All optical physiologyin vivoprovides a conduit for investigating the function of neural circuits in 3-D. Here, we report a new strategy for flexible, axially-decoupled photo-stimulation and two photon readout (ADePT) of neuronal activity. To achieve axially-contained widefield optogenetic patterned stimulation, we couple a digital micro-mirror device illuminated by a solid-state laser with a motorized holographic diffuser. In parallel, we use multiphoton imaging of neural activity across different z-planes. We useADePTto analyze the excitatory and inhibitory functional connectivity of the mouse early olfactory system. Specifically, we control the activity of individual input glomeruli on the olfactory bulb surface, and map the ensuing responses of output mitral and tufted cell bodies in deeper layers. This approach identifies cohorts ofsistermitral and tufted cells, whose firing is driven by the same parent glomerulus, and also reveals their differential inhibition by other glomeruli. In addition, selective optogenetic activation of glomerular GABAergic/dopaminergic (DAT+) interneurons triggers dense, but spatially heterogeneous suppression of mitral and tufted cell baseline activity and odor responses, further demonstrating specificity in the inhibitory olfactory bulb connectivity. In summary,ADePTenables high-throughput functional connectivity mapping in optically accessible brain regions.
", "doi": "10.1101/2025.02.24.639992", "publisher": "bioRxiv", "publication_date": "2025-06-01" }, { "id": "authors:sxje4-sj785", "collection": "authors", "collection_id": "sxje4-sj785", "cite_using_url": "https://authors.library.caltech.edu/records/sxje4-sj785", "type": "article", "title": "Characterization and quantification of adeno-associated virus capsid-loading states by multi-wavelength analytical ultracentrifugation with UltraScan", "author": [ { "family_name": "Henrickson", "given_name": "Amy", "orcid": "0000-0003-3266-5202", "clpid": "Henrickson-Amy" }, { "family_name": "Ding", "given_name": "Xiaozhe", "orcid": "0000-0002-0267-0791", "clpid": "Ding-Xiaozhe" }, { "family_name": "Seal", "given_name": "Austin G.", "orcid": "0009-0003-3417-1908", "clpid": "Seal-Austin-G" }, { "family_name": "Qu", "given_name": "Zhe", "orcid": "0009-0001-6323-9305", "clpid": "Qu-Zhe" }, { "family_name": "Tomlinson", "given_name": "Lauren", "orcid": "0000-0001-6936-1881", "clpid": "Tomlinson-Lauren-J" }, { "family_name": "Forsey", "given_name": "John", "orcid": "0009-0001-5557-4381", "clpid": "Forsey-John" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Oka", "given_name": "Kazuhiro", "orcid": "0000-0003-2159-3637", "clpid": "Oka-Kazuhiro" }, { "family_name": "Demeler", "given_name": "Borries", "orcid": "0000-0002-2414-9518", "clpid": "Demeler-Borries" } ], "abstract": "Aim: We present multi-wavelength (MW) analytical ultracentrifugation (AUC) methods offering superior accuracy for adeno-associated virus characterization and quantification.
Methods: Experimental design guidelines are presented for MW sedimentation velocity and analytical buoyant density equilibrium AUC.
Results: Our results were compared with dual-wavelength AUC, transmission electron microscopy and mass photometry. In contrast to dual-wavelength AUC, MW-AUC correctly quantifies adeno-associated virus capsid ratios and identifies contaminants. In contrast to transmission electron microscopy, partially filled capsids can also be detected and quantified. In contrast to mass photometry, first-principle results are obtained.
Conclusion: Our study demonstrates the improved information provided by MW-AUC, highlighting the utility of several recently integrated UltraScan programs, and reinforces AUC as the gold-standard analysis for viral vectors.
", "doi": "10.2217/nnm-2023-0156", "pmcid": "PMC10652292", "issn": "1743-5889", "publisher": "Future Medicine Ltd", "publication": "Nanomedicine", "publication_date": "2023-09", "series_number": "22", "volume": "18", "issue": "22", "pages": "1519-1534" }, { "id": "authors:1w82f-14a30", "collection": "authors", "collection_id": "1w82f-14a30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221209-478595000.5", "type": "article", "title": "Molecular basis of astrocyte diversity and morphology across the CNS in health and disease", "author": [ { "family_name": "Endo", "given_name": "Fumito", "orcid": "0000-0003-4445-6707", "clpid": "Endo-Fumito" }, { "family_name": "Kasai", "given_name": "Atsushi", "orcid": "0000-0002-1612-3078", "clpid": "Kasai-Atsushi" }, { "family_name": "Soto", "given_name": "Joselyn S.", "orcid": "0000-0002-5869-9091", "clpid": "Soto-Joselyn-S" }, { "family_name": "Yu", "given_name": "Xinzhu", "orcid": "0000-0003-1244-0110", "clpid": "Yu-Xinzhu" }, { "family_name": "Qu", "given_name": "Zhe", "clpid": "Qu-Zhe" }, { "family_name": "Hashimoto", "given_name": "Hitoshi", "orcid": "0000-0001-6548-4016", "clpid": "Hashimoto-Hitoshi" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Kawaguchi", "given_name": "Riki", "orcid": "0000-0002-2489-4825", "clpid": "Kawaguchi-Riki" }, { "family_name": "Khakh", "given_name": "Baljit S.", "orcid": "0000-0002-0939-1218", "clpid": "Khakh-Baljit-S" } ], "abstract": "Astrocytes, a type of glia, are abundant and morphologically complex cells. Here, we report astrocyte molecular profiles, diversity, and morphology across the mouse central nervous system (CNS). We identified shared and region-specific astrocytic genes and functions and explored the cellular origins of their regional diversity. We identified gene networks correlated with astrocyte morphology, several of which unexpectedly contained Alzheimer's disease (AD) risk genes. CRISPR/Cas9\u2013mediated reduction of candidate genes reduced astrocyte morphological complexity and resulted in cognitive deficits. The same genes were down-regulated in human AD, in an AD mouse model that displayed reduced astrocyte morphology, and in other human brain disorders. We thus provide comprehensive molecular data on astrocyte diversity and mechanisms across the CNS and on the molecular basis of astrocyte morphology in health and disease.", "doi": "10.1126/science.adc9020", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2022-11-04", "series_number": "6619", "volume": "378", "issue": "6619", "pages": "Art. No. adc9020" }, { "id": "authors:pg7h2-wsy12", "collection": "authors", "collection_id": "pg7h2-wsy12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210728-223917563", "type": "article", "title": "Brain-wide Cas9-mediated cleavage of a gene causing familial Alzheimer's disease alleviates amyloid-related pathologies in mice", "author": [ { "family_name": "Duan", "given_name": "Yangyang", "orcid": "0000-0002-0823-6574", "clpid": "Duan-Yangyang" }, { "family_name": "Ye", "given_name": "Tao", "orcid": "0000-0002-8075-7323", "clpid": "Ye-Tao" }, { "family_name": "Qu", "given_name": "Zhe", "clpid": "Qu-Zhe" }, { "family_name": "Chen", "given_name": "Yuewen", "clpid": "Chen-Yuewen" }, { "family_name": "Miranda", "given_name": "Abigail", "clpid": "Miranda-Abigail" }, { "family_name": "Zhou", "given_name": "Xiaopu", "clpid": "Zhou-Xiaopu" }, { "family_name": "Lok", "given_name": "Ka-Chun", "clpid": "Lok-Ka-Chun" }, { "family_name": "Chen", "given_name": "Yu", "clpid": "Chen-Yu" }, { "family_name": "Fu", "given_name": "Amy K. Y.", "clpid": "Fu-Amy-K-Y" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Ip", "given_name": "Nancy Y.", "orcid": "0000-0002-2763-8907", "clpid": "Ip-Nancy-Y" } ], "abstract": "The pathology of familial Alzheimer's disease, which is caused by dominant mutations in the gene that encodes amyloid-beta precursor protein (APP) and in those that encode presenilin 1 and presenilin 2, is characterized by extracellular amyloid plaques and intracellular neurofibrillary tangles in multiple brain regions. Here we show that the brain-wide selective disruption of a mutated APP allele in transgenic mouse models carrying the human APP Swedish mutation alleviates amyloid-beta-associated pathologies for at least six months after a single intrahippocampal administration of an adeno-associated virus that encodes both Cas9 and a single-guide RNA that targets the mutation. We also show that the deposition of amyloid-beta, as well as microgliosis, neurite dystrophy and the impairment of cognitive performance, can all be ameliorated when the CRISPR\u2013Cas9 construct is delivered intravenously via a modified adeno-associated virus that can cross the blood\u2013brain barrier. Brain-wide disease-modifying genome editing could represent a viable strategy for the treatment of familial Alzheimer's disease and other monogenic diseases that affect multiple brain regions.", "doi": "10.1038/s41551-021-00759-0", "issn": "2157-846X", "publisher": "Nature Publishing Group", "publication": "Nature Biomedical Engineering", "publication_date": "2022-02", "series_number": "2", "volume": "6", "issue": "2", "pages": "168-180" } ]