Article
Microbiology
Maria V. Kulakova, Eslam S. M. O. Ghazy, Fedor Ryabov, Yaroslav M. Stanishevskiy, Michael O. Agaphonov, Alexander I. Alexandrov
Summary: In this study, a method called Histone Abundance Quantification (HAQ) was developed to quantitatively measure the level of histones in live yeast cells. The HAQ method showed consistent results with DNA levels and can be used in conjunction with other fluorescent markers. This method provides a simple approach for directly monitoring the effects of various stimuli on the cell cycle.
Review
Biochemistry & Molecular Biology
Magdalena Foltman, Alberto Sanchez-Diaz
Summary: This article focuses on the significance of the highly conserved TOR signaling pathway, particularly the connection between TORC1 complex in budding yeast and the cell cycle, and the importance of this connection for cell size and chromosome stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Diwakar M. Awate, Cicero C. Pola, Erica Shumaker, Carmen L. Gomes, Jaime J. Juarez
Summary: Despite the limitations of flow cytometers, a 3D-printed imaging platform (3DPIP) has been developed to accurately count particles and conduct fluorescence microscopy efficiently. The 3DPIP utilizes a custom particle counter code and machine vision-based algorithm to identify and count particles, showing comparable accuracy to commercial particle counters. Additionally, the platform can perform static experiments and flow-through experiments effectively, making it a promising tool for use in resource-limited clinical environments.
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
Biotechnology & Applied Microbiology
Ming Lei, Vikas D. Trivedi, Nikhil U. Nair, Kyongbum Lee, James A. Van Deventer
Summary: Synthetic cell-cell interaction systems are important for understanding multicellular communities and screening binding molecules. In this study, a previously characterized set of synthetic nanobody-antigen pairs was adapted to a yeast-bacteria coincubation format and evaluated using flow cytometry and fluorescence-activated cell sorting. The results demonstrate the efficiency of this system in evaluating ligand-target interactions and its potential for systematic characterization and high-throughput discovery of bacterial surface-binding molecules.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemical Research Methods
Andreas P. Cuny, Aaron Ponti, Tomas Kundig, Fabian Rudolf, Jorg Stelling
Summary: TracX improves the accuracy of single-cell tracking using a fingerprinting approach to measure cell similarity across consecutive images. It is applicable across different cell types and image modalities, aiding in accurate cell observation and biological discovery in single-cell biology.
Article
Geosciences, Multidisciplinary
Changlin Li, Kuo-Ping Chiang, Edward A. Laws, Xin Liu, Jixin Chen, Yibin Huang, Bingzhang Chen, An-Yi Tsai, Bangqin Huang
Summary: Picophytoplankton, the smallest and most abundant photosynthetic organisms in the ocean, exhibit synchronized diel cycles in cell numbers and cell sizes/biomasses, which are in a quasi-antiphase relationship. The mortality rates indicate significant grazing pressure on Prochlorococcus and Synechococcus throughout the day and night. This study enhances our understanding of autotrophic picoplankton in the oligotrophic ocean.
GEOPHYSICAL RESEARCH LETTERS
(2022)
Article
Biochemical Research Methods
Chen Jia, Abhyudai Singh, Ramon Grima
Summary: This study investigates the dynamics of cell size in fission yeast, revealing the relationship between different cell growth phases and size control strategies, as well as their effects under various growth conditions. By matching experimental data with theoretical models, the size control strategy and model parameters of cell size distribution are determined.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Paul H. Dannenberg, Jisoo Kang, Nicola Martino, Anokhi Kashiparekh, Sarah Forward, Jiamin Wu, Andreas C. Liapis, Jie Wang, Seok-Hyun Yun
Summary: This article demonstrates a cell barcode technology using laser particles, which can be used for cell sorting and routing through a microfluidic platform integrated with a high-speed spectrometer. By utilizing the spectral emission of laser particles, individual cells labeled with different laser colors can be distinguished and sorted.
Article
Agricultural Engineering
Yangyang Wei, Zilin Zhao, Sumei Wan, Yi Li, Jiajia Feng, Qiankun Liu, Jingjing Zhai, Jianyu Wang, Yongqing Zhao, Xingyan Li, Yuling Liu, Tao Wang, Pengtao Li, Quanwei Lu, Baohong Zhang, Shoulin Hu, Renhai Peng
Summary: Cell cycle is crucial for plant growth and development, and synchronizing the cell cycle can provide insights into molecular mechanisms and cell growth for several purposes, including crop improvement. However, there is limited research on cell cycle synchronization and its application in transcriptome analysis. In this study, a cell cycle synchronization technology was developed using flow cytometry, and the gene expression profiling during the cell cycle was studied in cotton. The results identified important genes related to cell cycle regulation and revealed the involvement of tubulin family in the cell cycle.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Immunology
Claudia Andrade, Barbara Oliveira, Silvia Guatelli, Pedro Martinez, Beatriz Simoes, Claudia Bispo, Cinzia Ferrario, Francesco Bonasoro, Jose Rino, Michela Sugni, Rui Gardner, Rita Zilhao, Ana Varela Coelho
Summary: In this study, coelomocytes present in the coelomic fluid of Marthasterias glacialis were characterized using a combination of flow cytometry, imaging flow cytometry, and fluorescence plus transmission electron microscopy. Two distinct coelomocyte populations were identified and studied in terms of abundance, morphology, ultrastructure, cell viability, and cell cycle profiles. The integrative experimental workflow allowed for a better understanding of the heterogeneity within these coelomocyte populations.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
Ryley D. McClelland, Tyce N. Culp, David J. Marchant
Summary: Viruses use host factors to enter cells and cause disease, and imaging techniques are crucial for studying virus entry and replication processes, providing insights into viral infection mechanisms. Quantifying viral images and using cryo-electron microscopy to gather structural information of viruses can help identify novel targets for antiviral therapeutics and vaccines.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Chemistry, Analytical
Li Wu, Shihan Xu, Jingang Wang, Amy L. Paguirigan, Jerald P. Radich, Yuling Qin, Daniel T. Chiu
Summary: Researchers have developed a single cell dispenser inspired by electrohydrodynamic jet printing, which can be used for single-cell multiomics studies, achieving accurate droplet generation and single-cell dispensing through systematic parameter optimization.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Minh Doan, Claire Barnes, Claire McQuin, Juan C. Caicedo, Allen Goodman, Anne E. Carpenter, Paul Rees
Summary: This protocol describes an open-source application called Deepometry for supervised and weakly supervised deep learning analysis of imaging flow cytometry datasets. It explains the application of deep learning to single-cell images for supervised cell classification and weakly supervised learning, using example data from an experiment exploring red blood cell morphology. The protocol provides runtime scripts for Python, MATLAB, and a standalone application, allowing for flexible and user-friendly environment for morphological phenotyping and deep learning feature exploration.
Article
Cell Biology
Keiichiro Sakai, Yohei Kondo, Hiroyoshi Fujioka, Mako Kamiya, Kazuhiro Aoki, Yuhei Goto
Summary: The study demonstrates that phycocyanobilin (PCB) functions as a brighter chromophore for near-infrared fluorescent protein (iRFP) than biliverdin (BV), increasing the brightness of iRFP fluorescence. By introducing a PCB biosynthesis system and developing an endogenous gene tagging system along with integration plasmids carrying iRFP-fused marker proteins, multiplexed live-cell imaging in fission yeast becomes more accessible.
JOURNAL OF CELL SCIENCE
(2021)
Review
Biochemical Research Methods
Uta Erdbruegger, Joanne Lannigan
Article
Biochemical Research Methods
Graham M. Richardson, Joanne Lannigan, Ian G. Macara
Article
Biochemical Research Methods
Asya Smirnov, Michael D. Solga, Joanne Lannigan, Alison K. Criss
JOURNAL OF IMMUNOLOGICAL METHODS
(2015)
Article
Biochemical Research Methods
Lora W. Barsky, Michele Black, Matthew Cochran, Benjamin J. Daniel, Derek Davies, Monica DeLay, Rui Gardner, Michael Gregory, Desiree Kunkel, Joanne Lannigan, James Marvin, Robert Salomon, Carina Torres, Rachael Walker
Article
Biochemical Research Methods
Aldo Nascimento, Joanne Lannigan, David Kashatus
Editorial Material
Biochemical Research Methods
Joanne Lannigan, John P. Nolan, Robert Zucker
Article
Biochemical Research Methods
Joanne Lannigan, Uta Erdbruegger
Article
Biochemistry & Molecular Biology
Swati Mehrotra, Luciano Galdieri, Tiantian Zhang, Man Zhang, Lucy F. Pemberton, Ales Vancura
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2014)
Article
Mathematical & Computational Biology
Kevin M. D'Auria, Gina M. Donato, Mary C. Gray, Glynis L. Kolling, Cirle A. Warren, Lauren M. Cave, Michael D. Solga, Joanne A. Lannigan, Jason A. Papin, Erik L. Hewlett
BMC SYSTEMS BIOLOGY
(2012)
Article
Biochemical Research Methods
Christine M. Coquery, William Loo, Maja Buszko, Joanne Lannigan, Loren D. Erickson
Article
Biochemical Research Methods
Uta Erdbruegger, Christine K. Rudy, Mark E. Etter, Kelly A. Dryden, Mark Yeager, Alexander L. Klibanov, Joanne Lannigan
Article
Biochemistry & Molecular Biology
Yu-Ming Xue, Anna K. Kowalska, Kamila Grabowska, Katarzyna Przybyt, Magda A. Cichewicz, Brian C. Del Rosario, Lucy F. Pemberton
MOLECULAR AND CELLULAR BIOLOGY
(2013)
Article
Cell Biology
Kristin M. Keck, Lucy F. Pemberton
Article
Biology
Sierra M. Barone, Alberta G. A. Paul, Lyndsey M. Muehling, Joanne A. Lannigan, William W. Kwok, Ronald B. Turner, Judith A. Woodfolk, Jonathan M. Irish
Summary: T-REX is a machine learning workflow designed to identify changes in rare and common cells in human immune monitoring settings. It successfully identified hotspots of virus-specific T cells during rhinovirus and SARS-CoV-2 infections.
Article
Biochemical Research Methods
Maria C. Jaimes, Michael Leipold, Geoffrey Kraker, El-ad Amir, Holden Maecker, Joanne Lannigan
Summary: High-dimensional single-cell data is crucial in understanding the complexity of the immune system. The introduction of full spectrum flow cytometry has overcome the limitations of previous technologies. By comparing two platforms (mass cytometry and full spectrum flow cytometry), this study demonstrates their highly comparable results.