Article
Biochemistry & Molecular Biology
Yaqian Li, Jiabin Wang, Xuecheng Chen, Daniel M. Czajkowsky, Zhifeng Shao
Summary: This study used super-resolution optical microscopy to examine the amount of CENP-A and DNA in human centromeric chromatin. The researchers found that the amount of CENP-A remains unchanged in different sized domains, suggesting a strict relationship between CENP-A and microtubule stoichiometries. Additionally, the study revealed that the CENP-A centromeric domain is primarily composed of CENP-A nucleosomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Xian Hao, Jyotsana J. Parmar, Benoit Lelandais, Andrey Aristov, Wei Ouyang, Christian Weber, Christophe Zimmer
Summary: The 3D organization of chromatin fiber in cell nuclei is crucial for gene expression regulation. This study combines single-molecule localization microscopy with a low-cost fluorescence labeling strategy to visualize single human chromosomes at high resolution. The results suggest that there are 6-25 or more purely cohesin-dependent chromatin loops per megabase of DNA in single cells.
Review
Biochemistry & Molecular Biology
Jon Ander Nieto-Garai, June Olazar-Intxausti, Itxaso Anso, Maier Lorizate, Oihana Terrones, Francesc-Xabier Contreras
Summary: Interorganelle membrane contact sites (MCS) are areas of close vicinity between the membranes of two organelles that are maintained by protein tethers. The study of MCS is important due to its implication in various biological functions. Super-resolution fluorescence microscopy (SRFM) has emerged as a powerful tool for studying MCS. This review explores the characteristics and biological functions of MCS, summarizes different approaches for studying them, and focuses on the use of SRFM techniques in MCS research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Teodora Andrian, Pietro Delcanale, Silvia Pujals, Lorenzo Albertazzi
Summary: The functionalization of nanoparticles with functional moieties is important for achieving cell targeting in nanomedicine. The correlation between size and ligand number in nanoparticles is crucial for understanding structure-activity relations. A new method combining super-resolution microscopy and transmission electron microscopy, called super-resCLEM, has been introduced to accurately measure these parameters and address the issue of heterogeneity in nanoparticle populations.
Article
Biochemistry & Molecular Biology
Sang-Hee Shim
Summary: Recent advancements in sequencing and imaging technologies have provided new insights into the three-dimensional folding of the genome in the nucleus. These technologies have enabled visualization of chromatin structures at varying resolutions, revealing both ensemble behavior consistent with sequencing results and single-cell variations. However, they have also raised questions about the roles of architectural proteins and enhancer-promoter interactions, leading to contradictory results. Live-cell labeling methods, including the CRISPR/dCas9 system, offer potential for further understanding genome structural dynamics.
Article
Biochemistry & Molecular Biology
Ivona Kubalova, Alzbeta Nemeckova, Klaus Weisshart, Eva Hribova, Veit Schubert
Summary: Fluorescence light microscopy is important for studying cellular structures, but limited by light diffraction; super-resolution techniques like SIM are used to overcome this limitation; however, STED and SMLM, which offer higher resolution, are not widely applied in plant cell research due to specific sample preparation requirements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Seokran Go, Dokyung Jeong, Jinkyoung Chung, Geun-Ho Kim, Jaewoo Song, Eunyoung Moon, Yang Hoon Huh, Doory Kim
Summary: This research examines the ultrastructural organization of various organelles in different platelet intermediates using super-resolution microscopy. The study reveals that microtubules control the overall shape of platelet intermediates, while actin and microtubules regulate the distribution of organelles. These findings call for a reassessment of organelle redistribution in platelet intermediates.
Review
Cell Biology
Jianquan Xu, Yang Liu
Summary: Chromatin organization plays a crucial role in gene regulation and genome maintenance. Disruption of chromatin structure is associated with various pathological processes and diseases. Recent advances in single molecule localization microscopy (SMLM) provide new opportunities to visualize chromatin architecture at nanometer resolution and improve our understanding of diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Fabian Lang, Maria F. Contreras-Gerenas, Marton Gelleri, Jan Neumann, Ole Kroeger, Filip Sadlo, Krzysztof Berniak, Alexander Marx, Christoph Cremer, Hans-Achim Wagenknecht, Heike Allgayer
Summary: Tumour cell heterogeneity and its early individual diagnosis present a fundamental challenge in cancer diagnosis and therapy. Single molecule localisation microscopy (SMLM) has been used to analyze subcellular features, although primarily limited to cultured cell lines. A new approach using SMLM allows for quantitative analysis of chromatin nanostructure in individual cells from resected colorectal carcinoma patient tissue, providing insights into differences in chromatin architecture between normal and carcinoma tissues.
Article
Chemistry, Multidisciplinary
Emmanouil Archontakis, Linlin Deng, Peter Zijlstra, Anja R. A. Palmans, Lorenzo Albertazzi
Summary: Folding a polymer chain into a well-defined single chain polymeric nanoparticle (SCPN) is a fascinating approach to obtaining structured and functional nanoparticles. However, due to the heterogeneous nature of SCPNs, which arise from the polydispersity of their synthesis, there are nanoparticles with different physicochemical properties in a single batch. This poses a great challenge to characterizing SCPNs at a single-particle level. In this study, the NR-sPAINT super-resolution fluorescence technique was implemented to study SCPNs at a single-particle level, allowing the mapping of small-molecule binding rates and polarity on individual SCPNs. The experimental results revealed interparticle differences in binding rates within the same polymer design, as well as a marked polarity shift between different designs. This research sheds light on the importance of hydrophobic pendant groups in determining binding properties and inducing single-particle polarity diversity, and represents a significant step toward designing SCPNs for specific applications.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Huimin Chen, Han Wang, Yongchun Wei, Maomao Hu, Bo Dong, Hongbao Fang, Qixin Chen
Summary: In this study, researchers used structured illumination microscopy to investigate the distribution and cellular localization of Cy5-dextran in living cells. They found that Cy5-dextran could be absorbed by HeLa cells and exhibited differential distribution in lysosomes and mitochondria, triggering different biological responses.
CHINESE CHEMICAL LETTERS
(2022)
Article
Oncology
Dan Huang, Cristel V. Camacho, Sara Martire, Anusha Nagari, Rohit Setlem, Xuan Gong, Andrea D. Edwards, Shu-Ping Chiu, Laura A. Banaszynski, W. Lee Kraus
Summary: Recent studies have found cancer-associated mutations in histone genes, resulting in the expression of mutant core histones called oncohistones. These mutations affect cell growth and inhibit ADP-ribosylation at specific sites in wild-type histones. Some mutations significantly alter chromatin accessibility, gene expression, and acetylation modification. This study reveals the significance of cancer-driving mutations in histones as sites of ADP-ribosylation and their role in evading the growth-regulating effects of PARP1.
Article
Multidisciplinary Sciences
Yicong Wu, Xiaofei Han, Yijun Su, Melissa Glidewell, Jonathan S. Daniels, Jiamin Liu, Titas Sengupta, Ivan Rey-Suarez, Robert Fischer, Akshay Patel, Christian Combs, Junhui Sun, Xufeng Wu, Ryan Christensen, Corey Smith, Lingyu Bao, Yilun Sun, Leighton H. Duncan, Jiji Chen, Yves Pommier, Yun-Bo Shi, Elizabeth Murphy, Sougata Roy, Arpita Upadhyaya, Daniel Colon-Ramos, Patrick La Riviere, Hari Shroff
Summary: Researchers have enhanced the performance of confocal microscopy using four approaches: developing compact line scanners, combining multi-view imaging, adapting techniques from structured illumination microscopy, and utilizing deep learning. They successfully improved imaging resolution, reduced phototoxicity, and demonstrated these advancements on over 20 different samples.
Article
Biochemistry & Molecular Biology
Migle Tomkuvien, Markus Meier, Diana Ikasalaite, Julia Wildenauer, Visvaldas Kairys, Saulius Klimasauskas, Laura Manelyt
Summary: Methylation of cytosine is an important epigenetic mark that can alter DNA and chromatin structure. This study investigates how larger chemical variations in DNA affect chromatin structure and nucleosome formation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Agnieszka Pierzynska-Mach, Alberto Diaspro, Francesca Cella Zanacchi
Summary: This study used single-molecule localization microscopy (SMLM) to analyze the nanoscale organization of DEK protein. It found differences in cluster features of DEK protein in different breast cell types and showed that the nanoscale organization of DEK clusters remains stable regardless of protein overexpression or chromatin compaction changes.
Article
Biochemistry & Molecular Biology
Avinash Patel, Hyun O. Lee, Louise Jawerth, Shovamayee Maharana, Marcus Jahnel, Marco Y. Hein, Stoyno Stoynov, Julia Mahamid, Shambaditya Saha, Titus M. Franzmann, Andrej Pozniakovski, Ina Poser, Nicola Maghelli, Loic A. Royer, Martin Weigert, Eugene W. Myers, Stephan Grill, David Drechsel, Anthony A. Hyman, Simon Alberti
Article
Biology
Sonja Kroschwald, Shovamayee Maharana, Daniel Mateju, Liliana Malinovska, Elisabeth Nueske, Ina Poser, Doris Richter, Simon Alberti
Article
Biochemistry & Molecular Biology
Shovamayee Maharana, K. Venkatesan Iyer, Nikhil Jain, Mallika Nagarajan, Yejun Wang, G. V. Shivashankar
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biology
Matthias Christoph Munder, Daniel Midtvedt, Titus Franzmann, Elisabeth Nueske, Oliver Otto, Maik Herbig, Elke Ulbricht, Paul Mueller, Anna Taubenberger, Shovamayee Maharana, Liliana Malinovska, Doris Richter, Jochen Guck, Vasily Zaburdaev, Simon Alberti
Article
Biochemical Research Methods
Yejun Wang, Nikhil Jain, Mallika Nagarajan, Shovamayee Maharana, K. Venkatesan Iyer, Shefali Talwar, G. V. Shivashankar
Article
Biochemistry & Molecular Biology
Jie Wang, Jeong-Mo Choi, Alex S. Holehouse, Hyun O. Lee, Xiaojie Zhang, Marcus Jahnel, Shovamayee Maharana, Regis Lemaitre, Andrei Pozniakovsky, David Drechsel, Ina Poser, Rohit V. Pappu, Simon Alberti, Anthony A. Hyman
Article
Multidisciplinary Sciences
Shovamayee Maharana, Jie Wang, Dimitrios K. Papadopoulos, Doris Richter, Andrey Pozniakovsky, Ina Poser, Marc Bickle, Sandra Rizk, Jordina Guillen-Boixet, Titus M. Franzmann, Marcus Jahnel, Lara Marrone, Young-Tae Chang, Jared Sterneckert, Pavel Tomancak, Anthony A. Hyman, Simon Alberti
Article
Cell Biology
Sonja Kroschwald, Matthias C. Munder, Shovamayee Maharana, Titus M. Franzmann, Doris Richter, Martine Ruer, Anthony A. Hyman, Simon Alberti
Article
Biophysics
Deepak Kumar Sinha, Bidisha Banerjee, Shovamayee Maharana, G. V. Shivashankar
BIOPHYSICAL JOURNAL
(2008)
Meeting Abstract
Biophysics
Shovamayee Maharana, G. V. Shivashankar
BIOPHYSICAL JOURNAL
(2012)
Article
Biophysics
Shovamayee Maharana, Divya Sharma, Xianke Shi, G. V. Shivashankar
BIOPHYSICAL JOURNAL
(2012)
Article
Multidisciplinary Sciences
K. Venkatesan Iyer, Shovamayee Maharana, Soumya Gupta, Albert Libchaber, Tsvi Tlusty, G. V. Shivashankar
Article
Biochemistry & Molecular Biology
Daniel Mateju, Titus M. Franzmann, Avinash Patel, Andrii Kopach, Edgar E. Boczek, Shovamayee Maharana, Hyun O. Lee, Serena Carra, Anthony A. Hyman, Simon Alberti