[ { "key": "PEAQKQB9", "version": 27, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/PEAQKQB9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/PEAQKQB9", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/NCDCXRWD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } } }, "data": { "key": "PEAQKQB9", "version": 27, "parentItem": "NCDCXRWD", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-07-11T13:09:06Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/22017985", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-07-11T13:09:06Z", "dateModified": "2014-07-11T13:09:06Z" } }, { "key": "79ZGNGWJ", "version": 27, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/79ZGNGWJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/79ZGNGWJ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/NCDCXRWD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } } }, "data": { "key": "79ZGNGWJ", "version": 27, "parentItem": "NCDCXRWD", "itemType": "attachment", "linkMode": "linked_url", "title": "Full Text PDF", "accessDate": "2014-07-11T13:09:06Z", "url": "http://www.cell.com/article/S0896627311008725/pdf", "note": "", "contentType": "application/pdf", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-07-11T13:09:06Z", "dateModified": "2014-07-11T13:09:06Z" } }, { "key": "PRQ7XA9Q", "version": 27, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/PRQ7XA9Q", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/PRQ7XA9Q", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/NCDCXRWD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } } }, "data": { "key": "PRQ7XA9Q", "version": 27, "parentItem": "NCDCXRWD", "itemType": "attachment", "linkMode": "linked_url", "title": "Snapshot", "accessDate": "2014-07-11T13:09:06Z", "url": "http://www.cell.com/neuron/abstract/S0896-6273(11)00872-5", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-07-11T13:09:06Z", "dateModified": "2014-07-11T13:09:06Z" } }, { "key": "ITW62V6F", "version": 29, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/ITW62V6F", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/ITW62V6F", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Guo et al.", "parsedDate": "2009-12", "numChildren": 1 }, "data": { "key": "ITW62V6F", "version": 29, "itemType": "journalArticle", "title": "Optical interrogation of neural circuits in Caenorhabditis elegans", "creators": [ { "creatorType": "author", "firstName": "Zengcai V", "lastName": "Guo" }, { "creatorType": "author", "firstName": "Anne C", "lastName": "Hart" }, { "creatorType": "author", "firstName": "Sharad", "lastName": "Ramanathan" } ], "abstractNote": "The nematode Caenorhabditis elegans has a compact nervous system with only 302 neurons. Whereas most of the synaptic connections between these neurons have been identified by electron microscopy serial reconstructions, functional connections have been inferred between only a few neurons through combinations of electrophysiology, cell ablation, in vivo calcium imaging and genetic analysis. To map functional connections between neurons, we combined in vivo optical stimulation with simultaneous calcium imaging. We analyzed the connections from the ASH sensory neurons and RIM interneurons to the command interneurons AVA and AVD. Stimulation of ASH or RIM neurons using channelrhodopsin-2 (ChR2) resulted in activation of AVA neurons, evoking an avoidance behavior. Our results demonstrate that we can excite specific neurons expressing ChR2 while simultaneously monitoring G-CaMP fluorescence in several other neurons, making it possible to rapidly decipher functional connections in C. elegans neural circuits.", "publicationTitle": "Nature methods", "publisher": "", "place": "", "date": "Dec 2009", "volume": "6", "issue": "12", "section": "", "partNumber": "", "partTitle": "", "pages": "891-896", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Methods", "DOI": "10.1038/nmeth.1397", "citationKey": "", "url": "", "accessDate": "", "PMID": "19898486", "PMCID": "", "ISSN": "1548-7105", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Caenorhabditis elegans", "type": 1 }, { "tag": "Calcium", "type": 1 }, { "tag": "Interneurons", "type": 1 }, { "tag": "Optics and Photonics", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-07-10T13:51:47Z", "dateModified": "2014-07-10T13:51:47Z" } }, { "key": "ZWGWA392", "version": 26, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/ZWGWA392", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/ZWGWA392", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/ITW62V6F", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } } }, "data": { "key": "ZWGWA392", "version": 26, "parentItem": "ITW62V6F", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-06-03T16:17:35Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19898486", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-07-10T13:51:47Z", "dateModified": "2014-07-10T13:51:47Z" } }, { "key": "9NVGSI9K", "version": 25, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/9NVGSI9K", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/9NVGSI9K", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Ben Arous et al.", "parsedDate": "2010-03-30", "numChildren": 0 }, "data": { "key": "9NVGSI9K", "version": 25, "itemType": "journalArticle", "title": "Automated imaging of neuronal activity in freely behaving Caenorhabditis elegans", "creators": [ { "creatorType": "author", "firstName": "Juliette", "lastName": "Ben Arous" }, { "creatorType": "author", "firstName": "Yoshinori", "lastName": "Tanizawa" }, { "creatorType": "author", "firstName": "Ithai", "lastName": "Rabinowitch" }, { "creatorType": "author", "firstName": "Didier", "lastName": "Chatenay" }, { "creatorType": "author", "firstName": "William R.", "lastName": "Schafer" } ], "abstractNote": "In order to understand how neuronal circuits control locomotory patterns it is necessary to record neuronal activity of freely behaving animals. Here, using a new automated system for simultaneous recording of behavior and neuronal activity in freely moving Caenorhabditis elegans on standard agar plates, we show that spontaneous reversals from forward to backward locomotion reflect precisely the activity of the AVA command interneurons. We also witness spontaneous activity transients in the PLM sensory neurons during free behavior of the worm in standard conditions. We show that these activity transients are coupled to short spontaneous forward accelerations of the worm.", "publicationTitle": "Journal of Neuroscience Methods", "publisher": "", "place": "", "date": "March 30, 2010", "volume": "187", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "229-234", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.jneumeth.2010.01.011", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/B6T04-4Y6S7GN-3/2/f80f32c2892d34b07f1db80b870e4b53", "accessDate": "2010-12-21T00:19:32Z", "PMID": "", "PMCID": "", "ISSN": "0165-0270", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Behavior", "type": 1 }, { "tag": "C. elegans", "type": 1 }, { "tag": "Calcium imaging", "type": 1 }, { "tag": "Mechanosensory neurons", "type": 1 }, { "tag": "Tracking system", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-07-10T13:50:55Z", "dateModified": "2014-07-10T13:50:55Z" } }, { "key": "GEVRPVU7", "version": 29, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/GEVRPVU7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/GEVRPVU7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Schrödel et al.", "parsedDate": "2013-10", "numChildren": 1 }, "data": { "key": "GEVRPVU7", "version": 29, "itemType": "journalArticle", "title": "Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light", "creators": [ { "creatorType": "author", "firstName": "Tina", "lastName": "Schrödel" }, { "creatorType": "author", "firstName": "Robert", "lastName": "Prevedel" }, { "creatorType": "author", "firstName": "Karin", "lastName": "Aumayr" }, { "creatorType": "author", "firstName": "Manuel", "lastName": "Zimmer" }, { "creatorType": "author", "firstName": "Alipasha", "lastName": "Vaziri" } ], "abstractNote": "Recent efforts in neuroscience research have been aimed at obtaining detailed anatomical neuronal wiring maps as well as information on how neurons in these networks engage in dynamic activities. Although the entire connectivity map of the nervous system of Caenorhabditis elegans has been known for more than 25 years, this knowledge has not been sufficient to predict all functional connections underlying behavior. To approach this goal, we developed a two-photon technique for brain-wide calcium imaging in C. elegans, using wide-field temporal focusing (WF-TeFo). Pivotal to our results was the use of a nuclear-localized, genetically encoded calcium indicator, NLS-GCaMP5K, that permits unambiguous discrimination of individual neurons within the densely packed head ganglia of C. elegans. We demonstrate near-simultaneous recording of activity of up to 70% of all head neurons. In combination with a lab-on-a-chip device for stimulus delivery, this method provides an enabling platform for establishing functional maps of neuronal networks.", "publicationTitle": "Nature methods", "publisher": "", "place": "", "date": "Oct 2013", "volume": "10", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "1013-1020", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Methods", "DOI": "10.1038/nmeth.2637", "citationKey": "", "url": "", "accessDate": "", "PMID": "24013820", "PMCID": "", "ISSN": "1548-7105", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-07-09T12:43:58Z", "dateModified": "2014-07-09T12:43:58Z" } }, { "key": "HSKXIEXK", "version": 24, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/HSKXIEXK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/HSKXIEXK", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/GEVRPVU7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } } }, "data": { "key": "HSKXIEXK", "version": 24, "parentItem": "GEVRPVU7", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-10-02T22:49:27Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/24013820", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-07-09T12:43:58Z", "dateModified": "2014-07-09T12:43:58Z" } }, { "key": "4G52GKH8", "version": 23, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/4G52GKH8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/4G52GKH8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Stephens et al.", "parsedDate": "2010-11-16", "numChildren": 0 }, "data": { "key": "4G52GKH8", "version": 23, "itemType": "journalArticle", "title": "From Modes to Movement in the Behavior of Caenorhabditis elegans", "creators": [ { "creatorType": "author", "firstName": "Greg J.", "lastName": "Stephens" }, { "creatorType": "author", "firstName": "Bethany", "lastName": "Johnson-Kerner" }, { "creatorType": "author", "firstName": "William", "lastName": "Bialek" }, { "creatorType": "author", "firstName": "William S.", "lastName": "Ryu" } ], "abstractNote": "Organisms move through the world by changing their shape, and here we explore the mapping from shape space to movements in the nematode Caenorhabditis elegans as it crawls on an agar plate. We characterize the statistics of the trajectories through the correlation functions of the orientation angular velocity, orientation angle and the mean-squared displacement, and we find that the loss of orientational memory has significant contributions from both abrupt, large amplitude turning events and the continuous dynamics between these events. Further, we discover long-time persistence of orientational memory in the intervals between abrupt turns. Building on recent work demonstrating that C. elegans movements are restricted to a low-dimensional shape space, we construct a map from the dynamics in this shape space to the trajectory of the worm along the agar. We use this connection to illustrate that changes in the continuous dynamics reveal subtle differences in movement strategy that occur among mutants defective in two classes of dopamine receptors.", "publicationTitle": "PLoS ONE", "publisher": "", "place": "", "date": "November 16, 2010", "volume": "5", "issue": "11", "section": "", "partNumber": "", "partTitle": "", "pages": "e13914", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS ONE", "DOI": "10.1371/journal.pone.0013914", "citationKey": "", "url": "http://dx.doi.org/10.1371/journal.pone.0013914", "accessDate": "2011-06-06T14:29:31Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PLoS ONE", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-07-09T12:34:40Z", "dateModified": "2014-07-09T12:34:40Z" } }, { "key": "GU3A83ZX", "version": 29, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/GU3A83ZX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/GU3A83ZX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Larsch et al.", "parsedDate": "2013-11-05", "numChildren": 1 }, "data": { "key": "GU3A83ZX", "version": 29, "itemType": "journalArticle", "title": "High-throughput imaging of neuronal activity in Caenorhabditis elegans", "creators": [ { "creatorType": "author", "firstName": "Johannes", "lastName": "Larsch" }, { "creatorType": "author", "firstName": "Donovan", "lastName": "Ventimiglia" }, { "creatorType": "author", "firstName": "Cornelia I.", "lastName": "Bargmann" }, { "creatorType": "author", "firstName": "Dirk R.", "lastName": "Albrecht" } ], "abstractNote": "Neuronal responses to sensory inputs can vary based on genotype, development, experience, or stochastic factors. Existing neuronal recording techniques examine a single animal at a time, limiting understanding of the variability and range of potential responses. To scale up neuronal recordings, we here describe a system for simultaneous wide-field imaging of neuronal calcium activity from at least 20 Caenorhabditis elegans animals under precise microfluidic chemical stimulation. This increased experimental throughput was used to perform a systematic characterization of chemosensory neuron responses to multiple odors, odor concentrations, and temporal patterns, as well as responses to pharmacological manipulation. The system allowed recordings from sensory neurons and interneurons in freely moving animals, whose neuronal responses could be correlated with behavior. Wide-field imaging provides a tool for comprehensive circuit analysis with elevated throughput in C. elegans.", "publicationTitle": "Proceedings of the National Academy of Sciences of the United States of America", "publisher": "", "place": "", "date": "Nov 5, 2013", "volume": "110", "issue": "45", "section": "", "partNumber": "", "partTitle": "", "pages": "E4266-4273", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proc. Natl. Acad. Sci. U.S.A.", "DOI": "10.1073/pnas.1318325110", "citationKey": "", "url": "", "accessDate": "", "PMID": "24145415", "PMCID": "PMC3831453", "ISSN": "1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Analysis of Variance", "type": 1 }, { "tag": "Animals", "type": 1 }, { "tag": "Caenorhabditis elegans", "type": 1 }, { "tag": "Calcium", "type": 1 }, { "tag": "Chemoreceptor Cells", "type": 1 }, { "tag": "Microfluidic Analytical Techniques", "type": 1 }, { "tag": "Microscopy, Fluorescence", "type": 1 }, { "tag": "Neuroimaging", "type": 1 }, { "tag": "Odors", "type": 1 }, { "tag": "Stimulation, Chemical", "type": 1 }, { "tag": "Synaptic Transmission", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-07-08T13:42:59Z", "dateModified": "2014-07-08T13:42:59Z" } }, { "key": "QJDW7WGT", "version": 22, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/QJDW7WGT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/QJDW7WGT", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/GU3A83ZX", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } } }, "data": { "key": "QJDW7WGT", "version": 22, "parentItem": "GU3A83ZX", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-07-08T13:42:42Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/24145415", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-07-08T13:42:59Z", "dateModified": "2014-07-08T13:42:59Z" } }, { "key": "WCXMRZCI", "version": 29, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/WCXMRZCI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/WCXMRZCI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Stirman et al.", "parsedDate": "2012-02", "numChildren": 0 }, "data": { "key": "WCXMRZCI", "version": 29, "itemType": "journalArticle", "title": "A multispectral optical illumination system with precise spatiotemporal control for the manipulation of optogenetic reagents", "creators": [ { "creatorType": "author", "firstName": "Jeffrey N", "lastName": "Stirman" }, { "creatorType": "author", "firstName": "Matthew M", "lastName": "Crane" }, { "creatorType": "author", "firstName": "Steven J", "lastName": "Husson" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Gottschalk" }, { "creatorType": "author", "firstName": "Hang", "lastName": "Lu" } ], "abstractNote": "Optogenetics is an excellent tool for noninvasive activation and silencing of neurons and muscles. Although they have been widely adopted, illumination techniques for optogenetic tools remain limited and relatively nonstandardized. We present a protocol for constructing an illumination system capable of dynamic multispectral optical targeting of micrometer-sized structures in both stationary and moving objects. The initial steps of the protocol describe how to modify an off-the-shelf video projector by insertion of optical filters and modification of projector optics. Subsequent steps involve altering the microscope's epifluorescence optical train as well as alignment and characterization of the system. When fully assembled, the illumination system is capable of dynamically projecting multispectral patterns with a resolution better than 10 μm at medium magnifications. Compared with other custom-assembled systems and commercially available products, this protocol allows a researcher to assemble the illumination system for a fraction of the cost and can be completed within a few days.", "publicationTitle": "Nature protocols", "publisher": "", "place": "", "date": "Feb 2012", "volume": "7", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "207-220", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Protoc", "DOI": "10.1038/nprot.2011.433", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/22240583", "accessDate": "2012-05-09T23:15:51Z", "PMID": "22240583", "PMCID": "", "ISSN": "1750-2799", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-07-08T01:31:10Z", "dateModified": "2014-07-08T01:31:10Z" } }, { "key": "Z6W8ZN8W", "version": 20, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/Z6W8ZN8W", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/Z6W8ZN8W", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Kerr", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "Z6W8ZN8W", "version": 20, "itemType": "journalArticle", "title": "Imaging the activity of neurons and muscles", "creators": [ { "creatorType": "author", "firstName": "Rex", "lastName": "Kerr" } ], "abstractNote": "", "publicationTitle": "WormBook", "publisher": "", "place": "", "date": "2006", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1895/wormbook.1.113.1", "citationKey": "", "url": "http://www.wormbook.org/chapters/www_imagingneurons/imagingneurons.html", "accessDate": "2012-09-23T13:06:40Z", "PMID": "", "PMCID": "", "ISSN": "15518507", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-07-07T14:23:21Z", "dateModified": "2014-07-07T14:23:21Z" } }, { "key": "B8HIF8Q7", "version": 29, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/B8HIF8Q7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/B8HIF8Q7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Nagel et al.", "parsedDate": "2005-12-20", "numChildren": 1 }, "data": { "key": "B8HIF8Q7", "version": 29, "itemType": "journalArticle", "title": "Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses", "creators": [ { "creatorType": "author", "firstName": "Georg", "lastName": "Nagel" }, { "creatorType": "author", "firstName": "Martin", "lastName": "Brauner" }, { "creatorType": "author", "firstName": "Jana F", "lastName": "Liewald" }, { "creatorType": "author", "firstName": "Nona", "lastName": "Adeishvili" }, { "creatorType": "author", "firstName": "Ernst", "lastName": "Bamberg" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Gottschalk" } ], "abstractNote": "For studying the function of specific neurons in their native circuitry, it is desired to precisely control their activity. This often requires dissection to allow accurate electrical stimulation or neurotransmitter application , and it is thus inherently difficult in live animals, especially in small model organisms. Here, we employed channelrhodopsin-2 (ChR2), a directly light-gated cation channel from the green alga Chlamydomonas reinhardtii, in excitable cells of the nematode Caenorhabditis elegans, to trigger specific behaviors, simply by illumination. Channelrhodopsins are 7-transmembrane-helix proteins that resemble the light-driven proton pump bacteriorhodopsin , and they also utilize the chromophore all-trans retinal, but to open an intrinsic cation pore. In muscle cells, light-activated ChR2 evoked strong, simultaneous contractions, which were reduced in the background of mutated L-type, voltage-gated Ca2+-channels (VGCCs) and ryanodine receptors (RyRs). Electrophysiological analysis demonstrated rapid inward currents that persisted as long as the illumination. When ChR2 was expressed in mechanosensory neurons, light evoked withdrawal behaviors that are normally elicited by mechanical stimulation. Furthermore, ChR2 enabled activity of these neurons in mutants lacking the MEC-4/MEC-10 mechanosensory ion channel . Thus, specific neurons or muscles expressing ChR2 can be quickly and reversibly activated by light in live and behaving, as well as dissected, animals.", "publicationTitle": "Current biology: CB", "publisher": "", "place": "", "date": "Dec 20, 2005", "volume": "15", "issue": "24", "section": "", "partNumber": "", "partTitle": "", "pages": "2279-2284", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Curr. Biol.", "DOI": "10.1016/j.cub.2005.11.032", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/16360690", "accessDate": "2012-09-30T21:33:50Z", "PMID": "16360690", "PMCID": "", "ISSN": "0960-9822", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Chlamydomonas reinhardtii", "type": 1 }, { "tag": "DNA Primers", "type": 1 }, { "tag": "Electrophysiology", "type": 1 }, { "tag": "Gene Expression", "type": 1 }, { "tag": "Ion Channels", "type": 1 }, { "tag": "Light", "type": 1 }, { "tag": "Microscopy, Fluorescence", "type": 1 }, { "tag": "Muscle Contraction", "type": 1 }, { "tag": "Neurons, Afferent", "type": 1 }, { "tag": "Photochemistry", "type": 1 }, { "tag": "Sensory Rhodopsins", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-07-07T02:03:53Z", "dateModified": "2014-07-07T02:03:53Z" } }, { "key": "8F26FTR8", "version": 19, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/8F26FTR8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/8F26FTR8", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/B8HIF8Q7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "8F26FTR8", "version": 19, "parentItem": "B8HIF8Q7", "itemType": "note", "note": "

First optogenetics in worms.

", "tags": [], "relations": {}, "dateAdded": "2014-07-07T02:03:53Z", "dateModified": "2014-07-07T02:03:53Z" } }, { "key": "NXQIMGH2", "version": 18, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/NXQIMGH2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/NXQIMGH2", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Chung et al.", "parsedDate": "2013-04-10", "numChildren": 0 }, "data": { "key": "NXQIMGH2", "version": 18, "itemType": "journalArticle", "title": "Neuronal Calcium Imaging in C. elegans", "creators": [ { "creatorType": "author", "firstName": "Samuel H.", "lastName": "Chung" }, { "creatorType": "author", "firstName": "Lin", "lastName": "Sun" }, { "creatorType": "author", "firstName": "Christopher V.", "lastName": "Gabel" } ], "abstractNote": "", "publicationTitle": "Journal of Visualized Experiments", "publisher": "", "place": "", "date": "2013-4-10", "volume": "", "issue": "74", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.3791/50357", "citationKey": "", "url": "http://www.jove.com/video/50357/in-vivo-neuronal-calcium-imaging-in-c-elegans", "accessDate": "2014-07-07T01:58:10Z", "PMID": "", "PMCID": "", "ISSN": "1940-087X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-07-07T01:58:25Z", "dateModified": "2014-07-07T01:58:25Z" } }, { "key": "H72TDCFJ", "version": 17, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/H72TDCFJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/H72TDCFJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Husson", "parsedDate": "2012-09-10", "numChildren": 0 }, "data": { "key": "H72TDCFJ", "version": 17, "itemType": "journalArticle", "title": "Keeping track of worm trackers", "creators": [ { "creatorType": "author", "firstName": "Steven J.", "lastName": "Husson" } ], "abstractNote": "", "publicationTitle": "WormBook", "publisher": "", "place": "", "date": "2012-09-10", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "1-17", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1895/wormbook.1.156.1", "citationKey": "", "url": "http://www.wormbook.org/chapters/www_tracking/tracking.html", "accessDate": "2014-07-05T22:01:13Z", "PMID": "", "PMCID": "", "ISSN": "15518507", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-07-05T22:01:21Z", "dateModified": "2014-07-05T22:01:21Z" } }, { "key": "VRWISJHD", "version": 29, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/VRWISJHD", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/VRWISJHD", "type": "text/html" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "creatorSummary": "Stirman et al.", "parsedDate": "2011-02", "numChildren": 0 }, "data": { "key": "VRWISJHD", "version": 29, "itemType": "journalArticle", "title": "Real-time multimodal optical control of neurons and muscles in freely behaving Caenorhabditis elegans", "creators": [ { "creatorType": "author", "firstName": "Jeffrey N", "lastName": "Stirman" }, { "creatorType": "author", "firstName": "Matthew M", "lastName": "Crane" }, { "creatorType": "author", "firstName": "Steven J", "lastName": "Husson" }, { "creatorType": "author", "firstName": "Sebastian", "lastName": "Wabnig" }, { "creatorType": "author", "firstName": "Christian", "lastName": "Schultheis" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Gottschalk" }, { "creatorType": "author", "firstName": "Hang", "lastName": "Lu" } ], "abstractNote": "The ability to optically excite or silence specific cells using optogenetics has become a powerful tool to interrogate the nervous system. Optogenetic experiments in small organisms have mostly been performed using whole-field illumination and genetic targeting, but these strategies do not always provide adequate cellular specificity. Targeted illumination can be a valuable alternative but it has only been shown in motionless animals without the ability to observe behavior output. We present a real-time, multimodal illumination technology that allows both tracking and recording the behavior of freely moving C. elegans while stimulating specific cells that express channelrhodopsin-2 or MAC. We used this system to optically manipulate nodes in the C. elegans touch circuit and study the roles of sensory and command neurons and the ultimate behavioral output. This technology enhances our ability to control, alter, observe and investigate how neurons, muscles and circuits ultimately produce behavior in animals using optogenetics.", "publicationTitle": "Nature methods", "publisher": "", "place": "", "date": "Feb 2011", "volume": "8", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "153-158", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Methods", "DOI": "10.1038/nmeth.1555", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21240278", "accessDate": "2012-05-09T23:16:17Z", "PMID": "21240278", "PMCID": "", "ISSN": "1548-7105", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Behavior, Animal", "type": 1 }, { "tag": "Caenorhabditis elegans", "type": 1 }, { "tag": "Muscles", "type": 1 }, { "tag": "Neurons", "type": 1 }, { "tag": "Optical Processes", "type": 1 }, { "tag": "Photobiology", "type": 1 }, { "tag": "Time Factors", "type": 1 }, { "tag": "Visual Perception", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-07-05T21:59:09Z", "dateModified": "2014-07-05T21:59:09Z" } }, { "key": "5CMWFAD2", "version": 15, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/5CMWFAD2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/5CMWFAD2", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/ZBQFM5ZD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "5CMWFAD2", "version": 15, "parentItem": "ZBQFM5ZD", "itemType": "note", "note": "

Glued down worm with head free to move.

\n

 

\n

 

", "tags": [], "relations": {}, "dateAdded": "2014-07-03T22:07:04Z", "dateModified": "2014-07-05T20:49:45Z" } }, { "key": "47HVF3RM", "version": 15, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/47HVF3RM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/47HVF3RM", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/ZBQFM5ZD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "47HVF3RM", "version": 15, "parentItem": "ZBQFM5ZD", "itemType": "note", "note": "

First instance of recording from c. elegans using a dual objective setup.

", "tags": [], "relations": {}, "dateAdded": "2014-07-05T20:49:12Z", "dateModified": "2014-07-05T20:49:23Z" } }, { "key": "K38FC8KC", "version": 14, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/K38FC8KC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/K38FC8KC", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/PR6WFXVA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "K38FC8KC", "version": 14, "parentItem": "PR6WFXVA", "itemType": "note", "note": "

This is a commercial system that can be purchased in its entirety.

\n

 

", "tags": [], "relations": {}, "dateAdded": "2014-07-05T20:48:29Z", "dateModified": "2014-07-05T20:48:38Z" } }, { "key": "ZFNX3D27", "version": 14, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/ZFNX3D27", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/ZFNX3D27", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/PR6WFXVA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "ZFNX3D27", "version": 14, "parentItem": "PR6WFXVA", "itemType": "note", "note": "

First instance of fluorescence based real time tracking in C. elegans.

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First instances of calcium imaging in freely moving unrestrained C. elegans.

\n

 

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Review of optogenetic stimulation and inhibition in C. elegans.

", "tags": [], "relations": {}, "dateAdded": "2014-07-05T20:46:59Z", "dateModified": "2014-07-05T20:47:16Z" } }, { "key": "35CDVXW9", "version": 11, "library": { "type": "group", "id": 271076, "name": "CeNeuroWorkshop2014", "links": { "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/271076/items/35CDVXW9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/ceneuroworkshop2014/items/35CDVXW9", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/271076/items/M8CPSBTP", "type": "application/json" } }, "meta": { "createdByUser": { "id": 8015, "username": "Kramer", "name": "Andrew Leifer", "links": { "alternate": { "href": "https://www.zotero.org/kramer", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "35CDVXW9", "version": 11, "parentItem": "M8CPSBTP", "itemType": "note", "note": "

See especially intro & conclusion.

", "tags": [], "relations": {}, "dateAdded": "2014-07-05T20:46:40Z", "dateModified": "2014-07-05T20:46:40Z" } } ]