Optogenetics for gene expression in mammalian cells.

Molecular switches that are controlled by chemicals have evolved as central research instruments in mammalian cell biology. However, these tools are limited in terms of their spatiotemporal resolution due to freely diffusing inducers. These limitations have recently been addressed by the development of optogenetic, genetically encoded, and light-responsive tools that can be controlled with the unprecedented spatiotemporal precision of light. In this article, we first provide a brief overview of currently available optogenetic tools that have been designed to control diverse cellular processes. Then, we focus on recent developments in light-controlled gene expression technologies and provide the reader with a guideline for choosing the most suitable gene expression system.

An optogenetic upgrade for the Tet-OFF system.

The rapid development of mammalian optogenetics has produced an expanding number of gene switches that can be controlled with the unprecedented spatiotemporal resolution of light. However, in the "pre-optogenetic" era many networks, cell lines and transgenic organisms have been engineered that rely on chemically-inducible transgene expression systems but would benefit from the advantages of the traceless inducer light. To open the possibility for the effortless upgrade of such systems from chemical inducers to light, we capitalized on the specific Med25VBD inhibitor of the VP16/VP64 transactivation domain. In a first step, we demonstrated the efficiency and selectivity of Med25VBD in the inhibition of VP16/VP64-based transgene expression systems. Then, we fused the inhibitor to the blue light-responsive B-LID degron and optimized the performance of this construct with regard to the number of Med25VBD repeats. This approach resulted in an optogenetic upgrade of the popular Tet-OFF (TetR-VP64, tetO7 -PhCMVmin ) system that allows tunable, blue light-inducible transgene expression in HEK-293T cells.

Chemistry of Urban Grime: Inorganic Ion Composition of Grime vs Particles in Leipzig, Germany.

Deposition of atmospheric constituents--either gas phase or particulate--onto urban impervious surfaces gives rise to a thin "urban grime" film. The area exposed by these impervious surfaces in a typical urban environment is comparable to, or greater than, that of particles present in the urban boundary layer; however, it is largely overlooked as a site for heterogeneous reactions. Here we present the results of a field campaign to determine and compare the chemical composition of urban grime and of particles collected simultaneously during the autumn of 2014 at an urban site in central Leipzig, Germany. We see dramatically reduced ammonium and nitrate levels in the film as compared to particles, suggesting a significant loss of ammonium nitrate, thus enhancing the mobility of these species in the environment. Nitrate levels are 10% lower for films exposed to sunlight compared to those that were shielded from direct sun, indicating a possible mechanism for recycling nitrate anion to reactive nitrogen species. Finally, chloride levels in the film suggest that urban grime could represent an unrecognized source of continental chloride available for ClNO2 production even in times of low particulate chloride. Such source and recycling processes could prove to be important to local and regional air quality.

Multi-chromatic control of mammalian gene expression and signaling.

The emergence and future of mammalian synthetic biology depends on technologies for orchestrating and custom tailoring complementary gene expression and signaling processes in a predictable manner. Here, we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths. To this end, we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1. The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells. Based on a quantitative model, we determined critical system parameters. By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes. This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.

A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells.

Growth and differentiation of multicellular systems is orchestrated by spatially restricted gene expression programs in specialized subpopulations. The targeted manipulation of such processes by synthetic tools with high-spatiotemporal resolution could, therefore, enable a deepened understanding of developmental processes and open new opportunities in tissue engineering. Here, we describe the first red/far-red light-triggered gene switch for mammalian cells for achieving gene expression control in time and space. We show that the system can reversibly be toggled between stable on- and off-states using short light pulses at 660 or 740 nm. Red light-induced gene expression was shown to correlate with the applied photon number and was compatible with different mammalian cell lines, including human primary cells. The light-induced expression kinetics were quantitatively analyzed by a mathematical model. We apply the system for the spatially controlled engineering of angiogenesis in chicken embryos. The system's performance combined with cell- and tissue-compatible regulating red light will enable unprecedented spatiotemporally controlled molecular interventions in mammalian cells, tissues and organisms.

Deep treasury management for banks.

Retail banks use Asset Liability Management (ALM) to hedge interest rate risk associated with differences in maturity and predictability of their loan and deposit portfolios. The opposing goals of profiting from maturity transformation and hedging interest rate risk while adhering to numerous regulatory constraints make ALM a challenging problem. We formulate ALM as a high-dimensional stochastic control problem in which monthly investment and financing decisions drive the evolution of the bank's balance sheet. To find strategies that maximize long-term utility in the presence of constraints and stochastic interest rates, we train neural networks that parametrize the decision process. Our experiments provide practical insights and demonstrate that the approach of Deep ALM deduces dynamic strategies that outperform static benchmarks.

Dynamical Coulomb blockade observed in nanosized electrical contacts.

Electrical contacts between nanoengineered systems are expected to constitute the basic building blocks of future nanoscale electronics. However, the accurate characterization and understanding of electrical contacts at the nanoscale is an experimentally challenging task. Here, we employ low-temperature scanning tunneling spectroscopy to investigate the conductance of individual nanocontacts formed between flat Pb islands and their supporting substrates. We observe a suppression of the differential tunnel conductance at small bias voltages due to dynamical Coulomb blockade effects. The differential conductance spectra allow us to determine the capacitances and resistances of the electrical contacts which depend systematically on the island-substrate contact area. Calculations based on the theory of environmentally assisted tunneling agree well with the measurements.

Reduced expression of IL-18 is a marker of ultraviolet radiation-induced melanomas.

We previously showed that mice carrying an activated Cdk4 mutation together with melanocyte-specific mutant Hras (Cdk4(R24C/R24C)/TPras) develop melanoma spontaneously, but penetrance is increased and age of onset reduced after neonatal ultraviolet radiation (UVR) exposure. UVR-treated mice were more likely to develop multiple primary lesions, and these melanomas more often expressed Trp53, and less often expressed c-Myc, than melanomas from nonirradiated mice (Hacker et al., Cancer Res 2006;66:2946-52). These data suggest differences in mechanisms of tumorigenesis between melanomas developing spontaneously, or as a result of UVR exposure. To further delineate these differences, we compared global gene expression between spontaneous and UVR-induced melanomas from these mice using microarrays. We found 264 genes differentially expressed between these groups (ANOVA, p < 0.05). Selected candidate genes were validated using qRT-PCR, which confirmed upregulation of Gpr155 and Bmp7, and downregulation of Plagl1, Akap12 and Il18 in UVR-induced mouse melanomas. In humans, epidemiological studies suggest that there may be 2 predominant pathways to melanoma development. One characterized by chronic UVR exposure and which leads mainly to melanomas on sun-exposed sites; the other associated with low UVR exposure and leading predominantly to melanomas on less-exposed body sites. We found by immunohistochemical analysis that, comparing a series of human melanomas from the head (a chronically sun-exposed site; N = 82) with a set from the trunk (an intermittently exposed site; N = 65), the prevalence of IL-18 expression was significantly lower in melanomas on the head (16%) than on truncal melanomas (34%, p = 0.011). We conclude that loss of IL-18 is a marker of UVR-induced melanoma, both in animal models and humans.

Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells.

Optogenetic switches are emerging molecular tools for studying cellular processes as they offer higher spatiotemporal and quantitative precision than classical, chemical-based switches. Light-controllable gene expression systems designed to upregulate protein expression levels meanwhile show performances superior to their chemical-based counterparts. However, systems to reduce protein levels with similar efficiency are lagging behind. Here, we present a novel two-component, blue light-responsive optogenetic OFF switch ('Blue-OFF'), which enables a rapid and quantitative down-regulation of a protein upon illumination. Blue-OFF combines the first light responsive repressor KRAB-EL222 with the protein degradation module B-LID (blue light-inducible degradation domain) to simultaneously control gene expression and protein stability with a single wavelength. Blue-OFF thus outperforms current optogenetic systems for controlling protein levels. The system is described by a mathematical model which aids in the choice of experimental conditions such as light intensity and illumination regime to obtain the desired outcome. This approach represents an advancement of dual-controlled optogenetic systems in which multiple photosensory modules operate synergistically. As exemplified here for the control of apoptosis in mammalian cell culture, the approach opens up novel perspectives in fundamental research and applications such as tissue engineering.

Light-Responsive Promoters.

Recent advances in the development of light-inducible transgene expression systems have overcome many inherent drawbacks of conventional chemically regulated systems. The latest generation of those light-regulated systems that are specifically responsive to different wavelengths allows spatiotemporal control of gene expression in a so far unprecedented manner.In this chapter, we first describe the available light-inducible gene expression systems compatible with mammalian cells and explain their underlying mechanisms. Afterward, we give a detailed protocol for the implementation of a UVB light-inducible expression system in mammalian cells.

Optogenetics in Plants: Red/Far-Red Light Control of Gene Expression.

Optogenetic tools to control gene expression have many advantages over the classical chemically inducible systems, overcoming intrinsic limitations of chemical inducers such as solubility, diffusion, and cell toxicity. They offer an unmatched spatiotemporal resolution and permit quantitative and noninvasive control of the gene expression. Here we describe a protocol of a synthetic light-inducible system for the targeted control of gene expression in plants based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). The synthetic toggle switch system is in the ON state when plant protoplasts are illuminated with red light (660 nm) and can be returned to the OFF state by subsequent illumination with far-red light (760 nm). In this protocol, the implementation of a red light-inducible expression system in plants using Light-Emitting Diode (LED) illumination boxes is described, including the isolation and transient transformation of plant protoplasts from Arabidopsis thaliana and Nicotiana tabacum.

A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication.

BACKGROUND: Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to engineer well-defined systems that allow the convenient study and manipulation of intercellular communication networks. RESULTS: Here, we present the first mammalian synthetic network for reciprocal cell-cell communication to compute the border between a sender/receiver and a processing cell population. The two populations communicate via L-tryptophan and interleukin-4 to highlight the population border by the production of a fluorescent protein. The sharpness of that visualized edge can be adjusted by modulating key parameters of the network. CONCLUSIONS: We anticipate that this network will on the one hand be a useful tool to gain deeper insights into the mechanisms of tissue formation in nature and will on the other hand contribute to our ability to engineer artificial tissues.

Red Light-Regulated Reversible Nuclear Localization of Proteins in Mammalian Cells and Zebrafish.

Protein trafficking in and out of the nucleus represents a key step in controlling cell fate and function. Here we report the development of a red light-inducible and far-red light-reversible synthetic system for controlling nuclear localization of proteins in mammalian cells and zebrafish. First, we synthetically reconstructed and validated the red light-dependent Arabidopsis phytochrome B nuclear import mediated by phytochrome-interacting factor 3 in a nonplant environment and support current hypotheses on the import mechanism in planta. On the basis of this principle we next regulated nuclear import and activity of target proteins by the spatiotemporal projection of light patterns. A synthetic transcription factor was translocated into the nucleus of mammalian cells and zebrafish to drive transgene expression. These data demonstrate the first in vivo application of a plant phytochrome-based optogenetic tool in vertebrates and expand the repertoire of available light-regulated molecular devices.

Monoterpene emissions and carbonyl compound air concentrations during the blooming period of rape (Brassica napus).

An increasing percentage of agricultural land in Germany is used for oil seed plants. Hence, rape has become an important agricultural plant (in Saxony 1998: 12% of the farmland) in the recent years. During flowering of rape along with intensive radiation and high temperatures, a higher production and emission of biogenic VOC was observed. The emissions of terpenes were determined and more importantly, high concentrations of organic carbonyl compounds were observed during this field experiment. All measurements of interest have been carried out during two selected days with optimal weather conditions. It is found that the origin or the mechanism of formation of different group of compounds had strong influence on the day to day variation of their concentrations. The emission flux of terpenes from flowering rape plants was determined to be 16-32 microg h(-1) m(-2) (30-60 ng h(-1) per g dry plant-540-11080 ng h(-1) per plant), in total. Limonene, alpha-thujene and sabinene were the most important compounds (about 60% of total terpenes). For limonene and sabinene reference emission rates (Ms) and temperature coefficients were determined: beta(limonene) = 0.108 K(-1) and Ms = 14.57 microg h(-1) m(-2) beta(sabinene) = 0.095 K(-1) and Ms = 5.39 microg h(-1) m(-2). The detected carbonyl compound concentrations were unexpectedly high (maximum formaldehyde concentration was 18.1 ppbv and 3.4 ppbv for butyraldehyde) for an open field. Possible reasons for these concentrations are the combination of primary emission from the plants induced by high temperature and high ozone stress, the secondary formation from biogenically and advected anthropogenically emitted VOC at high radiation intensities and furthered by the low wind speeds at this time.

Control of gene expression using a red- and far-red light-responsive bi-stable toggle switch.

Light-triggered gene expression systems offer an unprecedented spatiotemporal resolution that cannot be achieved with classical chemically inducible genetic tools. Here we describe a protocol for red light-responsive gene expression in mammalian cells. This system can be toggled between stable ON and OFF states by short pulses of red and far-red light, respectively. In the protocol, CHO-K1 cells are transfected to allow red light-inducible expression of the secreted alkaline phosphatase (SEAP) reporter, and gene expression is tuned by illumination with light of increasing wavelengths. As a starting point for elaborate red light-responsive gene expression, we outline the reversible activation of gene expression and describe how a spatial pattern can be 'printed' on a monolayer of cells by using a photomask. The core protocol requires only 4 d from seeding of the cells to reporter quantification, and other than light-emitting diode (LED) illumination boxes no elaborate equipment is required.

Orthogonal optogenetic triple-gene control in Mammalian cells.

Optogenetic gene switches allow gene expression control at an unprecedented spatiotemporal resolution. Recently, light-responsive transgene expression systems that are activated by UV-B, blue, or red light have been developed. These systems perform well on their own, but their integration into genetic networks has been hampered by the overlapping absorbance spectra of the photoreceptors. We identified a lack of orthogonality between UV-B and blue light-controlled gene expression as the bottleneck and employed a model-based approach that identified the need for a blue light-responsive gene switch that is insensitive to low-intensity light. Based on this prediction, we developed a blue light-responsive and rapidly reversible expression system. Finally, we employed this expression system to demonstrate orthogonality between UV-B, blue, and red/far-red light-responsive gene switches in a single mammalian cell culture. We expect this approach to enable the spatiotemporal control of gene networks and to expand the applications of optogenetics in synthetic biology.

Optogenetic control of protein kinase activity in mammalian cells.

Light-dependent dimerization is the basis for recently developed noninvasive optogenetic tools. Here we present a novel tool combining optogenetics with the control of protein kinase activity to investigate signal transduction pathways. Mediated by Arabidopsis thaliana photoreceptor cryptochrome 2, we activated the protein kinase C-RAF by blue light-dependent dimerization, allowing for decoupling from upstream signaling events induced by surface receptors. The activation by light is fast, reversible, and not only time but also dose dependent as monitored by phosphorylation of ERK1/2. Additionally, light-activated C-RAF controls serum response factor-mediated gene expression. Light-induced heterodimerization of C-RAF with a kinase-dead mutant of B-RAF demonstrates the enhancing role of B-RAF as a scaffold for C-RAF activity, which leads to the paradoxical activation of C-RAF found in human cancers. This optogenetic tool enables reversible control of protein kinase activity in signal duration and strength. These properties can help to shed light onto downstream signaling processes of protein kinases in living cells.

A red light-controlled synthetic gene expression switch for plant systems.

On command control of gene expression in time and space is required for the comprehensive analysis of key plant cellular processes. Even though some chemical inducible systems showing satisfactory induction features have been developed, they are inherently limited in terms of spatiotemporal resolution and may be associated with toxic effects. We describe here the first synthetic light-inducible system for the targeted control of gene expression in plants. For this purpose, we applied an interdisciplinary synthetic biology approach comprising mammalian and plant cell systems to customize and optimize a split transcription factor based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). Implementation of the system in transient assays in tobacco protoplasts resulted in strong (95-fold) induction in red light (660 nm) and could be instantaneously returned to the OFF state by subsequent illumination with far-red light (740 nm). Capitalizing on this toggle switch-like characteristic, we demonstrate that the system can be kept in the OFF state in the presence of 740 nm-supplemented white light, opening up perspectives for future application of the system in whole plants. Finally we demonstrate the system's applicability in basic research, by the light-controlled tuning of auxin signalling networks in N. tabacum protoplasts, as well as its biotechnological potential for the chemical-inducer free production of therapeutic proteins in the moss P. patens.

Optogenetic tools for mammalian systems.

Light is fundamental to life on earth. Therefore, nature has evolved a multitude of photoreceptors that sense light across all kingdoms. This natural resource provides synthetic biology with a vast pool of light-sensing components with distinct spectral properties that can be harnessed to engineer novel optogenetic tools. These devices enable control over gene expression, cell morphology and signaling pathways with superior spatiotemporal resolution and are maturing towards elaborate applications in basic research, in the production of biopharmaceuticals and in biomedicine. This article provides a summary of the recent advances in optogenetics that use light for the precise control of biological functions in mammalian cells.

Synthesis of phycocyanobilin in mammalian cells.

The chromophore 3-Z phycocyanobilin (PCB, (2R,3Z)-8,12-bis(2-carboxyethyl)-18-ethyl-3-ethylidene-2,7,13,17-tetramethyl-2,3-dihydrobilin-1,19(21H,24H)-dione) mediates red and far-red light perception in natural and synthetic biological systems. Here we describe a PCB synthesis strategy in mammalian cells. We optimize the production by co-localizing the biocatalysts to the substrate source, by coordinating the availability of the biocatalysts and by reducing the degradation of the reaction product. We show that the resulting PCB levels of 2 µM are sufficient to sustain the functionality of red light-responsive optogenetic tools suitable for the light-inducible control of gene expression in mammalian cells.