Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics.

At around 150 000 neurons, the adult Drosophila melanogaster central nervous system is one of the largest species, for which a complete cellular catalogue is imminent. While numerically much simpler than mammalian brains, its complexity is still difficult to parse without grouping neurons into consistent types, which can number 1-1000 cells per hemisphere. We review how neuroanatomical and gene expression data are being used to discover neuronal types at scale. The correlation among multiple co-varying neuronal properties, including lineage, gene expression, morphology, connectivity, response properties and shared behavioral significance is essential to the definition of neuronal cell type. Initial studies comparing morphological and transcriptomic definitions of neuronal type suggest that these are highly consistent, but there is much to do to match these approaches brain-wide. Matched single-cell transcriptomic and morphological data provide an effective reference point to integrate other data types, including connectomics data. This will significantly enhance our ability to make functional predictions from brain wiring diagrams as well facilitating molecular genetic manipulation of neuronal types

The natverse, a versatile toolbox for combining and analysing neuroanatomical data.

To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation and clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison across many neurons of morphology and connectivity after imaging or co-registration within a common template space. The natverse also enables transformations between different template spaces and imaging modalities. We demonstrate tools that integrate the vast majority of Drosophila neuroanatomical light microscopy and electron microscopy connectomic datasets. The natverse is an easy-to-use environment for neuroscientists to solve complex, large-scale analysis challenges as well as an open platform to create new code and packages to share with the community

The natverse, a versatile toolbox for combining and analysing neuroanatomical data.

To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation and clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison across many neurons of morphology and connectivity after imaging or co-registration within a common template space. The natverse also enables transformations between different template spaces and imaging modalities. We demonstrate tools that integrate the vast majority of Drosophila neuroanatomical light microscopy and electron microscopy connectomic datasets. The natverse is an easy-to-use environment for neuroscientists to solve complex, large-scale analysis challenges as well as an open platform to create new code and packages to share with the community

Functional and anatomical specificity in a higher olfactory centre.

Most sensory systems are organized into parallel neuronal pathways that process distinct aspects of incoming stimuli. In the insect olfactory system, second order projection neurons target both the mushroom body, required for learning, and the lateral horn (LH), proposed to mediate innate olfactory behavior. Mushroom body neurons form a sparse olfactory population code, which is not stereotyped across animals. In contrast, odor coding in the LH remains poorly understood. We combine genetic driver lines, anatomical and functional criteria to show that the Drosophila LH has ~1400 neurons and >165 cell types. Genetically labeled LHNs have stereotyped odor responses across animals and on average respond to three times more odors than single projection neurons. LHNs are better odor categorizers than projection neurons, likely due to stereotyped pooling of related inputs. Our results reveal some of the principles by which a higher processing area can extract innate behavioral significance from sensory stimuli

Analysis and optimization of equitable US cancer clinical trial center access by travel time

Importance: Racially minoritized and socioeconomically disadvantaged populations are currently underrepresented in clinical trials. Data-driven, quantitative analyses and strategies are required to help address this inequity. Objective: To systematically analyze the geographical distribution of self-identified racial and socioeconomic demographics within commuting distance to cancer clinical trial centers and other hospitals in the US. Design, Setting, and Participants: This longitudinal quantitative study used data from the US Census 2020 Decennial and American community survey (which collects data from all US residents), OpenStreetMap, National Cancer Institute–designated Cancer Centers list, Nature Index of Cancer Research Health Institutions, National Trial registry, and National Homeland Infrastructure Foundation-Level Data. Statistical analyses were performed on data collected between 2006 and 2020. Main Outcomes and Measures: Population distributions of socioeconomic deprivation indices and self-identified race within 30-, 60-, and 120-minute 1-way driving commute times from US cancer trial sites. Map overlay of high deprivation index and high diversity areas with existing hospitals, existing major cancer trial centers, and commuting distance to the closest cancer trial center. Results: The 78 major US cancer trial centers that are involved in 94% of all US cancer trials and included in this study were found to be located in areas with socioeconomically more affluent populations with higher proportions of self-identified White individuals (+10.1% unpaired mean difference; 95% CI, +6.8% to +13.7%) compared with the national average. The top 10th percentile of all US hospitals has catchment populations with a range of absolute sum difference from 2.4% to 35% from one-third each of Asian/multiracial/other (Asian alone, American Indian or Alaska Native alone, Native Hawaiian or Other Pacific Islander alone, some other race alone, population of 2 or more races), Black or African American, and White populations. Currently available data are sufficient to identify diverse census tracks within preset commuting times (30, 60, or 120 minutes) from all hospitals in the US (N = 7623). Maps are presented for each US city above 500 000 inhabitants, which display all prospective hospitals and major cancer trial sites within commutable distance to racially diverse and socioeconomically disadvantaged populations. Conclusion and Relevance: This study identified biases in the sociodemographics of populations living within commuting distance to US-based cancer trial sites and enables the determination of more equitably commutable prospective satellite hospital sites that could be mobilized for enhanced racial and socioeconomic representation in clinical trials. The maps generated in this work may inform the design of future clinical trials or investigations in enrollment and retention strategies for clinical trials; however, other recruitment barriers still need to be addressed to ensure racial and socioeconomic demographics within the geographical vicinity of a clinical site can translate to equitable trial participant representation

Communication from Learned to Innate Olfactory Processing Centers Is Required for Memory Retrieval in Drosophila.

The behavioral response to a sensory stimulus may depend on both learned and innate neuronal representations. How these circuits interact to produce appropriate behavior is unknown. In Drosophila, the lateral horn (LH) and mushroom body (MB) are thought to mediate innate and learned olfactory behavior, respectively, although LH function has not been tested directly. Here we identify two LH cell types (PD2a1 and PD2b1) that receive input from an MB output neuron required for recall of aversive olfactory memories. These neurons are required for aversive memory retrieval and modulated by training. Connectomics data demonstrate that PD2a1 and PD2b1 neurons also receive direct input from food odor-encoding neurons. Consistent with this, PD2a1 and PD2b1 are also necessary for unlearned attraction to some odors, indicating that these neurons have a dual behavioral role. This provides a circuit mechanism by which learned and innate olfactory information can interact in identified neurons to produce appropriate behavior. VIDEO ABSTRACT.This work was supported by MRC LMB graduate studentships and Boehringer Ingelheim Fonds PhD fellowships (to M.-J.D. and A.S.B.) and a Janelia graduate research fellowship (to M.-J.D.), ERC starting (211089) and consolidator (649111) grants and core support from the MRC (MC-U105188491) (to G.S.X.E.J.), Agence Nationale de la Recherche funding of the MemoNetworks and MemoMap projects (to P.-Y.P. and T.P.) and the Labex Memolife PhD fellowship (to G.B.-G.), the Howard Hughes Medical Institute (to A.W. and G.M.R.), a Wellcome Trust collaborative award (203261/Z/16/Z to G.S.X.E.J., D.B., and G.M.R.), and a Cambridge Neuroscience-PSL collaborative grant supported by the Embassy of France in London (to G.S.X.E.J.). This work was also supported by the HHMI Janelia Visiting Scientist Program

Information flow, cell types and stereotypy in a full olfactory connectome

Funder: Howard Hughes Medical Institute; FundRef: http://dx.doi.org/10.13039/100000011The hemibrain connectome provides large-scale connectivity and morphology information for the majority of the central brain of Drosophila melanogaster. Using this data set, we provide a complete description of the Drosophila olfactory system, covering all first, second and lateral horn-associated third-order neurons. We develop a generally applicable strategy to extract information flow and layered organisation from connectome graphs, mapping olfactory input to descending interneurons. This identifies a range of motifs including highly lateralised circuits in the antennal lobe and patterns of convergence downstream of the mushroom body and lateral horn. Leveraging a second data set we provide a first quantitative assessment of inter- versus intra-individual stereotypy. Comparing neurons across two brains (three hemispheres) reveals striking similarity in neuronal morphology across brains. Connectivity correlates with morphology and neurons of the same morphological type show similar connection variability within the same brain as across two brains

Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body.

Animals exhibit innate behaviours to a variety of sensory stimuli including olfactory cues. In Drosophila, one higher olfactory centre, the lateral horn (LH), is implicated in innate behaviour. However, our structural and functional understanding of the LH is scant, in large part due to a lack of sparse neurogenetic tools for this region. We generate a collection of split-GAL4 driver lines providing genetic access to 82 LH cell types. We use these to create an anatomical and neurotransmitter map of the LH and link this to EM connectomics data. We find ~30% of LH projections converge with outputs from the mushroom body, site of olfactory learning and memory. Using optogenetic activation, we identify LH cell types that drive changes in valence behavior or specific locomotor programs. In summary, we have generated a resource for manipulating and mapping LH neurons, providing new insights into the circuit basis of innate and learned olfactory behavior

The organisation of a third-order olfactory brain region in the vinegar fly

Neural representations of the chemosensory world generate both learned and instinctive behaviours. Olfactory systems detect a huge range of volatiles by combining patterns of activity across input channels. The lateral horn of the fly informs innate behaviours by combining patterns of second-order olfactory projection neuron (PN) activity. While most odorants only elicit a strong behavioural response after associative learning, ecologically meaningful and evolutionarily significant odour channels trigger innate behavioural responses, likely through hard-wired, genetically and developmentally pre-programmed circuits. The identity and function of third-order neurons, particularly those outside the mushroom body, the centre for associative learning, are poorly understood. Here I present data and analyses for such third-order neurons as well as the tools I have helped to make my analyses possible. Using full synaptic reconstructions for neurons of the lateral horn, I investigate previously unknown connectivity motifs including local neuron feedback onto PN axons, the synaptic budget of olfactory interneurons, olfactory neurons that actually integrate multiple sensory modalities, and the existence of centrifugal connections from higher brain regions, including those involved in the output of associative learning. These motifs are novel findings for both insect and equivalent mammalian circuits. I attempt to relate my findings to physiological and morphological data collected by light microscopy, probe the correlation between morphology and connectivity, the degree of connection stereotypy within isomorphic cell types, and the developmental origins of neurons and their connections. These observations provide specific insights into the structure of this ‘innate behaviour’ brain region and the statistics of its constituent types’ connectivities, as well as circuit hypotheses for how learned and innate olfactory representations may interact.This work was supported by a Boehringer Ingelheim Fonds PhD Fellowship, a Herchel Smith Studentship and the MRC LMB