Author
Ivan V. Smirnov
Other affiliations: Russian National Research Medical University, National Research University – Higher School of Economics, Kazan Federal University ...read more
Bio: Ivan V. Smirnov is an academic researcher from Russian Academy of Sciences. The author has contributed to research in topics: Myelin basic protein & Microstructure. The author has an hindex of 21, co-authored 140 publications receiving 1441 citations. Previous affiliations of Ivan V. Smirnov include Russian National Research Medical University & National Research University – Higher School of Economics.
Topics: Myelin basic protein, Microstructure, Alloy, Pichia pastoris, Antibody
Papers published on a yearly basis
Papers
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TL;DR: The MDE–FACS platform allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon and predicted which genera were associated with inhibitory activity.
Abstract: Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus, and predicted which genera were associated with inhibitory activity.
169 citations
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TL;DR: Kinetic properties of the DNA autoantibody Fab fragment revealed a high affinity and considerable catalytic efficiency of the reaction and was shown to hydrolyze plasmid DNA by Mg(2+)-dependent single-strand multiple nicking of the substrate.
Abstract: A highly effective method consisting of two affinity chromatography steps and ion-exchange and gel-filtration chromatography steps was developed for purification of autoantibodies from human sera with DNA-hydrolyzing activity Antibody Fab fragment, which had been purified 130-fold, was shown to catalyze plasmid DNA cleavage The flow linear dichroism technique was used for quantitative and qualitative studying of supercoiled plasmid DNA cleavage by these autoantibodies in comparison with DNase I and EcoRI restriction endonuclease The DNA autoantibody Fab fragment was shown to hydrolyze plasmid DNA by Mg(2+)-dependent single-strand multiple nicking of the substrate Kinetic properties of the DNA autoantibody Fab fragment were evaluated from the flow linear dichroism and agarose gel electrophoresis data and revealed a high affinity (Kobsm = 43 nM) and considerable catalytic efficiency (kappcat/Kobsm = 032 min-1nM-1) of the reaction
109 citations
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TL;DR: In this article, the authors reported the identification of the fungal luciferase and three other key enzymes that together formed the biosynthetic cycle of the fungus luciferin from caffeic acid, a simple and widespread metabolite.
Abstract: Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering.
97 citations
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TL;DR: Polysialylation gives bioscavengers with enhanced pharmacokinetics which protect mice against 4.2 LD50 of S-(2-(diethylamino)ethyl) O-isobutyl methanephosphonothioate without perturbation of long-term behavior.
Abstract: The creation of effective bioscavengers as a pretreatment for exposure to nerve agents is a challenging medical objective. We report a recombinant method using chemical polysialylation to generate bioscavengers stable in the bloodstream. Development of a CHO-based expression system using genes encoding human butyrylcholinesterase and a proline-rich peptide under elongation factor promoter control resulted in self-assembling, active enzyme multimers. Polysialylation gives bioscavengers with enhanced pharmacokinetics which protect mice against 4.2 LD50 of S-(2-(diethylamino)ethyl) O-isobutyl methanephosphonothioate without perturbation of long-term behavior.
77 citations
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TL;DR: UHT quantitative single-cell analysis to estimate antibiotic efficacy toward different microbiomes and used it to determine the activity spectra of Ami toward human and Siberian bear microbiota is developed, showing that it could be effectively transferred to numerous applications in microbiology and biotechnology.
Abstract: Microbiome spectra serve as critical clues to elucidate the evolutionary biology pathways, potential pathologies, and even behavioral patterns of the host organisms. Furthermore, exotic sources of microbiota represent an unexplored niche to discover microbial secondary metabolites. However, establishing the bacterial functionality is complicated by an intricate web of interactions inside the microbiome. Here we apply an ultrahigh-throughput (uHT) microfluidic droplet platform for activity profiling of the entire oral microbial community of the Siberian bear to isolate Bacillus strains demonstrating antimicrobial activity against Staphylococcus aureus. Genome mining allowed us to identify antibiotic amicoumacin A (Ami) as responsible for inhibiting the growth of S. aureus. Proteomics and metabolomics revealed a unique mechanism of Bacillus self-resistance to Ami, based on a subtle equilibrium of its deactivation and activation by kinase AmiN and phosphatase AmiO, respectively. We developed uHT quantitative single-cell analysis to estimate antibiotic efficacy toward different microbiomes and used it to determine the activity spectra of Ami toward human and Siberian bear microbiota. Thus, uHT microfluidic droplet platform activity profiling is a powerful tool for discovering antibiotics and quantifying external influences on a microbiome.
77 citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
01 Jan 2005
TL;DR: In “Constructing a Language,” Tomasello presents a contrasting theory of how the child acquires language: It is not a universal grammar that allows for language development, but two sets of cognitive skills resulting from biological/phylogenetic adaptations are fundamental to the ontogenetic origins of language.
Abstract: Child psychiatrists, pediatricians, and other child clinicians need to have a solid understanding of child language development. There are at least four important reasons that make this necessary. First, slowing, arrest, and deviation of language development are highly associated with, and complicate the course of, child psychopathology. Second, language competence plays a crucial role in emotional and mood regulation, evaluation, and therapy. Third, language deficits are the most frequent underpinning of the learning disorders, ubiquitous in our clinical populations. Fourth, clinicians should not confuse the rich linguistic and dialectal diversity of our clinical populations with abnormalities in child language development. The challenge for the clinician becomes, then, how to get immersed in the captivating field of child language acquisition without getting overwhelmed by its conceptual and empirical complexity. In the past 50 years and since the seminal works of Roger Brown, Jerome Bruner, and Catherine Snow, child language researchers (often known as developmental psycholinguists) have produced a remarkable body of knowledge. Linguists such as Chomsky and philosophers such as Grice have strongly influenced the science of child language. One of the major tenets of Chomskian linguistics (known as generative grammar) is that children’s capacity to acquire language is “hardwired” with “universal grammar”—an innate language acquisition device (LAD), a language “instinct”—at its core. This view is in part supported by the assertion that the linguistic input that children receive is relatively dismal and of poor quality relative to the high quantity and quality of output that they manage to produce after age 2 and that only an advanced, innate capacity to decode and organize linguistic input can enable them to “get from here (prelinguistic infant) to there (linguistic child).” In “Constructing a Language,” Tomasello presents a contrasting theory of how the child acquires language: It is not a universal grammar that allows for language development. Rather, human cognition universals of communicative needs and vocal-auditory processing result in some language universals, such as nouns and verbs as expressions of reference and predication (p. 19). The author proposes that two sets of cognitive skills resulting from biological/phylogenetic adaptations are fundamental to the ontogenetic origins of language. These sets of inherited cognitive skills are intentionreading on the one hand and pattern-finding, on the other. Intention-reading skills encompass the prelinguistic infant’s capacities to share attention to outside events with other persons, establishing joint attentional frames, to understand other people’s communicative intentions, and to imitate the adult’s communicative intentions (an intersubjective form of imitation that requires symbolic understanding and perspective-taking). Pattern-finding skills include the ability of infants as young as 7 months old to analyze concepts and percepts (most relevant here, auditory or speech percepts) and create concrete or abstract categories that contain analogous items. Tomasello, a most prominent developmental scientist with research foci on child language acquisition and on social cognition and social learning in children and primates, succinctly and clearly introduces the major points of his theory and his views on the origins of language in the initial chapters. In subsequent chapters, he delves into the details by covering most language acquisition domains, namely, word (lexical) learning, syntax, and morphology and conversation, narrative, and extended discourse. Although one of the remaining domains (pragmatics) is at the core of his theory and permeates the text throughout, the relative paucity of passages explicitly devoted to discussing acquisition and proBOOK REVIEWS
1,757 citations
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1,388 citations
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TL;DR: In this article, the authors summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities, and discuss the potential of using natural products as drug leads.
Abstract: Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer and infectious diseases. Nevertheless, natural products also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization, which contributed to a decline in their pursuit by the pharmaceutical industry from the 1990s onwards. In recent years, several technological and scientific developments — including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances — are addressing such challenges and opening up new opportunities. Consequently, interest in natural products as drug leads is being revitalized, particularly for tackling antimicrobial resistance. Here, we summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities. Natural products have historically made a major contribution to pharmacotherapy, but also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization. This Review discusses recent technological developments — including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances — that are enabling a revitalization of natural product-based drug discovery.
1,297 citations