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BackgroundRegulated proteolysis by the proteasome is one of the fundamental mechanisms used in eukaryotic cells to control cellular behavior. Efficient tools to regulate protein stability offer synthetic influence on molecular level on a selected biological process. Optogenetic control of protein stability has been achieved with the photo-sensitive degron (psd) module. This engineered tool consists of the photoreceptor domain light oxygen voltage 2 (LOV2) from Arabidopsis thaliana phototropin1 fused to a sequence that induces direct proteasomal degradation, which was derived from the carboxy-terminal degron of murine ornithine decarboxylase. The abundance of target proteins tagged with the psd module can be regulated by blue light if the degradation tag is exposed to the cytoplasm or the nucleus.ResultsWe used the model organism Saccharomyces cerevisiae to generate psd module variants with increased and decreased stabilities in darkness or when exposed to blue light using site-specific and random mutagenesis. The variants were characterized as fusions to fluorescent reporter proteins and showed half-lives between 6 and 75 minutes in cells exposed to blue light and 14 to 187 minutes in darkness. In blue light, ten variants showed accelerated degradation and four variants increased stability compared to the original psd module. Measuring the dark/light ratio of selected constructs in yeast cells showed that two variants were obtained with ratios twice as high as in the wild type psd module. In silico modeling of photoreceptor variant characteristics suggested that for most cases alterations in behavior were induced by changes in the light-response of the LOV2 domain.ConclusionsIn total, the mutational analysis resulted in psd module variants, which provide tuning of protein stability over a broad range by blue light. Two variants showed characteristics that are profoundly improved compared to the original construct. The modular usage of the LOV2 domain in optogenetic tools allows the usage of the mutants in the context of other applications in synthetic and systems biology as well.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-014-0128-9) contains supplementary material, which is available to authorized users.

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MSC (2000) 49M37,65K10,65L10,65L80,90C06,90C30Nonlinear Differential Algebraic Equations (DAEs) are an important class of models for dynamic processes. To establish models that describe the process behavior in a quantitatvely correct way, often parameters in the model have to be determined from observations or measurements of the process. This paper reviews numerical methods for parameter estimation in DAEs. In particular the so-called boundary value problem approach and a versatile realisation, the multiple shooting method for parameter estimation, are discussed. Several applications are given to show the numerical performance and the wide applicability of the methods. A difficulty that occurs in practical applications is that the experiments performed to obtain measurements for parameter estimation are expensive, but nevertheless do not guarantee satisfactory parameter accuracy. The optimization of one or more dynamic experiments in order to maximize the accuracy of the results of a parameter estimation subject to cost and further technical inequality constraints leads to very complex non-standard optimal control problems. Newly developed methods for design of optimal experiments for nonlinear processes are briefly discussed.

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The paper discusses a new view on globalization techniques for Newton's method. In particular, strategies based on "natural level functions" are considered and their properties are investigated. A "restrictive mDnotonicity test" is introduced and theoretically motivated. Numerical results for a highly nonlinear optimal control problem from aerospace engineering and a parameter estimation for a chemical process are presented.

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