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Korkmaz N, Usman M, Kim M. Reprogramming Filamentous fd Viruses to Capture Copper Ions. Chembiochem 2024; 25:e202400237. [PMID: 38712989 DOI: 10.1002/cbic.202400237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/25/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
C-terminal truncated variants (A, VA, NVA, ANVA, FANVA and GFANVA) of our recently identified Cu(II) specific peptide "HGFANVA" were displayed on filamentous fd phages. Wild type fd-tet and engineered virus variants were treated with 100 mM Cu(II) solution at a final phage concentration of 1011 vir/ml and 1012 vir/ml. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) imaging before Cu(II) exposure showed ≈6-8 nm thick filamentous virus layer formation. Cu(II) treatment resulted in aggregated bundle-like assemblies with mineral deposition. HGFANVA phage formed aggregates with an excessive mineral coverage. As the virus concentration was 10-fold decreased, nanowire-like assemblies were observed for shorter peptide variants A, NVA and ANVA. Wild type fd phages did not show any mineral formation. Energy dispersive X-ray spectroscopy (EDX) analyses revealed the presence of C and N peaks on phage organic material. Cu peak was only detected for engineered viruses. Metal ion binding of viruses was next investigated by enzyme-linked immunosorbent assay (ELISA) analyses. Engineered viruses were able to bind Cu(II) forming mineralized intertwined structures although no His (H) unit was displayed. Such genetically reprogrammed virus based biological materials can be further applied for bioremediation studies to achieve a circular economy.
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Affiliation(s)
- Nuriye Korkmaz
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Muhammad Usman
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Minyoung Kim
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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Korkmaz N, Himawan S, Usman M, Baik S, Kim M. Bacteriophage Engineering for Improved Copper Ion Binding. Macromol Biosci 2024; 24:e2300354. [PMID: 37985183 DOI: 10.1002/mabi.202300354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/13/2023] [Indexed: 11/22/2023]
Abstract
In this study, fd viruses are genetically modified to display seven cropped versions (H, HG, HGF, HGFA, HGFAN, HGFANV and HGFANVA) of the previously identified Cu(II) specific peptide (HGFANVA). Atomic force microscopy (AFM) imaging reveals the typical filamentous structures of recombinant phages with thicknesses of ≈2-5 nm in dry state. Scanning electron microscopy (SEM) imaging shows that HGFANVA viruses form larger elongated assemblies than H viruses that are deposited with a mineral layer after Cu(II) treatment. C and N peaks are detected for virus samples through Energy dispersive X-ray spectroscopy (EDX) analyses confirming the presence of phage organic material. Cu peak is only detected for engineered viruses after Cu(II) exposure. Enzyme-linked immunosorbent assay (ELISA) analyses show the selective Cu(II) binding of engineered phages. Agarose gel electrophoresis (AGE) and zeta potential analyses reveal negative surface charges of engineered viral constructs. Positively charged Cytopore beads are coated with bacteriophages and used for Cu(II) ion sorption studies. ICP-MS analyses clearly show the improved Cu(II) binding of engineered viruses with respect to wild-type fd phages. Such bottom-up constructed, genetically engineered virus-based biomaterials may be applied in bioremediation studies targeting metal species from environmental samples.
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Affiliation(s)
- Nuriye Korkmaz
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Sandiego Himawan
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
- Bioprogrammable Materials Group, INM - Leibniz Institute for New Materials, Campus D 2.2, D-66123, Saarbrücken, Germany
| | - Muhammed Usman
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Seungyun Baik
- Environmental Safety Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Minyoung Kim
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
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Shimma Y, Sato T, Baglioni P, Ogura T. Hierarchical Emulsion Structure and Functionality Regulated by Coexisting Bicontinuous Microemulsion and Liquid Crystal Domains. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:4077-4086. [PMID: 38346388 DOI: 10.1021/acs.langmuir.3c02935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Since microemulsions are usually low viscosity fluids, enhanced rheological properties while maintaining their structure-derived functionality have long been desired from an industrial application point of view. However, for instance, it is practically difficult to thicken bicontinuous microemulsions (BCMEs) without perturbing their alternating domain structure or to emulsify oils using BCME having ultralow interfacial tension as an external phase. In this study, a methodology called a BCLC emulsification technique has been constructed to obtain oil-in-water emulsions stabilized by coexisting BCME and liquid crystal (LC) phases. The produced emulsions based on polyglyceryl-10 diisostearate, polyglyceryl-6 dicaprate, cetyl ethylhexanoate, and water are structurally scrutinized by means of small- and wide-angle X-ray scattering (SWAXS), freeze fracture transmission electron microscopy (FF-TEM), and scanning electron assisted dielectric microscopy (SE-ADM). The data provide experimental evidence that this methodology enables one to control the bending elasticity of the interfacial membranes and consequent long-range order of the BCME domains. Moreover, closely correlated with the interfacial membrane properties, submicrometer-sized fine oil droplets are supported by the LC networks and agglomerated into spongy or network-like phase-separation patterns. The resulting nonfluidic, jelly emulsions are particularly useful in cosmetics because of combined BCME-derived high cleansing performance and excellent usability owing to the enhanced viscosity. The thickening mechanisms are essentially different from those of common lamellar-gel-stabilized oil-in-water emulsions, which utilize crystalline lamellar gel networks as oil droplet stabilizers.
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Affiliation(s)
- Yuko Shimma
- ALBION Co., Ltd., 2-24-11 Higashi-Nihonbashi, Chuo-ku, Tokyo 103-0004, Japan
| | - Takaaki Sato
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
| | - Piero Baglioni
- Department of Chemistry and CSGI, University of Florence, 50019 Sesto Fiorentino, Florence, Italy
| | - Taku Ogura
- NIKKOL GROUP, Nikko Chemicals Co., Ltd., 1-4-8 Nihonbashibakurocho, Chuo-ku, Tokyo 103-0002, Japan
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Ogura T, Okada T, Hatano M, Nakamura M, Agemura T. Development of General-purpose Dielectric Constant Imaging Unit for SEM and Direct Observation of Samples in Aqueous Solution. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1037-1046. [PMID: 37749668 DOI: 10.1093/micmic/ozad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 09/27/2023]
Abstract
Electron microscopes can observe samples with a spatial resolution of 10 nm or higher; however, they cannot observe samples in solutions due to the vacuum conditions inside the sample chamber. Recently, we developed a scanning electron-assisted dielectric microscope (SE-ADM), based on scanning electron microscope, which enables the observation of various specimens in solution. Until now, the SE-ADM system used a custom-made SE-ADM stage with a built-in amplifier and could not be linked to the scanning electron microscopy (SEM) operation system. Therefore, it was necessary to manually acquire images from the SE-ADM system after setting the EB focus, astigmatism, and observation field-of-view from the SEM operating console. In this study, we developed a general-purpose dielectric constant imaging unit attached to commercially available SEMs. The new SE-ADM unit can be directly attached to the standard stage of an SEM, and the dielectric signal detected from this unit can be input to the external input terminal of the SEM, enabling simultaneous observation yielding SEM and SE-ADM images. Furthermore, 4.5 nm spatial resolution was achieved using a 10 nm thick silicon nitride film in the sample holder in the observation of aggregated PM2.5. We carried out the observation of cultured cells, PM2.5, and clay samples in solution.
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Affiliation(s)
- Toshihiko Ogura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Tomoko Okada
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Michio Hatano
- Hitachi High-Tech Corporation, Ichige 882, Hitachinaka, Ibaraki 312-8504, Japan
| | - Mitsuhiro Nakamura
- Hitachi High-Tech Corporation, Ichige 882, Hitachinaka, Ibaraki 312-8504, Japan
| | - Toshihide Agemura
- Hitachi High-Tech Corporation, Ichige 882, Hitachinaka, Ibaraki 312-8504, Japan
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Fukuta M, Ono A, Nawa Y, Inami W, Shen L, Kawata Y, Terekawa S. Cell structure imaging with bright and homogeneous nanometric light source. JOURNAL OF BIOPHOTONICS 2017; 10:503-510. [PMID: 27274004 DOI: 10.1002/jbio.201500308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/19/2016] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
Label-free optical nano-imaging of dendritic structures and intracellular granules in biological cells is demonstrated using a bright and homogeneous nanometric light source. The optical nanometric light source is excited using a focused electron beam. A zinc oxide (ZnO) luminescent thin film was fabricated by atomic layer deposition (ALD) to produce the nanoscale light source. The ZnO film formed by ALD emitted the bright, homogeneous light, unlike that deposited by another method. The dendritic structures of label-free macrophage receptor with collagenous structure-expressing CHO cells were clearly visualized below the diffraction limit. The inner fiber structure was observed with 120 nm spatial resolution. Because the bright homogeneous emission from the ZnO film suppresses the background noise, the signal-to-noise ratio (SNR) for the imaging results was greater than 10. The ALD method helps achieve an electron beam excitation assisted microscope with high spatial resolution and high SNR.
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Affiliation(s)
- Masahiro Fukuta
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
| | - Atsushi Ono
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Yasunori Nawa
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
| | - Wataru Inami
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Lin Shen
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Yoshimasa Kawata
- Research Institute of Electronics, Shizuoka University, 3-5-1 Johoku, Naka, Hamamatsu, 432-8561, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
| | - Susumu Terekawa
- CREST, Japan Science and Technology Agency, 4-1-8 Honmachi, Kawaguchi, Saitama, 332-0012, Japan
- Photon Medical Research Center, Hamamatsu University School of Medicine, 1-20-1 Hondayama, Higashi, Hamamatsu, 431-3192, Japan
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Ogura T. Direct observation of unstained biological specimens in water by the frequency transmission electric-field method using SEM. PLoS One 2014; 9:e92780. [PMID: 24651483 PMCID: PMC3961424 DOI: 10.1371/journal.pone.0092780] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/25/2014] [Indexed: 11/18/2022] Open
Abstract
Scanning electron microscopy (SEM) is a powerful tool for the direct visualization of biological specimens at nanometre-scale resolution. However, images of unstained specimens in water using an atmospheric holder exhibit very poor contrast and heavy radiation damage. Here, we present a new form of microscopy, the frequency transmission electric-field (FTE) method using SEM, that offers low radiation damage and high-contrast observation of unstained biological samples in water. The wet biological specimens are enclosed in two silicon nitride (SiN) films. The metal-coated SiN film is irradiated using a focused modulation electron beam (EB) at a low-accelerating voltage. A measurement terminal under the sample holder detects the electric-field frequency signal, which contains structural information relating to the biological specimens. Our results in very little radiation damage to the sample, and the observation image is similar to the transmission image, depending on the sample volume. Our developed method can easily be utilized for the observation of various biological specimens in water.
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Affiliation(s)
- Toshihiko Ogura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Umezono, Tsukuba, Ibaraki, Japan
- * E-mail:
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Harano K, Minami K, Noiri E, Okamoto K, Nakamura E. Protein-coated nanocapsules via multilevel surface modification. Controlled preparation and microscopic analysis at nanometer resolution. Chem Commun (Camb) 2013; 49:3525-7. [DOI: 10.1039/c3cc40752g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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