1
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Chen B, Chang BJ, Daetwyler S, Zhou F, Sharma S, Lee DM, Nayak A, Noh J, Dubrovinski K, Chen EH, Glotzer M, Fiolka R. Projective light-sheet microscopy with flexible parameter selection. Nat Commun 2024; 15:2755. [PMID: 38553438 PMCID: PMC10980818 DOI: 10.1038/s41467-024-46693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Projection imaging accelerates volumetric interrogation in fluorescence microscopy, but for multi-cellular samples, the resulting images may lack contrast, as many structures and haze are summed up. Here, we demonstrate rapid projective light-sheet imaging with parameter selection (props) of imaging depth, position and viewing angle. This allows us to selectively image different sub-volumes of a sample, rapidly switch between them and exclude background fluorescence. Here we demonstrate the power of props by functional imaging within distinct regions of the zebrafish brain, monitoring calcium firing inside muscle cells of moving Drosophila larvae, super-resolution imaging of selected cell layers, and by optically unwrapping the curved surface of a Drosophila embryo. We anticipate that props will accelerate volumetric interrogation, ranging from subcellular to mesoscopic scales.
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Affiliation(s)
- Bingying Chen
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Felix Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shiv Sharma
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Donghoon M Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amruta Nayak
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Konstantin Dubrovinski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth H Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Glotzer
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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McFadden C, Marin Z, Chen B, Daetwyler S, Wang X, Rajendran D, Dean KM, Fiolka R. Adaptive Optics in an Oblique Plane Microscope. bioRxiv 2024:2024.03.21.586191. [PMID: 38562744 PMCID: PMC10983975 DOI: 10.1101/2024.03.21.586191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Adaptive optics (AO) can restore diffraction limited performance when imaging beyond superficial cell layers in vivo and in vitro, and as such is of interest for advanced 3D microscopy methods such as light-sheet fluorescence microscopy (LSFM). In a typical LSFM system, the illumination and detection paths are separate and subject to different optical aberrations. To achieve optimal microscope performance, it is necessary to sense and correct these aberrations in both light paths, resulting in a complex microscope system. Here, we show that in an oblique plane microscope (OPM), a type of LSFM with a single primary objective lens, the same deformable mirror can correct both the illumination and fluorescence detection. Besides reducing the complexity, we show that AO in OPM also restores the relative alignment of the light-sheet and focal plane, and that a projection imaging mode can stabilize and improve the wavefront correction in a sensorless AO format. We demonstrate OPM with AO on fluorescent nanospheres and by imaging the vasculature and cancer cells in zebrafish embryos embedded in a glass capillary, restoring diffraction limited resolution and improving the signal strength twofold.
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Affiliation(s)
- Conor McFadden
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Zach Marin
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Bingying Chen
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Stephan Daetwyler
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Xiaoding Wang
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Kevin M. Dean
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Reto Fiolka
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
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3
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Marin Z, Wang X, Collison DW, McFadden C, Lin J, Borges H, Chen B, Mehra D, Shen Q, Galecki S, Daetwyler S, Fiolka R, Dean KM. navigate: an open-source platform for smart light-sheet microscopy. bioRxiv 2024:2024.02.09.579083. [PMID: 38370811 PMCID: PMC10871345 DOI: 10.1101/2024.02.09.579083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
navigate is a turnkey, open-source software solution designed to enhance light-sheet fluorescence microscopy (LSFM) by integrating smart microscopy techniques into a user-friendly framework. It enables automated, intelligent imaging with a Python-based control system that supports GUI-reconfigurable acquisition routines and the integration of diverse hardware sets. As a comprehensive package, navigate democratizes access to advanced LSFM capabilities, facilitating the development and implementation of smart microscopy workflows without requiring deep programming knowledge or specialized expertise in light-sheet microscopy.
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4
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Banerjee S, Daetwyler S, Bai X, Michaud M, Jouhet J, Madhugiri S, Johnson E, Wang CW, Fiolka R, Toulmay A, Prinz WA. The Vps13-like protein BLTP2 is pro-survival and regulates phosphatidylethanolamine levels in the plasma membrane to maintain its fluidity and function. bioRxiv 2024:2024.02.04.578804. [PMID: 38370643 PMCID: PMC10871178 DOI: 10.1101/2024.02.04.578804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Lipid transport proteins (LTPs) facilitate nonvesicular lipid exchange between cellular compartments and have critical roles in lipid homeostasis1. A new family of bridge-like LTPs (BLTPs) is thought to form lipid-transporting conduits between organelles2. One, BLTP2, is conserved across species but its function is not known. Here, we show that BLTP2 and its homolog directly regulate plasma membrane (PM) fluidity by increasing the phosphatidylethanolamine (PE) level in the PM. BLTP2 localizes to endoplasmic reticulum (ER)-PM contact sites34, 5, suggesting it transports PE from the ER to the PM. We find BLTP2 works in parallel with another pathway that regulates intracellular PE distribution and PM fluidity6, 7. BLTP2 expression correlates with breast cancer aggressiveness8-10. We found BLTP2 facilitates growth of a human cancer cell line and sustains its aggressiveness in an in vivo model of metastasis, suggesting maintenance of PM fluidity by BLTP2 may be critical for tumorigenesis in humans.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofei Bai
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Juliette Jouhet
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Shruthi Madhugiri
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emma Johnson
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao-Wen Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alexandre Toulmay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William A Prinz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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5
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Roudot P, Legant WR, Zou Q, Dean KM, Isogai T, Welf ES, David AF, Gerlich DW, Fiolka R, Betzig E, Danuser G. u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions. Cell Rep Methods 2023; 3:100655. [PMID: 38042149 PMCID: PMC10783629 DOI: 10.1016/j.crmeth.2023.100655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/04/2023]
Abstract
We describe u-track3D, a software package that extends the versatile u-track framework established in 2D to address the specific challenges of 3D particle tracking. First, we present the performance of the new package in quantifying a variety of intracellular dynamics imaged by multiple 3D microcopy platforms and on the standard 3D test dataset of the particle tracking challenge. These analyses indicate that u-track3D presents a tracking solution that is competitive to both conventional and deep-learning-based approaches. We then present the concept of dynamic region of interest (dynROI), which allows an experimenter to interact with dynamic 3D processes in 2D views amenable to visual inspection. Third, we present an estimator of trackability that automatically defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track3D provides a complete framework for unbiased studies of molecular processes in complex volumetric sequences.
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Affiliation(s)
- Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA; Aix Marseille University, CNRS, Centrale Marseille, I2M, Turing Centre for Living Systems, Marseille, France.
| | - Wesley R Legant
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Erik S Welf
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ana F David
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Eric Betzig
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
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6
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Chang BJ, Shepherd D, Fiolka R. Projective oblique plane structured illumination microscopy. bioRxiv 2023:2023.08.08.552447. [PMID: 37609312 PMCID: PMC10441343 DOI: 10.1101/2023.08.08.552447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Structured illumination microscopy (SIM) can double the spatial resolution of a fluorescence microscope and video rate live cell imaging in a two-dimensional format has been demonstrated. However, rapid implementations of 2D SIM typically only cover a narrow slice of the sample immediately at the coverslip, with most of the cellular volume out of reach. Here we implement oblique plane structured illumination microscopy (OPSIM) in a projection format to rapidly image an entire cell in a 2D SIM framework. As no mechanical scanning of the sample or objective is involved, this technique has the potential for rapid projection imaging with doubled resolution. We characterize the spatial resolution with fluorescent nanospheres, compare projection and 3D imaging using OPSIM and image mitochondria and ER dynamics across an entire cell at up to 2.7 Hz. To our knowledge, this represents the fastest whole cell SIM imaging to date.
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Affiliation(s)
- Bo-Jui Chang
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Douglas Shepherd
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ 82587, USA
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7
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Weems AD, Welf ES, Driscoll MK, Zhou FY, Mazloom-Farsibaf H, Chang BJ, Murali VS, Gihana GM, Weiss BG, Chi J, Rajendran D, Dean KM, Fiolka R, Danuser G. Blebs promote cell survival by assembling oncogenic signalling hubs. Nature 2023; 615:517-525. [PMID: 36859545 PMCID: PMC10881276 DOI: 10.1038/s41586-023-05758-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/25/2023] [Indexed: 03/03/2023]
Abstract
Most human cells require anchorage for survival. Cell-substrate adhesion activates diverse signalling pathways, without which cells undergo anoikis-a form of programmed cell death1. Acquisition of anoikis resistance is a pivotal step in cancer disease progression, as metastasizing cells often lose firm attachment to surrounding tissue2,3. In these poorly attached states, cells adopt rounded morphologies and form small hemispherical plasma membrane protrusions called blebs4-11. Bleb function has been thoroughly investigated in the context of amoeboid migration, but it has been examined far less in other scenarios12. Here we show by three-dimensional imaging and manipulation of cell morphological states that blebbing triggers the formation of plasma membrane-proximal signalling hubs that confer anoikis resistance. Specifically, in melanoma cells, blebbing generates plasma membrane contours that recruit curvature-sensing septin proteins as scaffolds for constitutively active mutant NRAS and effectors. These signalling hubs activate ERK and PI3K-well-established promoters of pro-survival pathways. Inhibition of blebs or septins has little effect on the survival of well-adhered cells, but in detached cells it causes NRAS mislocalization, reduced MAPK and PI3K activity, and ultimately, death. This unveils a morphological requirement for mutant NRAS to operate as an effective oncoprotein. Furthermore, whereas some BRAF-mutated melanoma cells do not rely on this survival pathway in a basal state, inhibition of BRAF and MEK strongly sensitizes them to both bleb and septin inhibition. Moreover, fibroblasts engineered to sustain blebbing acquire the same anoikis resistance as cancer cells even without harbouring oncogenic mutations. Thus, blebs are potent signalling organelles capable of integrating myriad cellular information flows into concerted cellular responses, in this case granting robust anoikis resistance.
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Affiliation(s)
- Andrew D Weems
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Erik S Welf
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Meghan K Driscoll
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Felix Y Zhou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Vasanth S Murali
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gabriel M Gihana
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Byron G Weiss
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joseph Chi
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Divya Rajendran
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
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8
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Segal D, Mazloom-Farsibaf H, Chang BJ, Roudot P, Rajendran D, Daetwyler S, Fiolka R, Warren M, Amatruda JF, Danuser G. In vivo 3D profiling of site-specific human cancer cell morphotypes in zebrafish. J Cell Biol 2022; 221:213501. [PMID: 36155740 PMCID: PMC9516844 DOI: 10.1083/jcb.202109100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 05/11/2022] [Accepted: 08/22/2022] [Indexed: 12/18/2022] Open
Abstract
Tissue microenvironments affect the functional states of cancer cells, but determining these influences in vivo has remained a challenge. We present a quantitative high-resolution imaging assay of single cancer cells in zebrafish xenografts to probe functional adaptation to variable cell-extrinsic cues and molecular interventions. Using cell morphology as a surrogate readout of cell functional states, we examine environmental influences on the morphotype distribution of Ewing Sarcoma, a pediatric cancer associated with the oncogene EWSR1-FLI1 and whose plasticity is thought to determine disease outcome through non-genomic mechanisms. Computer vision analysis reveals systematic shifts in the distribution of 3D morphotypes as a function of cell type and seeding site, as well as tissue-specific cellular organizations that recapitulate those observed in human tumors. Reduced expression of the EWSR1-FLI1 protein product causes a shift to more protrusive cells and decreased tissue specificity of the morphotype distribution. Overall, this work establishes a framework for a statistically robust study of cancer cell plasticity in diverse tissue microenvironments.
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Affiliation(s)
- Dagan Segal
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Hanieh Mazloom-Farsibaf
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Divya Rajendran
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
| | - Mikako Warren
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - James F Amatruda
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX.,Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX
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9
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Chen B, Chang BJ, Zhou FY, Daetwyler S, Sapoznik E, Nanes BA, Terrazas I, Gihana GM, Castro LP, Chan IS, Conacci-Sorrell M, Dean KM, Millett-Sikking A, York AG, Fiolka R. Increasing the field-of-view in oblique plane microscopy via optical tiling. Biomed Opt Express 2022; 13:5616-5627. [PMID: 36733723 PMCID: PMC9872888 DOI: 10.1364/boe.467969] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 05/20/2023]
Abstract
Fast volumetric imaging of large fluorescent samples with high-resolution is required for many biological applications. Oblique plane microscopy (OPM) provides high spatiotemporal resolution, but the field of view is typically limited by its optical train and the pixel number of the camera. Mechanically scanning the sample or decreasing the overall magnification of the imaging system can partially address this challenge, albeit by reducing the volumetric imaging speed or spatial resolution, respectively. Here, we introduce a novel dual-axis scan unit for OPM that facilitates rapid and high-resolution volumetric imaging throughout a volume of 800 × 500 × 200 microns. This enables us to perform volumetric imaging of cell monolayers, spheroids and zebrafish embryos with subcellular resolution. Furthermore, we combined this microscope with a multi-perspective projection imaging technique that increases the volumetric interrogation rate to more than 10 Hz. This allows us to rapidly probe a large field of view in a dimensionality reduced format, identify features of interest, and volumetrically image these regions with high spatiotemporal resolution.
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Affiliation(s)
- Bingying Chen
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Felix Y. Zhou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Etai Sapoznik
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Benjamin A Nanes
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Isabella Terrazas
- Department of Internal Medicine, Division of Hematology and Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Gabriel M. Gihana
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | - Isaac S. Chan
- Department of Internal Medicine, Division of Hematology and Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kevin M. Dean
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | | | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
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10
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Perez-Castro L, Venkateswaran N, Garcia R, Hao YH, Lafita-Navarro MC, Kim J, Segal D, Saponzik E, Chang BJ, Fiolka R, Danuser G, Xu L, Brabletz T, Conacci-Sorrell M. The AHR target gene scinderin activates the WNT pathway by facilitating the nuclear translocation of β-catenin. J Cell Sci 2022; 135:jcs260028. [PMID: 36148682 PMCID: PMC10658791 DOI: 10.1242/jcs.260028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/12/2022] [Indexed: 01/12/2023] Open
Abstract
The ligand-activated transcription factor aryl hydrocarbon receptor (AHR) regulates cellular detoxification, proliferation and immune evasion in a range of cell types and tissues, including cancer cells. In this study, we used RNA-sequencing to identify the signature of the AHR target genes regulated by the pollutant 2,3,7,8-tetrachlorodibenzodioxin (TCDD) and the endogenous ligand kynurenine (Kyn), a tryptophan-derived metabolite. This approach identified a signature of six genes (CYP1A1, ALDH1A3, ABCG2, ADGRF1 and SCIN) as commonly activated by endogenous or exogenous ligands of AHR in multiple colon cancer cell lines. Among these, the actin-severing protein scinderin (SCIN) was necessary for cell proliferation; SCIN downregulation limited cell proliferation and its expression increased it. SCIN expression was elevated in a subset of colon cancer patient samples, which also contained elevated β-catenin levels. Remarkably, SCIN expression promoted nuclear translocation of β-catenin and activates the WNT pathway. Our study identifies a new mechanism for adhesion-mediated signaling in which SCIN, likely via its ability to alter the actin cytoskeleton, facilitates the nuclear translocation of β-catenin. This article has an associated First Person interview with the first authors of the paper.
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Affiliation(s)
- Lizbeth Perez-Castro
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Roy Garcia
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi-Heng Hao
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - M. C. Lafita-Navarro
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dagan Segal
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Etai Saponzik
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gaudenz Danuser
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, Division of Hematology/Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas Brabletz
- Nikolaus-Fiebiger Center for Molecular Medicine, University Erlangen-Nurnberg, Erlangen 91054, Germany
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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11
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Liu H, Hiremath C, Patterson Q, Vora S, Shang Z, Jamieson AR, Fiolka R, Dean KM, Dellinger MT, Marciano DK. Heterozygous Mutation of Vegfr3 Reduces Renal Lymphatics without Renal Dysfunction. J Am Soc Nephrol 2021; 32:3099-3113. [PMID: 34551997 PMCID: PMC8638391 DOI: 10.1681/asn.2021010061] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/29/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Lymphatic abnormalities are observed in several types of kidney disease, but the relationship between the renal lymphatic system and renal function is unclear. The discovery of lymphatic-specific proteins, advances in microscopy, and available genetic mouse models provide the tools to help elucidate the role of renal lymphatics in physiology and disease. METHODS We utilized a mouse model containing a missense mutation in Vegfr3 (dubbed Chy ) that abrogates its kinase ability. Vegfr3 Chy/+ mice were examined for developmental abnormalities and kidney-specific outcomes. Control and Vegfr3 Chy/+ mice were subjected to cisplatin-mediated injury. We characterized renal lymphatics using tissue-clearing, light-sheet microscopy, and computational analyses. RESULTS In the kidney, VEGFR3 is expressed not only in lymphatic vessels but also, in various blood capillaries. Vegfr3 Chy/+ mice had severely reduced renal lymphatics with 100% penetrance, but we found no abnormalities in BP, serum creatinine, BUN, albuminuria, and histology. There was no difference in the degree of renal injury after low-dose cisplatin (5 mg/kg), although Vegfr3 Chy/+ mice developed perivascular inflammation. Cisplatin-treated controls had no difference in total cortical lymphatic volume and length but showed increased lymphatic density due to decreased cortical volume. CONCLUSIONS We demonstrate that VEGFR3 is required for development of renal lymphatics. Our studies reveal that reduced lymphatic density does not impair renal function at baseline and induces only modest histologic changes after mild injury. We introduce a novel quantification method to evaluate renal lymphatics in 3D and demonstrate that accurate measurement of lymphatic density in CKD requires assessment of changes to cortical volume.
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Affiliation(s)
- Hao Liu
- Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chitkale Hiremath
- Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Quinten Patterson
- Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Saumya Vora
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zhiguo Shang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Andrew R. Jamieson
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kevin M. Dean
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Michael T. Dellinger
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Denise K. Marciano
- Department of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
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12
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Chang BJ, Manton JD, Sapoznik E, Pohlkamp T, Terrones TS, Welf ES, Murali VS, Roudot P, Hake K, Whitehead L, York AG, Dean KM, Fiolka R. Real-time multi-angle projection imaging of biological dynamics. Nat Methods 2021; 18:829-834. [PMID: 34183831 PMCID: PMC9206531 DOI: 10.1038/s41592-021-01175-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/05/2021] [Indexed: 02/03/2023]
Abstract
We introduce a cost-effective and easily implementable scan unit that converts any camera-based microscope with optical sectioning capability into a multi-angle projection imaging system. Projection imaging reduces data overhead and accelerates imaging by a factor of >100, while also allowing users to readily view biological phenomena of interest from multiple perspectives on the fly. By rapidly interrogating the sample from just two perspectives, our method also enables real-time stereoscopic imaging and three-dimensional particle localization. We demonstrate projection imaging with spinning disk confocal, lattice light-sheet, multidirectional illumination light-sheet and oblique plane microscopes on specimens that range from organelles in single cells to the vasculature of a zebrafish embryo. Furthermore, we leverage our projection method to rapidly image cancer cell morphodynamics and calcium signaling in cultured neurons at rates up to 119 Hz as well as to simultaneously image orthogonal views of a beating embryonic zebrafish heart.
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Affiliation(s)
- Bo-Jui Chang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Etai Sapoznik
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Theresa Pohlkamp
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tamara S Terrones
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Erik S Welf
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vasanth S Murali
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Philippe Roudot
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kayley Hake
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Lachlan Whitehead
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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13
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Welf ES, Miles CE, Huh J, Sapoznik E, Chi J, Driscoll MK, Isogai T, Noh J, Weems AD, Pohlkamp T, Dean K, Fiolka R, Mogilner A, Danuser G. Actin-Membrane Release Initiates Cell Protrusions. Dev Cell 2020; 55:723-736.e8. [PMID: 33308479 DOI: 10.1016/j.devcel.2020.11.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/08/2020] [Accepted: 11/20/2020] [Indexed: 01/04/2023]
Abstract
Despite the well-established role of actin polymerization as a driving mechanism for cell protrusion, upregulated actin polymerization alone does not initiate protrusions. Using a combination of theoretical modeling and quantitative live-cell imaging experiments, we show that local depletion of actin-membrane links is needed for protrusion initiation. Specifically, we show that the actin-membrane linker ezrin is depleted prior to protrusion onset and that perturbation of ezrin's affinity for actin modulates protrusion frequency and efficiency. We also show how actin-membrane release works in concert with actin polymerization, leading to a comprehensive model for actin-driven shape changes. Actin-membrane release plays a similar role in protrusions driven by intracellular pressure. Thus, our findings suggest that protrusion initiation might be governed by a universal regulatory mechanism, whereas the mechanism of force generation determines the shape and expansion properties of the protrusion.
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Affiliation(s)
- Erik S Welf
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Christopher E Miles
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA; Department of Biology, New York University, New York, NY 10012, USA
| | - Jaewon Huh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Etai Sapoznik
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph Chi
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Meghan K Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew D Weems
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Theresa Pohlkamp
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alex Mogilner
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA; Department of Biology, New York University, New York, NY 10012, USA.
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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14
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Abstract
Annotation of time-lapse data provides an important tool to highlight dynamic processes. Particularly, arrows, circles and arrowheads are useful to pinpoint a specific process, stationary or evolving over time. Here, we describe a user-friendly Fiji plugin to facilitate annotation of movies with arrows, arrowheads and circles. The plugin also enables saving and loading of annotated tracks. This article has an associated First Person interview with the first author of the paper. Summary: We present a user-friendly Fiji plugin to annotate movies with custom arrows, thereby providing biologists with no coding experience an easy tool to highlight dynamic processes in their movies.
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Affiliation(s)
- Stephan Daetwyler
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, 75390, Texas, USA
| | - Carl D Modes
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, 01069 Dresden, Germany
| | - Reto Fiolka
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, 75390, Texas, USA.,Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, 75390, Texas, USA
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15
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Lomakin AJ, Cattin CJ, Cuvelier D, Alraies Z, Molina M, Nader GPF, Srivastava N, Sáez PJ, Garcia-Arcos JM, Zhitnyak IY, Bhargava A, Driscoll MK, Welf ES, Fiolka R, Petrie RJ, De Silva NS, González-Granado JM, Manel N, Lennon-Duménil AM, Müller DJ, Piel M. The nucleus acts as a ruler tailoring cell responses to spatial constraints. Science 2020; 370:eaba2894. [PMID: 33060332 PMCID: PMC8059074 DOI: 10.1126/science.aba2894] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/29/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022]
Abstract
The microscopic environment inside a metazoan organism is highly crowded. Whether individual cells can tailor their behavior to the limited space remains unclear. In this study, we found that cells measure the degree of spatial confinement by using their largest and stiffest organelle, the nucleus. Cell confinement below a resting nucleus size deforms the nucleus, which expands and stretches its envelope. This activates signaling to the actomyosin cortex via nuclear envelope stretch-sensitive proteins, up-regulating cell contractility. We established that the tailored contractile response constitutes a nuclear ruler-based signaling pathway involved in migratory cell behaviors. Cells rely on the nuclear ruler to modulate the motive force that enables their passage through restrictive pores in complex three-dimensional environments, a process relevant to cancer cell invasion, immune responses, and embryonic development.
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Affiliation(s)
- A J Lomakin
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences (ÖAW), Vienna, Austria
- Medical University of Vienna (MUV), Vienna, Austria
- Centre for Stem Cells and Regenerative Medicine, School of Basic and Medical Biosciences, King's College London, London, UK
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
| | - C J Cattin
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - D Cuvelier
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
| | - Z Alraies
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
- Institut Curie, PSL Research University, INSERM, U 932, Paris, France
| | - M Molina
- Centre for Stem Cells and Regenerative Medicine, School of Basic and Medical Biosciences, King's College London, London, UK
| | - G P F Nader
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
| | - N Srivastava
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
| | - P J Sáez
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
| | - J M Garcia-Arcos
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
| | - I Y Zhitnyak
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
- N.N. Blokhin Medical Research Center of Oncology, Moscow, Russia
| | - A Bhargava
- Institut Curie, PSL Research University, INSERM, U 932, Paris, France
| | - M K Driscoll
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E S Welf
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R J Petrie
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - N S De Silva
- Institut Curie, PSL Research University, INSERM, U 932, Paris, France
| | - J M González-Granado
- LamImSys Lab, Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre (imas12), Madrid, Spain
| | - N Manel
- Institut Curie, PSL Research University, INSERM, U 932, Paris, France
| | | | - D J Müller
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - M Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France.
- Institut Pierre Gilles de Gennes, PSL Research University, Paris, France
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16
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Chang BJ, Dean KM, Fiolka R. Systematic and quantitative comparison of lattice and Gaussian light-sheets. Opt Express 2020; 28:27052-27077. [PMID: 32906967 PMCID: PMC7679196 DOI: 10.1364/oe.400164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
The axial resolving power of a light-sheet microscope is determined by the thickness of the illumination beam and the numerical aperture of its detection optics. Bessel-beam based optical lattices have generated significant interest owing to their reportedly narrow beam waist and propagation-invariant characteristics. Yet, despite their significant use in lattice light-sheet microscopy and recent incorporation into commercialized systems, there are very few quantitative reports on their physical properties and how they compare to standard Gaussian illumination beams. Here, we measure the beam properties in the transmission of dithered square lattices, which is the most commonly used variant of lattice light-sheet microscopy, and Gaussian-based light-sheets. After a systematic analysis, we find that square lattices are very similar to Gaussian-based light-sheets in terms of thickness, confocal parameter, propagation length and overall imaging performance.
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Affiliation(s)
- Bo-Jui Chang
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Kevin M. Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
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17
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Chen B, Chakraborty T, Daetwyler S, Manton JD, Dean K, Fiolka R. Extended depth of focus multiphoton microscopy via incoherent pulse splitting. Biomed Opt Express 2020; 11:3830-3842. [PMID: 33014569 PMCID: PMC7510929 DOI: 10.1364/boe.393931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 06/01/2023]
Abstract
We present a beam splitter mask that can be easily added to a multiphoton raster scanning microscope to extend the depth of focus five-fold at a small loss in lateral resolution. The method is designed for ultrafast laser pulses or other light-sources featuring a low coherence length. In contrast to other methods of focus extension, our approach uniquely combines low complexity, high light-throughput and multicolor capability. We characterize the point spread function in a two-photon microscope and demonstrate fluorescence imaging of GFP labeled neurons in fixed brain samples as imaged with conventional and extended depth of focus two-photon microscopy.
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Affiliation(s)
- Bingying Chen
- Department of Cell Biology, University of
Texas Southwestern Medical Center, Dallas, TX 75390, USA
- These authors contributed equally to this
work
| | - Tonmoy Chakraborty
- Department of Cell Biology, University of
Texas Southwestern Medical Center, Dallas, TX 75390, USA
- These authors contributed equally to this
work
| | - Stephan Daetwyler
- Department of Cell Biology, University of
Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Kevin Dean
- Department of Cell Biology, University of
Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reto Fiolka
- Department of Cell Biology, University of
Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics,
University of Texas Southwestern Medical Center, Dallas, TX 75390,
USA
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18
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Segal D, Chang BJ, Mazloom-Farsibaf H, Fiolka R, Amatruda J, Danuser G. Abstract PHB01: The zebrafish as a mechanical filter: Using zebrafish xenografts to model Ewing sarcoma metastasis in vivo. Cancer Res 2020. [DOI: 10.1158/1538-7445.camodels2020-phb01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ewing Sarcoma (ES), a pediatric cancer driven by the oncogenic fusion protein EWS-FLI1, recurs or metastasizes in 1 in 3 patients with no clear correlation to accumulation of secondary mutations, raising the possibility that environmental cues may drive metastasis. Previous work in the field has observed distinct cellular morphologies of ES cells in cell culture as a function of EWS-FLI1 level and posited the idea that this may correlate with distinct functional cellular states.
In this work, we use zebrafish xenografts to investigate the effect of variable microenvironments on cellular morphologies of ES cells. We use high resolution light-sheet microscopy to focus on specific recurring seeding sites within the 3-day old zebrafish larvae. We then implement a unique cell-shape classification method to distinguish discrete 3D cellular morphologies in these datasets.
Using this workflow, we observe a variety of cellular morphologies within the fish, including elongated cellular protrusions, blebbing, and rounded cells. We demonstrate that ES cells take on distinct morphological states as a function of the region in which they reside. We find cell proliferation, but not cell death, vary greatly in the different regions, suggesting differences in the functional state of the ES cells. Interestingly, knockdown of EWS-FLI1 in xenografted cells leads to discrete switches between cellular morphologies, but only as a function of seeding site within the fish, suggesting a previously undescribed environmental cue that modulates cellular effects of EWS-FLI1. Overall, the xenograft model for ES in zebrafish embryos can be viewed as a “mechanical filter”, which provides unique, complex 3-dimensional environments to study cell behavior within an organism, while leveraging the advantages of the zebrafish system, namely higher throughput and high resolution in vivo imaging capabilities. This work establishes a pipeline for classification and distinction of morphological states within a living organism, and, more specifically, helps our understanding of cellular plasticity of ES cells in response to microenvironment.
Citation Format: Dagan Segal, Bo-Jui Chang, Hanieh Mazloom-Farsibaf, Reto Fiolka, James Amatruda, Gaudenz Danuser. The zebrafish as a mechanical filter: Using zebrafish xenografts to model Ewing sarcoma metastasis in vivo [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PHB01.
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Affiliation(s)
- Dagan Segal
- 1UT Southwestern Medical Center, Dallas, TX,
| | | | | | - Reto Fiolka
- 1UT Southwestern Medical Center, Dallas, TX,
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19
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Manton JD, Ströhl F, Fiolka R, Kaminski CF, Rees EJ. Concepts for structured illumination microscopy with extended axial resolution through mirrored illumination. Biomed Opt Express 2020; 11:2098-2108. [PMID: 32341869 PMCID: PMC7173891 DOI: 10.1364/boe.382398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 05/03/2023]
Abstract
Wide-field fluorescence microscopy, while much faster than confocal microscopy, suffers from a lack of optical sectioning and poor axial resolution. 3D structured illumination microscopy (SIM) has been demonstrated to provide optical sectioning and to double the resolution limit both laterally and axially, but even with this the axial resolution is still worse than the lateral resolution of unmodified wide-field microscopy. Interferometric schemes using two high numerical aperture objectives, such as 4Pi confocal and I5M microscopy, have improved the axial resolution beyond that of the lateral, but at the cost of a significantly more complex optical setup. Here, we theoretically and numerically investigate a simpler dual-objective scheme which we propose can be easily added to an existing 3D-SIM microscope, providing lateral and axial resolutions in excess of 125 nm with conventional fluorophores and without the need for interferometric detection.
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Affiliation(s)
- James D. Manton
- Department of Chemical Engineering & Biotechnology, University of Cambridge, CB3 0AS, UK
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Florian Ströhl
- Department of Chemical Engineering & Biotechnology, University of Cambridge, CB3 0AS, UK
- Present address: Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Reto Fiolka
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, USA
| | - Clemens F. Kaminski
- Department of Chemical Engineering & Biotechnology, University of Cambridge, CB3 0AS, UK
| | - Eric J. Rees
- Department of Chemical Engineering & Biotechnology, University of Cambridge, CB3 0AS, UK
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20
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Chakraborty T, Chen B, Daetwyler S, Chang BJ, Vanderpoorten O, Sapoznik E, Kaminski CF, Knowles TPJ, Dean KM, Fiolka R. Converting lateral scanning into axial focusing to speed up three-dimensional microscopy. Light Sci Appl 2020; 9:165. [PMID: 33024553 PMCID: PMC7501866 DOI: 10.1038/s41377-020-00401-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 05/04/2023]
Abstract
In optical microscopy, the slow axial scanning rate of the objective or the sample has traditionally limited the speed of volumetric imaging. Recently, by conjugating either a movable mirror to the image plane in a remote-focusing geometry or an electrically tuneable lens (ETL) to the back focal plane, rapid axial scanning has been achieved. However, mechanical actuation of a mirror limits the axial scanning rate (usually only 10-100 Hz for piezoelectric or voice coil-based actuators), while ETLs introduce spherical and higher-order aberrations that prevent high-resolution imaging. In an effort to overcome these limitations, we introduce a novel optical design that transforms a lateral-scan motion into a spherical aberration-free axial scan that can be used for high-resolution imaging. Using a galvanometric mirror, we scan a laser beam laterally in a remote-focusing arm, which is then back-reflected from different heights of a mirror in the image space. We characterize the optical performance of this remote-focusing technique and use it to accelerate axially swept light-sheet microscopy by an order of magnitude, allowing the quantification of rapid vesicular dynamics in three dimensions. We also demonstrate resonant remote focusing at 12 kHz with a two-photon raster-scanning microscope, which allows rapid imaging of brain tissues and zebrafish cardiac dynamics with diffraction-limited resolution.
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Affiliation(s)
- Tonmoy Chakraborty
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM USA
| | - Bingying Chen
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Stephan Daetwyler
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Bo-Jui Chang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Oliver Vanderpoorten
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS UK
| | - Etai Sapoznik
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS UK
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Kevin M. Dean
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Reto Fiolka
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
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21
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Chakraborty T, Driscoll MK, Jeffery E, Murphy MM, Roudot P, Chang BJ, Vora S, Wong WM, Nielson CD, Zhang H, Zhemkov V, Hiremath C, De La Cruz ED, Yi Y, Bezprozvanny I, Zhao H, Tomer R, Heintzmann R, Meeks JP, Marciano DK, Morrison SJ, Danuser G, Dean KM, Fiolka R. Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution. Nat Methods 2019; 16:1109-1113. [PMID: 31673159 PMCID: PMC6924633 DOI: 10.1038/s41592-019-0615-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/17/2019] [Indexed: 12/15/2022]
Abstract
We present cleared tissue Axially Swept Light-Sheet Microscopy (ctASLM), which enables isotropic, subcellular resolution, high optical sectioning capability, and large field of view imaging over a broad range of immersion media. ctASLM can image live, expanded, and both aqueous and organic chemically cleared tissue preparations. Depending on the optical configuration, ctASLM provides up to 260 nm axial resolution, an improvement over confocal and other reported cleared tissue light-sheet microscopes by a factor 3–10. We image millimeter-scale tissues with subcellular 3D resolution, which enabled us to automatically detect with computer vision multicellular tissue architectures, individual cells, synaptic spines, and rare cell-cell interactions.
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Affiliation(s)
- Tonmoy Chakraborty
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meghan K Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elise Jeffery
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Malea M Murphy
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Philippe Roudot
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Saumya Vora
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wen Mai Wong
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cara D Nielson
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vladimir Zhemkov
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chitkale Hiremath
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Yating Yi
- Department of Restorative Sciences, Texas A&M University, College Station, TX, USA
| | - Ilya Bezprozvanny
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hu Zhao
- Department of Restorative Sciences, Texas A&M University, College Station, TX, USA
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, NY, USA.,NeuroTechnology Center, Columbia University, New York, NY, USA.,Data Science Institute, Columbia University, New York, NY, USA
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
| | - Julian P Meeks
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Denise K Marciano
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean J Morrison
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gaudenz Danuser
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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22
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Murali VS, Chang BJ, Fiolka R, Danuser G, Cobanoglu MC, Welf ES. An image-based assay to quantify changes in proliferation and viability upon drug treatment in 3D microenvironments. BMC Cancer 2019; 19:502. [PMID: 31138163 PMCID: PMC6537405 DOI: 10.1186/s12885-019-5694-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 05/08/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Every biological experiment requires a choice of throughput balanced against physiological relevance. Most primary drug screens neglect critical parameters such as microenvironmental conditions, cell-cell heterogeneity, and specific readouts of cell fate for the sake of throughput. METHODS Here we describe a methodology to quantify proliferation and viability of single cells in 3D culture conditions by leveraging automated microscopy and image analysis to facilitate reliable and high-throughput measurements. We detail experimental conditions that can be adjusted to increase either throughput or robustness of the assay, and we provide a stand alone image analysis program for users who wish to implement this 3D drug screening assay in high throughput. RESULTS We demonstrate this approach by evaluating a combination of RAF and MEK inhibitors on melanoma cells, showing that cells cultured in 3D collagen-based matrices are more sensitive than cells grown in 2D culture, and that cell proliferation is much more sensitive than cell viability. We also find that cells grown in 3D cultured spheroids exhibit equivalent sensitivity to single cells grown in 3D collagen, suggesting that for the case of melanoma, a 3D single cell model may be equally effective for drug identification as 3D spheroids models. The single cell resolution of this approach enables stratification of heterogeneous populations of cells into differentially responsive subtypes upon drug treatment, which we demonstrate by determining the effect of RAK/MEK inhibition on melanoma cells co-cultured with fibroblasts. Furthermore, we show that spheroids grown from single cells exhibit dramatic heterogeneity to drug response, suggesting that heritable drug resistance can arise stochastically in single cells but be retained by subsequent generations. CONCLUSION In summary, image-based analysis renders cell fate detection robust, sensitive, and high-throughput, enabling cell fate evaluation of single cells in more complex microenvironmental conditions.
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Affiliation(s)
- Vasanth S. Murali
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
| | - Bo-Jui Chang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Reto Fiolka
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
| | - Gaudenz Danuser
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
| | - Murat Can Cobanoglu
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
| | - Erik S. Welf
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
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23
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Dean KM, Roudot P, Welf ES, Pohlkamp T, Garrelts G, Herz J, Fiolka R. Imaging Subcellular Dynamics with Fast and Light-Efficient Volumetrically Parallelized Microscopy. Optica 2017; 4:263-271. [PMID: 28944279 PMCID: PMC5609504 DOI: 10.1364/optica.4.000263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In fluorescence microscopy, the serial acquisition of 2D images to form a 3D volume limits the maximum imaging speed. This is particularly evident when imaging adherent cells in a light-sheet fluorescence microscopy format, as their elongated morphologies require ~200 image planes per image volume. Here, by illuminating the specimen with three light-sheets, each independently detected, we present a light-efficient, crosstalk free, and volumetrically parallelized 3D microscopy technique that is optimized for high-speed (up to 14 Hz) subcellular (300 nm lateral, 600 nm axial resolution) imaging of adherent cells. We demonstrate 3D imaging of intracellular processes, including cytoskeletal dynamics in single cell migration and collective wound healing for 1500 and 1000 time points, respectively. Further, we capture rapid biological processes, including trafficking of early endosomes with velocities exceeding 10 microns per second and calcium signaling in primary neurons.
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Affiliation(s)
- Kevin M. Dean
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Lyda Hill Department of Bioinformatics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Philippe Roudot
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Lyda Hill Department of Bioinformatics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Erik S. Welf
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Lyda Hill Department of Bioinformatics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Theresa Pohlkamp
- Department of Molecular Genetics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Gerard Garrelts
- Coleman Technologies. 5131 West Chester Pike, Newtown Square, Pennsylvania, United States of America
| | - Joachim Herz
- Department of Molecular Genetics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Reto Fiolka
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Corresponding author:
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24
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Abstract
In Total Internal Reflection Fluorescence (TIRF) microscopy, the sample is illuminated with an evanescent field that yields a thin optical section. However, its widefield detection has no rejection mechanism against out-of-focus blur from scattered light that can compromise TIRF images. Here I demonstrate that via structured illumination, out-of-focus blur can be effectively suppressed in TIRF microscopy, yielding strikingly clearer images. The same mechanism can also be applied to oblique illumination schemes that extend the reach of TIRF microscopy beyond the basal surface of the cell. The two imaging modes are used to image a biosensor, clathrin coated vesicles and the actin cytoskeleton in different cell types with improved contrast.
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25
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Welf ES, Driscoll MK, Dean KM, Schäfer C, Chu J, Davidson MW, Lin MZ, Danuser G, Fiolka R. Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments. Dev Cell 2016; 36:462-75. [PMID: 26906741 DOI: 10.1016/j.devcel.2016.01.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 11/11/2015] [Accepted: 01/26/2016] [Indexed: 12/30/2022]
Abstract
The microenvironment determines cell behavior, but the underlying molecular mechanisms are poorly understood because quantitative studies of cell signaling and behavior have been challenging due to insufficient spatial and/or temporal resolution and limitations on microenvironmental control. Here we introduce microenvironmental selective plane illumination microscopy (meSPIM) for imaging and quantification of intracellular signaling and submicrometer cellular structures as well as large-scale cell morphological and environmental features. We demonstrate the utility of this approach by showing that the mechanical properties of the microenvironment regulate the transition of melanoma cells from actin-driven protrusion to blebbing, and we present tools to quantify how cells manipulate individual collagen fibers. We leverage the nearly isotropic resolution of meSPIM to quantify the local concentration of actin and phosphatidylinositol 3-kinase signaling on the surfaces of cells deep within 3D collagen matrices and track the many small membrane protrusions that appear in these more physiologically relevant environments.
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Affiliation(s)
- Erik S Welf
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Meghan K Driscoll
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Claudia Schäfer
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Chu
- Departments of Bioengineering and Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Michael W Davidson
- National High Magnetic Field Laboratory, Department of Biological Science, Florida State University, Tallahassee, FL 32310, USA
| | - Michael Z Lin
- Departments of Bioengineering and Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Gaudenz Danuser
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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26
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Dean KM, Roudot P, Welf ES, Danuser G, Fiolka R. Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy. Biophys J 2016; 108:2807-15. [PMID: 26083920 PMCID: PMC4472079 DOI: 10.1016/j.bpj.2015.05.013] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 11/30/2022] Open
Abstract
The use of propagation invariant Bessel beams has enabled high-resolution subcellular light sheet fluorescence microscopy. However, the energy within the concentric side lobe structure of Bessel beams increases significantly with propagation length, generating unwanted out-of-focus fluorescence that enforces practical limits on the imaging field of view size. Here, we present a light sheet fluorescence microscope that achieves 390 nm isotropic resolution and high optical sectioning strength (i.e., out-of-focus blur is strongly suppressed) over large field of views, without the need for structured illumination or deconvolution-based postprocessing. We demonstrate simultaneous dual-color, high-contrast, and high-dynamic-range time-lapse imaging of migrating cells in complex three-dimensional microenvironments, three-dimensional tracking of clathrin-coated pits, and long-term imaging spanning >10 h and encompassing >2600 time points.
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Affiliation(s)
- Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Philippe Roudot
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Erik S Welf
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Gaudenz Danuser
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas.
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27
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Fiolková K, Biringer K, Hrtánková M, Fiolka R, Danko J. [Coeliac disease as a possible cause of some gynecological and obstetric abnormalities]. Ceska Gynekol 2016; 81:470-476. [PMID: 27918167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To bring a review of available literature sources on the prevalence of coeliac disease and its possible impact on gynecological and obstetric disorders. DESIGN Review article. SETTING Gynecology and Obstetrics Clinic, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia. METHODS Analysis of literary sources. CONCLUSION Coeliac disease is an autoimmune enteropathy caused by abnormal immune system response to gluten. Over the last decade when the prevalence of the disease increases rapidly confirming the relationship between coeliac disease and a range of reproductive disorders. Problems in this area are mostly confirmed in untreated women. Among the atypical symptoms of coeliac disease also include infertility such as delayed onset of menstruation, early menopause, secondary amenorrhea, infertility and pregnancy complications, such as recurrent abortions, intrauterine fetal growth restriction, small fetus for gestational age, low birth weight and premature birth.
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28
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Abstract
Light-sheet fluorescence microscopy (LSFM) affords highly parallelized 3D imaging with optical sectioning capability and minimal light exposure. However, using Gaussian beams for light-sheet generation results in a trade-off between beam waist thickness and the area over which the beam can approximate a light-sheet. Here, we present a novel form of LSFM that uses incoherent extended focusing to produce divergence free light-sheets with near diffraction-limited resolution and uniform intensity distribution along the propagation direction. We demonstrate the imaging performance of the new technique by volumetric imaging of beads, collagen fibers, and melanoma cancer cells with sub-cellular resolution.
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29
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Abstract
Structured illumination microscopy can achieve super-resolution in fluorescence imaging. The sample is illuminated with periodic light patterns, and a series of images are acquired for different pattern positions, also called phases. From these a super-resolution image can be computed. However, for an artefact-free reconstruction it is important that the pattern phases be known with very high precision. If the necessary precision cannot be guaranteed experimentally, the phase information has to be retrieved a posteriori from the acquired data. We present a fast and robust algorithm that iteratively determines these phases with a precision of typically below λ/100. Our method, which is based on cross-correlations, allows optimisation of pattern phase even when the pattern itself is too fine for detection, in which case most other methods inevitably fail. We analyse the performance of this method using simulated data from a synthetic 2D sample as well as experimental single-slice data from a 3D sample and compare it with another previously published approach.
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Affiliation(s)
- Kai Wicker
- Institute of Physical Chemistry, Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, Germany.
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30
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Abstract
Ultrasound pulse guided digital phase conjugation has emerged to realize fluorescence imaging inside random scattering media. Its major limitation is the slow imaging speed, as a new wavefront needs to be measured for each voxel. Therefore 3D or even 2D imaging can be time consuming. For practical applications on biological systems, we need to accelerate the imaging process by orders of magnitude. Here we propose and experimentally demonstrate a parallel wavefront measurement scheme towards such a goal. Multiple focused ultrasound pulses of different carrier frequencies can be simultaneously launched inside a scattering medium. Heterodyne interferometry is used to measure all of the wavefronts originating from every sound focus in parallel. We use these wavefronts in sequence to rapidly excite fluorescence at all the voxels defined by the focused ultrasound pulses. In this report, we employed a commercially available sound transducer to generate two sound foci in parallel, doubled the wavefront measurement speed, and reduced the mechanical scanning steps of the sound transducer to half.
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Affiliation(s)
- Reto Fiolka
- Howard Hughes Medical Institute’s Janelia Farm Research Campus 19700 Helix Drive, Ashburn, VA 20147, USA
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31
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Si K, Fiolka R, Cui M. Breaking the spatial resolution barrier via iterative sound-light interaction in deep tissue microscopy. Sci Rep 2012; 2:748. [PMID: 23087813 PMCID: PMC3475990 DOI: 10.1038/srep00748] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/24/2012] [Indexed: 01/01/2023] Open
Abstract
Optical microscopy has so far been restricted to superficial layers, leaving many important biological questions unanswered. Random scattering causes the ballistic focus, which is conventionally used for image formation, to decay exponentially with depth. Optical imaging beyond the ballistic regime has been demonstrated by hybrid techniques that combine light with the deeper penetration capability of sound waves. Deep inside highly scattering media, the sound focus dimensions restrict the imaging resolutions. Here we show that by iteratively focusing light into an ultrasound focus via phase conjugation, we can fundamentally overcome this resolution barrier in deep tissues and at the same time increase the focus to background ratio. We demonstrate fluorescence microscopy beyond the ballistic regime of light with a threefold improved resolution and a fivefold increase in contrast. This development opens up practical high resolution fluorescence imaging in deep tissues.
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Affiliation(s)
- Ke Si
- Howard Hughes Medical Institute, Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
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32
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Visnovsky J, Fiolka R, Dokus K, Kúdela E, Danko J. M030 CHLAMYDIA INFECTIONS IN RELATION TO STERILITY AND INFERTILITY. Int J Gynaecol Obstet 2012. [DOI: 10.1016/s0020-7292(12)61224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Abstract
Fluorescence imaging has revolutionized biomedical research over the past three decades. Its high molecular specificity and unrivaled single molecule level sensitivity have enabled breakthroughs in a variety of research fields. For in vivo applications, its major limitation is the superficial imaging depth as random scattering in biological tissues causes exponential attenuation of the ballistic component of a light wave. Here we present fluorescence imaging beyond the ballistic regime by combining single cycle pulsed ultrasound modulation and digital optical phase conjugation. We demonstrate a near isotropic 3D localized sound-light interaction zone. With the exceptionally high optical gain provided by the digital optical phase conjugation system, we can deliver sufficient optical power to a focus inside highly scattering media for not only fluorescence imaging but also a variety of linear and nonlinear spectroscopy measurements. This technology paves the way for many important applications in both fundamental biology research and clinical studies.
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Affiliation(s)
| | | | - Meng Cui
- Correspondence and request for materials should be addressed to Meng Cui, 571-209-4136
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34
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Cul'bová M, Lasabová Z, Stanclová A, Tilandyová P, Zúbor P, Fiolka R, Danko J, Visnovský J. [Methylation of selected tumor-supressor genes in benign and malignant ovarian tumors]. Ceska Gynekol 2011; 76:274-279. [PMID: 22026068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To evaluate the usefullness of examination of methylation status of selected tumor-supressor genes in early diagnosis of ovarian cancer. DESIGN Prospective clinical study. SETTING Department of Gynecology and Obstetrics, Department of Molecular Biology, Jessenius Medical Faculty, Commenius University, Martin, Slovak Republic. METHODS In this study we analyzed hypermethylation of 5 genes RASSF1A, GSTP, E-cadherin, p16 and APC in ovarian tumor samples from 34 patients - 13 patients with epithelial ovarian cancer, 2 patients with border-line ovarian tumors, 12 patients with benign lesions of ovaries and 7 patients with healthy ovarian tissue. The methylation status of promoter region of tumor-supressor genes was determined by Methylation Specific Polymerase Chain Reaction (MSP) using a nested two-step approach with bisulfite modified DNA template and specific primers. RESULTS Gene methylation analysis revealed hypermethylation of gene RASSF1A (46%) and GSTP (8%) only in malignant ovarian tissue samples. Ecad, p16 and APC genes were methylated both in maignant and benign tissue samples. Methylation positivity in observed genes was present independently to all clinical stages of ovarian cancer and to tumor grades. However, there was observed a trend of increased number and selective involvement of methylated genes with increasing disease stages. Furthermore, there was no association between positive methylation status and histological subtypes of ovarian carcinomas. CONCLUSION RASSF1A and GSTP promoter methylation positivity is associated with ovarian cancer. The revealed gene-selective methylation positivity and the increased number of methylated genes with advancing disease stages could be considered as a useful molecular marker for early detection of ovarian cancer. However, there is need to find diagnostic approach of specifically and frequently methylated genes to determining a methylation phenotype for early detection of ovarian malignancies.
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Affiliation(s)
- M Cul'bová
- Gynekologicko-pôrodnícka klinika JLF UK a UNM, Martin.
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35
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Abstract
We present a novel microscopy technique to measure the scattered wavefront emitted from an optically transparent microscopic object. The complex amplitude is decoded via phase stepping in a common-path interferometer, enabling high mechanical stability. We demonstrate theoretically and practically that the incoherent summation of multiple illumination directions into a single image increases the resolving power and facilitates image reconstruction in diffraction tomography. We propose a slice-by-slice object-scatter extraction algorithm entirely based in real space in combination with ordinary z-stepping. Thereby the computational complexity affiliated with tomographic methods is significantly reduced. Using the first order Born approximation for weakly scattering objects it is possible to obtain estimates of the scattering density from the exitwaves.
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Affiliation(s)
- Reto Fiolka
- Nanotechnology Group, Department of Mechanical and Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
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36
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Abstract
We present a polymeric optical phase retarder that is electrically tunable by a dielectric elastomer actuator. The soft material device affords a large tuning range (14pi at lambda=488 nm) combined with high accuracy in optical path length and low drift rate (8.3 nm/min). Furthermore, the phase retarder is not sensitive to polarization, introduces a wavefront distortion<lambda/30, and tolerates high power densities (>141 kW/cm2). We show the dynamics for periodic phase modulation and demonstrate a simple drive technique for fast phase stepping. The polymer-based device is inexpensive, easy to fabricate, and its design can be adapted to specific applications.
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Affiliation(s)
- Markus Beck
- Nanotechnology Group, Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
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Visnovsky J, Zubor P, Galo S, Klobusiaková D, Fiolka R, Kajo K. [Validity of hysteroscopy in clinical setting: single centre analysis of 605 consecutive hysteroscopies]. Ceska Gynekol 2008; 73:365-369. [PMID: 19170372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
OBJECTIVE Hysteroscopy represent standard diagnostic and therapeutic method in the treatment of endometrial pathology, where patient selection for this procedure depends in majority on preoperative uterine ultrasound scan. Hysteroscopy can be used for removal of polyps or myomas, endometrial tumor resection, synechiolysis, sterilisation or removal of remnants from pregnancy. Hysteroscopic surgery can be also an option for patients who wish to preserve the uterus for the treatment of recurrent bleeding. We aimed to evaluate the validity, complication rate and accuracy of hysteroscopy in correlation with preoperative ultrasound and postoperative histopathological findings. SETTING Department of Gynecology and Obstetrics, Jessenius Medical Faculty, Commenius University, Martin, Slovak Republic. SUBJECT AND METHOD Retrospective analysis of hysteroscopies for period of 24 months. RESULTS During study period a total of 605 hysteroscopies were performed. In three (0.5%) cases we did not acquired sufficient bioptic material required for histopathological diagnosis, thus only 602 cases were included in the final analyses. The most frequent indication for hysteroscopy was history of postmenopausal bleeding (35.88%), followed by endometrial polyp (30.9%), hyperplasia (28.24%), cervical polyp (2.32%), corpus alienum in the uterus (1.66%) and fertility disorders (1%). Multifactorial analysis of hysteroscopy, ultrasound and histopathological findings revealed 69.41% sensitivity rate for ultrasound finding of endometrial hyperplasia, 48.16% sensitivity rate for submucous myoma and 81.72% sensitivity for endometrial polyp. The last group of patients showed the highest correlation rate (r)=0.41, p<0.01. The false pozitivity of preoperative ultrasound was 30.59%, 51.84% and 18.28% for mentioned groups, respectively. The association between hysteroscopic and histopathological results showed a 97.1% agreement in patients with endometrial polyp and 89.3% agreement for cases with endometrial hyperplasia (p<0.05). In 66.45% was hysteroscopy associated with biopsy or curretage. The causally surgery (tumor or endometrium ablation, myoma or septum resection) was performed in 27.9% and in 5.65% others types of intrauterine hysteroscopic sugery were done. Out of all surgical procedures polyp ablation represented 63.2%, resection of submucous fibroids 21.2%, endometrial resection or ablation 7.2% and 8.4% others procedures. In studied population we diagnosed 18 (3%) cases of endometrial carcinoma (13 cases associated with hyperplasia, 5 with polyp). Complication rate was 0.66%. Diagnostic hysteroscopic procedures were associated with a significantly lower complication rate (0.19%) than operative procedures (0.82%; p<0.05). The most frequent surgical complication was perforation of the uterine cavity (three cases 0.50%), followed by fluid overload syndrome (0.17%). CONCLUSION Hysteroscopy is safe diagnostic and operative method with high sensitivity, particularly for endometrial polyps. The validity of sonography in case of hyperplasia prior surgery could be improved by control uterine ultrasound scan reflecting cycle phase one-two days before surgery.
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Affiliation(s)
- J Visnovsky
- Gynekologicko-pôrodnícka klinika JLF UK a MFN, Martin, Slovenská republika.
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Münzenberg C, Rossi A, Feldman K, Fiolka R, Stemmer A, Kita-Tokarczyk K, Meier W, Sakamoto J, Lukin O, Schlüter A. Synthesis of Compounds Presenting Three and Four Anthracene Units as Potential Connectors To Mediate Infinite Lateral Growth at the Air/Water Interface. Chemistry 2008; 14:10797-807. [DOI: 10.1002/chem.200800478] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fiolka R, Beck M, Stemmer A. Structured illumination in total internal reflection fluorescence microscopy using a spatial light modulator. Opt Lett 2008; 33:1629-31. [PMID: 18628820 DOI: 10.1364/ol.33.001629] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In wide-field fluorescence microscopy, illuminating the specimen with evanescent standing waves increases lateral resolution more than twofold. We report a versatile setup for standing-wave illumination in total internal reflection fluorescence microscopy. An adjustable diffraction grating written on a phase-only spatial light modulator controls the illumination field. Selecting appropriate diffraction orders and displaying a sheared (tilted) diffraction grating allows one to tune the penetration depth in very fine steps. The setup achieves 91 nm lateral resolution for green emission.
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Affiliation(s)
- Reto Fiolka
- Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
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Abstract
In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode.
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Affiliation(s)
- R Fiolka
- Nanotechnology Group, ETH Zurich, Tannenstrasse 3, CH-8092 Zurich, Switzerland
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Abstract
We present a novel slit scanning confocal microscope with a CCD camera image sensor and a virtual slit aperture for descanning that can be adjusted during post-processing. A very efficient data structure and mathematical criteria for aligning the virtual aperture guarantee the ease of use. We further introduce a method to reduce the anisotropic lateral resolution of slit scanning microscopes. System performance is evaluated against a spinning disk confocal microscope on identical specimens. The virtual slit scanning microscope works as the spinning disk type and outperforms on thick specimens.
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Affiliation(s)
- Reto Fiolka
- Nanotechnology Group, ETH Zurich, Tannenstrasse 3, 8092, Zurich, Switzerland
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