of accelerating networks, PRE, Vol: 79
Staniczenko PPA, Lee CF, Jones NS, 2009, Rapidly detecting disorder in rhythmic biological signals: A spectral entropy measure to identify cardiac arrhythmias, Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol: 79, Pages: 011915-011915
Jones NS, 2008, Using the Memories of Multiscale Machines to Characterize Complex Systems, PRL, Vol: 100
Jones NS, Masanes L, 2008, Key Distillation and the Secret-Bit Fraction, Information Theory, IEEE Transactions on, Vol: 54, Pages: 680-691, ISSN: 0018-9448
We consider distillation of secret bits from partially secret noisy correlations P<sub>ABE</sub>, shared between two honest parties and an eavesdropper. The most studied distillation scenario consists of joint operations on a large number of copies of the distribution (P<sub>ABE</sub>)<sup>N</sup>, assisted with public communication. Here we consider distillation with only one copy of the distribution, and instead of rates, the Â¿qualityÂ¿ of the distilled secret bits is optimized, where the Â¿qualityÂ¿ is quantified by the secret-bit fraction of the result. The secret-bit fraction of a binary distribution is the proportion which constitutes a secret bit between Alice and Bob. With local operations and public communication the maximal extractable secret-bit fraction from a distribution P<sub>ABE</sub> is found, and is denoted by Â¿[P<sub>ABE</sub>]. This quantity is shown to be nonincreasing under local operations and public communication, and nondecreasing under eavesdropper's local operations: Â¿ is a secrecy monotone. It is shown that if Â¿ [P<sub>ABE</sub>] > 1/2 then P<sub>ABE</sub> is distillable, thus providing a sufficient condition for distillability. A simple expression for Â¿[P<sub>ABE</sub>] is found when the eavesdropper is decoupled, and when the honest parties' information is binary and the local operations are reversible. Intriguingly, for general distributions the (optimal) operation requires local degradation of the data.
Jones NS, Stace TM, 2006, Photon frequency-mode matching using acousto-optic frequency beam splitters, PRA, Vol: 73
Jones NS, Masanes L, 2005, Interconversion of nonlocal correlations, PRA, Vol: 72
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