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Yu S, Wu H, Kang S, Ma J, Xie M, Dai L. Model-free robust motion control for biological optical microscopy using time-delay estimation with an adaptive RBFNN compensator. ISA TRANSACTIONS 2024; 149:365-372. [PMID: 38724294 DOI: 10.1016/j.isatra.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/06/2024] [Accepted: 04/19/2024] [Indexed: 06/05/2024]
Abstract
The field of large numerical aperture microscopy has witnessed significant advancements in spatial and temporal resolution, as well as improvements in optical microscope imaging quality. However, these advancements have concurrently raised the demand for enhanced precision, extended range, and increased load-bearing capacity in objective motion carrier (OMC). To address this challenge, this study introduces an innovative OMC that employs a ball screw mechanism as its primary driving component. Furthermore, a robust nonlinear motion control strategy has been developed, which integrates fast nonsingular terminal sliding mode, experimental estimation techniques, and adaptive radial basis neural network, to mitigate the impact of nonlinear friction within the ball screw mechanism on motion precision. The stability of the closed-loop control system has been rigorously demonstrated through Lyapunov theory. Compared with other enhanced sliding mode control strategies, the maximum error and root mean square error of this controller are improved by 33% and 34% respectively. The implementation of the novel OMC has enabled the establishment of a high-resolution bio-optical microscope, which has proven its effectiveness in the microscopic imaging of retinal organoids.
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Affiliation(s)
- Shengdong Yu
- Wenzhou Key Laboratory of Biomaterials and Engineering, Wenzhou Key Laboratory of Biomedical Imaging, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Hongyuan Wu
- College of Mechanical and Electrical Engineering, Wenzhou University, Wenzhou 325000, China
| | - Shengzheng Kang
- School of Automation in Nanjing University of Information Science and Technology, China
| | - Jinyu Ma
- School of Intelligent Manufacturing, Wenzhou Polytechnic, Wenzhou 325000, China.
| | - Mingyang Xie
- Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Luru Dai
- Wenzhou Key Laboratory of Biomaterials and Engineering, Wenzhou Key Laboratory of Biomedical Imaging, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China.
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Kalinichev AV, Zieger SE, Koren K. Optical sensors (optodes) for multiparameter chemical imaging: classification, challenges, and prospects. Analyst 2023; 149:29-45. [PMID: 37975528 DOI: 10.1039/d3an01661g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Chemical gradients and uneven distribution of analytes are common in natural and artificial systems. As a result, the ability to visualize chemical distributions in two or more dimensions has gained significant importance in recent years. This has led to the integration of chemical imaging techniques into all domains of analytical chemistry. In this review, we focus on the use of optical sensors, so-called optodes, to obtain real-time and multidimensional images of two or more parameters simultaneously. It is important to emphasize that multiparameter imaging in this context is not confined solely to multiple chemical parameters (analytes) but also encompasses physical (e.g., temperature or flow) or biological (e.g., metabolic activity) parameters. First, we discuss the technological milestones that have paved the way for chemical imaging using optodes. Later, we delve into various strategies that can be taken to enable multiparameter imaging. The latter spans from developing novel receptors that enable the recognition of multiple parameters to chemometrics and machine learning-based techniques for data analysis. We also explore ongoing trends, challenges, and prospects for future developments in this field. Optode-based multiparameter imaging is a rapidly expanding field that is being fueled by cutting-edge technologies. Chemical imaging possesses the potential to provide novel insights into complex samples, bridging not only across various scientific disciplines but also between research and society.
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Affiliation(s)
- Andrey V Kalinichev
- Aarhus University Centre for Water Technology, Department of Biology - Microbiology, Ny Munkegade 116, 8000 Aarhus C, Denmark.
| | - Silvia E Zieger
- Aarhus University Centre for Water Technology, Department of Biology - Microbiology, Ny Munkegade 116, 8000 Aarhus C, Denmark.
| | - Klaus Koren
- Aarhus University Centre for Water Technology, Department of Biology - Microbiology, Ny Munkegade 116, 8000 Aarhus C, Denmark.
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3
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He S, Xie L, Liu J, Zou L. Single-use flexible bronchoscopes vs traditional reusable flexible bronchoscopes: a prospective controlled study. BMC Pulm Med 2023; 23:202. [PMID: 37296389 DOI: 10.1186/s12890-023-02478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Single-use flexible bronchoscopes(SFB) eliminate the risk of bronchoscopy-related infection compared with traditional reusable flexible bronchoscopes(RFB). At present, there is no comparative study between SFB and RFB in the aspects of biopsy and interventional therapy. This study aims to explore whether SFB can perform complex bronchoscopic procedures such as transbronchial biopsies just like RFB. METHODS We conducted a prospective controlled study. A total of 45 patients who required bronchoscopic biopsy in our hospital from June 2022 to December 2022 were enrolled. The patients were divided into the SFB group and the RFB group, and routine bronchoscopy, bronchoalveolar lavage, and biopsy were performed respectively. Data on the time of routine bronchoscopy, the recovery rate of bronchoalveolar lavage fluid(BALF), biopsy time, and bleeding volume were collected. Then we used the two-sample t-test and the χ2 test to assess the performance differences between SFB and RFB. We also designed a questionnaire to compare the performance between SFB and RFB by different bronchoscope operators. RESULTS The routine examination time of SFB and RFB was 3.40 ± 0.50 min and 3.55 ± 0.42 min, respectively. There was no significant difference between the two groups (P = 0.308). The recovery rate of BALF was (46.56 ± 8.22) % in the SFB group and (47.00 ± 8.07) in the RFB group, without a significant difference between the two groups(P = 0.863). The biopsy time was similar(4.67 ± 0.51 min VS 4.57 ± 0.45 min) in both groups, with no significant difference(P = 0.512). The positive biopsy rate was 100% in both groups, with no significant difference. Overall, the bronchoscope operators were generally satisfied with SFB. CONCLUSION SFBs are non-inferior to RFBs in routine bronchoscopy, bronchoalveolar lavage, and biopsy. It is suggested that SFBs have a wider clinical application.
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Affiliation(s)
- Shuzhen He
- Department of Pulmonary and Critical Care Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Lihua Xie
- Department of Pulmonary and Critical Care Medicine, The Third Xiangya Hospital of Central South University, Changsha, China.
| | - Jianming Liu
- Department of Pulmonary and Critical Care Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Lijun Zou
- Department of Pulmonary and Critical Care Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
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Microscopy in Infectious Disease Research-Imaging Across Scales. J Mol Biol 2018; 430:2612-2625. [PMID: 29908150 DOI: 10.1016/j.jmb.2018.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/03/2018] [Accepted: 06/08/2018] [Indexed: 12/18/2022]
Abstract
A comprehensive understanding of host-pathogen interactions requires quantitative assessment of molecular events across a wide range of spatiotemporal scales and organizational complexities. Due to recent technical developments, this is currently only achievable with microscopy. This article is providing a general perspective on the importance of microscopy in infectious disease research, with a focus on new imaging modalities that promise to have a major impact in biomedical research in the years to come. Every major technological breakthrough in light microscopy depends on, and is supported by, advancements in computing and information technologies. Bioimage acquisition and analysis based on machine learning will pave the way toward more robust, automated and objective implementation of new imaging modalities and in biomedical research in general. The combination of novel imaging technologies with machine learning and near-physiological model systems promises to accelerate discoveries and breakthroughs in our understanding of infectious diseases, from basic research all the way to clinical applications.
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Chaddad A, Daniel P, Niazi T. Radiomics Evaluation of Histological Heterogeneity Using Multiscale Textures Derived From 3D Wavelet Transformation of Multispectral Images. Front Oncol 2018; 8:96. [PMID: 29670857 PMCID: PMC5893871 DOI: 10.3389/fonc.2018.00096] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/19/2018] [Indexed: 12/18/2022] Open
Abstract
Purpose Colorectal cancer (CRC) is markedly heterogeneous and develops progressively toward malignancy through several stages which include stroma (ST), benign hyperplasia (BH), intraepithelial neoplasia (IN) or precursor cancerous lesion, and carcinoma (CA). Identification of the malignancy stage of CRC pathology tissues (PT) allows the most appropriate therapeutic intervention. Methods This study investigates multiscale texture features extracted from CRC pathology sections using 3D wavelet transform (3D-WT) filter. Multiscale features were extracted from digital whole slide images of 39 patients that were segmented in a pre-processing step using an active contour model. The capacity for multiscale texture to compare and classify between PTs was investigated using ANOVA significance test and random forest classifier models, respectively. Results 12 significant features derived from the multiscale texture (i.e., variance, entropy, and energy) were found to discriminate between CRC grades at a significance value of p < 0.01 after correction. Combining multiscale texture features lead to a better predictive capacity compared to prediction models based on individual scale features with an average (±SD) classification accuracy of 93.33 (±3.52)%, sensitivity of 88.33 (± 4.12)%, and specificity of 96.89 (± 3.88)%. Entropy was found to be the best classifier feature across all the PT grades with an average of the area under the curve (AUC) value of 91.17, 94.21, 97.70, 100% for ST, BH, IN, and CA, respectively. Conclusion Our results suggest that multiscale texture features based on 3D-WT are sensitive enough to discriminate between CRC grades with the entropy feature, the best predictor of pathology grade.
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Affiliation(s)
- Ahmad Chaddad
- Division of Radiation Oncology, McGill University, Montreal, QC, Canada
| | - Paul Daniel
- Division of Radiation Oncology, McGill University, Montreal, QC, Canada
| | - Tamim Niazi
- Division of Radiation Oncology, McGill University, Montreal, QC, Canada
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Aoki K, Niki H. Release of condensin from mitotic chromosomes requires the Ran-GTP gradient in the reorganized nucleus. Biol Open 2017; 6:1614-1628. [PMID: 28954740 PMCID: PMC5703609 DOI: 10.1242/bio.027193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After mitosis, nuclear reorganization occurs together with decondensation of mitotic chromosomes and reformation of the nuclear envelope, thereby restoring the Ran-GTP gradient between the nucleus and cytoplasm. The Ran-GTP gradient is dependent on Pim1/RCC1. Interestingly, a defect in Pim1/RCC1 in Schizosaccharomyces pombe causes postmitotic condensation of chromatin, namely hypercondensation, suggesting a relationship between the Ran-GTP gradient and chromosome decondensation. However, how Ran-GTP interacts with chromosome decondensation is unresolved. To examine this interaction, we used Schizosaccharomyces japonicus, which is known to undergo partial breakdown of the nuclear membrane during mitosis. We found that Pim1/RCC1 was localized on nuclear pores, but this localization failed in a temperature-sensitive mutant of Pim1/RCC1. The mutant cells exhibited hypercondensed chromatin after mitosis due to prolonged association of condensin on the chromosomes. Conceivably, a condensin-dephosphorylation defect might cause hypercondensed chromatin, since chromosomal localization of condensin is dependent on phosphorylation by cyclin-dependent kinase (CDK). Indeed, CDK-phospho-mimic mutation of condensin alone caused untimely condensin localization, resulting in hypercondensed chromatin. Together, these results suggest that dephosphorylation of CDK sites of condensin might require the Ran-GTP gradient produced by nuclear pore-localized Pim1/RCC1. Summary: A mutant of Pim1/RCC1 caused hypercondensed chromatin after mitosis due to prolonged association of condensin on chromosomes, suggesting that dephosphorylation of CDK sites of condensin might require Ran-GTP after mitosis.
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Affiliation(s)
- Keita Aoki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan .,Department of Genetics, SOKENDAI, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, SOKENDAI, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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Texture Analysis of Abnormal Cell Images for Predicting the Continuum of Colorectal Cancer. Anal Cell Pathol (Amst) 2017; 2017:8428102. [PMID: 28331793 PMCID: PMC5282460 DOI: 10.1155/2017/8428102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/20/2015] [Indexed: 11/17/2022] Open
Abstract
Abnormal cell (ABC) is a markedly heterogeneous tissue area and can be categorized into three main types: benign hyperplasia (BH), carcinoma (Ca), and intraepithelial neoplasia (IN) or precursor cancerous lesion. In this study, the goal is to determine and characterize the continuum of colorectal cancer by using a 3D-texture approach. ABC was segmented in preprocessing step using an active contour segmentation technique. Cell types were analyzed based on textural features extracted from the gray level cooccurrence matrices (GLCMs). Significant texture features were selected using an analysis of variance (ANOVA) of ABC with a p value cutoff of p < 0.01. Features selected were reduced with a principal component analysis (PCA), which accounted for 97% of the cumulative variance from significant features. The simulation results identified 158 significant features based on ANOVA from a total of 624 texture features extracted from GLCMs. Performance metrics of ABC discrimination based on significant texture features showed 92.59% classification accuracy, 100% sensitivity, and 94.44% specificity. These findings suggest that texture features extracted from GLCMs are sensitive enough to discriminate between the ABC types and offer the opportunity to predict cell characteristics of colorectal cancer.
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Stuurman N, Vale RD. Impact of New Camera Technologies on Discoveries in Cell Biology. THE BIOLOGICAL BULLETIN 2016; 231:5-13. [PMID: 27638691 PMCID: PMC5100698 DOI: 10.1086/689587] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
New technologies can make previously invisible phenomena visible. Nowhere is this more obvious than in the field of light microscopy. Beginning with the observation of "animalcules" by Antonie van Leeuwenhoek, when he figured out how to achieve high magnification by shaping lenses, microscopy has advanced to this day by a continued march of discoveries driven by technical innovations. Recent advances in single-molecule-based technologies have achieved unprecedented resolution, and were the basis of the Nobel prize in Chemistry in 2014. In this article, we focus on developments in camera technologies and associated image processing that have been a major driver of technical innovations in light microscopy. We describe five types of developments in camera technology: video-based analog contrast enhancement, charge-coupled devices (CCDs), intensified sensors, electron multiplying gain, and scientific complementary metal-oxide-semiconductor cameras, which, together, have had major impacts in light microscopy.
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Affiliation(s)
- Nico Stuurman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, California 94143
| | - Ronald D Vale
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, California 94143
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9
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Chaddad A, Desrosiers C, Bouridane A, Toews M, Hassan L, Tanougast C. Multi Texture Analysis of Colorectal Cancer Continuum Using Multispectral Imagery. PLoS One 2016; 11:e0149893. [PMID: 26901134 PMCID: PMC4764026 DOI: 10.1371/journal.pone.0149893] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/05/2016] [Indexed: 01/05/2023] Open
Abstract
PURPOSE This paper proposes to characterize the continuum of colorectal cancer (CRC) using multiple texture features extracted from multispectral optical microscopy images. Three types of pathological tissues (PT) are considered: benign hyperplasia, intraepithelial neoplasia and carcinoma. MATERIALS AND METHODS In the proposed approach, the region of interest containing PT is first extracted from multispectral images using active contour segmentation. This region is then encoded using texture features based on the Laplacian-of-Gaussian (LoG) filter, discrete wavelets (DW) and gray level co-occurrence matrices (GLCM). To assess the significance of textural differences between PT types, a statistical analysis based on the Kruskal-Wallis test is performed. The usefulness of texture features is then evaluated quantitatively in terms of their ability to predict PT types using various classifier models. RESULTS Preliminary results show significant texture differences between PT types, for all texture features (p-value < 0.01). Individually, GLCM texture features outperform LoG and DW features in terms of PT type prediction. However, a higher performance can be achieved by combining all texture features, resulting in a mean classification accuracy of 98.92%, sensitivity of 98.12%, and specificity of 99.67%. CONCLUSIONS These results demonstrate the efficiency and effectiveness of combining multiple texture features for characterizing the continuum of CRC and discriminating between pathological tissues in multispectral images.
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Affiliation(s)
- Ahmad Chaddad
- Laboratory for Imagery, Vision and Artificial Intelligence, École de Technologie Supérieure, Montréal, Québec, Canada
- Laboratory of Conception, Optimization and Modelling of Systems, University of Lorraine, Metz, Lorraine, France
| | - Christian Desrosiers
- Laboratory for Imagery, Vision and Artificial Intelligence, École de Technologie Supérieure, Montréal, Québec, Canada
| | - Ahmed Bouridane
- School of Computing, Engineering and Information Sciences, Northumbria University, Newcastle, United Kingdom
| | - Matthew Toews
- Laboratory for Imagery, Vision and Artificial Intelligence, École de Technologie Supérieure, Montréal, Québec, Canada
| | - Lama Hassan
- Laboratory of Conception, Optimization and Modelling of Systems, University of Lorraine, Metz, Lorraine, France
| | - Camel Tanougast
- Laboratory of Conception, Optimization and Modelling of Systems, University of Lorraine, Metz, Lorraine, France
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Chaddad A, Tanougast C. Real-time abnormal cell detection using a deformable snake model. HEALTH AND TECHNOLOGY 2015. [DOI: 10.1007/s12553-015-0115-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
Lineage tracing is a widely used method for understanding cellular dynamics in multicellular organisms during processes such as development, adult tissue maintenance, injury repair and tumorigenesis. Advances in tracing or tracking methods, from light microscopy-based live cell tracking to fluorescent label-tracing with two-photon microscopy, together with emerging tissue clearing strategies and intravital imaging approaches have enabled scientists to decipher adult stem and progenitor cell properties in various tissues and in a wide variety of biological processes. Although technical advances have enabled time-controlled genetic labeling and simultaneous live imaging, a number of obstacles still need to be overcome. In this review, we aim to provide an in-depth description of the traditional use of lineage tracing as well as current strategies and upcoming new methods of labeling and imaging.
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Affiliation(s)
| | | | - Bon-Kyoung Koo
- Department of Genetics and Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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De Los Santos C, Chang CW, Mycek MA, Cardullo RA. FRAP, FLIM, and FRET: Detection and analysis of cellular dynamics on a molecular scale using fluorescence microscopy. Mol Reprod Dev 2015; 82:587-604. [PMID: 26010322 PMCID: PMC4515154 DOI: 10.1002/mrd.22501] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 05/01/2015] [Indexed: 01/01/2023]
Abstract
The combination of fluorescent-probe technology plus modern optical microscopes allows investigators to monitor dynamic events in living cells with exquisite temporal and spatial resolution. Fluorescence recovery after photobleaching (FRAP), for example, has long been used to monitor molecular dynamics both within cells and on cellular surfaces. Although bound by the diffraction limit imposed on all optical microscopes, the combination of digital cameras and the application of fluorescence intensity information on large-pixel arrays have allowed such dynamic information to be monitored and quantified. Fluorescence lifetime imaging microscopy (FLIM), on the other hand, utilizes the information from an ensemble of fluorophores to probe changes in the local environment. Using either fluorescence-intensity or lifetime approaches, fluorescence resonance energy transfer (FRET) microscopy provides information about molecular interactions, with Ångstrom resolution. In this review, we summarize the theoretical framework underlying these methods and illustrate their utility in addressing important problems in reproductive and developmental systems.
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Affiliation(s)
- Carla De Los Santos
- Departments of Biology and Bioengineering, University of California, Riverside, Riverside, CA 92501
| | - Ching-Wei Chang
- Department of Bioengineering, University of California, Berkeley 94720
| | - Mary-Ann Mycek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Richard A. Cardullo
- Departments of Biology and Bioengineering, University of California, Riverside, Riverside, CA 92501
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Wasserlauf I, Usov K, Artemov G, Anan'ina T, Stegniy V. Specific features in linear and spatial organizations of pericentromeric heterochromatin regions in polytene chromosomes of the closely related species Drosophila virilis and D. kanekoi (Diptera: Drosophilidae). Genetica 2015; 143:331-42. [PMID: 25721230 DOI: 10.1007/s10709-015-9832-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/23/2015] [Indexed: 12/17/2022]
Abstract
Heterochromatin plays an important role in the spatial arrangement and evolution of the eukaryotic genetic apparatus. The closely related species Drosophila virilis (phyla virilis) and D. kanekoi (phyla montana) differ in the amount of heterochromatin along the chromosomes as well as by the presence of the metacentric chromosome 2, which emerged as a result of a pericentric inversion during speciation, in the D. kanekoi karyotype. The purpose of this study was to establish if chromosome rearrangements have any influence on the linear redistribution of centromeric heterochromatin in polytene chromosomes and the spatial organization of chromosomes in the nuclei of nurse cell. We have microdissected the chromocenter of D. virilis salivary gland polytene chromosomes; obtained a DNA library of this region (DvirIII); and hybridized (FISH) DvirIII to the salivary gland and nurse cell polytene chromosomes of D. virilis and D. kanekoi. We demonstrated that DvirIII localizes to the pericentromeric heterochromatin regions of all chromosomes and peritelomeric region of chromosome 5 in both species. Unlike D. virilis, the DvirIII signal in D. kanekoi chromosomes is detectable in the telomeric region of chromosome 2. We have also conducted a 3D FISH of DvirIII probe to the D. virilis and D. kanekoi nurse cell chromosomes. In particular, the DvirIII signal in D. virilis was observed in the local chromocenter at one pole of the nucleus, while the signal belonging to the telomeric region of chromosome 5 was detectable at the other pole. In contrast, in D. kanekoi there exist two separate DvirIII-positive regions. One of these regions belongs to the pericentromeric region of chromosome 2 and the other, to pericentromeric regions of the remaining chromosomes. These results suggest that chromosome rearrangements play an important role in the redistribution of heterochromatin DNA sequences in the genome, representing a speciation mechanism, which, in general, could also affect the chromosome orientation in the 3D nuclear space.
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Affiliation(s)
- Irina Wasserlauf
- Tomsk State University, 36 Lenin Prospekt, Tomsk, 634050, Russian Federation,
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15
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Singh S, Bray MA, Jones TR, Carpenter AE. Pipeline for illumination correction of images for high-throughput microscopy. J Microsc 2014; 256:231-6. [PMID: 25228240 PMCID: PMC4359755 DOI: 10.1111/jmi.12178] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/12/2014] [Indexed: 12/24/2022]
Abstract
The presence of systematic noise in images in high-throughput microscopy experiments can significantly impact the accuracy of downstream results. Among the most common sources of systematic noise is non-homogeneous illumination across the image field. This often adds an unacceptable level of noise, obscures true quantitative differences and precludes biological experiments that rely on accurate fluorescence intensity measurements. In this paper, we seek to quantify the improvement in the quality of high-content screen readouts due to software-based illumination correction. We present a straightforward illumination correction pipeline that has been used by our group across many experiments. We test the pipeline on real-world high-throughput image sets and evaluate the performance of the pipeline at two levels: (a) Z′-factor to evaluate the effect of the image correction on a univariate readout, representative of a typical high-content screen, and (b) classification accuracy on phenotypic signatures derived from the images, representative of an experiment involving more complex data mining. We find that applying the proposed post-hoc correction method improves performance in both experiments, even when illumination correction has already been applied using software associated with the instrument. To facilitate the ready application and future development of illumination correction methods, we have made our complete test data sets as well as open-source image analysis pipelines publicly available. This software-based solution has the potential to improve outcomes for a wide-variety of image-based HTS experiments.
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Affiliation(s)
- S Singh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, U.S.A
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16
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Van PT, Bass V, Shiwarski D, Lanni F, Minden J. High dynamic range proteome imaging with the structured illumination gel imager. Electrophoresis 2014; 35:2642-55. [PMID: 24935033 DOI: 10.1002/elps.201400126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/14/2014] [Accepted: 06/10/2014] [Indexed: 11/08/2022]
Abstract
A current challenge for proteomics is detecting proteins over the large concentration ranges found in complex biological samples such as whole-cell extracts. Currently, no unbiased, whole-proteome analysis scheme is capable of detecting the full range of cellular proteins. This is due in part to the limited dynamic range of the detectors used to sense proteins or peptides. We present a new technology, structured illumination (SI) gel imager, which detects fluorescently labeled proteins in electrophoretic gels over a 1 000 000-fold concentration range. SI uses computer-generated masks to attenuate the illumination of highly abundant proteins, allowing for long exposures of low-abundance proteins, thus avoiding detector saturation. A series of progressively masked gel images are assembled into a single, very high dynamic range image. We demonstrate that the SI imager can detect proteins over a concentration range of approximately 1 000 000-fold, making it a useful tool for comprehensive, unbiased proteome-wide surveys.
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Affiliation(s)
- Phu T Van
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
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Diaz-de-Quijano D, Palacios P, Horňák K, Felip M. 3D restoration microscopy improves quantification of enzyme-labeled fluorescence-based single-cell phosphatase activity in plankton. Cytometry A 2014; 85:841-53. [PMID: 24845646 DOI: 10.1002/cyto.a.22486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 01/22/2014] [Accepted: 04/30/2014] [Indexed: 11/10/2022]
Abstract
The ELF or fluorescence-labeled enzyme activity (FLEA) technique is a culture-independent single-cell tool for assessing plankton enzyme activity in close-to-in situ conditions. We demonstrate that single-cell FLEA quantifications based on two-dimensional (2D) image analysis were biased by up to one order of magnitude relative to deconvolved 3D. This was basically attributed to out-of-focus light, and partially to object size. Nevertheless, if sufficient cells were measured (25-40 cells), biases in individual 2D cell measurements were partially compensated, providing useful and comparable results to deconvolved 3D. We also discuss how much caution should be used when comparing the single-cell enzyme activities of different sized bacterio- and/or phytoplankton populations measured on 2D images. Finally, a novel method based on deconvolved 3D images (wide field restoration microscopy; WFR) was devised to improve the discrimination of similar single-cell enzyme activities, the comparison of enzyme activities between different size cells, the measurement of low fluorescence intensities, the quantification of less numerous species, and the combination of the FLEA technique with other single-cell methods. These improvements in cell enzyme activity measurements will provide a more precise picture of individual species' behavior in nature, which is essential to understand their functional role and evolutionary history.
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Affiliation(s)
- Daniel Diaz-de-Quijano
- Unitat de Limnologia, Departament d'Ecologia i Centre de Recerca d'Alta Muntanya, CEAB-CSIC-Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
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Abstract
The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.
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Affiliation(s)
- Mariluce Riegel
- Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil . ; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Abstract
This chapter introduces to electronic cameras, discusses the various parameters considered for evaluating their performance, and describes some of the key features of different camera formats. The chapter also presents the basic understanding of functioning of the electronic cameras and how these properties can be exploited to optimize image quality under low-light conditions. Although there are many types of cameras available for microscopy, the most reliable type is the charge-coupled device (CCD) camera, which remains preferred for high-performance systems. If time resolution and frame rate are of no concern, slow-scan CCDs certainly offer the best available performance, both in terms of the signal-to-noise ratio and their spatial resolution. Slow-scan cameras are thus the first choice for experiments using fixed specimens such as measurements using immune fluorescence and fluorescence in situ hybridization. However, if video rate imaging is required, one need not evaluate slow-scan CCD cameras. A very basic video CCD may suffice if samples are heavily labeled or are not perturbed by high intensity illumination. When video rate imaging is required for very dim specimens, the electron multiplying CCD camera is probably the most appropriate at this technological stage. Intensified CCDs provide a unique tool for applications in which high-speed gating is required. The variable integration time video cameras are very attractive options if one needs to acquire images at video rate acquisition, as well as with longer integration times for less bright samples. This flexibility can facilitate many diverse applications with highly varied light levels.
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Coutu DL, Schroeder T. Probing cellular processes by long-term live imaging--historic problems and current solutions. J Cell Sci 2013; 126:3805-15. [PMID: 23943879 DOI: 10.1242/jcs.118349] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Living organisms, tissues, cells and molecules are highly dynamic. The importance of their continuous and long-term observation has been recognized for over a century but has been limited by technological hurdles. Improvements in imaging technologies, genetics, protein engineering and data analysis have more recently allowed us to answer long-standing questions in biology using quantitative continuous long-term imaging. This requires a multidisciplinary collaboration between scientists of various backgrounds: biologists asking relevant questions, imaging specialists and engineers developing hardware, and informaticians and mathematicians developing software for data acquisition, analysis and computational modeling. Despite recent improvements, there are still obstacles to be addressed before this technology can achieve its full potential. This Commentary aims at providing an overview of currently available technologies for quantitative continuous long-term single-cell imaging, their limitations and what is required to bring this field to the next level. We provide an historical perspective on the development of this technology and discuss key issues in time-lapse imaging: keeping cells alive, using labels, reporters and biosensors, and hardware and software requirements. We highlight crucial and often non-obvious problems for researchers venturing into the field and hope to inspire experts in the field and from related disciplines to contribute to future solutions.
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Affiliation(s)
- Daniel L Coutu
- ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
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Nuttall AL, Fridberger A. Instrumentation for studies of cochlear mechanics: from von Békésy forward. Hear Res 2012; 293:3-11. [PMID: 22975360 PMCID: PMC3483786 DOI: 10.1016/j.heares.2012.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/13/2012] [Accepted: 08/21/2012] [Indexed: 11/24/2022]
Abstract
Georg von Békésy designed the instruments needed for his research. He also created physical models of the cochlea allowing him to manipulate the parameters (such as volume elasticity) that could be involved in controlling traveling waves. This review is about the specific devices that he used to study the motion of the basilar membrane thus allowing the analysis that lead to his Nobel Prize Award. The review moves forward in time mentioning the subsequent use of von Békésy's methods and later technologies important for motion studies of the organ of Corti. Some of the seminal findings and the controversies of cochlear mechanics are mentioned in relation to the technical developments.
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Affiliation(s)
- Alfred L Nuttall
- Oregon Hearing Research Center, Dept. of Otolaryngology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR, USA.
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Abstract
The current revolution in biological microscopy stems from the realisation that advances in optics and computational tools and automation make the modern microscope an instrument that can access all scales relevant to modern biology – from individual molecules all the way to whole tissues and organisms and from single snapshots to time-lapse recordings sampling from milliseconds to days. As these and more new technologies appear, the challenges of delivering them to the community grows as well. I discuss some of these challenges, and the examples where openly shared technology have made an impact on the field.
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Affiliation(s)
- Jason R Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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Holmes TJ, Liu YH, Khosla D, Agard DA. Increased depth of field and stereo pairs of fluorescence micrographs via inverse filtering and maximum-likelihood estimation. J Microsc 2011. [DOI: 10.1111/j.1365-2818.1991.tb03209.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Shaw P, Highett M, Rawlins D. Confocal microscopy and image processing in the study of plant nuclear structure. J Microsc 2011. [DOI: 10.1111/j.1365-2818.1992.tb01508.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
INTRODUCTIONCharged-coupled device (CCD) cameras are commonly used to acquire wide-field, spinning-disk confocal, and total internal reflection fluorescence (TIRF) microscopy images. Collecting digital images for a live cell fluorescence microscopy experiment requires balancing the desire to acquire sufficiently high-quality images with the need to minimize exposure of the specimen to light to reduce phototoxicity and photobleaching. The choice of CCD camera and the camera acquisition settings are critical determinants in the quality of a digital image that one can acquire from a given fluorescent specimen. In this article, we discuss the characteristics of CCD cameras, how they affect digital-image quality, and how to properly use a CCD camera for fluorescence live cell imaging experiments.
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Miller MI, Joshi S, Maffitt DR, Mcnally JG, Grenander U. Membranes, mitochondria and amoebae: shape models. J Appl Stat 2011. [DOI: 10.1080/757582973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Michael I. Miller
- a Biomedical Computer Laboratory
- b Department of Electrical Engineering
| | | | | | - James G. Mcnally
- a Biomedical Computer Laboratory
- c Department of Biology , Washington University , St Louis, MO
| | - Ulf Grenander
- d Division of Applied Mathematics , Brown University , Biomedical Computer Laboratory, Providence , RI
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Davis BJ, Carney PS, Bhargava R. Theory of midinfrared absorption microspectroscopy: I. Homogeneous samples. Anal Chem 2010; 82:3474-86. [PMID: 20392063 DOI: 10.1021/ac902067p] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Midinfrared (IR) microspectroscopy is widely employed for spatially localized spectral analyses. A comprehensive theoretical model for the technique, however, has not been previously proposed. In this paper, rigorous theory is presented for IR absorption microspectroscopy by using Maxwell's equations to model beam propagation. Focusing effects, material dispersion, and the geometry of the sample are accounted to predict spectral response for homogeneous samples. Predictions are validated experimentally using Fourier transform IR (FT-IR) microspectroscopic examination of a photoresist. The results emphasize that meaningful interpretation of IR microspectroscopic data must involve an understanding of the coupled optical effects associated with the sample, substrate properties, and microscopy configuration. Simulations provide guidance for developing experimental methods and future instrument design by quantifying distortions in the recorded data. Distortions are especially severe for transflection mode and for samples mounted on certain substrates. Last, the model generalizes to rigorously consider the effects of focusing. While spectral analyses range from examining gross spectral features to assessing subtle features using advanced chemometrics, the limitations imposed by these effects in the data acquisition on the information available are less clear. The distorting effects are shown to be larger than noise levels seen in modern spectrometers. Hence, the model provides a framework to quantify spectral distortions that may limit the accuracy of information or present confounding effects in microspectroscopy.
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Affiliation(s)
- Brynmor J Davis
- Department of Bioengineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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31
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Awwad HO, Millman EE, Alpizar-Foster E, Moore RH, Knoll BJ. Mutating the dileucine motif of the human beta(2)-adrenoceptor reduces the high initial rate of receptor phosphorylation by GRK without affecting postendocytic sorting. Eur J Pharmacol 2010; 635:9-15. [PMID: 20193676 DOI: 10.1016/j.ejphar.2010.02.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 01/27/2010] [Accepted: 02/13/2010] [Indexed: 10/19/2022]
Abstract
The internalization of beta(2)-adrenoceptors after agonist activation results in a desensitized and phosphorylated receptor that either resensitizes by recycling to the cell surface or becomes degraded by postendocytic sorting to lysosomes. The duration and physiological effects of agonists therefore depend on beta(2)-adrenoceptor sorting, highlighting the importance of sorting signals. Dileucine motifs within other membrane proteins act as signals for endocytosis and/or postendocytic sorting, and the beta(2)-adrenoceptor has a dileucine motif within helix 8 that might play a role in efficient receptor recycling and/or downregulation. beta(2)-adrenoceptor internalization and sorting were studied in HEK293 cells stably expressing wild type or mutant dialanine L339A,L340A beta(2)-adrenoceptors. The mutant beta(2)-adrenoceptors showed a significantly lower initial rate of phosphorylation at the prominent G-protein coupled receptor kinase (GRK) sites Ser355 and 356 compared to wild type beta(2)-adrenoceptors. Furthermore, the agonist-induced endocytic rate constant for L339A,L340A beta(2)-adrenoceptors was reduced to approximately 25% that of wild type beta(2)-adrenoceptors, which resulted in a similar reduction in agonist-induced downregulation. Internalized L339A,L340A beta(2)-adrenoceptors recycled to the surface with a rate and extent similar to that of wild type beta(2)-adrenoceptors. Therefore, although the role of L339,L340 in beta(2)-adrenoceptor recycling or postendocytic sorting seems minimal, we conclude that L339,L340 is required for the initial high rate of phosphorylation by G-protein coupled receptor kinases at Ser355,356, which in turn is required for efficient beta(2)-adrenoceptors endocytosis.
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Affiliation(s)
- Hibah O Awwad
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA
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32
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Swedlow JR, Eliceiri KW. Open source bioimage informatics for cell biology. Trends Cell Biol 2009; 19:656-60. [PMID: 19833518 PMCID: PMC2789254 DOI: 10.1016/j.tcb.2009.08.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/23/2009] [Accepted: 08/25/2009] [Indexed: 01/02/2023]
Abstract
Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery.
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Affiliation(s)
- Jason R Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK.
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Cheong R, Wang CJ, Levchenko A. Using a microfluidic device for high-content analysis of cell signaling. Sci Signal 2009; 2:pl2. [PMID: 19531802 DOI: 10.1126/scisignal.275pl2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Quantitative analysis and understanding of signaling networks require measurements of the location and activities of key proteins over time, at the level of single cells, in response to various perturbations. Microfluidic devices enable such analyses to be conducted in a high-throughput and in a highly controlled manner. We describe in detail how to design and use a microfluidic device to perform such information-rich experiments.
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Affiliation(s)
- Raymond Cheong
- Department of Biomedical Engineering and Whitaker Institute of Biomedical Engineering and Institute for Cell Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
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34
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Cheong R, Wang CJ, Levchenko A. High content cell screening in a microfluidic device. Mol Cell Proteomics 2008; 8:433-42. [PMID: 18953019 DOI: 10.1074/mcp.m800291-mcp200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A comprehensive, systems level understanding of cell signaling networks requires methods to efficiently assay multiple signaling species, at the level of single cells, responding to a variety of stimulation protocols. Here we describe a microfluidic device that enables quantitative interrogation of signaling networks in thousands of individual cells using immunofluorescence-based readouts. The device is especially useful for measuring the signaling activity of kinases, transcription factors, and/or target genes in a high throughput, high content manner. We demonstrate how the device may be used to measure detailed time courses of signaling responses to one or more soluble stimuli and/or chemical inhibitors as well as responses to a complex temporal pattern of multiple stimuli. Furthermore we show how the throughput and resolution of the device may be exploited in investigating the differences, if any, of signaling at the level of a single cell versus at the level of the population. In particular, we show that NF-kappaB activity dynamics in individual cells are not asynchronous and instead resemble the dynamics of the population average in contrast to studies of cells overexpressing p65-EGFP.
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Affiliation(s)
- Raymond Cheong
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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Tanke HJ. Digital fluorescence microscopy. CURRENT PROTOCOLS IN CYTOMETRY 2008; Chapter 2:Unit 2.5. [PMID: 18770699 DOI: 10.1002/0471142956.cy0205s00] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fluorescence microscopy is a valuable tool for biomedical research, providing good sensitivity and high multiplicity. Specialized techniques (anisotropy measurement, resonance energy transfer) can provide information on cell spatial arrangement or label microenvironment. The unit discusses camera selection strategy, microscope hardware, and image acquisition and processing.
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Affiliation(s)
- H J Tanke
- Leiden University, Leiden, The Netherlands
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36
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Hom EFY, Marchis F, Lee TK, Haase S, Agard DA, Sedat JW. AIDA: an adaptive image deconvolution algorithm with application to multi-frame and three-dimensional data. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2007; 24:1580-600. [PMID: 17491626 PMCID: PMC3166524 DOI: 10.1364/josaa.24.001580] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We describe an adaptive image deconvolution algorithm (AIDA) for myopic deconvolution of multi-frame and three-dimensional data acquired through astronomical and microscopic imaging. AIDA is a reimplementation and extension of the MISTRAL method developed by Mugnier and co-workers and shown to yield object reconstructions with excellent edge preservation and photometric precision [J. Opt. Soc. Am. A21, 1841 (2004)]. Written in Numerical Python with calls to a robust constrained conjugate gradient method, AIDA has significantly improved run times over the original MISTRAL implementation. Included in AIDA is a scheme to automatically balance maximum-likelihood estimation and object regularization, which significantly decreases the amount of time and effort needed to generate satisfactory reconstructions. We validated AIDA using synthetic data spanning a broad range of signal-to-noise ratios and image types and demonstrated the algorithm to be effective for experimental data from adaptive optics-equipped telescope systems and wide-field microscopy.
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Affiliation(s)
- Erik F Y Hom
- Graduate Group in Biophysics and Department of Biochemistry and Biophysics, University of California, San Francisco 94143-2240, USA.
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Awwad HO, Iyer V, Rosenfeld JL, Millman EE, Foster E, Moore RH, Knoll BJ. Inhibitors of phosphoinositide 3-kinase cause defects in the postendocytic sorting of beta2-adrenergic receptors. Exp Cell Res 2007; 313:2586-96. [PMID: 17553490 PMCID: PMC2034330 DOI: 10.1016/j.yexcr.2007.04.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 04/18/2007] [Accepted: 04/18/2007] [Indexed: 11/16/2022]
Abstract
Phosphatidylinositol 3-kinase inhibitors have been shown to affect endocytosis or subsequent intracellular sorting in various receptor systems. Agonist-activated beta(2)-adrenergic receptors undergo desensitization by mechanisms that include the phosphorylation, endocytosis and degradation of receptors. Following endocytosis, most internalized receptors are sorted to the cell surface, but some proportion is sorted to lysosomes for degradation. It is not known what governs the ratio of receptors that recycle versus receptors that undergo degradation. To determine if phosphatidylinositol 3-kinases regulate beta(2)-adrenergic receptor trafficking, HEK293 cells stably expressing these receptors were treated with the phosphatidylinositol 3-kinase inhibitors LY294002 or wortmannin. We then studied agonist-induced receptor endocytosis and postendocytic sorting, including recycling and degradation of the internalized receptors. Both inhibitors amplified the internalization of receptors after exposure to the beta-agonist isoproterenol, which was attributable to the sorting of a significant fraction of receptors to an intracellular compartment from which receptor recycling did not occur. The initial rate of beta(2)-adrenergic receptor endocytosis and the default rate of receptor recycling were not significantly altered. During prolonged exposure to agonist, LY294002 slowed the degradation rate of beta(2)-adrenergic receptors and caused the accumulation of receptors within rab7-positive vesicles. These results suggest that phosphatidylinositol 3-kinase inhibitors (1) cause a misrouting of beta(2)-adrenergic receptors into vesicles that are neither able to efficiently recycle to the surface nor sort to lysosomes, and (2) delays the movement of receptors from late endosomes to lysosomes.
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Affiliation(s)
- Hibah O. Awwad
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, Texas 77204
| | - Varsha Iyer
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, Texas 77204
| | - Jennifer L. Rosenfeld
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, Texas 77204
| | - Ellen E. Millman
- Department of Pediatrics, Baylor College of Medicine, 6621 Fannin, CCC1040, Houston, Texas 77030
| | - Estrella Foster
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, Texas 77204
| | - Robert H. Moore
- Department of Pediatrics, Baylor College of Medicine, 6621 Fannin, CCC1040, Houston, Texas 77030
| | - Brian J. Knoll
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, Texas 77204
- **Corresponding author: Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Science and Research Bldg. 2, Rm. 521D, Houston, Texas 77204, Phone:713–743–1299; FAX 713–743–1229;
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Affiliation(s)
- Ivan Rasnik
- Physics Department, Emory University, Atlanta, Georgia 30322, USA
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Grattarola M, Borghi C, Emionite L, Lulli P, Chessa L, Vergani L. Modifications of nuclear architecture and chromatin organization in ataxia telangiectasia cells are coupled to changes of gene transcription. J Cell Biochem 2006; 99:1148-64. [PMID: 16795050 DOI: 10.1002/jcb.20895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ataxia telangiectasia (AT) is a rare genetic disorder caused by mutations of ATM gene. ATM kinase is a "master controller" of DNA-damage response and signal transducer of external stimuli. The complex role of ATM may explain the pleiotropic phenotype characteristic of AT syndrome, only partially. In our hypothesis, the multi-faceted phenotype of AT patients might depend on specific chromatin reorganization, which then reflects on the cellular transcription. We analyzed three lymphoblastoid cell-lines isolated from AT patients and one healthy control. The three-dimensional reconstruction disclosed marked changes of nuclear morphology and architecture in AT cells. When chromatin condensation was analyzed by differential scanning calorimetry, a remodeling was observed at the level of fiber folding and nucleosome conformation. Despite the structural differences, chromatin did not exhibit modifications of the average acetylation status in comparison to the control. Moreover, AT cells presented significant alterations in the transcription of genes involved in cell-cycle regulation and stress response. In AT3RM cells, the average chromatin decondensation went with the upregulation of c-fos, c-jun, and c-myc and downregulation of metallothioneins, p21 and p53. AT9RM and AT44RM cells were instead characterized by an increased chromatin condensation and presented a different transcription unbalance. Whereas in AT44RM all the considered genes were downregulated, in AT3RM the three oncogenes and metallothioneins were upregulated, but p53 and p21 were downregulated.
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Affiliation(s)
- Myriam Grattarola
- Department of Biophysical Sciences and Techologies M.&O.-Biophysical Division, University of Genova, Genova, Italy
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Abstract
The focus of this article is to provide an overview of the current technologies for the pharmaceutical and biotech industry. Disease processes express themselves in the functional and structural disturbance of cellular systems. Cells and their metabolites constitute the building blocks of tissues and entire organisms. Studying the spatial and temporal phenotype of disease processes in tissues at the cellular level reveals a multitude of information about the progress and status of a disease. Detailed exploration of tissues by slide-based cytometry is an important source of information about disease processes. Technological and analytical advances allow us to shed a new light on tissues and to come to a better understanding of the complexity of disease processes. Dealing with complex multidimensional datasets from tissue samples requires an advanced approach to image processing and data management. The increase in computing power and the continuing research into imaging algorithms allow us to improve the exploration of the data content of tissues.
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Narizzano R, Erokhin V, Nicolini C. A Heterostructure Composed of Conjugated Polymer and Copper Sulfide Nanoparticles. J Phys Chem B 2005; 109:15798-802. [PMID: 16853006 DOI: 10.1021/jp051954k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A heterostructure formed by a conjugated polymer and semiconducting nanoparticles was produced. The conjugated polymer was synthesized by oxidative copolymerization of 3-thiopheneacetic acid and 3-hexylthiophene, thus obtaining an amphiphilic polythiophene that allows the formation of a stable polymer layer at the air-water interface. Different numbers of monolayers were deposited on solid substrates. CuS nanoparticles were grown directly in the polymeric matrix using the carboxylic groups as nucleation centers. The reactions were monitored by quartz crystal microbalance, Brewster angle, and fluorescence microscopy. The heterostructure showed increased conductivity as compared to the pristine polymer.
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Affiliation(s)
- Riccardo Narizzano
- Nanoworld Institute and Biophysics Division, University of Genova, Corso Europa, 30, 16132 Genoa, Italy
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Roux P, Münter S, Frischknecht F, Herbomel P, Shorte SL. Focusing light on infection in four dimensions. Cell Microbiol 2004; 6:333-43. [PMID: 15009025 DOI: 10.1111/j.1462-5822.2004.00374.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The fusion of cell biology with microbiology has bred a new discipline, cellular microbiology, in which the primary aim is to understand host-pathogen interactions at a tissue, cellular and molecular level. In this context, we require techniques allowing us to probe infection in situ and extrapolate quantitative information on its spatiotemporal dynamics. To these ends, fluorescent light-based imaging techniques offer a powerful tool, and the state-of-the-art is defined by paradigms using so-called multidimensional (multi-D) imaging microscopy. Multi-D imaging aims to visualize and quantify biological events through time and space and, more specifically, refers to combinations of: three (3D, volume), four (4D, time) and five (5D, multiwavelength)-dimensional recordings. Successful multi-D imaging depends upon understanding the available technologies and their limitations. This is especially true in the field of microbiology where visualization of infectious/pathogenic activities inside living host systems presents particular technical challenges. Thus, as multi-D imaging rapidly becomes a common bench tool to the cellular microbiologist, this review provides the new user with some of the necessary technical insight required to get the best from these methods.
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Affiliation(s)
- Pascal Roux
- Plate-forme d'Imagerie Dynamique (PFID), Institut Pasteur, 25-28 rue du Dr Roux, 75015 Paris, France
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43
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Michalet X, Kapanidis AN, Laurence T, Pinaud F, Doose S, Pflughoefft M, Weiss S. The power and prospects of fluorescence microscopies and spectroscopies. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2003; 32:161-82. [PMID: 12598370 DOI: 10.1146/annurev.biophys.32.110601.142525] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.
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Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, UCLA, Young Hall, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA.
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Dahl KN, Parthasarathy R, Westhoff CM, Layton DM, Discher DE. Protein 4.2 is critical to CD47-membrane skeleton attachment in human red cells. Blood 2003; 103:1131-6. [PMID: 14551146 DOI: 10.1182/blood-2003-04-1331] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reduction in expression of the integral membrane protein CD47 in human red blood cells (RBCs) deficient in protein 4.2 suggests that protein 4.2 may mediate a linkage of CD47 to the membrane skeleton. We compared the fractions of membrane skeleton-attached CD47, Rh-associated glycoprotein (RhAG), Rh, and band 3 in normal and protein 4.2-deficient cells using fluorescence-imaged microdeformation. We found that CD47 attachment decreases from 55% in normal cells to 25% to 35% in 4.2-deficient cells. RhAG, which has been shown to have no significant variation in expression among the cells studied, shows a significant decrease in membrane skeleton attachment in 4.2-deficient cells from 60% to 40%. Both Rh and band 3, which have also been shown to have no change in expression, show a smaller decrease from 75% attached in normal RBCs to 55% attached in 4.2-deficient cells. In normal cells, Rh phenotype influences CD47 expression but not the level of membrane skeleton attachment of CD47. In contrast, the results indicate that protein 4.2 strongly influences CD47 levels as well as the extent of membrane skeleton attachment in the RBC, whereas protein 4.2 affects membrane skeletal attachment of RhAG, Rh, and band 3 to a lesser extent.
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Affiliation(s)
- Kris Noel Dahl
- Department of Chemical and Biomolecular Engineering and School of Engineering and Applied Science, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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45
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Femino AM, Fogarty K, Lifshitz LM, Carrington W, Singer RH. Visualization of single molecules of mRNA in situ. Methods Enzymol 2003; 361:245-304. [PMID: 12624916 DOI: 10.1016/s0076-6879(03)61015-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrea M Femino
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Affiliation(s)
- Keith Berland
- Physics Department, Emory University, Atlanta, Georgia 30322, USA
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47
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Spadiliero B, Nicolini C, Mascetti G, Henríquez D, Vergani L. Chromatin of Trypanosoma cruzi: in situ analysis revealed its unusual structure and nuclear organization. J Cell Biochem 2002; 85:798-808. [PMID: 11968019 DOI: 10.1002/jcb.10183] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromatin of Trypanosoma cruzi is known to be organized in classical nucleosomal filaments, but surprisingly, these filaments do not fold in visible chromosomes and the nuclear envelope is preserved during cell division. Our hypothesis about the role of chromatin structure in regulating gene expression and, more generally, cell functioning, pressed us to verify if chromatin organization is modulated during the parasite life-cycle. To this end, we analyzed in situ the fine structural organization of T. cruzi chromatin by means of an integrated biophysical approach, using differential scanning calorimetry and fluorescence microscopy. We observed that logarithmic forms exhibit a less condensed chromatin with respect to the stationary ones. Thermal analysis revealed that parasite chromatin is organized in three main levels of condensation, barring from the polynucleosomal filament till to superstructured fibers. Besides, the fluorescence images of nuclei showed a characteristic chromatin distribution, with defined domains localized near to the nuclear envelope. While in stationary parasites, these regions are highly condensed, in logarithmic forms they unfold by extending themselves toward the center of nucleus. These observations suggest that, in comparison with higher eukaryotes, in T. cruzi the nuclear envelope plays an unusual and pivotal role in interphase and in mitosis.
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Affiliation(s)
- Barbara Spadiliero
- Department of Cell Biology, Simón Bolívar University, Caracas 89 000, Venezuela.
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Affiliation(s)
- Daniel R Rines
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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49
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Andrews PD, Harper IS, Swedlow JR. To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era. Traffic 2002; 3:29-36. [PMID: 11872140 DOI: 10.1034/j.1600-0854.2002.30105.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Digital fluorescence microscopy is now a standard technology for assaying molecular localisation in cells and tissues. The choice of laser scanning (LSM) and wide-field microscopes (WFM) largely depends on the type of sample, with LSMs performing best on thick samples and WFMs performing best on thin ones. These systems are increasingly used to collect large multidimensional datasets. We propose a unified image structure that considers space, time, and fluorescence wavelength as integral parts of the image. Moreover, the application of fluorescence imaging to large-scale screening means that large datasets are now routinely acquired. We propose that analysis of these data requires querying tools based on relational databases and describe one such system.
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Affiliation(s)
- Paul D Andrews
- Division of Gene Regulation and Expression, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
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50
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Van Dort HM, Knowles DW, Chasis JA, Lee G, Mohandas N, Low PS. Analysis of integral membrane protein contributions to the deformability and stability of the human erythrocyte membrane. J Biol Chem 2001; 276:46968-74. [PMID: 11595743 DOI: 10.1074/jbc.m107855200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Three major hypotheses have been proposed to explain the role of membrane-spanning proteins in establishing/maintaining membrane stability. These hypotheses ascribe the essential contribution of integral membrane proteins to (i) their ability to anchor the membrane skeleton to the lipid bilayer, (ii) their capacity to bind and stabilize membrane lipids, and (iii) their ability to influence and regulate local membrane curvature. In an effort to test these hypotheses in greater detail, we have modified both the membrane skeletal and lipid binding interactions of band 3 (the major membrane-spanning and skeletal binding protein of the human erythrocyte membrane) and have examined the impact of these modifications on erythrocyte membrane morphology, deformability, and stability. The desired changes in membrane skeletal and protein-lipid interactions were induced by 1) reaction of the cells with 4,4'-diisothiocyanostilbene-2,2'-disulfonate (DIDS), an inhibitor of band 3-mediated anion transport that dissociates band 3 into dimers (increasing its surface area in contact with lipid) and severs band 3 linkages to the membrane skeleton; 2) a fragment of ankyrin that ruptures the same ankyrin-band 3 bridge to the membrane skeleton, but drives the band 3 subunit equilibrium toward the tetramer (i.e. decreasing the band 3 surface area in contact with lipid); and 3) an antibody to the ankyrin-binding site on band 3 that promotes the same changes in band 3 skeletal and lipid interactions as the ankyrin fragment. We observed that although DIDS induced echinocytic morphological changes in the treated erythrocytes, it had little impact on either membrane deformability or stability. In contrast, resealing of either the ankyrin fragment or anti-band 3 IgG into erythrocytes caused spontaneous membrane fragmentation and loss of deformability/stability. Because these and other new observations cannot all be reconciled with any single hypothesis on membrane stability, we suggest that more than one hypothesis may be operative and provide an explanation of how each might individually contribute to net membrane stability.
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Affiliation(s)
- H M Van Dort
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-1393, USA
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