Elena Koshel

ITMO University | SPbNRU ITMO · Laboratory of DNA-nanosensor diagnostics

The rapid and accurate diagnosis of meningitis is critical for preventing severe complications and fatalities. This study addresses the need for accessible diagnostics in the absence of specialized equipment by developing a novel diagnostic assay. The assay utilizes dual-priming isothermal amplification (DAMP) with unique internal primers to signif...

Colanic acid (CA) is an exopolysaccharide found in Enterobacteriaceae. Recently, its ability to stimulate physical activity in mice and to prolong the lifespan of invertebrates has been described. In the current work, we use standard MTT assay, fluorescence microscopy, and flow cytometry to describe CA action on several cell lines of different orig...

This paper discusses the pathway for obtaining a highly homologous gene of spider silk ADF4 from Araneus diadematus. The process of de novo synthesis of this gene is not only a process of PCR assembly, but also a detailed analysis of the gene sequence and its optimisation for synthesis in E. coli. This paper presents a sequence of actions for the a...

Objective: There is a large amount of data on fecal microbiome composition in inflammatory bowel disease and ulcerative colitis, but the mucosal microbiome is less described. Analysis of pathogenic determinants of microorganisms colonizing inflamed regions is promising for understanding their role in disease pathogenesis. The aim of this study is t...

Structural RNA is a challenging target for recognition by hybridization probes. This chapter addresses the recognition problem of RNA amplicons in samples obtained by multiplex nucleic acid sequence-based amplification (NASBA). The method describes the design of G-quadruplex binary (split) DNA peroxidase sensors that produces colorimetric signal up...

Bacterial infection is a major problem with diabetic wounds that may result in nonhealing chronic ulcers. Here, we report an approach to antibacterial hydrogel dressings for enhanced treatment of infected skin wounds. A fibrous hydrogel was derived from cellulose nanocrystals that were modified with dopamine and cross-linked with gelatin. The hydro...

It is believed that the nucleolus organizer region (NOR) in the ovary of adult birds is inactivated at all stages of oocyte growth. However, in the ovary of juvenile chicken (Gallus g. domesticus) one or two nucleoli were observed in 50% of early diplotene oocytes. These nucleoli were functioning up to the lampbrush stage. It was assumed that diplo...

The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at an improved understanding of the relationship between the human microbiot...

Organically-coated nanomaterials are intensively studied and find numerous applications in a wide range of areas from optics to biomedicine. One of the recent trends in material science is the application of bio-mimetic polydopamine coatings that can be produced on a variety of substrates in a cost-efficient way under mild conditions. Such coatings...

Since the outcome of an operation largely depends on the quality of wound healing, it is one of the most challenging stages in surgery. Today, wound closure is mostly undertaken by means of a surgical suture. Good surgical sutures are biocompatible and biodegradable and possess excellent mechanical properties. Preferably, these sutures demonstrate...

Bacterial biofilms play a major etiological role in dental diseases worldwide. Currently, toothpastes with bactericidal chemicals and abrasive materials are used as preventive care methods. However, chemicals can cause adverse side effects, with the use of antibiotics, fluorides, and antiseptics drastically reducing quality of life. At the same tim...

Organically-coated nanomaterials are intensively studied and find numerous applications in a wide range of areas ranging from optics to biomedicine. One of the recent trends in material science is the application of bio-mimetic polydopamine coatings that can be produced on a variety of substrates in a cost-efficient way under mild conditions. Such...

The newly prepared heparin-coated iron oxide nanoparticles (Hep-IONPs) contrasted cholangioma tumors in the liver in T2 MRI. NPs were not toxic to rats and rabbits after 14 days of consecutive...

Biofilms are the reason for a vast majority of chronic inflammation cases and most acute inflammation. The treatment of biofilms still is a complicated task due to the low efficiency of drug delivery and high resistivity of the involved bacteria to harmful factors. Here we describe a magnetically controlled nanocomposite with a stimuli-responsive r...

Hollow metallic capsules are of great interest given the large specific surface area and optical, electrical, and catalytic properties. To expand the possibilities of application and research of inorganic nano- and microparticles, new methodologies are being developed for obtaining metallic or multimetallic particles. For the first time, we propose...

The features of rDNA amplification have been studied in oocytes of the red-eared slider Trachemys scripta using a number of specific histochemical and cytomolecular methods. A single nucleolus in early diplotene oocytes is associated with the nucleolus organizer region (NOR). With oocyte growth, the number of nucleoli increases dramatically and rea...

Rapid and cost‐efficient methods for diagnostics of infectious diseases can expedite prescription of adequate treatment, thus shortening the patients’ recovery and reducing adverse side effects. In this study, we developed a procedure for visual detection of bacterial pathogens Gram‐negative Neisseria meningitidis and Gram‐positive Streptococcus pn...

Advanced wound dressings improve wound healing by releasing antibacterial agents, accelerating wound closure, and reporting (sensing) changes in the wound's state. The challenge with the release of antibacterial agents such as drugs, peptides, or nanoparticles is their unregulated administration. In addition, bacteria resistance to antibiotics stim...

Rapid development of antibiotic resistance in bacteria is a critical public health problem in the world. One of the main routes of resistance development is the transfer of genes containing antibiotic resistance cassettes. Gene transfer can be done through horizontal transfer of genes: transduction, conjugation, and transformation. Many factors in...

At present, there is an urgent need in medicine and industry to develop new approaches to eliminate bacterial biofilms. Considering the low efficiency of classical approaches to biofilm eradication and the growing problem of antibiotic resistance, the introduction of nanomaterials may be a promising solution. Outstanding antimicrobial properties ha...

A major obstacle in the introduction of nanoformulated drugs has been the fact that shape of the drug delivery systems (DDSs) - the most important parameter driven by nature for viruses and bacteria – remains almost out-of-scope for artificial systems. Here we propose a potential solution for this problem by developing a template-free approach towa...

In recent years, more and more data indicate the effect of human microbiota on carcinogenesis. Despite the numerous studies on the relationship between gut microbiota and carcinogenesis, the exact mechanisms of this interaction are not well studied. It becomes apparent that this relationship can be mediated by microbial metabolites. Mechanisms of s...

For the widespread application of nanotechnology in biomedicine, it is necessary to obtain information about their safety. A critical problem is presented by the host immune responses to nanomaterials. It is assumed that the innate immune system plays a crucial role in the interaction of nanomaterials with the host organism. However, there are only...

Amyloids are β-sheets-rich protein fibrils that cause neurodegenerative and other incurable human diseases affecting millions of people worldwide. However, a number of proteins is functional in the amyloid state in various organisms from bacteria to humans. Using an original proteomic approach, we identified a set of proteins forming amyloid-like a...

Different metal particles are increasingly used to target bacteria as an alternative to antibiotics. Despite numerous data about treating bacterial infections, the utilization of metal particles in antibacterial coatings for implantable devices and medicinal materials promoting wound healing. The antibacterial mechanisms of nanoscale and microscale...

Nanostructured drugs are being approved for clinical use, although there is a serious deficit of systematic studies of these materials. Data on toxicity of nanoparticles (NPs) can vary due to different methods of preparation, size and shape. We investigated the toxicity against cultured human cells, the acute toxicity in mice and the influence on c...

Biofilm-related diseases contribute to patient morbidity, increased mortality and represent a considerable economic burden. Despite numerous developments in the field of combating biofilms, the most effective treatment method is still the mechanical removal of biofilms or the replacement of a device overgrown with biofilm. Given that the main chall...

Albumins are very promising carrier family for various types of small functional molecules, including (pro)drugs, sensors, and imaging agents. In this study, we demonstrate that one of the most crucial features of albumin—its ability to internalize into cancer cells—is strongly affected by its aggregation state. We used 14 different luminescent com...

Functional amyloids regulate vital processes in a variety of organisms from bacteria to higher eukaryotes. The development of methods enabling large-scale screening for amyloids opens up opportunity for systemic analysis of the prevalence of amyloids in nature. Using an original proteomic approach, we identified several proteins forming amyloid-lik...

Alumina is one of the most promising carriers for drug delivery due to the long history of its usage as a vaccine adjuvant. Sol-gel synthesis provides excellent conditions for entrapment of biomolecules within an inorganic cage providing stabilization of proteins under the extremal conditions. In this paper, we show in vitro investigation of monodi...

One of the most urgent problems of modern medicine is bacterial resistance to antibiotics. Development of new treatment approaches is a laborious and expensive process. One of the strategies for developing new antimicrobial agents is a modification of existing antibiotics. Sonochemical nanostructuring (SN) of antibiotics can become a cheap alternat...

The development of stimuli-responsive nanocontainers is an issue of prime importance for many applications such as target drug delivery, regulation of the cell and tissue’s behavior, make bacteria do useful functions, here convert light. The present work shows a new contribution to the design of polyelectrolyte (PE) containers based on surface modi...

The focus of this study is to investigate influence of template functional groups on properties and morphology of alumina materials obtained by a combination of template and sol-gel synthesis. Cyanoethyl-, amidoethyl- and carboxymethylcellulose were synthesized and used as templates for alumina materials preparation. Alumina nanoparticles due to th...

The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo re...

Elena Gaginskaya is an outstanding scientist, doctor of biological sciences, professor, international expert, creator of the first core facility at St. Petersburg State University, and the founder of the Lampbrushology Scientific School. She celebrates her 85th birthday this year. Students, colleagues and friends congratulate Elena with all their h...

Lampbrush chromosomes are giant, transcriptionally active, meiotic chromosomes found in oocytes of all vertebrates with the exception of mammals. Lampbrush chromosomes offer a convenient tool for cytogenetic mapping and, in particular, have been instrumental in mapping genes and linkage groups on chicken (GGA) chromosomes. Whereas cytogenetic maps...

Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained...

Reptilians are a complex paraphyletic vertebrate group embracing representatives that acquired divergent oogenesis features independently of each other. To be noticed is that reptilian oocyte descriptions are mainly made at routine histological level, while reliable modern data on nucleoli or other nuclear structures are still practically absent. H...

The genes of rRNA in the nucleolar organizer region (NOR) are inactivated in the oocytes of adult birds despite the functioning of lampbrush chromosomes. The nucleolus is not formed during all stages of the oocyte development. On the other hand, two morphological forms of oocytes differing by the presence of nucleolus in the germinal vesicle are de...

Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITSs sequences in 24 species from 11 classes initially obtained...

Despite long-term exploration into ribosomal RNA gene functioning during the oogenesis of various organisms, many intriguing problems remain unsolved. In this review, we describe nucleolus organizer region (NOR) activity in avian oocytes. Whereas oocytes from an adult avian ovary never reveal the formation of the nucleolus in the germinal vesicle (...

In this study we have shown that substitution of chloride ligand for imidazole (Im) ring in cyclometalated platinum complex, Pt(phpy)(PPh3)Cl (1; phpy = 2-phenylpyridine; PPh3 = triphenylphosphine), which is non-emissive in solution, switches on phosphorescence of the resulting compound. Crystallographic and NMR spectroscopic studies of the substit...

Simultaneous fluorescence and phosphorescence lifetime imaging microscopy (FLIM and PLIM) of living cells makes it possible to obtain a more detailed picture of intracellular homeostasis. In particular, in situ measurement of oxygen concentration in biological objects and its effect on the metabolism of the cells can be measured with PLIM based on...

Metal-based phosphorescent probes are useful tools for bioimaging, including two-photon microscopy. In this study, we present investigation of a new phosphorescent homoleptic alkynyl gold(I) cluster, (AuC2R)10 (R – 2,6-dimethyl-4-heptanol) (Koshevoy et al., 2012), which demonstrates a selective staining of lipid droplets in animals tissues and huma...

Entomoparasitic nematodes are the natural regulators of numbers of fleas – plague vectors in natural plague foci. They have an impact on the intensity of epizootic process, progressing in these foci. Objective of the study is to examine entomoparasitic nematodes from fleas of the souslik and vole, collected in the territory of Povolzhsky Region. Ma...

The development of organelle-specific phosphorescent multiphoton probes is a rapidly growing area in biomedical imaging. Phosphorescent properties allow spectral or time-resolved discrimination from autofluorescence, while the use of two-photon microscopy provides higher spatial resolution as well as deeper penetration into the sample compared to c...

Heterocyclic fluorochrome 2-phenylpyrido[2,1-a]pyrrolo[3,2-c]isoquinoline (PPPI) has a high quantum yield of fluorescence in protic solvents (Tomashenko et al. 2015). In this study PPPI was investigated as a new nuclear dye during the structural and functional analysis of chicken oocyte nuclei. For this study metaphase chromosomes samples, cryosect...

Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5’ETS (1836...

18S rRNA gene sequence boundaries resulted from a multiple sequence alignment. Indications are the same as in S1 Fig. (TIF)

Chicken 5.8S rRNA gene sequence boundaries resulted from a multiple sequence alignment. Indications are the same as in S1 Fig. (TIF)

Chicken ITS2 sequence boundaries resulted from a multiple sequence alignment. Indications are the same as in S1 Fig. (TIF)

Chicken 28S rRNA gene sequence boundaries resulted from a multiple sequence alignment. Indications are the same as in S1 Fig. (TIF)

Chicken 5’ETS sequence boundaries resulted from a multiple sequence alignment. Black frames outline the elements of the ribosomal cluster. Cluster members are schematically indicated by colored boxes. Asterisk–chicken pre-rRNA transcription initiation site. Arrow–transcription direction. Double slashes schematically point the hidden area of alignme...

Raw read assembly verification using WGS contigs and annotated sequences. (PDF)

De novo and re-assembled rRNA gene cluster sequence alignment. (PDF)

Chicken ITS1 sequence boundaries resulted from a multiple sequence alignment. Indications are the same as in S1 Fig. (TIF)

Chicken ITS2 ssDNA secondary structures under the conditions of T = 60°C, [K+] = 50 mM. (PDF)

Chicken 3’ETS sequence boundaries resulted from a multiple sequence alignment. Indications are the same as in S1 Fig. (TIF)

Multiple alignment matrix for chicken rRNA gene cluster boundaries search using annotated fragments of ribosomal clusters of Homo sapiens, Rattus norvegicus, Mus musculus, Xenopus laevis and Crocodylus porosus. (PDF)

Chicken ITS1 ssDNA secondary structures under the conditions of T = 60°C, [K+] = 50 mM. (PDF)

Objective of the study is to explore the feasibility of the long-term persistence of Yersinia pestis strains in association with ameba - Acanthamoeba sp. Materials and methods. Investigated has been interaction of ameba - Acanthamoeba sp., isolated from rodent burrows in the Pre-Caspian sandy, Volga-Ural steppe, and Pre-Caspian North-Western steppe...

In this paper, we analyzed the distribution and the transcriptional activity of different repetitive elements in the sex chromosomes of chicken at the lampbrush stage. Based on these results, we suggest participation of interspersed repeats in the maintenance evolutionarily significant level of variability of heteromorphic sex chromosomes in birds....

Background Repeated clusters of ribosomal genes whose activity results in the nucleolus formation are extremely important in multicellular organism genome. Despite the extensive exploration into vertebrate genomes, in many model objects the ribosomal cluster structure is still underinvestigated. So far, complete description for primary structure of...

The results of a study on the taxonomy and quantitative abundance of free-living amoebas in soil samples from the Russian plague foci of the Northwestern Caspian steppe, the Caspian sand, and the Volga-Ural steppe are presented. Amoebas of the Willaertia and Hartmanella genera, as well as representatives of myxomycetes, were isolated from samples....

Entomoparasitic nematodes are natural control agents for many insect pests, including fleas that transmit Yersinia pestis, a causative agent of plague, in the natural foci of this extremely dangerous zoonosis. We examined the flea samples from the Volga-Ural natural focus of plague for their infestation with nematodes. Among the six flea species fe...

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##