[ { "id": "https://authors.library.caltech.edu/records/57jyj-3p616", "eprint_id": 81011, "eprint_status": "archive", "datestamp": "2023-08-19 02:42:57", "lastmod": "2024-01-14 05:22:32", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kim-Jinho", "name": { "family": "Kim", "given": "Jinho" } }, { "id": "Henley-Beverley-M", "name": { "family": "Henley", "given": "Beverley M." } }, { "id": "Kim-Charlene-H", "name": { "family": "Kim", "given": "Charlene H." } }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" }, { "id": "Yang-Changhuei", "name": { "family": "Yang", "given": "Changhuei" }, "orcid": "0000-0001-8791-0354" } ] }, "title": "Incubator embedded cell culture imaging system (EmSight) based on Fourier ptychographic microscopy", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2017 Society of Photo-Optical Instrumentation Engineers (SPIE).", "abstract": "Multi-day tracking of cells in culture systems can provide valuable information in bioscience experiments. We report the development of a cell culture imaging system, named EmSight, which incorporates multiple compact Fourier ptychographic microscopes with a standard multiwell imaging plate. The system is housed in an incubator and presently incorporates six microscopes, imaging an ANSI standard 6-well plate at the same time. By using the same low magnification objective lenses (NA of 0.1) as the objective and the tube lens, the EmSight is configured as a 1:1 imaging system that, providing large field-of-view (FOV) imaging (5.7 mm \u00d7 4.3 mm) onto a low-cost CMOS imaging sensor. The EmSight improves the image resolution by capturing a series of images of the sample at varying illumination angles; the instrument reconstructs a higher-resolution image by using the iterative Fourier ptychographic algorithm. In addition to providing high-resolution brightfield and phase imaging, the EmSight is also capable of fluorescence imaging at the native resolution of the objectives. We characterized the system using a phase Siemens star target, and show four-fold improved coherent resolution (synthetic NA of 0.42) and a depth of field of 0.2 mm. To conduct live, long-term dopaminergic neuron imaging, we cultured ventral midbrain from mice driving eGFP from the tyrosine hydroxylase promoter. The EmSight system tracks movements of dopaminergic neurons over a 21 day period.", "date": "2017-04-24", "date_type": "published", "publisher": "Society of Photo-Optical Instrumentation Engineers", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 100680X", "id_number": "CaltechAUTHORS:20170831-081004023", "isbn": "9781510605770", "book_title": "Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XV", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170831-081004023", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Farkas-Daniuel-L", "name": { "family": "Farkas", "given": "Daniel L." } }, { "id": "Nicolau-D-V", "name": { "family": "Nicolau", "given": "D. V." } }, { "id": "Leif-R-C", "name": { "family": "Leif", "given": "R. C." } } ] }, "doi": "10.1117/12.2249906", "resource_type": "book_section", "pub_year": "2017", "author_list": "Kim, Jinho; Henley, Beverley M.; et el." }, { "id": "https://authors.library.caltech.edu/records/x05mk-fhm54", "eprint_id": 27764, "eprint_status": "archive", "datestamp": "2023-08-19 04:54:59", "lastmod": "2024-01-13 05:47:13", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shanata-J-A-P", "name": { "family": "Shanata", "given": "Jai A. P." } }, { "id": "Frazier-S-J", "name": { "family": "Frazier", "given": "Shawnalea J." } }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" }, { "id": "Dougherty-D-A", "name": { "family": "Dougherty", "given": "Dennis A." }, "orcid": "0000-0003-1464-2461" } ] }, "title": "Using Mutant Cycle Analysis to Elucidate Long-Range Functional Coupling in Allosteric Receptors", "ispublished": "unpub", "full_text_status": "public", "keywords": "Allostery, Signal transduction, Conformational change, Coupling, Structure\u2013function\nstudy, Ion channel, Nicotinic receptor, Amino acids", "note": "\u00a9 2012 Springer Science+Business Media, LLC. \n\nWe thank Kristin Rule Gleitsman for essential discussions throughout the development of ELFCAR. This work was supported by the National Institutes of Health (NS 34407; NS 11756). J.A.P.S. and S.F. were partially supported by National Research Service Awards from the NIH.\n\n
Accepted Version - nihms561566.pdf
", "abstract": "Functional coupling of residues that are far apart in space is the quintessential property of allosteric\nreceptors. Data from functional studies of allosteric receptors, such as whole-cell dose\u2013response relations,\ncan be used to determine if mutation to a receptor significantly impacts agonist potency. However, the\nclassification of perturbations as primarily impacting binding or allosteric function is more challenging,\noften requiring detailed kinetic studies. This protocol describes a simple strategy, derived from mutant\ncycle analysis, for elucidating long-range functional coupling in allosteric receptors (ELFCAR). Introduction\nof a gain-of-function reporter mutation, followed by a mutant cycle analysis of the readily measured\nmacroscopic EC_(50) values can provide insight into the role of many physically distant targets. This new\nmethod should find broad application in determining the functional roles of residues in allosteric receptors.", "date": "2011", "date_type": "published", "publisher": "Springer", "pagerange": "97-113", "id_number": "CaltechAUTHORS:20111114-081228635", "isbn": "9781617793332", "book_title": "Allostery: Methods and Protocols", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111114-081228635", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS 34407" }, { "agency": "NIH", "grant_number": "NS 11756" } ] }, "contributors": { "items": [ { "id": "Fenton-A-W", "name": { "family": "Fenton", "given": "Aron W." } } ] }, "doi": "10.1007/978-1-61779-334-9_6", "pmcid": "PMC4006985", "primary_object": { "basename": "nihms561566.pdf", "url": "https://authors.library.caltech.edu/records/x05mk-fhm54/files/nihms561566.pdf" }, "resource_type": "book_section", "pub_year": "2011", "author_list": "Shanata, Jai A. P.; Frazier, Shawnalea J.; et el." }, { "id": "https://authors.library.caltech.edu/records/menwh-neb80", "eprint_id": 102625, "eprint_status": "archive", "datestamp": "2023-08-19 10:41:47", "lastmod": "2024-01-15 03:01:12", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Petersson-E-J", "name": { "family": "Petersson", "given": "E. James" }, "orcid": "0000-0003-3854-9210" }, { "id": "Brandt-G-S", "name": { "family": "Brandt", "given": "Gabriel S." } }, { "id": "Zacharias-N-M", "name": { "family": "Zacharias", "given": "Niki M." } }, { "id": "Dougherty-D-A", "name": { "family": "Dougherty", "given": "Dennis A." }, "orcid": "0000-0003-1464-2461" }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" } ] }, "title": "Caging proteins through unnatural amino acids mutagenesis", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2003 Published by Elsevier. \n\nThis work was supported by the National Institutes of Health (Grants GM-29836, NS-11756, NS-34407, and NS-11756).", "abstract": "The caging of specific residues of proteins is a powerful tool. This discussion attempts to alert the reader to the considerations that must be made in preparing and analyzing a caged protein through nonsense suppression. Although the suppression methodology is conceptually straightforward, it not possible to provide a failsafe \"cook book\" method for using caged unnaturals. We have emphasized the preparation of caged receptors expressed in Xenopus oocytes, but these approaches can clearly be adapted to many other systems.", "date": "2003", "date_type": "published", "publisher": "Academic Press", "place_of_pub": "San Diego, CA", "pagerange": "258-273", "id_number": "CaltechAUTHORS:20200417-142717296", "isbn": "9780121822637", "book_title": "Biophotonics, Part A", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200417-142717296", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-29836" }, { "agency": "NIH", "grant_number": "NS-11756" }, { "agency": "NIH", "grant_number": "NS-34407" } ] }, "contributors": { "items": [ { "id": "Marriott-G", "name": { "family": "Marriott", "given": "Gerard" } }, { "id": "Parker-I", "name": { "family": "Parker", "given": "Ian" } } ] }, "doi": "10.1016/s0076-6879(03)60114-x", "resource_type": "book_section", "pub_year": "2003", "author_list": "Petersson, E. James; Brandt, Gabriel S.; et el." }, { "id": "https://authors.library.caltech.edu/records/exrfx-m2z66", "eprint_id": 103242, "eprint_status": "archive", "datestamp": "2023-08-19 02:17:57", "lastmod": "2024-01-15 03:02:18", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nowak-M-W", "name": { "family": "Nowak", "given": "Mark W." } }, { "id": "Gallivan-J-P", "name": { "family": "Gallivan", "given": "Justin P." } }, { "id": "Silverman-S-K", "name": { "family": "Silverman", "given": "Scott K." } }, { "id": "Labarca-C-G", "name": { "family": "Labarca", "given": "Cesar G." } }, { "id": "Dougherty-D-A", "name": { "family": "Dougherty", "given": "Dennis A." }, "orcid": "0000-0003-1464-2461" }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" } ] }, "title": "In vivo incorporation of unnatural amino acids into ion channels in Xenopus oocyte expression system", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 1998 Published by Elsevier Inc. \n\nWe thank the NIH (NS-11756 and NS-34407) for support of this work.", "abstract": "This chapter has adapted the nonsense codon suppression method for the incorporation of unnatural amino acids into membrane proteins in a Xenopus oocyte expression system. Combining this method with electrophysiologic analysis allows it to probe structure-function relationships in ion channels and receptors in ways not possible with conventional mutagenesis. In the absence of atomic-scale, structural data for membrane proteins, these techniques can provide detailed structural information. In the nonsense codon suppression method, Xenopus oocytes are coinjected with two RNAs: (1) mRNA transcribed in vitro from a mutated cDNA containing a TAG nonsense (stop) codon at the position of interest and (2) a suppressor tRNA containing the corresponding anticodon, CUA, and chemically acylated at the end with an amino acid. During protein synthesis, the aminoacylated suppressor tRNA directs the incorporation of the amino acid into the desired position of the protein. Because the amino acid is appended synthetically, it is not limited to the natural, and many unnatural amino acids have been incorporated into various proteins using this method. This chapter describes suppressor tRNA design and synthesis, chemical acylation of the suppressor tRNA, relevant organic synthesis methods, and optimization of mRNA and suppressor tRNA for Xenopus oocyte expression.", "date": "1998", "date_type": "published", "publisher": "Academic Press", "place_of_pub": "San Diego, CA", "pagerange": "504-529", "id_number": "CaltechAUTHORS:20200515-134619162", "isbn": "978-0-12-182194-4", "book_title": "Ion Channels Part B", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200515-134619162", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS-11756" }, { "agency": "NIH", "grant_number": "NS-34407" } ] }, "contributors": { "items": [ { "id": "Conn-P-M", "name": { "family": "Conn", "given": "P. Michael" } } ] }, "doi": "10.1016/s0076-6879(98)93031-2", "resource_type": "book_section", "pub_year": "1998", "author_list": "Nowak, Mark W.; Gallivan, Justin P.; et el." }, { "id": "https://authors.library.caltech.edu/records/3hnnv-3jj71", "eprint_id": 106073, "eprint_status": "archive", "datestamp": "2023-08-22 05:39:00", "lastmod": "2024-01-15 18:13:34", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lester-H-A", "name": { "family": "Lester", "given": "H. A." }, "orcid": "0000-0002-5470-5255" }, { "id": "Snutch-T-P", "name": { "family": "Snutch", "given": "T. P." } }, { "id": "Leonard-J-P", "name": { "family": "Leonard", "given": "J. P." } }, { "id": "Nargeot-J", "name": { "family": "Nargeot", "given": "J." } }, { "id": "Davidson-N", "name": { "family": "Davidson", "given": "N." } } ] }, "title": "Expression of mRNA Encoding Rat Brain Ca\u00b2\u207a Channels in Xenopus Oocytes", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Xenopus Oocyte; Electrical Excitability; Macroscopic Current; Muscle Acetylcholine Receptor; Phorbol Ester Stimulation", "note": "\u00a9 Springer-Verlag Berlin Heidelberg 1988. \n\nThis research was sponsored by grants from the National Institutes of Health (GM-10991 and GM-29836), and by postdoctoral fellowships from the American Heart Association to T. P. S. J. P. L. and J.N. thanks Laboratoire Servier for a travel grant.", "abstract": "Our laboratory is seeking a mechanistic picture of the action of the voltage-dependent, Ca\u00b2\u207a-selective ion channels that partially underlie the electrical excitability of membranes. Full explanations will ultimately require pictures of such molecules at atomic resolution (as obtained with X-ray crystallography) in all their states (closed, open, inactivated, etc.). Such structural information is not yet available for any channel.", "date": "1988", "date_type": "published", "publisher": "Springer Berlin Heidelberg", "place_of_pub": "Berlin, Heidelberg", "pagerange": "272-280", "id_number": "CaltechAUTHORS:20201014-153713952", "isbn": "9783540500612", "book_title": "The Calcium Channel: Structure, Function and Implications", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201014-153713952", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM-10991" }, { "agency": "NIH", "grant_number": "GM-29836" }, { "agency": "American Heart Association" }, { "agency": "Laboratoire Servier" } ] }, "contributors": { "items": [ { "id": "Morad-M", "name": { "family": "Morad", "given": "Martin" } }, { "id": "Nayler-W-G", "name": { "family": "Nayler", "given": "Winifred G." } }, { "id": "Kazda-S", "name": { "family": "Kazda", "given": "Stanislav" } }, { "id": "Schramm-M", "name": { "family": "Schramm", "given": "Matthias" } } ] }, "doi": "10.1007/978-3-642-73914-9_22", "resource_type": "book_section", "pub_year": "1988", "author_list": "Lester, H. A.; Snutch, T. P.; et el." } ]