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    Introduction
    I am a postdoc between two labs: Physics: https://www.demarco-lab.com/ and Biology: https://www.researchgate.net/lab/Moira-K-OBryan-Lab My scientific interests are broad: electron and atomic force microscopy, biophysics of single cells and viruses, development of new scientific equipment and techniques. Now I am focused on cryo electron microscopy sample preparation and FIB-SEM technique for morphological studies. In addition, I am going to study of flagellar movement by PIV technique and numerical simulation.
    Research Experience
    Nov 2017
    Dec 2016 - Dec 2016
    Academic visitor
    Position
    • Academic visitor
    Jul 2016 - Sep 2016
    École Polytechnique Fédérale de Lausanne
    Position
    • Visitor (trainee)
    Education
    Oct 2016 - Oct 2016
    Lomonosov Moscow State University
    Field of study
    • Biophysics
    Sep 2003 - Jun 2011
    Novosibirsk State University
    Field of study
    • Physics (Biophysics)
    Current institution
    Monash University (Australia)
    Current position
    • Research Fellow
    Lab members (8)
    Brendan Houston
    Jessica Dunleavy
    Anne O'Connor
    Avinash Gaikwad
    Jinghua Hu
    Denis Korneev
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    Following
    Projects
    Projects (3)
    Project
    World Society for Virology was founded to build up a network of scientific collaboration among virologists worldwide. www.ws-virology.org 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).
    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.
    Research
    Research Items (34)
    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 incubating the tip with a virus suspension proved impossible. Force spectroscopy measurements were performed for the vaccinia virus, influenza virus, and bacteriophage AP22. ForceReader special software was designed for analyzing the force–distance curves.
    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 (SMDFS), enzyme immunoassay and optical surface waves-based biosensor measurements. The experiments were performed at neutral pH (7.4) and acid pH (5.3) conditions. The data obtained confirm the role of LBP as a cell receptor for two typical viral species of the Flavivirus genus. A comparison of these data with similar data obtained for another cell receptor of this family, namely human αVβ3 integrin, reveals that both these receptors are very important. Studying the specific interaction between the cell receptors in question and specially prepared monoclonal antibodies against them, we could show that both interaction sites involved in the process of virus–cell interaction remain intact at pH 5.3. At the same time, for these acid conditions characteristic for an endosome during flavivirus–cell membrane fusion, SMDFS data reveal the existence of a force-induced (effective already for forces as small as 30–70 pN) sharp globule–coil transition for LBP and LBP–fragments of protein E complexes. We argue that this conformational transformation, being an analog of abrupt first-order phase transition and having similarity with the famous Rayleigh hydrodynamic instability, might be indispensable for the flavivirus–cell membrane fusion process. Copyright © 2014 John Wiley & Sons, Ltd.
    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 high resolution images of ComiHIVvac microparticles showed that vaccine structure mimic the size and organization of native viruses and yields insights into how this structure relates to high immunogenisity of vaccine.
    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 and attracts the attention of researchers. In this work, we have made an attempt to clarify the mechanism of Glycyrrhizin activity on molecular and cellular level. The influence of GA on the functional properties of biomembranes was investigated via NMR spectroscopy and atomic force microscopy (AFM) using human erythrocytes as a model system. GA was shown to increase the permeability (about 60%) and to decrease elasticity modulus of cell membranes (by an order of magnitude) even in micromolar concentrations. Changes on the erythrocyte surface were also detected by AFM. These results could provide a new insight on the mechanism of bioavailability enhancement of some drugs in the presence of glycyrrhizin, as well as the mechanism of its own biological activity. The role of cholesterol-glycyrrhizin binding in the observed effects is also discussed.
    Question - Is there any working method for precipitation / concentration of a large virus?
    Answer
    Alexander Malogolovkin, yes, the liquid that passed through the filter is going to waste. We use the liquid above the filter, see the schematic illustration. The filter works like a sieve here.
    Question - Is there any working method for precipitation / concentration of a large virus?
    Answer
    Alexander Malogolovkin, I have never seen a special protocol of virus purification with centrifugal concentrators, it was just my own idea. I used it for influenza, vaccinia, bacteriophages (Myoviridae) and protein fibrils. It works well.
    E.g. for influenza virus and Vivaspin 6 (300.000 MWCO):
    0. Filtration with 220 nm filter.
    1. Put 2 ml of allantois liquid into a tube, then fill the tube with PBS (full volume is 6 ml) and shake.
    2. Centrifugate for 5 min with 3000 g (swing buckets). The time is depend on initial concentration and can be vary, the final level should be about 1 ml.
    3. Remove and empty the low part of the tube and install it back.
    4. Add PBS for 6 ml. Intensively (100 times) pipette or put the tube into a sonic bath for 5 min.
    5. Centrifugate with the same conditions.
    Repeat 10 times. In the final step the time of centrifugation can be increased for high concentration.
    Virus purification is a very important part of sample preparation in microscopy and biophysics of…
    Question - Is there any working method for precipitation / concentration of a large virus?
    Answer
    Saif Deis, you are welcome. This simple method can be used not only for concentration, with high MWCO (> 100.000) all small "garbage" (proteins, lipids, etc.) is going away through the membrane. I prepared extremely pure virus suspension for some biophysical experiments and microscopy with this simple way:
    - concentrate about 10 times;
    - add a buffer for the initial volume and remove old liquid from the low part of the tube (they are demountable);
    - intensive pipetting or sonication;
    - concentrate...
    Repeat 5-10 times. The result will be very nice and the process is more simple than ultracentrifugation in gradients.
    Good luck!
    Question - Is there any working method for precipitation / concentration of a large virus?
    Answer
    @Saif Deis,
    I used low-speed centrifuge with swing buckets, 3000 g, 5 min for Vivaspin 6 (300.000 MWCO). But the proper time is depend on the initial concentration. The best way is make a first step, e.g. 1 min 3000 g and estimate the level of the virus suspension in the tube.
    Don't forget to rinse the virions out from the membrane surface after concentration. It is possible to use intensive pipetting or sonication in a sonic bath.
    Good luck!
    Question - Hi, can anyone tell me that how to confirm the cell wall or membrane inhibition in aspergillus other than SEM or TEM imaging?. Thanks in advance.?
    Answer
    I don't have any experience with aspergillus, but the main principles are the same for all living cells:
    1. Differential staining for conventional light microscopy. It is a well-known technique and there are a lot of protocols and commercial chemicals.
    2. Biophysical methods. Cell wall or cell membrane conductivity is strictly depend on their conditions and can be studied by dielectrophoresis. For example:
    Good luck!
    Question - Global warming and climate change: Hoax or reality?
    Answer
    Dear Dr. Asit, the picture is just a piece of humor - Friday, evening... :-)
    Question - Global warming and climate change: Hoax or reality?
    Answer
    :)
    Question - How can I remove carbon film thickness from specimen thickness in electron energy-loss spectroscopy (EELS) ?
    Answer
    The simplest and self-evident way is just a comparison of three points: null (a hole in the film), carbon film and the sample on the film. Then it is possible to subtract the film thickness. I have never used DigitalMicrograph software and cannot say anything about the interface, but it is the main physical basis.
    Good luck!
    Question - Why use diffraction mode with an amorphous sample?
    Answer
    @Janez, nice picture. I used diffraction mode for cleaning (!) of sharp AFM tip which was installed in Jeol tomographic holder and rotated for 60 degree. It was a kind of perversion in conventional TEM practice :)
    Question - I have done FESEM and TEM analysis of carbon dots. TEM shows the size is of about 2 nm and FESEM shows diameter of about 4 nm. Is this right ?
    Answer
    Hi Janez, I don't trust DLS too :)
    When it was necessary to know really size of small particles, I used TEM and AFM simultaneously.
    The most precise way, obviously, is calculation of particle size from some crystallographic parameters obtained by HTEM.
    P.S. Are you going to IMC19 in Sydney?
    Question - I have done FESEM and TEM analysis of carbon dots. TEM shows the size is of about 2 nm and FESEM shows diameter of about 4 nm. Is this right ?
    Answer
    @Janez, I am totally agree about electron microscopy, but have a little remark about DLS :)
    DLS is not conventional light microscopy with well-known Rayleigh limit, it is another technique based on photon auto-correlation function and suitable for particles up to 1 nm. But the problem is in systematic error and electron microscopy is known as more reliable method. The best way is to use both techniques - microscopy and laser size analyzer simultaneously, because microscopy provides diameter just for a few particles and DLS gives it for billions.
    Question - I have done FESEM and TEM analysis of carbon dots. TEM shows the size is of about 2 nm and FESEM shows diameter of about 4 nm. Is this right ?
    Answer
    Theoretically, some additives which always exist in every solvent, can give a very thin film by drying. It could be an explanation. Just put your TEM grid with the sample in a FESEM and compare the results.
    Good luck!
    Question - I have done FESEM and TEM analysis of carbon dots. TEM shows the size is of about 2 nm and FESEM shows diameter of about 4 nm. Is this right ?
    Answer
    In general, TEM is more precise. Especially, for such small objects.
    But it is necessary to keep it in mind - both methods are techniques of visualization, not precise measurement. HTEM is suitable for some crystallographic measurements, but when we just try to measure some objects on the pictures, it is not a measurement, it is just an estimation.
    Good luck!
    Question - How can one remove a magnetic sample stuck inside TEM, probably in the pole-piece, very close to goniometer?
    Answer
    If the microscope is new, don't try to disassemble it yourself. It can be extremely expensive (damages and lost warranty). Call Jeol engineer.
    Perhaps, the problem is not so serious. It looks like a mechanical problem with goniometer. Remove the covers from goniometer mechanism and inspect carefully.
    Good luck!
    Question - Preparing the cross section of thin film on a plate for SEM analysis?
    Answer
    FIB-SEM technique could be more informative than conventional embedding-polishing way, but this kind of equipment is not very common.
    Good luck!
    Question - Your thoughts about using propylene oxide for TEM processing?
    Answer
    I use PO for epon embedding, but in comparison with ethanol the difference is not critical.
    Question - Why use diffraction mode with an amorphous sample?
    Answer
    Very strict teacher )))
    Question - Why use diffraction mode with an amorphous sample?
    Answer
    You are welcome, Matthew
    I wrote that answer before:
    " In addition, diffraction mode can be used in TEM adjustment (center apertures). "
    :-)
    Question - Is there any working method for precipitation / concentration of a large virus?
    Answer
    Centrifugal concentrators work very well. I used Vivaspin 6 (300,000 MWCO) for concentration and purification of poxviruses.
    Good luck!
    Question - How to separate nanoparticles from micro-nano particle mixture?
    Answer
    If it is possible to suspend the particles in liquid, there are two self-evident ways: filtration and centrifugation.
    Good luck!
    Question - What are the Applications of SEM and TEM on protein whipability and foaming properties?
    Answer
    Cryogenic sample preparation techniques are used in this area. It is possible to fix the foam structure with fast freezing. There are a lot of powerful cryogenic techniques, cryo FIB-SEM tomography looks one of the most promising.
    Good luck!
    Question - How to remove the wax covering layer of hemipterans ?
    Answer
    Chloroform can help. For example, such protocol:
    Immerse in Chloroform for 1 hr to dissolve the surface wax, finishing with a final rinse in 100% ethanol (from a newly opened bottle, to ensure no water was present).
    Good luck!
    Question - Influence of mounted sample height on SEM images?
    Answer
    As Dr. Dusevich said, just use Z axis movement and adjust the same WD for all samples. Be careful with the movement - samples with different height on the stage is the most common cause of mechanical damages: when one adjusts WD for the lowest sample, the highest can strike detectors and other interior parts of the SEM. It can be very expensive.
    Good luck!
    Question - Why does RBC crenate after attaching to glass surface?
    Answer
    High ion strength induces crenation. Low pH can give the same effect. As Dr. Ho Lee said, it can be just an effect of drying - decreasing of volume with increasing of ion concentration.
    We have used poly-l-lysine slides from Thermo and just conventional PBS (pH 7.2 - 7.3) for the same AFM experiments. All was Ok.
    Good luck!
    Question - How to extract the size from SEM image using the profile plot?
    Answer
    Just use any image measurement software and put the marks visually :-)
    You won't lose anything, because a SEM is not a measuring apparatus and the systematic error (defocus, calibration, aberrations, etc.), definitely is more than a few pixels...
    Good luck!
    Question - Does the EDX (EDS) element mapping of biological samples show protein-bound metal ions or mobile metal ions?
    Answer
    @ Zihui Wang
    Nevertheless, EDX just cannot help in this case. Sad but true. Just fundamental limitations.
    Sometimes people make EDX mapping and interpret it too optimistic. The difference between "elements distribution in the cell" and noise/artifacts is very tiny... ;-)
    In my opinion, scanning electrochemical microscopy and nanocapillary techniques are more suitable in this case.
    Good luck!
    Question - Does the EDX (EDS) element mapping of biological samples show protein-bound metal ions or mobile metal ions?
    Answer
    In general, it is a wrong way for soft biological samples. The precision of the method is not enough for soft tissues. It is acceptable (with accurate operation and using standards) for hard tissues - bones and teeth, but not for muscles, brain, liver, etc.
    Question - How to detach titania from titanium and how to perform hydroxylation and silanization of titania?
    Answer
    What about electrochemical dissolution of titanium?
    Theoretically, it can help, but most likely, the layer of TiO2 just doesn't have enough mechanical strength and will be destroyed, as Dr. Verlotski said.
    You can attach the oxide layer to some substrate surface and try to electrochemically dissolve the foil, but the success of such treatment looks not very likely.
    Good luck!
    Question - How do I take FESESM images of nanotubes at cross section of my sample?
    Answer
    FIB-SEM technique can help.
    Good luck!
    Question - Surface modification of pure Si nanoparticles?
    Answer
    An old good article about parameters of APTES deposition:
    From my experience, the best way is to use just fresh (it is important) 1% APTES water solution.
    Question - Surface modification of pure Si nanoparticles?
    Answer
    I have meant a thin silica layer which usually exists on the silicon surface. Sometimes it is enough for APTES functionalization without any additional preparations.
    From the fundamental point of view, obviously, pure Si surface doesn't have Si-OH groups, as Dr. Nematollahzadeh said. But it is a well-known fact in surface chemistry, that ideal pure surfaces just do not exist :)
    Question - Surface modification of pure Si nanoparticles?
    Answer
    APTES works for pure silicon too. In atomic force spectroscopy of biomolecules it is used for attachment of the molecules to silicon AFM cantilevers. Toluene, evaporation in a vacuum chamber or even fresh water solution of APTES (about 1%) is a conventional way. A typical protocol of silicon AFM cantilever functionalization:
    • 10 min in 1% APTES solution
    • rinse with deionized water
    • 10 min in 1% glutaraldehyde solution
    • rinse with deionized water
    • 10 min in protein (about 0.1 mg/ml) solution
    • rinse with a buffer
    It should work for silicon particles too.
    Good luck!
    Question - How to obtain more quantity of Silver Nanoparticles? How much quantity of AgNP is required for Electron Microscopy?
    Answer
    Just concentrate it by centrifugation. For electron microscopy (TEM) you need just a small droplet (5 or 10 microliter per one grid) with concentration about 1 mg/ml.
    Good luck!
    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 cement»). The protection of such implants by antibiotic impregnation is subjected to multiple criticisms; therefore, as an alternative to antibiotics, lytic bacteriophages with a number of unique advantages can be used - however, no experimental studies have been published on the possibility of impregnating bacteriophages into polymethyl methacrylate and their antibacterial activity assessment under such conditions. Aims: To evaluate the possibility of physical placement of bacteriophages in polymethylmethacrylate and to characterize the lytic antibacterial effect of two different strains of bacteriophages when impregnated into polymer carrier ex tempore during the polymerization process in in vitro model. Materials and methods: First stage - Atomic force microscopy (AFM) of polymethyl methacrylate samples for medical purposes was used to determine the presence and size of caverns in polymethyl methacrylate after completion of its polymerization at various reaction temperatures (+6...+25°C and +18...+50°C). The second stage was performed in vitro and included an impregnation of two different bacteriophage strains (phage ph20 active against S. aureus and ph57 active against P. aeruginosa) into polymethyl methacrylate during the polymerization process, followed by determination of their antibacterial activity. Results: ACM showed the possibility of bacteriophages placement in the cavities of polymethyl methacrylate - the median of the section and the depth of cavities on the outer surface of the polymer sample polymerized at +18...+50°C were 100.0 and 40.0 nm, respectively, and on the surface of the transverse cleavage of the sample - 120.0 and 100.0 nm, respectively, which statistically did not differ from the geometric dimensions of the caverns of the sample polymerized at a temperature of +6...+25°C. The study of antibacterial activity showed that the ph20 bacteriophage impregnated in polymethyl methacrylate at +6...+25°C lost its effective titer within the first six days after the start of the experiment, while the phage ph57 retained an effective titer for at least 13 days. Conclusion: the study confirmed the possibility of bacteriophages impregnation into medical grade polymethyl methacrylate, maintaining the effective titer of the bacteriophage during phage emission into the external environment, which opens the way for the possible application of this method of bacteriophage delivery in clinical practice. It is also assumed that certain bacteriophages are susceptible to aggressive influences from the chemical components of «bone cement» and/or polymerization reaction products which requires strict selection of bacteriophage strains that could be suitable for this method of delivery.
    Question - Why use diffraction mode with an amorphous sample?
    Answer
    An "exotic" application of diffraction mode is modification of beam-sensitive samples (a surrogate of FIB :)), but it is used extremely rarely...
    It would be very interesting to know the answer.
    Question - What's the best fixation method when preparing Fusarium spp. for SEM?
    Answer
    Most likely, these objects don't need any specific preparation for SEM: just make a dry monolayer on a conductive substrate and coat with gold (about 5 nm) using a conventional sputter.
    Good luck!
    Question - Why does glutaraldehyde cause chitosan/pva nanofibers to increase in diameter when imaged with SEM?
    Answer
    Most likely, there is just aggregation of the fibers - they are "glued" together with GA. Could you show a picture?
    Question - I'm looking for a postdoctoral position in microscopy and physics of microorganisms
    Answer
    Dear Foroogh,
    Thank you. I don't work with viruses now, but I use advanced microscopy and I'm very glad :)
    Question - Why use diffraction mode with an amorphous sample?
    Answer
    In addition, diffraction mode can be used in TEM adjustment (center apertures).
    Question - How can I prepare sample for SEM analysis to get accurate result??
    Answer
    Just drop a droplet (concentration about 1 mg/ml) to any conductive substrate (flat clean stub surface is Ok) and incubate about 10 min, then dry it off with a jet of pressured air or nitrogen and coat with carbon or gold (5 nm).
    I used a conventional TEM with negative staining (1% UA), it works very well for such objects.
    Good luck!
    Question - Negative stain of memrane protein??
    Answer
    Hi Haaris,
    Try to decrease the concentration.
    Good luck!
    Question - Hi, can anyone explain to me how I can identify the pixel intensity of each element from a gray SEM image?
    Answer
    Do you have BSE images? If you do, it is possible to just estimate of heterogeneity of the surface composition - it looks like spots. It is just a rough qualitative estimation, not analysis. It is fundamentally impossible to produce "a quantitative elements mapping" with any processing of images.
    If you want to have elements mapping, you have to do new SEM visualization of the samples in EDX-mapping mode.
    Good luck!
    Question - Hi, can anyone explain to me how I can identify the pixel intensity of each element from a gray SEM image?
    Answer
    Hi Elly,
    Mapping is a separate mode of analysis: EDX signal is collecting from a "grid" of points (usually less than full amount of pixels) on the scan. Then it is possible to mark each element by color, e.g. Fe - green, O - red, etc. There will be a SEM picture with a bunch of colored dots.
    If you have just a scan with a table of composition, you cannot transform it to an elements map. The table consists only sum composition for the scan area.
    Sometimes it is possible to speculate about elements distribution for BSE images (atomic weight), but it is just estimation and, obviously, it isn't EDX.
    Good luck!
    Question - How to avoid tissue falling off glass slide during AFM measurement?
    Answer
    Poly-L-lysine coated slides (Thermo, etc.) for use in immunohistology can help in this case.
    As Dr. Rebis said, it is necessary to be very careful when talk about "AFM measurement", because there are a lot of artifacts and, honestly speaking, it is more correct to call it "estimation" than "measurement".
    Good luck!
    Question - I'd like to know how could we measure the displacement of atoms in metals and ceramics during displacive transformation?
    Answer
    It is possible to use HR-TEM with a special holder for in situ microscopy:
    Deleted research item The research item mentioned here has been deleted
    Good luck!
    Question - There are some abnormal particles, on the SEM cross section images of NF membranes. What are these?Did any one see like this?
    Answer
    What a tremendous analogy - smallpox! :-)
    I think, there are just some structural elements of the material (like foam plastic balls). Usually such structures can be removed by a jet of compressed air.
    Good luck!
    Question - How the nano-materials affect the the health of humans in near future?
    Answer
    Who knows... There were a lot of tragic things in the history: radioactivity, cancerogenic materials, teratogenic drugs, etc. Sometimes new substances are more dangerous than it looks from first glance.
    But all is not so bad. Just google "nanotoxicology" - there are a lot of researches, reviews, even state regulations in this area.
    Question - Does TEM technique give only bulk composition in a nanoparticle?
    Answer
    Dear Irfan, you can answer yourself for the question about SEM EDS. Just simulate electron trajectory in solid and compare with diameter of your particles with this software:
    With SEM EDS you can only estimate the composition for bulk specimen (a lot of individual particles) and estimate their structure from the geometrical point of view (obviously, if the particles have similar shape and diameter). Such estimation will be extremely rough.
    Question - Does TEM technique give only bulk composition in a nanoparticle?
    Answer
    For nanoparticles (diameter < 100 nm) EDS can give only average composition for system "particle's surface, core, substrate (film, etc.)".
    Particles structure and composition (indirectly) can be resolved by HR-TEM and crystallographic methods.
    Good luck!
    Question - How we make sure nanoparticles are sterile?
    Answer
    It would be more correct to call these particles just "submicron", because "nano" usually means "less than 100 nm" :-)
    The method of sterilization is dependent on resistance of the particles: thermal, UV, high power sonication, ionizing radiation... In general, physical methods are more preferable, because antimicrobial chemicals can influence the cells.
    Good luck!
    Question - Can we take TEM image of the sample that is inside 2 mm Diameter and 0.01 mm thick capillaries? if not is there any way ?
    Answer
    It is necessary to remove the sample from the capillary. Then you can dissolve it in a buffer solution and drop to a TEM grid for negative staining and/or metal evaporation shadowing. Another way is an AFM. You can deposit the sample to a smooth surface (mica, silicon, graphite, etc.) and scan it with an AFM. Just google "DNA TEM" and "DNA AFM" - there are a lot of articles with detailed protocols of preparation. The best possible way is Cryo-TEM, but there are not so many places in the world where it can be conducted.
    In addition, if the capillary is transparent, it is possible to use microspectroscopy technique for estimation of the conformation.
    Good luck!
    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 controlled properties is a challenging task. This paper describes effect of catalyst deposition technique on the properties of hierarchically structured carbon-carbon nanocomposites. The synthesized samples were analyzed by XRD, SEM, TEM and BET. It was shown how the way of catalyst deposition affects both the yield and structure of the carbon nanofibers grown on the microfiber surface.
    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 effective for catalytic chemical vapor deposition of CF 2 Cl 2 with formation of bimodal carbon structures. It was demonstrated that interaction of nichrome with CF 2 Cl 2 /H 2 reaction mixture at 600 °C leads to its rapid disintegration caused by carbon erosion to form disperse active Ni-particles catalyzing the growth of carbon filaments. The resulted filamentous carbon material is characterized with high textural parameters.
    Project - Direct detection of bacteriophage (Myoviridae) tail contraction
    Update
    This project isn't active now.
    Question - What would you like to be?
    Answer
    A pilot :)
    Question - How can we differentiate the original size of core nanoparticles and the thickness of capping material through AFM or SEM image?
    Answer
    Asim, could you upload some TEM pictures?
    Just google "core-shell nanoparticles TEM". There are a lot of self-evident pictures.
    Good luck!
    Question - How can we differentiate the original size of core nanoparticles and the thickness of capping material through AFM or SEM image?
    Answer
    AFM cannot solve this problem. Theoretically, it is possible to use a SEM in BSD mode, but the result would be not evident. TEM is more suitable in this case.
    Good luck!
    Question - To explain the SEM image of SnS nanofilm?
    Answer
    Obviously, the picture contains just two mirror scans of the same area. Just check the parameters of your software. It is possible to estimate the grain size.
    Question - How do I prepare a diesel/fuel liquid sample for TEM viewing, I want to view suspended solids in the fuel?
    Answer
    Dear Dr. Kumar,
    A conventional diesel fuel contains hydrocarbons with carbon chain lengths between 10 and 30. The heaviest hydrocarbons can form an oil looking film on the grid's surface, which blurs the pictures. In additional, a TEM can be contaminated with hydrocarbons.
    I had a little experience in electron microscopy of used motor oil and strictly recommend to replace the heavy hydrocarbons.
    Best regards,
    Denis
    Question - How do I prepare a diesel/fuel liquid sample for TEM viewing, I want to view suspended solids in the fuel?
    Answer
    In additional, centrifugation or filtration provide a possibility to visualize the particles if their concentration is not so high.
    Question - How do I prepare a diesel/fuel liquid sample for TEM viewing, I want to view suspended solids in the fuel?
    Answer
    Indeed, a conventional way with dropping is not looking very well. I think, there are at least three other ways:
    • Centrifugation. Just deposit the particles on the bottom of a tube and carefully replace the diesel with ethanol, shake it and drop or spray to grids;
    • Filtration. Pump the diesel through a paper filter, dry it with ethanol, embed in epoxy resin and prepare thin sections with an ultratome. If the particles are hard (carbides, etc.) they can destroy the edge of a diamond knife. Use a glass knife;
    • Direct spraying of the diesel. It has high superficial tension and it is not so simple to make fine aerosol (few micrometers particles), but theoretically it is possible by using a very powerful sonic dispenser.
    Obviously, the first way is the simplest.
    Good luck!
    Question - How to discuss apparent conc.,intensity correction, standard level and factory standard for SEM-EDX?
    Answer
    You are welcome :)
    Question - How to discuss apparent conc.,intensity correction, standard level and factory standard for SEM-EDX?
    Answer
    It is very difficult to estimate the systematic error of the method. This task is more difficult than conventional statistical error calculations. Especially, for biological objects. Just for a tough illustration, I have painted this picture.
    Just use more suitable methods for analysis of chemical composition: chromatography, mass spectroscopy, methods of classical analytical chemistry, etc.
    Good luck!
    Question - How to discuss apparent conc.,intensity correction, standard level and factory standard for SEM-EDX?
    Answer
    Hi Nazia,
    In general, EDS is just a method of COARSE ESTIMATION. There are at least three fundamental limitations:
    1. Depth. Only few micrometer-thick layer is examined. Obviously, there are a lot of artifacts - oxides (for inorganic samples), contamination, heterogeneity (for biological samples), etc.
    2. Spatial resolution. The "X-rays source" on the surface is more than the beam spot. Typically, it is few cubic micrometers (well known bulb looking pictures from student books).
    3. Concentration. The method is not so sensitive in comparison with quantitative analytical methods.
    These limitation must be kept in mind. Especially, when you work with biological samples.
    Good luck!
    Question - I'm looking for a postdoctoral position in microscopy and physics of microorganisms
    Answer
    I have found the position. Thank you all!
    Project - WSVirology
    Update
    Dear colleagues, I'm glad to show you an example of virus particles manipulation.
    Dielectrophoresis of vaccinia virions.
    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 a conductive AFM tip or other sharp electrode; - Study of dielectric properties of virions (parameters of dielectrophoresis contain this information); - Concentration of virions; - Sorting of particles.
    Project - Dielectrophoresis as a tool for virus particles manipulation
    Update
    An example of DEP movement of virus particles.
    Project - WSVirology
    Update
    Dear colleagues,
    I defended my Ph.D. thesis ("Atomic force spectroscopy of single virus particles") in October 2016 (Moscow State University) and now I am looking for a postdoctoral position in microscopy (AFM, TEM, SEM) and biophysics of microorganisms (especially, viruses, I like them :)). My CV is attached.
    If there is an open position in your lab, please, write me.
    Best regards,
    Denis
    Question
    Question - Ionic liquid for Scanning Electron Microscopy samples preparation
    Answer
    There are some IL-based techniques of sample preparation for EM. But it is "exotic" and is used not so often. 
    Monica, why do you want to use such technique and what samples do you have?
    Question - What is the suitable sonication power to exfoliate expanded graphite?
    Answer
    Don't worry. Just use any commercial probe-sonicator. Sometimes, it is enough to put a tube to a sonic bath, but a probe-sonicator is more powerful and suitable.
    An important parameter is specific power - Watt per volume. It must be as high as possible. I think, it is almost impossible to destroy graphite sheets with too high power of the sonicator.
    Good luck! 
    Question - Electron beam evaporation of Graphite sample for carbon film coating is possible?
    Answer
    You are welcome)
    Question - What do the TEM images predict?
    Answer
    Sometimes particles agregate on the film surface. Try to sonicate the suspension before TEM grids preparation or use sonic spraying technique of particles deposition.
    Good luck!
    Question - What can be a good silane coupling agent to modify surface of silica nano particles?
    Question - How to get rid of crystal formation when imaging extracellular vesicles?
    Answer
    Usually, such structures appear when the concentration is too high. 
    Try to this simple protocol:
    1. Dilut the suspension 1:10 or 1:100 (try few concentrations) with a buffer (PBS or another).
    2. Drop 10 µl on Parafilm and put a grid (face side) on the droplet for 30 sec. Then dry it out with a piece of filter paper.
    3. Drop 10 µl of uranyl acetate water solution (1%) on Parafilm and put a grid (face side) on the droplet for 10 sec. Then dry it out with a piece of filter paper.
    Hope, it will be Ok.
    Good luck!
    Question - Electron beam evaporation of Graphite sample for carbon film coating is possible?
    Answer
    I'm not an expert in the carbon coating, but I weekly use thermal evaporation technique for TEM grids preparation (Jeol JEE 420 evaporator). The heating time is about 10-20 sec (few times). This old (more than 50 years) technique is well-known in electron microscopy.
    There are two carbon electrodes in the vacuum chamber. One is sharped to cone and the tip area has very high (white light) temperature when the currernt is going through the electrodes.
    This system is cheap, robust and works well. What advantages could have a high power e-beam system?
    E-beam evaporation technique is good for metal coating, because it provides very fine grain size. But what reason can be for a conventional carbon?  
    Question - What are the various methods to prepare the nanoparticles for TEM test?
    Answer
    Don't worry, all is Ok :)
    For the silica particles you can use a simple preparation technique:
    1. Prepare a water suspension with concentration about 1 mg/ml. Shake it with Vortex or sonicate.
    2. Drop a droplet (10 μ) on Parafilm surface and put a conventional TEM grid (e.g. Formvar film coated) at the droplet for 30 sec. Then just dry it out with a piece of filter paper and examine by TEM.
    Good luck!   
    Question - What are the various methods to prepare the nanoparticles for TEM test?
    Answer
    Dear Manaf,
    There are a lot of good books and articles about TEM and sample preparation. Just google it. The effect of the solvent, obviously, is depend on the chemical nature of the particles and film on the TEM grid. For example, some solvents destroy Formvar film on the grid.
    The preparation technique is depend on the properties of the sample too. There are few basic principles:
    • Just incubate the grid (carbon or Formvar film covered) on a drop of solution and dry it out (usually, with a piece of filter paper);
    • Sonic spraying technique;
    • Negative staining for soft particles like viruses and VLP; 
    • Ultrathin slices technique for bulk specimens.
    They all are described in literature. 
    Good luck!
    Question - What are the various methods to prepare the nanoparticles for TEM test?
    Answer
    Has Google banned you? :-)
    The question is too broad. Probably, you have any concrete questions: preparation of TEM-grids, concentration of particles, sonic spraying trchnique, etc.
    I would be glad to answer. 
    Good luck!
    Question - Which is the best method to study the thickness and roughness of my FET device layers?
    Answer
    The answer is depend on the size of your objects and type of substrate.
    In general, AFM and SEM are more suitable for such tasks. A sample for TEM must be such thin as possible (usually, about 50 nm or less), it isn't so simple to prepare it from a bulk specimen. 
    Good luck!  
    Question - Electron beam evaporation of Graphite sample for carbon film coating is possible?
    Answer
    Technically, it is possible, but for what? What advantages do you expect in comparison with the well-known thermal evaporation technique?
    Question - How can i measure the temperature of electrodes in Thermal Evaporation systems
    Answer
    There are few ways:
    1. Theoretical estimation from the current and the properties of the boat. Obviously, the precision is too low. 
    2. Use a high temperature thermocouple.
    3. Use a pyrometer.
    4. Calibrate the system with some pure compounds with well-known melting temperature and extrapolate the points.
    Good luck!  
    Question - How to save AFM true image?
    Answer
    There is just a tilt of substrate on the picture. I don't know Park software, but usually AFM soft has options "fit lines", "subtract plane", ect. Use such tools, then save the picture as an image file (bmp, tiff, etc.). Probably, it names "export as image".   
    Good luck!
    Question - Does anyone know how to clean a functionalized AFM cantilever after being used?
    Answer
    I have never seen a thermal shock broken cantilever. It looks strange, because the conventional thicknes is about 1÷2 µm and the thermal gradient is neglectable. For which cantilevers have you seen such effect? Sometimes cantilevers have been broken with hydrodinamic and meniscus forces in liquid with the intensive cleaning.
     Usually, Piranha don't destroy colloidal probes, the temperature is less than 100 C and the medium is not so agressive for conventional glues (epoxy epon). Nevertheless, it is possible to destroy it. It depends on the glue and conditions. In this case, one can use a mechanical cleaning technique:
    The mirror side of the cantilever (usually, thin gold layer) can be detached with a chemical cleaning. It can be restored with a simple sputtering with a conventional sputter for SEM sample preparation.
    Visualization of cantilevers is very important, because there can be anything. An example of "exotic"…
    Question - Does anybody know if is it possible to measure humidity in extracellular space in human body, if yes how are the values of humidity?
    Answer
    I think, the term "humidity" is incorrect in this case. Extracellular space is filled with a liquid and contains ions, a lot of free biomolecules, etc.
    It looks little strange to talk about humidity of the liquid :)
    But it is possible and necessary to care about pH, ion strength, etc.
    Question - How to get rid of crystal formation when imaging extracellular vesicles?
    Answer
    Hello Sören,
    What sample preparation technique do you use? Negative staining?
    Usually, crystals are not a problem. Try to put the prepared grid (face side) on a drop of water for 10-20 sec, then dry it out with a piece of filter paper.
    Could you upload an example of picture?
    Good luck!
    Question - Newcastle disease virus contamination: how do we remove it?
    Answer
    Dear Umar, you can use some antibiotics too. Sometimes it is possible to use them at concentration lethal for microbes, but almost nontoxic for the infecting cells.
    Question - Source of micro silicone tubing with wall thickness ~0.05mm?
    Answer
    Theoretically, it is possible to protect the interior chanel and etch the walls, e.g. by concentrated KOH or HF + HNO3. I am not sure about the tubing, but I have used such technique for AFM cantilevers (silicon) modification.
    Good luck! 
    Question - Is it possible to produce high chitosan nanoparticles concentrations?
    Answer
    It is possible to use membrane centrifugal concentrators - "Centricon" and others.
    Question - What is the sample prepration steps for Al203 Nano particles to see SEM mrphology.
    Answer
    The magnification is too low and there is a self-evident charging on the picture. Al2O3 is an insulator and it is necessary to use some special modes (low tension, VP, etc.) or coat it with a thin layer of gold or another metal. The simplest way is a conventional 5 nm gold coating by a sputter system.
    Good luck!
    Question - Newcastle disease virus contamination: how do we remove it?
    Answer
    Just use a conventional bacterial filter. The pore size is about 220 nm. It is an usual practice in virology. The other way is differential centrifugation. 
    The contamination could be not from the virus suspension. It is possible to contaminate the cells just with manipulations. Clean the laminar box, it can be contaminated too. In additional, you can check the virus suspension with optical or electron microscopy. Sometimes we use TEM with negative staining for virus suspensions check.   
    Good luck!
    Question - Does anyone know how to clean a functionalized AFM cantilever after being used?
    Answer
    Piranha solution is suitable. We use H2SO4 (concentrated) and H2O2 (30% in water) in rate 3:1. Mix the chemicals and immediately dip the cantilever to the solution for 10 min.
    Be careful. The reaction is exothermic and the solution will be hot.
    It would be very good to visualize the cantilevers after the cleaning.
    Good luck!
    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. Loading of M in the samples was varied in a range of 1–5 at.%. Pure nickel was used a reference. The kinetics of carbon deposition was investigated using flow reactor equipped with McBain balances. The samples of carbon product were characterized by nitrogen adsorption, scanning and transmission electron microscopies. The hydrogen addition into reaction mixture was shown to have opposite effect on both catalytic behavior and carbon yield depending on catalyst’s nature. Segmented structure of carbon filaments formed specifies its developed surface area. Both bulk chlorination of nickel particles and its blockage by dense carbon deposits in the case of mechanochemically prepared samples were suggested to be responsible for rapid deactivation of the catalyst.
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