| Partner: J.R.E. Davis |
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Ostatnie publikacje
| 1. | Finkenstädt B.♦, Woodcock D.J.♦, Komorowski M., Harper C.V.♦, Davis J.R.E.♦, White M.R.H.♦, Rand D.A.♦, Quantifying intrinsic and extrinsic noise in gene transcription using the linear noise approximation: An application to single cell data, Annals of Applied Statistics, ISSN: 1932-6157, DOI: 10.1214/13-AOAS669, Vol.7, No.4, pp.1960-1982, 2013 Streszczenie: A central challenge in computational modeling of dynamic biological systems is parameter inference from experimental time course measurements. However, one would not only like to infer kinetic parameters but also study their variability from cell to cell. Here we focus on the case where single-cell fluorescent protein imaging time series data are available for a population of cells. Based on van Kampen’s linear noise approximation, we derive a dynamic state space model for molecular populations which is then extended to a hierarchical model. This model has potential to address the sources of variability relevant to single-cell data, namely, intrinsic noise due to the stochastic nature of the birth and death processes involved in reactions and extrinsic noise arising from the cell-to-cell variation of kinetic parameters. In order to infer such a model from experimental data, one must also quantify the measurement process where one has to allow for nonmeasurable molecular species as well as measurement noise of unknown level and variance. The availability of multiple single-cell time series data here provides a unique testbed to fit such a model and quantify these different sources of variation from experimental data. Słowa kluczowe: Linear noise approximation, kinetic parameter estimation, intrinsic and extrinsic noise, state space model and Kalman filter, Bayesian hierarchical modeling Afiliacje autorów:
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| 2. | Harper Claire V.V.♦, Featherstone K.♦, Semprini S.♦, Friedrichsen S.♦, McNeilly J.♦, Paszek P.♦, Spiller David G.♦, McNeilly Alan S.♦, Mullins John J.♦, Davis Julian R.♦, White Michael R.R.♦, Dynamic organisation of prolactin gene expression in living pituitary tissue, Journal of Cell Science, ISSN: 0021-9533, DOI: 10.1242/jcs.060434, Vol.123, No.3, pp.424-430, 2010 Streszczenie: Gene expression in living cells is highly dynamic, but temporal patterns of gene expression in intact tissues are largely unknown. The mammalian pituitary gland comprises several intermingled cell types, organised as interdigitated networks that interact functionally to generate co-ordinated hormone secretion. Live-cell imaging was used to quantify patterns of reporter gene expression in dispersed lactotrophic cells or intact pituitary tissue from bacterial artificial chromosome (BAC) transgenic rats in which a large prolactin genomic fragment directed expression of luciferase or destabilised enhanced green fluorescent protein (d2EGFP). Prolactin promoter activity in transgenic pituitaries varied with time across different regions of the gland. Although amplitude of transcriptional responses differed, all regions of the gland displayed similar overall patterns of reporter gene expression over a 50-hour period, implying overall co-ordination of cellular behaviour. By contrast, enzymatically dispersed pituitary cell cultures showed unsynchronised fluctuations of promoter activity amongst different cells, suggesting that transcriptional patterns were constrained by tissue architecture. Short-term, high resolution, single cell analyses in prolactin-d2EGFP transgenic pituitary slice preparations showed varying transcriptional patterns with little correlation between adjacent cells. Together, these data suggest that pituitary tissue comprises a series of cell ensembles, which individually display a variety of patterns of short-term stochastic behaviour, but together yield long-range and long-term coordinated behaviour. Słowa kluczowe: Live-cell, Microscopy, Pituitary, Prolactin, Transcription Afiliacje autorów:
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