Article
Environmental Sciences
Man Ning, Huimin Li, Zheng Xu, Lei Chen, Yiliang He
Summary: This study developed a new methodology combining flow cytometric analysis and high-throughput sequencing for monitoring picophytoplankton in a clean reservoir, discovering more species of Pico-Cyanobacteria and Pico-Eukaryotes to improve monitoring accuracy.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Review
Chemistry, Analytical
Majood Haddad, Alex N. Frickenstein, Stefan Wilhelm
Summary: Understanding nanoparticle-cell interactions at single-nanoparticle and single-cell resolutions is crucial to improving the design of next-generation nanoparticles for safer, more effective, and more efficient applications in nanomedicine. This review focuses on recent advances in the continuous high-throughput analysis of nanoparticle-cell interactions at the single-cell level, discussing methods such as flow cytometry and inductively coupled plasma mass spectrometry, as well as their intersection in mass cytometry. The review also explores the challenges and opportunities in current single-cell analysis approaches and proposes directions for innovation in high-throughput analysis of nanoparticle-cell interactions.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Gerjen H. Tinnevelt, Kristiaan Wouters, Geert J. Postma, Rita Folcarelli, Jeroen J. Jansen
Summary: White blood cells play a crucial role in protecting the body from diseases, but can also be related to chronic inflammation, auto immune diseases, or leukemia. High-throughput analytical instruments have been developed to measure multiple proteins on millions of single cells to study the identity and function of different white blood cell types. Multivariate statistics are essential for fully extracting the information-rich biochemistry data. The process involves analyzing the study design, formulating a research question, preparing the data, converting single cells into a cellular distribution, and using clustering methods or models for analysis to differentiate cell (sub)types between groups.
ANALYTICA CHIMICA ACTA
(2021)
Review
Chemistry, Analytical
Zheng Zhou, Yao Chen, Shu Zhu, Linbo Liu, Zhonghua Ni, Nan Xiang
Summary: Inertial microfluidics, proposed in 2007, has been extensively studied and applied in the biomedical field, offering advantages such as high throughput, simplicity, and low cost. This technology is promising for rapid sample processing, cell analysis, and detection, playing a crucial role in cellular sample pretreatment.
Article
Medicine, General & Internal
Julien Demagny, Camille Roussel, Mailys Le Guyader, Eric Guiheneuf, Veronique Harrivel, Thomas Boyer, Momar Diouf, Michael Dussiot, Yohann Demont, Loic Garon
Summary: This study presents a method combining imaging flow cytometry and artificial intelligence for the direct label-free and operator-independent quantification of schistocytes in whole blood. By training a support vector machine blood elements' classifier, the method can reliably diagnose thrombotic microangiopathy syndrome in emergency situations.
Review
Chemistry, Analytical
Minruihong Wang, Hongyan Liang, Xiao Chen, Deyong Chen, Junbo Wang, Yuan Zhang, Jian Chen
Summary: Single-cell analysis plays a crucial role in scientific research and clinical diagnosis, especially in the study of dynamic immune processes and tumor research. The development of optoelectronic flow cytometry technology offers new possibilities for complete blood cell counting and is expected to become the standard for future blood analysis.
Review
Immunology
Marion Le Rochais, Patrice Hemon, Jacques-Olivier Pers, Arnaud Uguen
Summary: Imaging mass cytometry (IMC) allows for the analysis of in-depth-phenotyped cells in their native microenvironment within tissue sections, aiding in the identification of biomarkers for cancer treatment and improving understanding of cancer progression and immune system resistance mechanisms.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Masashi Ugawa, Sadao Ota
Summary: This study introduces a high-throughput 3D-imaging flow cytometry technique based on light-sheet microscopy, which can rapidly screen a large number of cells and obtain subcellular structural information.
Article
Chemistry, Multidisciplinary
Joshua A. Welsh, Bryce Killingsworth, Julia Kepley, Tim Traynor, Kathy McKinnon, Jason Savage, Deven Appel, Kenneth Aldape, Kevin Camphausen, Jay A. Berzofsky, Alexander R. Ivanov, Ionita H. Ghiran, Jennifer C. Jones
Summary: Evidence is increasing for the clinical utility of extracellular vesicles (EVs) as translational biomarkers, but there is a lack of methods for removing unbound labels. By developing a multi-modal resin method called EV-Clean, improvements have been demonstrated in flow cytometric EV analysis.
Article
Multidisciplinary Sciences
Yannik Severin, Benjamin D. Hale, Julien Mena, David Goslings, Beat M. Frey, Berend Snijder
Summary: Phenotypic plasticity in the immune system is influenced by donor age, gender, and blood pressure, resulting in distinct polarization and activation-associated phenotypes across immune cell classes. The morphology of T cells is associated with their transcriptional state, with inflammation-associated polarized T cell morphology and age-associated loss of mitochondria observed. This study reveals that immune cell phenotypes reflect both molecular and personal health information, providing new perspectives for deep immune phenotyping in individuals' health and disease.
Article
Biochemical Research Methods
Madeline E. McCarthy, William B. Dodd, Xiaoming Lu, Daniel J. Pritko, Nishi D. Patel, Charlotte V. Haskell, Hugo Sanabria, Mark A. Blenner, Marc R. Birtwistle
Summary: We propose a theory for high-throughput genetic interaction screens, which extends the Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to create 100,000 spectrally unique MuSIC barcodes. Experimental testing of this theory could revolutionize genetic perturbation technology and knowledge of genetic function. Additionally, a genome-scale spectral barcode library could have widespread applications in genetic screening and lineage tracing.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jaco Botha, Haley R. Pugsley, Aase Handberg
Summary: This study compared the performance of traditional flow cytometry with high-resolution imaging flow cytometry, finding the latter to have higher sensitivity and repeatability in detecting and quantifying extracellular vesicles. By selecting the appropriate flow cytometry platform, researchers can better conduct EV studies, improving the reliability and reproducibility of research results.
Review
Pharmacology & Pharmacy
Chelsea B. Pratt, Matt Alexander
Summary: The development of CAR-T cells is crucial for the success of adoptive T-cell immunotherapy. While the process of producing autologous CAR-T cells is time-consuming and expensive, the exploration of cost-effective allogeneic CAR-T cells is essential. High-throughput tools are used to monitor the entire process of CAR-T cell design, testing, manufacturing, and patient monitoring to ensure safety and efficacy.
DRUG DISCOVERY TODAY
(2022)
Article
Biology
Ziqi Zhang, Kelvin C. M. Lee, Dickson M. D. Siu, Michelle C. K. Lo, Queenie T. K. Lai, Edmund Y. Lam, Kevin K. Tsia
Summary: This article introduces an image-based approach that can quantify multiple biophysical fractal-related properties of single cells at subcellular resolution. This technique has high-throughput single-cell imaging performance and offers sufficient statistical power for cell classification, drug response assays, and cell-cycle progression tracking.
COMMUNICATIONS BIOLOGY
(2023)
Article
Physics, Applied
Julie Martin-Wortham, Steffen M. Recktenwald, Marcelle G. M. Lopes, Lars Kaestner, Christian Wagner, Stephan Quint
Summary: The proposed method combines spatial optical modulation and deep learning to detect cells label-free at high throughput while providing their brightfield images. It requires minimal optical components, suitable for lab-on-chip devices, and has been benchmarked with a dataset of red blood cell images.
APPLIED PHYSICS LETTERS
(2021)
Article
Biochemical Research Methods
Liran Ben Yaakov, Yael Mutsafi, Ziv Porat, Tali Dadosh, Abraham Minsky
Article
Biochemistry & Molecular Biology
Shiran Rabinovich, Alon Silberman, Lital Adler, Shani Agron, Smadar Levin-Zaidman, Amir Bahat, Ziv Porat, Efrat Ben-Zeev, Inbal Geva, Maxim Itkin, Sergey Malitsky, Adam Buchaklian, Daniel Helbling, David Dimmock, Ayelet Erez
Article
Cell Biology
Fatoumata Samassa, Mariana L. Ferrari, Julien Husson, Anastassia Mikhailova, Ziv Porat, Florence Sidaner, Katja Brunner, Teck-Hui Teo, Elisabetta Frigimelica, Jean-Yves Tinevez, Philippe J. Sansonetti, Maria-Isabel Thoulouze, Armelle Phalipon
CELLULAR MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Omer Karin, Amit Agrawal, Ziv Porat, Valery Krizhanovsky, Uri Alon
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Avital Eisenberg-Lerner, Ron Benyair, Noa Hizkiahou, Neta Nudel, Roey Maor, Matthias P. Kramer, Merav D. Shmueli, Inbal Zigdon, Marina Cherniavsky Lev, Adi Ulman, Jitka Yehudith Sagiv, Molly Dayan, Bareket Dassa, Mercedes Rosenwald, Idit Shachar, Jie Li, Yanzhuang Wang, Nili Dezorella, Suman Khan, Ziv Porat, Eyal Shimoni, Ori Avinoam, Yifat Merbl
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Elya Dekel, Paula Abou Karam, Yael Ohana-Daniel, Mirit Biton, Neta Regev-Rudzki, Ziv Porat
Article
Immunology
Shira Tabachnick-Cherny, Sivan Pinto, Dikla Berko, Caterina Curato, Yochai Wolf, Ziv Porat, Rotem Karmona, Boaz Tirosh, Steffen Jung, Ami Navon
JOURNAL OF IMMUNOLOGY
(2020)
Article
Multidisciplinary Sciences
Flora Vincent, Uri Sheyn, Ziv Porat, Daniella Schatz, Assaf Vardi
Summary: In this study, the quantification of active viral infection in marine phytoplankton revealed the significance of viral-induced cell lysis on the marine ecosystem. The use of high-throughput single-molecule messenger RNA in situ hybridization allowed for a mechanistic understanding of biotic interactions in the ocean.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Elya Dekel, Dana Yaffe, Irit Rosenhek-Goldian, Gili Ben-Nissan, Yifat Ofir-Birin, Mattia I. Morandi, Tamar Ziv, Xavier Sisquella, Matthew A. Pimentel, Thomas Nebl, Eugene Kapp, Yael Ohana Daniel, Paula Abou Karam, Daniel Alfandari, Ron Rotkopf, Shimrit Malihi, Tal Block Temin, Debakshi Mullick, Or-Yam Revach, Ariel Rudik, Nir S. Gov, Ido Azuri, Ziv Porat, Giulia Bergamaschi, Raya Sorkin, Gijs J. L. Wuite, Ori Avinoam, Teresa G. Carvalho, Sidney R. Cohen, Michal Sharon, Neta Regev-Rudzki
Summary: The study demonstrates that Plasmodium falciparum secretes extracellular vesicles (EVs) containing functional 20S proteasome complexes which remodel the cytoskeleton of naive human red blood cells, preparing them for parasite invasion.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Rita Manco, Inna Averbukh, Ziv Porat, Keren Bahar Halpern, Ido Amit, Shalev Itzkovitz
Summary: Combining single-cell RNA sequencing with spatial information allows for the reconstruction of spatially-resolved tissue cell atlases, which is challenging for rare cell types. The ClumpSeq approach presented in this study enables the establishment of spatial atlases for all epithelial cell types in the small intestine, revealing immune-modulatory gene expression in villus tip goblet and tuft cells as well as heterogeneous migration patterns of enteroendocrine cells.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Tom Kaufman, Erez Nitzan, Nir Firestein, Miriam Bracha Ginzberg, Seshu Iyengar, Nish Patel, Rotem Ben-Hamo, Ziv Porat, Jaryd Hunter, Andreas Hilfinger, Varda Rotter, Ran Kafri, Ravid Straussman
Summary: In this study, the authors developed a fluorescence imaging-based visual barcode for livecell clonal-multiplexing, which allows the identification of signalling pathways clusters in response to different chemotherapy compounds. They also demonstrated the use of visual barcodes to generate 'Signalome' cell-lines, enabling the simultaneous monitoring of the activity in 12 branches of signaling at clonal resolution.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Tamar Sapir, Aditya Kshirsagar, Anna Gorelik, Tsviya Olender, Ziv Porat, Ingrid E. Scheffer, David B. Goldstein, Orrin Devinsky, Orly Reiner
Summary: HNRNPU loss of function leads to rapid cell death of both postmitotic neurons and neural progenitors, with a higher sensitivity of the latter. The expression and alternative splicing of multiple genes involved in cell survival, cell motility, and synapse formation are affected following Hnrnpu's conditional truncation. Pharmaceutical and genetic agents have been identified to partially reverse the loss of cortical structures in Hnrnpu mutated embryonic brains.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Zhana Haimon, Gal Ronit Frumer, Jung-Seok Kim, Sebastien Trzebanski, Rebecca Haffner-Krausz, Shifra Ben-Dor, Ziv Porat, Andreas Muschaweckh, Louise Chappell-Maor, Sigalit Boura-Halfon, Thomas Korn, Steffen Jung
Summary: Microglia, the brain macrophages, play a critical role in brain development and homeostasis. They interact with T cells through antigen presentation, costimulation, and coinhibition. In autoimmune neuroinflammation, microglia have significant non-redundant cognate and cytokine-mediated interactions with regulatory T cells.
Article
Multidisciplinary Sciences
N. Zioni, A. Akhiad Bercovich, N. Chapal-Ilani, Tal Bacharach, N. Rappoport, A. Solomon, R. Avraham, E. Kopitman, Z. Porat, M. Sacma, G. Hartmut, M. Scheller, C. Muller-Tidow, D. Lipka, E. Shlush, M. Minden, N. Kaushansky, Liran Shlush
Summary: The accumulation of fatty bone marrow and somatic mutations in hematopoietic stem cells (HSCs) increases with aging. In preclinical mouse models, it is found that fatty bone marrow can enhance the self-renewal of HSCs and activate inflammatory signaling. The inflammatory cytokines, such as IL-6, in fatty bone marrow promote DNMT3a-driven clonal hematopoiesis, which can be inhibited by blocking the IL-6 pathway.
NATURE COMMUNICATIONS
(2023)
Review
Cell Biology
Gabriela Koifman, Ronit Aloni-Grinstein, Varda Rotter
JOURNAL OF MOLECULAR CELL BIOLOGY
(2019)