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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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Chen J. Crystallization and Assembly-Driven Nanostructures for Energy, Electronics, Environment, and Emerging Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:637. [PMID: 36839005 PMCID: PMC9963978 DOI: 10.3390/nano13040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
This manuscript has been authored by UT-Battelle, LLC, under Contract No [...].
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Affiliation(s)
- Jihua Chen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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Dubashynskaya NV, Gasilova ER, Skorik YA. Nano-Sized Fucoidan Interpolyelectrolyte Complexes: Recent Advances in Design and Prospects for Biomedical Applications. Int J Mol Sci 2023; 24:ijms24032615. [PMID: 36768936 PMCID: PMC9916530 DOI: 10.3390/ijms24032615] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
The marine polysaccharide fucoidan (FUC) is a promising polymer for pharmaceutical research and development of novel drug delivery systems with modified release and targeted delivery. The presence of a sulfate group in the polysaccharide makes FUC an excellent candidate for the formation of interpolyelectrolyte complexes (PECs) with various polycations. However, due to the structural diversity of FUC, the design of FUC-based nanoformulations is challenging. This review describes the main strategies for the use of FUC-based PECs to develop drug delivery systems with improved biopharmaceutical properties, including nanocarriers in the form of FUC-chitosan PECs for pH-sensitive oral delivery, targeted delivery systems, and polymeric nanoparticles for improved hydrophobic drug delivery (e.g., FUC-zein PECs, core-shell structures obtained by the layer-by-layer self-assembly method, and self-assembled hydrophobically modified FUC particles). The importance of a complex study of the FUC structure, and the formation process of PECs based on it for obtaining reproducible polymeric nanoformulations with the desired properties, is also discussed.
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He J, Tao L, Xian W, Arbaugh T, Li Y. Molecular self-assembled monolayers anomalously enhance thermal conductance across polymer-semiconductor interfaces. NANOSCALE 2022; 14:17681-17693. [PMID: 36416469 DOI: 10.1039/d2nr04936h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Thermal issues have become increasingly important for the performance and lifetime of highly miniaturized and integrated devices. However, the high thermal resistance across the polymer/semiconductor interface greatly weakens the fast heat dissipation. In this study, applying the self-assembled monolayer (SAM) technique, organic molecules are employed as heat regulators to mediate interfacial thermal conductance (ITC) between semiconductors (silicon or Si) and polymers (polystyrene or PS). Silane-based SAM molecules with unique functional groups, such as -NH2, -CH3, -SH, and -Cl, are orderly assembled into Si-PS interfaces. Their roles in ITC and the heat transfer mechanism were systematically investigated. Molecular simulations demonstrate that the Si-PS interface decorated with SAM molecules can significantly facilitate heat transfer in varying degrees. Such a difference is primarily due to the different non-bonded interactions and compatibility between SAMs and PS. Compared with the pristine Si-PS interface, the interface incorporated with 3-chloropropyl trimethoxysilane shows the greatest improvement in ITC, about 507.02%. Such improvements are largely attributed to the SAM molecules, as the thermal bridges straighten the molecular SAM chains, develop strong non-bonded interactions with PS, provide the covalent bonding between Si and PS, exhibit a strong coupling effect between two materials' vibrational modes, and eliminate the discontinuities in the temperature field. Eventually, these demonstrations are expected to offer molecular insights to enable effective thermal management through surface engineering for critical-heat transfer materials and microelectronic devices.
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Affiliation(s)
- Jinlong He
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1572, USA.
| | - Lei Tao
- Department of Mechanical Engineering, University of Connecticut, Storrs, Connecticut 06269-3139, USA
| | - Weikang Xian
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1572, USA.
| | - Tom Arbaugh
- Department of Physics, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Ying Li
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1572, USA.
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Botifoll M, Pinto-Huguet I, Arbiol J. Machine learning in electron microscopy for advanced nanocharacterization: current developments, available tools and future outlook. NANOSCALE HORIZONS 2022; 7:1427-1477. [PMID: 36239693 DOI: 10.1039/d2nh00377e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the last few years, electron microscopy has experienced a new methodological paradigm aimed to fix the bottlenecks and overcome the challenges of its analytical workflow. Machine learning and artificial intelligence are answering this call providing powerful resources towards automation, exploration, and development. In this review, we evaluate the state-of-the-art of machine learning applied to electron microscopy (and obliquely, to materials and nano-sciences). We start from the traditional imaging techniques to reach the newest higher-dimensionality ones, also covering the recent advances in spectroscopy and tomography. Additionally, the present review provides a practical guide for microscopists, and in general for material scientists, but not necessarily advanced machine learning practitioners, to straightforwardly apply the offered set of tools to their own research. To conclude, we explore the state-of-the-art of other disciplines with a broader experience in applying artificial intelligence methods to their research (e.g., high-energy physics, astronomy, Earth sciences, and even robotics, videogames, or marketing and finances), in order to narrow down the incoming future of electron microscopy, its challenges and outlook.
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Affiliation(s)
- Marc Botifoll
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain.
| | - Ivan Pinto-Huguet
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain.
| | - Jordi Arbiol
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain.
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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Weng S, Li Y, Wang X. Cryo-EM for battery materials and interfaces: Workflow, achievements, and perspectives. iScience 2021; 24:103402. [PMID: 34849466 PMCID: PMC8607198 DOI: 10.1016/j.isci.2021.103402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The emerging cryogenic electron microscopy (cryo-EM) has demonstrated its power and essential role in probing the beam-sensitive battery materials and delivering new insights. With the increasing interest in cryo-EM for battery materials and interfaces, herein we provide the strategies of obtaining fresh and native structural information with minimal artifacts, including sample preparation, transferring, imaging, and data interpretation. We summarize the recent achievements enabled by cryo-EM and point out some unsolved/potential questions in terms of the bulk materials, solid-solid interface, and solid-liquid interfaces of batteries. Finally, we conclude with perspectives on the future developments and applications of cryo-EM in battery materials and interfaces.
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Affiliation(s)
- Suting Weng
- Laboratory for Advanced Materials and Electron Microscopy, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yejing Li
- Laboratory for Advanced Materials and Electron Microscopy, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xuefeng Wang
- Laboratory for Advanced Materials and Electron Microscopy, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Tianmu Lake Institute of Advanced Energy Storage Technologies Co. Ltd., Liyang, Jiangsu 213300, China
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