Article
Multidisciplinary Sciences
Michele Gabriele, Hugo B. Brandao, Simon Grosse-Holz, Asmita Jha, Gina M. Dailey, Claudia Cattoglio, Tsung-Han S. Hsieh, Leonid Mirny, Christoph Zechner, Anders S. Hansen
Summary: This study reveals the rare and dynamic nature of chromatin looping in the Fbn2 TAD, with a looped fraction of approximately 3 to 6.5% and a median loop lifetime of approximately 10 to 30 minutes. The results suggest that functional interactions may be primarily regulated by single CTCF boundaries rather than the fully CTCF-CTCF looped state.
Article
Biology
Francesco Padovani, Benedikt Mairhoermann, Pascal Falter-Braun, Jette Lengefeld, Kurt M. Schmoller
Summary: Cell-ACDC is an open-source user-friendly framework written in Python for segmentation, tracking, and cell cycle annotations in live cell imaging data. It includes state-of-the-art deep learning models, visualization and error correction tools, and allows for fast integration of new methods.
Article
Chemistry, Organic
Rabi Sankar Das, Ayan Mukherjee, Samiran Kar, Tapas Bera, Shreya Das, Arunima Sengupta, Samit Guha
Summary: This article describes a novel red fluorescent mechanically interlocked molecule with dual targeting functionality for live cancer cell specific active targeting and imaging of malignant lysosomes.
Article
Chemistry, Multidisciplinary
Michael Holtmannspoetter, Eike Wienbeuker, Timo Dellmann, Isabelle Watrinet, Ana J. Garcia-Saez, Kai Johnsson, Rainer Kurre, Jacob Piehler
Summary: Self-labeling enzymes (SLE) like the HaloTag are valuable tools in high and super-resolution fluorescence microscopy. New fluorogenic substrates for SLE allow imaging with excess dye. Two engineered variants of HaloTag7 with restored dehalogenase activity, reHaloTagS (approx. 0.006 s(-1)) and reHaloTagF (approx. 0.055 s(-1)), showed different turnover kinetics in vitro. Imaging with reHaloTag labeling demonstrated 3-5 times enhanced photostability, and single molecule imaging enabled controlled and stable labeling density over extended periods. Combination with structured illumination allowed simultaneous visualization of single molecule diffusion and organellar dynamics. These applications showcase the potential of reHaloTag labeling in advancing fluorescence microscopy techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biology
Thomas G. W. Graham, John Joseph Ferrie, Gina M. Dailey, Robert Tjian, Xavier Darzacq
Summary: Single-molecule imaging is a powerful tool for studying biochemical processes in live cells, but tracking single molecules and detecting their interactions simultaneously remains challenging. This study describes a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), which allows the detection of protein-protein interactions in live cells using two different labeled protein complexes in proximity.
Article
Chemistry, Physical
Zhiyuan Han, Rohit M. Vaidya, Opeyemi H. Arogundade, Liang Ma, Mohammad U. Zahid, Suresh Sarkar, Chia-Wei Kuo, Paul R. Selvin, Andrew M. Smith
Summary: Quantum dots (QDs) are widely used semiconductor nanocrystals in life science studies. A focus of research is to reduce the size of QDs to enhance their accessibility to biological targets. By coating QDs with multidentate polymer coatings, the researchers were able to achieve compact and stable QDs with smaller hydrodynamic sizes. The study also found that the structural characteristics of the polymers play a crucial role in determining the hydrodynamic size, colloidal stability, and biomolecular interactions of the coated QDs. The findings provide insights for the design of next-generation QDs with sizes approaching fluorescent protein labels.
CHEMISTRY OF MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Weina Liu, Md Noor A. Alam, Yan Liu, Viatcheslav N. Agafonov, Haoyuan Qi, Kaloian Koynov, Valery A. Davydov, Rustem Uzbekov, Ute Kaiser, Theo Lasser, Fedor Jelezko, Anna Ermakova, Tanja Weil
Summary: The article introduces new applications of nanodiamonds with silicon-vacancy centers for bioimaging and biosensing. The results demonstrate for the first time the use of nanodiamonds with silicon-vacancy centers for live-cell dual-color imaging and intracellular tracking. The challenges associated with silicon-vacancy atomic defects are also discussed.
Article
Chemistry, Analytical
Yi-Fan Tian, Yu-Peng Zhang, Qiu-Mei Wu, Dai-Wen Pang, Shu-Lin Liu, Zhi-Gang Wang
Summary: Translation is a critical cellular activity regulated by viruses, and studying its kinetics and subcellular localization requires real-time visualization techniques. This study presents a new method using the CRISPR/dCas13 system and specific complementary guide RNAs to dynamically image translation without altering the coding regions. This tool provides promising opportunities for further investigating translation mechanisms.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Yi-Fan Tian, Yu-Peng Zhang, Qiu-Mei Wu, Dai-Wen Pang, Shu-Lin Liu, Zhi-Gang Wang
Summary: This article introduces a method for real-time dynamic translation imaging using the CRISPR/dCas13 system. The method labels the unmodified coding regions of target mRNA, enabling real-time visualization of the translation process, and is promising for further investigations into translation mechanisms.
ANALYTICAL CHEMISTRY
(2023)
Article
Biology
Jeremy Copperman, Sean M. Gross, Young Hwan Chang, Laura M. Heiser, Daniel M. Zuckerman
Summary: Time-lapse imaging is a powerful tool to study cell dynamics, but analyzing morphological changes over time is challenging. In this study, we use trajectory embedding to analyze cellular behavior based on multiple time points simultaneously. We apply this method to study the effects of microenvironmental perturbagens on MCF10A mammary epithelial cells. Our analysis reveals ligand-specific regulation of cell state transitions and provides descriptive models of single-cell trajectories. Incorporating trajectories improves the characterization of cell states and enables better identification of phenotypes compared to snapshot-based analysis. This approach has broad applications in live-cell imaging for studying cell responses.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Analytical
Su Liang, Zeyu Wang, Luyu Qi, Chao Tang, Yiming Zhang, Qun Luo, Yayun Wu, Jinghe Yuan, Yao Zhao, Yanyan Zhang, Xiaohong Fang, Shijun Wang, Fuyi Wang
Summary: This study designed a fluorescent probe, ATTO565-WGN, which showed similar anti-proliferative activity to wogonin against human cancer cell lines and demonstrated mitochondrial localization through confocal fluorescence imaging. The conjugated ATTO565 fluorophore enabled STED fluorescence living cell imaging with ultrahigh spatial resolution, facilitating the investigation of wogonin-biological target interactions in living cells at mitochondria. This work provides novel insights into rational design of mitochondrion targeting fluorescence probes for ultrahigh resolution living cell imaging.
Article
Chemistry, Multidisciplinary
Danyang Wang, Ana Shalamberidze, Emilia Arguello, Byron W. Purse, Ralph E. Kleiner
Summary: The article introduces a platform for fluorescence imaging of bulk RNA dynamics in living cells and uses this platform to study RNA metabolism and localization during oxidative stress. The study found that bulk RNA turnover is accelerated upon oxidative stress treatment and identified new cytoplasmic RNA granules that co-localize with RNA helicase.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Dana Al Kelabi, Avishek Dey, Lukman O. Alimi, Hubert Piwonski, Satoshi Habuchi, Niveen M. Khashab
Summary: Fluorescent microscopy is a powerful technique for studying cellular dynamics. The organic fluorophore OC1, with high cell permeability, photostability, and selectivity for mitochondria, has been identified. The keto-enol tautomerization of OC1 allows for consistent fluorescence in dilute solutions through supramolecular self-assembly.
Article
Biology
Tania Mendonca, Katarzyna Lis-Slimak, Andrew B. Matheson, Matthew G. Smith, Akosua B. Anane-Adjei, Jennifer C. Ashworth, Robert Cavanagh, Lynn Paterson, Paul A. Dalgarno, Cameron Alexander, Manlio Tassieri, Catherine L. R. Merry, Amanda J. Wright
Summary: OptoRheo, a new instrument combining light sheet fluorescence microscopy and particle tracking microrheology, allows for live imaging and micromechanical sensing of extracellular matrix-cell interactions. By developing OptoRheo, we can image cells in 3D while simultaneously sensing the mechanical properties of the surrounding extracellular and pericellular matrix at a sub-cellular length scale. OptoRheo can be operated in two modes (with and without an optical trap) to extend the dynamic range of microrheology measurements. We validated this by characterizing the extracellular matrix surrounding live breast cancer cells in two different culture systems.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Andreas Boden, Francesca Pennacchietti, Giovanna Coceano, Martina Damenti, Michael Ratz, Ilaria Testa
Summary: A new 3D pRESOLFT microscope method with sub-80-nm resolution has been developed to visualize the volumetric architecture of organelles and molecules inside whole living cells, allowing for targeted 3D confinement of fluorescence and observation of dynamic structural alterations in cells.
NATURE BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Abdulmajeed Fahad Alrefaei, Andrea E. Munsterberg, Grant N. Wheeler
Article
Developmental Biology
Camille Viaut, Shannon Weldon, Andrea Munsterberg
Summary: miR-128 is involved in regulating skeletal myogenesis by directly targeting EYA4 with indirect effects on other PSED members, including SIX4 and PAX3. Multiple muscle-enriched microRNAs co-regulate the PSED network of transcription factors. The inhibitory effect of miR-128 can be rescued by concomitant knockdown of PAX3.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Developmental Biology
Abdulmajeed Fahad Alrefaei, Andrea E. Munsterberg, Grant N. Wheeler
Summary: Frizzled receptors, transducing signals through Wnts, are crucial for neural tube development. Specific expression profiles of FZD receptors offer basis for future functional studies, showing interactions of Wnts-FZDs during spinal cord neurogenesis.
GENE EXPRESSION PATTERNS
(2021)
Article
Multidisciplinary Sciences
Gi Fay Mok, Leighton Folkes, Shannon A. Weldon, Eirini Maniou, Victor Martinez-Heredia, Alice M. Godden, Ruth M. Williams, Tatjana Sauka-Spengler, Grant N. Wheeler, Simon Moxon, Andrea E. Muensterberg
Summary: This study used ATAC-seq and RNA-seq to analyze the spatiotemporal dynamics along the chick embryonic axis, identifying differential binding site coverage for key transcription factors and connecting accessible chromatin with nearby expressed genes. The authors determined cis-regulatory elements for TCF15 and MEOX1, investigated their spatiotemporal activity and evolutionary conservation, and disrupted their expression through epigenome silencing to recapitulate phenotypic abnormalities of anterior-posterior axis extension. This integrated approach allows for dissection of paraxial mesoderm regulatory circuits in vivo and has implications for investigating gene regulatory networks.
NATURE COMMUNICATIONS
(2021)
Review
Cell Biology
Shannon A. Weldon, Andrea E. Munsterberg
Summary: A critical stage in vertebrate embryonic development is the formation and regionalization of the body plan, including the axial skeleton. This review focuses on axial patterning of somites in amniote model systems, such as birds and mice. It summarizes the molecular and cellular mechanisms involved in generating paraxial mesoderm and discusses how different regions of the vertebral column acquire specific identities that shape the body plan. The review also examines the generation of organoids and embryo-like structures from embryonic stem cells, offering insights into axis formation and potential applications in disease modeling.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Marco Antonaci, Grant N. Wheeler
Summary: This article explores the importance of the neural crest in neurocristopathies and introduces the potential role of non-coding gene miRNA in neural crest development and pathology.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Review
Biochemistry & Molecular Biology
Emily Louise Smith, Gi Fay Mok, Andrea Munsterberg
Summary: Mapping accessible chromatin across time scales can provide insights into its dynamic nature and help identify functional cis-regulatory elements and transcription factor binding sites. ATAC-seq is a powerful approach that allows for quick analysis of differentially accessible regions of chromatin in different cell populations, and it has been used to uncover the highly dynamic nature of chromatin during vertebrate embryonic development.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Developmental Biology
Alice M. Godden, Marco Antonaci, Nicole J. Ward, Michael van der Lee, Anita Abu-Daya, Matthew Guille, Grant N. Wheeler
Summary: Researchers used CRISPR-Cas9 knockout methods to study the role of miRNAs in the development of Xenopus neural crest. They designed a new approach to effectively 'drop out' miRNAs and studied their functions and effects through phenotype validation and gene analysis.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Isis Atallah, Dominique McCormick, Jean-Marc Good, Mohammed Barigou, Montserrat Fraga, Christine Sempoux, Andrea Superti-Furga, Robert K. Semple, Christel Tran
Summary: This article describes a case of Werner syndrome presenting with early onset diabetes, partial lipodystrophy, severe dyslipidaemia, and rapidly progressive liver fibrosis. Molecular diagnosis revealed compound heterozygous mutations in the WRN gene. The study suggests that including WRN gene analysis in patients with early onset diabetes, lipodystrophy, or dyslipidaemia can allow for early detection of Werner syndrome and implementation of preventive interventions.
JOURNAL OF CLINICAL LIPIDOLOGY
(2022)
Meeting Abstract
Toxicology
S. E. Wyville, G. N. Wheeler
TOXICOLOGY LETTERS
(2022)
Article
Multidisciplinary Sciences
Eudald Pascual-Carreras, Marta Marin-Barba, Sergio Castillo-Lara, Pablo Coronel-Cordoba, Marta Silvia Magri, Grant N. Wheeler, Jose Luis Gomez-Skarmeta, Josep F. Abril, Emili Salo, Teresa Adell
Summary: Any planarian fragment can regenerate the missing head and tail properly by activating the Wnt/beta-catenin signaling pathway, which changes the chromatin accessibility of the wound cells. The determination of missing tissue identity relies on pre-existing tissue. Planarians are perfect organisms for studying this mechanism, as the same group of cells can regenerate a head or a tail depending on the injured body part. The differential activation of the Wnt/beta-catenin signal after amputation specifies anterior or posterior identity. The chromatin accessibility of wound cells shifts according to the polarity of pre-existing tissue in a Wnt/beta-catenin-dependent manner within 12 hours.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Ximena Ibarra-Soria, Elodie Thierion, Gi Fay Mok, Andrea E. Mu euro Nsterberg, Duncan T. Odom, John C. Marioni
Summary: The mammalian body plan is formed by the segmentation of the mesoderm into somites, which are transient embryonic structures. Through a genomic analysis, we studied the transcriptional and chromatin dynamics during somitogenesis, revealing an accelerated rate of somite differentiation as development progresses. We also identified a conserved maturation program followed by all somites, as well as differentiation programs in more developed embryos.
DEVELOPMENTAL CELL
(2023)