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Whittington AA, Keimowitz AR, Tanski JM. Crystal structures of three uranyl-acetate-bipyridine complexes crystallized from hydraulic fracking fluid. Acta Crystallogr C Struct Chem 2024; 80:1-8. [PMID: 38054474 DOI: 10.1107/s2053229623010288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023] Open
Abstract
Hydraulic fracking exposes shale plays to acidic hydraulic fracking fluid (HFF), releasing toxic uranium (U) along with the desired oil and gas. With no existing methods to ensure U remains sequestered in the shale, this study sought to add organic ligands to HFF to explore potential U retention in shale plays. To test this possibility, incubations were set up in which uranyl acetate and one organic bipyridine ligand (either 2,2'-, 2,3'-, 2,4'-, or 4,4'-bipyridine) were added to pristine HFF as the crystallization medium. After several months and complete evaporation of all volatiles, bulk yellow crystalline material was obtained from the incubations, three of which yielded crystals suitable for single-crystal analysis, resulting in two novel structures and a high-quality structure of a previously described compound. The UO2VI acetate complexes bis(acetato-κ2O,O')(2,2'-bipyridine-κ2N,N')dioxidouranium(VI), [U(C2H3O2)2O2(C10H8N2)2] or [2,2'-bipyridine]UVIO2(CH3CO2)2, (I), and bis(acetato-κ2O,O')(2,4'-bipyridine-κN1')dioxidouranium(VI), [U(C2H3O2)2O2(C10H8N2)2] or [2,4'-bipyridine]2UVIO2(CH3CO2)2, (III), contain eight-coordinate UVI in a pseudo-hexagonal bipyramidal coordination geometry and are molecular, packing via weak C-H...O/N interactions, whereas catena-poly[bis(2,3'-bipyridinium) [di-μ-acetato-μ3-hydroxido-μ-hydroxido-di-μ3-oxido-hexaoxidotriuranium(VI)]-2,3'-bipyridine-water (1/1/1)], (C10H9N2)2[U3(C2H3O2)2O8(OH)2]·C10H8N2·H2O or {[2,3'-bipyridinium]2[2,3'-bipyridine][(UVIO2)3(O)2(OH)2(CH3CO2)2·H2O]}n, (II), forms an ionic one-dimensional polymer with seven-coordinate pentagonal bipyramidal UVI centers and hydrogen-bonding interactions within each chain. The formation of these crystals could indicate the potential for bipyridine to bind with U in shale during fracking, which will be explored in a future study via ICP-MS (inductively coupled plasma mass spectrometry) analyses of U concentration in HFF/bipyridine/shale incubations. The variation seen here between the molecular structures may indicate variance in the ability of bipyridine isomers to form complexes with U, which could impact their ability to retain U within shale in the context of fracking.
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Affiliation(s)
| | | | - Joseph M Tanski
- Department of Chemistry, Vassar College, Poughkeepsie, NY 12604, USA
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Sheikh A, Zechmann B, Sayes CM, Taube JH, Greathouse KL. A preparation of bacterial outer membrane with osmium tetroxide and uranyl acetate co-stain enables improved structural determination by transmission electron microscopy. Microscopy (Oxf) 2023; 72:515-519. [PMID: 37148329 PMCID: PMC10673695 DOI: 10.1093/jmicro/dfad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/10/2023] [Accepted: 05/04/2023] [Indexed: 05/08/2023] Open
Abstract
Biological nanoparticles, such as bacterial outer membrane vesicles (OMVs), are routinely characterized through transmission electron microscopy (TEM). In this study, we report a novel method to prepare OMVs for TEM imaging. To preserve vesicular shape and structure, we developed a dual fixation protocol involving osmium tetroxide incubation prior to negative staining with uranyl acetate. Combining osmium tetroxide with uranyl acetate resulted in preservation of sub-50 nm vesicles and improved morphological stability, enhancing characterization of lipid-based nanoparticles by TEM.
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Affiliation(s)
- Aadil Sheikh
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Bernd Zechmann
- Center for Microscopy and Imaging, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Christie M Sayes
- Department of Environmental Science, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Joseph H Taube
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - K. Leigh Greathouse
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
- Nutrition Sciences, Baylor University, One Bear Place #97311, Waco, TX 76798, USA
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Mrazova K, Bacovsky J, Sedrlova Z, Slaninova E, Obruca S, Fritz I, Krzyzanek V. Urany-Less Low Voltage Transmission Electron Microscopy: A Powerful Tool for Ultrastructural Studying of Cyanobacterial Cells. Microorganisms 2023; 11:888. [PMID: 37110311 PMCID: PMC10146862 DOI: 10.3390/microorganisms11040888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Sample preparation protocols for conventional high voltage transmission electron microscopy (TEM) heavily rely on the usage of staining agents containing various heavy metals, most commonly uranyl acetate and lead citrate. However high toxicity, rising legal regulations, and problematic waste disposal of uranyl acetate have increased calls for the reduction or even complete replacement of this staining agent. One of the strategies for uranyless imaging is the employment of low-voltage transmission electron microscopy. To investigate the influence of different imaging and staining strategies on the final image of cyanobacterial cells, samples stained by uranyl acetate with lead citrate, as well as unstained samples, were observed using TEM and accelerating voltages of 200 kV or 25 kV. Moreover, to examine the possibilities of reducing chromatic aberration, which often causes issues when imaging using electrons of lower energies, samples were also imaged using a scanning transmission electron microscopy at 15 kV accelerating voltages. The results of this study demonstrate that low-voltage electron microscopy offers great potential for uranyless electron microscopy.
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Affiliation(s)
- Katerina Mrazova
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Kralovopolska 147, 612 64 Brno, Czech Republic;
| | - Jaromir Bacovsky
- Delong Instruments a.s., Palackeho Trida 3019/153 b, 612 00 Brno, Czech Republic;
| | - Zuzana Sedrlova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (Z.S.); (E.S.); (S.O.)
| | - Eva Slaninova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (Z.S.); (E.S.); (S.O.)
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (Z.S.); (E.S.); (S.O.)
| | - Ines Fritz
- Institute of Environmental Biotechnology, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Konrad-Lorenz-Strase 20, 3430 Tulln an der Donau, Austria;
| | - Vladislav Krzyzanek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Kralovopolska 147, 612 64 Brno, Czech Republic;
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Pinto AL, Rai RK, Shoemark A, Hogg C, Burgoyne T. UA-Zero as a Uranyl Acetate Replacement When Diagnosing Primary Ciliary Dyskinesia by Transmission Electron Microscopy. Diagnostics (Basel) 2021; 11:1063. [PMID: 34207629 DOI: 10.3390/diagnostics11061063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a disorder affecting motile cilia. An early accurate diagnosis helps prevent lung damage and preserve lung function. To make a diagnostic assessment, one of the commonly used methods that allows for the examination of ciliary ultrastructure is transmission electron microscopy (TEM). This allows for a quantitative assessment of ciliary components to identify defects associated with PCD. Heavy metal staining is required to provide a contrast when imaging cilia in the TEM. One of the most commonly used stains is uranyl acetate (UA). UA can be applied to cellular material before embedding (en bloc), or to ultrathin sections of embedded samples (grid staining). UA is radioactive and, due to growing safety concerns and restrictions by government bodies, universities and hospitals, it is essential to find a suitable alternative. We show UA-zero (UAZ), when used en bloc, provides a high contrast and is a suitable replacement for UA. PCD diagnostic experts, having reviewed ciliary cross-sections stained with UAZ en bloc, are confident that the staining and PCD defects are readily detectable similar to samples that have been stained with UA.
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Abstract
Structural DNA nanotechnology can produce a wide range of 3D nanostructures with programmable structure and size at <5 nm resolution. However, it is challenging to dry these structures without capillary force-induced damage. As a result, the applications of 3D DNA nanostructures have long been limited in aqueous environments. Ready access to free-standing 3D DNA nanostructures in the dry state could revolutionize many research areas, especially in the development of low-density, high-strength materials. Here we report a method to obtain free-standing wireframe 3D DNA tetrahedra in air on a solid substrate, such as SiO2 and mica, by absorbing uranyl acetate and lyophilization. The dried DNA tetrahedron structure, 93 ± 2 nm in height, withstands 42 ± 22 nN of loading force. The effective hardness (9.1 ± 5.1 MPa) and Young's modulus (77 ± 48 MPa) of this low-density (70.7 kg/m3) DNA-inorganic hybrid nanostructure are comparable to other reported low-density high-strength materials.
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Affiliation(s)
- Feng Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Wei Sun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chen Zhang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jie Shen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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He X, Guo F, Liu B. Oolong tea and LR-White resin: a new method of plant sample preparation for transmission electron microscopy. J Microsc 2018; 270:244-251. [PMID: 29334400 DOI: 10.1111/jmi.12678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/22/2017] [Accepted: 12/17/2017] [Indexed: 11/27/2022]
Abstract
Simplifying sample processing, shortening the sample preparation time, and adjusting procedures to suitable for new health and safety regulations, these issues are the current challenges which electron microscopic examinations need to face. In order to resolve these problems, new plant tissue sample processing protocols for transmission electron microscopy should be developed. In the present study, we chose the LR-White resin-assisted processing protocol for the ultrastructural observation of different types of plant tissues. Moreover, we explored Oolong tea extract (OTE) as a substitute for UA in staining ultrathin sections of plant samples. The results revealed that there was no significant difference between the OTE double staining method and the traditional double staining method. Furthermore, in some organelles, such as mitochondria in root cells of tomatoes and chloroplast in leaf cells of watermelons, the OTE double staining method achieved little better results than the traditional double staining method. Therefore, OTE demonstrated good potentials in replacing UA as a counterstain on ultrathin sections. In addition, sample preparation time was significantly shortened and simplified using LR-White resin. This novel protocol reduced the time for preparing plant samples, and hazardous reagents in traditional method (acetone and UA) were also replaced by less toxic ones (ethanol and OTE).
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Affiliation(s)
- Xiaohua He
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Fuzhen Guo
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi, China
| | - Bin Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
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Iwakura T, Fujigaki Y, Fujikura T, Ohashi N, Kato A, Yasuda H. Acquired resistance to rechallenge injury after acute kidney injury in rats is associated with cell cycle arrest in proximal tubule cells. Am J Physiol Renal Physiol 2016; 310:F872-84. [PMID: 26823281 DOI: 10.1152/ajprenal.00380.2015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/27/2016] [Indexed: 01/26/2023] Open
Abstract
Rats that have recovered from severe proximal tubule (PT) injury induced by uranyl acetate (UA), a toxic stimulus, developed resistance to subsequent UA treatment. We investigated cell cycle status and progression in PT cells in relation to this acquired resistance. Fourteen days after pretreatment with saline (vehicle group) or UA [acute kidney injury (AKI) group], rats were injected with UA or lead acetate (a proliferative stimulus). Cell cycle status (G0/G1/S/G2/M) was analyzed by flow cytometry. The expression of cell cycle markers, cyclin-dependent kinase inhibitors, and phenotypic markers were examined by immunohistochemistry. Cell cycle status in PT cells in the AKI group was comparable to those of the vehicle group. However, more early G1-phase cells (cyclin D1- or Ki67-) and p21+ or p27+ cells were found in the PT of the AKI group than in that of the vehicle group. UA induced G1 arrest and inhibited S phase progression with earlier dedifferentiation and less apoptosis in PT cells of the AKI group. Lead acetate induced proliferation without dedifferentiation but with delayed G0-G1 transition and inhibited S phase progression in PT cells in the AKI group. Sustained p21 and increased p27 expression in PT cells were found in the AKI group in response to UA and lead acetate. PT cells in the AKI group inhibited cell cycle progression by enhanced G1 arrest, probably via p21/p27 modulation as an injury or proliferation response, resulting in cytoresistance to rechallenge injury.
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Affiliation(s)
- Takamasa Iwakura
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yoshihide Fujigaki
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan; Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan; and
| | - Tomoyuki Fujikura
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naro Ohashi
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akihiko Kato
- Blood Purification Unit, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hideo Yasuda
- Internal Medicine I, Division of Nephrology, Hamamatsu University School of Medicine, Hamamatsu, Japan
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Kaku H, Inoue K, Muranaka Y, Park P, Ikeda K. Rapid contrast evaluation method based on affinity beads and backscattered electron imaging for the screening of electron stains. Microscopy (Oxf) 2015. [PMID: 26199255 DOI: 10.1093/jmicro/dfv041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Uranyl salts are toxic and radioactive; therefore, several studies have been conducted to screen for substitutes of electron stains. In this regard, the contrast evaluation process is time consuming and the results obtained are inconsistent. In this study, we developed a novel contrast evaluation method using affinity beads and a backscattered electron image (BSEI), obtained using scanning electron microscopy. The contrast ratios of BSEI in each electron stain treatment were correlated with those of transmission electron microscopic images. The affinity beads bound to cell components independently. Protein and DNA samples were enhanced by image contrast treated with electron stains; however, this was not observed for sugars. Protein-conjugated beads showed an additive effect of image contrast when double-stained with lead. However, additive effect of double staining was not observed in DNA-conjugated beads. The varying chemical properties of oligopeptides showed differences in image contrast when treated with each electron stain. This BSEI-based evaluation method not only enables screening for alternate electron stains, but also helps analyze the underlying mechanisms of electron staining of cellular structures.
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Affiliation(s)
- Hiroki Kaku
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kanako Inoue
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yoshinori Muranaka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Pyoyun Park
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kenichi Ikeda
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
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9
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Kemmerling S, Arnold SA, Bircher BA, Sauter N, Escobedo C, Dernick G, Hierlemann A, Stahlberg H, Braun T. Single-cell lysis for visual analysis by electron microscopy. J Struct Biol 2013; 183:467-473. [PMID: 23816812 DOI: 10.1016/j.jsb.2013.06.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 06/20/2013] [Accepted: 06/24/2013] [Indexed: 01/22/2023]
Abstract
The stochastic nature of biological systems makes the study of individual cells a necessity in systems biology. Yet, handling and disruption of single cells and the analysis of the relatively low concentrations of their protein components still challenges available techniques. Transmission electron microscopy (TEM) allows for the analysis of proteins at the single-molecule level. Here, we present a system for single-cell lysis under light microscopy observation, followed by rapid uptake of the cell lysate. Eukaryotic cells were grown on conductively coated glass slides and observed by light microscopy. A custom-designed microcapillary electrode was used to target and lyse individual cells with electrical pulses. Nanoliter volumes were subsequently aspirated into the microcapillary and dispensed onto an electron microscopy grid for TEM inspection. We show, that the cell lysis and preparation method conserves protein structures well and is suitable for visual analysis by TEM.
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Affiliation(s)
- Simon Kemmerling
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Stefan A Arnold
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Benjamin A Bircher
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Nora Sauter
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Carlos Escobedo
- Bio Engineering Laboratory (BEL), Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
| | - Gregor Dernick
- Discovery Technologies, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Andreas Hierlemann
- Bio Engineering Laboratory (BEL), Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Braun
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland.
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Ikeda KI, Inoue K, Kanematsu S, Horiuchi Y, Park P. Enhanced effects of nonisotopic hafnium chloride in methanol as a substitute for uranyl acetate in TEM contrast of ultrastructure of fungal and plant cells. Microsc Res Tech 2010; 74:825-30. [PMID: 23939670 DOI: 10.1002/jemt.20964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 10/03/2010] [Indexed: 11/09/2022]
Abstract
This ultrastructural study showed that nonisotopic methanolic hafnium chloride and aqueous lead solution was an excellent new electron stain for enhancing TEM contrasts of fungal and plant cell structures. The ultrastructural definition provided by the new stain was often superior to that provided by conventional staining with uranyl acetate and lead. Definition of fine ultrastructure was also supported by quantitative data on TEM contrast ratios of organelles and components in fungal and plant cells. In particular, polysaccharides, which were localized in cell walls, glycogen particles, starch grains, and plant Golgi vesicle components, were much more reactive to the new stain than to the conventional one. The new nonisotopic stain is useful for enhancing the contrast of ultrastructure in biological tissues and is a safer alternative to uranyl acetate.
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Affiliation(s)
- Ken-Ichi Ikeda
- Graduate School of Agricultural Science, Kobe University, Rokkodai-cho, Nada Ward, Kobe 657-8501, Japan
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