{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/129579"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/129579","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Development and application of innovative technologies to unravel neuronal systems: From optogenetics to neural interfaces to spatial transcriptomics","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-05-01","abstract_has_math":false,"creators":["Fan, Huaxun"],"institution":"University of Illinois Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biochemistry","degree_department":null,"school":null,"contributors":["Zhang, Kai","Yang, Jing","Christian-Hinman, Catherine","Kalsotra, Auinash"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-04-27","date_published":"2025-04-27","updated_at":"2026-07-22T22:25:05Z","subjects":["Biotechnologies","Neuroscience","Optogenetics","Spatial Transcriptomics"],"languages":["en","eng"],"rights":["Copyright 2025 Huaxun Fan"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/129579","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Zhang, Kai","Yang, Jing","Christian-Hinman, Catherine","Kalsotra, Auinash"]},{"key":"dc:creator","label":"Author","values":["Fan, Huaxun"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-04-27","2025-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biochemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biotechnologies","Neuroscience","Optogenetics","Spatial Transcriptomics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Huaxun Fan"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/129579"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-05-01","The student, Huaxun Fan, accepted the attached license on 2025-04-24 at 17:47.","The student, Huaxun Fan, submitted this Dissertation for approval on 2025-04-25 at 09:17.","This Dissertation was approved for publication on 2025-04-27 at 20:33.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21965 on 2025-10-19 at 19:16:12","The neuronal system represents one of the final frontiers of biological research, as it underpinning cognitive function and behavior. However, the immense complexity of neuronal systems has hindered our ability to fully understand the underlying mechanisms. This dissertation presents the development and application of innovative technologies, including optogenetics, neural interfaces and spatial transcriptomics, to provide deeper understanding of cell signaling pathways, neural communication, and the intricate architecture of brain function. Cell signaling pathways constitute the molecular machinery that regulates cellular behavior. Among them, the Raf/ERK and AKT pathways play key roles in neuronal development, survival, regeneration, and plasticity. We developed optogenetic systems, termed optoRaf and optoAKT, to enable precise control of corresponding signaling pathways in both invertebrate and vertebrate models. In Drosophila, optoRaf or optoAKT activation not only enhanced axon regeneration in both regeneration-competent and incompetent sensory neurons in the peripheral nervous system (PNS) but also enabled temporal modulation and spatial guidance of axon regrowth. Importantly in the central nervous system (CNS), activation of these systems promoted axon regrowth and functional recovery of thermonociceptive behavior. We further engineered the optoRaf system to be compatible with the adeno-associate virus (AAV) delivery system, facilitating mammalian applications. Non-invasive light delivery through transcranial window successfully activates optoRaf system in the mouse motor cortex. Optical activation of ERK signaling pathway increased calcium activity frequency and amplitude, inducing neuronal excitability. Importantly, ambient illumination in freely moving animals trigger similar activation, highlighting the potential of the optoRaf system for studying ERK-dependent neuronal plasticity in freely behaving animals and across diverse behavioral contexts. Neural communication is the foundation for cognitive function, the efficiency of neuronal information processing is orders of magnitude higher than the most advanced silicon-based semiconductors. We developed a transformative bionanotechnology platform that enables the guided formation of cultured neural networks with complex and well-defined 3D topologies. Meanwhile, these neuronal cells are seamlessly interfaced with advanced electronic devices, allowing us to administer and monitor the neuronal and synaptic activities with unprecedented high spatiotemporal resolution. Finally, the spatial context of gene expression is critical for understanding the organization and function of neuronal systems. To address this, we developed Single Nuclei Imaging-guided sPatial transcriptomics for Enhanced genome-wide coveRage (SNIPER), a technology capable of capturing whole-transcriptome profiles at single-cell resolution. This methodology offers unparalleled precision and enables comprehensive characterization of neuronal heterogeneity and spatial architecture. Collectively, these innovative technologies significantly advance our ability to investigate neuronal systems at the molecular, cellular, and network levels. Beyond providing fundamental insights into neuronal function, these tools hold potential for therapeutic applications and broader interdisciplinary research. It is our aspiration that these technological innovations will equip researchers to advance the frontiers of neuroscience and biology."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Development and application of innovative technologies to unravel neuronal systems: From optogenetics to neural interfaces to spatial transcriptomics"]}]}],"canonical_facts":{"dc:contributor":["Zhang, Kai","Yang, Jing","Christian-Hinman, Catherine","Kalsotra, Auinash"],"dc:creator":["Fan, Huaxun"],"dc:date":["2025-04-27","2025-05"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2027-05-01","The student, Huaxun Fan, accepted the attached license on 2025-04-24 at 17:47.","The student, Huaxun Fan, submitted this Dissertation for approval on 2025-04-25 at 09:17.","This Dissertation was approved for publication on 2025-04-27 at 20:33.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21965 on 2025-10-19 at 19:16:12","The neuronal system represents one of the final frontiers of biological research, as it underpinning cognitive function and behavior. However, the immense complexity of neuronal systems has hindered our ability to fully understand the underlying mechanisms. This dissertation presents the development and application of innovative technologies, including optogenetics, neural interfaces and spatial transcriptomics, to provide deeper understanding of cell signaling pathways, neural communication, and the intricate architecture of brain function. Cell signaling pathways constitute the molecular machinery that regulates cellular behavior. Among them, the Raf/ERK and AKT pathways play key roles in neuronal development, survival, regeneration, and plasticity. We developed optogenetic systems, termed optoRaf and optoAKT, to enable precise control of corresponding signaling pathways in both invertebrate and vertebrate models. In Drosophila, optoRaf or optoAKT activation not only enhanced axon regeneration in both regeneration-competent and incompetent sensory neurons in the peripheral nervous system (PNS) but also enabled temporal modulation and spatial guidance of axon regrowth. Importantly in the central nervous system (CNS), activation of these systems promoted axon regrowth and functional recovery of thermonociceptive behavior. We further engineered the optoRaf system to be compatible with the adeno-associate virus (AAV) delivery system, facilitating mammalian applications. Non-invasive light delivery through transcranial window successfully activates optoRaf system in the mouse motor cortex. Optical activation of ERK signaling pathway increased calcium activity frequency and amplitude, inducing neuronal excitability. Importantly, ambient illumination in freely moving animals trigger similar activation, highlighting the potential of the optoRaf system for studying ERK-dependent neuronal plasticity in freely behaving animals and across diverse behavioral contexts. Neural communication is the foundation for cognitive function, the efficiency of neuronal information processing is orders of magnitude higher than the most advanced silicon-based semiconductors. We developed a transformative bionanotechnology platform that enables the guided formation of cultured neural networks with complex and well-defined 3D topologies. Meanwhile, these neuronal cells are seamlessly interfaced with advanced electronic devices, allowing us to administer and monitor the neuronal and synaptic activities with unprecedented high spatiotemporal resolution. Finally, the spatial context of gene expression is critical for understanding the organization and function of neuronal systems. To address this, we developed Single Nuclei Imaging-guided sPatial transcriptomics for Enhanced genome-wide coveRage (SNIPER), a technology capable of capturing whole-transcriptome profiles at single-cell resolution. This methodology offers unparalleled precision and enables comprehensive characterization of neuronal heterogeneity and spatial architecture. Collectively, these innovative technologies significantly advance our ability to investigate neuronal systems at the molecular, cellular, and network levels. Beyond providing fundamental insights into neuronal function, these tools hold potential for therapeutic applications and broader interdisciplinary research. It is our aspiration that these technological innovations will equip researchers to advance the frontiers of neuroscience and biology."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/129579"],"dc:language":["en","eng"],"dc:rights":["Copyright 2025 Huaxun Fan"],"dc:subject":["Biotechnologies","Neuroscience","Optogenetics","Spatial Transcriptomics"],"dc:title":["Development and application of innovative technologies to unravel neuronal systems: From optogenetics to neural interfaces to spatial transcriptomics"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Biochemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:05Z"}