[ { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ckx23-fcn21", "eprint_id": 122065, "eprint_status": "archive", "datestamp": "2024-01-09 20:10:24", "lastmod": "2024-01-10 16:56:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Haomin", "name": { "family": "Wang", "given": "Haomin" }, "orcid": "0000-0001-7193-8651" }, { "id": "Lee-Dongkwan", "name": { "family": "Lee", "given": "Dongkwan" }, "orcid": "0000-0001-6091-1349" }, { "id": "Cao-Yulu", "name": { "family": "Cao", "given": "Yulu" } }, { "id": "Bi-Xiaotian", "name": { "family": "Bi", "given": "Xiaotian" }, "orcid": "0000-0003-4449-7488" }, { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" }, "orcid": "0000-0003-2693-834X" }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Bond-selective fluorescence imaging with single-molecule sensitivity", "ispublished": "pub", "full_text_status": "public", "keywords": "Atomic and Molecular Physics, and Optics; Electronic, Optical and Magnetic Materials", "note": "\u00a9 The Author(s), under exclusive licence to Springer Nature Limited 2023. \n\nWe thank Caltech Beckman Institute Laser Resource Center (BILRC) and the Office of Laboratory Animal Resources (OLAR) for research resources. We thank M. Okumura and S. Cushing for kindly sharing research resources. We thank X. Tao and T. Begusic for calculating the Frank\u2013Condon factors and A. Colazo and P. Kocheril for helpful discussions. This work is supported by an NIH Director's New Innovator Award (DP2 GM140919-01 for L.W.) and an Alfred P. Sloan Research Fellowship (L.W.). L.W. is a Heritage Principal Investigator supported by the Heritage Medical Research Institute at Caltech. \n\nThese authors contributed equally: Haomin Wang, Dongkwan Lee. \n\nContributions. H.W., D.L. and L.W. conceived and designed the research. H.W. and D.L. built the BonFIRE set-up and performed solution measurements. H.W. wrote the LabVIEW scripts and conducted single-molecule measurements. D.L. conducted biological sample preparation and bioimaging experiments. H.W., D.L. and Y.C. collected and analysed the data. X.B. and K.M. helped provide cell, neuronal and brain tissue samples. J.D. synthesized BF dyes. L.W. supervised the experiments. The manuscript was written by H.W., D.L. and L.W., with input from all authors. \n\nData availability. The minimum dataset necessary to reproduce the results is available from the corresponding author. \n\nCode availability. The codes for experimental data acquisition, physical model simulation and Franck\u2013Condon factor calculation are available from the corresponding author. \n\nThe authors have filed a provisional patent application (63/462,131) based on this work.\n\n
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", "abstract": "Bioimaging harnessing optical contrasts and chemical specificity is of vital importance in probing complex biology. Vibrational spectroscopy based on mid-infrared excitation can reveal rich chemical information about molecular distributions. However, its full potential for bioimaging is hindered by the achievable sensitivity. Here we report bond-selective fluorescence-detected infrared-excited (BonFIRE) spectro-microscopy. BonFIRE employs two-photon excitation in the mid- and near-infrared to upconvert vibrational excitations to electronic states for fluorescence detection, thus encoding vibrational information into fluorescence. The system utilizes tunable narrowband picosecond pulses to ensure high sensitivity, biocompatibility and robustness for bond-selective biological interrogations over a wide spectrum of reporter molecules. We demonstrate BonFIRE spectral imaging in both fingerprint and cell-silent spectroscopic windows with single-molecule sensitivity for common fluorescent dyes. We then demonstrate BonFIRE imaging on various intracellular targets in fixed and live cells, neurons and tissues, with promise for further vibrational multiplexing. For dynamic bioanalysis in living systems, we implement a high-frequency modulation scheme and demonstrate time-lapse BonFIRE microscopy of live HeLa cells. We expect BonFIRE to expand the bioimaging toolbox by providing a new level of bond-specific vibrational information and facilitate functional imaging and sensing for biological investigations.", "date": "2023-10", "date_type": "published", "publication": "Nature Photonics", "volume": "17", "number": "10", "publisher": "Nature Publishing Group", "pagerange": "846-855", "id_number": "CaltechAUTHORS:20230630-744789000.1", "issn": "1749-4885", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230630-744789000.1", "funders": { "items": [ { "agency": "NIH", "grant_number": "DP2 GM140919-01" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Heritage Medical Research Institute" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1038/s41566-023-01243-8", "pmcid": "PMC10756635", "primary_object": { "basename": "nihms-1943181.pdf", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/nihms-1943181.pdf" }, "related_objects": [ { "basename": "41566_2023_1243_Fig10_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig10_ESM.jpg" }, { "basename": "41566_2023_1243_Fig11_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig11_ESM.jpg" }, { "basename": "41566_2023_1243_Fig13_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig13_ESM.jpg" }, { "basename": "41566_2023_1243_Fig15_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig15_ESM.jpg" }, { "basename": "41566_2023_1243_Fig12_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig12_ESM.jpg" }, { "basename": "41566_2023_1243_Fig14_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig14_ESM.jpg" }, { "basename": "41566_2023_1243_Fig7_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig7_ESM.jpg" }, { "basename": "41566_2023_1243_Fig8_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig8_ESM.jpg" }, { "basename": "41566_2023_1243_Fig9_ESM.jpg", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_Fig9_ESM.jpg" }, { "basename": "41566_2023_1243_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/ckx23-fcn21/files/41566_2023_1243_MOESM1_ESM.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Wang, Haomin; Lee, Dongkwan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rhdcj-29j60", "eprint_id": 122456, "eprint_status": "archive", "datestamp": "2023-08-22 21:22:15", "lastmod": "2023-10-20 20:34:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" }, "orcid": "0000-0001-8490-6413" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Raman Imaging Reveals Insights into Membrane Phase Biophysics in Cells", "ispublished": "pub", "full_text_status": "public", "keywords": "Materials Chemistry; Surfaces, Coatings and Films; Physical and Theoretical Chemistry", "note": "\u00a9 2023 American Chemical Society. \n\nW.M. acknowledges the support from National Institute of Health (R01 EB029523) and Multi-University Research Initiative (MURI) of the Air Force Office of Scientific Research (FA9550-21-1-0170). This project has been made possible in part by Grant Number 2023-321166 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. L.W. is a Heritage Principal Investigator supported by the Heritage Medical Research Institute at the California Institute of Technology.", "abstract": "Cellular membranes are essential components of all living organisms. They are composed of a complex mixture of lipids with diverse chemical structures and crucial biological functions. The dynamic and heterogeneous nature of cellular membranes presents a challenge for studying their biophysical properties and organization in vivo. Raman imaging, particularly coherent Raman scattering techniques such as stimulated Raman scattering (SRS) microscopy, have emerged as powerful tools for studying cellular membranes with high spatial and temporal resolution and minimal perturbation. In this Review, we discuss the scientific importance and technical challenges of characterizing membrane composition in cellular contexts and how the advances of Raman imaging can provide unique insights into membrane phase behavior and organization. We also highlight recent applications of Raman imaging in studying cellular membranes and implications in diseases. In particular, the discovery of phase separation and a solid-phase intracellular membrane on endoplasmic reticulum is reviewed in detail, shedding light on the biology of lipotoxicity.", "date": "2023-07-11", "date_type": "published", "publication": "Journal of Physical Chemistry B", "volume": "127", "number": "28", "publisher": "American Chemical Society", "pagerange": "6233-6240", "id_number": "CaltechAUTHORS:20230725-856924000.24", "issn": "1520-6106", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230725-856924000.24", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 EB029523" }, { "agency": "Air Force Office of Scientific Research (AFOSR)", "grant_number": "FA9550-21-1-0170" }, { "agency": "Chan Zuckerberg Initiative", "grant_number": "2023-321166" }, { "agency": "Silicon Valley Community Foundation" }, { "agency": "Heritage Medical Research Institute" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" } ] }, "doi": "10.1021/acs.jpcb.3c03125", "resource_type": "article", "pub_year": "2023", "author_list": "Shen, Yihui; Wei, Lu; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bhmhk-wbp71", "eprint_id": 122065, "eprint_status": "archive", "datestamp": "2023-08-22 21:16:40", "lastmod": "2023-10-20 16:56:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Haomin", "name": { "family": "Wang", "given": "Haomin" }, "orcid": "0000-0001-7193-8651" }, { "id": "Lee-Dongkwan", "name": { "family": "Lee", "given": "Dongkwan" }, "orcid": "0000-0001-6091-1349" }, { "id": "Cao-Yulu", "name": { "family": "Cao", "given": "Yulu" } }, { "id": "Bi-Xiaotian", "name": { "family": "Bi", "given": "Xiaotian" }, "orcid": "0000-0003-4449-7488" }, { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" }, "orcid": "0000-0003-2693-834X" }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Bond-selective fluorescence imaging with single-molecule sensitivity", "ispublished": "pub", "full_text_status": "public", "keywords": "Atomic and Molecular Physics, and Optics; Electronic, Optical and Magnetic Materials", "note": "\u00a9 The Author(s), under exclusive licence to Springer Nature Limited 2023. \n\nWe thank Caltech Beckman Institute Laser Resource Center (BILRC) and the Office of Laboratory Animal Resources (OLAR) for research resources. We thank M. Okumura and S. Cushing for kindly sharing research resources. We thank X. Tao and T. Begusic for calculating the Frank\u2013Condon factors and A. Colazo and P. Kocheril for helpful discussions. This work is supported by an NIH Director's New Innovator Award (DP2 GM140919-01 for L.W.) and an Alfred P. Sloan Research Fellowship (L.W.). L.W. is a Heritage Principal Investigator supported by the Heritage Medical Research Institute at Caltech. \n\nThese authors contributed equally: Haomin Wang, Dongkwan Lee. \n\nContributions. H.W., D.L. and L.W. conceived and designed the research. H.W. and D.L. built the BonFIRE set-up and performed solution measurements. H.W. wrote the LabVIEW scripts and conducted single-molecule measurements. D.L. conducted biological sample preparation and bioimaging experiments. H.W., D.L. and Y.C. collected and analysed the data. X.B. and K.M. helped provide cell, neuronal and brain tissue samples. J.D. synthesized BF dyes. L.W. supervised the experiments. The manuscript was written by H.W., D.L. and L.W., with input from all authors. \n\nData availability. The minimum dataset necessary to reproduce the results is available from the corresponding author. \n\nCode availability. The codes for experimental data acquisition, physical model simulation and Franck\u2013Condon factor calculation are available from the corresponding author. \n\nThe authors have filed a provisional patent application (63/462,131) based on this work.\n\nSupplemental Material - 41566_2023_1243_Fig10_ESM.jpg
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", "abstract": "Bioimaging harnessing optical contrasts and chemical specificity is of vital importance in probing complex biology. Vibrational spectroscopy based on mid-infrared excitation can reveal rich chemical information about molecular distributions. However, its full potential for bioimaging is hindered by the achievable sensitivity. Here we report bond-selective fluorescence-detected infrared-excited (BonFIRE) spectro-microscopy. BonFIRE employs two-photon excitation in the mid- and near-infrared to upconvert vibrational excitations to electronic states for fluorescence detection, thus encoding vibrational information into fluorescence. The system utilizes tunable narrowband picosecond pulses to ensure high sensitivity, biocompatibility and robustness for bond-selective biological interrogations over a wide spectrum of reporter molecules. We demonstrate BonFIRE spectral imaging in both fingerprint and cell-silent spectroscopic windows with single-molecule sensitivity for common fluorescent dyes. We then demonstrate BonFIRE imaging on various intracellular targets in fixed and live cells, neurons and tissues, with promise for further vibrational multiplexing. For dynamic bioanalysis in living systems, we implement a high-frequency modulation scheme and demonstrate time-lapse BonFIRE microscopy of live HeLa cells. We expect BonFIRE to expand the bioimaging toolbox by providing a new level of bond-specific vibrational information and facilitate functional imaging and sensing for biological investigations.", "date": "2023-07-01", "date_type": "published", "publication": "Nature Photonics", "publisher": "Nature Publishing Group", "id_number": "CaltechAUTHORS:20230630-744789000.1", "issn": "1749-4885", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230630-744789000.1", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DP2 GM140919-01" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Heritage Medical Research Institute" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1038/s41566-023-01243-8", "primary_object": { "basename": "41566_2023_1243_Fig14_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig14_ESM.jpg" }, "related_objects": [ { "basename": "41566_2023_1243_Fig15_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig15_ESM.jpg" }, { "basename": "41566_2023_1243_Fig8_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig8_ESM.jpg" }, { "basename": "41566_2023_1243_Fig9_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig9_ESM.jpg" }, { "basename": "41566_2023_1243_Fig7_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig7_ESM.jpg" }, { "basename": "41566_2023_1243_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_MOESM1_ESM.pdf" }, { "basename": "41566_2023_1243_Fig10_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig10_ESM.jpg" }, { "basename": "41566_2023_1243_Fig11_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig11_ESM.jpg" }, { "basename": "41566_2023_1243_Fig12_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig12_ESM.jpg" }, { "basename": "41566_2023_1243_Fig13_ESM.jpg", "url": "https://authors.library.caltech.edu/records/bhmhk-wbp71/files/41566_2023_1243_Fig13_ESM.jpg" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Wang, Haomin; Lee, Dongkwan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/209qm-2my05", "eprint_id": 122439, "eprint_status": "archive", "datestamp": "2023-11-30 17:14:21", "lastmod": "2023-11-30 17:19:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" }, "orcid": "0000-0003-2693-834X" }, { "id": "Tao-Xuecheng", "name": { "family": "Tao", "given": "Xuecheng" }, "orcid": "0000-0003-2907-3839" }, { "id": "Begu\u0161i\u0107-Tomislav", "name": { "family": "Begu\u0161i\u0107", "given": "Tomislav" }, "orcid": "0000-0002-7942-4134" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Computational Design of Molecular Probes for Electronic Preresonance Raman Scattering Microscopy", "ispublished": "pub", "full_text_status": "public", "keywords": "Materials Chemistry; Surfaces, Coatings and Films; Physical and Theoretical Chemistry", "note": "\u00a9 2023 American Chemical Society. \n\nL.W. acknowledges support from NIH Director's New Innovator Award (GM140919). T.B. acknowledges financial support from the Swiss National Science Foundation through the Early Postdoc Mobility Fellowship (Grant Number P2ELP2-199757). We thank Dr. Martin J. Schnermann for sharing the FC10 dye. The computations presented here were conducted in the Resnick High Performance Computing Center, a facility supported by the Resnick Sustainability Institute at the California Institute of Technology. \n\nAuthor Contributions: J.D. and X.T. contributed equally to this work. \n\nThe authors declare no competing financial interest.\n\nSupplemental Material - jp3c00699_si_001.pdf
", "abstract": "Recently developed electronic preresonance stimulated Raman scattering (epr-SRS) microscopy, in which the Raman signal of a dye is significantly boosted by setting the incident laser frequency near the electronic excitation energy, has pushed the sensitivity of SRS microscopy close to that offered by confocal fluorescence microscopy. Prominently, the maintained narrow line-width of epr-SRS also offers high multiplexity that breaks the \"color barrier\" in optical microscopy. However, detailed understanding of the fundamental mechanism in these epr-SRS dyes still remains elusive. Here, we combine experiments with theoretical modeling to investigate the structure\u2013function relationship, aiming to facilitate the design of new probes and expanding epr-SRS palettes. Our ab initio approach employing the displaced harmonic oscillator (DHO) model provides a consistent agreement between simulated and experimental SRS intensities of various triple-bond bearing epr-SRS probes with distinct scaffolds. We further review two popular approximate expressions for epr-SRS, namely the short-time and Albrecht A-term equations, and compare them to the DHO model. Overall, the theory allows us to illustrate how the observed intensity differences between molecular scaffolds stem from the coupling strength between the electronic excitation and the targeted vibrational mode, leading to a general design strategy for highly sensitive next-generation vibrational imaging probes.", "date": "2023-06-08", "date_type": "published", "publication": "Journal of Physical Chemistry B", "volume": "127", "number": "22", "publisher": "American Chemical Society", "pagerange": "4979-4988", "id_number": "CaltechAUTHORS:20230725-856834000.3", "issn": "1520-6106", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230725-856834000.3", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM140919" }, { "agency": "Swiss National Science Foundation (SNSF)", "grant_number": "P2ELP2-199757" }, { "agency": "Resnick Sustainability Institute" } ] }, "local_group": { "items": [ { "id": "Resnick-Sustainability-Institute" } ] }, "doi": "10.1021/acs.jpcb.3c00699", "pmcid": "PMC10676804", "primary_object": { "basename": "nihms-1943187.pdf", "url": "https://authors.library.caltech.edu/records/209qm-2my05/files/nihms-1943187.pdf" }, "related_objects": [ { "basename": "jp3c00699_si_001.pdf", "url": "https://authors.library.caltech.edu/records/209qm-2my05/files/jp3c00699_si_001.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Du, Jiajun; Tao, Xuecheng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x1cq9-y3414", "eprint_id": 122081, "eprint_status": "archive", "datestamp": "2023-08-20 16:49:34", "lastmod": "2023-10-20 16:57:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Haomin", "name": { "family": "Wang", "given": "Haomin" }, "orcid": "0000-0001-7193-8651" }, { "id": "Lee-Dongkwan", "name": { "family": "Lee", "given": "Dongkwan" }, "orcid": "0000-0001-6091-1349" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Toward the Next Frontiers of Vibrational Bioimaging", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2023 The Authors. Co-published by Nanjing University and American Chemical Society. Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).\n\nThe authors would like to thank the support from NIH Director's New Innovator Award, DP2 GM140919-01. \n\nThe authors declare no competing financial interest.\n\nPublished - im3c00004.pdf
", "abstract": "Chemical imaging based on vibrational contrasts can extract molecular information entangled in complex biological systems. To this end, nonlinear Raman scattering microscopy, mid-infrared photothermal (MIP) microscopy, and atomic force microscopy (AFM)-based force-detected photothermal microscopies are emerging with better chemical sensitivity, molecular specificity, and spatial resolution than conventional vibrational methods. Their utilization in bioimaging applications has provided biological knowledge in unprecedented detail. This Perspective outlines key methodological developments, bioimaging applications, and recent technical innovations of the three techniques. Representative biological demonstrations are also highlighted to exemplify the unique advantages of obtaining vibrational contrasts. With years of effort, these three methods compose an expanding vibrational bioimaging toolbox to tackle specific bioimaging needs, benefiting many biological investigations with rich information in both label-free and labeling manners. Each technique will be discussed and compared in the outlook, leading to possible future directions to accommodate growing needs in vibrational bioimaging.", "date": "2023-04-24", "date_type": "published", "publication": "Chemical and Biomedical Imaging", "volume": "1", "number": "1", "publisher": "American Chemical Society", "pagerange": "3-17", "id_number": "CaltechAUTHORS:20230630-537228000.5", "issn": "2832-3637", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230630-537228000.5", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DP2 GM140919-01" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1021/cbmi.3c00004", "pmcid": "PMC10131268", "primary_object": { "basename": "im3c00004.pdf", "url": "https://authors.library.caltech.edu/records/x1cq9-y3414/files/im3c00004.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Wang, Haomin; Lee, Dongkwan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1rrr7-zvg77", "eprint_id": 115746, "eprint_status": "archive", "datestamp": "2023-12-08 00:55:01", "lastmod": "2023-12-08 00:55:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" }, "orcid": "0000-0003-2693-834X" }, { "id": "Wang-Haomin", "name": { "family": "Wang", "given": "Haomin" }, "orcid": "0000-0001-7193-8651" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Bringing Vibrational Imaging to Chemical Biology with Molecular Probes", "ispublished": "pub", "full_text_status": "public", "keywords": "Biological imaging, Hydrocarbons, Labeling, Lipids, Probes; Molecular Medicine; General Medicine; Biochemistry", "note": "\u00a9 2022 American Chemical Society. \n\nPublished online 30 June 2022. Published in issue 15 July 2022. \n\nL. Wei acknowledges startup funds from California Institute of Technology and Grant No. DP2 GM140919 from the National Institutes of Health. We thank A. Colazo for helpful discussion. \n\nThe authors declare no competing financial interest.", "abstract": "As an emerging optical imaging modality, stimulated Raman scattering (SRS) microscopy provides invaluable opportunities for chemical biology studies using its rich chemical information. Through rapid progress over the past decade, the development of Raman probes harnessing the chemical biology toolbox has proven to play a key role in advancing SRS microscopy and expanding biological applications. In this perspective, we first discuss the development of biorthogonal SRS imaging using small tagging of triple bonds or isotopes and highlight their unique advantages for metabolic pathway analysis and microbiology investigations. Potential opportunities for chemical biology studies integrating small tagging with SRS imaging are also proposed. We next summarize the current designs of highly sensitive and super-multiplexed SRS probes, as well as provide future directions and considerations for next-generation functional probe design. These rationally designed SRS probes are envisioned to bridge the gap between SRS microscopy and chemical biology research and should benefit their mutual development.", "date": "2022-07-15", "date_type": "published", "publication": "ACS Chemical Biology", "volume": "17", "number": "7", "publisher": "American Chemical Society", "pagerange": "1621-1637", "id_number": "CaltechAUTHORS:20220721-8927000", "issn": "1554-8929", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220721-8927000", "funders": { "items": [ { "agency": "Caltech" }, { "agency": "NIH", "grant_number": "DP2 GM140919" } ] }, "doi": "10.1021/acschembio.2c00200", "pmcid": "PMC10676805", "primary_object": { "basename": "nihms-1938094.pdf", "url": "https://authors.library.caltech.edu/records/1rrr7-zvg77/files/nihms-1938094.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Du, Jiajun; Wang, Haomin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0fyaa-sn944", "eprint_id": 114830, "eprint_status": "archive", "datestamp": "2023-08-22 15:39:31", "lastmod": "2023-10-24 15:12:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Bi-Xiaotian", "name": { "family": "Bi", "given": "Xiaotian" }, "orcid": "0000-0003-4449-7488" }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen\u2013Deuterium Exchange", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics, Hydrocarbons, Kinetics, Oligomers, Probes; Colloid and Surface Chemistry; Biochemistry; General Chemistry; Catalysis", "note": "\u00a9 2022 American Chemical Society. \n\nReceived 21 July 2021. Published online 4 May 2022. Published in issue 18 May 2022. \n\nWe acknowledge the Caltech Biological Imaging Facility for providing the instrument. We thank Prof. Jacqueline Barton, Prof. Jesse Beauchamp, Amy-Doan P. Vo, Jiajun Du, Jolena Zhou, and Heyun Li for fruitful discussions. L.W. is a Heritage Principal Investigator supported by the Heritage Medical Research Institute. L.W. also acknowledges the support of the start-up funds from the California Institute of Technology and the Shurl and Kay Curci Foundation grant. \n\nThe authors declare no competing financial interest.\n\nSupplemental Material - ja2c01991_si_001.pdf
", "abstract": "Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen\u2013deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm\u20131, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pKas and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.", "date": "2022-05-18", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "144", "number": "19", "publisher": "American Chemical Society", "pagerange": "8504-8514", "id_number": "CaltechAUTHORS:20220520-649607000", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220520-649607000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Heritage Medical Research Institute" }, { "agency": "Caltech" }, { "agency": "Shurl and Kay Curci Foundation" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" } ] }, "doi": "10.1021/jacs.2c01991", "primary_object": { "basename": "ja2c01991_si_001.pdf", "url": "https://authors.library.caltech.edu/records/0fyaa-sn944/files/ja2c01991_si_001.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Bi, Xiaotian; Miao, Kun; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p3am9-etp54", "eprint_id": 116907, "eprint_status": "archive", "datestamp": "2023-08-22 15:39:36", "lastmod": "2023-10-24 21:10:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Lin-Li-En", "name": { "family": "Lin", "given": "Li-En" }, "orcid": "0000-0003-3086-6991" }, { "id": "Qian-Chenxi", "name": { "family": "Qian", "given": "Chenxi" }, "orcid": "0000-0003-4815-5565" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Label-free Super-resolution Imaging Enabled by Vibrational Imaging of Swelled Tissue and Analysis", "ispublished": "pub", "full_text_status": "public", "keywords": "General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; General Chemical Engineering; General Neuroscience", "note": "We acknowledge the Caltech Biological Imaging Facility for software support. L.W. acknowledges the support of the National Institutes of Health (NIH Director's New Innovator Award, DP2 GM140919-01), Amgen (Amgen Early Innovation Award), and the start-up funds from the California Institute of Technology. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1838830.pdf
Supplemental Material - NIHMS1838830-supplement-Supplementary_table.xlsx
", "abstract": "The universal utilization of fluorescence microscopy, especially super-resolution microscopy, has greatly advanced knowledge about modern biology. Conversely, the requirement of fluorophore labeling in fluorescent techniques poses significant challenges, such as photobleaching and non-uniform labeling of fluorescent probes and prolonged sample processing. In this protocol, the detailed working procedures of vibrational imaging of swelled tissue and analysis (VISTA) are presented. VISTA circumvents obstacles associated with fluorophores and achieves label-free super-resolution volumetric imaging in biological samples with spatial resolution down to 78 nm. The procedure is established by embedding cells and tissues in hydrogel, isotropically expanding the hydrogel sample hybrid, and visualizing endogenous protein distributions by vibrational imaging with stimulated Raman scattering microscopy. The method is demonstrated on both cells and mouse brain tissues. Highly correlative VISTA and immunofluorescence images were observed, validating the protein origin of imaging specificities. Exploiting such correlation, a machine learning-based image-segmentation algorithm was trained to achieve multi-component prediction of nuclei, blood vessels, neuronal cells, and dendrites from label-free mouse brain images. The procedure was further adapted to investigate pathological poly-glutamine (polyQ) aggregates in cells and amyloid-beta (A\u03b2) plaques in brain tissues with high throughput, justifying its potential for large-scale clinical samples.", "date": "2022-05-18", "date_type": "published", "publication": "Journal of Visualized Experiments", "volume": "17", "number": "183", "publisher": "JoVE", "pagerange": "Art. No. e63824", "id_number": "CaltechAUTHORS:20220913-219244900", "issn": "1940-087X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220913-219244900", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DP2 GM140919-01" }, { "agency": "Amgen" }, { "agency": "Caltech" } ] }, "doi": "10.3791/63824", "pmcid": "PMC9549918", "primary_object": { "basename": "NIHMS1838830-supplement-Supplementary_table.xlsx", "url": "https://authors.library.caltech.edu/records/p3am9-etp54/files/NIHMS1838830-supplement-Supplementary_table.xlsx" }, "related_objects": [ { "basename": "nihms-1838830.pdf", "url": "https://authors.library.caltech.edu/records/p3am9-etp54/files/nihms-1838830.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Miao, Kun; Lin, Li-En; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/8zwrw-r8s18", "eprint_id": 112616, "eprint_status": "archive", "datestamp": "2023-09-22 22:32:03", "lastmod": "2023-10-23 23:23:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" }, "orcid": "0000-0003-2693-834X" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Multicolor Photoactivatable Raman Probes for Subcellular Imaging and Tracking by Cyclopropenone Caging", "ispublished": "pub", "full_text_status": "public", "keywords": "Optical imaging, Hydrocarbons, Fluorescence imaging, Mitochondria, Probes; Colloid and Surface Chemistry; Biochemistry; General Chemistry; Catalysis", "note": "\u00a9 2021 American Chemical Society. \n\nReceived: September 13, 2021; Published: December 16, 2021. \n\nThe authors would like to thank Prof. Brian Stoltz for helpful discussions, the Center for Catalysis and Chemical Synthesis for access to LCMS and HPLC equipment and Dr. Mona Shahgholi of CCE Multiuser Mass Spectrometry Laboratory for assistance with high-resolution mass spectrometry, Xiaotian Bi for the assistance on preparing cell samples, and Amy-Doan Vo and Quan Gan for helpful discussion of the manuscript. L.W. acknowledges the startup funds from California Institute of Technology and the support from an Amgen early innovator award. \n\nThe authors declare the following competing financial interest(s): L.W. and J.D are inventors of a patent application covering multicolor photoactivatable Raman probes.\n\nSupplemental Material - ja1c09689_si_001.pdf
", "abstract": "Photoactivatable probes, with high-precision spatial and temporal control, have largely advanced bioimaging applications, particularly for fluorescence microscopy. While emerging Raman probes have recently pushed the frontiers of Raman microscopy for noninvasive small-molecule imaging and supermultiplex optical imaging with superb sensitivity and specificity, photoactivatable Raman probes remain less explored. Here, we report the first general design of multicolor photoactivatable alkyne Raman probes based on cyclopropenone caging for live-cell imaging and tracking. The fast photochemically generated alkynes from cyclopropenones enable background-free Raman imaging with desired photocontrollable features. We first synthesized and spectroscopically characterized a series of model cyclopropenones and identified the suitable light-activating scaffold. We further engineered the scaffold for enhanced chemical stability in a live-cell environment and improved Raman sensitivity. Organelle-targeting probes were then generated to achieve targeted imaging of mitochondria, lipid droplets, endoplasmic reticulum, and lysosomes. Multiplexed photoactivated imaging and tracking at both subcellular and single-cell levels was next demonstrated to monitor the dynamic migration and interactions of the cellular contents. We envision that this general design of multicolor photoactivatable Raman probes would open up new ways for spatial\u2013temporal controlled profiling and interrogations in complex biological systems with high information throughput.", "date": "2022-01-19", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "144", "number": "2", "publisher": "American Chemical Society", "pagerange": "777-786", "id_number": "CaltechAUTHORS:20211221-866869000", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211221-866869000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech" }, { "agency": "Amgen" } ] }, "doi": "10.1021/jacs.1c09689", "primary_object": { "basename": "ja1c09689_si_001.pdf", "url": "https://authors.library.caltech.edu/records/8zwrw-r8s18/files/ja1c09689_si_001.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Du, Jiajun and Wei, Lu" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/2n95a-dwn37", "eprint_id": 112584, "eprint_status": "archive", "datestamp": "2023-08-22 12:41:54", "lastmod": "2023-10-23 22:37:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Aguado-Brian", "name": { "family": "Aguado", "given": "Brian" } }, { "name": { "family": "Bray", "given": "Laura J." } }, { "name": { "family": "Caneva", "given": "Sabina" } }, { "name": { "family": "Correa-Baena", "given": "Juan-Pablo" } }, { "name": { "family": "Di Martino", "given": "Giuliana" } }, { "name": { "family": "Fang", "given": "Chengcheng" } }, { "name": { "family": "Fang", "given": "Yin" } }, { "name": { "family": "Gehring", "given": "Pascal" } }, { "name": { "family": "Grosso", "given": "Gabriele" } }, { "name": { "family": "Gu", "given": "Xiaodan" } }, { "name": { "family": "Guo", "given": "Peijun" } }, { "name": { "family": "He", "given": "Yu" } }, { "name": { "family": "Kempa", "given": "Thomas J." } }, { "name": { "family": "Kutys", "given": "Matthew" } }, { "name": { "family": "Li", "given": "Jinxing" } }, { "name": { "family": "Li", "given": "Tian" } }, { "name": { "family": "Liao", "given": "Bolin" } }, { "name": { "family": "Liu", "given": "Fang" } }, { "name": { "family": "Molina-Lopez", "given": "Francisco" } }, { "name": { "family": "Pickel", "given": "Andrea" } }, { "name": { "family": "Porras", "given": "Ana M." } }, { "name": { "family": "Raman", "given": "Ritu" } }, { "name": { "family": "Sletten", "given": "Ellen M." } }, { "name": { "family": "Smith", "given": "Quinton" } }, { "name": { "family": "Tan", "given": "Chaoliang" } }, { "name": { "family": "Wang", "given": "Haotian" } }, { "name": { "family": "Wang", "given": "Huiliang" } }, { "name": { "family": "Wang", "given": "Sihong" } }, { "name": { "family": "Wang", "given": "Zhongrui" } }, { "name": { "family": "Wehmeyer", "given": "Geoffrey" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "name": { "family": "Yang", "given": "Yuan" } }, { "name": { "family": "Zarzar", "given": "Lauren D." } }, { "name": { "family": "Zhao", "given": "Meiting" } }, { "name": { "family": "Zheng", "given": "Yuqing" } }, { "name": { "family": "Cranford", "given": "Steve" } } ] }, "title": "35 challenges in materials science being tackled by PIs under 35(ish) in 2021", "ispublished": "pub", "full_text_status": "restricted", "keywords": "General Materials Science", "note": "\u00a9 2021 Elsevier. \n\nAvailable online 1 December 2021.", "abstract": "Here we highlight 35 researchers approximately under the age of 35. Age, of course, is just a number\u2014our target was emerging early-career academics. Contributors were recruited in a self-propagating \"pay-it-forward\" manner, with each invitee being suggested by a peer who had already contributed. The final collection is an inspiring look at the challenges the current generation of materials researchers are tackling.", "date": "2021-12-01", "date_type": "published", "publication": "Matter", "volume": "4", "number": "12", "publisher": "Cell Press", "pagerange": "3804-3810", "id_number": "CaltechAUTHORS:20211220-955732000", "issn": "2590-2385", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211220-955732000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.matt.2021.11.003", "resource_type": "article", "pub_year": "2021", "author_list": "Aguado, Brian; Bray, Laura J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rmnf5-24v90", "eprint_id": 109103, "eprint_status": "archive", "datestamp": "2023-08-20 04:11:16", "lastmod": "2023-10-23 17:39:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lin-Li-En", "name": { "family": "Lin", "given": "Li-En" }, "orcid": "0000-0003-3086-6991" }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Qian-Chenxi", "name": { "family": "Qian", "given": "Chenxi" }, "orcid": "0000-0003-4815-5565" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "High spatial-resolution imaging of label-free in vivo protein aggregates by VISTA", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Royal Society of Chemistry 2021. \n\nReceived 11th January 2021, Accepted 7th April 2021, First published on 12th April 2021. \n\nWe thank the Caltech Biological Imaging Facility for software support. We are grateful to Bryce Manifold (University of Washington) and the Caltech OLAR staffs for technical support. Chenxi Qian acknowledges the support of the Natural Sciences and Engineering Research Council of Canada (NSERC Postdoctoral Fellowship). Lu Wei acknowledges the support of National Institutes of Health (DP2GM140919-01), Amgen (Amgen Early Innovation Award), and the start-up funds from California Institute of Technology. \n\nData and code availability: All data supporting the findings of the present study are available in the article and its supplementary figures, or from the corresponding author upon request. The code for U-Net training, prediction, and evaluation in this paper is available at https://github.com/Li-En-Good/VISTA. \n\nThe authors declare no conflicts of interest.\n\nAccepted Version - nihms-1703089.pdf
Supplemental Material - d1an00060h1.pdf
", "abstract": "Amyloid aggregation, formed by aberrant proteins, is a pathological hallmark for neurodegenerative diseases, including Alzheimer's disease and Huntington's disease. High-resolution holistic mapping of the fine structures from these aggregates should facilitate our understanding of their pathological roles. Here, we achieved label-free high-resolution imaging of the polyQ and the amyloid-beta (A\u03b2) aggregates in cells and tissues utilizing a sample-expansion stimulated Raman strategy. We further focused on characterizing the A\u03b2 plaques in 5XFAD mouse brain tissues. 3D volumetric imaging enabled visualization of the whole plaques, resolving both the fine protein filaments and the surrounding components. Coupling our expanded label-free Raman imaging with machine learning, we obtained specific segmentation of aggregate cores, peripheral filaments together with cell nuclei and blood vessels by pre-trained convolutional neural network models. Combining with 2-channel fluorescence imaging, we achieved a 6-color holistic view of the same sample. This ability for precise and multiplex high-resolution imaging of the protein aggregates and their micro-environment without the requirement of labeling would open new biomedical applications.", "date": "2021-07-07", "date_type": "published", "publication": "Analyst", "volume": "146", "number": "13", "publisher": "Royal Society of Chemistry", "pagerange": "4135-4145", "id_number": "CaltechAUTHORS:20210512-125027084", "issn": "0003-2654", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210512-125027084", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "NIH", "grant_number": "DP2GM140919-01" }, { "agency": "Amgen" }, { "agency": "Caltech" } ] }, "doi": "10.1039/d1an00060h", "pmcid": "PMC8238904", "primary_object": { "basename": "d1an00060h1.pdf", "url": "https://authors.library.caltech.edu/records/rmnf5-24v90/files/d1an00060h1.pdf" }, "related_objects": [ { "basename": "nihms-1703089.pdf", "url": "https://authors.library.caltech.edu/records/rmnf5-24v90/files/nihms-1703089.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Lin, Li-En; Miao, Kun; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/bnzh9-vj406", "eprint_id": 107395, "eprint_status": "archive", "datestamp": "2023-08-22 10:11:50", "lastmod": "2023-10-23 16:58:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qian-Chenxi", "name": { "family": "Qian", "given": "Chenxi" }, "orcid": "0000-0003-4815-5565" }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Lin-Li-En", "name": { "family": "Lin", "given": "Li-En" }, "orcid": "0000-0003-3086-6991" }, { "id": "Chen-Xinhong", "name": { "family": "Chen", "given": "Xinhong" }, "orcid": "0000-0003-0408-0813" }, { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Super-resolution label-free volumetric vibrational imaging", "ispublished": "pub", "full_text_status": "public", "keywords": "Optical imaging; Raman spectroscopy; Super-resolution microscopy", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 17 December 2020; Accepted 07 May 2021; Published 15 June 2021. \n\nWe thank Xun Wang and Dr. Lilien Voong for fruitful discussions. We are grateful to Can Li and Prof. Marianne Bronner for sharing the zebrafish embryo slices. We acknowledge Prof. Viviana Gradinaru for sharing resources and the helpful discussions. Chenxi Qian acknowledges the support of the Natural Sciences and Engineering Research Council of Canada (NSERC Postdoctoral Fellowship). Lu Wei acknowledges the support of the National Institutes of Health (NIH Director's New Innovator Award, DP2 GM140919-01), Amgen (Amgen Early Innovation Award), and the start-up funds from the California Institute of Technology. \n\nData availability: The authors declare that all data supporting the findings of the present study are available in the article and its supplementary figures and tables, or from the corresponding author upon request. \n\nCode availability: MATLAB code used for PSF determination and Python code for U-Net training and prediction in this paper is available at https://github.com/Li-En-Good/VISTA (10.5281/zenodo.4717251). \n\nThese authors contributed equally: Chenxi Qian, Kun Miao. \n\nAuthor Contributions: L.W. conceived the study and supervised the project. C.Q., K.M., and L.W. designed the experiments and analyzed the data. C.Q. characterized the technical aspects of VISTA. C.Q., K.M., X.C., and J.D. performed the experiments. L.-E.L. performed U-Net training for multiplexed VISTA. C.Q., K.M., and L.W. wrote the paper with input from all the authors. \n\nThe authors declare no competing interests. \n\nPeer review information: Nature Communications thanks Sang-Hee Shim and the other anonymous reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.\n\nPublished - s41467-021-23951-x.pdf
Submitted - 2021.01.08.425961v1.full.pdf
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", "abstract": "Innovations in high-resolution optical imaging have allowed visualization of nanoscale biological structures and connections. However, super-resolution fluorescence techniques, including both optics-oriented and sample-expansion based, are limited in quantification and throughput especially in tissues from photobleaching or quenching of the fluorophores, and low-efficiency or non-uniform delivery of the probes. Here, we report a general sample-expansion vibrational imaging strategy, termed VISTA, for scalable label-free high-resolution interrogations of protein-rich biological structures with resolution down to 78\u2009nm. VISTA achieves decent three-dimensional image quality through optimal retention of endogenous proteins, isotropic sample expansion, and deprivation of scattering lipids. Free from probe-labeling associated issues, VISTA offers unbiased and high-throughput tissue investigations. With correlative VISTA and immunofluorescence, we further validated the imaging specificity of VISTA and trained an image-segmentation model for label-free multi-component and volumetric prediction of nucleus, blood vessels, neuronal cells and dendrites in complex mouse brain tissues. VISTA could hence open new avenues for versatile biomedical studies.", "date": "2021-06-15", "date_type": "published", "publication": "Nature Communications", "volume": "12", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 3648", "id_number": "CaltechAUTHORS:20210111-140338961", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210111-140338961", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "NIH", "grant_number": "DP2 GM140919-01" }, { "agency": "Amgen" }, { "agency": "Caltech" } ] }, "doi": "10.1038/s41467-021-23951-x", "pmcid": "PMC8206358", "primary_object": { "basename": "2021.01.08.425961v1.full.pdf", "url": "https://authors.library.caltech.edu/records/bnzh9-vj406/files/2021.01.08.425961v1.full.pdf" }, "related_objects": [ { "basename": "41467_2021_23951_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/bnzh9-vj406/files/41467_2021_23951_MOESM1_ESM.pdf" }, { "basename": "41467_2021_23951_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/bnzh9-vj406/files/41467_2021_23951_MOESM2_ESM.pdf" }, { "basename": "41467_2021_23951_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/bnzh9-vj406/files/41467_2021_23951_MOESM3_ESM.pdf" }, { "basename": "s41467-021-23951-x.pdf", "url": "https://authors.library.caltech.edu/records/bnzh9-vj406/files/s41467-021-23951-x.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Qian, Chenxi; Miao, Kun; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/91na4-n8n08", "eprint_id": 108748, "eprint_status": "archive", "datestamp": "2023-08-20 02:40:22", "lastmod": "2023-10-23 17:17:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Dongkwan", "name": { "family": "Lee", "given": "Dongkwan" }, "orcid": "0000-0001-6091-1349" }, { "id": "Qian-Chenxi", "name": { "family": "Qian", "given": "Chenxi" }, "orcid": "0000-0003-4815-5565" }, { "id": "Wang-Haomin", "name": { "family": "Wang", "given": "Haomin" }, "orcid": "0000-0001-7193-8651" }, { "id": "Li-Lei", "name": { "family": "Li", "given": "Lei" }, "orcid": "0000-0001-6164-2646" }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" }, "orcid": "0000-0003-2693-834X" }, { "id": "Shcherbakova-Daria-M", "name": { "family": "Shcherbakova", "given": "Daria M." }, "orcid": "0000-0003-3384-6363" }, { "id": "Verkhusha-Vladislav-V", "name": { "family": "Verkhusha", "given": "Vladislav V." }, "orcid": "0000-0002-2083-8121" }, { "id": "Wang-Lihong-V", "name": { "family": "Wang", "given": "Lihong V." }, "orcid": "0000-0001-9783-4383" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Toward photoswitchable electronic pre-resonance stimulated Raman probes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Published under license by AIP Publishing. \n\nSubmitted: 11 January 2021; Accepted: 15 March 2021; Published Online: 2 April 2021. \n\nThis work was supported by the grants from the National Institutes of Health, Grant No. DP2 GM140919 (to L.W.) and Grant No. R35 GM122567 (to V.V.), and by the start-up fund from the California Institute of Technology (to L.W.). \n\nData Availability: The data that support the findings of this study are available from the corresponding author upon reasonable request.\n\nPublished - 5.0043791.pdf
Supplemental Material - supplementary_032802021_final.pdf
", "abstract": "Reversibly photoswitchable probes allow for a wide variety of optical imaging applications. In particular, photoswitchable fluorescent probes have significantly facilitated the development of super-resolution microscopy. Recently, stimulated Raman scattering (SRS) imaging, a sensitive and chemical-specific optical microscopy, has proven to be a powerful live-cell imaging strategy. Driven by the advances of newly developed Raman probes, in particular the pre-resonance enhanced narrow-band vibrational probes, electronic pre-resonance SRS (epr-SRS) has achieved super-multiplex imaging with sensitivity down to 250 nM and multiplexity up to 24 colors. However, despite the high demand, photoswitchable Raman probes have yet to be developed. Here, we propose a general strategy for devising photoswitchable epr-SRS probes. Toward this goal, we exploit the molecular electronic and vibrational coupling, in which we switch the electronic states of the molecules to four different states to turn their ground-state epr-SRS signals on and off. First, we showed that inducing transitions to both the electronic excited state and triplet state can effectively diminish the SRS peaks. Second, we revealed that the epr-SRS signals can be effectively switched off in red-absorbing organic molecules through light-facilitated transitions to a reduced state. Third, we identified that photoswitchable proteins with near-infrared photoswitchable absorbance, whose states are modulable with their electronic resonances detunable toward and away from the pump photon energy, can function as the photoswitchable epr-SRS probes with desirable sensitivity (<1 \u00b5M) and low photofatigue (>40 cycles). These photophysical characterizations and proof-of-concept demonstrations should advance the development of novel photoswitchable Raman probes and open up the unexplored Raman imaging capabilities.", "date": "2021-04-07", "date_type": "published", "publication": "Journal of Chemical Physics", "volume": "154", "number": "13", "publisher": "American Institute of Physics", "pagerange": "Art. No. 135102", "id_number": "CaltechAUTHORS:20210416-071920882", "issn": "0021-9606", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210416-071920882", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "DP2 GM140919" }, { "agency": "NIH", "grant_number": "R35 GM122567" }, { "agency": "Caltech" } ] }, "doi": "10.1063/5.0043791", "pmcid": "PMC8019356", "primary_object": { "basename": "5.0043791.pdf", "url": "https://authors.library.caltech.edu/records/91na4-n8n08/files/5.0043791.pdf" }, "related_objects": [ { "basename": "supplementary_032802021_final.pdf", "url": "https://authors.library.caltech.edu/records/91na4-n8n08/files/supplementary_032802021_final.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Lee, Dongkwan; Qian, Chenxi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/m20x1-9kw24", "eprint_id": 105346, "eprint_status": "archive", "datestamp": "2023-11-30 17:17:24", "lastmod": "2023-11-30 17:17:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Dongkwan", "name": { "family": "Lee", "given": "Dongkwan" } }, { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" } }, { "id": "Yu-Rona", "name": { "family": "Yu", "given": "Rona" } }, { "id": "Su-Yapeng", "name": { "family": "Su", "given": "Yapeng" }, "orcid": "0000-0002-6305-8467" }, { "id": "Heath-J-R", "name": { "family": "Heath", "given": "James R." }, "orcid": "0000-0001-5356-4385" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Visualizing Subcellular Enrichment of Glycogen in Live Cancer Cells by Stimulated Raman Scattering", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 American Chemical Society. \n\nReceived: June 1, 2020; Accepted: September 9, 2020; Published: September 9, 2020. \n\nWe thank Dr. Antoni Ribas for sharing the melanoma cell lines. We also thank Dr. Otto Baba and Dr. Morita for sharing the antiglycogen antibodies. We thank Dr. C. Qian, K. Miao, X. Bi, L. Lin, and Dr. L. Voong for helpful discussions. We acknowledge the following agencies and foundations for support: NIH Grant U01 CA217655 (to J.R.H.), the WA State Andy Hill CARE Foundation (to J.R.H.), and an ISB Innovator Award (Y.S.). L.W. acknowledges the support for start-up funds from California Institute of Technology. \n\nThe authors declare no competing financial interest.\n\nSupplemental Material - ac0c02348_si_001.pdf
", "abstract": "Glycogen, a branched glucose polymer, helps regulate glucose homeostasis through immediate storage and release of glucose. Reprogramming of glycogen metabolism has recently been suggested to play an emerging role in cancer progression and tumorigenesis. However, regulation of metabolic rewiring for glycogen synthesis and breakdown in cancer cells remains less understood. Despite the availability of various glycogen detection methods, selective visualization of glycogen in living cells with high spatial resolution has proven to be highly challenging. Here, we present an optical imaging strategy to visualize glycogen in live cancer cells with minimal perturbation by combining stimulated Raman scattering microscopy with metabolic incorporation of deuterium-labeled glucose. We revealed the subcellular enrichment of glycogen in live cancer cells and achieved specific glycogen mapping through distinct spectral identification. Using this method, different glycogen metabolic phenotypes were characterized in a series of patient-derived BRAF mutant melanoma cell lines. Our results indicate that cell lines manifesting high glycogen storage level showed increased tolerance to glucose deficiency among the studied melanoma phenotypes. This method opens up the possibility for noninvasive study of complex glycogen metabolism at subcellular resolution and may help reveal new features of glycogen regulation in cancer systems.", "date": "2020-10-06", "date_type": "published", "publication": "Analytical Chemistry", "volume": "92", "number": "19", "publisher": "American Chemical Society", "pagerange": "13182-13191", "id_number": "CaltechAUTHORS:20200911-133137005", "issn": "0003-2700", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200911-133137005", "funders": { "items": [ { "agency": "NIH", "grant_number": "U01 CA217655" }, { "agency": "Andy Hill CARE Foundation" }, { "agency": "Institute for Systems Biology" }, { "agency": "Caltech" } ] }, "doi": "10.1021/acs.analchem.0c02348", "pmcid": "PMC10676777", "primary_object": { "basename": "nihms-1943194.pdf", "url": "https://authors.library.caltech.edu/records/m20x1-9kw24/files/nihms-1943194.pdf" }, "related_objects": [ { "basename": "ac0c02348_si_001.pdf", "url": "https://authors.library.caltech.edu/records/m20x1-9kw24/files/ac0c02348_si_001.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Lee, Dongkwan; Du, Jiajun; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/n0npk-4qf04", "eprint_id": 105516, "eprint_status": "archive", "datestamp": "2023-08-22 06:27:50", "lastmod": "2023-10-23 17:21:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" } }, { "id": "Su-Yapeng", "name": { "family": "Su", "given": "Yapeng" }, "orcid": "0000-0002-6305-8467" }, { "id": "Qian-Chenxi", "name": { "family": "Qian", "given": "Chenxi" }, "orcid": "0000-0003-4815-5565" }, { "id": "Yuan-Dan", "name": { "family": "Yuan", "given": "Dan" } }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Lee-Dongkwan", "name": { "family": "Lee", "given": "Dongkwan" } }, { "id": "Ng-Alphonsus-H-C", "name": { "family": "Ng", "given": "Alphonsus H. C." }, "orcid": "0000-0003-0074-4598" }, { "id": "Wijker-Reto-S", "name": { "family": "Wijker", "given": "Reto S." }, "orcid": "0000-0001-5104-9849" }, { "id": "Ribas-Antoni", "name": { "family": "Ribas", "given": "Antoni" }, "orcid": "0000-0003-3669-8458" }, { "id": "Levine-Raphael-D", "name": { "family": "Levine", "given": "Raphael D." } }, { "id": "Heath-J-R", "name": { "family": "Heath", "given": "James R." }, "orcid": "0000-0001-5356-4385" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells", "ispublished": "pub", "full_text_status": "public", "keywords": "Cancer metabolism; Cellular imaging; Lipids; Raman spectroscopy; Target identification", "note": "\u00a9 The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 21 January 2020; Accepted 14 August 2020; Published 24 September 2020. \n\nL.W. acknowledges start-up fund support from California Institute of Technology. We acknowledge the following agencies and foundations for support: NIH Grant U01 CA217655 (to J.R.H.); the Parker Institute for Cancer Immunotherapy (J.R.H. and A.R.), the WA State Andy Hill CARE Foundation (J.R.H.), and an ISB Innovator Award (Y.S.). \n\nData availability: All the data supporting the findings of this study are available within the article and its Supplementary Information files and from the corresponding author upon reasonable request. The following databases are used: Human Reference Genome (UCSC hg 19), Gene Expression Omnibus database (GEO), Molecular Signatures Database (MSigDB). RNA-seq data have been deposited to array express with accession number of E-MTAB-8842. Source data are provided with this paper. \n\nCode availability: Custom code for the surprisal analysis of Raman spectra has previously been published and deposited on GitHub (https://github.com/mesako/Melanoma-Publication) 36. Source data are provided with this paper. \n\nThese authors contributed equally: Jiajun Du, Yapeng Su. \n\nAuthor Contributions: L.W., J.R.H., J.D., and Y.S. conceived the study and designed the experiments. J.D., Y.S., C.Q., D.Y., K.M., D.L., A.N., and R.W. performed the experiments. J.D. and Y.S. analyzed and interpreted the data. L.W., J.R.H., A.R., and R.L. provided conceptual advice on data analysis and interpretation. L.W., J.D., J.R.H., and Y.S. wrote the manuscript. L.W. and J.R.H. supervised this study. \n\nThe authors declare no competing interests. \n\nPeer review information: Nature Communications thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.\n\nPublished - s41467-020-18376-x.pdf
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", "abstract": "Non-invasively probing metabolites within single live cells is highly desired but challenging. Here we utilize Raman spectro-microscopy for spatial mapping of metabolites within single cells, with the specific goal of identifying druggable metabolic susceptibilities from a series of patient-derived melanoma cell lines. Each cell line represents a different characteristic level of cancer cell de-differentiation. First, with Raman spectroscopy, followed by stimulated Raman scattering (SRS) microscopy and transcriptomics analysis, we identify the fatty acid synthesis pathway as a druggable susceptibility for differentiated melanocytic cells. We then utilize hyperspectral-SRS imaging of intracellular lipid droplets to identify a previously unknown susceptibility of lipid mono-unsaturation within de-differentiated mesenchymal cells with innate resistance to BRAF inhibition. Drugging this target leads to cellular apoptosis accompanied by the formation of phase-separated intracellular membrane domains. The integration of subcellular Raman spectro-microscopy with lipidomics and transcriptomics suggests possible lipid regulatory mechanisms underlying this pharmacological treatment. Our method should provide a general approach in spatially-resolved single cell metabolomics studies.", "date": "2020-09-24", "date_type": "published", "publication": "Nature Communications", "volume": "11", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 4830", "id_number": "CaltechAUTHORS:20200924-122708002", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200924-122708002", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech" }, { "agency": "NIH", "grant_number": "U01 CA217655" }, { "agency": "Parker Institute for Cancer Immunotherapy" }, { "agency": "Washington State Andy Hill CARE Foundation" }, { "agency": "Institute for Systems Biology" } ] }, "doi": "10.1038/s41467-020-18376-x", "pmcid": "PMC7518429", "primary_object": { "basename": "41467_2020_18376_MOESM6_ESM.pdf", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/41467_2020_18376_MOESM6_ESM.pdf" }, "related_objects": [ { "basename": "41467_2020_18376_MOESM7_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/41467_2020_18376_MOESM7_ESM.xlsx" }, { "basename": "s41467-020-18376-x.pdf", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/s41467-020-18376-x.pdf" }, { "basename": "41467_2020_18376_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/41467_2020_18376_MOESM1_ESM.pdf" }, { "basename": "41467_2020_18376_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/41467_2020_18376_MOESM2_ESM.pdf" }, { "basename": "41467_2020_18376_MOESM3_ESM.docx", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/41467_2020_18376_MOESM3_ESM.docx" }, { "basename": "41467_2020_18376_MOESM4_ESM.avi", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/41467_2020_18376_MOESM4_ESM.avi" }, { "basename": "41467_2020_18376_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/n0npk-4qf04/files/41467_2020_18376_MOESM5_ESM.xlsx" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Du, Jiajun; Su, Yapeng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pba3w-s1n51", "eprint_id": 107235, "eprint_status": "archive", "datestamp": "2023-08-19 22:47:57", "lastmod": "2023-10-20 22:54:17", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" } }, { "id": "Su-Yapeng", "name": { "family": "Su", "given": "Yapeng" }, "orcid": "0000-0002-6305-8467" }, { "id": "Heath-J-R", "name": { "family": "Heath", "given": "James Richard" }, "orcid": "0000-0001-5356-4385" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2020 American Chemical Society.", "abstract": "We utilized Raman spectro-microscopy to non-invasively probe metabomics within single live cells, aiming to identify\ndruggable metabolic susceptibilities from a series of patient-derived BRAF mutant melanoma cell lines. Each cell line\nrepresents a phenotype with different characteristic level of de-differentiation and BRAFi (BRAF inhibitor) resistance.\nFirst, with single-cell Raman spectroscopy and stimulated Raman scattering (SRS) microscopy, followed by\ntranscriptomics anal., we identified lipid processes as major metabolic functional difference between different\nphenotypes. We then utilized hyperspectral-SRS imaging on intracellular single organelles to identify a previously\nunknown susceptibility of lipid desatn. within de-differentiated cell lines. Drugging this target leads to cellular apoptosis\naccompanied by phase sepd. intracellular domains. The integration of subcellular Raman spectro-microscopy with\nlipidomics and transcriptomics suggests highly heterogenous metabolic responses and possible lipid regulatory\nmechanisms underlying this pharmacol. treatment. Our method should provide a general approach in spatially-resolved\nsingle cell metabolomics studies.", "date": "2020-08", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20201221-101511711", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201221-101511711", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "conference_item", "pub_year": "2020", "author_list": "Du, Jiajun; Su, Yapeng; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5ns69-76r34", "eprint_id": 99535, "eprint_status": "archive", "datestamp": "2023-08-19 21:02:19", "lastmod": "2023-10-20 22:21:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Live-Cell Imaging and Quantification of PolyQ Aggregates by Stimulated Raman Scattering of Selective Deuterium Labeling", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 American Chemical Society. This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. \n\nReceived: November 19, 2019; Published: March 6, 2020. \n\nWe would like to thank Dr. C. Qian, D. Lee, J. Du, and Dr. L. Voong for helpful discussions. We are grateful for the plasmid (mHtt-97Q-GFP) shared by Prof. R. Kopito and Prof. F.-U. Hartl. We thank Prof. Z. Liu for sharing the stable embryonic stem cell-lines. L.W. acknowledges the support of start-up funds from California Institute of Technology. \n\nThe authors declare no competing financial interest.\n\nPublished - acscentsci.9b01196.pdf
Submitted - 820217.full.pdf
Supplemental Material - oc9b01196_si_001.pdf
", "abstract": "Polyglutamine (polyQ) diseases are a group of neurodegenerative disorders, involving the deposition of aggregation-prone proteins with long polyQ expansions. However, the cytotoxic roles of these aggregates remain highly controversial, largely due to a lack of proper tools for quantitative and nonperturbative interrogations. Common methods including in vitro biochemical, spectroscopic assays, and live-cell fluorescence imaging all suffer from certain limitations. Here, we propose coupling stimulated Raman scattering microscopy with deuterium-labeled glutamine for live-cell imaging, quantification, and spectral analysis of native polyQ aggregates with subcellular resolution. First, through the enrichment of deuterated glutamine in the polyQ sequence of mutant Huntingtin (mHtt) exon1 proteins for Huntington's disease, we achieved sensitive and specific stimulated Raman scattering (SRS) imaging of carbon\u2013deuterium bonds (C\u2013D) from aggregates without GFP labeling, which is commonly employed in fluorescence microscopy. We revealed that these aggregates became 1.8-fold denser compared to those with GFP. Second, we performed ratiometric quantifications, which indicate a surprising dependence of protein compositions on aggregation sizes. Our further calculations, for the first time, reported the absolute concentrations for sequestered mHtt and non-mHtt proteins within the same aggregates. Third, we adopted hyperspectral SRS for Raman spectroscopic studies of aggregate structures. By inducing a cellular heat shock response, a potential therapeutic approach for inhibiting aggregate formation, we found a possible aggregate intermediate state with changed solvation microenvironments. Our method may hence readily unveil new features and mechanistic insight of polyQ aggregates and pave the way for comprehensive in vivo investigations.", "date": "2020-04-22", "date_type": "published", "publication": "ACS Central Science", "volume": "6", "number": "4", "publisher": "American Chemical Society", "pagerange": "478-486", "id_number": "CaltechAUTHORS:20191029-113111264", "issn": "2374-7943", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191029-113111264", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech" } ] }, "doi": "10.1021/acscentsci.9b01196", "pmcid": "PMC7181319", "primary_object": { "basename": "oc9b01196_si_001.pdf", "url": "https://authors.library.caltech.edu/records/5ns69-76r34/files/oc9b01196_si_001.pdf" }, "related_objects": [ { "basename": "820217.full.pdf", "url": "https://authors.library.caltech.edu/records/5ns69-76r34/files/820217.full.pdf" }, { "basename": "acscentsci.9b01196.pdf", "url": "https://authors.library.caltech.edu/records/5ns69-76r34/files/acscentsci.9b01196.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Miao, Kun and Wei, Lu" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7v1t3-a9k53", "eprint_id": 101868, "eprint_status": "archive", "datestamp": "2023-08-19 20:32:21", "lastmod": "2024-01-14 23:03:47", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Chemical probes for optical bio-imaging (Conference Presentation)", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2020 Society of Photo-Optical Instrumentation Engineers (SPIE).", "abstract": "Innovations in novel probes have significantly push the development of new optical spectroscopy and microscopy methods for revealing new information in biological systems. In this talk, I will discuss our recent development by introducing chemical probes to stimulated Raman scattering (SRS) microscopy that could allow multi-functional imaging at sub-cellular level. Both physical and chemical principles underlying the investigation and design of new probes when coupled to the Raman imaging modalities will be presented, as well as our efforts in biomedical applications including cancer- and neuronal- metabolism.", "date": "2020-03-10", "date_type": "published", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 112560E", "id_number": "CaltechAUTHORS:20200311-151708752", "isbn": "9781510632752", "book_title": "Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications XII", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200311-151708752", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Achilefu-S", "name": { "family": "Achilefu", "given": "Samuel" } }, { "id": "Raghavachari-R", "name": { "family": "Raghavachari", "given": "Ramesh" } } ] }, "doi": "10.1117/12.2551679", "resource_type": "book_section", "pub_year": "2020", "author_list": "Wei, Lu" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0mg92-hqq16", "eprint_id": 101862, "eprint_status": "archive", "datestamp": "2023-08-19 20:31:59", "lastmod": "2024-01-14 23:03:36", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "High-sensitivity stimulated Raman imaging with chemical tags (Conference Presentation)", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2020 Society of Photo-Optical Instrumentation Engineers (SPIE).", "abstract": "Innovations in optical spectroscopy and microscopy have revolutionized our understanding in biological systems. In this talk, I will discuss our recent development by coupling stimulated Raman scattering (SRS) microscopy with chemical probes that could allow high-sensitivity bio-analysis with fast speed at the sub-cellular level. Both physical and chemical principles underlying the optical microscopy will be presented, as well as our efforts in biomedical applications including cancer- and neuronal- metabolism.", "date": "2020-03-10", "date_type": "published", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 112500R", "id_number": "CaltechAUTHORS:20200311-151707376", "isbn": "9781510632639", "book_title": "High-Speed Biomedical Imaging and Spectroscopy V", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200311-151707376", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Tsia-Kevin-K", "name": { "family": "Tsia", "given": "Kevin K." } }, { "id": "Goda-Keisuke", "name": { "family": "Goda", "given": "Keisuke" } } ] }, "doi": "10.1117/12.2548543", "resource_type": "book_section", "pub_year": "2020", "author_list": "Wei, Lu" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y15wz-q2q45", "eprint_id": 101861, "eprint_status": "archive", "datestamp": "2023-08-19 20:31:56", "lastmod": "2024-01-14 23:03:34", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Miao-Kun", "name": { "family": "Miao", "given": "Kun" }, "orcid": "0000-0001-6567-3650" }, { "id": "Du-Jiajun", "name": { "family": "Du", "given": "Jiajun" } } ] }, "title": "Stimulated Raman imaging with chemical probes for subcellular bioanalysis (Conference Presentation)", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2020 Society of Photo-Optical Instrumentation Engineers (SPIE).", "abstract": "Innovations in optical spectroscopy and microscopy have revolutionized our understanding in biological systems at sub-cellular levels. In this talk, I will discuss about our recent development by coupling stimulated Raman scattering (SRS) microscopy with chemical probes that could allow new subcellular bioanalysis in live cells. The introduced tags offer additional SRS contrast channel for quantification of biological contents that were previously difficult. Both physical and chemical principles underlying the optical microscopy will be presented, as well as our efforts in biomedical applications including cancer- and neuronal- metabolism.", "date": "2020-03-10", "date_type": "published", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 112521S", "id_number": "CaltechAUTHORS:20200311-151707274", "isbn": "9781510632677", "book_title": "Advanced Chemical Microscopy for Life Science and Translational Medicine", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200311-151707274", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Cheng-Ji-Xin", "name": { "family": "Cheng", "given": "Ji-Xin" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" } }, { "id": "Simpson-G-J", "name": { "family": "Simpson", "given": "Garth J." } } ] }, "doi": "10.1117/12.2546942", "resource_type": "book_section", "pub_year": "2020", "author_list": "Wei, Lu; Miao, Kun; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7v12z-vb272", "eprint_id": 97792, "eprint_status": "archive", "datestamp": "2023-08-19 17:05:22", "lastmod": "2023-10-18 16:44:31", "type": "conference_item", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Stimulated Raman imaging with chemical probes for subcellular bioanalysis", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2019 American Chemical Society.", "abstract": "Innovations in optical spectroscopy and microscopy have revolutionized our understanding in biol. systems at subcellular levels. In this talk, I will present recent advances of two chem. imaging strategies addressing two fundamental challenges in optical bio-imaging. First, we devised a live-cell Bioorthogonal Chem. Imaging platform suited for probing the metabolic dynamics of small bio-mols., which cannot be effectively labeled by bulky fluorophores. This scheme couples the stimulated Raman scattering (SRS) microscopy, a nonlinear vibrational imaging modality that offers rich chem. information, with small vibrational tags including stable isotopes and triple bonds. We applied this platform to a variety of dynamical biol. systems and revealed previously less-known heterogeneity in metabolic signatures governing the obversed cell phenotypes. Second, we developed a supermultiplex optical imaging technique enabled by preresonant SRS microscopy of a newly designed palette of vibrational dyes. This work allows for simultaneous imaging of a large no. of mol. species in live cells and tissues with high sensitivity and specificity, bridging imaging and omics paradigms. Both phys. and chem. principles underlying the optical microscopy will be presented, as well as our recent efforts in biomedical applications including cancer- and neuronal- metab.", "date": "2019-08", "date_type": "published", "publisher": "Caltech Library", "id_number": "CaltechAUTHORS:20190812-141405591", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190812-141405591", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "resource_type": "conference_item", "pub_year": "2019", "author_list": "Wei, Lu" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/kqk29-9mq27", "eprint_id": 111913, "eprint_status": "archive", "datestamp": "2023-08-22 01:46:05", "lastmod": "2023-10-23 20:48:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Xiong-Hanqing", "name": { "family": "Xiong", "given": "Hanqing" } }, { "id": "Shi-Lixue", "name": { "family": "Shi", "given": "Lixue" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Long-Rong", "name": { "family": "Long", "given": "Rong" } }, { "id": "Zhao-Zhilun", "name": { "family": "Zhao", "given": "Zhilun" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Stimulated Raman excited fluorescence spectroscopy and imaging", "ispublished": "pub", "full_text_status": "public", "keywords": "Fluorescence spectroscopy; Imaging and sensing; Microscopy; Raman spectroscopy; Optical spectroscopy", "note": "\u00a9 2019 Nature Publishing Group. \n\nReceived 18 January 2019; Accepted 20 February 2019; \nPublished 01 April 2019. \n\nWe are grateful for discussions with L. E. Brus and X. Y. Zhu. This work was supported by grant R01GM128214 from the NIH, and by the Camille and Henry Dreyfus Foundation. \n\nThese authors contributed equally: Hanqing Xiong, Lixue Shi. \n\nAuthor Contributions: H.X. and L.S. collected and analysed all the data; H.X. designed and constructed the instrument with the help of L.S. and Z.Z. under the guidance of W.M.; L.W. and Y.S. contributed to the early phase of the spectroscopy project; R.L. performed chemical synthesis; W.M. conceived the concept; H.X., L.S. and W.M. wrote the manuscript with input from all authors. \n\nData availability: The data that support the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.\n\nAccepted Version - nihms-1522289.pdf
Supplemental Material - 41566_2019_396_MOESM1_ESM.pdf
", "abstract": "Powerful optical tools have revolutionized science and technology. The prevalent fluorescence detection offers superb sensitivity down to single molecules but lacks sufficient chemical information1. In contrast, Raman-based vibrational spectroscopy provides exquisite chemical specificity about molecular structure, dynamics and coupling, but is notoriously insensitive. Here, we report a hybrid technique of stimulated Raman excited fluorescence (SREF) that integrates superb detection sensitivity and fine chemical specificity. Through stimulated Raman pumping to an intermediate vibrational eigenstate, followed by an upconversion to an electronic fluorescent state, SREF encodes vibrational resonance into the excitation spectrum of fluorescence emission. By harnessing the narrow vibrational linewidth, we demonstrated multiplexed SREF imaging in cells, breaking the 'colour barrier' of fluorescence. By leveraging the superb sensitivity of SREF, we achieved all-far-field single-molecule Raman spectroscopy and imaging without plasmonic enhancement, a long-sought-after goal in photonics. Thus, through merging Raman and fluorescence spectroscopy, SREF would be a valuable tool for chemistry and biology.", "date": "2019-06", "date_type": "published", "publication": "Nature Photonics", "volume": "13", "number": "6", "publisher": "Nature Publishing Group", "pagerange": "412-417", "id_number": "CaltechAUTHORS:20211117-150753305", "issn": "1749-4885", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211117-150753305", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM128214" }, { "agency": "Camille and Henry Dreyfus Foundation" } ] }, "doi": "10.1038/s41566-019-0396-4", "pmcid": "PMC7326316", "primary_object": { "basename": "41566_2019_396_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/kqk29-9mq27/files/41566_2019_396_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "nihms-1522289.pdf", "url": "https://authors.library.caltech.edu/records/kqk29-9mq27/files/nihms-1522289.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Xiong, Hanqing; Shi, Lixue; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cp84r-7mf78", "eprint_id": 93811, "eprint_status": "archive", "datestamp": "2023-08-22 01:19:09", "lastmod": "2023-10-20 17:26:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Mian", "name": { "family": "Wei", "given": "Mian" } }, { "id": "Shi-Lingyan", "name": { "family": "Shi", "given": "Lingyan" } }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Zhao-Zhilun", "name": { "family": "Zhao", "given": "Zhilun" } }, { "id": "Guzman-A", "name": { "family": "Guzman", "given": "Asja" } }, { "id": "Kaufman-L-J", "name": { "family": "Kaufman", "given": "Laura J." } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy", "ispublished": "pub", "full_text_status": "public", "keywords": "volumetric imaging; stimulated Raman scattering; tissue clearing; metabolic imaging; cancer metabolism", "note": "\u00a9 2019 National Academy of Sciences. Published under the PNAS license. \n\nEdited by Lance L. Munn, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, and accepted by Editorial Board Member Rakesh K. Jain February 19, 2019 (received for review July 29, 2018). PNAS published ahead of print March 14, 2019. \n\nWe thank E. Silveira for technical assistance; Y. Yang and X. Qu for discussion; and T. Swayne and the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University for help with 3D image analysis, supported by NIH Grant P30 CA013696. W.M. acknowledges support of R01EB020892 from the NIH and the Camille and Henry Dreyfus Foundation. \n\nM.W. and L.S. contributed equally to this work. \n\nAuthor contributions: M.W., L.S., L.W., and W.M. designed research; M.W. and L.S. performed research; Y.S., Z.Z., A.G., and L.J.K. contributed new reagents/analytic tools; M.W. analyzed data; and M.W., L.S., L.W., and W.M. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. L.L.M. is a guest editor invited by the Editorial Board. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813044116/-/DCSupplemental.\n\nPublished - 6608.full.pdf
Supplemental Material - pnas.1813044116.sapp.pdf
", "abstract": "Three-dimensional visualization of tissue structures using optical microscopy facilitates the understanding of biological functions. However, optical microscopy is limited in tissue penetration due to severe light scattering. Recently, a series of tissue-clearing techniques have emerged to allow significant depth-extension for fluorescence imaging. Inspired by these advances, we develop a volumetric chemical imaging technique that couples Raman-tailored tissue-clearing with stimulated Raman scattering (SRS) microscopy. Compared with the standard SRS, the clearing-enhanced SRS achieves greater than 10-times depth increase. Based on the extracted spatial distribution of proteins and lipids, our method reveals intricate 3D organizations of tumor spheroids, mouse brain tissues, and tumor xenografts. We further develop volumetric phasor analysis of multispectral SRS images for chemically specific clustering and segmentation in 3D. Moreover, going beyond the conventional label-free paradigm, we demonstrate metabolic volumetric chemical imaging, which allows us to simultaneously map out metabolic activities of protein and lipid synthesis in glioblastoma. Together, these results support volumetric chemical imaging as a valuable tool for elucidating comprehensive 3D structures, compositions, and functions in diverse biological contexts, complementing the prevailing volumetric fluorescence microscopy.", "date": "2019-04-02", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "116", "number": "14", "publisher": "National Academy of Sciences", "pagerange": "6608-6617", "id_number": "CaltechAUTHORS:20190314-130512034", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190314-130512034", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P30 CA013696" }, { "agency": "NIH", "grant_number": "R01EB020892" }, { "agency": "Camille and Henry Dreyfus Foundation" } ] }, "doi": "10.1073/pnas.1813044116", "pmcid": "PMC6452712", "primary_object": { "basename": "6608.full.pdf", "url": "https://authors.library.caltech.edu/records/cp84r-7mf78/files/6608.full.pdf" }, "related_objects": [ { "basename": "pnas.1813044116.sapp.pdf", "url": "https://authors.library.caltech.edu/records/cp84r-7mf78/files/pnas.1813044116.sapp.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Wei, Mian; Shi, Lingyan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9gtaz-ymb50", "eprint_id": 91008, "eprint_status": "archive", "datestamp": "2023-08-19 11:53:04", "lastmod": "2023-10-19 22:03:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shi-Lixue", "name": { "family": "Shi", "given": "Lixue" } }, { "id": "Xiong-Hanqing", "name": { "family": "Xiong", "given": "Hanqing" } }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Long-Rong", "name": { "family": "Long", "given": "Rong" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Electronic Resonant Stimulated Raman Scattering Micro-Spectroscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 American Chemical Society. \n\nReceived: July 22, 2018. Revised: September 8, 2018. Published: September 12, 2018. \n\nPublished as part of The Journal of Physical Chemistry virtual special issue \"Young Scientists\". \n\nW.M. acknowledges support from the US Army Research Office (W911NF-12-1-0594) and R01 (EB020892) and the Camille and Henry Dreyfus Foundation. \n\nThe authors declare no competing financial interest.\n\nAccepted Version - nihms-1017006.pdf
Supplemental Material - jp8b07037_si_001.pdf
", "abstract": "Recently we have reported electronic pre-resonance stimulated Raman scattering (epr-SRS) microscopy as a powerful technique for super-multiplex imaging (Wei, L.; Nature 2017, 544, 465\u2212470). However, under rigorous electronic resonance, background signal, which mainly originates from pump\u2013probe process, overwhelms the desired vibrational signature of the chromophores. Here we demonstrate electronic resonant stimulated Raman scattering (er-SRS) microspectroscopy and imaging through suppression of electronic background and subsequent retrieval of vibrational peaks. We observed a change of the vibrational band shapes from normal Lorentzian, through dispersive shapes, to inverted Lorentzian as the electronic resonance was approached, in agreement with theoretical prediction. In addition, resonant Raman cross sections have been determined after power-dependence study as well as Raman excitation profile calculation. As large as 10\u207b\u00b2\u00b3 cm\u00b2 of resonance Raman cross section is estimated in er-SRS, which is about 100 times higher than previously reported in epr-SRS. These results of er-SRS microspectroscopy pave the way for the single-molecule Raman detection and ultrasensitive biological imaging.", "date": "2018-10-04", "date_type": "published", "publication": "Journal of Physical Chemistry B", "volume": "122", "number": "39", "publisher": "American Chemical Society", "pagerange": "9218-9224", "id_number": "CaltechAUTHORS:20181119-102039172", "issn": "1520-6106", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102039172", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "NIH", "grant_number": "R01 EB020892" }, { "agency": "Camille and Henry Dreyfus Foundation" } ] }, "doi": "10.1021/acs.jpcb.8b07037", "pmcid": "PMC6425473", "primary_object": { "basename": "jp8b07037_si_001.pdf", "url": "https://authors.library.caltech.edu/records/9gtaz-ymb50/files/jp8b07037_si_001.pdf" }, "related_objects": [ { "basename": "nihms-1017006.pdf", "url": "https://authors.library.caltech.edu/records/9gtaz-ymb50/files/nihms-1017006.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Shi, Lixue; Xiong, Hanqing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7jexz-ngd44", "eprint_id": 91009, "eprint_status": "archive", "datestamp": "2023-08-19 10:58:52", "lastmod": "2023-10-19 22:03:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Electronic Preresonance Stimulated Raman Scattering Microscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 American Chemical Society. ACS Editors' Choice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. \n\nReceived: January 21, 2018. Accepted: July 12, 2018. Published: July 12, 2018. \n\nWe are grateful for discussions with Lixue Shi, Zhixing Chen, Louis Brus, and Sunney Xie. W.M. acknowledges support from NIH Director's New Innovator Award (1DP2EB016573) and R01 (EB020892) and the Camille and Henry Dreyfus Foundation. \n\nThe authors declare no competing financial interest.\n\nPublished - acs.jpclett.8b00204
Cover Image - jpclcd_v009i015.jpg
", "abstract": "Optical microscopy has generated great impact for modern research. While fluorescence microscopy provides the ultimate sensitivity, it generally lacks chemical information. Complementarily, vibrational imaging methods provide rich chemical-bond-specific contrasts. Nonetheless, they usually suffer from unsatisfying sensitivity or compromised biocompatibility. Recently, electronic preresonance stimulated Raman scattering (EPR-SRS) microscopy was reported, achieving simultaneous high detection sensitivity and superb vibrational specificity of chromophores. With newly synthesized Raman-active dyes, this method readily breaks the optical color barrier of fluorescence microscopy and is well-suited for supermultiplex imaging in biological samples. In this Perspective, we first review previous utilizations of electronic resonance in various Raman spectroscopy and microscopy. We then discuss the physical origin and uniqueness of the electronic preresonance region, followed by quantitative analysis of the enhancement factors involved in EPR-SRS microscopy. On this basis, we provide an outlook for future development as well as the broad applications in biophotonics.", "date": "2018-08-02", "date_type": "published", "publication": "Journal of Physical Chemistry Letters", "volume": "9", "number": "15", "publisher": "American Chemical Society", "pagerange": "4294-4301", "id_number": "CaltechAUTHORS:20181119-102039337", "issn": "1948-7185", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102039337", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1DP2EB016573" }, { "agency": "NIH", "grant_number": "R01 EB020892" }, { "agency": "Camille and Henry Dreyfus Foundation" } ] }, "doi": "10.1021/acs.jpclett.8b00204", "pmcid": "PMC6077771", "primary_object": { "basename": "acs.jpclett.8b00204", "url": "https://authors.library.caltech.edu/records/7jexz-ngd44/files/acs.jpclett.8b00204" }, "related_objects": [ { "basename": "jpclcd_v009i015.jpg", "url": "https://authors.library.caltech.edu/records/7jexz-ngd44/files/jpclcd_v009i015.jpg" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Wei, Lu and Min, Wei" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0carm-zdm78", "eprint_id": 91010, "eprint_status": "archive", "datestamp": "2023-08-19 10:37:58", "lastmod": "2023-10-19 22:03:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cheng-Qian", "name": { "family": "Cheng", "given": "Qian" }, "orcid": "0000-0001-5510-2977" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Liu-Zhe", "name": { "family": "Liu", "given": "Zhe" } }, { "id": "Ni-Nan", "name": { "family": "Ni", "given": "Nan" } }, { "id": "Sang-Zhe", "name": { "family": "Sang", "given": "Zhe" } }, { "id": "Zhu-Bin", "name": { "family": "Zhu", "given": "Bin" }, "orcid": "0000-0001-6165-3994" }, { "id": "Xu-Weiheng", "name": { "family": "Xu", "given": "Weiheng" } }, { "id": "Meijie-Chen", "name": { "family": "Chen", "given": "Meijie" } }, { "id": "Mao-Yupeng", "name": { "family": "Miao", "given": "Yupeng" } }, { "id": "Chen-Long-Qing", "name": { "family": "Chen", "given": "Long-Qing" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" }, { "id": "Yang-Yuan", "name": { "family": "Yang", "given": "Yuan" }, "orcid": "0000-0003-0264-2640" } ] }, "title": "Operando and three-dimensional visualization of anion depletion and lithium growth by stimulated Raman scattering microscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 The Author(s). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived: 12 December 2017 Accepted: 24 June 2018. Published online: 30 July 2018. \n\nWe acknowledge seed funding support from Columbia University's Research Initiatives in Science & Engineering competition, started in 2004 to trigger high-risk, high-reward, and innovative collaborations in the basic sciences, engineering, and medicine. Y.Y. acknowledges support from startup funding by Columbia University. W.M. acknowledges support from the US Army Research Office (W911NF-12-1-0594), NIH Director's New Innovator Award (1DP2EB016573) and R01 (EB020892), and the Camille and Henry Dreyfus Foundation. Z.L and L.-Q.C. acknowledge the support from the Department of Energy, Office of Energy Efficiency and Renewable Energy (EERE), under the Award (DE-EE0007803). Y.Y and Q.C. also want to thank Prof. Alan West at Columbia University for his kind help. \n\nThese authors contributed equally: Qian Cheng, Lu Wei. \n\nAuthor Contributions: Y.Y., W.M., Q.C., and L.W. conceived the idea and designed the experiments. Q.C. and L.W. performed all the experiments and measurements. Z.L, Z.S. and L-Q. C. performed simulations. N.N., B.Z., W.X., M.C., and Y.M. helped prepare and perform experiments. All authors discussed the results. Q.C., L.W., Y.Y., W.M. and Z.L. wrote the paper with the input from all authors. \n\nData availability: The data that support the findings of this study are available from the corresponding author upon reasonable request. \n\nThe authors declare no competing interests.\n\nPublished - s41467-018-05289-z.pdf
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", "abstract": "Visualization of ion transport in electrolytes provides fundamental understandings of electrolyte dynamics and electrolyte-electrode interactions. However, this is challenging because existing techniques are hard to capture low ionic concentrations and fast electrolyte dynamics. Here we show that stimulated Raman scattering microscopy offers required resolutions to address a long-lasting question: how does the lithium-ion concentration correlate to uneven lithium deposition? In this study, anions are used to represent lithium ions since their concentrations should not deviate for more than 0.1\u2009mM, even near nanoelectrodes. A three-stage lithium deposition process is uncovered, corresponding to no depletion, partial depletion, and full depletion of lithium ions. Further analysis reveals a feedback mechanism between the lithium dendrite growth and heterogeneity of local ionic concentration, which can be suppressed by artificial solid electrolyte interphase. This study shows that stimulated Raman scattering microscopy is a powerful tool for the materials and energy field.", "date": "2018-07-30", "date_type": "published", "publication": "Nature Communications", "volume": "9", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 2942", "id_number": "CaltechAUTHORS:20181119-102039470", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102039470", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Columbia University" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "NIH", "grant_number": "1DP2EB016573" }, { "agency": "NIH", "grant_number": "R01 EB020892" }, { "agency": "Camille and Henry Dreyfus Foundation" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-EE0007803" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1038/s41467-018-05289-z", "pmcid": "PMC6065384", "primary_object": { "basename": "41467_2018_5289_MOESM5_ESM.avi", "url": "https://authors.library.caltech.edu/records/0carm-zdm78/files/41467_2018_5289_MOESM5_ESM.avi" }, "related_objects": [ { "basename": "41467_2018_5289_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/0carm-zdm78/files/41467_2018_5289_MOESM1_ESM.pdf" }, { "basename": "s41467-018-05289-z.pdf", "url": "https://authors.library.caltech.edu/records/0carm-zdm78/files/s41467-018-05289-z.pdf" }, { "basename": "41467_2018_5289_MOESM4_ESM.avi", "url": "https://authors.library.caltech.edu/records/0carm-zdm78/files/41467_2018_5289_MOESM4_ESM.avi" }, { "basename": "41467_2018_5289_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/0carm-zdm78/files/41467_2018_5289_MOESM3_ESM.pdf" }, { "basename": "41467_2018_5289_MOESM6_ESM.avi", "url": "https://authors.library.caltech.edu/records/0carm-zdm78/files/41467_2018_5289_MOESM6_ESM.avi" }, { "basename": "41467_2018_5289_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/0carm-zdm78/files/41467_2018_5289_MOESM2_ESM.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Cheng, Qian; Wei, Lu; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f98vy-5sc63", "eprint_id": 86925, "eprint_status": "archive", "datestamp": "2023-08-20 04:18:31", "lastmod": "2023-10-18 20:42:46", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" } ] }, "title": "Nonlinear optical microscopy for the invisible: vibrational imaging of small molecules in live cells and electronic imaging of fluorophores into the ultra deep", "ispublished": "unpub", "full_text_status": "public", "note": "Accepted Version - Wei_columbia_0054D_12908.pdf
", "abstract": "Nonlinear optical microscopy (NOM) has become increasingly popular in biomedical research in recent years with the developments of laser sources, contrast mechanisms, novel probes and etc. One of the advantages of NOM over the linear counterpart is the ability to image deep into scattering tissues or even on the whole animals. This is due to the adoption of near-infrared excitation that is of less scattering than visible excitation, and the intrinsic optical sectioning capability minimizing the excitation background beyond focal volume. Such an advantage is particularly prominent in two-photon fluorescence microscopy compared to one-photon fluorescence microscopy. In addition, NOM may provide extra molecular information (e.g. second harmonic generation and third harmonic generation) or stronger signal (e.g. stimulated Raman scattering and coherent anti-Stokes Raman scattering compared to spontaneous Raman scattering), because of the nonlinear interaction between strong optical fields and molecules. However, the merits of NOM are not yet fully exploited to tackle important questions in biomedical research. This thesis contributes to the developments of NOM in two aspects that correspond to two fundamental problems in biomedical imaging: first, how to non invasively image small functional biomolecules in live biological systems (Chapters 1-4); second, how to extend the optical imaging depth inside scattering tissues (Chapters 5-6). The ability to non-perturbatively image vital small biomolecules is crucial for understanding the complex functions of biological systems. However, it has proven to be highly challenging with the prevailing method of fluorescence microscopy. Because it requires the utilization of large-size fluorophore tagging (e.g., the Green Fluorescent Protein tagging) that would severely perturb the natural functions of small bio-molecules. Hence, we devise and construct a nonlinear Raman imaging platform, with the coupling of the emerging stimulated Raman scattering (SRS) microscopy and tiny vibrational tags, which provides superb sensitivity, specificity and biocompatibility for imaging small biomolecules (Chapters 1-4). Chapter 1 outlines the theoretical background for Raman scattering. Chapter 2 describes the instrumentation for SRS microscopy, followed with an overview of recent technical developments. Chapter 3 depicts the coupling of SRS microscopy with small alkyne tags (C\u2261C) to sensitively and specifically image a broad spectrum of small and functionally vital biomolecules (i.e. nucleic acids, amino acids, choline, fatty acids and small molecule drugs) in live cells, tissues and animals. Chapter 4 reports the combination of SRS microscopy with small carbon-deuterium (C-D) bonds to probe the complex and dynamic protein metabolism, including protein synthesis, degradation and trafficking, with subcellular resolution through metabolic labeling. It is to my belief that the coupling of SRS microscopy with alkyne or C-D tags will be readily applied in answering key biological questions in the near future. The remaining chapters of this thesis (Chapters 5-6) present the super-nonlinear fluorescence microscopy (SNFM) techniques for extending the optical imaging depth into scattering tissues. Unlike SRS microscopy that is an emerging technique, multiphoton microscopy (mainly referred as two-photon fluorescence microscopy), has matured over 20 years with its setup scheme and biological applications. Although it offers the deepest penetration in the optical microscopy, it still poses a fundamental depth limit set by the signal-to-background ratio when imaging into scattering tissues. Three SNFM techniques are proposed to extend such a depth limit: unlike the conventional multiphoton microscopy whose nonlinearity stems from virtual-states mediated simultaneous interactions between the incident photons and the molecules, the high-order nonlinearity of the SNFM techniques that we have conceived is generated through real-state mediated population-transfer kinetics. In particular, Chapter 5 demonstrates the multiphoton activation and imaging (MPAI) microscopy, which adopts a new class of fluorophores, the photoactivatable fluorophores, to significantly extend the fundamental imaging depth limit. Chapter 6 theoretically and analytically depicts two additional SNFM techniques of stimulated emission reduced fluorescence (SERF) microscopy and focal saturation microscopy. Both MPAI and focal saturation microscopies exhibit a fourth order power dependence, which is effectively a four-photon process. SERF presents a third order power dependence for a three-photon process.", "date": "2018-06-11", "date_type": "published", "id_number": "CaltechAUTHORS:20180608-131246246", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-131246246", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.7916/D81J991F", "primary_object": { "basename": "Wei_columbia_0054D_12908.pdf", "url": "https://authors.library.caltech.edu/records/f98vy-5sc63/files/Wei_columbia_0054D_12908.pdf" }, "resource_type": "thesis", "pub_year": "2018", "author_list": "Wei, Lu" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/wexeq-yeg77", "eprint_id": 86924, "eprint_status": "archive", "datestamp": "2023-08-19 08:08:07", "lastmod": "2023-10-18 20:42:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Zeng-Chen", "name": { "family": "Zeng", "given": "Chen" }, "orcid": "0000-0003-2829-5018" }, { "id": "Long-Rong", "name": { "family": "Long", "given": "Rong" } }, { "id": "Mao-Yupeng", "name": { "family": "Miao", "given": "Yupeng" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Xu-Qizhi", "name": { "family": "Xu", "given": "Qizhi" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Supermultiplexed optical imaging and barcoding with engineered polyynes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 Macmillan Publishers Limited. \n\nReceived: 23 August 2017. Accepted: 05 December 2017. Published: 15 January 2018. \n\nWe are grateful for the discussion with L. Brus, Y. Shen and Z. Chen. W.M. acknowledges support from NIH Director's New Innovator Award (1DP2EB016573), R01 (EB020892), the US Army Research Office (W911NF-12-1-0594), and the Camille and Henry Dreyfus Foundation. \n\nAuthor Contributions: F.H. performed the spectroscopy, microscopy and biological studies and analyzed the data with the help of Y.M., L.W. and Q.X.; C.Z. performed the chemical synthesis together with R.L.; F.H. and W.M. conceived the concept; F.H., C.Z. and W.M. designed the experiments and wrote the manuscript with input from all authors. \n\nCompeting interests: Columbia University has filed a patent application (US 62/540,953) based on this study. \n\nCode availability. The MATLAB code is available from the corresponding author upon request. \n\nLife Sciences Reporting Summary. Further information on experimental design is available in the Life Sciences Reporting Summary. \n\nData availability. The data that support the findings of this study are provided in Supplementary Figures 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, Supplementary Tables 1\u20133 and Supplementary Note 1 and are available from the corresponding author upon request.\n\nSupplemental Material - nmeth.4578-S1.pdf
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", "abstract": "Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability. Moreover, we realized optical data storage and identification by combinatorial barcoding, yielding to our knowledge the largest number of distinct spectral barcodes to date. Therefore, these polyynes hold great promise in live-cell imaging and sorting as well as in high-throughput diagnostics and screening.", "date": "2018-03", "date_type": "published", "publication": "Nature Methods", "volume": "15", "number": "3", "publisher": "Nature Publishing Group", "pagerange": "194-200", "id_number": "CaltechAUTHORS:20180608-125759681", "issn": "1548-7091", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-125759681", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1DP2EB016573" }, { "agency": "NIH", "grant_number": "R01 EB020892" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "Camille and Henry Dreyfus Foundation" } ] }, "doi": "10.1038/nmeth.4578", "pmcid": "PMC5831481", "primary_object": { "basename": "nmeth.4578-SF2.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF2.jpg" }, "related_objects": [ { "basename": "nmeth.4578-SF4.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF4.jpg" }, { "basename": "nmeth.4578-SF6.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF6.jpg" }, { "basename": "nmeth.4578-SF9.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF9.jpg" }, { "basename": "nmeth.4578-SF1.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF1.jpg" }, { "basename": "nmeth.4578-SF10.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF10.jpg" }, { "basename": "nmeth.4578-SF13.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF13.jpg" }, { "basename": "nmeth.4578-SF5.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF5.jpg" }, { "basename": "nmeth.4578-SF8.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF8.jpg" }, { "basename": "nmeth.4578-S1.pdf", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-S1.pdf" }, { "basename": "nmeth.4578-SF11.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF11.jpg" }, { "basename": "nmeth.4578-SF12.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF12.jpg" }, { "basename": "nmeth.4578-S2.pdf", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-S2.pdf" }, { "basename": "nmeth.4578-SF3.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF3.jpg" }, { "basename": "nmeth.4578-SF7.jpg", "url": "https://authors.library.caltech.edu/records/wexeq-yeg77/files/nmeth.4578-SF7.jpg" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Hu, Fanghao; Zeng, Chen; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/thdkc-52h59", "eprint_id": 86916, "eprint_status": "archive", "datestamp": "2023-08-19 02:45:34", "lastmod": "2023-10-23 15:08:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Shi-Lixue", "name": { "family": "Shi", "given": "Lixue" } }, { "id": "Long-Rong", "name": { "family": "Long", "given": "Rong" } }, { "id": "Anzalone-A-V", "name": { "family": "Anzalone", "given": "Andrew V." } }, { "id": "Zhang-Liyuan", "name": { "family": "Zhang", "given": "Liyuan" }, "orcid": "0000-0002-0898-787X" }, { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Yuste-R", "name": { "family": "Yuste", "given": "Rafael" } }, { "id": "Cornish-V-W", "name": { "family": "Cornish", "given": "Virginia W." } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Super-multiplex vibrational imaging", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Macmillan Publishers Limited. \n\nreceived 21 September 2016; accepted 3 March 2017. Published online 19 April 2017. \n\nWe thank L. Brus and A. McDermott for discussions, M. Jimenez and C. Dupre for suggestions, and L. Shi for technical assistance. W.M. acknowledges support from an NIH Director's New Innovator Award (1DP2EB016573), R01 (EB020892), the US Army Research Office (W911NF-12-1-0594), the Alfred P. Sloan Foundation and the Camille and Henry Dreyfus Foundation. R.Y. is supported by the NEI (EY024503, EY011787) and NIMH (MH101218, MH100561). \n\nAuthor Contributions: L.W. carried out the spectroscopy, microscopy and biological studies together with L.S. and with the help of L.Z., F.H. and R.Y.; Z.C. designed and performed chemical synthesis together with R.L., A.V.A. and L.W. under the guidance of V.W.C. and W.M.; L.W. and W.M. conceived the concept; and L.W., Z.C. and W.M. wrote the manuscript with input from all authors. \n\nData availability: All data that support this study are available from the corresponding author on request. Source Data for Fig. 4e are available in the online version of the paper. \n\nCompeting interests: Columbia University has filed a patent application based on this work.\n\nAccepted Version - nihms858426.pdf
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", "abstract": "The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure\u2013function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions. For instance, fluorescence microscopy faces a 'colour barrier', owing to the intrinsically broad (about 1,500 inverse centimetres) and featureless nature of fluorescence spectra that limits the number of resolvable colours to two to five (or seven to nine if using complicated instrumentation and analysis). Spontaneous Raman microscopy probes vibrational transitions with much narrower resonances (peak width of about 10 inverse centimetres) and so does not suffer from this problem, but weak signals make many bio-imaging applications impossible. Although surface-enhanced Raman scattering offers high sensitivity and multiplicity, it cannot be readily used to image specific molecular targets quantitatively inside live cells. Here we use stimulated Raman scattering under electronic pre-resonance conditions to image target molecules inside living cells with very high vibrational selectivity and sensitivity (down to 250 nanomolar with a time constant of 1 millisecond). We create a palette of triple-bond-conjugated near-infrared dyes that each displays a single peak in the cell-silent Raman spectral window; when combined with available fluorescent probes, this palette provides 24 resolvable colours, with the potential for further expansion. Proof-of-principle experiments on neuronal co-cultures and brain tissues reveal cell-type-dependent heterogeneities in DNA and protein metabolism under physiological and pathological conditions, underscoring the potential of this 24-colour (super-multiplex) optical imaging approach for elucidating intricate interactions in complex biological systems.", "date": "2017-04-27", "date_type": "published", "publication": "Nature", "volume": "544", "number": "7651", "publisher": "Nature Publishing Group", "pagerange": "465-470", "id_number": "CaltechAUTHORS:20180608-105013735", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-105013735", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1DP2EB016573" }, { "agency": "NIH", "grant_number": "R01 EB020892" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Camille and Henry Dreyfus Foundation" }, { "agency": "NIH", "grant_number": "EY024503" }, { "agency": "NIH", "grant_number": "EY011787" }, { "agency": "NIH", "grant_number": "MH101218" }, { "agency": "NIH", "grant_number": "MH100561" } ] }, "doi": "10.1038/nature22051", "pmcid": "PMC5939925", "primary_object": { "basename": "nature22051-sf2.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf2.jpg" }, "related_objects": [ { "basename": "nature22051-st2.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-st2.jpg" }, { "basename": "nature22051-s1.pdf", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-s1.pdf" }, { "basename": "nature22051-sf3.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf3.jpg" }, { "basename": "nature22051-sf5.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf5.jpg" }, { "basename": "nature22051-sf7.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf7.jpg" }, { "basename": "nature22051-sf9.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf9.jpg" }, { "basename": "nature22051-st1.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-st1.jpg" }, { "basename": "nature22051-sf4.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf4.jpg" }, { "basename": "nature22051-sf8.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf8.jpg" }, { "basename": "nature22051-sf1.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf1.jpg" }, { "basename": "nature22051-sf6.jpg", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nature22051-sf6.jpg" }, { "basename": "nihms858426.pdf", "url": "https://authors.library.caltech.edu/records/thdkc-52h59/files/nihms858426.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Wei, Lu; Chen, Zhixing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fdy1h-cb684", "eprint_id": 86919, "eprint_status": "archive", "datestamp": "2023-08-19 00:37:34", "lastmod": "2023-10-18 20:42:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Lamprecht-M-R", "name": { "family": "Lamprecht", "given": "Michael R." } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Morrison-B", "name": { "family": "Morrison", "given": "Barclay" } }, { "id": "Wei-Min", "name": { "family": "Min", "given": "Wei" } } ] }, "title": "Bioorthogonal chemical imaging of metabolic activities in live mammalian hippocampal tissues with stimulated Raman scattering", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 The Author(s). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ \n\nreceived: 30 September 2016, accepted: 25 November 2016. Published: 21 December 2016. \n\nWe thank Y. Shen and L. Shi for helpful discussions. W. M. acknowledges support from NIH Director's New Innovator Award (Grant 1DP2EB016573), NIH R01 (Grant EB020892), the US Army Research Office (Grant W911NF-12-1-0594), the Alfred P. Sloan Foundation, and the Camille and Henry Dreyfus Foundation. B.M. acknowledges support from the Army Research Laboratory (Grant W911NF-10-1-0526). M.R.L acknowledges support from a National Science Foundation Graduate Research Fellowship. \n\nAuthor Contributions: F.H., B.M. and W.M. conceived the concept and designed the experiments. F.H., M.R.L. and L.W. performed the experiments. F.H. analyzed the data and wrote the manusript. B.M. and W.M. oversaw the study and edited the manuscript. All authors reviewed the manusript. \n\nThe authors declare no competing financial interests.\n\nPublished - srep39660.pdf
Supplemental Material - srep39660-s1.pdf
", "abstract": "Brain is an immensely complex system displaying dynamic and heterogeneous metabolic activities. Visualizing cellular metabolism of nucleic acids, proteins, and lipids in brain with chemical specificity has been a long-standing challenge. Recent development in metabolic labeling of small biomolecules allows the study of these metabolisms at the global level. However, these techniques generally require nonphysiological sample preparation for either destructive mass spectrometry imaging or secondary labeling with relatively bulky fluorescent labels. In this study, we have demonstrated bioorthogonal chemical imaging of DNA, RNA, protein and lipid metabolism in live rat brain hippocampal tissues by coupling stimulated Raman scattering microscopy with integrated deuterium and alkyne labeling. Heterogeneous metabolic incorporations for different molecular species and neurogenesis with newly-incorporated DNA were observed in the dentate gyrus of hippocampus at the single cell level. We further applied this platform to study metabolic responses to traumatic brain injury in hippocampal slice cultures, and observed marked upregulation of protein and lipid metabolism particularly in the hilus region of the hippocampus within days of mechanical injury. Thus, our method paves the way for the study of complex metabolic profiles in live brain tissue under both physiological and pathological conditions with single-cell resolution and minimal perturbation.", "date": "2016-12-21", "date_type": "published", "publication": "Scientific Reports", "volume": "6", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 39660", "id_number": "CaltechAUTHORS:20180608-112524422", "issn": "2045-2322", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-112524422", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1DP2EB016573" }, { "agency": "NIH", "grant_number": "R01 EB020892" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Camille and Henry Dreyfus Foundation" }, { "agency": "Army Research Laboratory", "grant_number": "W911NF-10-1-0526" }, { "agency": "NSF Graduate Research Fellowship" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1038/srep39660", "pmcid": "PMC5175176", "primary_object": { "basename": "srep39660-s1.pdf", "url": "https://authors.library.caltech.edu/records/fdy1h-cb684/files/srep39660-s1.pdf" }, "related_objects": [ { "basename": "srep39660.pdf", "url": "https://authors.library.caltech.edu/records/fdy1h-cb684/files/srep39660.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Hu, Fanghao; Lamprecht, Michael R.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cffaa-aa371", "eprint_id": 86920, "eprint_status": "archive", "datestamp": "2023-08-20 13:26:03", "lastmod": "2023-10-18 20:42:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Zhang-Luyuan", "name": { "family": "Zhang", "given": "Luyuan" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Live-Cell Bioorthogonal Chemical Imaging: Stimulated Raman Scattering Microscopy of Vibrational Probes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 American Chemical Society. \n\nReceived: May 2, 2016. Published: August 3, 2016. \n\nWe appreciate helpful discussions with Meng Wang, Colin Nuckolls, Louis Brus, Ann McDermott, Ronald Breslow, Virginia Cornish, Rafael Yuste, Sunney Xie, and Steven Boxer. This work is supported by NIH Director's New Innovator Award (Grant 1DP2EB016573), R01 (Grant EB020892), the US Army Research Office (Grant W911NF-12-1-0594), the Alfred P. Sloan Foundation, and the Camille and Henry Dreyfus Foundation. Y. Shen acknowledges support from HHMI International Student Research Fellowship. \n\nThe authors declare the following competing financial interest(s): Columbia University has filed a patent application based on this work.\n\nAccepted Version - nihms865024.pdf
", "abstract": "Innovations in light microscopy have tremendously revolutionized the way researchers study biological systems with subcellular resolution. In particular, fluorescence microscopy with the expanding choices of fluorescent probes has provided a comprehensive toolkit to tag and visualize various molecules of interest with exquisite specificity and high sensitivity. Although fluorescence microscopy is currently the method of choice for cellular imaging, it faces fundamental limitations for studying the vast number of small biomolecules. This is because common fluorescent labels, which are relatively bulky, could introduce considerable perturbation to or even completely alter the native functions of vital small biomolecules. Hence, despite their immense functional importance, these small biomolecules remain largely undetectable by fluorescence microscopy. \n\nTo address this challenge, a bioorthogonal chemical imaging platform has recently been introduced. By coupling stimulated Raman scattering (SRS) microscopy, an emerging nonlinear Raman microscopy technique, with tiny and Raman-active vibrational probes (e.g., alkynes and stable isotopes), bioorthogonal chemical imaging exhibits superb sensitivity, specificity, and biocompatibility for imaging small biomolecules in live systems. In this Account, we review recent technical achievements for visualizing a broad spectrum of small biomolecules, including ribonucleosides and deoxyribonucleosides, amino acids, fatty acids, choline, glucose, cholesterol, and small-molecule drugs in live biological systems ranging from individual cells to animal tissues and model organisms. Importantly, this platform is compatible with live-cell biology, thus allowing real-time imaging of small-molecule dynamics. Moreover, we discuss further chemical and spectroscopic strategies for multicolor bioorthogonal chemical imaging, a valuable technique in the era of \"omics\". \n\nAs a unique tool for biological discovery, this platform has been applied to studying various metabolic processes under both physiological and pathological states, including protein synthesis activity of neuronal systems, protein aggregations in Huntington disease models, glucose uptake in tumor xenografts, and drug penetration through skin tissues. We envision that the coupling of SRS microscopy with vibrational probes would do for small biomolecules what fluorescence microscopy of fluorophores has done for larger molecular species.", "date": "2016-08-16", "date_type": "published", "publication": "Accounts of Chemical Research", "volume": "49", "number": "8", "publisher": "American Chemical Society", "pagerange": "1494-1502", "id_number": "CaltechAUTHORS:20180608-113519551", "issn": "0001-4842", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-113519551", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1DP2EB016573" }, { "agency": "NIH", "grant_number": "R01 EB020892" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "Camille and Henry Dreyfus Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1021/acs.accounts.6b00210", "pmcid": "PMC5704954", "primary_object": { "basename": "nihms865024.pdf", "url": "https://authors.library.caltech.edu/records/cffaa-aa371/files/nihms865024.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Wei, Lu; Hu, Fanghao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/30ep4-vys47", "eprint_id": 86921, "eprint_status": "archive", "datestamp": "2023-08-20 11:23:01", "lastmod": "2024-01-14 20:14:33", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanhao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Zhang-Luyuan", "name": { "family": "Zhang", "given": "Luyuan" } }, { "id": "Shen-Yuhui", "name": { "family": "Shen", "given": "Yuhui" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Vibrational imaging of glucose uptake activity in live cells and tissues by stimulated Raman scattering microscopy", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2016 Society of Photo-Optical Instrumentation Engineers (SPIE).", "abstract": "Glucose is consumed as an energy source by virtually all living organisms, from bacteria to humans. Its uptake activity closely reflects the cellular metabolic status in various pathophysiological transformations, such as diabetes and cancer. Extensive efforts such as positron emission tomography, magnetic resonance imaging and fluorescence microscopy have been made to specifically image glucose uptake activity but all with technical limitations. Here, we report a new platform to visualize glucose uptake activity in live cells and tissues with subcellular resolution and minimal perturbation. A novel glucose analogue with a small alkyne tag (carbon-carbon triple bond) is developed to mimic natural glucose for cellular uptake, which can be imaged with high sensitivity and specificity by targeting the strong and characteristic alkyne vibration on stimulated Raman scattering (SRS) microscope to generate a quantitative three dimensional concentration map. Cancer cells with differing metabolic characteristics can be distinguished. Heterogeneous uptake patterns are observed in tumor xenograft tissues, neuronal culture and mouse brain tissues with clear cell-cell variations. Therefore, by offering the distinct advantage of optical resolution but without the undesirable influence of bulky fluorophores, our method of coupling SRS with alkyne labeled glucose will be an attractive tool to study energy demands of living systems at the single cell level.", "date": "2016-04-27", "date_type": "published", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 97230B", "id_number": "CaltechAUTHORS:20180608-114633492", "isbn": "9781628419573", "book_title": "Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications VIII", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-114633492", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Achilefu-S", "name": { "family": "Achilefu", "given": "Samuel" } }, { "id": "Raghavachari-R", "name": { "family": "Raghavachari", "given": "Ramesh" } } ] }, "doi": "10.1117/12.2211787", "resource_type": "book_section", "pub_year": "2016", "author_list": "Hu, Fanhao; Chen, Zhixing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/z03bm-g1e67", "eprint_id": 86922, "eprint_status": "archive", "datestamp": "2023-08-20 11:09:37", "lastmod": "2023-10-18 20:42:35", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Optical Imaging of Vibrationally-Tagged Small molecules for Biomedicine", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2016 Optical Society of America.", "abstract": "We report a novel imaging platform, by coupling stimulated Raman scattering microscopy with small vibrational tags (including isotopes and alkynes), to probe dynamics of small biomolecules in living organisms with superb sensitivity, specificity and biocompatibility.", "date": "2016-04", "date_type": "published", "publisher": "Optical Society of America", "place_of_pub": "Washington, DC", "pagerange": "Art. No. BTh2D.2", "id_number": "CaltechAUTHORS:20180608-115332345", "isbn": "978-1-943580-10-1", "book_title": "Biomedical Optics 2016", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-115332345", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1364/BRAIN.2016.BTh2D.2", "resource_type": "book_section", "pub_year": "2016", "author_list": "Wei, Lu and Min, Wei" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/498s5-88p84", "eprint_id": 86923, "eprint_status": "archive", "datestamp": "2023-08-20 07:46:59", "lastmod": "2023-10-18 20:42:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Zhang-Luyuan", "name": { "family": "Zhang", "given": "Luyuan" } }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Vibrational Imaging of Glucose Uptake Activity in Live Cells and Tissues by Stimulated Raman Scattering", "ispublished": "pub", "full_text_status": "public", "keywords": "alkyne tags \u00b7 glucose uptake \u00b7 imaging agents \u00b7 Raman spectroscopy \u00b7 SRS microscopy", "note": "\u00a9 2015 WILEY\u2010VCH. \n\nReceived: March 18, 2015. Revised: April 26, 2015. Published online: July 16, 2015. \n\nWe thank Y. Shin for providing hippocampal neurons and J. Hirtz for assistance on mouse brain tissues. W.M. acknowledges support from the NIH Director's New Innovator Award, ARO MURI W911NF-12-1-0594, and a Alfred P. Sloan Research Fellowship.\n\nAccepted Version - nihms732618.pdf
Supplemental Material - anie_201502543_sm_miscellaneous_information.pdf
", "abstract": "Glucose is a ubiquitous energy source for most living organisms. Its uptake activity closely reflects cellular metabolic demand in various physiopathological conditions. Extensive efforts have been made to specifically image glucose uptake, such as with positron emission tomography, magnetic resonance imaging, and fluorescence microscopy, but all have limitations. A new platform to visualize glucose uptake activity in live cells and tissues is presented that involves performing stimulated Raman scattering on a novel glucose analogue labeled with a small alkyne moiety. Cancer cells with differing metabolic activities can be distinguished. Heterogeneous uptake patterns are observed with clear cell-cell variations in tumor xenograft tissues, neuronal culture, and mouse brain tissues. By offering the distinct advantage of optical resolution but without the undesirable influence of fluorophores, this method will facilitate the study of energy demands of living systems with subcellular resolution.", "date": "2015-08-17", "date_type": "published", "publication": "Angewandte Chemie International Edition", "volume": "54", "number": "34", "publisher": "Wiley", "pagerange": "9821-9825", "id_number": "CaltechAUTHORS:20180608-124956778", "issn": "1433-7851", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-124956778", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "Alfred P. Sloan Foundation" } ] }, "doi": "10.1002/anie.201502543", "pmcid": "PMC4644272", "primary_object": { "basename": "anie_201502543_sm_miscellaneous_information.pdf", "url": "https://authors.library.caltech.edu/records/498s5-88p84/files/anie_201502543_sm_miscellaneous_information.pdf" }, "related_objects": [ { "basename": "nihms732618.pdf", "url": "https://authors.library.caltech.edu/records/498s5-88p84/files/nihms732618.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Hu, Fanghao; Chen, Zhixing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6czm6-hyv42", "eprint_id": 86926, "eprint_status": "archive", "datestamp": "2023-08-20 05:30:11", "lastmod": "2023-10-18 20:42:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Xu-Fang", "name": { "family": "Xu", "given": "Fang" } }, { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Harrington-J-K", "name": { "family": "Harrington", "given": "Jamie K." } }, { "id": "Targoff-K-L", "name": { "family": "Targoff", "given": "Kimara L." } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Imaging complex protein metabolism in live organisms by stimulated Raman scattering microscopy with isotope labeling", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 American Chemical Society. ACS AuthorChoice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. \n\nReceived: September 30, 2014. Accepted: January 5, 2015. Published: January 5, 2015. \n\nWe thank J. Jackson and C. Dupre for assistance with the brain slices and J. C. Tapia, M. C. Wang, Z. Chen, D. Peterka, and R. Yuste for helpful discussions. We are grateful to Y. Shin for technical assistance with the in vivo mice experiments. W.M. acknowledges support from Columbia University, an National Institutes of Health Director's New Innovator Award, the U.S. Army Research Office (W911NF-12-1-0594), the Brain Research Foundation, and an Alfred P. Sloan Research Fellowship. \n\nAuthor Contributions: L.W., Y.S., F.X., F.H., J.K.H., and K.L.T. performed experiments and analyzed data. L.W., Y.S., and W.M. designed the experiments. L.W. and W.M. conceived the concept and wrote the article. \n\nThe authors declare the following competing financial interest(s): Columbia University has filed a patent application based on this work.\n\nPublished - cb500787b.pdf
Supplemental Material - cb500787b_si_001.pdf
", "abstract": "Protein metabolism, consisting of both synthesis and degradation, is highly complex, playing an indispensable regulatory role throughout physiological and pathological processes. Over recent decades, extensive efforts, using approaches such as autoradiography, mass spectrometry, and fluorescence microscopy, have been devoted to the study of protein metabolism. However, noninvasive and global visualization of protein metabolism has proven to be highly challenging, especially in live systems. Recently, stimulated Raman scattering (SRS) microscopy coupled with metabolic labeling of deuterated amino acids (D-AAs) was demonstrated for use in imaging newly synthesized proteins in cultured cell lines. Herein, we significantly generalize this notion to develop a comprehensive labeling and imaging platform for live visualization of complex protein metabolism, including synthesis, degradation, and pulse-chase analysis of two temporally defined populations. First, the deuterium labeling efficiency was optimized, allowing time-lapse imaging of protein synthesis dynamics within individual live cells with high spatial-temporal resolution. Second, by tracking the methyl group (CH3) distribution attributed to pre-existing proteins, this platform also enables us to map protein degradation inside live cells. Third, using two subsets of structurally and spectroscopically distinct D-AAs, we achieved two-color pulse-chase imaging, as demonstrated by observing aggregate formation of mutant hungtingtin proteins. Finally, going beyond simple cell lines, we demonstrated the imaging ability of protein synthesis in brain tissues, zebrafish, and mice in vivo. Hence, the presented labeling and imaging platform would be a valuable tool to study complex protein metabolism with high sensitivity, resolution, and biocompatibility for a broad spectrum of systems ranging from cells to model animals and possibly to humans.", "date": "2015-03-20", "date_type": "published", "publication": "ACS Chemical Biology", "volume": "10", "number": "3", "publisher": "American Chemical Society", "pagerange": "901-908", "id_number": "CaltechAUTHORS:20180608-131444540", "issn": "1554-8929", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-131444540", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Columbia University" }, { "agency": "NIH" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "Brain Research Foundation" }, { "agency": "Alfred P. Sloan Foundation" } ] }, "doi": "10.1021/cb500787b", "pmcid": "PMC4610303", "primary_object": { "basename": "cb500787b.pdf", "url": "https://authors.library.caltech.edu/records/6czm6-hyv42/files/cb500787b.pdf" }, "related_objects": [ { "basename": "cb500787b_si_001.pdf", "url": "https://authors.library.caltech.edu/records/6czm6-hyv42/files/cb500787b_si_001.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Wei, Lu; Shen, Yihui; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p3dt6-d3w20", "eprint_id": 86931, "eprint_status": "archive", "datestamp": "2023-08-20 04:40:48", "lastmod": "2023-10-18 20:43:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Zhang-Luyuan", "name": { "family": "Zhang", "given": "Luyuan" } }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Vibrational Imaging of Glucose Uptake in Live Cells and Tissues by Stimulated Raman Scattering Microscopy", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2015 Biophysical Society. Published by Elsevier Inc. \n\nAvailable online 27 January 2015. \n\nMeeting Abstract: 2420-Pos B557.", "abstract": "Glucose is a ubiquitous energy source for virtually all living organisms. Its uptake activity closely reflects the cellular metabolic status in various physiological and pathological conditions. Extensive efforts such as positron emission tomography (PET), magnetic resonance imaging (MRI) and fluorescence microscopy have been made to image glucose uptake but all with technical limitations. Here, we report a novel vibrational microscopy platform to visualize glucose uptake in living cells and tissues with subcellular resolution and minimal perturbation by performing stimulated Raman scattering (SRS) on a new glucose analogue. Cancer cells with differing metabolic characteristics can be distinguished. Moreover, heterogeneous glucose uptake patterns are observed with clear cell-cell variations in tumor xenograft tissues as well as in neuronal culture and mouse brain tissues. Therefore, by offering the distinct advantage of optical resolution yet without the undesirable influence of bulky fluorophores, SRS imaging of glucose uptake will be a valuable tool to study energy demands of living systems, particularly in tumors and brain.", "date": "2015-01-27", "date_type": "published", "publication": "Biophysical Journal", "volume": "108", "number": "2", "publisher": "Biophysical Society", "pagerange": "480A", "id_number": "CaltechAUTHORS:20180608-135537234", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-135537234", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2014.11.2621", "resource_type": "article", "pub_year": "2015", "author_list": "Hu, Fanghao; Chen, Zhixing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/9j6v0-03397", "eprint_id": 91011, "eprint_status": "archive", "datestamp": "2023-08-20 01:21:37", "lastmod": "2023-10-19 22:03:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Paley-D-W", "name": { "family": "Paley", "given": "Daniel W." } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Weisman-A-L", "name": { "family": "Weisman", "given": "Andrew L." } }, { "id": "Friesner-R-A", "name": { "family": "Friesner", "given": "Richard A." } }, { "id": "Nuckolls-C", "name": { "family": "Nuckolls", "given": "Colin" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Multicolor Live-Cell Chemical Imaging by Isotopically Edited Alkyne Vibrational Palette", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 American Chemical Society. ACS AuthorChoice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. \n\nReceived: March 17, 2014. Published: May 21, 2014. \n\nWe thank F. Hu, Y. Shen, and M. Jimenez for helpful discussions. D.W.P. and C.N. acknowledge support from the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, U.S. Department of Energy (DOE) under award number DE-FG02-01ER15264. W.M. acknowledges support from NIH Director's New Innovator Award and Alfred P. Sloan Research Fellowship. \n\nThe authors declare the following competing financial interest(s): Z.C., L.W., and W.M. are the inventors of a patent application filed by Columbia University. R.A.F. has an interest in Schrodinger, Inc. R.A.F. has a significant financial stake in Schr\u00f6dinger, Inc., is a consultant to Schr\u00f6dinger, Inc. and is on the Scientific Advisory Board of Schr\u00f6dinger, Inc.\n\nPublished - ja502706q.pdf
Supplemental Material - ja502706q_si_001.pdf
", "abstract": "Vibrational imaging such as Raman microscopy is a powerful technique for visualizing a variety of molecules in live cells and tissues with chemical contrast. Going beyond the conventional label-free modality, recent advance of coupling alkyne vibrational tags with stimulated Raman scattering microscopy paves the way for imaging a wide spectrum of alkyne-labeled small biomolecules with superb sensitivity, specificity, resolution, biocompatibility, and minimal perturbation. Unfortunately, the currently available alkyne tag only processes a single vibrational \"color\", which prohibits multiplex chemical imaging of small molecules in a way that is being routinely practiced in fluorescence microscopy. Herein we develop a three-color vibrational palette of alkyne tags using a ^(13)C-based isotopic editing strategy. We first synthesized ^(13)C isotopologues of EdU, a DNA metabolic reporter, by using the newly developed alkyne cross-metathesis reaction. Consistent with theoretical predictions, the mono-^(13)C (^(13)C\u2261^(12)C) and bis-^(13)C (^(13)C\u2261^(13)C) labeled alkyne isotopologues display Raman peaks that are red-shifted and spectrally resolved from the originally unlabeled (^(12)C\u2261^(12)C) alkynyl probe. We further demonstrated three-color chemical imaging of nascent DNA, RNA, and newly uptaken fatty-acid in live mammalian cells with a simultaneous treatment of three different isotopically edited alkynyl metabolic reporters. The alkyne vibrational palette presented here thus opens up multicolor imaging of small biomolecules, enlightening a new dimension of chemical imaging.", "date": "2014-06-04", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "136", "number": "22", "publisher": "American Chemical Society", "pagerange": "8027-8033", "id_number": "CaltechAUTHORS:20181119-102039582", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102039582", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-01ER15264" }, { "agency": "NIH" }, { "agency": "Alfred P. Sloan Foundation" } ] }, "doi": "10.1021/ja502706q", "pmcid": "PMC4063185", "primary_object": { "basename": "ja502706q.pdf", "url": "https://authors.library.caltech.edu/records/9j6v0-03397/files/ja502706q.pdf" }, "related_objects": [ { "basename": "ja502706q_si_001.pdf", "url": "https://authors.library.caltech.edu/records/9j6v0-03397/files/ja502706q_si_001.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Chen, Zhixing; Paley, Daniel W.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/tdnry-rg894", "eprint_id": 86927, "eprint_status": "archive", "datestamp": "2023-08-22 12:44:28", "lastmod": "2023-10-18 20:42:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Xu-Fang", "name": { "family": "Xu", "given": "Fang" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Live-cell quantitative imaging of proteome degradation by stimulated Raman scattering", "ispublished": "pub", "full_text_status": "public", "keywords": "Raman spectroscopy; SRS microscopy; isotope labeling; protein aggregation; protein degradation", "note": "\u00a9 2014 WILEY\u2010VCH. \n\nReceived: December 10, 2013. Published online: April 15, 2014. \n\nW.M. acknowledges support from National Institutes of Health Director's New Innovator Award and Sloan Research Fellowship.\n\nAccepted Version - nihms597333.pdf
Supplemental Material - anie_201310725_sm_miscellaneous_information.pdf
", "abstract": "Protein degradation is a regulatory process essential to cell viability and its dysfunction is implicated in many diseases, such as aging and neurodegeneration. In this report, stimulated Raman scattering microscopy coupled with metabolic labeling with ^(13)C-phenylalanine is used to visualize protein degradation in living cells with subcellular resolution. We choose the ring breathing modes of endogenous ^(12)C-phenylalanine and incorporated ^(13)C-phenylalanine as protein markers for the original and nascent proteomes, respectively, and the decay of the former wasquantified through ^(12)C/(^(12)C + ^(13)C) ratio maps. We demonstrate time-dependent imaging of proteomic degradation in mammalian cells under steady-state conditions and various perturbations, including oxidative stress, cell differentiation, and huntingtin protein aggregation.", "date": "2014-05-26", "date_type": "published", "publication": "Angewandte Chemie International Edition", "volume": "53", "number": "22", "publisher": "Wiley", "pagerange": "5596-5599", "id_number": "CaltechAUTHORS:20180608-133129304", "issn": "1433-7851", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-133129304", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Alfred P. Sloan Foundation" } ] }, "doi": "10.1002/anie.201310725", "pmcid": "PMC4231775", "primary_object": { "basename": "anie_201310725_sm_miscellaneous_information.pdf", "url": "https://authors.library.caltech.edu/records/tdnry-rg894/files/anie_201310725_sm_miscellaneous_information.pdf" }, "related_objects": [ { "basename": "nihms597333.pdf", "url": "https://authors.library.caltech.edu/records/tdnry-rg894/files/nihms597333.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Shen, Yihui; Xu, Fang; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1xa86-9e809", "eprint_id": 91012, "eprint_status": "archive", "datestamp": "2023-08-20 01:00:28", "lastmod": "2023-10-19 22:03:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Zheng-Chaogu", "name": { "family": "Zheng", "given": "Chaogu" } }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Live-cell vibrational imaging of choline metabolites by stimulated Raman scattering coupled with isotope-based metabolic labeling", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 Royal Society of Chemistry 2014. \n\nReceived 11th December 2013, Accepted 18th January 2014, First published on 20th January 2014. \n\nWe thank M. Chalfie, Z. Chen and L. Zhang for stimulating discussion and Dr Y. Shin for providing mouse hippocampal neurons. W. Min acknowledges support from NIH Director's New Innovator Award. \n\nThe authors declare no competing financial interest.\n\nAccepted Version - nihms577413.pdf
Supplemental Material - c3an02281a.pdf
Cover Image - Get.gif
", "abstract": "Choline is a small molecule that occupies a key position in the biochemistry of all living organisms. Recent studies have strongly implicated choline metabolites in cancer, atherosclerosis and nervous system development. To detect choline and its metabolites, existing physical methods such as magnetic resonance spectroscopy and positron emission tomography are often limited by the poor spatial resolution and substantial radiation dose. Fluorescence imaging, although with submicrometer resolution, requires introduction of bulky fluorophores and thus is difficult in labeling the small choline molecule. By combining the emerging bond-selective stimulated Raman scattering microscopy with metabolic incorporation of deuterated choline, herein we have achieved high resolution imaging of choline-containing metabolites in living mammalian cell lines, primary hippocampal neurons and the multicellular organism C. elegans. Different subcellular distributions of choline metabolites are observed between cancer cells and non-cancer cells, which may reveal a functional difference in the choline metabolism and lipid-mediated signaling events. In neurons, choline incorporation is visualized within both soma and neurites, where choline metabolites are more evenly distributed compared to proteins. Furthermore, choline localization is also observed in the pharynx region of C. elegans larvae, consistent with its organogenesis mechanism. These applications demonstrate the potential of isotope-based stimulated Raman scattering microscopy for future choline-related disease detection and development monitoring in vivo.", "date": "2014-05-21", "date_type": "published", "publication": "Analyst", "volume": "139", "number": "10", "publisher": "Royal Society of Chemistry", "pagerange": "2312-2317", "id_number": "CaltechAUTHORS:20181119-102039701", "issn": "0003-2654", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102039701", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" } ] }, "doi": "10.1039/c3an02281a", "pmcid": "PMC4069604", "primary_object": { "basename": "Get.gif", "url": "https://authors.library.caltech.edu/records/1xa86-9e809/files/Get.gif" }, "related_objects": [ { "basename": "c3an02281a.pdf", "url": "https://authors.library.caltech.edu/records/1xa86-9e809/files/c3an02281a.pdf" }, { "basename": "nihms577413.pdf", "url": "https://authors.library.caltech.edu/records/1xa86-9e809/files/nihms577413.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Hu, Fanghao; Wei, Lu; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/avc7k-gkg83", "eprint_id": 86929, "eprint_status": "archive", "datestamp": "2023-08-20 00:17:58", "lastmod": "2023-10-18 20:42:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Hu-Fanghao", "name": { "family": "Hu", "given": "Fanghao" }, "orcid": "0000-0002-8659-4027" }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Yu-Yong", "name": { "family": "Yu", "given": "Yong" } }, { "id": "Lin-Chih-Chun", "name": { "family": "Lin", "given": "Chih-Chun" } }, { "id": "Wang-Meng-C", "name": { "family": "Wang", "given": "Meng C." } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Macmillan Publishers Limited. \n\nReceived 2 October 2013; accepted 29 January 2014; published online 2 March 2014. \n\nWe thank L. Zhang, L. Brus, V.W. Cornish, D. Peterka and R. Yuste for helpful discussions. We are grateful to Y. Shin and X. Gao for technical assistance. W.M. acknowledges support from Columbia University, a US National Institutes of Health Director's New Innovator Award, the US Army Research Office (W911NF-12-1-0594) and an Alfred P. Sloan Research Fellowship. \n\nAuthor Contributions: L.W., F.H., Y.S., Z.C., Y.Y., C.-C.L. and M.C.W. performed experiments and analyzed data. L.W. and W.M. conceived the concept, designed the experiments and wrote the paper. \n\nCompeting interests: Columbia University, which L.W., F.H., Y.S., Z.C. and W.M. are affiliated with, has filed a patent application based on this work.\n\nAccepted Version - nihms-566357.pdf
Supplemental Material - nmeth.2878-S1.pdf
", "abstract": "Sensitive and specific visualization of small biomolecules in living systems is highly challenging. We report stimulated Raman-scattering imaging of alkyne tags as a general strategy for studying a broad spectrum of small biomolecules in live cells and animals. We demonstrate this technique by tracking alkyne-bearing drugs in mouse tissues and visualizing de novo synthesis of DNA, RNA, proteins, phospholipids and triglycerides through metabolic incorporation of alkyne-tagged small precursors.", "date": "2014-04", "date_type": "published", "publication": "Nature Methods", "volume": "11", "number": "4", "publisher": "Nature Publishing Group", "pagerange": "410-412", "id_number": "CaltechAUTHORS:20180608-133705699", "issn": "1548-7091", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-133705699", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Columbia University" }, { "agency": "NIH" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-12-1-0594" }, { "agency": "Alfred P. Sloan Foundation" } ] }, "doi": "10.1038/nmeth.2878", "pmcid": "PMC4040164", "primary_object": { "basename": "nihms-566357.pdf", "url": "https://authors.library.caltech.edu/records/avc7k-gkg83/files/nihms-566357.pdf" }, "related_objects": [ { "basename": "nmeth.2878-S1.pdf", "url": "https://authors.library.caltech.edu/records/avc7k-gkg83/files/nmeth.2878-S1.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Wei, Lu; Hu, Fanghao; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/w08d5-fb045", "eprint_id": 86928, "eprint_status": "archive", "datestamp": "2023-08-19 23:34:41", "lastmod": "2024-01-14 20:14:36", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Zhu-Xinxin", "name": { "family": "Zhu", "given": "Xinxin" } }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Super-nonlinear fluorescence microscopy for high-contrast deep tissue imaging", "ispublished": "unpub", "full_text_status": "public", "keywords": "Nonlinear microscopy, multiphoton microscopy, imaging-depth limit, real population transfer, deep-tissue imaging", "note": "\u00a9 2014 Society of Photo-Optical Instrumentation Engineers (SPIE).\n\nPublished - 894825.pdf
", "abstract": "Two-photon excited fluorescence microscopy (TPFM) offers the highest penetration depth with subcellular resolution in light microscopy, due to its unique advantage of nonlinear excitation. However, a fundamental imaging-depth limit, accompanied by a vanishing signal-to-background contrast, still exists for TPFM when imaging deep into scattering samples. Formally, the focusing depth, at which the in-focus signal and the out-of-focus background are equal to each other, is defined as the fundamental imaging-depth limit. To go beyond this imaging-depth limit of TPFM, we report a new class of super-nonlinear fluorescence microscopy for high-contrast deep tissue imaging, including multiphoton activation and imaging (MPAI) harnessing novel photo-activatable fluorophores, stimulated emission reduced fluorescence (SERF) microscopy by adding a weak laser beam for stimulated emission, and two-photon induced focal saturation imaging with preferential depletion of ground-state fluorophores at focus. The resulting image contrasts all exhibit a higher-order (third- or fourth- order) nonlinear signal dependence on laser intensity than that in the standard TPFM. Both the physical principles and the imaging demonstrations will be provided for each super-nonlinear microscopy. In all these techniques, the created super-nonlinearity significantly enhances the imaging contrast and concurrently extends the imaging depth-limit of TPFM. Conceptually different from conventional multiphoton processes mediated by virtual states, our strategy constitutes a new class of fluorescence microscopy where high-order nonlinearity is mediated by real population transfer.", "date": "2014-02-28", "date_type": "published", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 894825", "id_number": "CaltechAUTHORS:20180608-133651608", "isbn": "9780819498618", "book_title": "Multiphoton Microscopy in the Biomedical Sciences XIV", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180608-133651608", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Periasamy-A", "name": { "family": "Periasamy", "given": "Ammasi" } }, { "id": "So-Peter-T-C", "name": { "family": "So", "given": "Peter T. C." } }, { "id": "K\u00f6nig-K", "name": { "family": "K\u00f6nig", "given": "Karsten" } } ] }, "doi": "10.1117/12.2038753", "primary_object": { "basename": "894825.pdf", "url": "https://authors.library.caltech.edu/records/w08d5-fb045/files/894825.pdf" }, "resource_type": "book_section", "pub_year": "2014", "author_list": "Wei, Lu; Zhu, Xinxin; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t7b49-ssp47", "eprint_id": 91013, "eprint_status": "archive", "datestamp": "2023-08-19 20:43:44", "lastmod": "2023-10-19 22:03:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Yu-Yong", "name": { "family": "Yu", "given": "Yong" } }, { "id": "Shen-Yihui", "name": { "family": "Shen", "given": "Yihui" } }, { "id": "Wang-Meng-C", "name": { "family": "Wang", "given": "Meng C." } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Vibrational imaging of newly synthesized proteins in live cells by stimulated Raman scattering microscopy", "ispublished": "pub", "full_text_status": "public", "keywords": "stable isotope labeling | stimulated Raman microscopy | protein synthesis", "note": "\u00a9 2013 National Academy of Sciences. \n\nEdited by David A. Tirrell, California Institute of Technology, Pasadena, CA, and approved May 31, 2013 (received for review February 27, 2013) \n\nWe thank F. Hu, Z. Chen, V. W. Cornish, D. Peterka, and R. Yuste for helpful discussion. We are grateful to S. Buffington, M. Costa-Mattioli, and M. Sakamoto for providing hippocampal neurons, and Y. Li for his assistance on the spontaneous Raman microscope. We acknowledge support from Ellison Medical Foundation fellowships (to M.C.W.) and National Institutes of Health Director's New Innovator Award (to W.M.). \n\nAuthor contributions: L.W., M.C.W., and W.M. designed research; L.W., Y.Y., and Y.S. performed research; L.W. analyzed data; and L.W., Y.Y., Y.S., M.C.W., and W.M. wrote the paper. \n\nConflict of interest statement: Columbia University has filed a patent application based on this work. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1303768110/-/DCSupplemental.\n\nPublished - 11226.full.pdf
Supplemental Material - pnas.201303768SI.pdf
", "abstract": "Synthesis of new proteins, a key step in the central dogma of molecular biology, has been a major biological process by which cells respond rapidly to environmental cues in both physiological and pathological conditions. However, the selective visualization of a newly synthesized proteome in living systems with subcellular resolution has proven to be rather challenging, despite the extensive efforts along the lines of fluorescence staining, autoradiography, and mass spectrometry. Herein, we report an imaging technique to visualize nascent proteins by harnessing the emerging stimulated Raman scattering (SRS) microscopy coupled with metabolic incorporation of deuterium-labeled amino acids. As a first demonstration, we imaged newly synthesized proteins in live mammalian cells with high spatial\u2013temporal resolution without fixation or staining. Subcellular compartments with fast protein turnover in HeLa and HEK293T cells, and newly grown neurites in differentiating neuron-like N2A cells, are clearly identified via this imaging technique. Technically, incorporation of deuterium-labeled amino acids is minimally perturbative to live cells, whereas SRS imaging of exogenous carbon\u2013deuterium bonds (C\u2013D) in the cell-silent Raman region is highly sensitive, specific, and compatible with living systems. Moreover, coupled with label-free SRS imaging of the total proteome, our method can readily generate spatial maps of the quantitative ratio between new and total proteomes. Thus, this technique of nonlinear vibrational imaging of stable isotope incorporation will be a valuable tool to advance our understanding of the complex spatial and temporal dynamics of newly synthesized proteome in vivo.", "date": "2013-07-09", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "110", "number": "28", "publisher": "National Academy of Sciences", "pagerange": "11226-11231", "id_number": "CaltechAUTHORS:20181119-102039803", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102039803", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ellison Medical Foundation" }, { "agency": "NIH" } ] }, "doi": "10.1073/pnas.1303768110", "pmcid": "PMC3710790", "primary_object": { "basename": "11226.full.pdf", "url": "https://authors.library.caltech.edu/records/t7b49-ssp47/files/11226.full.pdf" }, "related_objects": [ { "basename": "pnas.201303768SI.pdf", "url": "https://authors.library.caltech.edu/records/t7b49-ssp47/files/pnas.201303768SI.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Wei, Lu; Yu, Yong; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6yey0-zwb88", "eprint_id": 91015, "eprint_status": "archive", "datestamp": "2023-08-22 09:48:21", "lastmod": "2023-10-19 22:04:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "What can stimulated emission do for bioimaging?", "ispublished": "pub", "full_text_status": "restricted", "keywords": "deep tissue imaging; imaging-depth limit; nonfluorescent chromophore; pump-probe microscopy; stimulated emission; superresolution", "note": "\u00a9 2013 New York Academy of Sciences.\n\nThe authors thank Zhixing Chen and Rafael Yuste for helpful discussions. W.M. acknowledges the start\u2010up funds from Columbia University, and grant support from the Kavli Institute for Brain Science. \n\nThe authors declare no conflicts of interest. \n\nIssue: Blavatnik Awards for Young Scientists 2012.", "abstract": "Advances in bioimaging have revolutionized our ability to study life phenomena at a microscopic scale. In particular, the stimulated emission process, a universal mechanism that competes with spontaneous emission, has emerged as a powerful driving force for advancing light microscopy. The present review summarizes and compares three related techniques that each measure a different physical quantity involved in the stimulated emission process in order to tackle various challenges in light microscopy. Stimulated emission depletion microscopy, which detects the residual fluorescence after quenching, can break the diffraction\u2010limited resolution barrier in fluorescence microscopy. Stimulated emission microscopy is capable of imaging nonfluorescent but absorbing chromophores by detecting the intensity gain of the stimulated emission beam. Very recently, stimulated emission reduced fluorescence microscopy has been proposed, in which the reduced fluorescence due to focal stimulation is measured to extend the fundamental imaging\u2010depth limit of two\u2010photon microscopy. Thus, through ingenious spectroscopy design in distinct microscopy contexts, stimulated emission has opened up several new territories for bioimaging, allowing examination of biological structures that are ever smaller, darker, and deeper.", "date": "2013-07", "date_type": "published", "publication": "Annals of the New York Academy of Sciences", "volume": "1293", "publisher": "New York Academy of Sciences", "pagerange": "1-7", "id_number": "CaltechAUTHORS:20181119-102040019", "issn": "0077-8923", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102040019", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Columbia University" }, { "agency": "Kavli Institute for Brain Science" } ] }, "doi": "10.1111/nyas.12079", "resource_type": "article", "pub_year": "2013", "author_list": "Wei, Lu and Min, Wei" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ya4e3-wrn16", "eprint_id": 91014, "eprint_status": "archive", "datestamp": "2023-08-19 20:26:41", "lastmod": "2023-10-19 22:03:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Xu-Fang", "name": { "family": "Xu", "given": "Fang" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Frustrated FRET for high-contrast high-resolution two-photon imaging", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Optical Society of America. \n\nReceived 20 Feb 2013; revised 1 Apr 2013; accepted 2 Apr 2013; published 5 Jun 2013. \n\nWe thank L. Zhang, X. Zhu, L. Brus, R. Yuste, D. Peterka, V. Cornish and M. Jimenez for helpful discussions. W.M. acknowledges support from Kavli Institute for Brain Science and RISE program of Columbia University.\n\nPublished - oe-21-12-14097.pdf
", "abstract": "Two-photon fluorescence microscopy has become increasingly popular in biomedical research as it allows high-resolution imaging of thick biological specimen with superior contrast and penetration than confocal microscopy. However, two-photon microscopy still faces two fundamental limitations: 1) image-contrast deterioration with imaging depth due to out-of-focus background and 2) diffraction-limited spatial resolution. Herein we propose to create and detect high-order (more than quadratic) nonlinear signals by harnessing the frustrated fluorescence resonance energy transfer (FRET) effect within a specially designed donor-acceptor probe pair. Two distinct techniques are described. In the first method, donor fluorescence generated by a two-photon laser at the focus is preferentially switched on and off by a modulated and focused one-photon laser beam that is able to block FRET via direct acceptor excitation. The resulting image, constructed from the enhanced donor fluorescence signal, turns out to be an overall three-photon process. In the second method, a two-photon laser at a proper wavelength is capable of simultaneously exciting both the donor and the acceptor. By sinusoidally modulating the two-photon excitation laser at a fundamental frequency \u03c9, an overall four-photon signal can be isolated by demodulating the donor fluorescence at the third harmonic frequency 3\u03c9. We show that both the image contrast and the spatial resolution of the standard two-photon fluorescence microscopy can be substantially improved by virtue of the high-order nonlinearity. This frustrated FRET approach represents a strategy that is based on extracting the inherent nonlinear photophysical response of the specially designed imaging probes.", "date": "2013-06-17", "date_type": "published", "publication": "Optics Express", "volume": "21", "number": "12", "publisher": "Optical Society of America", "pagerange": "14097-14108", "id_number": "CaltechAUTHORS:20181119-102039911", "issn": "1094-4087", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102039911", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Kavli Institute for Brain Science" }, { "agency": "Columbia University" } ] }, "doi": "10.1364/oe.21.014097", "primary_object": { "basename": "oe-21-12-14097.pdf", "url": "https://authors.library.caltech.edu/records/ya4e3-wrn16/files/oe-21-12-14097.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Xu, Fang; Wei, Lu; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gattv-2jc52", "eprint_id": 91017, "eprint_status": "archive", "datestamp": "2023-08-19 12:40:26", "lastmod": "2023-10-19 22:04:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gatzogiannis-E", "name": { "family": "Gatzogiannis", "given": "Evangelos" } }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Wombacher-R", "name": { "family": "Wombacher", "given": "Richard" } }, { "id": "Kao-Ya-Ting", "name": { "family": "Kao", "given": "Ya-Ting" } }, { "id": "Yefremov-G", "name": { "family": "Yefremov", "given": "Grygorii" } }, { "id": "Cornish-V-W", "name": { "family": "Cornish", "given": "Virginia W." } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Mapping protein-specific micro-environments in live cells by fluorescence lifetime imaging of a hybrid genetic-chemical molecular rotor tag", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 Royal Society of Chemistry 2012. \n\nReceived 1st May 2012, Accepted 6th July 2012. \n\nThis work was supported by the National Institutes of Health (U54 GM087519 and RC1GM091804 to V. W. C) and by the start up funds from Columbia University (to W. M.). We thank Dr Steffen Jockusch for experimental assistance. \n\nV. W. C. holds patents on the TMP-tag technology, and the technology is licensed and commercialized by Active Motif.\n\nAccepted Version - nihms401554.pdf
Supplemental Material - c2cc33133k.pdf
", "abstract": "The micro-viscosity and molecular crowding experienced by specific proteins can regulate their dynamics and function within live cells. Taking advantage of the emerging TMP-tag technology, we present the design, synthesis and application of a hybrid genetic-chemical molecular rotor probe whose fluorescence lifetime can report protein-specific micro-environments in live cells.", "date": "2012-09-07", "date_type": "published", "publication": "Chemical Communications", "volume": "48", "number": "69", "publisher": "Royal Society of Chemistry", "pagerange": "8694-8696", "id_number": "CaltechAUTHORS:20181119-102040204", "issn": "1359-7345", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102040204", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54 GM087519" }, { "agency": "NIH", "grant_number": "RC1 GM091804" }, { "agency": "Columbia University" } ] }, "doi": "10.1039/c2cc33133k", "pmcid": "PMC3775488", "primary_object": { "basename": "c2cc33133k.pdf", "url": "https://authors.library.caltech.edu/records/gattv-2jc52/files/c2cc33133k.pdf" }, "related_objects": [ { "basename": "nihms401554.pdf", "url": "https://authors.library.caltech.edu/records/gattv-2jc52/files/nihms401554.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Gatzogiannis, Evangelos; Chen, Zhixing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/g7b9e-tad38", "eprint_id": 91018, "eprint_status": "archive", "datestamp": "2023-09-15 06:11:17", "lastmod": "2023-10-23 21:24:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Zhu-Xinxin", "name": { "family": "Zhu", "given": "Xinxin" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Extending the fundamental imaging-depth limit of multi-photon microscopy by imaging with photo-activatable fluorophores", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Optical Society of America. \n\nReceived 12 Apr 2012; revised 18 Jun 2012; accepted 19 Jun 2012; published 30 Jul 2012. \n\nZhixing Chen, Lu Wei and Xinxin Zhu contributed equally to this work. We thank Ya-Ting Kao, Fang Xu, Louis Brus, Rafael Yuste, Nicholas Turro, Virginia Cornish, Darcy Peterka, Christophe Dupre and Miguel Jimenez for helpful discussions. We are grateful to Virginia Cornish for sharing lab equipments and Keith Yeager for assistance on Leica microscope. W.M. acknowledges the startup funds from Columbia University, and grant support from Kavli Institute for Brain Science.\n\nPublished - oe-20-17-18525.pdf
", "abstract": "It is highly desirable to be able to optically probe biological activities deep inside live organisms. By employing a spatially confined excitation via a nonlinear transition, multiphoton fluorescence microscopy has become indispensable for imaging scattering samples. However, as the incident laser power drops exponentially with imaging depth due to scattering loss, the out-of-focus fluorescence eventually overwhelms the in-focal signal. The resulting loss of imaging contrast defines a fundamental imaging-depth limit, which cannot be overcome by increasing excitation intensity. Herein we propose to significantly extend this depth limit by multiphoton activation and imaging (MPAI) of photo-activatable fluorophores. The imaging contrast is drastically improved due to the created disparity of bright-dark quantum states in space. We demonstrate this new principle by both analytical theory and experiments on tissue phantoms labeled with synthetic caged fluorescein dye or genetically encodable photoactivatable GFP.", "date": "2012-08-13", "date_type": "published", "publication": "Optics Express", "volume": "20", "number": "17", "publisher": "Optical Society of America", "pagerange": "18525-18536", "id_number": "CaltechAUTHORS:20181119-102040297", "issn": "1094-4087", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102040297", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Columbia University" }, { "agency": "Kavli Institute for Brain Science" } ] }, "doi": "10.1364/oe.20.018525", "primary_object": { "basename": "oe-20-17-18525.pdf", "url": "https://authors.library.caltech.edu/records/g7b9e-tad38/files/oe-20-17-18525.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Chen, Zhixing; Wei, Lu; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/f820v-mtx07", "eprint_id": 91019, "eprint_status": "archive", "datestamp": "2023-08-19 11:17:16", "lastmod": "2023-10-19 22:04:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Chen-Zhixing", "name": { "family": "Chen", "given": "Zhixing" } }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Stimulated emission reduced fluorescence microscopy: a concept for extending the fundamental depth limit of two-photon fluorescence imaging", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Optical Society of America. \n\nReceived 27 Apr 2012; revised 19 May 2012; accepted 19 May 2012; published 22 May 2012. \n\nWe thank Ya-Ting Kao, Xinxin Zhu, Louis Brus, Rafael Yuste, Darcy Peterka, Virginia Cornish, Christophe Dupre and Miguel Jimenez for helpful discussions. W. M. acknowledges the startup funds from Columbia University, and grant support from Kavli Institute for Brain Science.\n\nPublished - boe-3-6-1465.pdf
", "abstract": "Two-photon fluorescence microscopy has become an indispensable tool for imaging scattering biological samples by detecting scattered fluorescence photons generated from a spatially confined excitation volume. However, this optical sectioning capability breaks down eventually when imaging much deeper, as the out-of-focus fluorescence gradually overwhelms the in-focal signal in the scattering samples. The resulting loss of image contrast defines a fundamental imaging-depth limit, which cannot be overcome by increasing excitation efficiency. Herein we propose to extend this depth limit by performing stimulated emission reduced fluorescence (SERF) microscopy in which the two-photon excited fluorescence at the focus is preferentially switched on and off by a modulated and focused laser beam that is capable of inducing stimulated emission of the fluorophores from the excited states. The resulting image, constructed from the reduced fluorescence signal, is found to exhibit a significantly improved signal-to-background contrast owing to its overall higher-order nonlinear dependence on the incident laser intensity. We demonstrate this new concept by both analytical theory and numerical simulations. For brain tissues, SERF is expected to extend the imaging depth limit of two-photon fluorescence microscopy by a factor of more than 1.8.", "date": "2012-06-01", "date_type": "published", "publication": "Biomedical Optics Express", "volume": "3", "number": "6", "publisher": "Optical Society of America", "pagerange": "1465-1475", "id_number": "CaltechAUTHORS:20181119-102040395", "issn": "2156-7085", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102040395", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Columbia University" }, { "agency": "Kavli Institute for Brain Science" } ] }, "doi": "10.1364/boe.3.001465", "pmcid": "PMC3370985", "primary_object": { "basename": "boe-3-6-1465.pdf", "url": "https://authors.library.caltech.edu/records/f820v-mtx07/files/boe-3-6-1465.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Wei, Lu; Chen, Zhixing; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/dh12p-1kt72", "eprint_id": 91016, "eprint_status": "archive", "datestamp": "2023-08-19 11:14:26", "lastmod": "2023-10-19 22:04:08", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wei-Lu", "name": { "family": "Wei", "given": "Lu" }, "orcid": "0000-0001-9170-2283" }, { "id": "Min-Wei", "name": { "family": "Min", "given": "Wei" }, "orcid": "0000-0003-2570-3557" } ] }, "title": "Pump-probe optical microscopy for imaging nonfluorescent chromophores", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Pump-probe microscopy. Label-free imaging . Excited state absorption . Stimulated emission . Ground state depletion . Nonfluorescent chromophore", "note": "\u00a9 Springer-Verlag 2012. \n\nReceived: 5 December 2011 /Revised: 16 February 2012 / Accepted: 20 February 2012 / Published online: 13 March 2012. \n\nWe acknowledge discussions with X. S. Xie, C. W. Freudiger, S. Lu, S. Chong, B. G. Saar, G. R. Holtom, M. Roeffaers, D. Fu, X. Zhang, and R. Roy. \n\nPublished in the special issue Young Investigators in Analytical and Bioanalytical Science with Guest Editors S. Daunert, J. Bettmer, T. Hasegawa, Q. Wang and Y. Wei.", "abstract": "Many chromophores absorb light intensely but have undetectable fluorescence. Hence microscopy techniques other than fluorescence are highly desirable for imaging these chromophores inside live cells, tissues, and organisms. The recently developed pump-probe optical microscopy techniques provide fluorescence-free contrast mechanisms by employing several fundamental light\u2013molecule interactions including excited state absorption, stimulated emission, ground state depletion, and the photothermal effect. By using the pump pulse to excite molecules and the subsequent probe pulse to interrogate the created transient states on a laser scanning microscope, pump-probe microscopy offers imaging capability with high sensitivity and specificity toward nonfluorescent chromophores. Single-molecule sensitivity has even been demonstrated. Here we review and summarize the underlying principles of this emerging class of molecular imaging techniques.", "date": "2012-06", "date_type": "published", "publication": "Analytical and Bioanalytical Chemistry", "volume": "403", "number": "8", "publisher": "Springer", "pagerange": "2197-2202", "id_number": "CaltechAUTHORS:20181119-102040116", "issn": "1618-2642", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181119-102040116", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1007/s00216-012-5890-1", "resource_type": "article", "pub_year": "2012", "author_list": "Wei, Lu and Min, Wei" } ]