Index of papers in April 2015 that mention
  • cell population
Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs Greber, Holger Fröhlich, Niko Beerenwinkel
Abstract
As a consequence of this cellular heterogeneity, knockdowns result in variable effects among cells and lead to weak average phenotypes on the cell population level.
Application to pathogen infection experiments
Like for the simulation study, we derived the cell population effects for the NEM from Wilcoxon tests, comparing the knockdown experiment to the control.
Author Summary
Nested effects models, a method tailored to reconstruct signaling networks from high-dimensional readouts of gene silencing experiments, have so far been only applied on the cell population level.
Discussion
Here, we have identified one confounding factor, namely heterogeneous signaling pathway activation within a cell population , and incorporated it directly into a novel probabilistic model for pathway reconstruction.
Discussion
Only at this data resolution, the heterogeneity within a cell population can be accounted for and it becomes possible to investigate potentially confounding factors, such as, for example, pathway activity.
Introduction
Otherwise, an ambiguous signal is obtained, when averaging over the cell population of a knockdown.
Simulation study
To assess the impact that pathway disruption has on the cell population level, we ran the simulations on a standard NEM using the log-likelihood model introduced in [23].
Simulation study
For these gene-level data sets we used p-values of a Wilcoxon test comparing the cell population of a knockdown to the control distribution.
cell population is mentioned in 8 sentences in this paper.
Topics mentioned in this paper:
Kevin Thurley, Daniel Gerecht, Elfriede Friedmann, Thomas Höfer
Discussion
In this theoretical study, we cannot address the question to what extent such a mechanism is responsible for the activation of T cell populations in vivo.
Discussion
That means, the cell population recognizes relative rather than absolute increases in the stimulus strength (here, the amount of secreted cyto-kine molecules per time).
In silico T cell population
In silico T cell population
Introduction
upon receiving an antigen stimulus, only about one quarter of a Th cell population releases IL-2 molecules [34—36].
Software
For the simulations of the three-dimensional in silico T cell population (Figs 3—5), a problem specific software was developed in the Heidelberg Numerical Methods Group, based on the open source C++ library deal.II [41].
lL-2 producers surrounded by lL-2-responsive cells produce short-range paracrine signals
Although we use the specific parameters for IL-2 here, this model is of more general interest and applies to other situations with few signaling cells and many responder cells (e.g., IL-4 secreting Th cells in a B cell population [9]), or can be thought of as representing a cluster of several cytokine secreting cells in a population with a small density of cytokine secreting cells elsewhere.
ln-silico Th cell culture exhibits localized paracrine lL-2 signaling
To investigate the origins and consequences of spatially inhomogeneous dynamics of cyto-kine signaling, we performed extensive three-dimensional simulations of a T cell population (Fig 3A and 3B).
ln-silico Th cell culture exhibits localized paracrine lL-2 signaling
However, competition for the cytokine can cause heterogeneity in the response of a cell population and result in bulk IL-2 levels that are much lower than local concentration peaks and in agreement With concentration levels measured by ELISA (see Discussion).
cell population is mentioned in 8 sentences in this paper.
Topics mentioned in this paper:
Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff
Abstract
Bursting transcription can cause individual cells to remain in synchrony transiently, offering an explanation of transcriptional cycling as observed in cell populations , both on promoter chromatin status and mRNA levels.
Author Summary
This provides an explanation for transient transcriptional cycles observed at the level of cell populations .
Bursts in the system
This finding is in good agreement with experimental observations that mRNA burst-size distributions for regulated genes across a cell population are often geometric [54, 55].
Bursts in the system
If no mRNA degradation occurred on the considered timescale the bursts led to stepwise accumulation of mRNA in individual cells (Fig 5D) as well as on the cell population level (Fig 5F).
Discussion
The model does not, however, exclude a possibility of the transcription cycle times being less precise, due, for instance, to the presence of a very slow step in one or more of the cycle transitions, or a possibility of variable gene induction times due to heterogeneity of the initial promoter states in a cell population .
Introduction
In some cases transcription dynamics at the cell population level proceeds in an oscillatory fashion [23—28] at frequencies between 30 and 60 min [24, 27], i.e.
cell population is mentioned in 6 sentences in this paper.
Topics mentioned in this paper:
Thomas W. Spiesser, Clemens Kühn, Marcus Krantz, Edda Klipp
Introduction
Through inheritance, we let the culture evolve over time, generating fully traceable cell populations for analysis [32].
Supporting Information
Model-1 and Model-2 within the cell populations simulator.
Supporting Information
The script can be used to simulate complete pedigrees of growing and dividing cells from single progenitor cells and contains routines to create basic plots for analysis of the resulting cell population .
cell population is mentioned in 3 sentences in this paper.
Topics mentioned in this paper: