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Kalitnik A, Lassota A, Polańska O, Gąsior‐Głogowska M, Szefczyk M, Barbach A, Chilimoniuk J, Jęśkowiak‐Kossakowska I, Wojciechowska AW, Wojciechowski JW, Szulc N, Kotulska M, Burdukiewicz M. Experimental methods for studying amyloid cross-interactions. Protein Sci 2025; 34:e70151. [PMID: 40384558 PMCID: PMC12086524 DOI: 10.1002/pro.70151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 04/16/2025] [Accepted: 04/20/2025] [Indexed: 05/20/2025]
Abstract
Interactions between amyloid proteins represent the cornerstone of various pathogenic pathways, including prion conversion and co-development of distinct kinds of systemic amyloidosis. Various experimental methodologies provide insights into the effects of such cross-interactions on amyloid self-assembly, which range from acceleration to complete inhibition. Here, we present a comprehensive review of experimental methods most commonly used to study amyloid cross-interactions both in vitro and in vivo, such as fluorescence-based techniques, high-resolution imaging, and spectroscopic methods. Although each method provides distinct information on amyloid interactions, we highlight that no method can fully capture the complexity of this process. In order to achieve an exhaustive portrayal, it is necessary to employ a hybrid strategy combining different experimental techniques. A core set of fluorescence methods (e.g., thioflavin T) and high-resolution imaging techniques (e.g., atomic force microscopy or Cryo-EM) are required to verify the lack of self-assembly or alterations in fibril morphology. At the same time, immuno-electron microscopy, mass spectrometry, or solid-state NMR can confirm the presence of heterotypic fibrils.
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Affiliation(s)
- Aleksandra Kalitnik
- Department of Biomedical Engineering, Faculty of Fundamental Problems of TechnologyWroclaw University of Science and TechnologyWrocławPoland
| | - Anna Lassota
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamBirminghamUK
| | - Oliwia Polańska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of TechnologyWroclaw University of Science and TechnologyWrocławPoland
| | - Marlena Gąsior‐Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of TechnologyWroclaw University of Science and TechnologyWrocławPoland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of ChemistryWroclaw University of Science and TechnologyWrocławPoland
| | - Agnieszka Barbach
- Department of Experimental OncologyHirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | | | | | - Alicja W. Wojciechowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of TechnologyWroclaw University of Science and TechnologyWrocławPoland
| | - Jakub W. Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of TechnologyWroclaw University of Science and TechnologyWrocławPoland
- Sano Centre for Computational MedicineKrakówPoland
| | - Natalia Szulc
- Department of Physics and BiophysicsWrocław University of Environmental and Life SciencesWrocławPoland
| | - Małgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of TechnologyWroclaw University of Science and TechnologyWrocławPoland
| | - Michał Burdukiewicz
- Clinical Research CentreMedical University of BiałystokBiałystokPoland
- Institute of BiotechnologyVilnius UniversityVilniausLithuania
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Sisó S, Kavirayani AM, Couto S, Stierstorfer B, Mohanan S, Morel C, Marella M, Bangari DS, Clark E, Schwartz A, Carreira V. Trends and Challenges of the Modern Pathology Laboratory for Biopharmaceutical Research Excellence. Toxicol Pathol 2025; 53:5-20. [PMID: 39673215 DOI: 10.1177/01926233241303898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2024]
Abstract
Pathology, a fundamental discipline that bridges basic scientific discovery to the clinic, is integral to successful drug development. Intrinsically multimodal and multidimensional, anatomic pathology continues to be empowered by advancements in molecular and digital technologies enabling the spatial tissue detection of biomolecules such as genes, transcripts, and proteins. Over the past two decades, breakthroughs in spatial molecular biology technologies and advancements in automation and digitization of laboratory processes have enabled the implementation of higher throughput assays and the generation of extensive molecular data sets from tissue sections in biopharmaceutical research and development research units. It is our goal to provide readers with some rationale, advice, and ideas to help establish a modern molecular pathology laboratory to meet the emerging needs of biopharmaceutical research. This manuscript provides (1) a high-level overview of the current state and future vision for excellence in research pathology practice and (2) shared perspectives on how to optimally leverage the expertise of discovery, toxicologic, and translational pathologists to provide effective spatial, molecular, and digital pathology data to support modern drug discovery. It captures insights from the experiences, challenges, and solutions from pathology laboratories of various biopharmaceutical organizations, including their approaches to troubleshooting and adopting new technologies.
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Affiliation(s)
- Sílvia Sisó
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | | | | | | | | | | | - Mathiew Marella
- Janssen Research & Development, LLC, La Jolla, California, USA
| | | | - Elizabeth Clark
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut, USA
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Pellequer JL. Perspectives Toward an Integrative Structural Biology Pipeline With Atomic Force Microscopy Topographic Images. J Mol Recognit 2024; 37:e3102. [PMID: 39329418 DOI: 10.1002/jmr.3102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/21/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024]
Abstract
After the recent double revolutions in structural biology, which include the use of direct detectors for cryo-electron microscopy resulting in a significant improvement in the expected resolution of large macromolecule structures, and the advent of AlphaFold which allows for near-accurate prediction of any protein structures, the field of structural biology is now pursuing more ambitious targets, including several MDa assemblies. But complex target systems cannot be tackled using a single biophysical technique. The field of integrative structural biology has emerged as a global solution. The aim is to integrate data from multiple complementary techniques to produce a final three-dimensional model that cannot be obtained from any single technique. The absence of atomic force microscopy data from integrative structural biology platforms is not necessarily due to its nm resolution, as opposed to Å resolution for x-ray crystallography, nuclear magnetic resonance, or electron microscopy. Rather a significant issue was that the AFM topographic data lacked interpretability. Fortunately, with the introduction of the AFM-Assembly pipeline and other similar tools, it is now possible to integrate AFM topographic data into integrative modeling platforms. The advantages of single molecule techniques, such as AFM, include the ability to confirm experimentally any assembled molecular models or to produce alternative conformations that mimic the inherent flexibility of large proteins or complexes. The review begins with a brief overview of the historical developments of AFM data in structural biology, followed by an examination of the strengths and limitations of AFM imaging, which have hindered its integration into modern modeling platforms. This review discusses the correction and improvement of AFM topographic images, as well as the principles behind the AFM-Assembly pipeline. It also presents and discusses a series of challenges that need to be addressed in order to improve the incorporation of AFM data into integrative modeling platform.
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Affiliation(s)
- Jean-Luc Pellequer
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
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Liu Z, Zhang M, Hao Y, Hu W, Zhu W, Wang H, Li L. Application of surface-modified functional packaging in food storage: A comprehensive review. Compr Rev Food Sci Food Saf 2024; 23:e13343. [PMID: 38629458 DOI: 10.1111/1541-4337.13343] [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: 10/22/2023] [Revised: 03/13/2024] [Accepted: 03/24/2024] [Indexed: 04/19/2024]
Abstract
Innovations in food packaging systems could meet the evolving needs of the market; emerging concepts of non-migrating technologies reduce the negative migration of preservatives from packaging materials, extend shelf life, and improve food quality and safety. Non-migratory packaging activates the surface of inert materials through pretreatment to generate different active groups. The preservative is covalently grafted with the resin of the pretreated packaging substrate through the graft polymerization of the monomer and the coupling reaction of the polymer chain. The covalent link not only provides the required surface properties of the material for a long time but also retains the inherent properties of the polymer. This technique is applied to the processing for durable, stable, and easily controllable packaging widely. This article reviews the principles of various techniques for packaging materials, surface graft modification, and performance characterization of materials after grafting modification. Potential applications in the food industry and future research trends are also discussed.
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Affiliation(s)
- Zhuolin Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai, China
| | - Mengmeng Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai, China
| | - Yi Hao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai, China
| | - Wenqing Hu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai, China
| | - Weizhong Zhu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai, China
| | - He Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai, China
| | - Li Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai, China
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Byvalov AA, Belozerov VS, Ananchenko BA, Konyshev IV. Specific and Nonspecific Interactions of Yersinia pseudotuberculosis Lipopolysaccharide with Monoclonal Antibodies Assessed by Atomic Force Microscopy. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922060033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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Bonet NF, Cava DG, Vélez M. Quartz crystal microbalance and atomic force microscopy to characterize mimetic systems based on supported lipids bilayer. Front Mol Biosci 2022; 9:935376. [PMID: 35992275 PMCID: PMC9382308 DOI: 10.3389/fmolb.2022.935376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/23/2022] Open
Abstract
Quartz Crystal Microbalance (QCM) with dissipation and Atomic Force Microscopy (AFM) are two characterization techniques that allow describing processes taking place at solid-liquid interfaces. Both are label-free and, when used in combination, provide kinetic, thermodynamic and structural information at the nanometer scale of events taking place at surfaces. Here we describe the basic operation principles of both techniques, addressing a non-specialized audience, and provide some examples of their use for describing biological events taking place at supported lipid bilayers (SLBs). The aim is to illustrate current strengths and limitations of the techniques and to show their potential as biophysical characterization techniques.
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Cava DG, Vélez M. Study of Amyloid Fibers Using Atomic Force Microscopy. Methods Mol Biol 2022; 2538:1-11. [PMID: 35951289 DOI: 10.1007/978-1-0716-2529-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic force microscopy (AFM) provides high-resolution images of the topography of amyloid fibers adsorbed on surfaces. This information is very useful to study their molecular assembly under various conditions. This chapter describes the basic protocols required to deposit fibers on flat surfaces and discusses some of the practical issues required to operate a good commercial microscope setup to obtain appropriate high-resolution AFM topographic images of amyloid fibers.
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Affiliation(s)
- Daniel G Cava
- Instituto de Catálisis y Petroleoquímica (CSIC), (Cantoblanco) Madrid, Spain
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica (CSIC), (Cantoblanco) Madrid, Spain.
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Albonetti C, ValdrÈ G. Preface to StSPM2019EV special issue. J Microsc 2021; 280:181-182. [PMID: 33180974 DOI: 10.1111/jmi.12966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C Albonetti
- Institute for the Study on Nanostructured Materials ISMN, National Research Council of Italy (CNR), Bologna, Italy
| | - G ValdrÈ
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna 'Alma Mater Studiorum' Piazza di Porta San Donato 1, Bologna, Italy.,Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Università di Bologna 'Alma Mater Studiorum' Piazza di Porta San Donato 1, Bologna, Italy
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