A guide to the optogenetic regulation of endogenous molecules

Genetically encoded tools for the regulation of endogenous molecules (RNA, DNA elements and protein) are needed to study and control biological processes with minimal interference caused by protein overexpression and overactivation of signaling pathways. Here we focus on light-controlled optogenetic tools (OTs) that allow spatiotemporally precise regulation of gene expression and protein function. To control endogenous molecules, OTs combine light-sensing modules from natural photoreceptors with specific protein or nucleic acid binders. We discuss OT designs and group OTs according to the principles of their regulation. We outline characteristics of OT performance, discuss considerations for their use in vivo and review available OTs and their applications in cells and in vivo. Finally, we provide a brief outlook on the development of OTs. This Review discusses optogenetic tools for manipulating endogenous targets such as genes and signaling pathways in a physiological range.Peer reviewe

Near-Infrared Fluorescent Proteins : Multiplexing and Optogenetics across Scales

Since mammalian tissue is relatively transparent to near-infrared (NIR) light, NIR fluorescentproteins(FPs) engineeredfrombacterialphytochromeshave become widely used probes for non-invasive in vivo imaging. Recently, these genetically encoded NIR probes have been substantially improved, enabling imaging experiments that were not possible previously. Here, we discuss the use of monomeric NIR FPs and NIR biosensors for multiplexed imaging with common visible GFP-based probes and blue light-activatable optogenetic tools. These NIR probes are suitable for visualization of functional activities from molecular to organismal levels. In combination with advanced imaging techniques, such as two-photon microscopy with adaptive optics, photoacoustic tomography and its recent modification reversibly switchable photoacoustic computed tomography, NIR probes allow subcellular resolution at millimeter depths.Peer reviewe

Nuclear Localization Signals for Optimization of Genetically Encoded Tools in Neurons

Nuclear transport in neurons differs from that in non-neuronal cells. Here we developed a non-opsin optogenetic tool (OT) for the nuclear export of a protein of interest induced by near-infrared (NIR) light. In darkness, nuclear import reverses the OT action. We used this tool for comparative analysis of nuclear transport dynamics mediated by nuclear localization signals (NLSs) with different importin specificities. We found that widely used KPNA2-binding NLSs, such as Myc and SV40, are suboptimal in neurons. We identified uncommon NLSs mediating fast nuclear import and demonstrated that the performance of the OT for nuclear export can be adjusted by varying NLSs. Using these NLSs, we optimized the NIR OT for light-controlled gene expression for lower background and higher contrast in neurons. The selected NLSs binding importins abundant in neurons could improve performance of genetically encoded tools in these cells, including OTs and gene-editing tools.Peer reviewe

Co-application of Difenoconazole with Thymol Results in Suppression of a Parastagonospora Nodorum Mutant Strain Resistant to this Triazole

Results of in vitro study of thymol, a natural chemosensitizer, as a potential agent for overcoming of difenoconazole resistance of Parastagonospora nodorum causing glume and leaf blotch of wheat are first reported. The level of difenoconazole resistance of a natural mutant PNm1 strain with low sensitivity to the Dividend fungicide (a.i. difenoconazole) was determined by the cultivation of this isolate on potato dextrose agar in the presence of the fungicide at sub-lethal and lethal (in relation to the initial fungicide-sensitive strain) concentrations. A principal possibility of the thymol use to overcome resistance of P. nodorum to DMI (demethylation inhibitors) fungicides is shown. Co-application of this compound with Dividend SC, 3 % resulted in a significant reduction of resistance of the mutant strain and enhancement of its sensitivity to difenoconazole up to the level corresponding to the initial non-resistant isolate

Multicontrast photoacoustic in vivo imaging using near-infrared fluorescent proteins

Non-invasive imaging of biological processes in vivo is invaluable in advancing biology. Photoacoustic tomography is a scalable imaging technique that provides higher resolution at greater depths in tissue than achievable by purely optical methods. Here we report the application of two spectrally distinct near-infrared fluorescent proteins, iRFP670 and iRFP720, engineered from bacterial phytochromes, as photoacoustic contrast agents. iRFPs provide tissue-specific contrast without the need for delivery of any additional substances. Compared to conventional GFP-like red-shifted fluorescent proteins, iRFP670 and iRFP720 demonstrate stronger photoacoustic signals at longer wavelengths, and can be spectrally resolved from each other and hemoglobin. We simultaneously visualized two differently labeled tumors, one with iRFP670 and the other with iRFP720, as well as blood vessels. We acquired images of a mouse as 2D sections of a whole animal, and as localized 3D volumetric images with high contrast and sub-millimeter resolution at depths up to 8 mm. Our results suggest iRFPs are genetically-encoded probes of choice for simultaneous photoacoustic imaging of several tissues or processes in vivo

City as an Object of Ecological and Economic Researches: the Example of Russian Cities

The growth of environmental pollution especially in big cities dictates the need to search for the reasons of this trend, most of which refer to the economic sphere. The aim of this work is not only to describe the state of environment in Russian cities with the population of 100 thousand inhabitants and more, but also to reveal the main economic factors that influence on the intensity of their environmental pollution. The ecological and economic analysis of Russian cities, fulfilled in this work, helped to identify the most unfavourable of them in terms of the level of environmental impact. The low quality of environment in these cities is largely due to natural and climatic conditions (bad conditions for contaminants dispersion) and specifics of their economic development: functioning of large industrial enterprises of ferrous and non-ferrous metallurgy, petro chemistry, construction industry. The conclusion is that to improve the environmental quality in these cities comprehensive social, environmental and economic solutions are required

Single-component near-infrared optogenetic systems for gene transcription regulation

Near-infrared (NIR) optogenetic systems for transcription regulation are in high demand because NIR light exhibits low phototoxicity, low scattering, and allows combining with probes of visible range. However, available NIR optogenetic systems consist of several protein components of large size and multidomain structure. Here, we engineer single-component NIR systems consisting of evolved photosensory core module of Idiomarina sp. bacterial phytochrome, named iLight, which are smaller and packable in adeno-associated virus. We characterize iLight in vitro and in gene transcription repression in bacterial and gene transcription activation in mammalian cells. Bacterial iLight system shows 115-fold repression of protein production. Comparing to multi-component NIR systems, mammalian iLight system exhibits higher activation of 65-fold in cells and faster 6-fold activation in deep tissues of mice. Neurons transduced with viral-encoded iLight system exhibit 50-fold induction of fluorescent reporter. NIR light-induced neuronal expression of green-light-activatable CheRiff channelrhodopsin causes 20-fold increase of photocurrent and demonstrates efficient spectral multiplexing. Current near-IR optogenetic systems to regulate transcription consist of a number of large protein components. Here the authors report a smaller single-component near-IR system, iLight, developed from a bacterial phytochrome that they use to control gene transcription in bacterial and mammalian cells.Peer reviewe

Синтез философии и искусства в "готическом" рассказе О. Уайльда "Кентервильское привидение"

The article analyzes O. Wilde's story The Canterville Ghost in the context of using the genre of the "Gothic" story to embody the writer's philosophical views. The article studies the causes of Wilde's appeal to the "Gothic" story, its interpretation by foreign and Russian researchers. The purpose of the article is to prove the synthesis of art and philosophy in the story. The multi-layers of the writer's works reflect his un­derstanding of the multi-layered nature of the world, and Wilde's text combines reflections on topical social, moral and philosophical problems with an individual author's vision of reality. In The Canterville Ghost Wilde begins to comprehend the „American theme", which highlights the problems of interaction between civiliza­tions, the victory of rationality over spirituality and the tragedy behind it. Wilde's negative attitude towards materialism, practicality of modern times is also manifested in depicting false messages based on logic.В статье проанализирован рассказ О. Уайльда "Кентервильское привидение" с точки зрения использования жанра "готического" рассказа для воплощения философских взглядов писателя

Interaction of Biliverdin Chromophore with Near-Infrared Fluorescent Protein BphP1-FP Engineered from Bacterial Phytochrome

Near-infrared (NIR) fluorescent proteins (FPs) designed from PAS (Per-ARNT-Sim repeats) and GAF (cGMP phosphodiesterase/adenylate cyclase/FhlA transcriptional activator) domains of bacterial phytochromes covalently bind biliverdin (BV) chromophore via one or two Cys residues. We studied BV interaction with a series of NIR FP variants derived from the recently reported BphP1-FP protein. The latter was engineered from a bacterial phytochrome RpBphP1, and has two reactive Cys residues (Cys15 in the PAS domain and Cys256 in the GAF domain), whereas its mutants contain single Cys residues either in the PAS domain or in the GAF domain, or no Cys residues. We characterized BphP1-FP and its mutants biochemically and spectroscopically in the absence and in the presence of denaturant. We found that all BphP1-FP variants are monomers. We revealed that spectral properties of the BphP1-FP variants containing either Cys15 or Cys256, or both, are determined by the covalently bound BV chromophore only. Consequently, this suggests an involvement of the inter-monomeric allosteric effects in the BV interaction with monomers in dimeric NIR FPs, such as iRFPs. Likely, insertion of the Cys15 residue, in addition to the Cys256 residue, in dimeric NIR FPs influences BV binding by promoting the BV chromophore covalent cross-linking to both PAS and GAF domains.Peer reviewe