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Boyden, Edward S. Orozco Cosio, Danielle Marie Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences 2022-09-27T20:16:29Z 2022-09-27T20:16:29Z 2022-05 2022-09-27T16:57:52.735Z https://hdl.handle.net/1721.1/145601 Optical methods to study C. elegans behavior and neural activity are popular and wellestablished in the field, but many of the most commonly used optical tools leave much to be improved upon. In this research I sought to establish the utility of new optical tools in C. elegans to address the shortcomings of commonly used ones. First, I present the properties and demonstrate the functionality of an improved near-infrared negative calcium ion indicator, NIR-GECO2, for imaging olfactory stimulated and optogenetically evoked neural activity. Next, I present the properties and demonstrate the functionality of a tool to strategically arrange GCaMP in clusters, STARC, to enable imaging of compartmentalized neural activity in regions dense with neural projections. Finally, I present a novel computational and RNA fluorescent in-situ hybridization-based method for unique identification of C. elegans neurons which allows for experiments to be performed in any C. elegans strain and can be flexibly applied to new applications and organisms. When appropriately combined with existing methods, these tools and techniques enable experiments that can push the field of C. elegans systems neuroscience towards a functional connectomic understanding of the neural control of the animal’s behavior. Ph.D. Massachusetts Institute of Technology In Copyright - Educational Use Permitted Copyright MIT http://rightsstatements.org/page/InC-EDU/1.0/ Development of Optical Tools and Techniques Toward a Functional Connectomic Understanding of C. elegans Thesis application/pdf Doctoral Doctor of Philosophy Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="827ffcf6-8118-44d8-a54a-074a929b2738"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Title>Development of Optical Tools and Techniques Toward a Functional Connectomic Understanding of C. elegans</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2022-05</PublicationDate> <Authors> <Author> <DisplayName>Orozco Cosio, Danielle Marie</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://rightsstatements.org/page/InC-EDU/1.0/</License> <Abstract>Optical methods to study C. elegans behavior and neural activity are popular and wellestablished in the field, but many of the most commonly used optical tools leave much to be improved upon. In this research I sought to establish the utility of new optical tools in C. elegans to address the shortcomings of commonly used ones. First, I present the properties and demonstrate the functionality of an improved near-infrared negative calcium ion indicator, NIR-GECO2, for imaging olfactory stimulated and optogenetically evoked neural activity. Next, I present the properties and demonstrate the functionality of a tool to strategically arrange GCaMP in clusters, STARC, to enable imaging of compartmentalized neural activity in regions dense with neural projections. Finally, I present a novel computational and RNA fluorescent in-situ hybridization-based method for unique identification of C. elegans neurons which allows for experiments to be performed in any C. elegans strain and can be flexibly applied to new applications and organisms. When appropriately combined with existing methods, these tools and techniques enable experiments that can push the field of C. elegans systems neuroscience towards a functional connectomic understanding of the neural control of the animal’s behavior.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>