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Kilner J, Waby JS, Chowdry J, Khan AQ, Noirel J, Wright PC, Corfe BM, Evans CA. A proteomic analysis of differential cellular responses to the short-chain fatty acids butyrate, valerate and propionate in colon epithelial cancer cells. MOLECULAR BIOSYSTEMS 2011; 8:1146-56. [PMID: 22075547 DOI: 10.1039/c1mb05219e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The short chain fatty acids (SCFAs) are inhibitors of histone deacetylases (HDACi); they are produced naturally in the colon by fermentation. They affect cellular processes at a molecular and transcriptional level, the mechanisms of which may involve large numbers of proteins and integrated pathways. Butyrate is the most biologically potent of the SCFAs in colon epithelial cells, inhibiting human colon carcinoma cell proliferation and inducing apoptosis in vitro. In order to investigate the hypothesis that propionate and valerate possess unique and independent actions from butyrate, we combined proteomic and cellomic approaches for large-scale comparative analysis. Proteomic evaluation was undertaken using an iTRAQ tandem mass-spectrometry workflow and high-throughput High-content Analysis microscopy (HCA) was applied to generate cellomic information on the cell cycle and the cytoskeletal structure. Our results show that these SCFAs possess specific effects. Butyrate was shown to have more pronounced effects on the keratins and intermediate filaments (IFs); while valerate altered the β-tubulin isotypes' expression and the microtubules (MTs); propionate was involved in both mechanisms, displaying intermediate effects. These data suggest distinct physiological roles for SCFAs in colon epithelial function, offering new possibilities for cancer therapeutics.
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Affiliation(s)
- Josephine Kilner
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
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52
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Tejada A, den Dekker AJ, Van den Broek W. Introducing measure-by-wire, the systematic use of systems and control theory in transmission electron microscopy. Ultramicroscopy 2011; 111:1581-91. [DOI: 10.1016/j.ultramic.2011.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 05/08/2011] [Accepted: 08/22/2011] [Indexed: 11/16/2022]
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53
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Valenzano KJ, Khanna R, Powe AC, Boyd R, Lee G, Flanagan JJ, Benjamin ER. Identification and characterization of pharmacological chaperones to correct enzyme deficiencies in lysosomal storage disorders. Assay Drug Dev Technol 2011; 9:213-35. [PMID: 21612550 PMCID: PMC3102255 DOI: 10.1089/adt.2011.0370] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many human diseases result from mutations in specific genes. Once translated, the resulting aberrant proteins may be functionally competent and produced at near-normal levels. However, because of the mutations, the proteins are recognized by the quality control system of the endoplasmic reticulum and are not processed or trafficked correctly, ultimately leading to cellular dysfunction and disease. Pharmacological chaperones (PCs) are small molecules designed to mitigate this problem by selectively binding and stabilizing their target protein, thus reducing premature degradation, facilitating intracellular trafficking, and increasing cellular activity. Partial or complete restoration of normal function by PCs has been shown for numerous types of mutant proteins, including secreted proteins, transcription factors, ion channels, G protein-coupled receptors, and, importantly, lysosomal enzymes. Collectively, lysosomal storage disorders (LSDs) result from genetic mutations in the genes that encode specific lysosomal enzymes, leading to a deficiency in essential enzymatic activity and cellular accumulation of the respective substrate. To date, over 50 different LSDs have been identified, several of which are treated clinically with enzyme replacement therapy or substrate reduction therapy, although insufficiently in some cases. Importantly, a wide range of in vitro assays are now available to measure mutant lysosomal enzyme interaction with and stabilization by PCs, as well as subsequent increases in cellular enzyme levels and function. The application of these assays to the identification and characterization of candidate PCs for mutant lysosomal enzymes will be discussed in this review. In addition, considerations for the successful in vivo use and development of PCs to treat LSDs will be discussed.
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Abstract
Embryonic stem (ES) cells and their differentiated progeny offer tremendous potential for regenerative medicine, even in the field of drug discovery. There is an urgent need for clinically relevant assays that make use of ES cells because of their rich biological utility. Attention has been focused on small molecules that allow the precise manipulation of cells in vitro, which could allow researchers to obtain homogeneous cell types for cell-based therapies and discover drugs for stimulating the regeneration of endogenous cells. Such therapeutics can act on target cells or their niches in vivo to promote cell survival, proliferation, differentiation, and homing. In the present paper, we reviewed the use of ES cell models for high-throughput/content drug screening and toxicity assessment. In addition, we examined the role of stem cells in large pharmaceutical companies' R&D and discussed a novel subject, nicheology, in stem cell-related research fields.
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Sun H, Aidun CK, Egertsdotter U. Possible effect from shear stress on maturation of somatic embryos of Norway spruce (Picea abies). Biotechnol Bioeng 2011; 108:1089-99. [PMID: 21449024 DOI: 10.1002/bit.23040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 12/01/2010] [Accepted: 12/09/2010] [Indexed: 01/07/2023]
Abstract
Somatic embryogenesis is the only method with the potential for industrial scale clonal propagation of conifers. Implementation of the method has so far been hampered by the extensive manual labor required for development of the somatic embryos into plants. The utilization of bioreactors is limited since the somatic embryos will not mature and germinate under liquid culture conditions. The negative effect on mature embryo yields from liquid culture conditions has been previously described. We have described the negative effects of shear stress on the development of early stage somatic embryos (proembryogenic masses; PEMs) at shear stresses of 0.086 and 0.14 N/m(2). In the present study, additional flow rates were studied to determine the effects of shear stress at lower rates resembling shear stress in a suspension culture flask. The results showed that shear stress at 0.009, 0.014, and 0.029 N/m(2) inhibited the PEM expansions comparing with the control group without shear stress. This study also provides validation for the cross-correlation method previously developed to show the effect of shear stress on early stage embryo suspensor cell formation and polarization. Furthermore, shear stress was shown to positively affect the uptake of water into the cells. The results indicate that the plasmolyzing effect from macromolecules added to liquid culture medium to stimulate maturation of the embryos are affected by liquid culture conditions and thus can affect the conversion of PEMs into mature somatic embryos.
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Affiliation(s)
- Hong Sun
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia
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56
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Integrating semantic annotation and information visualization for the analysis of multichannel fluorescence micrographs from pancreatic tissue. Comput Med Imaging Graph 2010; 34:446-52. [DOI: 10.1016/j.compmedimag.2009.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/27/2009] [Accepted: 10/29/2009] [Indexed: 11/21/2022]
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57
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Palmieri M, Nowell CJ, Condron M, Gardiner J, Holmes AB, Desai J, Burgess AW, Catimel B. Analysis of cellular phosphatidylinositol (3,4,5)-trisphosphate levels and distribution using confocal fluorescent microscopy. Anal Biochem 2010; 406:41-50. [PMID: 20599646 DOI: 10.1016/j.ab.2010.06.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/18/2010] [Accepted: 06/22/2010] [Indexed: 11/29/2022]
Abstract
We have developed an immunocytochemistry method for the semiquantitative detection of phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P3) at the cell plasma membrane. This protocol combines the use of a glutathione S-transferase-tagged pleckstrin homology (PH) domain of the general phosphoinositides-1 receptor (GST-GRP1PH) with fluorescence confocal microscopy and image segmentation using cell mask software analysis. This methodology allows the analysis of PI(3,4,5)P3 subcellular distribution in resting and epidermal growth factor (EGF)-stimulated HEK293T cells and in LIM1215 (wild-type phosphoinositide 3-kinase (PI3K)) and LIM2550 (H1047R mutation in PI3K catalytic domain) colonic carcinoma cells. Formation of PI(3,4,5)P3 was observed 5min following EGF stimulation and resulted in an increase of the membrane/cytoplasm fluorescence ratio from 1.03 to 1.53 for HEK293T cells and from 2.2 to 3.3 for LIM1215 cells. Resting LIM2550 cells stained with GST-GRP1PH had an elevated membrane/cytoplasm fluorescence ratio of 9.8, suggesting constitutive PI3K activation. The increase in the membrane/cytoplasm fluorescent ratio was inhibited in a concentration-dependent manner by the PI3K inhibitor LY294002. This cellular confocal imaging assay can be used to directly assess the effects of PI3K mutations in cancer cell lines and to determine the potential specificity and effectiveness of PI3K inhibitors in cancer cells.
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Affiliation(s)
- Michelle Palmieri
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victsoria, Australia
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58
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59
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Abstract
Stochastic profiling, a method to rank heterogeneity of gene expression in a cell population, shows that quantifying cell-to-cell variability has come of age and leads to biological insight.
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Ozaki YI, Uda S, Saito TH, Chung J, Kubota H, Kuroda S. A quantitative image cytometry technique for time series or population analyses of signaling networks. PLoS One 2010; 5:e9955. [PMID: 20376360 PMCID: PMC2848603 DOI: 10.1371/journal.pone.0009955] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 03/06/2010] [Indexed: 11/18/2022] Open
Abstract
Background Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. Methodology/Principal Findings We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. Conclusions/Significance The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.
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Affiliation(s)
- Yu-ichi Ozaki
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (YO); (SK)
| | - Shinsuke Uda
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takeshi H. Saito
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Jaehoon Chung
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Kubota
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shinya Kuroda
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
- CREST, Japan Science and Technology Agency, University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (YO); (SK)
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61
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Bisubstrate fluorescent probes and biosensors in binding assays for HTS of protein kinase inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:541-6. [DOI: 10.1016/j.bbapap.2009.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 10/18/2009] [Accepted: 10/21/2009] [Indexed: 11/20/2022]
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62
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Matthews DR, Carlin LM, Ofo E, Barber PR, Vojnovic B, Irving M, Ng T, Ameer-Beg SM. Time-lapse FRET microscopy using fluorescence anisotropy. J Microsc 2010; 237:51-62. [PMID: 20055918 DOI: 10.1111/j.1365-2818.2009.03301.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present recent data on dynamic imaging of Rac1 activity in live T-cells. Förster resonance energy transfer between enhanced green and monomeric red fluorescent protein pairs which form part of a biosensor molecule provides a metric of this activity. Microscopy is performed using a multi-functional high-content screening instrument using fluorescence anisotropy to provide a means of monitoring protein-protein activity with high temporal resolution. Specifically, the response of T-cells upon interaction of a cell surface receptor with an antibody coated multi-well chamber was measured. We observed dynamic changes in the activity of the biosensor molecules with a time resolution that is difficult to achieve with traditional methodologies for observing Förster resonance energy transfer (fluorescence lifetime imaging using single photon counting or frequency domain techniques) and without spectral corrections that are normally required for intensity based methodologies.
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Affiliation(s)
- D R Matthews
- Richard Dimbleby Department of Cancer Research, New Hunts House, Kings College London, Guy's Medical School Campus, SE11UL, UK.
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63
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Hsu YY, Liu YN, Lu WW, Kung SH. Visualizing and quantifying the differential cleavages of the eukaryotic translation initiation factors eIF4GI and eIF4GII in the enterovirus-infected cell. Biotechnol Bioeng 2009; 104:1142-52. [PMID: 19655339 DOI: 10.1002/bit.22495] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Enterovirus (EV) infection has been shown to cause a marked shutoff of host protein synthesis, an event mainly achieved through the cleavages of eukaryotic translation initiation factors eIF4GI and eIF4GII that are mediated by viral 2A protease (2A(pro)). Using fluorescence resonance energy transfer (FRET), we developed genetically encoded and FRET-based biosensors to visualize and quantify the specific proteolytic process in intact cells. This was accomplished by stable expression of a fusion substrate construct composed of the green fluorescent protein 2 (GFP(2)) and red fluorescent protein 2 (DsRed2), with a cleavage motif on eIF4GI or eIF4GII connected in between. The FRET biosensor showed a real-time and quantifiable impairment of FRET upon EV infection. Levels of the reduced FRET closely correlated with the cleavage kinetics of the endogenous eIF4Gs isoforms. The FRET impairments were solely attributed to 2A(pro) catalytic activity, irrespective of other viral-encoded protease, the activated caspases or general inhibition of protein synthesis in the EV-infected cells. The FRET biosensors appeared to be a universal platform for several related EVs. The spatiotemporal and quantitative imaging enabled by FRET can shed light on the protease-substrate behaviors in their normal milieu, permitting investigation into the molecular mechanism underlying virus-induced host translation inhibition.
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Affiliation(s)
- Yueh-Ying Hsu
- Department of Biotechnology, National Yang-Ming University, Taipei, Taiwan, R.O.C
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64
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Hart T, Zhao A, Garg A, Bolusani S, Marcotte EM. Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays. PLoS One 2009; 4:e7088. [PMID: 19862318 PMCID: PMC2760726 DOI: 10.1371/journal.pone.0007088] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 08/13/2009] [Indexed: 11/21/2022] Open
Abstract
Here we describe human spotted cell chips, a technology for determining cellular state across arrays of cells subjected to chemical or genetic perturbation. Cells are grown and treated under standard tissue culture conditions before being fixed and printed onto replicate glass slides, effectively decoupling the experimental conditions from the assay technique. Each slide is then probed using immunofluorescence or other optical reporter and assayed by automated microscopy. We show potential applications of the cell chip by assaying HeLa and A549 samples for changes in target protein abundance (of the dsRNA-activated protein kinase PKR), subcellular localization (nuclear translocation of NFκB) and activation state (phosphorylation of STAT1 and of the p38 and JNK stress kinases) in response to treatment by several chemical effectors (anisomycin, TNFα, and interferon), and we demonstrate scalability by printing a chip with ∼4,700 discrete samples of HeLa cells. Coupling this technology to high-throughput methods for culturing and treating cell lines could enable researchers to examine the impact of exogenous effectors on the same population of experimentally treated cells across multiple reporter targets potentially representing a variety of molecular systems, thus producing a highly multiplexed dataset with minimized experimental variance and at reduced reagent cost compared to alternative techniques. The ability to prepare and store chips also allows researchers to follow up on observations gleaned from initial screens with maximal repeatability.
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Affiliation(s)
- Traver Hart
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Alice Zhao
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Ankit Garg
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Swetha Bolusani
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of America
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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65
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Blanco AM, Rausell L, Aguado B, Perez-Alonso M, Artero R. A FRET-based assay for characterization of alternative splicing events using peptide nucleic acid fluorescence in situ hybridization. Nucleic Acids Res 2009; 37:e116. [PMID: 19561195 PMCID: PMC2761257 DOI: 10.1093/nar/gkp551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We describe a quantitative method for detecting RNA alternative splicing variants that combines in situ hybridization of fluorescently labeled peptide nucleic acid (PNA) probes with confocal microscopy Förster resonance energy transfer (FRET). The use of PNA probes complementary to sequences flanking a given splice junction allows to specifically quantify, within the cell, the RNA isoform generating such splice junction by FRET measure. As a proof of concept we analyzed two alternative splicing events originating from lymphocyte antigen 6 (LY6) complex, locus G5B (LY6G5B) pre-mRNA. These are characterized by the removal of the first intron (Fully Spliced Isoform, FSI) or by retention of such intron (Intron-Retained Isoform, IRI). The use of PNA probe pairs labeled with donor (Cy3) and acceptor (Cy5) fluorophores, suitable to FRET, flanking FSI and IRI specific splice junctions specifically detected both mRNA isoforms in HeLa cells. We have observed that the method works efficiently with probes 5–11 nt apart. The data supports that this FRET-based PNA fluorescence in situ hybridization (FP–FISH) method offers a conceptually new approach for characterizing at the subcellular level not only splice variant isoform structure, location and dynamics but also potentially a wide variety of close range RNA–RNA interactions.
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Affiliation(s)
- Ana M Blanco
- Sistemas Genómicos S.L., Parque Tecnológico de Valencia, Ronda G. Marconi 6, E-46980 Paterna, Spain
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66
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Eriksson E, Engström D, Scrimgeour J, Goksör M. Automated focusing of nuclei for time lapse experiments on single cells using holographic optical tweezers. OPTICS EXPRESS 2009; 17:5585-5594. [PMID: 19333326 DOI: 10.1364/oe.17.005585] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Experiments on single cells are currently gaining more and more interest. Single cell studies often concerns the spatio-temporal distribution of fluorescent proteins inside living cells, visualized using fluorescence microscopy. In order to extract quantitative information from such experiments it is necessary to image the sample with high spatial and temporal resolution while keeping the photobleaching to a minimum. The analysis of the spatial distribution of proteins often requires stacks of images at each time point, which exposes the sample to unnecessary amounts of excitation light. In this paper we show how holographic optical tweezers combined with image analysis can be used to optimize the axial position of trapped cells in an array in order to bring the nuclei into a single imaging plane, thus eliminating the need for stacks of images and consequently reducing photobleaching. This allows more images to be collected, as well as increasing the time span and/or the time resolution in time lapse studies of single cells.
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Affiliation(s)
- Emma Eriksson
- Department of Physics, University of Gothenburg, Gothenburg, Sweden
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67
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Wolinski H, Petrovic U, Mattiazzi M, Petschnigg J, Heise B, Natter K, Kohlwein SD. Imaging-based live cell yeast screen identifies novel factors involved in peroxisome assembly. J Proteome Res 2009; 8:20-7. [PMID: 19118449 DOI: 10.1021/pr800782n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We describe an imaging-based method in intact cells to systematically screen yeast mutant libraries for abnormal morphology and distribution of fluorescently labeled subcellular structures. In this study, chromosomally expressed green fluorescent protein (GFP) fused to the peroxisomal targeting sequence 1, consisting of serine-lysine-leucine, was introduced into 4740 viable yeast deletion mutants using a modified synthetic genetic array (SGA) technology. A benchtop robot was used to create ordered high-density arrays of GFP-expressing yeast mutants on solid media plates. Immobilized live yeast colonies were subjected to high-resolution, multidimensional confocal imaging. A software tool was designed for automated processing and quantitative analysis of acquired multichannel three-dimensional image data. The study resulted in the identification of two novel proteins, as well as of all previously known proteins required for import of proteins bearing peroxisomal targeting signal PTS1, into yeast peroxisomes. The modular method enables reliable microscopic analysis of live yeast mutant libraries in a universally applicable format on standard microscope slides, and provides a step toward fully automated high-resolution imaging of intact yeast cells.
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Affiliation(s)
- Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Austria
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68
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Abstract
In this chapter the authors describe automated imaging methods to quantify the transport rates of transmembrane as well as soluble cargo, and to evaluate the integrity of the Golgi complex. The quantification of cargo transport rates serves as an example of fluorescence intensity-based assays, the quantification of the Golgi complex integrity--as an example of morphology-based assays. These quantitative assays could be applied for single experiments as well as for middle- and high-throughput screening approaches. Each of these assays can be used to appreciate effects caused by gene silencing by RNAi, cDNA overexpression or application of chemical compounds. For each assay the authors discuss protocols for sample preparation, parameters for automated image acquisition, strategies of image analysis, and data quantification.
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69
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Quaranta V, Tyson DR, Garbett SP, Weidow B, Harris MP, Georgescu W. Trait variability of cancer cells quantified by high-content automated microscopy of single cells. Methods Enzymol 2009; 467:23-57. [PMID: 19897088 DOI: 10.1016/s0076-6879(09)67002-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Mapping quantitative cell traits (QCT) to underlying molecular defects is a central challenge in cancer research because heterogeneity at all biological scales, from genes to cells to populations, is recognized as the main driver of cancer progression and treatment resistance. A major roadblock to a multiscale framework linking cell to signaling to genetic cancer heterogeneity is the dearth of large-scale, single-cell data on QCT-such as proliferation, death sensitivity, motility, metabolism, and other hallmarks of cancer. High-volume single-cell data can be used to represent cell-to-cell genetic and nongenetic QCT variability in cancer cell populations as averages, distributions, and statistical subpopulations. By matching the abundance of available data on cancer genetic and molecular variability, QCT data should enable quantitative mapping of phenotype to genotype in cancer. This challenge is being met by high-content automated microscopy (HCAM), based on the convergence of several technologies including computerized microscopy, image processing, computation, and heterogeneity science. In this chapter, we describe an HCAM workflow that can be set up in a medium size interdisciplinary laboratory, and its application to produce high-throughput QCT data for cancer cell motility and proliferation. This type of data is ideally suited to populate cell-scale computational and mathematical models of cancer progression for quantitatively and predictively evaluating cancer drug discovery and treatment.
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Affiliation(s)
- Vito Quaranta
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Integrative Cancer Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Darren R Tyson
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Integrative Cancer Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shawn P Garbett
- Vanderbilt Integrative Cancer Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Brandy Weidow
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt Integrative Cancer Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mark P Harris
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Walter Georgescu
- Vanderbilt Integrative Cancer Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biomedical Engineering, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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70
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Abstract
Living cells are remarkably complex. To unravel this complexity, living-cell assays have been developed that allow delivery of experimental stimuli and measurement of the resulting cellular responses. High-throughput adaptations of these assays, known as living-cell microarrays, which are based on microtiter plates, high-density spotting, microfabrication, and microfluidics technologies, are being developed for two general applications: (a) to screen large-scale chemical and genomic libraries and (b) to systematically investigate the local cellular microenvironment. These emerging experimental platforms offer exciting opportunities to rapidly identify genetic determinants of disease, to discover modulators of cellular function, and to probe the complex and dynamic relationships between cells and their local environment.
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Affiliation(s)
- Martin L Yarmush
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School, Massachusetts 02139, USA.
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71
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Justice BA, Badr NA, Felder RA. 3D cell culture opens new dimensions in cell-based assays. Drug Discov Today 2008; 14:102-7. [PMID: 19049902 DOI: 10.1016/j.drudis.2008.11.006] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 11/18/2008] [Accepted: 11/18/2008] [Indexed: 12/13/2022]
Abstract
3D cell culture technologies have revolutionized our understanding of cellular behavior, both in culture and in vivo, but adoption by cell-based screening groups has been slow owing to problems of consistency, scale and cost. The evolving field of high content screening technologies will, however, require a rethinking of 3D cell culture adoption to ensure the next generation of cells provide relevant in vivo-like data. Three current technologies are presented in this review: membranes, sponges/gels and microcarriers. A short history of these technologies and unique research applications are discussed. Also, the technologies are evaluated for usefulness in modern automated cell-based screening equipment.
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Affiliation(s)
- Bradley A Justice
- Global Cell Solutions, Inc., 770 Harris Street, Suite 104, Charlottesville, VA 22903, USA.
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72
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Drake PJM, Griffiths GJ, Shaw L, Benson RP, Corfe BM. Application of High-Content Analysis to the Study of Post-Translational Modifications of the Cytoskeleton. J Proteome Res 2008; 8:28-34. [DOI: 10.1021/pr8006396] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Peter J. M. Drake
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Gareth J. Griffiths
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Leila Shaw
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Rod P. Benson
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Bernard M. Corfe
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
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73
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Horowitz VR, Awschalom DD, Pennathur S. Optofluidics: field or technique? LAB ON A CHIP 2008; 8:1856-1863. [PMID: 18941686 DOI: 10.1039/b816416a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Viva R Horowitz
- Department of Physics, University of California, Santa Barbara, USA
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74
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Vermot J, Fraser SE, Liebling M. Fast fluorescence microscopy for imaging the dynamics of embryonic development. HFSP JOURNAL 2008; 2:143-55. [PMID: 19404468 DOI: 10.2976/1.2907579] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 03/19/2008] [Indexed: 11/19/2022]
Abstract
Live imaging has gained a pivotal role in developmental biology since it increasingly allows real-time observation of cell behavior in intact organisms. Microscopes that can capture the dynamics of ever-faster biological events, fluorescent markers optimal for in vivo imaging, and, finally, adapted reconstruction and analysis programs to complete data flow all contribute to this success. Focusing on temporal resolution, we discuss how fast imaging can be achieved with minimal prejudice to spatial resolution, photon count, or to reliably and automatically analyze images. In particular, we show how integrated approaches to imaging that combine bright fluorescent probes, fast microscopes, and custom post-processing techniques can address the kinetics of biological systems at multiple scales. Finally, we discuss remaining challenges and opportunities for further advances in this field.
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75
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Challenges in discovering bioactives for the food industry. Curr Opin Biotechnol 2008; 19:66-72. [DOI: 10.1016/j.copbio.2008.02.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 02/28/2008] [Accepted: 02/28/2008] [Indexed: 11/21/2022]
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76
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Hwang YC, Chu JJH, Yang PL, Chen W, Yates MV. Rapid identification of inhibitors that interfere with poliovirus replication using a cell-based assay. Antiviral Res 2008; 77:232-6. [PMID: 18243348 PMCID: PMC7114228 DOI: 10.1016/j.antiviral.2007.12.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 12/13/2007] [Accepted: 12/15/2007] [Indexed: 11/28/2022]
Abstract
A small molecule library containing 480 known bioactive compounds was screened for antiviral activity against poliovirus (PV) using a cellular fluorescence resonance energy transfer (FRET) assay for viral protease activity. The infected reporter cells treated with the viral replication-suppressing compounds were examined via fluorescence microscope 7.5 h postinfection. Twelve molecules showed moderate to potent antiviral activity at concentrations less than 32 μM during the primary screening. Three compounds, anisomycin, linoleic acid, and lycorine, were chosen for validation. A dose-dependent cytotoxicity assay and a secondary screening using conventional plaque assay were conducted to confirm the results. The developed method can be used for rapid screening for molecules with antiviral activity.
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Affiliation(s)
- Yu-Chen Hwang
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
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77
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Gribbon P. High-throughput hit finding and compound-profiling technologies for academic drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2008; 5:e1-e34. [PMID: 24125500 DOI: 10.1016/j.ddtec.2009.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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78
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Capelle MAH, Arvinte T. High-throughput formulation screening of therapeutic proteins. DRUG DISCOVERY TODAY. TECHNOLOGIES 2008; 5:e71-e79. [PMID: 24981094 DOI: 10.1016/j.ddtec.2009.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
High-throughput screening (HTS) is used extensively in drug discovery to identify active compounds. Automated preparation and sample analysis in multiwell plates using a combination of liquid and/or powder handling stations, robotics and sensitive detection devices provide powerful tools. At present, protein formulation remains a slow process and will benefit from a fast formulation screening approach. The use of multiwell plates enables the simultaneous screening of many excipients and experimental conditions, such as buffers, salts, surfactants, sugars, storage temperature and mechanical stress. This article reviews the application of the HTS methodology for the development of different protein formulations, such as stable liquids, lyophilisates and slow release forms.:
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Affiliation(s)
- Martinus A H Capelle
- Therapeomic Inc., c/o University of Geneva, Quai E-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Tudor Arvinte
- Department of Pharmaceutics and Biopharmaceutics, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai E-Ansermet 30, 1211 Geneva 4, Switzerland.
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79
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Barbe L, Lundberg E, Oksvold P, Stenius A, Lewin E, Björling E, Asplund A, Pontén F, Brismar H, Uhlén M, Andersson-Svahn H. Toward a confocal subcellular atlas of the human proteome. Mol Cell Proteomics 2007; 7:499-508. [PMID: 18029348 DOI: 10.1074/mcp.m700325-mcp200] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Information on protein localization on the subcellular level is important to map and characterize the proteome and to better understand cellular functions of proteins. Here we report on a pilot study of 466 proteins in three human cell lines aimed to allow large scale confocal microscopy analysis using protein-specific antibodies. Approximately 3000 high resolution images were generated, and more than 80% of the analyzed proteins could be classified in one or multiple subcellular compartment(s). The localizations of the proteins showed, in many cases, good agreement with the Gene Ontology localization prediction model. This is the first large scale antibody-based study to localize proteins into subcellular compartments using antibodies and confocal microscopy. The results suggest that this approach might be a valuable tool in conjunction with predictive models for protein localization.
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Affiliation(s)
- Laurent Barbe
- Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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80
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Oheim M. High-throughput microscopy must re-invent the microscope rather than speed up its functions. Br J Pharmacol 2007; 152:1-4. [PMID: 17603553 PMCID: PMC1978271 DOI: 10.1038/sj.bjp.0707348] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Knowledge gained from the revolutions in genomics and proteomics has helped to identify many of the key molecules involved in cellular signalling. Researchers, both in academia and in the pharmaceutical industry, now screen, at a sub-cellular level, where and when these proteins interact. Fluorescence imaging and molecular labelling combine to provide a powerful tool for real-time functional biochemistry with molecular resolution. However, they traditionally have been work-intensive, required trained personnel, and suffered from low through-put due to sample preparation, loading and handling. The need for speeding up microscopy is apparent from the tremendous complexity of cellular signalling pathways, the inherent biological variability, as well as the possibility that the same molecule plays different roles in different sub-cellular compartments. Research institutes and companies have teamed up to develop imaging cytometers of ever-increasing complexity. However, to truly go high-speed, sub-cellular imaging must free itself from the rigid framework of current microscopes.
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Affiliation(s)
- M Oheim
- INSERM U603, and Centre National de la Recherche Scientifique (CNRS) UMR 8154, University Paris Descartes, 45 rue des Saints Pères, F-75006 Paris, France.
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