Article
Biology
Bronwyn A. Lucas, Benjamin A. Himes, Liang Xue, Timothy Grant, Julia Mahamid, Nikolaus Grigorieff
Summary: The study emphasizes the importance of understanding molecular mechanisms within the broader context of the cell and introduces a 2D template matching method to address technical limitations. By implementing GPU acceleration in the cisTEM software, the approach becomes more scalable and accessible. Experimental results demonstrate that 2D template matching is a versatile tool for in situ visual proteomics and in situ structure determination, showcasing its precision and sensitivity in identifying molecular complexes.
Article
Polymer Science
Mahdi Hamidinejad, Taib Arif, Guorui Wang, Sasan Rezaei, Peter Serles, Hayden K. . Taylor, Chul B. Park, Tobin Filleter
Summary: The study directly images the sectorization of polymer single crystals through anisotropic elastic deformation on the crystal surface. By utilizing a variant of friction force microscopy, the scanning direction of the probe tip parallel to the cantilever axis allows for high contrast imaging of sectorization in polymer single crystals. This approach provides a fast, easy, and nondestructive characterization of the microstructure and in-plane elastic anisotropy of compliant crystalline materials such as polymers.
Article
Biochemical Research Methods
Xuefeng Du, Haohan Wang, Zhenxi Zhu, Xiangrui Zeng, Yi-Wei Chang, Jing Zhang, Eric Xing, Min Xu
Summary: In this study, a Hybrid Active Learning (HAL) framework is proposed to alleviate the labeling burden by querying a large pool of unlabeled subtomograms. HAL framework utilizes uncertainty sampling and a discriminator to optimize subtomogram selection, achieving comparable testing performance with less labeled resources.
Article
Multidisciplinary Sciences
Jiro Usukura, Akihiro Narita, Tomoharu Matsumoto, Eiji Usukura, Takeshi Sunaoshi, Syunya Watanabe, Yusuke Tamba, Yasuhira Nagakubo, Takashi Mizuo, Junzo Azuma, Masako Osumi, Kazutaka Nimura, Ryuichiro Tamochi, Yoichi Ose
Summary: The new type of cryo-electron microscope allows simultaneous acquisition of transmission and surface images, with high-quality images at 30 kV. Using the unroofing method, fine structures near the cell membrane become visible, including the cytoskeleton, polyribosome chains, and endoplasmic reticulum.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Interdisciplinary Applications
E. Moebel, C. Kervrann
Summary: This paper presents a weakly supervised subtomogram classification method based on transfer learning, using a deep neural network to learn a clustering friendly representation capable of capturing 3D shapes in the presence of noise and artifacts. By applying k-means clustering to a learning-based representation, real subtomograms can be classified satisfactorily according to structural similarity without manual annotation.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Multidisciplinary Sciences
Huaipeng Xing, Reiya Taniguchi, Iskander Khusainov, Jan Philipp Kreysing, Sonja Welsch, Beata Turonova, Martin Beck
Summary: Using cryo-electron tomography, we resolved high-resolution ribosome structures inside human cells, revealing their distribution of functional states, including the elongation cycle, Z transfer RNA binding site, and ribosome expansion segments dynamics. Studying ribosome structures from cells treated with Homoharringtonine, a drug used against chronic myeloid leukemia, we discovered how translation dynamics were altered in situ and identified small molecules within the active site of the ribosome. Thus, we can assess structural dynamics and drug effects at high resolution within human cells.
Article
Chemistry, Physical
Ji Hun Wi, Cheol Ho Heo, HyeRan Gwak, Cheulhee Jung, So Yeon Kim
Summary: This study investigated the impact of cellular senescence on membrane properties through different imaging techniques. The research found that as cells undergo senescence, there is an increase in ceramide-rich lipid rafts in the membrane, highlighting the importance of membrane properties in cellular senescence.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Katrin Walter, Jan Bourquin, Anahid Amiri, Niklas Scheer, Martin Dehnert, Anna Lisa Eichhorn, Christian Dietz
Summary: Directly sensing focal adhesions and cell-cell contacts with a force sensor can provide information on the migration and invasion potential of cells. The technique quantifies the lateral forces of anchoring points and reveals local lateral forces of 1.0-1.5 nN for focal adhesions and slightly higher values at cell-cell contact interfaces. This method has the potential to improve our understanding of the relationship between mechanical properties of cell connections and disease states in the future.
Article
Physics, Multidisciplinary
Shadi Fatayer, Florian Albrecht, Ivano Tavernelli, Mats Persson, Nikolaj Moll, Leo Gross
Summary: By using single charge injections with an atomic force microscope, redox reactions of a molecule on a multilayer insulating film were investigated. Three channels for neutralization were observed and corresponding to transitions to different excited states. Energy differences between these transitions were measured using single-electron tunneling spectroscopy, and compared with density functional theory calculations. The results show that excited states of molecules can be prepared and their optical gap energies can be quantified through controlled single-charge injections.
PHYSICAL REVIEW LETTERS
(2021)
Review
Chemistry, Multidisciplinary
Peter Tieu, Xingxu Yan, Mingjie Xu, Phillip Christopher, Xiaoqing Pan
Summary: The development of single atom catalysts (SACs) with carefully controlled properties has been driven by the need for atom efficient catalysts. Advances in transmission electron microscopy (TEM) techniques, including aberration correction, spectroscopy, and in situ/operando observation, have enabled researchers to study SACs at an atomic scale, providing crucial information about their location, characteristics, and stability.
Article
Biochemistry & Molecular Biology
Maryna Loewe, Sebastian Haensch, Eymen Hachani, Lutz Schmitt, Stefanie Weidtkamp-Peters, Alexej Kedrov
Summary: Biochemical processes in crowded cellular environments, such as membranes, are affected by macromolecular crowding. Researchers developed a fluorescence-based sensor to quantify macromolecular crowding at membrane interfaces, and validated its dynamics in Escherichia coli inner membrane vesicles.
Review
Chemistry, Multidisciplinary
Ruichun Luo, Meng Gao, Chunwen Wang, Juntong Zhu, Roger Guzman, Wu Zhou
Summary: This review provides an overview of the static and in situ investigation of functional structures, defects, and interfaces in 2D transition metal dichalcogenides (TMDs), primarily utilizing scanning transmission electron microscopy and electron energy loss spectroscopy. Recent advancements in in situ visualization and manipulation of 2D TMDs using electron beams are also highlighted.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Spectroscopy
Heera Jayan, Hongbin Pu, Da-Wen Sun
Summary: In this study, Raman spectroscopy combined with deuterium labelling was used to analyze the metabolic activity of Escherichia coli cells. The method could semi-quantitatively determine total metabolic activity, macromolecule specific identification, and lipid and protein metabolism in a single cell.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Agriculture, Multidisciplinary
Mengxue Diao, Chi Li, Jianxiu Li, Jian Lu, Nengzhong Xie
Summary: This study investigates the dynamic process of sclareol biotransformation and proposes a potential transformation pathway of sclareol in Hyphozyma roseonigra based on detected intermediates.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemical Research Methods
Chia Ying Huang, Sylvain Aumonier, Sylvain Engilberge, Deniz Eris, Kate Mary Louise Smith, Filip Leonarski, Justyna Aleksandra Wojdyla, John H. Beale, Dominik Buntschu, Anuschka Pauluhn, May Elizabeth Sharpe, Alexander Metz, Vincent Olieric, Meitian Wang
Summary: Continuous developments in cryogenic X-ray crystallography have provided us with most of our understanding of 3D protein structures. However, the use of cryogenic temperatures may result in fictitious structures, limiting our knowledge of protein dynamics. In this study, a room-temperature X-ray crystallographic method was developed to capture structural snapshots under physiological conditions, revealing surprising binding discrepancies and capturing multiple binding poses and their interactions with DMSO. This opens up new prospects for structure determination and interpretation at physiological temperatures.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Microscopy
M. K. Morphew, E. T. O'Toole, C. L. Page, M. Pagratis, J. Meehl, T. Giddings, J. M. Gardner, C. Ackerson, S. L. Jaspersen, M. Winey, A. Hoenger, J. R. Mcintosh
JOURNAL OF MICROSCOPY
(2015)
Article
Cell Biology
Anand N. Rao, Aditi Falnikar, Eileen T. O'Toole, Mary K. Morphew, Andreas Hoenger, Michael W. Davidson, Xiaobing Yuan, Peter W. Baas
JOURNAL OF CELL BIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Joanna R. Brown, Cindi L. Schwartz, Johil. M. Heumann, Scott C. Dawson, Andreas Hoenger
JOURNAL OF STRUCTURAL BIOLOGY
(2016)
Review
Biochemistry & Molecular Biology
Eva A. Rog-Zielinska, Callum M. Johnston, Eileen T. O'Toole, Mary Morphew, Andreas Hoenger, Peter Kohl
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2016)
Article
Infectious Diseases
Johanna L. Hoeoeg, Sylvain Lacomble, Cedric Bouchet-Marquis, Laura Briggs, Kristin Park, Andreas Hoenger, Keith Gull
PLOS NEGLECTED TROPICAL DISEASES
(2016)
Article
Cell Biology
Chris N. Goulbourne, Peter Gin, Angelica Tatar, Chika Nobumori, Andreas Hoenger, Haibo Jiang, Chris R. M. Grovenor, Oludotun Adeyo, Jeffrey D. Esko, Ira J. Goldberg, Karen Reue, Peter Tontonoz, Andre Bensadoun, Anne P. Beigneux, Stephen G. Young, Loren G. Fong
Article
Biochemistry & Molecular Biology
Vassiliki A. Iconomidou, Aristeidis Leontis, Andreas Hoenger, Stavros J. Hamodrakas
Article
Cell Biology
Katherine C. Rank, Chun Ju Chen, Julia Cope, Ken Porche, Andreas Hoenger, Susan P. Gilbert, Ivan Rayment
JOURNAL OF CELL BIOLOGY
(2012)
Article
Biochemistry & Molecular Biology
Johanna L. Hoeoeg, Cedric Bouchet-Marquis, J. Richard McIntosh, Andreas Hoenger, Keith Gull
JOURNAL OF STRUCTURAL BIOLOGY
(2012)
Article
Biochemistry & Molecular Biology
Miguel A. Gonzalez, Julia Cope, Katherine C. Rank, Chun Ju Chen, Peter Tittmann, Ivan Rayment, Susan P. Gilbert, Andreas Hoenger
JOURNAL OF STRUCTURAL BIOLOGY
(2013)
Article
Multidisciplinary Sciences
Julia Cope, Katherine C. Rank, Susan P. Gilbert, Ivan Rayment, Andreas Hoenger
Article
Plant Sciences
Andreas Hoenger
Article
Biology
Johanna L. Hoeoeg, Sylvain Lacomble, Eileen T. O'Toole, Andreas Hoenger, J. Richard McIntosh, Keith Gull
Article
Biology
Minghua Liu, Maria B. Heimlicher, Mirjam Bachler, Chieze C. Ibeneche-Nnewihe, Ernst-Ludwig Florin, Damian Brunner, Andreas Hoenger
Article
Cell Biology
Maria B. Heimlicher, Mirjam Bachler, Minghua Liu, Chieze Ibeneche-Nnewihe, Ernst-Ludwig Florin, Andreas Hoenger, Damian Brunner
JOURNAL OF CELL SCIENCE
(2019)