Boards, Advisory Committees, Professional Organizations

  • Member, Stanford Biology Postdoc Committee (2022 - Present)
  • Member, Stanford Biology Diversity, Equity, Inclusion and Belonging Committee (2023 - Present)

Professional Education

  • Doctor of Philosophy, Cornell University (2021)
  • Ph.D., Cornell University, Applied and Engineering Physics (2021)

Stanford Advisors

All Publications

  • Label-free, whole-brain in vivo mapping in an adult vertebrate with third harmonic generation microscopy JOURNAL OF COMPARATIVE NEUROLOGY Akbari, N., Tatarsky, R. L., Kolkman, K. E., Fetcho, J. R., Xu, C., Bass, A. H. 2024; 532 (4): e25614


    Comprehensive understanding of interconnected networks within the brain requires access to high resolution information within large field of views and over time. Currently, methods that enable mapping structural changes of the entire brain in vivo are extremely limited. Third harmonic generation (THG) can resolve myelinated structures, blood vessels, and cell bodies throughout the brain without the need for any exogenous labeling. Together with deep penetration of long wavelengths, this enables in vivo brain-mapping of large fractions of the brain in small animals and over time. Here, we demonstrate that THG microscopy allows non-invasive label-free mapping of the entire brain of an adult vertebrate, Danionella dracula, which is a miniature species of cyprinid fish. We show this capability in multiple brain regions and in particular the identification of major commissural fiber bundles in the midbrain and the hindbrain. These features provide readily discernable landmarks for navigation and identification of regional-specific neuronal groups and even single neurons during in vivo experiments. We further show how this label-free technique can easily be coupled with fluorescence microscopy and used as a comparative tool for studies of other species with similar body features to Danionella, such as zebrafish (Danio rerio) and tetras (Trochilocharax ornatus). This new evidence, building on previous studies, demonstrates how small size and relative transparency, combined with the unique capabilities of THG microscopy, can enable label-free access to the entire adult vertebrate brain.

    View details for DOI 10.1002/cne.25614

    View details for Web of Science ID 001203534700001

    View details for PubMedID 38616537

  • Midbrain node for context-specific vocalisation in fish. Nature communications Schuppe, E. R., Ballagh, I., Akbari, N., Fang, W., Perelmuter, J. T., Radtke, C. H., Marchaterre, M. A., Bass, A. H. 2024; 15 (1): 189


    Vocalizations communicate information indicative of behavioural state across divergent social contexts. Yet, how brain regions actively pattern the acoustic features of context-specific vocal signals remains largely unexplored. The midbrain periaqueductal gray (PAG) is a major site for initiating vocalization among mammals, including primates. We show that PAG neurons in a highly vocal fish species (Porichthys notatus) are activated in distinct patterns during agonistic versus courtship calling by males, with few co-activated during a non-vocal behaviour, foraging. Pharmacological manipulations within vocally active PAG, but not hindbrain, sites evoke vocal network output to sonic muscles matching the temporal features of courtship and agonistic calls, showing that a balance of inhibitory and excitatory dynamics is likely necessary for patterning different call types. Collectively, these findings support the hypothesis that vocal species of fish and mammals share functionally comparable PAG nodes that in some species can influence the acoustic structure of social context-specific vocal signals.

    View details for DOI 10.1038/s41467-023-43794-y

    View details for PubMedID 38167237

    View details for PubMedCentralID PMC10762186

  • Midbrain node for context-specific vocalisation in fish NATURE COMMUNICATIONS Schuppe, E. R., Ballagh, I., Akbari, N., Fang, W., Perelmuter, J. T., Radtke, C. H., Marchaterre, M. A., Bass, A. H. 2024; 15 (1)
  • Tissue-specific in vivo transformation of plasmid DNA in Neotropical tadpoles using electroporation. PloS one Delia, J., Gaines-Richardson, M., Ludington, S. C., Akbari, N., Vasek, C., Shaykevich, D., O'Connell, L. A. 2023; 18 (8): e0289361


    Electroporation is an increasingly common technique used for exogenous gene expression in live animals, but protocols are largely limited to traditional laboratory organisms. The goal of this protocol is to test in vivo electroporation techniques in a diverse array of tadpole species. We explore electroporation efficiency in tissue-specific cells of five species from across three families of tropical frogs: poison frogs (Dendrobatidae), cryptic forest/poison frogs (Aromobatidae), and glassfrogs (Centrolenidae). These species are well known for their diverse social behaviors and intriguing physiologies that coordinate chemical defenses, aposematism, and/or tissue transparency. Specifically, we examine the effects of electrical pulse and injection parameters on species- and tissue-specific transfection of plasmid DNA in tadpoles. After electroporation of a plasmid encoding green fluorescent protein (GFP), we found strong GFP fluorescence within brain and muscle cells that increased with the amount of DNA injected and electrical pulse number. We discuss species-related challenges, troubleshooting, and outline ideas for improvement. Extending in vivo electroporation to non-model amphibian species could provide new opportunities for exploring topics in genetics, behavior, and organismal biology.

    View details for DOI 10.1371/journal.pone.0289361

    View details for PubMedID 37590232

  • Whole-brain optical access in a small adult vertebrate with two- and three-photon microscopy ISCIENCE Akbari, N., Tatarsky, R. L., Kolkman, K. E., Fetcho, J. R., Bass, A. H., Xu, C. 2022; 25 (10): 105191


    Although optical microscopy has allowed scientists to study the entire brain in early developmental stages, access to the brains of live, adult vertebrates has been limited. Danionella, a genus of miniature, transparent fish closely related to zebrafish has been introduced as a neuroscience model to study the adult vertebrate brain. However, the extent of optically accessible depth in these animals has not been quantitatively characterized. Here, we show that both two- and three-photon microscopy can access the entire depth and rostral-caudal extent of the adult wildtype Danionella dracula brain without any modifications to the animal other than mechanical stabilization. Three-photon microscopy provides higher signal-to-background ratio and optical sectioning of fluorescently labeled vasculature through the deepest part of the brain, the hypothalamus. Hence, we use multiphoton microscopy to penetrate the entire adult brain within the geometry of this genus' head structures and without the need for pigment removal.

    View details for DOI 10.1016/j.isci.2022.105191

    View details for Web of Science ID 000869487400006

    View details for PubMedID 36248737

    View details for PubMedCentralID PMC9557827