Review
Biochemistry & Molecular Biology
Shuo Huang, Rui Dai, Zhiqi Zhang, Han Zhang, Meng Zhang, Zhangjun Li, Kangrui Zhao, Wenjun Xiong, Siyu Cheng, Buhua Wang, Yi Wan
Summary: CRISPR/Cas systems are widely used in gene editing due to their accuracy, programmability, ease of use, and affordability. Additionally, they have been applied in live-cell imaging and bioanalysis, expanding the scope of their use beyond gene editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Narendra Chaudhary, Jae-Kyeong Im, Si-Hyeong Nho, Hajin Kim
Summary: The three-dimensional organization and time-dependent changes of chromatin significantly influence cellular functions, and visualizing these changes in individual cells remains challenging. CRISPR systems offer promising strategies for this visualization, but face limitations such as background signals, non-specific binding, and rapid photobleaching. Modifications to the CRISPR system aim to enhance target detection reliability and reduce required target size.
MOLECULES AND CELLS
(2021)
Article
Biochemical Research Methods
Li Jiang, Xin Xie, Ni Su, Dasheng Zhang, Xianjun Chen, Xiaochen Xu, Bibi Zhang, Kaiyi Huang, Jingwei Yu, Mengyue Fang, Bingkun Bao, Fangting Zuo, Lipeng Yang, Rui Zhang, Huiwen Li, Xinyi Huang, Zhengda Chen, Qingmei Zeng, Renmei Liu, Qiuning Lin, Yuzheng Zhao, Aiming Ren, Linyong Zhu, Yi Yang
Summary: A team of researchers has developed a fluorescent RNA called Clivias, which is small and stable and can be used to visualize and track the localization and functionality of RNA. When combined with Pepper fluorescent RNA, it enables the simultaneous imaging of multiple RNAs and can also detect RNA-protein interactions.
Article
Physiology
Ashraf N. Abdo, Carola Rintisch, Christian H. Gabriel, Achim Kramer
Summary: Using CRISPR/Cas9 technology, the researchers created a CLOCK knockout and rescue system to investigate the functionality of individual amino acids within the CLOCK exon 19-domain. The results showed that CLOCK/BMAL1 oligomerization mediated by the exon 19-domain is important for circadian dynamics and the exon 19-domain provides a platform for binding coactivators and repressors, which is required for normal circadian rhythms.
Article
Cell Biology
Sabrina Klemz, Thomas Wallach, Sandra Korge, Mechthild Rosing, Roman Klemz, Bert Maier, Nicholas C. Fiorenza, Irem Kaymak, Anna K. Fritzsche, Erik D. Herzog, Ralf Stanewsky, Achim Kramer
Summary: In organisms with circadian clocks, the post-translational modifications of clock proteins, particularly phosphorylation, play a crucial role in controlling circadian rhythms. Protein phosphatase 4 (PPP4) and its regulatory subunit PPP4R2 have been identified as critical components in mammals and Drosophila, affecting the circadian system by regulating phosphorylation and transactivation activity of CLOCK/BMAL1.
GENES & DEVELOPMENT
(2021)
Editorial Material
Cell Biology
Ueli Schibler
Summary: Mammalian body cells have cell-autonomous and self-sustained circadian oscillators relying on delayed negative feedback loops in gene expression. Transcriptional activation and repression, as well as post-translational mechanisms like phosphorylation and dephosphorylation, play crucial roles in setting the pace of these timekeepers. The study by Klemz and colleagues in Genes & Development demonstrates how dephosphorylation of BMAL1 by protein phosphatase 4 (PPP4) participates in the modulation of circadian timing.
GENES & DEVELOPMENT
(2021)
Article
Genetics & Heredity
Ziyan Wang, Bradley M. Bartholomai, Jennifer J. Loros, Jay C. Dunlap
Summary: Filamentous fungi have been slower in adopting fluorescence imaging tools developed for animal systems and yeast. This study analyzes fluorescent proteins in Neurospora crassa and provides genetic tools for their expression, expanding research capabilities in cell biology.
FUNGAL GENETICS AND BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Nina Reuven, Yosef Shaul
Summary: CRISPR technology provides a powerful tool for editing cell genomes, but specific mutations at certain sites remain challenging. Various strategies have been developed to select successfully edited cells in order to improve efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Mathematics, Applied
Jiaxin Zhou, Hongli Wang, Qi Ouyang
Summary: This paper proposes a temporal SCN network model and investigates the effects of dynamical rewiring and flexible coupling due to synaptic plasticity on the synchronization of the neural network in SCN. The results suggest that both dynamical rewiring and coupling plasticity enhance the synchronization in inhomogeneous networks, and a proper network model for the master SCN circadian rhythm needs to take into account the effects of dynamical changes in topology and plasticity in neuron interactions.
Article
Developmental Biology
Yu Shi, Nitya Kopparapu, Lauren Ohler, Daniel J. Dickinson
Summary: Fluorescent protein tagging is a crucial method for studying protein behavior in living cells. However, overexpression of tagged proteins can disrupt cell behavior. This study presents an improved method for inserting fluorescent proteins directly into native genes in mammalian cells using the CRISPaint system. The protocol is efficient and enables live imaging in less than two weeks post-transfection, increasing the versatility of fluorescent protein knock-in.
Article
Multidisciplinary Sciences
William Dion, Heather Ballance, Jane Lee, Yinghong Pan, Saad Irfan, Casey Edwards, Michelle Sun, Jing Zhang, Xin Zhang, Silvia Liu, Bokai Zhu
Summary: This study identified a cell-autonomous 12-hour ultradian rhythm mechanism in mammals that is separate from the 24-hour circadian clock and the cell cycle. By modulating the temporal dynamics of proteostasis, the nuclear speckle LLPS may represent a previously unidentified therapeutic target for pathologies associated with dysregulated proteostasis.
Review
Cell Biology
Huake Cao, Yuechen Wang, Ning Zhang, Siyuan Xia, Pengfei Tian, Li Lu, Juan Du, Yinan Du
Summary: This article reviews the progress in RNA imaging and mapping RNA-protein interactions, with a focus on the precise CRISPR-Cas13-mediated method. This method has potential for real-time RNA imaging and recognition of RNA-protein interactions, and provides new ideas for optimizing the method.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xiao-Lan Wang, Sander Kooijman, Yuanqing Gao, Laura Tzeplaeff, Brigitte Cosquer, Irina Milanova, Samantha E. C. Wolff, Nikita Korpel, Marie-France Champy, Benoit Petit-Demouliere, Isabelle Goncalves Da Cruz, Tania Sorg-Guss, Patrick C. N. Rensen, Jean-Christophe Cassel, Andries Kalsbeek, Anne-Laurence Boutillier, Chun-Xia Yi
Summary: The study found that microglial Bmal1 plays a crucial role in metabolic stress and memory formation, as knocking it down led to enhanced phagocytosis activity and positive effects on neuronal activity in the brain, helping to combat obesity and improve memory test performance.
MOLECULAR PSYCHIATRY
(2021)
Article
Biophysics
Mengyue Fang, Huiwen Li, Xin Xie, Hui Wang, Ying Jiang, Tianyu Li, Bibi Zhang, Xin Jiang, Yueyang Cao, Rui Zhang, Dasheng Zhang, Yuzheng Zhao, Linyong Zhu, Xianjun Chen, Yi Yang
Summary: Engineered fluorescent RNA (FR)-based sensors have been used to detect essential metabolites in living systems, but their unfavorable characteristics limit their applications. Here, we demonstrate a strategy for converting Pepper fluorescent RNA into sensors with improved characteristics. These Pepper-based sensors showed expanded emission and improved brightness, allowing robust monitoring of intracellular changes and protein translocation in live cells. Furthermore, the use of Pepper-based sensors in the CRISPR-display strategy achieved signal amplification in fluorescence imaging. These results highlight the potential of Pepper as a high-performance FR-based sensor for detecting cellular targets.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Multidisciplinary Sciences
Shirley L. Zhang, Nicholas F. Lahens, Zhifeng Yue, Denice M. Arnold, Peter P. Pakstis, Jessica E. Schwarz, Amita Sehgal
Summary: The blood-brain barrier is critical for neural function, and this study shows that efflux of xenobiotics through the BBB follows a circadian rhythm in mice and human cells. Interestingly, limited circadian regulation of transcription was detected in brain endothelial cells, with no evident oscillations in efflux transporters. The molecular clock drives cycling of intracellular magnesium through transcriptional regulation, contributing to the rhythm in efflux.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Anne Pelikan, Hanspeter Herzel, Achim Kramer, Bharath Ananthasubramaniam
Summary: The circadian clock plays a crucial role in regulating physiological processes, but Venn diagram analysis may lead to overestimation of differential rhythmic transcripts. New methods for comparing circadian amplitude and phase offer more accurate results and reveal categories of transcript changes missed by VDA. These findings suggest the need to avoid Venn diagrams in circadian studies for improved reliability.
Article
Physiology
Ashraf N. Abdo, Carola Rintisch, Christian H. Gabriel, Achim Kramer
Summary: Using CRISPR/Cas9 technology, the researchers created a CLOCK knockout and rescue system to investigate the functionality of individual amino acids within the CLOCK exon 19-domain. The results showed that CLOCK/BMAL1 oligomerization mediated by the exon 19-domain is important for circadian dynamics and the exon 19-domain provides a platform for binding coactivators and repressors, which is required for normal circadian rhythms.
Article
Biochemistry & Molecular Biology
Marie Coutelier, Manuel Holtgrewe, Marten Jaeger, Ricarda Floettman, Martin A. Mensah, Malte Spielmann, Peter Krawitz, Denise Horn, Dieter Beule, Stefan Mundlos
Summary: Copy Number Variants (CNVs) are deletions, duplications, or insertions larger than 50 base pairs that contribute to normal genome variation and have significant implications in human pathology. While traditional array-based approaches have been used for CNV detection, whole-genome sequencing (WGS) offers the potential for comprehensive exploration of CNVs and smaller variants. This study evaluates practical calling options for CNV detection from WGS data, highlighting the need to strike a balance between sensitivity and sensibility. Combining multiple callers and tools like SV2 shows promising results in terms of computation time and accuracy compared to array-based methods like aCGH.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Multidisciplinary Sciences
Yang Zhang, Laura Garcia-Ibanez, Carolin Ulbricht, Laurence S. C. Lok, Jeremy A. Pike, Jennifer Mueller-Winkler, Thomas W. Dennison, John R. Ferdinand, Cameron J. M. Burnett, Juan C. Yam-Puc, Lingling Zhang, Raul Maqueda Alfaro, Yousuke Takahama, Izumi Ohigashi, Geoffrey Brown, Tomohiro Kurosaki, Victor L. J. Tybulewicz, Antal Rot, Anja E. Hauser, Menna R. Clatworthy, Kai-Michael Toellner
Summary: This study demonstrates that memory B cells can recycle back to germinal centers via CCL-21 mediated chemotaxis to transport antigens, potentially contributing to affinity maturation and antigenic drift.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Carola Sparn, Eleni Dimou, Annalena Meyer, Roberto Saleppico, Sabine Wegehingel, Matthias Gerstner, Severina Klaus, Helge Ewers, Walter Nickel
Summary: The study reveals that Glypican-1 (GPC1) is the primary factor driving the unconventional secretion of Fibroblast growth factor 2 (FGF2), while its role in FGF2 signaling into cells is dispensable. Furthermore, the research provides insights into the structural basis of GPC1-dependent FGF2 secretion. These findings have significant implications for the key role of GPC1 in tumor progression.
Article
Cell Biology
Fabio Lolicato, Roberto Saleppico, Alessandra Griffo, Annalena Meyer, Federica Scollo, Bianca Pokrandt, Hans-Michael Muller, Helge Ewers, Hendrik Hahl, Jean-Baptiste Fleury, Ralf Seemann, Martin Hof, Britta Brugger, Karin Jacobs, Ilpo Vattulainen, Walter Nickel
Summary: This study found that cholesterol can promote the recruitment and translocation of FGF2 in cells, as well as enhance its binding to PI(4,5)P2. Through molecular dynamics simulations and experiments, it was revealed that cholesterol modulates the binding of FGF2 to PI(4,5)P2 by increasing the visibility of PI(4,5)P2 on the membrane surface, inducing the clustering of PI(4,5)P2 molecules, and increasing membrane tension.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Critical Care Medicine
Matthias Felten, Sebastian Ferencik, Luiz-Gustavo Teixeira Alves, Eleftheria Letsiou, Jasmin Lienau, Holger C. Mueller-Redetzky, Alina Katharina Langenhagen, Anne Voss, Kristina Dietert, Olivia Kershaw, Achim D. Gruber, Laura Michalick, Wolfgang M. Kuebler, Bharath Ananthasubramaniam, Bert Maier, Henriette Uhlenhaut, Achim Kramer, Martin Witzenrath
Summary: This study investigated the role of the core clock component BMAL1 in myeloid cells in modulating the severity of ventilator-induced lung injury (VILI). The results showed that inflammatory response and lung barrier dysfunction during mechanical ventilation exhibit diurnal variations regulated by the circadian clock. Mice without BMAL1 are less susceptible to VILI and do not show circadian variation in severity.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Editorial Material
Multidisciplinary Sciences
Christian H. Gabriel, Achim Kramer
Summary: Daily rhythms have an impact on various aspects of mammalian biology. A recent discovery in mice suggests that the activity of a specific type of immune cell is regulated by these rhythms, potentially influencing cancer treatment strategies.
Article
Multidisciplinary Sciences
Georgia Katsioudi, Rene Dreos, Enes S. Arpa, Sevasti Gaspari, Angelica Liechti, Miho Sato, Christian H. Gabriel, Achim Kramer, Steven A. Brown, David Gatfield
Summary: The study demonstrates the importance of nonsense-mediated mRNA decay (NMD) in physiological control, particularly in regulating the circadian clock and gene expression.
Review
Physiology
Matthias Felten, Christof Dame, Gunnar Lachmann, Claudia Spies, Kerstin Rubarth, Felix Balzer, Achim Kramer, Martin Witzenrath
Summary: Patients in the ICU require continuous organ replacement strategies and specialized care, which can disrupt their circadian rhythms and impact their condition. Understanding the complex interactions of circadian effectors and tissue-specific molecular clocks could potentially improve personalized treatment and accelerate recovery for critically ill patients.
Article
Chemistry, Multidisciplinary
Ria Thielhorn, Isabelle Heing-Becker, Nadja Huempfer, Jakob Rentsch, Rainer Haag, Kai Licha, Helge Ewers
Summary: Expansion microscopy (ExM) is a technique that enlarges a hydrogel-embedded facsimile of a biological sample to improve resolution below the diffraction limit. However, gel formation and digestion cause a loss in label. In this study, a small molecule agent combining targeting, fluorescent labeling, and gel linkage was developed to overcome this issue, resulting in improved fluorescence signal retention and the resolution of nuclear pores. Mechanistic insight into dye retention in ExM was also provided.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Editorial Material
Cell Biology
Serge Mostowy, Aurelie Bertin, Helge Ewers
Article
Multidisciplinary Sciences
Michael C. A. Dyhr, Mohsen Sadeghi, Ralitsa Moynova, Carolin Knappe, Burcu Kepsutlu Cakmak, Stephan Werner, Gerd Schneider, James McNally, Frank Noe, Helge Ewers
Summary: Cryo-soft X-ray tomography (cryo-SXT) is a powerful method for investigating cell ultrastructure, offering high resolution and contrast without the need for labeling. A new automated 3D segmentation pipeline based on semi-supervised deep learning enables high-throughput analysis of tomographic data with limited manual annotations and variations in conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Marta del Olmo, Florian Spoerl, Sandra Korge, Karsten Juerchott, Matthias Felten, Astrid Grudziecki, Jan de Zeeuw, Claudia Nowozin, Hendrik Reuter, Thomas Blatt, Hanspeter Herzel, Dieter Kunz, Achim Kramer, Bharath Ananthasubramaniam
Summary: This study reports 24-hour gene expression rhythms in the epidermis and dermis layers of human skin, showing differences between the layers and identifying biomarkers for internal clock phase. This research is significant in advancing our understanding of human skin and quantifying sources of variability in circadian rhythms.
NAR GENOMICS AND BIOINFORMATICS
(2022)
