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
Medicine, General & Internal
Lindsey A. George, Paul E. Monahan, M. Elaine Eyster, Spencer K. Sullivan, Margaret Ragni, Stacy E. Croteau, John E. J. Rasko, Michael Recht, Benjamin J. Samelson-Jones, Amy MacDougall, Kristen Jaworski, Robert Noble, Marla Curran, Klaudia Kuranda, Federico Mingozzi, Tiffany Chang, Kathleen Z. Reape, Xavier M. Anguela, Katherine A. High
Summary: A gene therapy trial using an AAV vector (SPK-8011) for factor VIII expression in 18 men with hemophilia A showed sustained expression in most participants, leading to reduced bleeding events and discontinuation of prophylaxis.
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
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)
Article
Chemistry, Multidisciplinary
Jared Peck, Jonathan F. Fay, Joshua D. Strauss
Summary: This study tested key parameters to increase the data collection speed in single-particle cryo-EM and successfully obtained high-resolution EM maps of mouse apoferritin. By using specific methods and operating procedures, rapid determination of single-particle cryo-EM structures can be achieved.
Article
Multidisciplinary Sciences
Kayo Nozawa, Yoshimasa Takizawa, Leonidas Pierrakeas, Chizuru Sogawa-Fujiwara, Kazumi Saikusa, Satoko Akashi, Ed Luk, Hitoshi Kurumizaka
Summary: The canonical nucleosome is the major packaging unit of eukaryotic chromatin, and the H3-H4 octasome is a nucleosome-like particle with alternative histone stoichiometry. The structure of the H3-H4 octasome is flexible.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Lunda Shen, Zhaoming Su, Kailu Yang, Cheng Wu, Thomas Becker, Deborah Bell-Pedersen, Junjie Zhang, Matthew S. Sachs
Summary: The study elucidated the mechanism of action of CHX in inhibiting protein synthesis by arresting the ribosome in the classical PRE translocation state, without interfering with A-site reactivity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Gabriel Javitt, Deborah Fass
Summary: The glycoprotein von Willebrand factor (VWF) plays a crucial role in hemostasis, and its assembly into tubular structures is a key feature. This study demonstrates that a segment of the human intestinal gel-forming mucin (MUC2) also has the ability to form tubules similar to VWF. This suggests a possible evolutionary origin for VWF tubules and provides insights into the design principles of mucins and VWF.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Sepideh Valimehr, Ashish Sethi, Manjari Shukla, Sudipta Bhattacharyya, Mohsen Kazemi, Isabelle Rouiller
Summary: p97/VCP, a highly conserved AAA+ ATPase, is a significant therapeutic target in the treatment of neurodegenerative diseases and cancer. This review provides an understanding of p97's molecular mechanism during the ATPase cycle and its regulation by cofactors and inhibitors. It compares structural information obtained in different nucleotide states and discusses the impact of pathogenic mutations on p97's conformational changes. Overall, the review emphasizes how the mechanistic knowledge of p97 contributes to the design of pathway-specific modulators and inhibitors.
Article
Biochemical Research Methods
Xiangwen Wang, Yonggang Lu, Xianghong Lin
Summary: This paper proposes a two-stage spectral clustering algorithm for the classification of heterogeneous cryo-EM projection images, and designs two novel distance measures. Experimental results demonstrate that these two new methods can improve the classification performance of spectral clustering, and using the proposed algorithm can achieve higher classification and reconstruction accuracy compared to existing methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
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
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
Biochemistry & Molecular Biology
Sarah M. Smith, Gabrielle Larocque, Katherine M. Wood, Kyle L. Morris, Alan M. Roseman, Richard B. Sessions, Stephen J. Royle, Corinne J. Smith
Summary: The interaction between Clathrin and the AP2 complex plays a crucial role in coated-pit assembly, with a beta 2 appendage able to bind in at least two positions in the clathrin cage. This multi-modal binding is shown to be a fundamental property of clathrin-AP2 interactions.
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
Multidisciplinary Sciences
Michael Laue, Anne Kauter, Tobias Hoffmann, Lars Moeller, Janine Michel, Andreas Nitsche
Summary: The study compared the ultrastructure of SARS-CoV-2 and SARS-CoV, finding that they were virtually identical in virus morphology and morphometry, but SARS-CoV had approximately 30% more spikes per virus particle than SARS-CoV-2.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Ruohua Shi, Keyan Bi, Kai Du, Lei Ma, Fang Fang, Lingyu Duan, Tingting Jiang, Tiejun Huang
Summary: Cell membrane segmentation in electron microscopy (EM) images is an important task. Current approaches perform well on low-resolution datasets but struggle with high-resolution datasets. Through eye movement and perceptual consistency experiments, we found that humans are more sensitive to membrane structure and can tolerate misalignment. Based on these findings, we propose a computational framework that incorporates human perception characteristics, including the perceptual Hausdorff distance (PHD) evaluation metric and a PHD-guided segmentation network (PS-Net).
Article
Chemistry, Applied
Christos Soukoulis, Solmaz Behboudi-Jobbehdar, William Macnaughtan, Christopher Parmenter, Ian D. Fisk
FOOD HYDROCOLLOIDS
(2017)
Article
Chemistry, Applied
Natalie Chiu, Amparo Tarrega, Christopher Parmenter, Louise Hewson, Bettina Wolf, Ian D. Fisk
FOOD HYDROCOLLOIDS
(2017)
Article
Chemistry, Multidisciplinary
David E. Clarke, Christopher D. J. Parmenter, Oren A. Scherman
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2018)
Correction
Multidisciplinary Sciences
Qin Hu, Xue-Zhong Sun, Christopher D. J. Parmenter, Michael W. Fay, Emily F. Smith, Graham A. Rance, Yinfeng He, Fan Zhang, Yaan Liu, Derek Irvine, Christopher Tuck, Richard Hague, Ricky Wildman
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Zubair Nizamudeen, Robert Markus, Rhys Lodge, Christopher Parmenter, Mark Platt, Lisa Chakrabarti, Virginie Sottile
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2018)
Article
Chemistry, Multidisciplinary
Thomas M. Bennett, Guping He, Ryan R. Larder, Michael G. Fischer, Graham A. Rance, Michael W. Fay, Amanda K. Pearce, Christopher D. J. Parmenter, Ullrich Steiner, Steven M. Howdle
Article
Nanoscience & Nanotechnology
Alistair Speidel, James W. Murray, Ivan Bisterov, Jonathon Mitchell-Smith, Christopher Parmenter, Adam T. Clare
ACS APPLIED MATERIALS & INTERFACES
(2020)
Article
Multidisciplinary Sciences
Vlad Dinu, Yudong Lu, Nicola Weston, Ryan Lithgo, Hayley Coupe, Guy Channell, Gary G. Adams, Amelia Torcello Gomez, Carlos Sabater, Alan Mackie, Christopher Parmenter, Ian Fisk, Mary K. Phillips-Jones, Stephen E. Harding
SCIENTIFIC REPORTS
(2020)
Article
Microscopy
Christopher David Parmenter, Zubair Ahmed Nizamudeen
Summary: This paper explores the development of the Cryo-Lift-Out technique for cryo-TEM preparation, presenting key hardware, basic principles, and practical considerations for new users. It also provides detailed protocols and discussions on further development, aiming to educate and guide beginners in the field.
JOURNAL OF MICROSCOPY
(2021)
Editorial Material
Microscopy
D. A. M. de Winter, C. D. J. Parmenter
JOURNAL OF MICROSCOPY
(2021)
Article
Multidisciplinary Sciences
Aleksandra Gonciaruk, Matthew R. Hall, Michael W. Fay, Christopher D. J. Parmenter, Christopher H. Vane, Andrei N. Khlobystov, Nino Ripepi
Summary: Gas storage and recovery processes in shales are influenced by nano-scale porosity and chemical composition. Research shows that gas adsorption at low pressure is controlled by pore width rather than chemical composition. Nanoscale structure of kerogen includes various forms, allowing accurate prediction of gas sorption, storage, and diffusion properties in shales.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Zubair Ahmed Nizamudeen, Rachael Xerri, Christopher Parmenter, Kiran Suain, Robert Markus, Lisa Chakrabarti, Virginie Sottile
Summary: The study found that low-power sonication on extracellular vesicles collected from mesenchymal stem cells not only had significant disaggregation effects, but also altered the size distribution and membrane integrity of EVs, affecting their uptake by cells. These results highlight the need for a more systematic analysis of sonication procedures to improve reproducibility in EV-based cellular experiments.
Article
Chemistry, Multidisciplinary
Jisun Im, Yaan Liu, Qin Hu, Gustavo F. Trindade, Christopher Parmenter, Michael Fay, Yinfeng He, Derek J. Irvine, Christopher Tuck, Ricky D. Wildman, Richard Hague, Lyudmila Turyanska
Summary: This study successfully fabricates complex 3D metal nanoparticle-polymer nanocomposites using two-photon polymerization (2PP). Three complementary strategies are described: in situ formation of metal nanoparticles (MeNPs) through a single-step photoreduction process, integration of pre-formed MeNPs into 2PP resin, and site-selective MeNPs decoration of 3D 2PP structures. These strategies offer exciting opportunities for the fabrication of MeNP composites with sub-micron resolution for various applications.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Microscopy
Daniel J. Merryweather, Nicola Weston, Jordan Roe, Christopher Parmenter, Mark P. Lewis, Paul Roach
Summary: Collagen hydrogels have wide applications in bioengineering and soft material engineering, particularly in medical therapeutics, medical devices, and biosensors. However, studying the microstructure of collagen gels is challenging due to the relationship between hydration and molecular organization. Robust sample preparation and handling protocols are needed to visualize and explore the microscale organization of collagen hydrogels.
JOURNAL OF MICROSCOPY
(2023)
Article
Chemistry, Multidisciplinary
Craig T. Stoppiello, Helena Isla, Marta Martinez-Abadia, Michael W. Fay, Christopher D. J. Parmenter, Martin J. Roe, Belen Lerma-Berlanga, Carlos Marti-Gastaldo, Aurelio Mateo-Alonso, Andrei N. Khlobystov
