DOCSLIB.ORG

CHARACTERIZING and MANIPULATING BIOLOGICAL INTERACTIONS of VIRUSES by NEETU MEHEK GULATI Submitted in Partial Fulfillment Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
CHARACTERIZING and MANIPULATING BIOLOGICAL INTERACTIONS of VIRUSES by NEETU MEHEK GULATI Submitted in Partial Fulfillment Of CHARACTERIZING AND MANIPULATING BIOLOGICAL INTERACTIONS OF VIRUSES by NEETU MEHEK GULATI Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Dissertation Advisors: Dr. Phoebe L. Stewart and Dr. Nicole F. Steinmetz Department of Pharmacology CASE WESTERN RESERVE UNIVERSITY January 2018 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of Neetu Mehek Gulati candidate for the Doctor of Philosophy degree*. (signed) Vera Moiseenkova-Bell (chair of the committee) Phoebe L. Stewart Nicole F. Steinmetz Derek J. Taylor Jun Qin Vivien C. Yee (date) September 8, 2017 *We also certify that written approval has been obtained for any proprietary material contained therein. Table of Contents List of Tables ..................................................................................................... vii List of Figures .................................................................................................. viii Acknowledgements ........................................................................................... xi List of Abbreviations ....................................................................................... xiv Abstract ............................................................................................................ xxi Chapter 1: Introduction ...................................................................................... 1 1.1 Viruses – for good and bad ................................................................. 1 1.2 Bioinspired shielding strategies for nanotechnology applications . 2 1.2.1 Abstract ....................................................................................... 2 1.2.2 Introduction .................................................................................. 3 1.2.3 PEG and other synthetic polymeric shielding strategies .............. 4 1.2.4 Bio-inspired shielding strategies .................................................. 9 1.2.5 Beyond shielding – Immune editing ........................................... 21 1.2.6 Conclusions ............................................................................... 22 1.3 Tobacco mosaic virus as a nanotechnology platform .................... 25 1.3.1 Tobacco mosaic virus infection and production ......................... 25 1.3.2 Tobacco mosaic virus structure ................................................. 25 1.3.3 Tobacco mosaic virus nanoparticles .......................................... 28 1.4 Human papillomavirus infection and neutralization ........................ 28 1.4.1 Human papillomavirus and cancer ............................................ 28 1.4.2 Human papillomavirus vaccines ................................................ 29 i 1.4.3 Human papillomavirus structure ................................................ 30 1.4.4 Human papillomavirus cell entry mechanism and infection pathway .............................................................................................. 35 1.4.5 Human papillomavirus and human alpha-defensin 5 ................. 37 1.5 Aims of dissertation ........................................................................... 40 Chapter 2: Structural characterization of SA-TMV ........................................ 41 2.1 Abstract ............................................................................................... 41 2.2 Introduction ......................................................................................... 42 2.3 Materials and Methods ....................................................................... 45 2.3.1 Virus propagation and purification ............................................. 45 2.3.2 TMV sCy5 labeling .................................................................... 45 2.3.3 TMV conjugation ........................................................................ 46 2.3.4 SDS-PAGE analysis .................................................................. 47 2.3.5 Western blot analysis ................................................................ 47 2.3.6 Immuno-dot blots ....................................................................... 48 2.3.7 Negative stain transmission electron microscopy ...................... 48 2.3.8 Cryo-electron microscopy and tomography ............................... 48 2.3.9 Subtomogram averaging of SA .................................................. 49 2.3.10 Subtomogram averaging of SA-TMV segment ........................ 50 2.3.11 Analysis of volume coverage ................................................... 50 2.3.12 Analysis of surface coverage ................................................... 51 2.4 Results and Discussion ..................................................................... 51 2.4.1 Particle preparation ................................................................... 51 ii 2.4.2 Imaging and processing of naked and SA-coated particles ....... 57 2.4.3 Quantification of TMV coverage ................................................ 66 2.5 Conclusions ........................................................................................ 69 2.6 Acknowledgements ............................................................................ 70 2.7 Supplementary information ............................................................... 71 Chapter 3: Immune recognition of SA-TMV .................................................... 72 3.1 Abstract ............................................................................................... 72 3.2 Introduction ......................................................................................... 73 3.3 Materials and Methods ....................................................................... 76 3.3.1 Virus propagation and purification ............................................. 76 3.3.2 TMV sCy5 labeling .................................................................... 77 3.3.3 TMV external conjugation .......................................................... 77 3.3.4 SDS-PAGE analysis .................................................................. 78 3.3.5 Western blot analysis ................................................................ 79 3.3.6 Negative stain transmission electron microscopy ...................... 79 3.3.7 Dot blots .................................................................................... 80 3.3.8 In vivo studies and ELISA assays .............................................. 80 3.3.9 Confocal microscopy ................................................................. 81 3.3.10 Lysosomal extraction experiments ........................................... 82 3.4 Results and Discussion ..................................................................... 83 3.4.1 Synthesis and characterization of SA-TMV constructs .............. 83 3.4.2 Effects of SA coverage and linker length on shielding TMV ....... 92 iii 3.4.3 Antibody response to multiple administrations of SA-TMV constructs ........................................................................................... 97 3.4.4 Trafficking of SA-TMV nanoparticles upon cell uptake ............ 103 3.4.5 SA-TMV cleavage and degradation in the lysosome ............... 109 3.5 Conclusions ...................................................................................... 112 3.6 Acknowledgements .......................................................................... 113 Chapter 4: cryoEM of HPV PsV with HD5 ..................................................... 114 4.1 Introduction ....................................................................................... 114 4.2 Materials and Methods ..................................................................... 119 4.2.1 Protein disorder prediction and modeling ................................. 119 4.2.2 HPV16 pseudovirus production ................................................119 4.2.3 CryoEM grid preparation ..........................................................119 4.2.4 CryoEM imaging and data collection ....................................... 120 4.2.5 Particle picking and CTF correction ......................................... 120 4.2.6 3D structure determination and filtering ................................... 120 4.3 Results and Discussion ................................................................... 121 4.3.1 Sub-nanometer resolution structures of HPV16 and HPV16+HD5 by RELION ....................................................................................... 121 4.3.2 Gaussian filtered HPV16 and HPV16+HD5 maps reveal additional density in the HD5 structure ............................................. 126 4.4 Conclusions ...................................................................................... 135 Chapter 5: Conclusions and Future Directions ........................................... 137 5.1 Scope of work ................................................................................... 137 iv 5.2 Viruses in nanomedicine: evading immune recognition of TMV nanoparticles by stealth-camouflage with SA ..................................... 138 5.2.1 Tobacco mosaic virus as a nanocarrier for drug delivery applications ...................................................................................... 140 5.2.2 Novel SA self-camouflage platform .......................................... 143 5.2.3 Considerations beyond SA-TMV ............................................. 149 5.3. Viruses in human disease:
Load more

Recommended publications
  • Negative Stain Grid Preparation
    Negative Stain Grid Preparation Generic Protocol for Single Particle – Page 2 Example For Bacteria – Page 5 Example For Viruses – Page 6 Example For Purified Bacterial Flagella – Page 7 Drafted by E. Montemayor, 6/15/2020. Revisions by EJM, JCS, ERW, 1/6/2021 1 Generic protocol for negative stain grid preparation Think of this as a “try this first” pipeline for new samples. Sample concentration and type of stain tend to be the most important variables, then additives like detergents or crosslinking should be tried next. Overview at a glance: Step 1: Prepare serial four-fold dilutions of your sample, covering at least two order of magnitude in sample concentration. Typical ceiling for sample concentration is ~ 1 mg/mL. Step 2: Prepare negative stain solution. Uranyl stains are most popular as a first pass, especially for single particle work. Consider filtering (0.1 µm or 0.2 µm syringe filters) and centrifuging (5-15 min, 15,000 rpm, and at room temperature (RT)) your stain to reduce crystals and debris. Step 3: Glow discharge grids. Standard thickness carbon on a 200 copper mesh is a popular support. Step 4: Place grid in self closing tweezers. Use a microscope or magnifying lens to help you touch only the edge of the grid with the tweezers. Step 5: Set up 2x 20 µL drops of buffer and 3x 20 µL drops of stain on a strip of parafilm. Apply 3 µL of sample to carbon side of grid and incubate for 1 minute. Step 6: Side blot to remove sample but do not let grid dry out.
    [Show full text]
  • Electron Microscopy of Negatively Stained and Unstained Fibrinogen (Scanning Transmission Electron Microscopy) LEONARD F
    Proc. Natl. Acad. Sci. USA Vol. 77, No. 6, pp. 3139-3143, June 1980 Biochemistry Electron microscopy of negatively stained and unstained fibrinogen (scanning transmission electron microscopy) LEONARD F. ESTIS* AND RUDY H. HASCHEMEYER Department of Biochemistry, Cornell University Medical College, 1300 York Avenue, New York, New York 10021 Communicated by Alton Meister, December 26,1979 ABSTRACT Electron microscopic images of negatively are always met: (i) The great majority of images of "apparent stained fibrinogen are predominantly asymmetric rods 450 A particles" in any field are of fibrinogen molecules. (Ui) The in length and about 60 A in width. The molecules appear to have considerable flexibility, and mass distribution along the major number of identifiable fibrinogen molecules is defined by fi- axis is not uniquely distinguished despite apparent beading in brinogen concentration and application time and not by the some particles. Scanning transmission electron microscopy of buffer, pH, or staining conditions. (Mii) Large-field views of unstained fibrinogen again demonstrates that a majority of fibrinogen contain predominantly well-separated molecules molecules are rodlike. The results differ from those obtained with clearly defined morphology and dimensions. by negative staining in that a substantial fraction of images are Conditions trinodular with striking resemblance to those obtained by C. required to achieve these goals are primarily E. Hall and H. S. Slayter IJ Biophys. Bioehem. Cytol. (1959) 5, related to attachment of fibrinogen to the substrate film. Once 11-161 using the mica replictecaique. The above results were this problem was solved, images of the unstained molecule were obtained on glow-discharged carbon substrate films by a simple also obtained by high-resolution scanning transmission electron low-concentration, lon&-attachment-time modification of microscopy (STEM).
    [Show full text]
  • Immunoelectron Microscopy for Virus Identification
    Chapter 7 ROBERT G. MILNE Immunoelectron Microscopy for Virus Identification 1 Introduction I am going to discuss immunonegative staining-the immunoelectron microscopy (!EM) of virus (or other pathogen-related) particles in suspension-with only short excursions into the topic of immune reactions on or in thin sections, as these are considered elsewhere in this book. As the field has been thoroughly reviewed, what I shall say will be more an informal commentary than an exhaustive survey, and I shall not necessarily follow each statement by a precise citation, or attempt to mention all the interesting papers. In places I shall use the term "grid" to mean support film. As all those know, who have worked with viruses both in negative stain and in thin sections, resolution is much higher in negative stain, and intensity and fidelity of immunolabeling is also greater; you would never work with sections again if they did not furnish positional information that is lost when you make an extract. This loss means that in negative stain you can only work with structures that can be recognizcd out of context-virus particles, subviral components, or certain virus­ induced inclusions; perhaps also mycoplasmas or their fragments. However, sometimes the same structures can be recognized both in vitro and in situ; and with the advantage of immune labeling we can, with luck, identify an antigen in both contexts. In that case we can obtain both positional or contextual information as well as high-resolution details of structure or antigen location. An interesting technique that I will not discuss, but which may prove a valuable compromise, is immunonegative staining of thin cryosections.
    [Show full text]
  • Electron Microscopy of Satellite Tobacco Mosaic Virus Crystals: Metal-Coated, Negatively Stained and Stereo Pairs
    © Japanese Society of Electron Microscopy Journal of Electron Microscopy (49)3: 509-514 (2000) Full-length paper Electron microscopy of satellite tobacco mosaic virus crystals: metal-coated, negatively stained and stereo pairs Paul R. Desjardins1*, Nenad Ban2-3, Deborah M. Mathews1, John T. Kitasako1-4, J. Allan Dodds1, and Alexander McPherson2-5 'Department of Plant Pathology and 2Department of Biochemistry, University of California, Riverside, CA 92521, USA *To whom correspondence should be addressed 'Present address: Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA 4Present address: Department of Neuroscience, University of California, Riverside, CA 92521, USA 'Present address: Department of Molecular Biology and Biochemistry, 3205 BS II, University of California, Irvine, CA 92697-3900, USA Abstract Highly purified virions of satellite tobacco mosaic virus (STMV) were found to crystallize at relatively low concentrations (300-500 \ig ml~l) in pure water. Small crystals of these preparations were examined in the transmission electron microscope after either being rotary shadowcast with metal or negatively stained with 4% uranyl acetate. Stereo views were also obtained of both types of preparations. Stereo pairs of metal-coated crystals provided good three-dimensional images. When stereo pairs of negatively stained crystals were printed from second negatives, they provided striking images although the three-dimensional aspect was not so pronounced. Images of both types of preparations were compared with a computer-generated model of the virus. This model was based on data obtained in earlier X-ray diffraction crystallographic studies. Measurements of crystal axes on the EM images were somewhat lower than those of the computer model.
    [Show full text]
  • Analysis of Macromolecules by Negative Stain Tomography
    Analysis of Macromolecules by Negative Stain Tomography Andrea Fera*, Jane E. Farrington‡, Joshua Zimmerberg‡ and Thomas S. Reese* (*) Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke (‡) Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health, Bethesda, Maryland 20892, USA Abstract We report on the use of EM tomography to visualize individual proteins in negative stained samples. A negative stain for tomography must not degrade under the electron dose used to collect a set of dual axis tomographic images at the necessary magnification. This precondition was verified experimentally for a tungsten-based stain for pixel sizes as small as 0.3 nm. Results show individual molecules on the surfaces of influenza virus and in post synaptic densities. Corresponding surface renderings of proteins obtained from virtual sections by thresholding demonstrate a good fit to known structures. Negative stain tomography thus provides a way to visualizing both the conformational richness and clustering properties of some complex proteins. Negative staining has been a pivotal technique for visualizing in exquisite detail the structure of protein molecules and oligomers. The most abundant glycoprotein of the influenza virus, hemagglutinin, was observed for the first time after extraction from the virions [1]. Later, the structure of the holoenzyme, calcium calmodulin kinase II (CaMKII), a major component of synapses, was determined by imaging negative stained extracts with electron microscopy [2]. More recently there has been new evidence that this holoenzyme assumes a disk-shape in solution [3]. Current methods allow tomograms to be calculated by back projection from series of tilt images collected at high resolution by electron microscopy (EM).
    [Show full text]
  • Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy
    micromachines Communication Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy Ibolya E. Kepiro 1 , Brunello Nardone 2, Anton Page 3 and Maxim G Ryadnov 1,* 1 National Physical Laboratory, Teddington, Middlesex TW11 0LW, UK; [email protected] 2 CEM Corporation, Buckingham Industrial Park, Buckingham MK18 1WA, UK; [email protected] 3 Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; [email protected] * Correspondence: [email protected] Received: 21 January 2020; Accepted: 26 February 2020; Published: 27 February 2020 Abstract: Electron microscopy plays an important role in the analysis of functional nano-to-microstructures. Substrates and staining procedures present common sources of variation for the analysis. However, systematic investigations on the impact of these sources on data interpretation are lacking. Here we pinpoint key determinants associated with reproducibility issues in the imaging of archetypal protein assemblies, protein shells, and filaments. The effect of staining on the morphological characteristics of the assemblies was assessed to reveal differential features for anisotropic (filaments) and isotropic (shells) forms. Commercial substrates and coatings under the same staining conditions gave comparable results for the same model assembly, while highlighting intrinsic sample variations including the density and heterogenous distribution of assemblies on the substrate surface. With no aberrant or disrupted structures observed, and putative artefacts limited to substrate-associated markings, the study emphasizes that reproducible imaging must correlate with an optimal combination of substrate stability, stain homogeneity, accelerating voltage, and magnification. Keywords: protein self-assembly; protein filaments; virus-like capsids; electron microscopy; negative staining 1.
    [Show full text]
  • Replicas, Shadowing, and Negative Staining
    8 Replicas, Shadowing, and Negative Staining Contrast in transmission electron microscopic (TEM) specimens occurs when there are specimen areas that stop (scatter) electrons and also areas that let most of the electrons pass through. Thus, the image results from subtractive contrast. We impregnate tissues and sections with a variety of heavy metals to scatter electrons as discussed in Chapter 4, but we can also surround particulates with heavy metals (negative staining) or cover particulates, cells, and tissues with thin metal films that have areas of differential beam-stopping capability (replicas produced by shadowing). This chapter will discuss these two added techniques for building subtractive contrast, pointing out the commonly used techniques and a few remedies to specific problems that may be encountered. I. SHADOW CASTING Shadowing casting (shadowing) and making replicas both involve coating a specimen sur­ face with metals. A shadowed preparation is one in which metals are evaporated at an angle to the specimen so that the metal is preferentially condensed on the high points of the sample surface toward the evaporated metal source (Fig. 159). If the specimen consists of a thin layer of particu­ lates such as bacterial flagella, the specimen with its overlying shadow of metal may be viewed in toto. However, if the specimen is a relatively thick sample (e.g., a layer of mammalian cells), a conventional electron microscope beam would have difficulty penetrating both the thin film of evaporated metal and the biological material beneath. In this case, after the tissue is shadowed, all SHADOW Figure 159. Diagram of a sample of particulates (Pl.
    [Show full text]
  • Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems
    Journal of Visualized Experiments www.jove.com Video Article Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems Charlotte A. Scarff1, Martin J. G. Fuller2, Rebecca F. Thompson2, Matthew G. Iadanza1 1 Astbury Centre for Structural Molecular Biology, University of Leeds 2 Astbury Biostructure Laboratory, University of Leeds Correspondence to: Matthew G. Iadanza at [email protected] URL: https://www.jove.com/video/57199 DOI: doi:10.3791/57199 Keywords: Biochemistry, Issue 132, Electron microscopy, Negative stain, Biological TEM, Blotting, Electron microscopy grids, Carbon coating Date Published: 2/6/2018 Citation: Scarff, C.A., Fuller, M.J.G., Thompson, R.F., Iadanza, M.G. Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems. J. Vis. Exp. (132), e57199, doi:10.3791/57199 (2018). Abstract Negative stain electron microscopy (EM) allows relatively simple and quick observation of macromolecules and macromolecular complexes through the use of contrast enhancing stain reagent. Although limited in resolution to a maximum of ~18 - 20 Å, negative stain EM is useful for a variety of biological problems and also provides a rapid means of assessing samples for cryo-electron microscopy (cryo-EM). The negative stain workflow is straightforward method; the sample is adsorbed onto a substrate, then a stain is applied, blotted, and dried to produce a thin layer of electron dense stain in which the particles are embedded. Individual samples can, however, behave in markedly different ways under varying staining conditions. This has led to the development of a large variety of substrate preparation techniques, negative staining reagents, and grid washing and blotting techniques.
    [Show full text]
  • Direct and Indirect Stains Will Be Used in This Laboratory, and Are Sometimes Used in Combination
    Exercise 6-A STAINING OF MICROORGANISMS DIRECT VS INDIRECT STAINING Introduction The morphological features of individual microorganisms may be examined either by observing living, unstained materials, or by observing prepared slides containing killed organisms stained or colored with some type of dye. Observing dead, stained, microorganisms has certain advantages over observing living forms, as follows: 1. Staining increases the contrast between microorganisms (sometimes transparent) and their background, making them more readily visible. 2. Certain stains make cellular structures (internal or external) visible that otherwise cannot be seen. 3. Stained preparations are easier to observe under high magnification because dead cells do not swim, i.e., cannot exit the viewing field or focal plane. 4. The organisms present in stained preparations are dead, and if they were potentially pathogenic, are no longer capable of causing infection. When a staining procedure colors the cells present in a preparation, but leaves the background colorless (appearing as white), it is called a direct stain. If a procedure colors the background, leaving the cells colorless (white) it is called an indirect or negative stain. Both direct and indirect stains will be used in this laboratory, and are sometimes used in combination. For example, the Gram stain, acid-fast stain, and Shaeffer-Fulton endospore stain are all direct stains. The capsule stains and Dorner method endospore stain are a combination of direct and indirect stains. Stains or dyes are generally salts with one ion being colored and the other not. The colored ion is called a chromophore. If color is associated with the positive ion (cation), the stain is called a basic stain; if color is associated with the negative ion (anion), the stain is said to be acidic.
    [Show full text]
  • Negative Stain of Small Molecules and Protein Complexes Melissa Chambers Vanderbilt University, Nashville, Tennessee, United States
    2092 Microsc. Microanal. 26 (Suppl 2), 2020 doi:10.1017/S1431927620020413 © Microscopy Society of America 2020 Negative Stain of Small Molecules and Protein Complexes Melissa Chambers Vanderbilt University, Nashville, Tennessee, United States Negative stain of small molecules and protein complexes has useful applications to a range of biological studies. Negative stains are heavy metal solutions that significantly increase the contrast of the sample in the electron microscope and allow detail of the molecules to be visualized with a resolution limit of around 18Å. Samples must be biochemically pure and conformationally homogeneous, preferably involving gel filtration as the final purification step. Each continuous carbon grid requires only 2.5μl of sample at a low concentration of ~10 μg/ml. A variety of stains can be used, with uranyl formate and uranyl acetate being best suited to small complexes. Most biological buffers are well tolerated with these stains, however it is preferable to avoid glycerol, phosphate (such as PBS) and high salt concentrations. There are also a variety of methods for applying stain and sample to the grids than can have an effect on the thickness and quality of the stain. Every sample is unique, and these methods are widely adaptable. Negative stain is a relatively quick way to assess the condition of the sample and ideal for troubleshooting purification and buffer conditions before continuing on with cryo-EM work. 2D class averages from negative stain images can reveal a lot about the homogeneity, composition, and flexibility of a complex, guiding the best conditions to be used when preparing vitrified grids for cryo-EM.
    [Show full text]
  • Enhanced Imaging of Lipid Rich Nanoparticles Embedded in Methylcellulose films for Transmission Electron Microscopy Using Mixtures of Heavy Metals MARK
    Micron 99 (2017) 40–48 Contents lists available at ScienceDirect Micron journal homepage: www.elsevier.com/locate/micron Enhanced imaging of lipid rich nanoparticles embedded in methylcellulose films for transmission electron microscopy using mixtures of heavy metals MARK Jalal Asadia, Sophie Fergusona, Hussain Rajaa, Christian Hackera,1, Phedra Mariusb, ⁎ Richard Wardb, Christos Pliotasb, James Naismithb, John Lucocqa, a School of Medicine, University of St Andrews, St. Andrews, Fife, KY16 9TF, UK b Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, St. Andrews, Scotland, UK ARTICLE INFO ABSTRACT Keywords: Synthetic and naturally occurring lipid-rich nanoparticles are of wide ranging importance in biomedicine. They Bicelles include liposomes, bicelles, nanodiscs, exosomes and virus particles. The quantitative study of these particles Phospholipids requires methods for high-resolution visualization of the whole population. One powerful imaging method is Membranes cryo-EM of vitrified samples, but this is technically demanding, requires specialized equipment, provides low Lipids contrast and does not reveal all particles present in a population. Another approach is classical negative stain- Methylcellulose EM, which is more accessible but is difficult to standardize for larger lipidic structures, which are prone to Uranyl acetate fi Phosphotungstic acid artifacts of structure collapse and contrast variability. A third method uses embedment in methylcellulose lms Sodium silicotungstate containing uranyl acetate as a contrasting agent. Methylcellulose embedment has been widely used for Negative stain contrasting and supporting cryosections but only sporadically for visualizing lipid rich vesicular structures Liposomes such as endosomes and exosomes. Here we present a simple methylcellulose-based method for routine and Nanodiscs comprehensive visualization of synthetic lipid rich nanoparticles preparations, such as liposomes, bicelles and nanodiscs.
    [Show full text]
  • Negative Staining 271 CHAPTER 8 TECHNIQUES
    Replicas, Shadowing, and Negative Staining 271 CHAPTER 8 TECHNIQUES Vacuum Evaporation Vacuum evaporators are used to coat substrates or specimens with carbon and/or metals and to pro­ duce pure carbon substrates for specimen support. The duration of evaporation, temperature of electrodes during evaporation (amperage used), angle of evaporation, vacuum at the time of evaporation, material being evaporated, and the temperature of the stage holding the specimen or support being coated are all factors for the end-product desired. As stated earlier, the shortest duration that delivers a usable coat, the lowest source (electrode) temperature that will cause evaporation, the largest angle between the source and substrate, the highest vacuum, the metal with the smallest grain structure, and a cooled stage will work together to produce the finest grain structure on the coated substrate. However, since other factors must be considered, all of these conditions cannot always be met. When shadowing a substrate with topography (e.g., a freeze-fracture specimen), contrast is developed by the dep­ osition of metal/carbon on one side of a particulate specimen, with a clear area behind the specimen that is not coated. This area is known as the shadow. Taller objects (like protozoan cells) are typically shadowed from one direction with metal at an angle of 45°, followed by a stabilizing carbon coat from sources directly overhead. Alternatively, carbon and metal are deposited simultaneously at a 45" angle. Specimens with little relief (nucleic acids, bacterial pili, viruses) are shadowed at a lower (10°) angle (Fig. 165A). If specimens are supported on a stage that is rotated rapidly during evaporation, the specimen is coated from all sides, producing very little shadow, but giving overall bulk to the sample (Fig.
    [Show full text]