Noise-based switches and amplifiers for gene expression

The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own expression or the production of protein in another network. Engineered control of cellular function through the design and manipulation of such networks lies within the constraints of current technology. Here we develop a model describing the regulation of gene expression, and elucidate the effects of noise on the formulation. We consider a single network derived from bacteriophage $\lambda$, and construct a two-parameter deterministic model describing the temporal evolution of the concentration of $\lambda$ repressor protein. Bistability in the steady-state protein concentration arises naturally, and we show how the bistable regime is enhanced with the addition of the first operator site in the promotor region. We then show how additive and multiplicative external noise can be used to regulate expression. In the additive case, we demonstrate the utility of such control through the construction of a protein switch, whereby protein production is turned ``on'' and ``off'' using short noise pulses. In the multiplicative case, we show that small deviations in the transcription rate can lead to large fluctuations in the production of protein, and describe how these fluctuations can be used to amplify protein production significantly. These novel results suggest that an external noise source could be used as a switch and/or amplifier for gene expression. Such a development could have important implications for gene therapy.Comment: 21 pages, 3 figure

Evidence for strong lattice effects as revealed from huge unconventional oxygen isotope effects on the pseudogap temperature in La2−x_{2-x}Srx_{x}CuO4_{4}

The oxygen isotope ($^{16}$O/$^{18}$O) effect (OIE) on the pseudogap (charge-stripe ordering) temperature $T^{\ast}$ is investigated for the cuprate superconductor La$_{2-x}$Sr$_{x}$CuO$_{4}$ as a function of doping $x$ by means of x-ray absorption near edge structure (XANES) studies. A strong $x$ dependent and sign reversed OIE on $T^{\ast}$ is observed. The OIE exponent $\alpha_{T^{\ast}}$ systematically decreases from $\alpha_{T^{\ast}} = - 0.6(1.3)$ for $x = 0.15$ to $\alpha_{T^{\ast}} = - 4.4(1.1)$ for $x = 0.06$, corresponding to increasing $T^{\ast}$ and decreasing superconducting transition temperature $T_{c}$. Both $T^{\ast}(^{16}{\rm O})$ and $T^{\ast}(^{18}{\rm O})$ exhibit a linear doping dependence with different slopes and critical end points (where $T^{\ast}(^{16}{\rm O})$ and $T^{\ast}(^{18}{\rm O})$ fall to zero) at $x_{c}(^{16}{\rm O}) = 0.201(4)$ and $x_{c}(^{18}{\rm O}) = 0.182(3)$, indicating a large positive OIE of $x_{c}$ with an exponent of $\alpha_{x_{c}} = 0.84(22)$. The remarkably large and strongly doping dependent OIE on $T^{\ast}$ signals a substantial involvement of the lattice in the formation of the pseudogap, consistent with a polaronic approach to cuprate superconductivity and the vibronic character of its ground state

Formation of clumps and patches in self-aggregation of finite size particles

New model equations are derived for dynamics of self-aggregation of finite-size particles. Differences from standard Debye-Huckel and Keller-Segel models are: a) the mobility $\mu$ of particles depends on the locally-averaged particle density and b) linear diffusion acts on that locally-averaged particle density. The cases both with and without diffusion are considered here. Surprisingly, these simple modifications of standard models allow progress in the analytical description of evolution as well as the complete analysis of stationary states. When $\mu$ remains positive, the evolution of collapsed states in our model reduces exactly to finite-dimensional dynamics of interacting particle clumps. Simulations show these collapsed (clumped) states emerging from smooth initial conditions, even in one spatial dimension. If $\mu$ vanishes for some averaged density, the evolution leads to spontaneous formation of \emph{jammed patches} (weak solution with density having compact support). Simulations confirm that a combination of these patches forms the final state for the system.Comment: 38 pages, 8 figures; submitted to Physica

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. We also find that communication between different disciplines goes through specific "trading zones", ie sub-communities that create an interface around specific tools (a DNA microchip) or concepts (a network).Comment: Journal of the American Society for Information Science and Technology (2012) 10.1002/asi.2264

Ein Sternlein stand am Himmel

http://tartu.ester.ee/record=b2415320~S1*es

Ein Sternlein stand am Himmel

http://tartu.ester.ee/record=b2410364~S1*es

Photometry Results for the Globular Clusters M10 and M12: Extinction Maps, Color-Magnitude Diagrams, and Variable Star Candidates

We report on photometry results of the equatorial globular clusters (GCs) M10 and M12. These two clusters are part of our sample of GCs which we are probing for the existence of photometrically varying eclipsing binary stars. During the search for binaries in M10 and M12, we discovered the signature of differential reddening across the fields of the clusters. The effect is stronger for M10 than for M12. Using our previously described dereddening technique, we create differential extinction maps for the clusters which dramatically improve the appearance of the color-magnitude diagrams (CMDs). Comparison of our maps with the dust emissivity maps of Schlegel, Finkbeiner, & Davis (SFD) shows good agreement in terms of spatial extinction features. Several methods of adding an E_{V-I} zero point to our differential maps are presented of which isochrone fitting proved to be the most successful. Our E_{V-I} values fall within the range of widely varying literature values. More specifically, our reddening zero point estimate for M12 agrees well with the SFD estimate, whereas the one for M10 falls below the SFD value. Our search for variable stars in the clusters produced a total of five variables: three in M10 and two in M12. The M10 variables include a binary system of the W Ursa Majoris (W UMa) type, a background RR Lyrae star, and an SX Phoenicis pulsator, none of which is physically associated with M10. M12's variables are two W UMa binaries, one of which is most likely a member of the cluster. We present the phased photometry lightcurves for the variable stars, estimate their distances, and show their locations in the fields and the CMDs of the GCs.Comment: 22 pages, 21 figures, to be published in AJ October 2002. For a higher-resolution version of this paper, please visit http://www.astro.lsa.umich.edu/~kaspar/M10_M12_photometry.ps.gz (gzipped postscript) or http://www.astro.lsa.umich.edu/~kaspar/M10_M12_photometry.pdf (pdf file

Digital detox: An effective solution in the smartphone era? A systematic literature review

Smartphone use, e.g., on social network sites or instant messaging, can impair well-being and is related to clinical phenomena, like depression. Digital detox interventions have been suggested as a solution to reduce negative impacts from smartphone use on outcomes like well-being or social relationships. Digital detox is defined as timeouts from using electronic devices (e.g., smartphones), either completely or for specific subsets of smartphone use. However, until now, it has been unclear whether digital detox interventions are effective at promoting a healthy way of life in the digital era. This systematic literature review aimed to answer the question of whether digital detox interventions are effective at improving outcomes like health and well-being, social relationships, self-control or performance. Systematic searches of seven databases were carried out according to PRISMA guidelines, and intervention studies were extracted that examined timeouts from smartphone use and/or smartphone-related use of social network sites and instant messaging. The review yielded k = 21 extracted studies (total N = 3,625 participants). The studies included interventions in the field, from which 12 were identified as randomized controlled trials. The results showed that the effects from digital detox interventions varied across studies on health and well-being, social relationships, self-control, or performance. For example, some studies found positive intervention effects, whereas others found no effect or even negative consequences for well-being. Reasons for these mixed findings are discussed. Research is needed to examine mechanisms of change to derive implications for the development of successful digital detox interventions