Yuliya G. Ermakova


PeriodCountry, cityEducation institutionAdditional info
2008–2013 Moscow Moscow State University diploma with honors

Selected publications

  1. Ermakova Y.G., Sen T., Bogdanova Y.A., Smirnov A.Y., Baleeva N.S., Krylov A.I., Baranov M.S. (2018). Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes With Large Solvent-Dependent Stokes Shift. J Phys Chem Lett , [+]

    Novel fluorogenic dyes based on the GFP chromophore are developed. The compounds contain a pyridinium ring instead of phenolate and feature large Stokes shifts and solvent-dependent variations in the fluorescence quantum yield, which facilitates their use for imaging the membrane structure of endoplasmic reticulum. Electronic structure calculations explain the trends in solvatochromic behavior.

  2. Ermakova Y.G., Pak V.V., Bogdanova Y.A., Kotlobay A.A., Yampolsky I.V., Shokhina A.G., Panova A.S., Marygin R.A., Staroverov D.B., Bilan D.S., Sies H., Belousov V.V. (2018). SypHer3s: a genetically encoded fluorescent ratiometric probe with enhanced brightness and an improved dynamic range. Chem. Commun. (Camb.) 54 (23), 2898–2901 [+]

    We designed a genetically encoded ratiometric fluorescent probe, SypHer3s, with enhanced brightness and optimized pK, which responds to pH changes in different cellular compartments. SypHer3s was successfully utilized for imaging the pH dynamics in mitochondria of living neurons and in quantitative pH measurement in zebrafish embryos.

  3. Ermakova Y.G., Lanin A.A., Fedotov I.V., Roshchin M., Kelmanson I.V., Kulik D., Bogdanova Y.A., Shokhina A.G., Bilan D.S., Staroverov D.B., Balaban P.M., Fedotov A.B., SidorovBiryukov D.A., Nikitin E.S., Zheltikov A.M., Belousov V.V. (2017). Thermogenetic neurostimulation with single-cell resolution. Nat Commun 8, 15362 [+]

    Thermogenetics is a promising innovative neurostimulation technique, which enables robust activation of neurons using thermosensitive transient receptor potential (TRP) cation channels. Broader application of this approach in neuroscience is, however, hindered by a limited variety of suitable ion channels, and by low spatial and temporal resolution of neuronal activation when TRP channels are activated by ambient temperature variations or chemical agonists. Here, we demonstrate rapid, robust and reproducible repeated activation of snake TRPA1 channels heterologously expressed in non-neuronal cells, mouse neurons and zebrafish neurons in vivo by infrared (IR) laser radiation. A fibre-optic probe that integrates a nitrogen-vacancy (NV) diamond quantum sensor with optical and microwave waveguide delivery enables thermometry with single-cell resolution, allowing neurons to be activated by exceptionally mild heating, thus preventing the damaging effects of excessive heat. The neuronal responses to the activation by IR laser radiation are fully characterized using Ca(2+) imaging and electrophysiology, providing, for the first time, a complete framework for a thermogenetic manipulation of individual neurons using IR light.

  4. Lanin A.A., Fedotov I.V., Ermakova Y.G., SidorovBiryukov D.A., Fedotov A.B., Hemmer P., Belousov V.V., Zheltikov A.M. (2016). Fiber-optic electron-spin-resonance thermometry of single laser-activated neurons. Opt Lett 41 (23), 5563–5566 [+]

    Optically detected electron spin resonance in fiber-coupled nitrogen-vacancy (NV) centers of diamond is used to demonstrate a fiber-optic quantum thermometry of individual thermogenetically activated neurons. Laser-induced temperature variations read out from single neurons with the NV-diamond fiber sensor are shown to strongly correlate with the fluorescence of calcium-ion sensors, serving as online indicators of the inward Ca2+ current across the cell membrane of neurons expressing transient receptor potential (TRP) cation channels. Local laser heating above the TRP-channel activation threshold is shown to reproducibly evoke robust action potentials, visualized by calcium-ion-sensor-aided fluorescence imaging and detected as prominent characteristic waveforms in the time-resolved response of fluorescence Ca2+ sensors.

  5. Fedotov I.V., Safronov N.A., Ermakova Y.G., Matlashov M.E., SidorovBiryukov D.A., Fedotov A.B., Belousov V.V., Zheltikov A.M. (2015). Fiber-optic control and thermometry of single-cell thermosensation logic. Sci Rep 5, 15737 [+]Thermal activation of transient receptor potential (TRP) cation channels is one of the most striking examples of temperature-controlled processes in cell biology. As the evidence indicating the fundamental role of such processes in thermosensation builds at a fast pace, adequately accurate tools that would allow heat receptor logic behind thermosensation to be examined on a single-cell level are in great demand. Here, we demonstrate a specifically designed fiber-optic probe that enables thermal activation with simultaneous online thermometry of individual cells expressing genetically encoded TRP channels. This probe integrates a fiber-optic tract for the delivery of laser light with a two-wire microwave transmission line. A diamond microcrystal fixed on the fiber tip is heated by laser radiation transmitted through the fiber, providing a local heating of a cell culture, enabling a well-controlled TRP-assisted thermal activation of cells. Online local temperature measurements are performed by using the temperature-dependent frequency shift of optically detected magnetic resonance, induced by coupling the microwave field, delivered by the microwave transmission line, to nitrogen-vacancy centers in the diamond microcrystal. Activation of TRP channels is verified by using genetically encoded fluorescence indicators, visualizing an increase in the calcium flow through activated TRP channels. ID:1328
  6. Matlashov M.E., Bogdanova Y.A., Ermakova G.V., Mishina N.M., Ermakova Y.G., Nikitin E.S., Balaban P.M., Okabe S., Lukyanov S., Enikolopov G., Zaraisky A.G., Belousov V.V. (2015). Fluorescent ratiometric pH indicator SypHer2: applications in neuroscience and regenerative biology. Biochim. Biophys. Acta 1850 (11), 2318–2328 [+]


    SypHer is a genetically encoded fluorescent pH-indicator with a ratiometric readout, suitable for measuring fast intracellular pH shifts. However, a relatively low brightness of the indicator limits its use.



    Here we designed a new version of pH-sensor - SypHer-2, that has up to three times brighter fluorescence signal in cultured mammalian cells compared to the SypHer.



    Using the new indicator we registered activity-associated pH oscillations in neuronal cell culture. We observed prominent temporal neuronal cytoplasm acidification that occurs in parallel with calcium entry. Furthermore, we monitored pH in presynaptic and postsynaptic termini by targeting SypHer-2 directly to these compartments and revealed marked differences in pH dynamics between synaptic boutons and dendritic spines. Finally, we were able to reveal for the first time the intracellular pH drop which occurs within an extended region of the amputated tail of the Xenopus laevis tadpole before it begins to regenerate.



    SypHer2 is suitable for quantitative monitoring of pH in biological systems of different scales, from small cellular subcompartments to animal tissues in vivo.



    The new pH-sensor will help to investigate pH-dependent processes in both in vitro and in vivo studies.


  7. Schwarzländer M., Wagner S., Ermakova Y.G., Belousov V.V., Radi R., Beckman J.S., Buettner G.R., Demaurex N., Duchen M.R., Forman H.J., Fricker M.D., Gems D., Halestrap A.P., Halliwell B., Jakob U., Johnston I.G., Jones N.S., Logan D.C., Morgan B., Müller F.L., Nicholls D.G., Remington S.J., Schumacker P.T., Winterbourn C.C., Sweetlove L.J., Meyer A.J., Dick T.P., Murphy M.P. (2014). The 'mitoflash' probe cpYFP does not respond to superoxide. Nature 514 (7523), E12–4 ID:1094
  8. Ermakova Y.G., Bilan D.S., Matlashov M.E., Mishina N.M., Markvicheva K.N., Subach O.M., Subach F.V., Bogeski I., Hoth M., Enikolopov G., Belousov V.V. (2014). Red fluorescent genetically encoded indicator for intracellular hydrogen peroxide. Nat Commun 5, 5222 [+]

    Reactive oxygen species (ROS) are conserved regulators of numerous cellular functions, and overproduction of ROS is a hallmark of various pathological processes. Genetically encoded fluorescent probes are unique tools to study ROS production in living systems of different scale and complexity. However, the currently available recombinant redox sensors have green emission, which overlaps with the spectra of many other probes. Expanding the spectral range of recombinant in vivo ROS probes would enable multiparametric in vivo ROS detection. Here we present the first genetically encoded red fluorescent sensor for hydrogen peroxide detection, HyPerRed. The performance of this sensor is similar to its green analogues. We demonstrate the utility of the sensor by tracing low concentrations of H2O2 produced in the cytoplasm of cultured cells upon growth factor stimulation. Moreover, using HyPerRed we detect local and transient H2O2 production in the mitochondrial matrix upon inhibition of the endoplasmic reticulum Ca(2+) uptake.

  9. Bilan D.S., Pase L., Joosen L., Gorokhovatsky A.Y., Ermakova Y.G., Gadella T.W., Grabher C., Schultz C., Lukyanov S., Belousov V.V. (2013). HyPer-3: a genetically encoded H(2)O(2) probe with improved performance for ratiometric and fluorescence lifetime imaging. ACS Chem. Biol. 8 (3), 535–42 [+]

    High-performance sensors for reactive oxygen species are instrumental to monitor dynamic events in cells and organisms. Here, we present HyPer-3, a genetically encoded fluorescent indicator for intracellular H2O2 exhibiting improved performance with respect to response time and speed. HyPer-3 has an expanded dynamic range compared to HyPer and significantly faster oxidation/reduction dynamics compared to HyPer-2. We demonstrate this performance by in vivo imaging of tissue-scale H2O2 gradients in zebrafish larvae. Moreover, HyPer-3 was successfully employed for single-wavelength fluorescent lifetime imaging of H2O2 levels both in vitro and in vivo.

  10. Safronov N.A., Fedotov I.V., Ermakova Yu.G., Matlashov M.E., SidorovBiryukov D.A., Fedotov A.B., Belousov V.V., Zheltikov A.M. (1970). Microwave-induced thermogenetic activation of single cells. Appl. Phys. Lett. 106 (163), 163702–1–4 [+]

    Exposure to a microwave field is shown to enable thermogenetic activation of individual cells in a culture of cell expressing thermosensitive ion channels. Integration of a microwave transmission line with an optical fiber and a diamond quantum thermometer has been shown to allow thermogenetic single-cell activation to be combined with accurate local online temperature measurements based on an optical detection of electron spin resonance in nitrogen–vacancy centers in diamond.