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Han K, Liu X, Sun G, Wang Z, Shi C, Liu W, Huang M, Liu S, Guo Q. Enhancing subcellular protein localization mapping analysis using Sc2promap utilizing attention mechanisms. Biochim Biophys Acta Gen Subj 2024:130601. [PMID: 38522679 DOI: 10.1016/j.bbagen.2024.130601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Aberrant protein localization is a prominent feature in many human diseases and can have detrimental effects on the function of specific tissues and organs. High-throughput technologies, which continue to advance with iterations of automated equipment and the development of bioinformatics, enable the acquisition of large-scale data that are more pattern-rich, allowing for the use of a wider range of methods to extract useful patterns and knowledge from them. METHODS The proposed sc2promap (Spatial and Channel for SubCellular Protein Localization Mapping) model, designed to proficiently extract meaningful features from a vast repository of single-channel grayscale protein images for the purposes of protein localization analysis and clustering. Sc2promap incorporates a prediction head component enriched with supplementary protein annotations, along with the integration of a spatial-channel attention mechanism within the encoder to enables the generation of high-resolution protein localization maps that encapsulate the fundamental characteristics of cells, including elemental cellular localizations such as nuclear and non-nuclear domains. RESULTS Qualitative and quantitative comparisons were conducted across internal and external clustering evaluation metrics, as well as various facets of the clustering results. The study also explored different components of the model. The research outcomes conclusively indicate that, in comparison to previous methods, Sc2promap exhibits superior performance. CONCLUSIONS The amalgamation of the attention mechanism and prediction head components has led the model to excel in protein localization clustering and analysis tasks. GENERAL SIGNIFICANCE The model effectively enhances the capability to extract features and knowledge from protein fluorescence images.
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Affiliation(s)
- Kaitai Han
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Xi Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Guocheng Sun
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Zijun Wang
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Chaojing Shi
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Wu Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Mengyuan Huang
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Shitou Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Qianjin Guo
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
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2
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Paran Y, Liron Y, Batsir S, Mabjeesh N, Geiger B, Kam Z. Multi-parametric characterization of drug effects on cells. F1000Res 2021; 9. [PMID: 33363713 PMCID: PMC7737707 DOI: 10.12688/f1000research.26254.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 12/28/2022] Open
Abstract
We present here a novel multi-parametric approach for the characterization of multiple cellular features, using images acquired by high-throughput and high-definition light microscopy. We specifically used this approach for deep and unbiased analysis of the effects of a drug library on five cultured cell lines. The presented method enables the acquisition and analysis of millions of images, of treated and control cells, followed by an automated identification of drugs inducing strong responses, evaluating the median effect concentrations and those cellular properties that are most highly affected by the drug. The tools described here provide standardized quantification of multiple attributes for systems level dissection of complex functions in normal and diseased cells, using multiple perturbations. Such analysis of cells, derived from pathological samples, may help in the diagnosis and follow-up of treatment in patients.
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Affiliation(s)
- Yael Paran
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel.,IDEA Biomedical Ltd., Rehovot, 76705, Israel
| | - Yuvalal Liron
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Sarit Batsir
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nicola Mabjeesh
- Department of Urology, Tel Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel
| | - Benjamin Geiger
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel.,Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Zvi Kam
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel
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3
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Hwang W, Seo J, Kim D, Lee CJ, Choi IH, Yoo KH, Kim DY. Large field-of-view nanometer-sectioning microscopy by using metal-induced energy transfer and biexponential lifetime analysis. Commun Biol 2021; 4:91. [PMID: 33469155 PMCID: PMC7815909 DOI: 10.1038/s42003-020-01628-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/24/2020] [Indexed: 12/04/2022] Open
Abstract
Total internal reflection fluorescence (TIRF) microscopy, which has about 100-nm axial excitation depth, is the method of choice for nanometer-sectioning imaging for decades. Lately, several new imaging techniques, such as variable angle TIRF microscopy, supercritical-angle fluorescence microscopy, and metal-induced energy transfer imaging, have been proposed to enhance the axial resolution of TIRF. However, all of these methods use high numerical aperture (NA) objectives, and measured images inevitably have small field-of-views (FOVs). Small-FOV can be a serious limitation when multiple cells need to be observed. We propose large-FOV nanometer-sectioning microscopy, which breaks the complementary relations between the depth of focus and axial sectioning by using MIET. Large-FOV imaging is achieved with a low-magnification objective, while nanometer-sectioning is realized utilizing metal-induced energy transfer and biexponential fluorescence lifetime analysis. The feasibility of our proposed method was demonstrated by imaging nanometer-scale distances between the basal membrane of human aortic endothelial cells and a substrate. Hwang et al. demonstrate that a high axial resolution can be achieved even with low numerical aperture (NA) objectives. They show the nano-profile of a basal cell membrane using metal-induced energy transfer and biexponential fluorescence lifetime analysis. The low-NA objective provides a larger field-of-view (FOV), thereby overcoming the limitations of a small FOV of the usually used high-NA objectives.
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Affiliation(s)
- Wonsang Hwang
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Jinwon Seo
- Department of Microbiology, Institute for Immunology and Immunological Diseases, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - DongEun Kim
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Chang Jun Lee
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - In-Hong Choi
- Department of Microbiology, Institute for Immunology and Immunological Diseases, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Kyung-Hwa Yoo
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Dug Young Kim
- Department of Physics, Yonsei University, Seoul, Republic of Korea.
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4
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Herbst RH, Bar-Zvi D, Reikhav S, Soifer I, Breker M, Jona G, Shimoni E, Schuldiner M, Levy AA, Barkai N. Heterosis as a consequence of regulatory incompatibility. BMC Biol 2017; 15:38. [PMID: 28494792 PMCID: PMC5426048 DOI: 10.1186/s12915-017-0373-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The merging of genomes in inter-specific hybrids can result in novel phenotypes, including increased growth rate and biomass yield, a phenomenon known as heterosis. Heterosis is typically viewed as the opposite of hybrid incompatibility. In this view, the superior performance of the hybrid is attributed to heterozygote combinations that compensate for deleterious mutations accumulating in each individual genome, or lead to new, over-dominating interactions with improved performance. Still, only fragmented knowledge is available on genes and processes contributing to heterosis. RESULTS We describe a budding yeast hybrid that grows faster than both its parents under different environments. Phenotypically, the hybrid progresses more rapidly through cell cycle checkpoints, relieves the repression of respiration in fast growing conditions, does not slow down its growth when presented with ethanol stress, and shows increased signs of DNA damage. A systematic genetic screen identified hundreds of S. cerevisiae alleles whose deletion reduced growth of the hybrid. These growth-affecting alleles were condition-dependent, and differed greatly from alleles that reduced the growth of the S. cerevisiae parent. CONCLUSIONS Our results define a budding yeast hybrid that is perturbed in multiple regulatory processes but still shows a clear growth heterosis. We propose that heterosis results from incompatibilities that perturb regulatory mechanisms, which evolved to protect cells against damage or prepare them for future challenges by limiting cell growth.
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Affiliation(s)
- Rebecca H Herbst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02114, USA
| | - Dana Bar-Zvi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sharon Reikhav
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ilya Soifer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Current affiliation: Calico Labs, South San Francisco, CA, 94080, USA
| | - Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Avraham A Levy
- Plant and Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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5
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Multiplexed imaging of intracellular protein networks. Cytometry A 2016; 89:761-75. [DOI: 10.1002/cyto.a.22876] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/19/2022]
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6
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Single-Cell Analysis of Growth in Budding Yeast and Bacteria Reveals a Common Size Regulation Strategy. Curr Biol 2016; 26:356-61. [PMID: 26776734 DOI: 10.1016/j.cub.2015.11.067] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/29/2015] [Accepted: 11/30/2015] [Indexed: 12/29/2022]
Abstract
To maintain a constant cell size, dividing cells have to coordinate cell-cycle events with cell growth. This coordination has long been supposed to rely on the existence of size thresholds determining cell-cycle progression [1]. In budding yeast, size is controlled at the G1/S transition [2]. In agreement with this hypothesis, the size at birth influences the time spent in G1: smaller cells have a longer G1 period [3]. Nevertheless, even though cells born smaller have a longer G1, the compensation is imperfect and they still bud at smaller cell sizes. In bacteria, several recent studies have shown that the incremental model of size control, in which size is controlled by addition of a constant volume (in contrast to a size threshold), is able to quantitatively explain the experimental data on four different bacterial species [4-7]. Here, we report on experimental results for the budding yeast Saccharomyces cerevisiae, finding, surprisingly, that cell size control in this organism is very well described by the incremental model, suggesting a common strategy for cell size control with bacteria. Additionally, we argue that for S. cerevisiae the "volume increment" is not added from birth to division, but rather between two budding events.
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7
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Abstract
Cell size is determined by a complex interplay between growth and division, involving multiple
cellular pathways. To identify systematically processes affecting size control in G1 in budding
yeast, we imaged and analyzed the cell cycle of millions of individual cells representing 591
mutants implicated in size control. Quantitative metric distinguished mutants affecting the
mechanism of size control from the majority of mutants that have a perturbed size due to indirect
effects modulating cell growth. Overall, we identified 17 negative and dozens positive size control
regulators, with the negative regulators forming a small network centered on elements of mitotic
exit network. Some elements of the translation machinery affected size control with a notable
distinction between the deletions of parts of small and large ribosomal subunit: parts of small
ribosomal subunit tended to regulate size control, while parts of the large subunit affected cell
growth. Analysis of small cells revealed additional size control mechanism that functions in G2/M,
complementing the primary size control in G1. Our study provides new insights about size control
mechanisms in budding yeast.
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Affiliation(s)
- Ilya Soifer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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8
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Elosegui-Artola A, Jorge-Peñas A, Moreno-Arotzena O, Oregi A, Lasa M, García-Aznar JM, De Juan-Pardo EM, Aldabe R. Image analysis for the quantitative comparison of stress fibers and focal adhesions. PLoS One 2014; 9:e107393. [PMID: 25269086 PMCID: PMC4182299 DOI: 10.1371/journal.pone.0107393] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 08/15/2014] [Indexed: 01/08/2023] Open
Abstract
Actin stress fibers (SFs) detect and transmit forces to the extracellular matrix through focal adhesions (FAs), and molecules in this pathway determine cellular behavior. Here, we designed two different computational tools to quantify actin SFs and the distribution of actin cytoskeletal proteins within a normalized cellular morphology. Moreover, a systematic cell response comparison between the control cells and those with impaired actin cytoskeleton polymerization was performed to demonstrate the reliability of the tools. Indeed, a variety of proteins that were present within the string beginning at the focal adhesions (vinculin) up to the actin SFs contraction (non-muscle myosin II (NMMII)) were analyzed. Finally, the software used allows for the quantification of the SFs based on the relative positions of FAs. Therefore, it provides a better insight into the cell mechanics and broadens the knowledge of the nature of SFs.
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Affiliation(s)
- Alberto Elosegui-Artola
- Tissue Engineering and Biomaterials Unit, Centro de Estudios e Investigaciones Técnicas and Tecnun, University of Navarra, San Sebastian, Spain
| | - Alvaro Jorge-Peñas
- Tissue Engineering and Biomaterials Unit, Centro de Estudios e Investigaciones Técnicas and Tecnun, University of Navarra, San Sebastian, Spain
| | - Oihana Moreno-Arotzena
- Multiscale in Mechanical and Biological Engineering, Aragón Institute of Engineering Research, Universidad de Zaragoza, Zaragoza, Spain
| | - Amaia Oregi
- Tissue Engineering and Biomaterials Unit, Centro de Estudios e Investigaciones Técnicas and Tecnun, University of Navarra, San Sebastian, Spain
| | - Marta Lasa
- Gene Therapy and Hepatology Area, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - José Manuel García-Aznar
- Multiscale in Mechanical and Biological Engineering, Aragón Institute of Engineering Research, Universidad de Zaragoza, Zaragoza, Spain
| | - Elena M. De Juan-Pardo
- Tissue Engineering and Biomaterials Unit, Centro de Estudios e Investigaciones Técnicas and Tecnun, University of Navarra, San Sebastian, Spain
- * E-mail: (RA); (EMDJ)
| | - Rafael Aldabe
- Gene Therapy and Hepatology Area, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- * E-mail: (RA); (EMDJ)
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9
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Lu S, Wang Y. Single-cell imaging of mechanotransduction in endothelial cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 126:25-51. [PMID: 25081613 DOI: 10.1016/b978-0-12-394624-9.00002-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Endothelial cells (ECs) are constantly exposed to chemical and mechanical microenvironment in vivo. In mechanotransduction, cells can sense and translate the extracellular mechanical cues into intracellular biochemical signals, to regulate cellular processes. This regulation is crucial for many physiological functions, such as cell adhesion, migration, proliferation, and survival, as well as the progression of disease such as atherosclerosis. Here, we overview the current molecular understanding of mechanotransduction in ECs associated with atherosclerosis, especially those in response to physiological shear stress. The enabling technology of live-cell imaging has allowed the study of spatiotemporal molecular events and unprecedented understanding of intracellular signaling responses in mechanotransduction. Hence, we also introduce recent studies on mechanotransduction using single-cell imaging technologies.
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Affiliation(s)
- Shaoying Lu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA
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10
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Vardi N, Levy S, Assaf M, Carmi M, Barkai N. Budding Yeast Escape Commitment to the Phosphate Starvation Program Using Gene Expression Noise. Curr Biol 2013; 23:2051-7. [DOI: 10.1016/j.cub.2013.08.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 12/30/2022]
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11
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Adiga U, Bell BL, Ponomareva L, Taylor D, Saldanha R, Nelson S, Lamkin TJ. Mapping infected cell phenotype. IEEE Trans Biomed Eng 2012; 59:2362-71. [PMID: 22711766 DOI: 10.1109/tbme.2012.2204746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Quantitative modeling of the phenotypic changes in the host cell during the bacterial infection makes it possible to explore an empirical relation between the infection stages and the quantifiable host-cell phenotype. A statistically reliable model of this relation can facilitate therapeutic defense against threats due to natural and genetically engineered bacterium. In the preliminary experiment, we have collected several thousand cell images over a period of 72 h of infection with a 2-h sampling frequency that covers various stages of infection by Francisella tularenesis (Ft). Segmentation of macrophages in images was accomplished using a fully automatic, parallel region growing technique. Over two thousand feature descriptors for the host cell were calculated. Multidimensional scaling, followed by hierarchical clustering, was used to group the cells. Preliminary results show that the host-cell phenotype, as defined by the set of measureable features, groups into different classes that can be mapped to the stages of infection.
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Affiliation(s)
- U Adiga
- UES, Inc., Dayton, OH 45432, USA.
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12
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Regulation of integrin adhesions by varying the density of substrate-bound epidermal growth factor. Biointerphases 2012; 7:23. [PMID: 22589066 DOI: 10.1007/s13758-012-0023-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 02/13/2012] [Indexed: 01/25/2023] Open
Abstract
Substrates coated with specific bioactive ligands are important for tissue engineering, enabling the local presentation of extracellular stimulants at controlled positions and densities. In this study, we examined the cross-talk between integrin and epidermal growth factor (EGF) receptors following their interaction with surface-immobilized Arg-Gly-Asp (RGD) and EGF ligands, respectively. Surfaces of glass coverslips, modified with biotinylated silane-polyethylene glycol, were functionalized by either biotinylated RGD or EGF (or both) via the biotin-NeutrAvidin interaction. Fluorescent labeling of the adhering A431 epidermoid carcinoma cells for zyxin or actin indicated that EGF had a dual effect on focal adhesions (FA) and stress fibers: at low concentrations (0.1; 1 ng/ml), it stimulated their growth; whereas at higher concentrations, on surfaces with low to intermediate RGD densities, it induced their disassembly, leading to cell detachment. The EGF-dependent dissociation of FAs was, however, attenuated on higher RGD density surfaces. Simultaneous stimulation by both immobilized RGD and EGF suggest a strong synergy between integrin and EGFR signaling, in FA induction and cell spreading. A critical threshold level of EGF was required to induce significant variation in cell adhesion; beyond this critical density, the immobilized molecule had a considerably stronger effect on cell adhesion than did soluble EGF. The mechanisms underlying this synergy between the adhesion ligand and EGF are discussed.
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13
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Prot JM, Leclerc E. The Current Status of Alternatives to Animal Testing and Predictive Toxicology Methods Using Liver Microfluidic Biochips. Ann Biomed Eng 2011; 40:1228-43. [DOI: 10.1007/s10439-011-0480-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/23/2011] [Indexed: 01/17/2023]
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14
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Baradez MO, Marshall D. The use of multidimensional image-based analysis to accurately monitor cell growth in 3D bioreactor culture. PLoS One 2011; 6:e26104. [PMID: 22028809 PMCID: PMC3197601 DOI: 10.1371/journal.pone.0026104] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 09/19/2011] [Indexed: 12/21/2022] Open
Abstract
The transition from traditional culture methods towards bioreactor based bioprocessing to produce cells in commercially viable quantities for cell therapy applications requires the development of robust methods to ensure the quality of the cells produced. Standard methods for measuring cell quality parameters such as viability provide only limited information making process monitoring and optimisation difficult. Here we describe a 3D image-based approach to develop cell distribution maps which can be used to simultaneously measure the number, confluency and morphology of cells attached to microcarriers in a stirred tank bioreactor. The accuracy of the cell distribution measurements is validated using in silico modelling of synthetic image datasets and is shown to have an accuracy >90%. Using the cell distribution mapping process and principal component analysis we show how cell growth can be quantitatively monitored over a 13 day bioreactor culture period and how changes to manufacture processes such as initial cell seeding density can significantly influence cell morphology and the rate at which cells are produced. Taken together, these results demonstrate how image-based analysis can be incorporated in cell quality control processes facilitating the transition towards bioreactor based manufacture for clinical grade cells.
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Affiliation(s)
| | - Damian Marshall
- Science and Technology Division, LGC, Teddington, Middlesex, United Kingdom
- * E-mail:
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15
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Berginski ME, Vitriol EA, Hahn KM, Gomez SM. High-resolution quantification of focal adhesion spatiotemporal dynamics in living cells. PLoS One 2011; 6:e22025. [PMID: 21779367 PMCID: PMC3136503 DOI: 10.1371/journal.pone.0022025] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 06/12/2011] [Indexed: 01/09/2023] Open
Abstract
Focal adhesions (FAs) are macromolecular complexes that provide a linkage between the cell and its external environment. In a motile cell, focal adhesions change size and position to govern cell migration, through the dynamic processes of assembly and disassembly. To better understand the dynamic regulation of focal adhesions, we have developed an analysis system for the automated detection, tracking, and data extraction of these structures in living cells. This analysis system was used to quantify the dynamics of fluorescently tagged Paxillin and FAK in NIH 3T3 fibroblasts followed via Total Internal Reflection Fluorescence Microscopy (TIRF). High content time series included the size, shape, intensity, and position of every adhesion present in a living cell. These properties were followed over time, revealing adhesion lifetime and turnover rates, and segregation of properties into distinct zones. As a proof-of-concept, we show how a single point mutation in Paxillin at the Jun-kinase phosphorylation site Serine 178 changes FA size, distribution, and rate of assembly. This study provides a detailed, quantitative picture of FA spatiotemporal dynamics as well as a set of tools and methodologies for advancing our understanding of how focal adhesions are dynamically regulated in living cells. A full, open-source software implementation of this pipeline is provided at http://gomezlab.bme.unc.edu/tools.
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Affiliation(s)
- Mathew E. Berginski
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Eric A. Vitriol
- Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Klaus M. Hahn
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (KMH); (SMG)
| | - Shawn M. Gomez
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (KMH); (SMG)
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16
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Le Dévédec SE, Yan K, de Bont H, Ghotra V, Truong H, Danen EH, Verbeek F, van de Water B. Systems microscopy approaches to understand cancer cell migration and metastasis. Cell Mol Life Sci 2010; 67:3219-40. [PMID: 20556632 PMCID: PMC2933849 DOI: 10.1007/s00018-010-0419-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 04/21/2010] [Accepted: 05/14/2010] [Indexed: 01/15/2023]
Abstract
Cell migration is essential in a number of processes, including wound healing, angiogenesis and cancer metastasis. Especially, invasion of cancer cells in the surrounding tissue is a crucial step that requires increased cell motility. Cell migration is a well-orchestrated process that involves the continuous formation and disassembly of matrix adhesions. Those structural anchor points interact with the extra-cellular matrix and also participate in adhesion-dependent signalling. Although these processes are essential for cancer metastasis, little is known about the molecular mechanisms that regulate adhesion dynamics during tumour cell migration. In this review, we provide an overview of recent advanced imaging strategies together with quantitative image analysis that can be implemented to understand the dynamics of matrix adhesions and its molecular components in relation to tumour cell migration. This dynamic cell imaging together with multiparametric image analysis will help in understanding the molecular mechanisms that define cancer cell migration.
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Affiliation(s)
- Sylvia E. Le Dévédec
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Kuan Yan
- Imaging and BioInformatics, Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands
| | - Hans de Bont
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Veerander Ghotra
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Hoa Truong
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Erik H. Danen
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Fons Verbeek
- Imaging and BioInformatics, Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands
| | - Bob van de Water
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
- Leiden/Amsterdam Center for Drug Research, Gorleaus Laboratories, Leiden University, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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17
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Abstract
High-content screening (HCS) was introduced in 1997 based on light microscope imaging technologies to address the need for an automated platform that could analyze large numbers of individual cells with subcellular resolution using standard microplates. Molecular specificity based on fluorescence was a central element of the platform taking advantage of the growing list of reagent classes and the ability to multiplex. In addition, image analysis coupled to data management, data mining, and data visualization created a tool that focused on biological information and knowledge to begin exploring the functions of genes identified in the genomics revolution. This overview looks at the development of HCS, the evolution of the technologies, and the market up to the present day. In addition, the options for adopting uniform definitions is suggested along with a perspective on what advances are needed to continue building the value of HCS in biomedical research, drug discovery, and development and diagnostics.
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The beautiful cell: high-content screening in drug discovery. Anal Bioanal Chem 2010; 398:219-26. [DOI: 10.1007/s00216-010-3788-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 04/21/2010] [Accepted: 04/24/2010] [Indexed: 01/22/2023]
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19
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Weichsel J, Herold N, Lehmann MJ, Kräusslich HG, Schwarz US. A quantitative measure for alterations in the actin cytoskeleton investigated with automated high-throughput microscopy. Cytometry A 2010; 77:52-63. [PMID: 19899129 DOI: 10.1002/cyto.a.20818] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The actin cytoskeleton modulates a large variety of physiological and disease-related processes in the cell. For example, actin has been shown to be a crucial host factor for successful infection by HIV-1, but the underlying mechanistic details are still unknown. Automated approaches open up the perspective to clarify such an issue by processing many samples in a high-throughput manner. To analyze the alterations in the actin cytoskeleton within an automated setting, large-scale image acquisition and analysis were established for JC-53 cells stained for actin. As a quantitative measure in such an automated approach, we suggest a parameter called image coherency. We successfully benchmarked our analysis by calculating coherency for both a biophysical model of the actin cytoskeleton and for cells whose actin architecture had been disturbed pharmacologically by latrunculin B or cytochalasin D. We then tested the influence of HIV-1 infection on actin coherency, but observed no significant differences between uninfected and infected cells.
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20
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Winograd-Katz SE, Itzkovitz S, Kam Z, Geiger B. Multiparametric analysis of focal adhesion formation by RNAi-mediated gene knockdown. ACTA ACUST UNITED AC 2009; 186:423-36. [PMID: 19667130 PMCID: PMC2728402 DOI: 10.1083/jcb.200901105] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell adhesion to the extracellular matrix is mediated by elaborate networks of multiprotein complexes consisting of adhesion receptors, cytoskeletal components, signaling molecules, and diverse adaptor proteins. To explore how specific molecular pathways function in the assembly of focal adhesions (FAs), we performed a high-throughput, high-resolution, microscopy-based screen. We used small interfering RNAs (siRNAs) to target human kinases, phosphatases, and migration- and adhesion-related genes. Multiparametric image analysis of control and of siRNA-treated cells revealed major correlations between distinct morphological FA features. Clustering analysis identified different gene families whose perturbation induced similar effects, some of which uncoupled the interfeature correlations. Based on these findings, we propose a model for the molecular hierarchy of FA formation, and tested its validity by dynamic analysis of FA formation and turnover. This study provides a comprehensive information resource on the molecular regulation of multiple cell adhesion features, and sheds light on signaling mechanisms regulating the formation of integrin adhesions.
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Affiliation(s)
- Sabina E Winograd-Katz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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21
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Vizeacoumar FJ, Chong Y, Boone C, Andrews BJ. A picture is worth a thousand words: Genomics to phenomics in the yeastSaccharomyces cerevisiae. FEBS Lett 2009; 583:1656-61. [DOI: 10.1016/j.febslet.2009.03.068] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 03/26/2009] [Accepted: 03/31/2009] [Indexed: 11/28/2022]
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22
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Rosivatz E. Imaging the boundaries-innovative tools for microscopy of living cells and real-time imaging. J Chem Biol 2008; 1:3-15. [PMID: 19568794 PMCID: PMC2698318 DOI: 10.1007/s12154-008-0004-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 03/11/2008] [Indexed: 01/17/2023] Open
Abstract
Recently, light microscopy moved back into the spotlight, which is mainly due to the development of revolutionary technologies for imaging real-time events in living cells. It is truly fascinating to see enzymes “at work” and optically acquired images certainly help us to understand biological processes better than any abstract measurements. This review aims to point out elegant examples of recent cell-biological imaging applications that have been developed with a chemical approach. The discussed technologies include nanoscale fluorescence microscopy, imaging of model membranes, automated high-throughput microscopy control and analysis, and fluorescent probes with a special focus on visualizing enzyme activity, free radicals, and protein–protein interaction designed for use in living cells.
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Affiliation(s)
- Erika Rosivatz
- Division of Cell and Molecular Biology, Imperial College London, SW7 2AZ, London, UK,
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23
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Wollman R, Stuurman N. High throughput microscopy: from raw images to discoveries. J Cell Sci 2008; 120:3715-22. [PMID: 17959627 DOI: 10.1242/jcs.013623] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Technological advances in automated microscopy now allow rapid acquisition of many images without human intervention, images that can be used for large-scale screens. The main challenge in such screens is the conversion of the raw images into interpretable information and hence discoveries. This post-acquisition component of image-based screens requires computational steps to identify cells, choose the cells of interest, assess their phenotype, and identify statistically significant 'hits'. Designing such an analysis pipeline requires careful consideration of the necessary hardware and software components, image analysis, statistical analysis and data presentation tools. Given the increasing availability of such hardware and software, these types of experiments have come within the reach of individual labs, heralding many interesting new ways of acquiring biological knowledge.
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Affiliation(s)
- Roy Wollman
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
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24
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Naffar-Abu-Amara S, Shay T, Galun M, Cohen N, Isakoff SJ, Kam Z, Geiger B. Identification of novel pro-migratory, cancer-associated genes using quantitative, microscopy-based screening. PLoS One 2008; 3:e1457. [PMID: 18213366 PMCID: PMC2195451 DOI: 10.1371/journal.pone.0001457] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Accepted: 12/18/2007] [Indexed: 01/22/2023] Open
Abstract
Background Cell migration is a highly complex process, regulated by multiple genes, signaling pathways and external stimuli. To discover genes or pharmacological agents that can modulate the migratory activity of cells, screening strategies that enable the monitoring of diverse migratory parameters in a large number of samples are necessary. Methodology In the present study, we describe the development of a quantitative, high-throughput cell migration assay, based on a modified phagokinetic tracks (PKT) procedure, and apply it for identifying novel pro-migratory genes in a cancer-related gene library. In brief, cells are seeded on fibronectin-coated 96-well plates, covered with a monolayer of carboxylated latex beads. Motile cells clear the beads, located along their migratory paths, forming tracks that are visualized using an automated, transmitted-light screening microscope. The tracks are then segmented and characterized by multi-parametric, morphometric analysis, resolving a variety of morphological and kinetic features. Conclusions In this screen we identified 4 novel genes derived from breast carcinoma related cDNA library, whose over-expression induces major alteration in the migration of the stationary MCF7 cells. This approach can serve for high throughput screening for novel ways to modulate cellular migration in pathological states such as tumor metastasis and invasion.
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Affiliation(s)
- Suha Naffar-Abu-Amara
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Shay
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Meirav Galun
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Cohen
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Steven J. Isakoff
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, United States of America
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zvi Kam
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail:
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25
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Lock JG, Wehrle-Haller B, Strömblad S. Cell-matrix adhesion complexes: master control machinery of cell migration. Semin Cancer Biol 2007; 18:65-76. [PMID: 18023204 DOI: 10.1016/j.semcancer.2007.10.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 09/26/2007] [Accepted: 10/01/2007] [Indexed: 01/09/2023]
Abstract
Cell-matrix adhesion complexes (CMACs) are foci of cellular attachment to the extracellular matrix (ECM). This attachment, mediated by integrins and adaptor proteins, provides both physical and regulatory links between the ECM and the cellular microfilament system. Through continual regulation and rearrangement of both ECM adhesion and actin structures, CMACs constitute core machineries of cell migration. To fulfill this role, CMACs are exceptionally flexible and dynamic complexes, and their components undergo rapid and regulated turn-over to maintain delicately balanced streams of mechanical and chemical information. Besides the critical role of CMACs in cell migration, signaling through these complexes provides influence over virtually every major cellular function, including for example cell survival, cell differentiation and cell proliferation. This review depicts the roles of CMACs in cell migration and discusses how CMACs integrate with other sub-cellular systems involved in cell motility. Importantly, we also present a rationalized view of CMACs as information handling machines, and suggest strategies that may facilitate better understanding of the complex cell migration phenomenon as a whole, through quantitative and integrative (systems biology) approaches.
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Affiliation(s)
- John G Lock
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, Huddinge, Sweden
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26
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Abstract
Technological advances have made it feasible to conduct high-throughput small-molecule screens based on visual phenotypes of individual cells, using automated imaging and analysis. These screens are rapidly moving from being small, proof-of-principle tests to robust and widespread screens of hundreds of thousands of compounds. Automated imaging screens maximize the information obtained in an initial screen and improve the ability to select high-quality leads. In this Perspective, I highlight the key steps necessary for conducting a high-throughput image-based chemical compound screen.
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Affiliation(s)
- Anne E Carpenter
- Broad Institute Imaging Platform, 7 Cambridge Center, Room 6011, Cambridge, Massachusetts 02142, USA.
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