Denis Korneev

Denis Korneev
Monash University (Australia) · Department of Biochemistry and Molecular Biology

Ph.D. in Biophysics

About

48
Publications
97,438
Reads
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441
Citations
Introduction
I work in the Imaging and technology development Lab (Monash University): https://www.demarco-lab.com/ My scientific interests: electron microscopy (SEM, TEM, FIB-SEM, Cryo); large volume imaging and data processing; atomic force microscopy (AFM); advanced sample preparation and developing of nonstandard protocols and tools; I'm associated (honorary fellow) with the University of Melbourne, working with Moira O'Bryan's Lab: https://obryan.science.unimelb.edu.au/
Additional affiliations
November 2017 - present
Monash University (Australia)
Position
  • PostDoc Position
December 2016 - December 2016
École Polytechnique Fédérale de Lausanne
Position
  • Academic visitor
July 2016 - September 2016
École Polytechnique Fédérale de Lausanne
Position
  • Visitor (trainee)
Education
October 2016 - October 2016
Lomonosov Moscow State University
Field of study
  • Biophysics
September 2003 - June 2011
Novosibirsk State University
Field of study
  • Physics (Biophysics)

Publications

Publications (48)
Article
Full-text available
The analysis of spermatozoa morphology is fundamental to understand male fertility and the etiology of infertility. Traditionally scanning electron microscopy (SEM) has been used to define surface topology. Recently, however, it has become a critical tool for three-dimensional analysis of internal cellular ultrastructure. Modern SEM provides nanome...
Article
Full-text available
We characterized two bacteriophages, ΦFG02 and ΦCO01, against clinical isolates of Acinetobacter baumannii and established that the bacterial capsule is the receptor for these phages. Phage-resistant mutants harboured loss-of-function mutations in genes responsible for capsule biosynthesis, resulting in capsule loss and disruption of phage adsorpti...
Article
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Human Cytomegalovirus (HCMV) infects over half the world's population, is a leading cause of congenital birth defects, and poses serious risks for immuno-compromised individuals. To expand the molecular knowledge governing virion maturation, we analysed HCMV virions using proteomics, and identified a significant proportion of host exosome constitue...
Article
Full-text available
Ultrastructural studies revealing morphological differences between intact and photodynamically inactivated virions can point to inactivation mechanisms and molecular targets. Using influenza as a model system, we show that photodynamic virus inactivation is possible without total virion destruction. Indeed, irradiation with a relatively low concen...
Preprint
Full-text available
Over the past decade, gallium Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) has been established as a key technology for cellular tomography. The utility of this approach, however, is severely limited both by throughput and the limited selection of compatible sample preparation protocols. Here, we address these limitations and present oxy...
Article
The majority of viruses within the gut are obligate bacterial viruses known as bacteriophages (phages). Their bacteriotropism underscores the study of phage ecology in the gut, where they modulate and coevolve with gut bacterial communities. Traditionally, these ecological and evolutionary questions were investigated empirically via in vitro experi...
Article
Full-text available
Background Clinical phage therapy is often delivered alongside antibiotics. However, the phenomenon of phage-antibiotic synergy has been mostly studied in vitro. Here, we assessed the in vivo bactericidal effect of a phage-antibiotic combination on Acinetobacter baumannii AB900 using phage øFG02, which binds to capsular polysaccharides and leads to...
Article
The process of a metal dusting of the nichrome alloy in the atmosphere of chlorinated hydrocarbon was investigated. A series of samples with different exposure times was prepared to study the bulk NiCr evolution. The X-ray diffraction data revealed no changes in the phase composition of the nichrome alloy after 1-h treatment, since the amount of de...
Article
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Owing to the high hydrogen content, hydrocarbons are considered as an alternative source for hydrogen energy purposes. Complete decomposition of hydrocarbons results in the formation of gaseous hydrogen and solid carbonaceous by-product. The process is complicated by the methane formation reaction when the released hydrogen interacts with the forme...
Preprint
Full-text available
The analysis of spermatozoa morphology is fundamental to understand male fertility and the aetiology of infertility. Traditionally scanning electron microscopy (SEM) has been used to define surface topology. Recently, however, it has become a critical tool for three dimensionally analyse of internal cellular ultrastructure. Modern SEM provides nano...
Article
Optical elements rely on refraction, diffraction, or reflection for light manipulation. Fusing diffractive and refractive functions in a single element provides an extra layer of control over the wave propagation, allowing complex beam shaping through self-aligned, monolithic and miniaturized optics. Using gray-scale lithography with high-current f...
Preprint
Full-text available
Carbapenem-resistant Acinetobacter baumannii is responsible for frequent, hard-to-treat and often fatal healthcare-associated infections. Phage therapy, the use of viruses that infect and kill bacteria, is an approach gaining significant clinical interest to combat antibiotic-resistant infections. However, a major limitation is that bacteria can de...
Article
Full-text available
A series of micro-disperse Ni-Mo alloys with the sponge-like structure was prepared by a simultaneous precipitation method followed by sintering of the sediment in H2 atmosphere at 800 °C. According to XRD data, the formation of single-phase solid solution Ni1-xMox took place for the samples with Mo content of 0.6-8.3 wt.%. Synthesized samples were...
Article
A series of micro-disperse Ni1-xPtx alloys with the sponge-like structure was prepared by a simultaneous precipitation method with subsequent sintering of the sediment in H2 atmosphere at 800 °C. The formation of single-phase solid solution Ni1-xPtx was confirmed by powder XRD analysis for entire range of Pt concentrations (1.3–75.9 wt.%). The synt...
Article
The Ni-Pd alloys synthesized by coprecipitation method were studied as precursors for the self-organizing particles catalyzing the growth of carbon nanofibers. Addition of palladium was found to enhance both the activity, stability and productivity of the catalyst in the hydrogen-assisted decomposition of 1,2-dichloroethane. Evolution of reflex (33...
Article
Full-text available
Background: The problem of bacterial colonization of implants used in medical practice continues to be relevant regardless of the material of the implant. Particular attention should be given to polymeric implants which are produced "ex tempore" from polymethyl methacrylate, for example, during orthopedic surgical interventions (so-called «bone cem...
Article
The hierarchically structured carbon-carbon nanocomposites represent carbon microfibers covered with a layer of carbon nanomaterials. Having properties of both micro- and nano-level, such nanocomposites demonstrate perspectives in polymer reinforcement, membrane technologies and catalysis. The synthesis of the carbon-carbon nanocomposites with cont...
Article
The way to produce the nanostructured carbon filaments via H 2 -assisted catalytic decomposition of CF 2 Cl 2 over self-organizing Ni-based catalyst has been reported. The self-organizing 6%Ni/CNM catalyst, where CNM is a carbon nanomaterial, resulted from carbon erosion of bulk Ni-Cr alloy (nichrome) in C 2 H 4 Cl 2 vapors was also shown to be eff...
Article
Catalytic chemical vapor deposition of 1,2-dichlorethane over Ni-based catalysts into carbon nanostructured materials was studied. The catalysts were prepared by mechanochemical activation and by metal dusting of bulk nickel-containing alloy precursors. Model Ni-M alloys, where M is Co, Cu, and Fe, were obtained by coprecipitation technique. Loadin...
Article
A novel hybrid material Bi(III)@MIL-101 (Bi(III) = Bi-containing oxoclusters and MIL-101 = chromium(III) oxoterephthalate) was obtained by the intra-pore hydrolysis of guest bismuth(III) chloride in ammonia solution. This compound was characterized by chemical analysis, powder X-ray diffraction, nitrogen sorption and TEM techniques. According to th...
Article
The features of the catalytic pyrolysis of chlorohydrocarbons over resistive Ni–Cr alloy were studied using 1,2-dichloroethane as a model substrate. The heating of the catalyst was provided by a direct supply of current on nichrome spiral wire. Such parameters as the temperature of spiral wire (550–700 °C), hydrogen concentration (0–60 vol%) and pr...
Article
Full-text available
We developed a candidate vaccine CombiHIVvac, which combines the conserved polyepitope immunogens approaches in a novel self-adjuvanted microparticle concept. The experimental visualization of a theoretical predicted formation of microparticles was performed using the method of transmission electron microscopy (TEM) with negative staining. Obtained...
Article
The alloyed Ni-Pd system with Pd content of 3 wt.% was prepared by coprecipitation method followed by reduction in hydrogen atmosphere at 800 °C. The formation of single-phase solid solution with unit cell parameter a = 3.532(1) Å (determined by (331) reflex at 2θ ≈ 145°) corresponding to NiPd alloy with weight ratio 97:3 was confirmed by XRD analy...
Article
The surface of fiberglass cloth, carbon and basalt microfibers was modified with carbon nanostructured coating via catalytic chemical vapor deposition (CCVD) of 1,2-dichloroethane. Incipient wetness impregnation and solution combustion synthesis (SCS) methods were used to deposit nickel catalyst on the surface of microfibrous support. Prepared NiO/...
Article
Full-text available
The complete genome sequence was determined for avian paramyxovirus (APMV-6) serotype 6 strain teal/Chany/455/2009, isolated from a teal (Anas crecca) in Siberia. Siberia is crossed by four major migration flyways and represents the major breeding area for many wild bird species in the Palearctic. Strain teal/Chany/455/2009 is genetically closely r...
Article
Full-text available
This paper presents the results of research on the regularities of the formation of carbon nanofibrous materials, as well as the influence of the composition of the model mixture of hydrocarbons С1–С4 on the morphological features and textural characteristics of the resulting carbon nanofibres (CNF). One of the most urgent issues faced by the oil a...
Article
Full-text available
Atomic force microscopy-based single virus particle force spectroscopy was developed using dielectrophoresis for fixing virions at the tip of an atomic force microscope (AFM) probe. Electron microscopic visualization was found to be necessary to prove the deposition of virus particles on the tip of the AFM probe, while fixation of single virions by...
Article
The study performed a comparative estimation of the detection systems with the use of conjugates based on peroxidase, alkaline phosphatase, colloidal gold, and the amplification system "Super-CARD" for multiplex dot-immunoassay of antibodies. The results of the study show that the sensitivity of the detection system with colloidal gold was approxim...
Article
Problems of multiplex test development for the detection of antibodies to a number of infectious agents in clinical blood samples using protein arrays are discussed. Experimental data on the evaluation of microstructure and adsorption properties of synthetic materials for protein chip substrate are presented. The synthetic paper Pentaprint PR-M480/...
Article
Full-text available
Objective: to develop a technology for obtaining the molded sorbent VNIITU-1, to study its physicochemical and biomedical properties, and to evaluate its efficacy in preventing and treating pyoinflammatory complications in obstetrics. Materials and methods. The molded sorbent VNIITU-1 was designed from the carbon porous material based on nanodisper...
Article
The method of synthesis of CNF/MF carbon-carbon composites by growing carbon nanofibers (CNFs) on a surface of carbon macrofibres (CMFs) is described. The method is based on catalytic gas-phase deposition of carbon (using C1, C2 hydrocarbons and the mix of C2-C4). Depending on the conditions of modification (composition of catalytic particles, type...
Article
The specific interactions of the pairs laminin binding protein (LBP)–purified tick-borne encephalitis viral surface protein E and certain recombinant fragments of this protein, as well as West Nile viral surface protein E and certain recombinant fragments of that protein, are studied by combined methods of single-molecule dynamic force spectroscopy...
Article
Full-text available
The application of high�frequency ultrasonic spray pyrolysis (USP) of aqueous solutions for the preparation of the NiO�CuO/10%MgO catalyst is discussed. The installation for the catalyst synthesis com� prises a household humidifier, a furnace for drying the formed aerosol, and an electric precipitator for col� lecting the product particles. The sec...
Article
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Abstract Glycyrrhizin or glycyrrhizic acid (GA) - triterpene glycoside extracted from licorice root - has been intensively studied over the past decade and is considered to be a potential drug delivery system. Glycyrrhizin was found to enhance the therapeutic effect of various drugs; however the detailed mechanism of these effects is still unknown...
Article
Due to amphiphilic properties, glycyrrhizic acid is capable of forming water�soluble conju� gates with a wide variety of hydrophobic pharmaceutical compounds. This results in a signifi� cant reduction in the therapeutic dose of the drugs. To enlighten the molecular and cellular mechanisms of the observed effects, the influence of glycyrrhizic acid...
Article
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A molecular construct of a spherical shape containing double-stranded RNA (dsRNA) in the center, coated by a spermidine-polyglucine coat, and carrying recombinant deltaferon—an analogue of recombinant interferon-gamma—has been designed. It is shown that deltaferon in this construct retains its specific activity at a level of 9 × 104 U/mg. It was fo...
Article
A multiplex polymerase chain reaction (PCR) for identification of four viruses causing acute respiratory diseases in human beings was developed. The analytical sensitivity of developed RT-PCR for identification of adenovirus, respiratory-syncytial virus, flu viruses types A and B, and actual subtypes of type A flu virus (seasonal and pandemic varia...
Article
Full-text available
The interaction of 1,2-dichloroethane (DCE) vapors with bulk NiCr alloy resulting in complete metal wastage with the formation of carbon nanofibers (CNFs) has been described from mechanistic point of view. The genesis of surface transformations of the bulk NiCr alloy exposed to corrosive reaction mix Ar/H2/DCE at 550 °C was studied by AFM, SEM and...
Article
Aiming at creation of prolonged-action medicine, the new macromolecular system has been developed. The unit contains dsRNA (double-stranded) and ssRNA (single-stranded) covered by polyanionic nuclease-protecting envelope, containing etiotropic antiviral agent - aprotinin. It has been demonstrated that the speed of dsRNA migration during the electro...
Article
Full-text available
To study the effect of nanoscale titanium dioxide (TiO(2)) on cell responses, we synthesized four modifications of the TiO(2) (amorphous, anatase, brookite, and rutile) capable of keeping their physicochemical characteristics in a cell culture medium. The modifications of nanoscale TiO(2) were obtained by hydrolysis of TiCl(4) and Ti(i-OC(3)H(7))(4...
Article
Full-text available
The effect of neutralization conditions of TiO2 acid sol obtained by hydrolysis of titanium tetraisopropoxide (the nature of monovalent cation (Li+, Na+, NH4+) of electrolyte, chemical nature of a dialyzing solution, and surface modification of nanoparticles with glycidyl isopropyl ether (GE)) on TiO2 dispersion and cytotoxic properties was investi...

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Projects (3)
Archived project
I have used dielectrophoresis (DEP) as a method of single virion position on the AFM tip for atomic force spectroscopy experiments: https://www.researchgate.net/publication/306140340_Atomic_force_microscopy-based_single_virus_particle_spectroscopy Dielectrophoretic properties of few viruses were studied. As an example you can see the DEP movement of vaccinia virions on the conventional flat DEP-chamber. The movie is attached. Frequency is 200 kHz, amplitude is slowly varying from 0 to 6 V few times. It is possible to see how virions are collected on the electrodes and skipped when the voltage was decreasing. The virions are labeled with FITC. Movie is monochromic, because the camera was used in fast white-black mode. There are different applications of such technique: - Position of single particles onto conductive AFM tip or other sharp electrode; - Study of dielectric properties of virions (parameters of dielectrophoresis contain this information); - Concentration of virions for some practical approaches; - Sorting of particles.
Project
World Society for Virology was founded to build up a network of scientific collaboration among virologists worldwide. www.ws-virology.org Join us: www.ws-virology.org/membership Email: info@ws-virology.org https://www.linkedin.com/in/ws-virology-748b49155/ https://twitter.com/WSVirology https://www.facebook.com/WSVirology/ https://www.instagram.com/WSVirology/
Archived project
A phage is attached to an AFM tip with dielectrophoresis. Then the tip is manually approached to bacterial film surface with Picoangler unit. The main goal is the detection of phage tail contraction (the cantilever is very soft, k is about 0.005 N/m).