Review
Plant Sciences
Maria Ada Prusicki, Martina Balboni, Kostika Sofroni, Yuki Hamamura, Arp Schnittger
Summary: Live-cell imaging is a powerful tool for understanding cellular processes, especially in meiosis where chromosomes and cellular components exhibit complex dynamics over a short period of time. Recent advances in live-cell imaging now allow real-time analysis of meiotic events in plants.
FRONTIERS IN PLANT SCIENCE
(2021)
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
Physics, Multidisciplinary
Arthur Genthon, Reinaldo Garcia-Garcia, David Lacoste
Summary: Using a theoretical framework based on branching processes with resetting, this study explores the stochastic thermodynamics of cell growth and division. The first and second laws of stochastic thermodynamics are derived, and separate contributions of branching and resetting are identified. Applying the framework to cell size control models, such as the sizer, the timer, and the adder, it is found that the entropy production of resetting is negative while that of branching is positive during exponential colony growth. These findings suggest an analogy between our model for cell growth and division and heat engines, along with the introduction of a thermodynamic efficiency that quantifies the conversion between different forms of entropy production.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
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
Microbiology
Richard S. Muniz, Paul C. Campbell, Thomas E. Sladewski, Lars D. Renner, Christopher L. de Graffenried
Summary: Researchers have developed a method for long-term live-cell imaging of Trypanosoma brucei using agarose microwells, allowing high spatial and temporal resolution imaging of cell division and monitoring of cell toxicity. With this approach, they found that asymmetric daughter cells produced during T. brucei division divide at different rates.
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
Optics
Xuanwen Hua, Wenhao Liu, Shu Jia
Summary: The study introduces a high-resolution Fourier light-field microscopy (HR-FLFM) for fast and volumetric live-cell imaging, enabling exploration of intracellular organization and processes for understanding cell physiology, development, and pathology. HR-FLFM offers near-diffraction-limited resolution in all three dimensions, an extended focal depth to several micrometers, and faster volume acquisition time. This system demonstrates easy instrumentation access, low photo damage for continuous observation, and high compatibility with general cell assays, providing a promising methodological pathway to investigate a wide range of intracellular processes and functions with precise spatiotemporal contextual details.
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
Biochemistry & Molecular Biology
Ana Domingo-Muelas, Robin M. Skory, Adam A. Moverley, Goli Ardestani, Oz Pomp, Carmen Rubio, Piotr Tetlak, Blake Hernandez, Eric A. Rhon-Calderon, Luis Navarro-Sanchez, Carmen M. Garcia-Pascual, Stephanie Bissiere, Marisa S. Bartolomei, Denny Sakkas, Carlos Simon, Nicolas Plachta
Summary: Combining fluorescent dyes with live imaging, this study reveals the dynamics of early development in human embryos, including chromosome segregation, compaction, polarization, blastocyst formation, and hatching. The study also shows that blastocyst expansion mechanically affects trophectoderm cells, causing nuclear budding and DNA shedding into the cytoplasm. Moreover, the study suggests that aneuploidies in human embryos may not only result from chromosome segregation errors during mitosis, but also from nuclear DNA shedding.
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
Developmental Biology
Gema Villa-Fombuena, Maria Lobo-Pecellin, Miriam Marin-Menguiano, Patricia Rojas-Rios, Acaimo Gonzalez-Reyes
Summary: By studying Drosophila female germline stem cells, researchers found that the spectrosomes within GSCs and cystoblasts undergo shape changes depending on the cell cycle phase and are essential for spindle orientation during mitosis. The asymmetric division of GSCs is influenced by the niche environment, as demonstrated by symmetric division of GSC-like cells located outside the niche.
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
Cell & Tissue Engineering
Smrithi Rajendiran, Stephanie Smith-Berdan, Leo Kunz, Maurizio Risolino, Licia Selleri, Timm Schroeder, E. Camilla Forsberg
Article
Hematology
Konstantinos D. Kokkaliaris, Leo Kunz, Nina Cabezas-Wallscheid, Constantina Christodoulou, Simon Renders, Fernando Camargo, Andreas Trumpp, David T. Scadden, Timm Schroeder
Article
Cell & Tissue Engineering
Nouraiz Ahmed, Leo Kunz, Philipp S. Hoppe, Dirk Loeffler, Martin Etzrodt, German Camargo Ortega, Oliver Hilsenbeck, Konstantinos Anastassiadis, Timm Schroeder
Article
Cell Biology
Cinzia Donato, Leo Kunz, Francesc Castro-Giner, Aino Paasinen-Sohns, Karin Strittmatter, Barbara Maria Szczerba, Ramona Scherrer, Nunzia Di Maggio, Wolf Heusermann, Oliver Biehlmaier, Christian Beisel, Marcus Vetter, Christoph Rochlitz, Walter Paul Weber, Andrea Banfi, Timm Schroeder, Nicola Aceto
Article
Hematology
Tata Nageswara Rao, Nils Hansen, Jan Stetka, Damien Luque Paz, Milena Kalmer, Julian Hilfiker, Max Endele, Nouraiz Ahmed, Lucia Kubovcakova, Margareta Rybarikova, Hui Hao-Shen, Florian Geier, Christian Beisel, Stefan Dirnhofer, Timm Schroeder, Tim H. Brummendorf, Dominik Wolf, Steffen Koschmieder, Radek C. Skoda
Summary: The study revealed a bias of CD41(hi) HSCs towards megakaryocyte differentiation and aberrant function in relation to MPN and JAK2-V617F mutation. CD41(hi) HSCs exhibited higher cell cycle activity and gene expression levels related to oxidative phosphorylation.
Article
Immunology
Anais Wanet, Mahmoud A. Bassal, Sweta B. Patel, Francisco Marchi, Samanta A. Mariani, Nouraiz Ahmed, Haoran Zhang, Marta Borchiellini, Sisi Chen, Junyan Zhang, Annalisa Di Ruscio, Kensuke Miyake, Mindy Tsai, Anuya Paranjape, Shin-Young Park, Hajime Karasuyama, Timm Schroeder, Elaine Dzierzak, Stephen J. Galli, Daniel G. Tenen, Robert S. Welner
Summary: E-cadherin expression in the hematopoietic system was studied using single-cell RNA-sequencing analyses and immunophenotyping. High levels of E-cadherin were found in progenitors within the granulocyte-monocyte progenitors (GMPs) fraction, with an enriched capacity to differentiate into basophils and mast cells. The transcriptional priming of these progenitors to the basophil and mast cell lineages was observed, with GATA-2 directly regulating E-cadherin expression in these lineages.
SCIENCE IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Alan Le Mercier, Remy Bonnavion, Weijia Yu, Mohamad Wessam Alnouri, Sophie Ramas, Yang Zhang, Yannick Jaeger, Kenneth Anthony Roquid, Hyun-Woo Jeong, Kishor Kumar Sivaraj, Haaglim Cho, Xinyi Chen, Boris Strilic, Tjeerd Sijmonsma, Ralf Adams, Timm Schroeder, Michael A. Rieger, Stefan Offemanns
Summary: GPR182 is a new atypical chemokine receptor for CXCL10, CXCL12, and CXCL13, involved in regulating hematopoietic stem cell homeostasis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Immunology
Tobias Kull, Timm Schroeder
Summary: Cells constantly adapt their behavior to changing needs by sensing their environment, and compute fine-tuned responses to complex inputs through signaling pathways. Despite progress, our understanding of the precise implementation, relevance, and manipulation of cellular signaling remains limited.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Chemistry, Analytical
David W. Inglis, Robert E. Nordon, Jason P. Beech, Gary Rosengarten
Summary: Research shows that red blood cells undergo reversible deformation under certain shear stress, taking on characteristic shapes not previously seen in physiological buffers. The rates of deformation and recovery are negatively correlated with flow rates, while the degree of deformation saturates with increasing shear stress.
Review
Oncology
Tiffany C. Y. Tang, Ning Xu, Robert Nordon, Michelle Haber, Kenneth Micklethwaite, Alla Dolnikov
Summary: Adoptive cell therapy using patient-derived CAR T cells has shown success in treating hematologic cancers, but accessibility needs to be improved. Donor T cells can be used to generate off-the-shelf CAR T cells, but safety and efficacy enhancements are required.
BIOMARKER RESEARCH
(2022)
Article
Cell Biology
Jingjing Li, Osmond Lao, Freya F. Bruveris, Liyuan Wang, Kajal Chaudry, Ziqi Yang, Nona Farbehi, Elizabeth S. Ng, Edouard G. Stanley, Richard P. Harvey, Andrew G. Elefanty, Robert E. Nordon
Summary: A microfluidic culture system was developed to simulate embryonic circulation and investigate the role of circulatory flow and shear stress in embryonic blood development. Human pluripotent stem cells were differentiated into embryonic hematopoietic cells, and the pathways of extra-embryonic and embryonic blood differentiation were delineated using single-cell transcriptomic analysis. The study found that circulatory flow and specific signaling molecules promote the formation of precursor cells that differentiate into different blood cell types.
Article
Oncology
Stephanie Z. Xie, Kerstin B. Kaufmann, Weijia Wang, Michelle Chan-Seng-Yue, Olga Gan, Elisa Laurenti, Laura Garcia-Prat, Shin-Ichiro Takayanagi, Stanley W. K. Ng, ChangJiang Xu, Andy G. X. Zeng, Liqing Jin, Jessica McLeod, Elvin Wagenblast, Amanda Mitchell, James A. Kennedy, Qiang Liu, Helena Boutzen, Melissa Kleinau, Joseph Jargstorf, Gareth Holmes, Yang Zhang, Veronique Voisin, Gary D. Bader, Jean C. Y. Wang, Yusuf A. Hannun, Chiara Luberto, Timm Schroeder, Mark D. Minden, John E. Dick
Summary: The study reveals the important regulatory role of S1PR3 in AML patients, promoting myeloid differentiation and activating inflammatory programs, showing a continuous variation from primitive to mature myeloid states. This finding opens new avenues for specific therapeutic target identification in different AML subsets.
BLOOD CANCER DISCOVERY
(2021)
Article
Multidisciplinary Sciences
Jingjing Li, Osmond Lao, Robert E. Nordon
Summary: This study utilizes microfluidic chips to mimic embryonic circulation of different types of PSC, creating pulsatile circulatory flow with pressure-driven microfluidic devices that simulate ventricles. Moulds are manufactured using standard and 3D laser lithography, surface chemistry is modified to support cell growth, and cellular responses can be directly observed.
Article
Biology
Nona Farbehi, Vaibhao Janbandhu, Robert E. Nordon, Richard P. Harvey
Summary: In addition to cardiomyocytes, the heart also contains various types of interstitial cells that play important roles in heart repair, regeneration, and disease. A comprehensive map of cardiac stromal cell heterogeneity and flux in healthy and infarcted hearts was recently published using single-cell RNA sequencing. The study described a FACS-based method for isolating two cardiac cell fractions from adult mouse ventricles.
Article
Biochemical Research Methods
Philip Dettinger, Weijia Wang, Nouraiz Ahmed, Yang Zhang, Dirk Loeffler, Tobias Kull, Martin Etzrodt, Claudia Lengerke, Timm Schroeder
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
