Biology subjects

Sarah Filippi

Publications and source records attributed to Sarah Filippi.

4 recordsLinked to original sources

bioRxiv2016

Nanog fluctuations in ES cells highlight the problem of measurement in cell biology

A number of important pluripotency regulators, including the transcription factor Nanog, are observed to fluctuate stochastically in individual embryonic stem (ES) cells. By transiently priming cells for commitment to different lineages, these fluctuations are thought to be important to the maintenance of, and exit from, pluripotency. However, since temporal changes in intracellular protein abundances cannot be measured directly in live cells, these fluctuations are typically assessed using genetically engineered reporter cell lines that produce a fluorescent signal as a proxy for protein expression. Here, using a combination of mathematical modeling and experiment, we show that there are unforeseen ways in which widely used reporter strategies can systemically disturb the dynamics they are intended to monitor, sometimes giving profoundly misleading results. In the case of Nanog we show how genetic reporters can compromise the behavior of important pluripotency-sustaining positive feedback loops, and induce a bifurcation in the underlying dynamics that gives rise to heterogeneous Nanog expression patterns in reporter cell lines that are not representative of the wild-type. These findings help explain the range of published observations of Nanog variability and highlight a fundamental measurement problem in cell biology.

Cell Biology↗

bioRxiv2015

Information Processing by Simple Molecular Motifs and Susceptibility to Noise

Biological organisms rely on their ability to sense and respond appropriately to their environment. The molecular mechanisms that facilitate these essential processes are however subject to a range of random effects and stochastic processes, which jointly affect the reliability of information transmission between receptors and e.g. the physiological downstream response. Information is mathematically defined in terms of the entropy; and the extent of information flowing across an information channel or signalling system is typically measured by the \"mutual information\", or the reduction in the uncertainty about the output once the input signal is known. Here we quantify how extrinsic and intrinsic noise affect the transmission of simple signals along simple motifs of molecular interaction networks. Even for very simple systems the effects of the different sources of variability alone and in combination can give rise to bewildering complexity. In particular extrinsic variability is apt to generate \"apparent\" information that can in extreme cases mask the actual information that for a single system would flow between the different molecular components making up cellular signalling pathways. We show how this artificial inflation in apparent information arises and how the effects of different types of noise alone and in combination can be understood.

Systems Biology↗

bioRxiv2015

Origins of cell-to-cell variability, kinetic proof-reading and the robustness of MAPK signal transduction

Cellular signalling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how individual cells respond differentially to the same environmental stimulus. However, the origins of cell-to-cell variability in cellular signalling systems remain poorly understood. Here we measure the temporal evolution of phosphorylated MEK and ERK dynamics across populations of cells and quantify the levels of population heterogeneity over time using high-throughput image cytometry. We use a statistical modelling framework to show that upstream noise is the dominant factor causing cell-to-cell variability in ERK phosphorylation, rather than stochasticity in the phosphorylation/dephosphorylation of ERK. In particular, the cell-to-cell variability during sustained phosphorylation stems from random fluctuations in the background upstream signalling processes, while during transient phosphorylation, the heterogeneity is primarily due to noise in the intensity of the upstream signal(s). We show that the core MEK/ERK system uses kinetic proof-reading to faithfully and robustly transmits these variable inputs. The MAPK cascade thus propagates cell-to-cell variability at the population level, rather than attenuating or increasing it.

Systems Biology↗

bioRxiv2015

Analog nitrogen sensing in Escherichia coli enables high fidelity information processing

The molecular reaction networks that coordinate the response of an organism to changing environmental conditions are central for survival and reproduction. Escherchia coli employs an accurate and flexible signalling system that is capable of processing ambient nitrogen availability rapidly and with high accuracy. Carefully orchestrated post-translational modifications of PII and the glutamine synthetase allow E. coli to trace nitrogen availability in a continuous, decidedly non-digital fashion. We measure the dynamic proteomic and metabolomic responses to trace the analog computations, and use an information theoretical framework to characterize the information capacity of E. colis nitrogen sensing network: we find that this system can transmit up to 9bits of information about the nitrogen state. This allows cells to respond rapidly and accurately even to small differences in metabolite concentrations.

Systems Biology↗