Кельмансон Илья Владимирович

Кандидат биологических наук

Научный сотрудник (Лаборатория молекулярных технологий)

Эл. почта: ikelmanson@gmail.com

Избранные публикации

  1. Shagin D.A., Shagina I.A., Zaretsky A.R., Barsova E.V., Kelmanson I.V., Lukyanov S., Chudakov D.M., Shugay M. (2017). A high-throughput assay for quantitative measurement of PCR errors. Sci Rep 7 (1), 2718 [+]

    The accuracy with which DNA polymerase can replicate a template DNA sequence is an extremely important property that can vary by an order of magnitude from one enzyme to another. The rate of nucleotide misincorporation is shaped by multiple factors, including PCR conditions and proofreading capabilities, and proper assessment of polymerase error rate is essential for a wide range of sensitive PCR-based assays. In this paper, we describe a method for studying polymerase errors with exceptional resolution, which combines unique molecular identifier tagging and high-throughput sequencing. Our protocol is less laborious than commonly-used methods, and is also scalable, robust and accurate. In a series of nine PCR assays, we have measured a range of polymerase accuracies that is in line with previous observations. However, we were also able to comprehensively describe individual errors introduced by each polymerase after either 20 PCR cycles or a linear amplification, revealing specific substitution preferences and the diversity of PCR error frequency profiles. We also demonstrate that the detected high-frequency PCR errors are highly recurrent and that the position in the template sequence and polymerase-specific substitution preferences are among the major factors influencing the observed PCR error rate.

  2. 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.

  3. Bogdanov E.A., Shagina I., Barsova E.V., Kelmanson I., Shagin D.A., Lukyanov S.A. (2010). Normalizing cDNA libraries. Curr Protoc Mol Biol Chapter 5, Unit 5.12.1–27 [+]

    The characterization of rare messages in cDNA libraries is complicated by the substantial variations that exist in the abundance levels of different transcripts in cells and tissues. The equalization (normalization) of cDNA is a helpful approach for decreasing the prevalence of abundant transcripts, thereby facilitating the assessment of rare transcripts. This unit provides a method for duplex-specific nuclease (DSN)-based normalization, which allows for the fast and reliable equalization of cDNA, thereby facilitating the generation of normalized, full-length-enriched cDNA libraries, and enabling efficient RNA analyses.

  4. Samarkina O.N., Popova A.G., Gvozdik E.Y., Chkalina A.V., Zvyagin I.V., Rylova Y.V., Rudenko N.V., Lusta K.A., Kelmanson I.V., Gorokhovatsky A.Y., Vinokurov L.M. (2009). Universal and rapid method for purification of GFP-like proteins by the ethanol extraction. Protein Expr. Purif. 65 (1), 108–13 [+]

    GFP-like fluorescent proteins (FPs) are crucial in biological and biomedical studies. The majority of FP purification techniques either include multiple time-consuming chromatography steps with a low yield of the desired product or require prior protein modification (addition of special tags). In the present work, we propose an alternative ethanol extraction-based technique previously used for GFP purification and then modified for diverse FPs originated from different sources. The following recombinant FPs were expressed using Escherichia coli M15 (pREP4) strain as a host transformed with pQE30 plasmid bearing one of the target FP genes: TagCFP, TagGFP, TagYFP, TagRFP, TurboGFP, TurboRFP, Dendra2, TurboFP602 and KillerRed. Despite their diversity, all tested recombinant FPs were successfully purified and yielded a highly homogeneous product. The method is easily scalable for purification of any amount of protein and requires no expensive reagents and equipment.

  5. Field S.F., Bulina M.Y., Kelmanson I.V., Bielawski J.P., Matz M.V. (2006). Adaptive evolution of multicolored fluorescent proteins in reef-building corals. J. Mol. Evol. 62 (3), 332–9 [+]

    Here we investigate the evolutionary scenarios that led to the appearance of fluorescent color diversity in reef-building corals. We show that the mutations that have been responsible for the generation of new cyan and red phenotypes from the ancestral green were fixed with the help of positive natural selection. This fact strongly suggests that the color diversity is a product of adaptive evolution. An unexpected finding was a set of residues arranged as an intermolecular binding interface, which was also identified as a target of positive selection but is nevertheless not related to color diversification. We hypothesize that multicolored fluorescent proteins evolved as part of a mechanism regulating the relationships between the coral and its algal endosymbionts (zooxanthellae). We envision that the effect of the proteins' fluorescence on algal physiology may be achieved not only through photosynthesis modulation, but also through regulatory photosensors analogous to phytochromes and cryptochromes of higher plants. Such a regulation would require relatively subtle, but spectrally precise, modifications of the light field. Evolution of such a mechanism would explain both the adaptive diversification of colors and the coevolutionary chase at the putative algae-protein binding interface in coral fluorescent proteins.

  6. Baranova A., Ivanov D., Petrash N., Pestova A., Skoblov M., Kelmanson I., Shagin D., Nazarenko S., Geraymovych E., Litvin O., Tiunova A., Born T.L., Usman N., Staroverov D., Lukyanov S., Panchin Y. (2004). The mammalian pannexin family is homologous to the invertebrate innexin gap junction proteins. Genomics 83 (4), 706–16 [+]

    We have cloned the genes PANX1, PANX2 and PANX3, encoding putative gap junction proteins homologous to invertebrate innexins, which constitute a new family of mammalian proteins called pannexins. Phylogenetic analysis revealed that pannexins are highly conserved in worms, mollusks, insects and mammals, pointing to their important function. Both innexins and pannexins are predicted to have four transmembrane regions, two extracellular loops, one intracellular loop and intracellular N and C termini. Both the human and mouse genomes contain three pannexin-encoding genes. Mammalian pannexins PANX1 and PANX3 are closely related, with PANX2 more distant. The human and mouse pannexin-1 mRNAs are ubiquitously, although disproportionately, expressed in normal tissues. Human PANX2 is a brain-specific gene; its mouse orthologue, Panx2, is also expressed in certain cell types in developing brain. In silico evaluation of Panx3 expression predicts gene expression in osteoblasts and synovial fibroblasts. The apparent conservation of pannexins between species merits further investigation.

  7. Kelmanson I.V., Matz M.V. (2003). Molecular basis and evolutionary origins of color diversity in great star coral Montastraea cavernosa (Scleractinia: Faviida). Mol. Biol. Evol. 20 (7), 1125–33 [+]

    Natural pigments are normally products of complex biosynthesis pathways where many different enzymes are involved. Corals and related organisms of class Anthozoa represent the only known exception: in these organisms, each of the host-tissue colors is essentially determined by a sequence of a single protein, homologous to the green fluorescent protein (GFP) from Aequorea victoria. This direct sequence-color linkage provides unique opportunity for color evolution studies. We previously reported the general phylogenetic analysis of GFP-like proteins, which suggested that the present-day diversity of reef colors originated relatively recently and independently within several lineages. The present work was done to get insight into the mechanisms that gave rise to this diversity. Three colonies of the great star coral Montastraea cavernosa (Scleractinia, Faviida) were studied, representing distinct color morphs. Unexpectedly, these specimens were found to express the same collection of GFP-like proteins, produced by at least four, and possibly up to seven, different genetic loci. These genes code for three basic colors-cyan, green, and red-and are expressed differently relative to one another in different morphs. Phylogenetic analysis of the new sequences indicated that the three major gene lineages diverged before separation of some coral families. Our results suggest that color variation in M. cavernosa is not a true polymorphism, but rather a manifestation of phenotypic plasticity (polyphenism). The family level depth of its evolutionary roots indicates that the color diversity is adaptively significant. Relative roles of gene duplication, gene conversion, and point mutations in its evolution are discussed.

  8. Kelmanson I.V., Shagin D.A., Usman N., Matz M.V., Lukyanov S.A., Panchin Y.V. (2002). Altering electrical connections in the nervous system of the pteropod mollusc Clione limacina by neuronal injections of gap junction mRNA. Eur. J. Neurosci. 16 (12), 2475–6 [+]

    Neurons can communicate with each other either via exchange of specific molecules at synapses or by direct electrical connections between the cytoplasm of either cell [for review see Bruzzone et al. (1996) Eur. J. Biochem., 238, 1-27]. Although electrical connections are abundant in many nervous systems, little is known about the mechanisms which govern the specificity of their formation. Recent cloning of the innexins--gap junction proteins responsible for electrical coupling in invertebrates (Phelan et al. (1998) Trends Genet., 14, 348-349], has made it possible to study the molecular mechanisms of patterning of the electrical connections between individual neurons in model systems. Here we demonstrate that intracellular injection of mRNA encoding the molluscan innexin Panx1 (Panchin et al. 2000 Curr. Biol., 10, R473-R474) drastically alters the specificity of electrical coupling between identified neurons of the pteropod mollusc Clione limacina.

  9. Panchin Y., Kelmanson I., Matz M., Lukyanov K., Usman N., Lukyanov S. (2000). A ubiquitous family of putative gap junction molecules. Curr. Biol. 10 (13), R473–4 ID:1350
  10. Panchin Y.V., Kelmanson I.V. (2000). Short-circuited neuron: a note. Neuroscience 96 (3), 597–9 [+]

    Here, we demonstrate in a direct electrophysiological experiment that a neuron can form electrical connections to itself. An isolated identified neuron with a long axon was plated in culture and the axon was looped so that its distal end contacted the cell body. After two days in culture, the cell body and the axon were both impaled with microelectrodes and the axon segment between the recording electrodes was cut. Electrotonic coupling was revealed between the separated cell compartments immediately after axon transection. In contrast to an earlier publication [Guthrie P. B. et al. (1994) J. Neurosci. 14, 1477-1485], no constraints on the formation of the electrical connections between different parts of the same neuron were revealed in our experiments.Thus, these experiments demonstrate that in vitro culture of a single neuron can form reflexive electrical connections which may strongly affect the basic properties of the neuron and should be taken into account in both experimental and model electrophysiological studies.