Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression

We present an analytical framework describing the steady-state distribution of protein concentration in live cells, considering that protein production occurs in random bursts with an exponentially distributed number of molecules. We extend this framework for cases of transcription autoregulation and noise propagation in a simple genetic network. This model allows for the extraction of kinetic parameters of gene expression from steady-state distributions of protein concentration in a cell population, which are available from single cell data obtained by flow cytometry or fluorescence microscopy

Emergent Dark Matter in Late Time Universe on Holographic Screen

We discuss a scenario that the dark matter in late time universe emerges as part of the holographic stress-energy tensor on the hypersurface in higher dimensional flat spacetime. Firstly we construct a toy model with a de Sitter hypersurface as the holographic screen in the flat bulk. After adding the baryonic matter on the screen, we assume that both of the dark matter and dark energy can be described by the Brown-York stress-energy tensor. From the Hamiltonian constraint equation in the flat bulk, we find an interesting relation between the dark matter and baryonic matter's energy density parameters, by comparing with the Lambda cold dark matter parameterization. We further compare this holographic embedding of emergent dark matter with traditional braneworld scenario and present an alternative interpretation as the holographic universe. It can be reduced to our toy constraint in the late time universe, with the new parameterization of the Friedmann equation. We also comment on the possible connection with Verlinde's emergent gravity, where the dark matter is treated as the elastic response of the baryonic matter on the de Sitter spacetime background. We show that from the holographic de Sitter model with elasticity, the Tully-Fisher relation and the dark matter distribution in the galaxy scale can be derived.Comment: 28 pages, 2 figures; Matches published version and we thank the referees for many insightful comments; v3: typos in the Friedmann equations are fixe

Frequency-modulated nuclear localization bursts coordinate gene regulation

In yeast, the transcription factor Crz1 is dephosphorylated and translocates into the nucleus in response to extracellular calcium. Here we show, using time-lapse microscopy, that Crz1 exhibits short bursts of nuclear localization (typically lasting 2 min) that occur stochastically in individual cells and propagate to the expression of downstream genes. Strikingly, calcium concentration controls the frequency, but not the duration, of localization bursts. Using an analytic model, we also show that this frequency modulation of bursts ensures proportional expression of multiple target genes across a wide dynamic range of expression levels, independent of promoter characteristics. We experimentally confirm this theory with natural and synthetic Crz1 target promoters. Another stress-response transcription factor, Msn2, exhibits similar, but largely uncorrelated, localization bursts under calcium stress suggesting that frequency-modulation regulation of localization bursts may be a general control strategy used by the cell to coordinate multi-gene responses to external signals