A feedback quenched oscillator produces turing patterning with one diffuser

Efforts to engineer synthetic gene networks that spontaneously produce patterning in multicellular ensembles have focused on Turing's original model and the "activator-inhibitor" models of Meinhardt and Gierer. Systems based on this model are notoriously difficult to engineer. We present the first demonstration that Turing pattern formation can arise in a new family of oscillator-driven gene network topologies, specifically when a second feedback loop is introduced which quenches oscillations and incorporates a diffusible molecule. We provide an analysis of the system that predicts the range of kinetic parameters over which patterning should emerge and demonstrate the system's viability using stochastic simulations of a field of cells using realistic parameters. The primary goal of this paper is to provide a circuit architecture which can be implemented with relative ease by practitioners and which could serve as a model system for pattern generation in synthetic multicellular systems. Given the wide range of oscillatory circuits in natural systems, our system supports the tantalizing possibility that Turing pattern formation in natural multicellular systems can arise from oscillator-driven mechanisms.     

A genetic bistable switch utilizing nonlinear protein degradation

Background

Fluorescent reporter proteins have revolutionized our understanding of cellular bioprocesses by enabling live cell imaging with exquisite spatio-temporal resolution. Existing fluorescent proteins are predominantly based on the green fluorescent protein (GFP) and related analogs. However, GFP-family proteins strictly require molecular oxygen for maturation of fluorescence, which precludes their application for investigating biological processes in low-oxygen environments. A new class of oxygen-independent fluorescent reporter proteins was recently reported based on flavin-binding photosensors from Bacillus subtilis and Pseudomonas putida. However, flavin-binding fluorescent proteins show very limited brightness, which restricts their utility as biological imaging probes.

Results

In this work, we report the discovery of bright mutants of a flavin-binding fluorescent protein from P. putida using directed evolution by site saturation mutagenesis. We discovered two mutations at a chromophore-proximal amino acid (F37S and F37T) that confer a twofold enhancement in brightness relative to the wild type fluorescent protein through improvements in quantum yield and holoprotein fraction. In addition, we observed that substitution with other aromatic amino acids at this residue (F37Y and F37W) severely diminishes fluorescence emission. Therefore, we identify F37 as a key amino acid residue in determining fluorescence.

Conclusions

To increase the scope and utility of flavin-binding fluorescent proteins as practical fluorescent reporters, there is a strong need for improved variants of the wild type protein. Our work reports on the application of site saturation mutagenesis to isolate brighter variants of a flavin-binding fluorescent protein, which is a first-of-its-kind approach. Overall, we anticipate that the improved variants will find pervasive use as fluorescent reporters for biological studies in low-oxygen environments.     

Varying coefficient model with unknown within-subject covariance for analysis of tumor growth curves

SUMMARY: In this article we develop a nonparametric estimation procedure for the varying coefficient model when the within-subject covariance is unknown. Extending the idea of iterative reweighted least squares to the functional setting, we iterate between estimating the coefficients conditional on the covariance and estimating the functional covariance conditional on the coefficients. Smoothing splines for correlated errors are used to estimate the functional coefficients with smoothing parameters selected via the generalized maximum likelihood. The covariance is nonparametrically estimated using a penalized estimator with smoothing parameters chosen via a Kullback-Leibler criterion. Empirical properties of the proposed method are demonstrated in simulations and the method is applied to the data collected from an ovarian tumor study in mice to analyze the effects of different chemotherapy treatments on the volumes of two classes of tumors.     

Cyst bank life-history model for a fairy shrimp from ephemeral ponds

1. Ephemeral wetland habitats provide a useful model system for studying how life‐history patterns enable populations to persist despite high environmental variation. One important life‐history trait of both plants and crustaceans in such habitats involves hatching/germination of only some of the eggs/seeds at any time. This bet‐hedging leads to the development of a bank composed of dormant propagules of many ages. 2. The San Diego fairy shrimp, Branchinecta sandiegonensis (Crustacea: Anostraca), a dominant faunal element of ephemeral ponds in San Diego, California, is a suitable organism for studying the consequences of highly fluctuating environmental conditions. As a result of large‐scale habitat loss, the species is also endangered, and this motivated our specific study towards understanding the hatching dynamics of its egg bank for planning conservation efforts such as pool restoration and re‐creation. 3. We formulated a matrix population model using egg age within the bank to study the relationship between adult survival and reproduction, and survival in and hatching from the egg bank. As vital rates for fairy shrimp are only poorly known, we generated 48 matrices with parameters encompassing ranges of likely values for the vital rates of B. sandiegonensis. We calculated population growth rates and eigenvalue elasticities both for a static model and a model with periodic reproductive failure. 4. The model shows that in good filling events, population growth rate is very high and the egg bank is increased dramatically. While population growth rate is insensitive to long‐term survival in the egg bank in our static deterministic model, it becomes sensitive to survival in the egg bank when a regime of periodically failed reproductive events is imposed. 5. Under favourable conditions, it was best for shrimp to hatch from eggs as soon as possible. However, under a regime where failed reproductive events were common, it was best to hatch after several pool fillings. Because conditions change from favourable to unfavourable unpredictably, variation in age within the egg bank appears to be critical for the persistence of the population. This attribute needs to be carefully considered when restoring or creating new pools for conservation purposes.     

Beschreibung

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