Article
Biochemistry & Molecular Biology
Jie E. Yang, Matthew R. Larson, Bryan S. Sibert, Samantha Shrum, Elizabeth R. Wright
Summary: Cryo-correlative light and electron microscopy (CLEM) combines the advantages of fluorescence light microscopy (FLM) and cryo-electron microscopy (cryo-EM) for high-resolution ultrastructure analysis of biological samples. Challenges lie in implementing correlation workflows and software tools on different microscope platforms to support automated cryo-EM data acquisition. CorRelator is an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection, providing flexible and high accuracy correlation for cryo-CLEM workflows.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hong-Lim Kim, Tae-Ryong Riew, Jieun Park, Youngchun Lee, In-Beom Kim
Summary: Researchers have developed a new method by combining light and electron microscopy with immunolabeling, to overcome technical barriers in immuno-electron microscopy. This method allows for excellent antigenicity of target proteins and preservation of ultrastructure, without the need for specifically designed correlative light and electron microscopy devices. It can be easily applied in many biomedical studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ryan Lane, Anouk H. G. Wolters, Ben N. G. Giepmans, Jacob P. Hoogenboom
Summary: We developed a 3D image acquisition and reconstruction pipeline that integrates widefield fluorescence microscopy with scanning electron microscopy, overcoming the limitations of slow acquisition rates and difficulty in providing targeted biological information. By using cathodoluminescent markers, we achieved high precision EM-FM overlay. Our proof-of-concept on immunolabelled serial sections of tissues demonstrated expedited acquisition times and reduced data burden.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xuyuan Kuang, Kyle Nunn, Jennifer Jiang, Paul Castellano, Uttara Hardikar, Arianna Horgan, Joyce Kong, Zhiqun Tan, Wei Dai
Summary: Studies have shown that mHTT can spread between cells, leading to the propagation of misfolded protein pathology. By using correlative light and electron microscopy and cryo-electron tomography, researchers identified the structure of transmissive mHTT species and highlighted the potential role of extracellular vesicles (EVs) in the transmission process.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Joseph George Beton, Jim Monistrol, Anne Wentink, Erin C. Johnston, Anthony John Roberts, Bernd Gerhard Bukau, Bart W. Hoogenboom, Helen R. Saibil
Summary: Specific combinations of molecular chaperones in the human body can disassemble protein aggregates, which is important for combating disease-related fiber formation. This study reveals the mechanism of this disassembly process and the localization and activity of molecular chaperones on the fibers using techniques such as atomic force microscopy.
Article
Biochemistry & Molecular Biology
Gabriele Bongiovanni, Oliver F. Harder, Marcel Drabbels, Ulrich J. Lorenz
Summary: This study introduces a novel approach to time-resolved cryo-electron microscopy with microsecond time resolution. It involves melting a cryo sample with a laser beam to allow dynamics of the embedded particles. The sample revitrifies within microseconds after the laser beam is switched off, trapping the particles in their transient configurations, which can be imaged to obtain a snap shot of the dynamics at that point in time.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Jie E. Yang, Matthew R. Larson, Bryan S. Sibert, Joseph Y. Kim, Daniel Parrell, Juan C. Sanchez, Victoria Pappas, Anil Kumar, Kai Cai, Keith Thompson, Elizabeth R. Wright
Summary: In this paper, robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens are presented, which can image large fields of view while preserving high-resolution structural information. The combination of multiple techniques in MPACT supports studies that contextually define the three-dimensional architecture of cells, and it provides flexibility and efficient data processing and analysis.
Review
Biochemistry & Molecular Biology
Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai
Summary: The different oligomeric forms of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) have defined cellular and subcellular distributions. While crystal structures of AChE and BChE have been available for many years, structures of the physiologically relevant cholinesterase tetramer were only recently solved by cryo-electron microscopy (cryo-EM). The next frontier in cholinesterase structural biology is to image membrane-anchored ChE oligomers directly in their native environment - the cell.
JOURNAL OF NEUROCHEMISTRY
(2021)
Review
Anatomy & Morphology
Hugh Tanner, Olivia Sherwin, Paul Verkade
Summary: Imaging is a crucial technology in biomedical research, but each technique only offers specific information. The combination of light and electron microscopy in CLEM allows for the advantages of both techniques. However, finding suitable markers for a Correlative Microscopy workflow remains a challenge.
MICROSCOPY RESEARCH AND TECHNIQUE
(2023)
Article
Neurosciences
Vladan Lucic
Summary: This article reviews the importance of electron microscopy in the study of neuronal synapse structures and discusses the use of image processing software methods. Special attention is given to the application of recent cryo-electron microscopy and tomography methods in molecular level analysis.
CURRENT OPINION IN NEUROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
John Sedat, Angus McDonald, Hu Cang, Joseph Lucas, Muthuvel Arigovindan, Zvi Kam, Cornelis Murre, Michael Elbaum
Summary: Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has revealed a large-scale chromosome structure. This study further investigates and analyzes these structures, proposing a unified architecture for interphase chromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Matthew Croxford, Michael Elbaum, Muthuvel Arigovindan, Zvi Kam, David Agard, Elizabeth Villa, John Sedat
Summary: Entropy-regularized deconvolution (ER-DC) was applied to cryo-electron tomography (cryo-ET) data to address limitations in signal-to-noise ratio and Z resolution, with assessment conducted through Fourier analysis and subtomogram analysis (STA).
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Samantha J. Ziegler, Sam J. B. Mallinson, Peter C. St John, Yannick J. Bomble
Summary: Microorganisms rely on protein interactions for signaling, stimuli response, and growth. Recent developments in structural biology, particularly integrative structural biology, have provided insight into how large protein complexes interact in their native environment. This mini-review discusses the past, present, and potential future of integrative structural biology in characterizing protein interactions in their cellular context.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Linhua Tai, Guoliang Yin, Fei Sun, Yun Zhu
Summary: The nuclear pore complex (NPC) is a large protein assembly that penetrates the nuclear membrane. Recent breakthroughs in cryo-EM and artificial intelligence-based modeling have allowed for improved understanding of the complex structure of the NPC. This review article summarizes the history and latest advancements in studying the architecture of the NPC, as well as future directions for research.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Microscopy
Jakub Kuba, John Mitchels, Milos Hovorka, Philipp Erdmann, Lukas Berka, Robert Kirmse, Julia Koenig, Jan De Bock, Bernhard Goetze, Alexander Rigort
Summary: Cryo-electron tomography (cryo-ET) is a groundbreaking technology that allows for 3D visualization and analysis of biomolecules within cellular structures. The introduction of focused ion beam (FIB) technology has made sample preparation for electron tomography easier and faster. The combination of cryo-microscopy, cryo-FIB, and cryo-ET has led to new insights into cellular processes and provided new 3D image data of cells.
JOURNAL OF MICROSCOPY
(2021)
Article
Microscopy
Jakub Kuba, John Mitchels, Milos Hovorka, Philipp Erdmann, Lukas Berka, Robert Kirmse, Julia Koenig, Jan De Bock, Bernhard Goetze, Alexander Rigort
Summary: Cryo-electron tomography (cryo-ET) is a groundbreaking technology that allows for 3D visualization and analysis of biomolecules within cellular structures. The introduction of focused ion beam (FIB) technology has made sample preparation for electron tomography easier and faster. The combination of cryo-microscopy, cryo-FIB, and cryo-ET has led to new insights into cellular processes and provided new 3D image data of cells.
JOURNAL OF MICROSCOPY
(2021)
Article
Biochemistry & Molecular Biology
Sebastian Tacke, Philipp Erdmann, Zhexin Wang, Sven Klumpe, Michael Grange, Jurgen Plitzko, Stefan Raunser
Summary: Cryo-electron tomography is a technique used to study cellular architecture and protein structure at high resolution, but is often hindered by ice contamination during cryo-FIB milling. Researchers have developed new hardware and software solutions to overcome contamination, simplify sample handling, and enable high-quality, high-throughput cryo-FIB milling. These improvements pave the way for new types of experiments that were previously deemed unfeasible.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tilak Kumar Gupta, Sven Klumpe, Karin Gries, Steffen Heinz, Wojciech Wietrzynski, Norikazu Ohnishi, Justus Niemeyer, Benjamin Spaniol, Miroslava Schaffer, Anna Rast, Matthias Ostermeier, Mike Strauss, Juergen M. Plitzko, Wolfgang Baumeister, Till Rudack, Wataru Sakamoto, Joerg Nickelsen, Jan M. Schuller, Michael Schroda, Benjamin D. Engel
Summary: This study reveals the structures of cyanobacterial VIPP1 rings using cryo-electron microscopy, showing how VIPP1 monomers flex and interweave to form basket-like assemblies. The research also demonstrates the essential role of VIPP1 lipid binding in resisting stress-induced damage, as mutations in hydrophobic surfaces lead to extreme thylakoid swelling under high light. Additionally, cryo-CLEM observations provide insights into how VIPP1 coats encapsulate membrane tubules within chloroplasts.
Article
Biochemistry & Molecular Biology
Luca Zinzula, Florian Beck, Sven Klumpe, Stefan Bohn, Guenter Pfeifer, Daniel Bollschweiler, Istvan Nagy, Juergen M. Plitzko, Wolfgang Baumeister
Summary: Cetacean morbillivirus (CeMV) is a highly infectious paramyxovirus that poses a major threat to biodiversity and conservation of endangered marine mammal populations. The structure of CeMV RNP complex reveals unique interactions compared to other morbilliviruses and MeV orthologs, suggesting potential implications for viral phenotype and host adaptation.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Laura Burbaum, Jonathan Schneider, Sarah Scholze, Ralph T. Boettcher, Wolfgang Baumeister, Petra Schwille, Juergen M. Plitzko, Marion Jasnin
Summary: The study visualizes sarcomere organization in neonatal cardiomyocytes using in situ cryo-electron tomography, revealing the hexagonal lattice of thick filaments and the arrangement of thin filaments. It provides direct evidence for thin filament sliding during muscle contraction, showcasing their overlapping arrays of opposite polarity in the fully activated state.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Philipp S. Erdmann, Zhen Hou, Sven Klumpe, Sagar Khavnekar, Florian Beck, Florian Wilfling, Juergen M. Plitzko, Wolfgang Baumeister
Summary: The large and small subunits of the ribosome are synthesized independently within the nucleolus before being exported into the cytoplasm, where they assemble into functional ribosomes. Using in situ cryo-electron tomography, the researchers observed ribosome maturation and revealed the native organization of the nucleolus, providing new insights into ribosome biogenesis.
NATURE COMMUNICATIONS
(2021)
Article
Materials Science, Biomaterials
Frank Mickoleit, Sabine Rosenfeldt, Mauricio Toro-Nahuelpan, Miroslava Schaffer, Anna S. Schenk, Jurgen M. Plitzko, Dirk Schueler
Summary: By optimizing temperature and light intensity, high-efficiency magnetite biomineralization in synthetic R. rubrum magneticum was achieved in this study. The findings demonstrated the high yield of magnetosomes and the efficient expression of enzyme proteins on the magnetosome surface in photoheterotrophic large-scale cultivation.
Article
Multidisciplinary Sciences
Zhong Yan Gan, Sylvie Callegari, Simon A. Cobbold, Thomas R. Cotton, Michael J. Mlodzianoski, Alexander F. Schubert, Niall D. Geoghegan, Kelly L. Rogers, Andrew Leis, Grant Dewson, Alisa Glukhova, David Komander
Summary: The research on the activation mechanism of PINK1 using crystallography and cryo-electron microscopy revealed the orientation of unphosphorylated yet active PINK1 on mitochondria, conformational changes to an active ubiquitin kinase state, and the role of regulatory PINK1 oxidation. The study also elucidates how PINK1 interacts with the mitochondrial outer membrane and suggests that PINK1 activity may be modulated by mitochondrial reactive oxygen species.
Article
Biology
Matthias Poege, Julia Mahamid, Sanae S. Imanishi, Juergen M. Plitzko, Krzysztof Palczewski, Wolfgang Baumeister
Summary: Studies have identified two molecular connectors/spacers in the membrane structure of rod outer segment (ROS) that likely contribute to the precise stacking of ROS disks. Additionally, a continuous supramolecular assembly composed of peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) oligomers enforces the extreme radius of curvature at the disk rims. Together, these molecular assemblies constitute the structural basis of the highly specialized ROS functional architecture.
Article
Multidisciplinary Sciences
Anna Bieber, Cristina Capitanio, Florian Wilfling, Jurgen Plitzko, Philipp S. Erdmann
Summary: This method describes how to target specific cellular sites during FIB milling using a 3D-correlative approach, which combines three-dimensional fluorescence microscopy data with information from the FIB-scanning electron microscope. Rare cellular events and structures can be targeted with high accuracy and visualized at molecular resolution using cryo-transmission electron microscopy (cryo-TEM).
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Mauricio Toro-Nahuelpan, Juergen M. Plitzko, Dirk Schueler, Daniel Pfeiffer
Summary: This study used Volta phase plate cryoelectron tomography to reveal the three-dimensional ultrastructural organization of PopZ in two different bacteria. The results show that PopZ forms a porous network structure.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wenhong Jiang, Jonathan Wagner, Wenjing Du, Juergen Plitzko, Wolfgang Baumeister, Florian Beck, Qiang Guo
Summary: Improvements in cryo-electron tomography sample preparation, electron-microscopy instrumentations, and image processing algorithms have advanced the structural analysis of macromolecules in situ. The study of their interactions with functionally related neighbors, i.e. molecular sociology, is of fundamental importance in biology. The NEighboring Molecule TOpology Clustering (NEMO-TOC) algorithm was presented and optimized for the detection and profiling of polyribosomes in this study. Results suggest synchronous translation in polysomes formed by connecting multiple nonstochastic blocks.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Hugo van den Hoek, Nikolai Klena, Mareike A. Jordan, Gonzalo Alvarez Viar, Ricardo D. Righetto, Miroslava Schaffer, Philipp S. Erdmann, William Wan, Stefan Geimer, Jurgen M. Plitzko, Wolfgang Baumeister, Gaia Pigino, Virginie Hamel, Paul Guichard, Benjamin D. Engel
Summary: The cilium is an organelle similar to an antenna that plays various important roles in cellular functions. The base of the cilium has a selective barrier that controls the entry of large cargo proteins required for ciliary assembly and maintenance. This study used in situ cryo-electron tomography and ultrastructure expansion microscopy to reveal the native structures of the ciliary base and the assembly process of IFT trains.
Article
Biology
Daan B. Boltje, Jacob P. Hoogenboom, Arjen J. Jakobi, Grant J. Jensen, Caspar T. H. Jonker, Max J. Kaag, Abraham J. Koster, Mart G. F. Last, Cecilia de Agrela Pinto, Juergen M. Plitzko, Stefan Raunser, Sebastian Tacke, Zhexin Wang, Ernest B. van der Wee, Roger Wepf, Sander den Hoedt, Suzanne R. Pfeffer
Summary: Cryo-ET combined with subtomogram averaging is a powerful technique for visualizing and determining the structure of macromolecular complexes. However, standard cryo-FIB fabrication used for sample preparation is blind to the precise location of structures or proteins of interest. In this study, a fluorescence microscopy-guided FIB fabrication method was developed to address this issue. By retrofitting a cryogenic microcooler and a fluorescence microscope onto an existing FIB scanning electron microscope, precise targeting at every milling step in the lamella fabrication process was achieved, resulting in improved success rate and throughput for high-resolution imaging.
Article
Biology
Maud Dumoux, Thomas Glen, Jake L. R. Smith, Elaine M. L. Ho, Luis M. A. Perdigao, Avery Pennington, Sven Klumpe, Neville B. Y. Yee, David Andrew Farmer, Pui Y. A. Lai, William Bowles, Ron Kelley, Juergen M. Plitzko, Liang Wu, Mark Basham, Daniel K. Clare, C. Alistair Siebert, Michele C. Darrow, James H. Naismith, Michael Grange, Giulia Zanetti
Summary: Cryogenic plasma FIB/SEM overcomes challenges in imaging non-stained biological samples, producing high-quality images with automated workflows. This technique allows for three-dimensional imaging of bacteria, human cells, and tissue with resolutions typically ranging from 20-50 nm.