Review
Biotechnology & Applied Microbiology
Paige Allard, Fotini Papazotos, Laurent Potvin-Trottier
Summary: Cells are dynamic, and the development of microfluidic methods allows for tracking and long-term observation of bacterial cells. This review focuses on the recent developments of a microfluidic device known as the mother machine, and discusses the associated analysis methods and modifications to the experimental setup.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang, Xiaowo Wang
Summary: Recent advances in long-term time-lapse microscopy have enabled researchers to quantify cell behavior and molecular dynamics with ease. However, the lack of user-friendly software tools optimized for customized research remains a major challenge. CellTracker is a highly integrated graphical user interface software that automates cell segmentation and tracking in time-lapse microscopy images, offering features such as project management, image pre-processing, and statistical analysis.
Article
Computer Science, Interdisciplinary Applications
Yu-Ting Su, Yao Lu, Jing Liu, Mei Chen, An-An Liu
Summary: This study reports the results of the first international contest on mitosis detection in phase-contrast microscopy image sequences, where ten different detection methods were evaluated on a large-scale dataset, providing insights and directions for future research in the field of mitosis detection.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2021)
Article
Biology
Edward R. Polanco, Tarek E. Moustafa, Andrew Butterfield, Sandra D. Scherer, Emilio Cortes-Sanchez, Tyler Bodily, Benjamin T. Spike, Bryan E. Welm, Philip S. Bernard, Thomas A. Zangle
Summary: This article introduces a real-time and label-free approach based on quantitative phase imaging to determine drug sensitivity, which has significant advantages over endpoint viability or metabolic assays, and reveals single cell response heterogeneity.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ghazal Azarfar, Ebrahim Aboualizadeh, Simona Ratti, Camilla Olivieri, Alessandra Norici, Michael J. Nasse, Mario Giordano, Carol J. Hirschmugl
Summary: This study utilized mid-infrared spectroscopy to investigate individual Thalassiosira weissflogii cells in water, revealing significant compositional changes in organic pools within the algal cells in response to elevated CO2 concentrations.
SCIENTIFIC REPORTS
(2021)
Article
Optics
Zhichao Liu, Heng Zhang, Luhong Jin, Jincheng Chen, Alexander Nedzved, Sergey Ablameyko, Qing Ma, Jiahui Yu, Yingke Xu
Summary: Fluorescence microscopy is essential for biologists to observe intracellular dynamics. We proposed a novel deep learning-based method for intracellular vesicle tracking, which significantly improved performance with the combination of a fan-shaped tracker. The method has shown promising outcomes in analyzing vesicle dynamics in living cells at different temperatures.
JOURNAL OF INNOVATIVE OPTICAL HEALTH SCIENCES
(2022)
Article
Microbiology
Setsu Kato, Kenta Suzuki, Taiki Kenjo, Junya Kato, Yoshiteru Aoi, Yutaka Nakashimada
Summary: Saccharomyces cerevisiae is widely used as a model organism for aging and longevity studies. In a clonal population, cell death in the stationary phase is asynchronous, highlighting heterogeneity in survival at a single-cell level. Cell size heterogeneity and its correlation with death rate are observed, with cells shrinking upon death and a constant proportion between cell size and shrinkage noted in different strains. Further investigation is needed to understand the mechanisms behind this shrinkage event and its implications for cell death and survival heterogeneity.
Article
Multidisciplinary Sciences
Ashley Teufel, Wu Liu, Jeremy A. Draghi, Craig E. Cameron, Claus O. Wilke
Summary: Viruses experience selective pressure on the timing and order of events during infection. A method has been developed to examine the dynamic phenotypic landscape that viruses must face during replication. Parameters associated with translation and early stage viral replication processes are essential for capturing experimentally observed dynamics.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Andy Goldschmidt, James Kunert-Graf, Adrian C. Scott, Zhihao Tan, Aimee M. Dudley, J. Nathan Kutz
Summary: Baker's yeast is a model organism for studying morphology at the scale of multi-cell colonies, with texture score development trajectories used for hierarchical clustering.
Article
Medicine, General & Internal
Max Masthoff, Felix Noah Freppon, Lisa Zondler, Enrica Wilken, Lydia Wachsmuth, Silke Niemann, Christian Schwarz, Ina Fredrich, Asli Havlas, Helena Block, Mirjam Gerwing, Anne Helfen, Walter Heindel, Alexander Zarbock, Moritz Wildgruber, Cornelius Faber
Summary: This study used time-lapse MRI to track the behavior of single circulating monocytes dynamically. It was found that the patrolling behavior of monocytes is influenced by both local and systemic stimuli, and varies depending on the type, duration, and strength of the stimulus.
Review
Pharmacology & Pharmacy
Fabio Stossi, Pankaj K. Singh, Kazem Safari, Michela Marini, Demetrio Labate, Michael A. Mancini
Summary: Measuring single cell responses to chemicals is crucial for human health, and high throughput, microscopy-based assays coupled with multi-dimensional single cell analysis methods are being used to address this problem. This article summarizes efforts in this field, focusing on environmental toxicology and drug screening, and discusses the advantages and limitations of high throughput assays.
BIOCHEMICAL PHARMACOLOGY
(2023)
Article
Biochemical Research Methods
Yanming Zhu, Erik Meijering
Summary: This study proposed a novel NAS-based solution for deep learning-based live cell segmentation in time-lapse microscopy images. By jointly searching non-repeatable micro architectures to construct the macro network and defining a specific search space suitable for the task, as well as exploring temporal information in cell sequences, the method demonstrated more competitive performance, showing more consistent top performance across all datasets in the experiments.
Article
Biochemical Research Methods
Saoirse Amarteifio, Todd Fallesen, Gunnar Pruessner, Giovanni Sena
Summary: This study introduces an algorithm to optimize 3D object tracking by combining registration and tracking tasks into one algorithm, using random sampling to solve the identity management problem. The algorithm is designed and applied in the field of plant biology, and is open-source. It fills a gap in existing tracking techniques by tracking mitotic events in challenging datasets using transient fluorescent markers in unregistered images.
Article
Computer Science, Artificial Intelligence
Pasquale Cascarano, Maria Colomba Comes, Arianna Mencattini, Maria Carla Parrini, Elena Loli Piccolomini, Eugenio Martinelli
Summary: A new deep learning-based algorithm is proposed for TLM Video Super Resolution without requiring any training, showing outstanding performances on synthetic and real videos related to tumor-immune interaction. The method introduces new approaches for initializing network weights and penalizing the DIP loss function.
MEDICAL IMAGE ANALYSIS
(2021)
Article
Biotechnology & Applied Microbiology
Xinyang Li, Yixin Li, Yiliang Zhou, Jiamin Wu, Zhifeng Zhao, Jiaqi Fan, Fei Deng, Zhaofa Wu, Guihua Xiao, Jing He, Yuanlong Zhang, Guoxun Zhang, Xiaowan Hu, Xingye Chen, Yi Zhang, Hui Qiao, Hao Xie, Yulong Li, Haoqian Wang, Lu Fang, Qionghai Dai
Summary: DeepCAD-RT is a real-time denoising method for fluorescence time-lapse images, which uses self-supervised deep learning for noise suppression. Compared to traditional methods, DeepCAD-RT significantly reduces the number of network parameters, memory consumption, and processing time, and achieves high imaging signal-to-noise ratio with one-tenth of the photons. In various photon-limited experiments, DeepCAD-RT demonstrates its utility in morphological and functional interrogation of biological dynamics.
NATURE BIOTECHNOLOGY
(2023)
Article
Physics, Multidisciplinary
Colas Droin, Eric R. Paquet, Felix Naef
Article
Multidisciplinary Sciences
Cedric Gobet, Benjamin Dieter Weger, Julien Marquis, Eva Martin, Nagammal Neelagandan, Frederic Gachon, Felix Naef
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Benjamin D. Weger, Cedric Gobet, Fabrice P. A. David, Florian Atger, Eva Martin, Nicholas E. Phillips, Aline Charpagne, Meltem Weger, Felix Naef, Frederic Gachon
Summary: The study investigated the roles of the circadian clock and feeding rhythms in regulating rhythmic gene expression in the liver, highlighting their importance and differential contributions. Both feeding patterns and the circadian clock influence gene expression rhythms, with distinct amplitudes. By analyzing multiple core clock regulators, the research revealed their varying impacts on liver gene expression regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Nagammal Neelagandan, Irene Lamberti, Hugo J. F. Carvalho, Cedric Gobet, Felix Naef
Article
Genetics & Heredity
Jerome Mermet, Jake Yeung, Felix Naef
Summary: The study reveals that both clock-controlled and clock-independent chromatin topology play a role in regulating the rhythmic physiology of the liver in mice. Dynamic and static DNA contacts contribute to the circadian transcription of liver physiology.
Article
Biochemistry & Molecular Biology
Nicholas E. Phillips, Alice Hugues, Jake Yeung, Eric Durandau, Damien Nicolas, Felix Naef
Summary: Research on single-cell mRNA dynamics of core clock genes in mouse fibroblasts using single-molecule fluorescence technology revealed significant variability between cells. A probabilistic model was developed to account for transcriptional bursting, circadian time, and cell-to-cell heterogeneity, with clock time contributing only a small fraction to mRNA number variability between cells.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Editorial Material
Multidisciplinary Sciences
Katharine C. Abruzzi, Cedric Gobet, Felix Naef, Michael Rosbash
Summary: The study by Ray et al. claimed the presence of temperature-compensated free-running mRNA oscillations in Bmal1(-/-) liver slices and skin fibroblasts. However, upon reanalysis, fewer reproducible mRNA oscillations were found in this genotype, along with errors and potentially inappropriate analyses.
Article
Biology
Paule Dagenais, Simon Blanchoud, David Pury, Catherine Pfefferli, Tinri Aegerter-Wilmsen, Christof M. Aegerter, Anna Jazwinska
Summary: Understanding how external factors modulate genetically encoded information to produce specific phenotypes is a key scientific interest. By manipulating the external environment of regenerating fish fins, researchers were able to induce structural and phenotypic responses. Mechanical forces were found to play a role in fine-tuning locomotory organs during fin morphogenesis.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2021)
Article
Developmental Biology
Marta K. Wawrzyniak, Lluis Albert Matas Serrato, Simon Blanchoud
Summary: Tunicates, closely related to vertebrates, are diverse marine invertebrate filter-feeders with colonial ascidians being established models for important biological processes including allorecognition. A flexible recirculating husbandry setup has been developed to promote the scientific spreading and popularity of colonial ascidians, allowing for successful long-term in-lab culture and research. The system, inspired by coastal ascidian labs and zebrafish research, provides a modular structure that can be scaled and adapted to specific species and laboratory needs.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Marta K. Wawrzyniak, Lluis Albert Matas Serrato, Simon Blanchoud
Summary: This article presents data on monitoring a marine recirculating artificial seawater husbandry system for breeding colonial ascidians over three years. The datasets include abiotic parameters, concentrations of noxious ions, animal countings, and animal survival, providing insights into the impact of culturing conditions on the breeding of colonial ascidians.
Article
Genetics & Heredity
Clemence S. Hurni, Benjamin Weger, Cedric S. Gobet, Felix Naef
Summary: This study analyzed the temporal regulation of RNA synthesis, splicing, nuclear export, and degradation in eukaryotes, specifically focusing on the circadian cycle. The researchers found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs.
Article
Multidisciplinary Sciences
Lorenzo Talamanca, Cedric Gobet, Felix Naef
Summary: The study revealed that the circadian clock regulates human physiology, but the specific gene expression rhythms and their dependence on age and sex in humans were not well-defined. By combining data from the GTEx project and an algorithm, the researchers identified mRNA rhythms in 46 tissues and found that they varied in breadth and were affected by sex and age. The overall gene expression rhythms were more sustained in females, while rhythmic programs generally dampened with age.
Article
Endocrinology & Metabolism
Colas Droin, Jakob El Kholtei, Keren Bahar Halpern, Clemence Hurni, Milena Rozenberg, Sapir Muvkadi, Shalev Itzkovitz, Felix Naef
Summary: This study reveals the interplay between gene regulation in space and time in the liver using single-cell RNA-seq, showing that many genes exhibit both zonation and rhythmic expression, covering key hepatic functions as well as other processes such as protein chaperones. Additionally, the expression of Wnt target genes is shown to be rhythmic and localized, potentially influenced by rhythmically expressed Wnt ligands from non-parenchymal cells near the central vein.
Article
Multidisciplinary Sciences
Onur Tidin, Elias T. Friman, Felix Naef, David M. Suter
SCIENTIFIC REPORTS
(2019)
Review
Physiology
Anna Jazwinska, Simon Blanchoud
CURRENT OPINION IN PHYSIOLOGY
(2020)
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.