Article
Biochemistry & Molecular Biology
Sabrina Koch, Anne-Bart Seinen, Michael Kamel, Daniel Kuckla, Cornelia Monzel, Alexej Kedrov, Arnold J. M. Driessen
Summary: This study uses total internal reflection fluorescence microscopy to investigate the oligomeric state and diffusion of SecYEG translocons in supported lipid bilayers at the single-molecule level. The findings suggest that the complex mobility of SecYEG arises from the conformational dynamics of the translocon and protein-lipid interactions.
Article
Virology
R. A. Petazzi, A. A. Koikkarah, N. D. Tischler, S. Chiantia
Summary: Hantaviruses are newly emerging pathogens that can cause deadly outbreaks in the human population. This study investigates the protein-protein interactions driving the assembly of the hantavirus envelope using advanced fluorescence microscopy methods. The results support a model where viral spikes are formed through clustering of hetero-dimers of the viral glycoproteins Gn and Gc, providing possible evidence for the initial assembly steps of the viral envelope in the Golgi apparatus of living cells.
JOURNAL OF VIROLOGY
(2021)
Article
Multidisciplinary Sciences
Christian Niederauer, Chikim Nguyen, Miles Wang-Henderson, Johannes Stein, Sebastian Strauss, Alexander Cumberworth, Florian Stehr, Ralf Jungmann, Petra Schwille, Kristina A. Ganzinger
Summary: DNA-PAINT-SPT technique overcomes the limitations of fluorophore photobleaching and significantly improves observation times in in vitro SPT experiments. It is now extended to enable simultaneous dual-colour detection, allowing the quantification of protein dimerization and live cell membrane protein tracking. The technique demonstrates improved performance compared to single-dye SPT.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Chenyi Liao, Ye Liu, Dinglin Zhang, Guohui Li
Summary: This review summarizes the recent progress in integrating cryoelectron microscopy and multiscale molecular modeling to understand the dynamics and function-related mechanism in various types of protein complexes. The future direction of multiscale simulations is to interpret the regulation and function enhancement of large complex multibodies using advanced structural-biology techniques and computing architectures.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Review
Plant Sciences
Yaning Cui, Xi Zhang, Xiaojuan Li, Jinxing Lin
Summary: New imaging methodologies with high contrast and molecular specificity have enabled researchers to analyze dynamic processes in plant cells at various scales. This review focuses on selected microscopy techniques, discussing their principles, applications, pros and cons, and methods for quantitative analysis. It provides guidance for plant scientists in selecting appropriate techniques to study structures and dynamic processes in plants.
Article
Chemistry, Multidisciplinary
Wenjie Liu, Abinash Padhi, Xiaohui Zhang, Jairaj Narendran, Mark A. Anastasio, Amrinder S. Nain, Joseph Irudayaraj
Summary: This study elucidates the spatiotemporal organization of heterochromatin in the elongated nuclei of cells on aligned nanofibers. The findings suggest that the anisotropy of nuclei is sufficient to drive heterochromatin alterations, and reveal an unconventional H3K9me3 heterochromatin distribution.
Article
Biology
George L. Hamilton, Nabanita Saikia, Sujit Basak, Franceine S. Welcome, Fang Wu, Jakub Kubiak, Changcheng Zhang, Yan Hao, Claus A. M. Seidel, Feng Ding, Hugo Sanabria, Mark E. Bowen
Summary: PSD-95 is a scaffold protein that links postsynaptic receptors to presynaptic neurotransmitter release sites. The study combines discrete molecular dynamics and single molecule FRET to characterize the supertertiary structure of PSD-95. The results reveal the conformational changes of PDZ3 and its binding ability to neuroligin.
Article
Multidisciplinary Sciences
Sara Marsango, Laura Jenkins, John D. Pediani, Sophie J. Bradley, Richard J. Ward, Sarah Hesse, Gabriel Biener, Michael R. Stoneman, Andrew B. Tobin, Valerica Raicu, Graeme Milligan
Summary: This study investigated the quaternary organization of the M-1 muscarinic acetylcholine receptor in native tissues using transgenic mice. The receptor was found to exist as a mixture of monomers, dimers, and higher-order oligomeric complexes. Treatment with both agonist and antagonist ligands promoted monomerization of the receptor.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
R. Pinto-Camara, A. Linares, D. S. Moreno-Gutierrez, H. O. Hernandez, J. D. Martinez-Reyes, J. M. Rendon-Mancha, C. D. Wood, A. Guerrero
Summary: FCSlib is an open-source R tool specially designed for analyzing fluorescence fluctuation spectroscopy data, covering various techniques.
Review
Cell Biology
Yicong Wu, Hari Shroff
Summary: This article reviews the importance of multiscale fluorescence imaging in biological research, discusses fundamental challenges, and highlights successful examples in the field. By synthesizing these cases, the aim is to identify general strategies to accelerate progress in this area.
HISTOCHEMISTRY AND CELL BIOLOGY
(2022)
Article
Chemistry, Physical
Koen Kennes, Alexey Kubarev, Coralie Demaret, Laureline Treps, Olivier Delpoux, Mickael Rivallan, Emmanuelle Guillon, Alain Methivier, Theodorus de Bruin, Axel Gomez, Bogdan Harbuzaru, Maarten B. J. Roeffaers, Celine Chizallet
Summary: Shaping has a significant impact on the acidity and catalytic properties of acid zeolite catalysts. The choice and use of binders can greatly affect the performance of the catalyst, with migration of cations and pore blockage being the most detrimental effects.
Article
Optics
Ida S. Opstad, Daniel H. Hansen, Sebastian Acuna, Florian Strohl, Anish Priyadarshi, Jean-Claude Tinguely, Firehun T. Dullo, Roy A. Dalmo, Tore Seternes, Balpreet S. Ahluwalia, Krishna Agarwal
Summary: Photon chip-based total internal reflection fluorescence microscopy (c-TIRFM) is a new technology that allows for the introduction of temporal fluctuations in the illumination pattern in wide waveguides, exploiting the multimodal nature for super-resolution imaging using the multiple signal classification algorithm. The resolution improvement compared to conventional images was measured to be 2.2-3.6-fold.
Article
Biochemistry & Molecular Biology
Colin Farrell, Maria Vaquero-Sedas, Maria D. Cubiles, Michael Thompson, Alejandro Vega-Vaquero, Matteo Pellegrini, Miguel A. Vega-Palas
Summary: DNA methylation modulates telomere function in Arabidopsis thaliana, where subtelomeric DNA methylation extends from Interstitial Telomeric Sequences (ITSs) near telomeres. However, it drops at the telomeric side and disappears at the inner part of telomeres.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Ji Zhang, Yibo Wang, Eric D. Donarski, Tanjin T. Toma, Madeline T. Miles, Scott T. Acton, Andreas Gahlmann
Summary: Accurate detection and segmentation of single cells in 3D fluorescence time-lapse images is crucial for studying individual cell behaviors in bacterial biofilms. A machine-learning-based image analysis approach called BCM3D, which combines deep learning with conventional image analysis, has been developed to achieve high accuracies. The new version, BCM3D 2.0, improves segmentation results by translating images into intermediate 3D representations, allowing better accuracy even in challenging conditions. This capability enables further investigation of time-dependent phenomena in bacterial biofilms.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Biotechnology & Applied Microbiology
Ruochi Zhang, Tianming Zhou, Jian Ma
Summary: Higashi is an algorithm based on hypergraph representation learning that outperforms existing methods for embedding and imputation of scHi-C data, and can identify multiscale 3D genome features in single cells. Furthermore, Higashi can incorporate epigenomic signals jointly profiled in the same cell, leading to improved embeddings for single-nucleus methyl-3C data.
NATURE BIOTECHNOLOGY
(2022)
Article
Cell Biology
Karsten Rippe
Summary: Self-organizing membraneless chromatin subcompartments play a crucial role in eukaryotic cells by efficiently conducting genome activities and establishing specific cellular programs. However, the mechanisms for their formation are only partially understood, with recent studies suggesting liquid-liquid phase separation (LLPS) of proteins and RNAs. Additionally, the folding of chromatin can partition the genome into distinct domains. This article discusses the interplay between chromatin organization, chromatin binding, and LLPS by comparing three prototypical chromatin subcompartments.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2022)
Article
Oncology
Christopher Berlin, Felicie Cottard, Dominica Willmann, Sylvia Urban, Stephan M. Tirier, Lisa Marx, Karsten Rippe, Mark Schmitt, Valentina Petrocelli, Florian R. Greten, Stefan Fichtner-Feigl, Rebecca Kesselring, Eric Metzger, Roland Schuele
Summary: This study identifies lysine methyltransferase 9 (KMT9) as an important regulator in colorectal tumorigenesis. KMT9 alpha and KMT9 beta are overexpressed in colorectal cancer and colocalize with H4K12me1 at promoters of proliferation-related target genes. Ablation of KMT9 alpha significantly reduces colorectal tumorigenesis and prevents the growth of tumor organoids. Loss of KMT9 alpha impairs the maintenance and function of colorectal cancer stem/initiating cells and induces apoptosis specifically in this cellular compartment. These findings suggest that KMT9 could be a promising therapeutic target for colorectal cancer treatment.
Article
Cell Biology
Karsten Rippe, Argyris Papantonis
Summary: This study explores the functional attributes of distinct clusters of RNA polymerase II inside eukaryotic cell nuclei and the mechanisms underlying their formation. It also discusses how the concept of proteins and RNA phase-separating into liquid-like droplets drives the formation of transcriptionally-active subcompartments and how the different ways of assembling the active RNA polymerase II transcriptional machinery relate to nuclear compartmentalization.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lukas Frank, Anne Rademacher, Norbert Muecke, Stephan M. Tirier, Emma Koeleman, Caroline Knotz, Sabrina Schumacher, Sabine A. Stainczyk, Frank Westermann, Stefan Froehling, Priya Chudasama, Karsten Rippe
Summary: This study introduces a new method called ALT-FISH to quantitate ALT activity in single cells by detecting the accumulation of single-stranded telomeric DNA and RNA. The method successfully identified ALT in cancer cell lines and primary tissue sections from different tumor entities, and it is suitable for high-throughput applications, which will facilitate screening for ALT-specific drugs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jorge Trojanowski, Lukas Frank, Anne Rademacher, Norbert Muecke, Pranas Grigaitis, Karsten Rippe
Summary: This study investigates the transcriptional activation process by comparing synthetic transcription factors (TFs) at a reporter gene array. The results show that the physicochemical properties of the activation domain (AD) can control TF assembly at chromatin. It was found that while the propensity for phase separation and activation strength of the AD were correlated, the actual formation of liquid-like TF droplets had a neutral or inhibitory effect on transcription activation. The study concludes that multivalent AD-mediated interactions enhance transcription activation capacity by increasing the TF's residence time in the chromatin-bound state and facilitating the recruitment of coactivators, independent of phase separation.
Article
Oncology
Alexandra M. Poos, Cornelia Schroeder, Neeraja Jaishankar, Daniela Roell, Marcus Oswald, Jan Meiners, Delia M. Braun, Caroline Knotz, Lukas Frank, Manuel Gunkel, Roman Spilger, Thomas Wollmann, Adam Polonski, Georgia Makrypidi-Fraune, Christoph Fraune, Markus Graefen, Inn Chung, Alexander Stenzel, Holger Erfle, Karl Rohr, Aria Baniahmad, Guido Sauter, Karsten Rippe, Ronald Simon, Rainer Koenig
Summary: Most prostate cancer is curable, but some aggressive subtypes require immediate and invasive therapies. The gene PITX1 has been identified as potentially playing a key role in both diagnosis and treatment of prostate cancer.
Article
Biology
Markus Muckenhuber, Isabelle Seufert, Katharina Mueller-Ott, Jan-Philipp Mallm, Lara C. Klett, Caroline Knotz, Jana Hechler, Nick Kepper, Fabian Erdel, Karsten Rippe
Summary: The antiviral response induced by type I interferon via the JAK-STAT signaling cascade activates hundreds of IFN-stimulated genes across human and mouse tissues but varies between cell types. However, the links between the underlying epigenetic features and the ISG profile are not well understood.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Fabian Erdel
Summary: This paragraph discusses heterochromatin formation involving phase transitions and liquid-liquid demixing of heterochromatin proteins. The author outlines the hallmarks of these transitions and the challenges to detect them in living cells. The author further discusses the abundance and properties of prominent heterochromatin proteins and their potential role in driving phase transitions. Recent data from mouse fibroblasts suggest that pericentric heterochromatin is organized through a reordering transition on the level of heterochromatin regions, which may not involve liquid-liquid demixing of heterochromatin proteins. Evaluating key hallmarks of different phase transition mechanisms across cell types and species will be necessary to have a complete understanding.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ulla Dolde, Fernando Muzzopappa, Charlotte Delesalle, Julie Neveu, Fabian Erdel, Gregory Vert
Summary: The transcription factor LEAFY (LFY) activates floral homeotic genes for flower development. The E3 ubiquitin ligase UFO interacts with LFY to mark it for degradation. LFY accumulates in biomolecular condensates in the cytoplasm and relocalizes to the nucleus upon perturbation of these condensates, leading to the activation of LFY target genes.
Review
Biochemistry & Molecular Biology
Pooja Sant, Karsten Rippe, Jan-Philipp Mallm
Summary: Single-cell sequencing of RNA (scRNA-seq) has greatly improved our understanding of cellular heterogeneity and signaling in developmental biology and disease. Various complementary assays have been developed to profile transcriptomes of individual cells, including chromatin accessibility and protein surface marker analysis. However, due to the rapid advancement of scRNA-seq technologies, establishing robust workflows and protocols to address research questions has become challenging.
TRANSCRIPTION-AUSTIN
(2023)
Review
Cell Biology
Maud Hertzog, Fabian Erdel
Summary: Chromatin regulatory processes occur in the cell nucleus, which contains various macromolecular assemblies of different sizes. This multiscale organization affects nuclear transport processes, mechanical properties, and mechanical sensing and reactions. Recent work has focused on assessing the material properties of the nucleus and its subcomponents through microrheology and micromanipulation experiments.
Article
Biochemistry & Molecular Biology
Robin Weinmann, Lukas Frank, Karsten Rippe
Summary: This article discusses recent advancements in studying the local properties and compositional dynamics of chromatin, as well as their functional implications in protein and RNA enrichment and genome accessibility.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jorge Trojanowski, Karsten Rippe
Summary: This article summarizes recent findings on the interplay between transcription factor binding, chromatin organization, and gene activation, highlighting the features that need to be considered for constructing quantitative models of eukaryotic gene regulation.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2022)