A GAL4-driver line resource for Drosophila neurobiology

Cholinergic and Glutamatergic Axons Differentially Require Glial Support in the Drosophila PNS

In vertebrates, there is a differential interaction between peripheral axons and their associated glial cells. While large-caliber axons are covered by a myelin sheath, small-diameter axons are simply wrapped in Remak fibers. In peripheral nerves of Drosophila larvae, axons are covered by wrapping glial cell processes similar to vertebrate Remak fibers. Whether differences in axonal diameter influence the interaction with glial processes in Drosophila has not yet been analyzed. Likewise, it is not understood whether the modality of the neuron affects the interaction with the wrapping glia. To start to decipher the mechanisms underlying glial wrapping, we employed APEX2 labeling in larval filet preparations. This allowed us to follow individual axons of defined segmental nerves at ultrastructural resolution in the presence or absence of wrapping glia. Using these tools, we first demonstrate that motor axons are larger compared to sensory axons. Sensory axons fasciculate in larger groups than motor axons, suggesting that they do not require direct contact with wrapping glia. However, unlike motor axons, sensory axons show length-dependent degeneration upon ablation of wrapping glia. These data suggest that Drosophila may help to understand peripheral neuropathies caused by defects in Schwann cell function, in which a similar degeneration of sensory axons is observed.

Synaptic defects in adult drosophila motor neurons in a model of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that primarily affects motor neurons in the brain and spinal cord. Like other neurodegenerative diseases, defects in synaptic integrity are among the earliest hallmarks of ALS. However, the specific impairments to synaptic integrity remain unclear. To better understand synaptic defects in ALS, we expressed either wild-type or mutant Fused in Sarcoma (FUS), an RNA binding protein that is often mis-localized in ALS, in adult motor neurons. Using optogenetic stimulation of the motor neurons innervating the Ventral Abdominal Muscles (VAMs), we found that expression of mutant FUS disrupted the functional integrity of these synapses. This functional deficit was followed by disruption of synaptic gross morphology, localization of pre- and post-synaptic proteins, and cytoskeleton integrity. We found similar synaptic defects using the motor neurons innervating the Dorsal Longitudinal Muscles (DLMs), where expression of mutant FUS resulted in a progressive loss of flight ability along with disruption of active zone distribution. Our findings uncover defects in synaptic function that precede changes in synaptic structure, suggesting that synaptic function is more sensitive to this ALS model. Highlighting the earliest synaptic defects in this disease model should help to identify strategies for preventing later stages of disease progression.

Sleep pressure accumulates in a voltage-gated lipid peroxidation memory

Voltage-gated potassium (KV) channels contain cytoplasmically exposed β-subunits1-5 whose aldo-keto reductase activity6-8 is required for the homeostatic regulation of sleep9. Here we show that Hyperkinetic, the β-subunit of the KV1 channel Shaker in Drosophila7, forms a dynamic lipid peroxidation memory. Information is stored in the oxidation state of Hyperkinetic's nicotinamide adenine dinucleotide phosphate (NADPH) cofactor, which changes when lipid-derived carbonyls10-13, such as 4-oxo-2-nonenal or an endogenous analogue generated by illuminating a membrane-bound photosensitizer9,14, abstract an electron pair. NADP+ remains locked in the active site of KVβ until membrane depolarization permits its release and replacement with NADPH. Sleep-inducing neurons15-17 use this voltage-gated oxidoreductase cycle to encode their recent lipid peroxidation history in the collective binary states of their KVβ subunits; this biochemical memory influences-and is erased by-spike discharges driving sleep. The presence of a lipid peroxidation sensor at the core of homeostatic sleep control16,17 suggests that sleep protects neuronal membranes against oxidative damage. Indeed, brain phospholipids are depleted of vulnerable polyunsaturated fatty acyl chains after enforced waking, and slowing the removal of their carbonylic breakdown products increases the demand for sleep.

Connectome-driven neural inventory of a complete visual system

Vision provides animals with detailed information about their surroundings and conveys diverse features such as colour, form and movement across the visual scene. Computing these parallel spatial features requires a large and diverse network of neurons. Consequently, from flies to humans, visual regions in the brain constitute half its volume. These visual regions often have marked structure-function relationships, with neurons organized along spatial maps and with shapes that directly relate to their roles in visual processing. More than a century of anatomical studies have catalogued in detail cell types in fly visual systems1-3, and parallel behavioural and physiological experiments have examined the visual capabilities of flies. To unravel the diversity of a complex visual system, careful mapping of the neural architecture matched to tools for targeted exploration of this circuitry is essential. Here we present a connectome of the right optic lobe from a male Drosophila melanogaster acquired using focused ion beam milling and scanning electron microscopy. We established a comprehensive inventory of the visual neurons and developed a computational framework to quantify their anatomy. Together, these data establish a basis for interpreting how the shapes of visual neurons relate to spatial vision. By integrating this analysis with connectivity information, neurotransmitter identity and expert curation, we classified the approximately 53,000 neurons into 732 types. These types are systematically described and about half are newly named. Finally, we share an extensive collection of split-GAL4 lines matched to our neuron-type catalogue. Overall, this comprehensive set of tools and data unlocks new possibilities for systematic investigations of vision in Drosophila and provides a foundation for a deeper understanding of sensory processing.

The Glutamate-gated Chloride Channel Facilitates Sleep by Enhancing the Excitability of Two Pairs of Neurons in the Ventral Nerve Cord of Drosophila

Sleep, an essential and evolutionarily conserved behavior, is regulated by numerous neurotransmitter systems. In mammals, glutamate serves as the wake-promoting signaling agent, whereas in Drosophila, it functions as the sleep-promoting signal. However, the precise molecular and cellular mechanisms through which glutamate promotes sleep remain elusive. Our study reveals that disruption of glutamate signaling significantly diminishes nocturnal sleep, and a neural cell-specific knockdown of the glutamate-gated chloride channel (GluClα) markedly reduces nocturnal sleep. We identified two pairs of neurons in the ventral nerve cord (VNC) that receive glutamate signaling input, and the GluClα derived from these neurons is crucial for sleep promotion. Furthermore, we demonstrated that GluClα mediates the glutamate-gated inhibitory input to these VNC neurons, thereby promoting sleep. Our findings elucidate that GluClα enhances nocturnal sleep by mediating the glutamate-gated inhibitory input to two pairs of VNC neurons, providing insights into the mechanism of sleep promotion in Drosophila.

Comparative connectomics of Drosophila descending and ascending neurons

In most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains most of the final motor outputs necessary for behaviour, and the brain. In insects, the neck connective is both a physical and an information bottleneck connecting the brain and the ventral nerve cord (an analogue of the spinal cord) and comprises diverse populations of descending neurons (DNs), ascending neurons (ANs) and sensory ascending neurons, which are crucial for sensorimotor signalling and control. Here, by integrating three separate electron microscopy (EM) datasets1-4, we provide a complete connectomic description of the ANs and DNs of the Drosophila female nervous system and compare them with neurons of the male nerve cord. Proofread neuronal reconstructions are matched across hemispheres, datasets and sexes. Crucially, we also match 51% of DN cell types to light-level data5 defining specific driver lines, as well as classifying all ascending populations. We use these results to reveal the anatomical and circuit logic of neck connective neurons. We observe connected chains of DNs and ANs spanning the neck, which may subserve motor sequences. We provide a complete description of sexually dimorphic DN and AN populations, with detailed analyses of selected circuits for reproductive behaviours, including male courtship6 (DNa12; also known as aSP22) and song production7 (AN neurons from hemilineage 08B) and female ovipositor extrusion8 (DNp13). Our work provides EM-level circuit analyses that span the entire central nervous system of an adult animal.

Olfactory projection neuron rewiring in the brain of an ecological specialist

Animal behaviors can differ greatly between closely related species. These behavioral changes are frequently linked to sensory system modifications, but central brain cell-type alterations might also be involved. Here, we develop advanced genetic tools to compare homologous central neurons in Drosophila sechellia, an ecological specialist, with the generalist Drosophila melanogaster. Through systematic morphological analysis of olfactory projection neurons (PNs), we reveal that the global anatomy of these second-order neurons is conserved. However, high-resolution, quantitative comparisons identify a striking case of convergent rewiring of PNs in two olfactory pathways critical for D. sechellia's host location. Calcium imaging and labeling of pre-synaptic sites in these evolved D. sechellia PNs indicate that species-specific connections with third-order partners are formed. This work demonstrates that peripheral sensory evolution is accompanied by selective wiring changes in the central brain to facilitate ecological specialization and paves the way to compare other cell types throughout the nervous system.

Dynamics of glia and neurons regulate homeostatic rest, sleep and feeding behavior in Drosophila

Homeostatic processes, including sleep, are critical for brain function. Here we identify astrocyte-like glia (or astrocytes, AL) and ensheathing glia (EG), the two major classes of glia that arborize inside the brain, as brain-wide, locally acting homeostats for the short, naturally occurring rest and sleep bouts of Drosophila, and show that a subset of neurons in the fan-shaped body encodes feeding homeostasis. We show that the metabolic gas carbon dioxide, changes in pH and behavioral activity all induce long-lasting calcium responses in EG and AL, and that calcium levels in both glia types show circadian modulation. The homeostatic dynamics of these glia can be modeled based on behavior. Additionally, local optogenetic activation of AL or EG is sufficient to induce rest. Together, these results suggest that glial calcium levels are homeostatic controllers of metabolic activity, thus establishing a link between metabolism, rest and sleep.

Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, and knowledge of what neurotransmitters and neuromodulators they express, will be required to gain mechanistic understanding of how these functions are implemented. We generated and characterized split-GAL4 driver lines that express in individual or small subsets of about half of CX cell types. We surveyed neuropeptide and neuropeptide receptor expression in the central brain using fluorescent in situ hybridization. About half of the neuropeptides we examined were expressed in only a few cells, while the rest were expressed in dozens to hundreds of cells. Neuropeptide receptors were expressed more broadly and at lower levels. Using our GAL4 drivers to mark individual cell types, we found that 51 of the 85 CX cell types we examined expressed at least one neuropeptide and 21 expressed multiple neuropeptides. Surprisingly, all co-expressed a small molecule neurotransmitter. Finally, we used our driver lines to identify CX cell types whose activation affects sleep, and identified other central brain cell types that link the circadian clock to the CX. The well-characterized genetic tools and information on neuropeptide and neurotransmitter expression we provide should enhance studies of the CX.

Functional dissection of a neuronal brain circuit mediating higher-order associative learning

A central feature characterizing the neural architecture of many species' brains is their capacity to form associative chains through learning. In elementary forms of associative learning, stimuli coinciding with reward or punishment become attractive or repulsive. Notably, stimuli previously learned as attractive or repulsive can themselves serve as reinforcers, establishing a cascading effect whereby they become associated with additional stimuli. When this iterative process is perpetuated, it results in higher-order associations. Here, we use odor conditioning in Drosophila and computational modeling to dissect the architecture of neuronal networks underlying higher-order associative learning. We show that the responsible circuit, situated in the mushroom bodies of the brain, is characterized by parallel processing of odor information and by recurrent excitatory and inhibitory feedback loops that empower odors to gain control over the dopaminergic valence-signaling system. Our findings establish a paradigmatic framework of a neuronal circuit diagram enabling the acquisition of associative chains.

Neurofibromin Deficiency Alters the Patterning and Prioritization of Motor Behaviors in a State-Dependent Manner

Genetic disorders such as neurofibromatosis type 1 (Nf1) increase vulnerability to cognitive and behavioral disorders, such as autism spectrum disorder and attention-deficit/hyperactivity disorder. Nf1 results from mutations in the neurofibromin gene that can reduce levels of the neurofibromin protein. While the mechanisms have yet to be fully elucidated, loss of Nf1 may alter neuronal circuit activity leading to changes in behavior and susceptibility to cognitive and behavioral comorbidities. Here we show that mutations decreasing Nf1 expression alter motor behaviors, impacting the patterning, prioritization, and behavioral state dependence in a Drosophila model of Nf1. Loss of Nf1 increased spontaneous grooming in male and female flies. This followed a nonlinear spatial pattern, with Nf1 deficiency increasing grooming of certain body parts differentially, including the abdomen, head, and wings. The increase in grooming could be overridden by hunger in foraging animals, demonstrating that the Nf1 effect is plastic and internal state dependent. Stimulus-evoked grooming patterns were altered as well, suggesting that hierarchical recruitment of grooming command circuits was altered. Yet loss of Nf1 in sensory neurons and/or grooming command neurons did not alter grooming frequency, suggesting that Nf1 affects grooming via higher-order circuit alterations. Changes in grooming coincided with alterations in walking. Flies lacking Nf1 walked with increased forward velocity on a spherical treadmill, yet there was no detectable change in leg kinematics or gait. These results demonstrate that loss of Nf1 alters the patterning and prioritization of repetitive behaviors, in a state-dependent manner, without affecting low-level motor functions.

The fruit fly, Drosophila melanogaster, as a microrobotics platform

Engineering small autonomous agents capable of operating in the microscale environment remains a key challenge, with current systems still evolving. Our study explores the fruit fly, Drosophila melanogaster, a classic model system in biology and a species adept at microscale interaction, as a biological platform for microrobotics. Initially, we focus on remotely directing the walking paths of fruit flies in an experimental arena. We accomplish this through two distinct approaches: harnessing the fruit flies' optomotor response and optogenetic modulation of its olfactory system. These techniques facilitate reliable and repeated guidance of flies between arbitrary spatial locations. We guide flies along predetermined trajectories, enabling them to scribe patterns resembling textual characters through their locomotion. We enhance olfactory-guided navigation through additional optogenetic activation of attraction-inducing mushroom body output neurons. We extend this control to collective behaviors in shared spaces and navigation through constrained maze-like environments. We further use our guidance technique to enable flies to carry a load across designated points in space, establishing the upper bound on their weight-carrying capabilities. Additionally, we demonstrate that visual guidance can facilitate novel interactions between flies and objects, showing that flies can consistently relocate a small spherical object over significant distances. Last, we demonstrate multiagent formation control, with flies alternating between distinct spatial patterns. Beyond expanding tools available for microrobotics, these behavioral contexts can provide insights into the neurological basis of behavior in fruit flies.

Synaptic deregulation of cholinergic projection neurons causes olfactory dysfunction across five fly Parkinsonism models

The classical diagnosis of Parkinsonism is based on motor symptoms that are the consequence of nigrostriatal pathway dysfunction and reduced dopaminergic output. However, a decade prior to the emergence of motor issues, patients frequently experience non-motor symptoms, such as a reduced sense of smell (hyposmia). The cellular and molecular bases for these early defects remain enigmatic. To explore this, we developed a new collection of five fruit fly models of familial Parkinsonism and conducted single-cell RNA sequencing on young brains of these models. Interestingly, cholinergic projection neurons are the most vulnerable cells, and genes associated with presynaptic function are the most deregulated. Additional single nucleus sequencing of three specific brain regions of Parkinson's disease patients confirms these findings. Indeed, the disturbances lead to early synaptic dysfunction, notably affecting cholinergic olfactory projection neurons crucial for olfactory function in flies. Correcting these defects specifically in olfactory cholinergic interneurons in flies or inducing cholinergic signaling in Parkinson mutant human induced dopaminergic neurons in vitro using nicotine, both rescue age-dependent dopaminergic neuron decline. Hence, our research uncovers that one of the earliest indicators of disease in five different models of familial Parkinsonism is synaptic dysfunction in higher-order cholinergic projection neurons and this contributes to the development of hyposmia. Furthermore, the shared pathways of synaptic failure in these cholinergic neurons ultimately contribute to dopaminergic dysfunction later in life.

RNAi-based screen for pigmentation in Drosophila melanogaster reveals regulators of brain dopamine and sleep

The dopaminergic system has been extensively studied for its role in behavior in animals as well as human neuropsychiatric and neurological diseases. However, we still know little about how dopamine levels are tightly regulated in vivo . To identify novel regulators of dopamine, we utilized Drosophila melanogaster cuticle pigmentation as a readout, where dopamine is a precursor to melanin. We measured dopamine from genes known to be critical for cuticle pigmentation and performed an RNAi-based screen to identify new regulators of pigmentation. We found 153 potential pigmentation genes, which were enriched for conserved homologs and disease- associated genes as well as developmental signaling pathways and mitochondria-associated proteins. From 35 prioritized candidates, we found 10 caused significant reduction in head dopamine levels and one caused an increase. Two genes, clueless and mask (multiple ankyrin repeats single KH domain), upon knockdown, reduced dopamine levels in the brain. Further examination suggests that Mask regulates the transcription of the rate-limiting dopamine synthesis enzyme, tyrosine hydroxylase , and its knockdown causes dopamine-dependent sleep phenotypes. In summary, by studying genes that affect cuticle pigmentation, a phenotype seemingly unrelated to the nervous system, we were able to identify several genes that affect dopamine metabolism as well as a novel regulator of behavior.

Developmental Genetic and Molecular Analysis of Drosophila Central Complex Lineages

Complex behaviors are mediated by a diverse class of neurons and glia produced during development. Both neural stem cell-intrinsic and -extrinsic temporal cues regulate the appropriate number, molecular identity, and circuit assembly of neurons. The Drosophila central complex (CX) is a higher-order brain structure regulating various behaviors, including sensory-motor integration, celestial navigation, and sleep. Most neurons and glia in the adult CX are formed during larval development by 16 Type II neural stem cells (NSCs). Unlike Type I NSCs, which directly give rise to the ganglion mother cells (GMCs), Type II NSCs give rise to multiple intermediate neural progenitors (INPs), and each INP in turn generates multiple GMCs, hence fostering the generation of longer and more diverse lineages. This makes Type II NSCs a suitable model to unravel the molecular mechanisms regulating neural diversity in more complex lineages. In this review, we elaborate on the classification and identification of NSCs based on the types of division adopted and the molecular markers expressed in each type. In the end, we discuss genetic methods for lineage analysis and birthdating. We also explain the temporal expression of stem cell factors and genetic techniques to study how stem cell factors may regulate neural fate specification.

Columnar cholinergic neurotransmission onto T5 cells of Drosophila

Several nicotinic and muscarinic acetylcholine receptors (AChRs) are expressed in the brain of Drosophila melanogaster. However, the contribution of different AChRs to visual information processing remains poorly understood. T5 cells are the primary motion-sensing neurons in the OFF pathway and receive input from four different columnar cholinergic neurons, Tm1, Tm2, Tm4, and Tm9. We reasoned that different AChRs in T5 postsynaptic sites might contribute to direction selectivity, a central feature of motion detection. We show that the nicotinic nAChRα1, nAChRα3, nAChRα4, nAChRα5, nAChRα7, and nAChβ1 subunits localize on T5 dendrites. By targeting synaptic markers specifically to each cholinergic input neuron, we find a prevalence of the nAChRα5 in Tm1, Tm2, and Tm4-to-T5 synapses and of nAChRα7 in Tm9-to-T5 synapses. Knockdown of nAChRα4, nAChRα5, nAChRα7, or mAChR-B individually in T5 cells alters the optomotor response and reduces T5 directional selectivity. Our findings indicate the contribution of a consortium of postsynaptic receptors to input visual processing and, thus, to the computation of motion direction in T5 cells.

Protocol for cell-type-specific single-cell labeling and manipulation in Drosophila using a sparse driver system

Here, we present a protocol for cell-type-specific single-cell labeling and manipulation in Drosophila using a sparse driver system. We describe steps for generating constructs and fly lines, titrating heat-shocked durations for precise temporal control and desired sparsity, and co-expressing multiple transgenes for experiments. We demonstrate that this generalizable toolkit enables tunable sparsity, multi-color staining, single-cell trans-synaptic tracing, single-cell manipulation, and cell-autonomous gene function analysis. For complete details on the use and execution of this protocol, please refer to Xu et al.1.

Activation of a Src-JNK pathway in unscheduled endocycling cells of the Drosophila wing disc induces a chronic wounding response

The endocycle is a specialized cell cycle during which cells undergo repeated G / S phases to replicate DNA without division, leading to large polyploid cells. The transition from a mitotic cycle to an endocycle can be triggered by various stresses, which results in unscheduled, or induced endocycling cells (iECs). While iECs can be beneficial for wound healing, they can also be detrimental by impairing tissue growth or promoting cancer. However, the regulation of endocycling and its role in tissue growth remain poorly understood. Using the Drosophila wing disc as a model, we previously demonstrated that iEC growth is arrested through a Jun N-Terminal Kinase (JNK)-dependent, reversible senescence-like response. However, it remains unclear how JNK is activated in iECs and how iECs impact overall tissue structure. In this study, we performed a genetic screen and identified the Src42A-Shark-Slpr pathway as an upstream regulator of JNK in iECs, leading to their senescence-like arrest. We found that tissues recognize iECs as wounds, releasing wound-related signals that induce a JNK-dependent developmental delay. Similar to wound closure, this response triggers Src-JNK-mediated actomyosin remodeling, yet iECs persist rather than being eliminated. Our findings suggest that the tissue response to iECs shares key signaling and cytoskeletal regulatory mechanisms with wound healing and dorsal closure, a developmental process during Drosophila embryogenesis. However, because iECs are retained within the tissue, they create a unique system that may serve as a model for studying chronic wounds and tumor progression.

Molecular profiling of invertebrate glia

Caenorhabditis elegans and Drosophila melanogaster are powerful experimental models for uncovering fundamental tenets of nervous system organization and function. Findings over the last two decades show that molecular and cellular features are broadly conserved between invertebrates and vertebrates, indicating that insights derived from invertebrate models can broadly inform our understanding of glial operating principles across diverse species. In recent years, these model systems have led to exciting discoveries in glial biology and mechanisms of glia-neuron interactions. Here, we summarize studies that have applied current state-of-the-art "-omics" techniques to C. elegans and D. melanogaster glia. Coupled with the remarkable acceleration in the pace of mechanistic studies of glia biology in recent years, these indicate that invertebrate glia also exhibit striking molecular complexity, specificity, and heterogeneity. We provide an overview of these studies and discuss their implications as well as emerging questions where C. elegans and D. melanogaster are well-poised to fill critical knowledge gaps in our understanding of glial biology.

The dorsal fan-shaped body is a neurochemically heterogeneous sleep-regulating center in Drosophila

Sleep is a behavior that is conserved throughout the animal kingdom. Yet, despite extensive studies in humans and animal models, the exact function or functions of sleep remain(s) unknown. A complicating factor in trying to elucidate the function of sleep is the complexity and multiplicity of neuronal circuits that are involved in sleep regulation. It is conceivable that distinct sleep-regulating circuits are only involved in specific aspects of sleep and may underlie different sleep functions. Thus, it would be beneficial to assess the contribution of individual circuits in sleep's putative functions. The intricacy of the mammalian brain makes this task extremely difficult. However, the fruit fly Drosophila melanogaster, with its simpler brain organization, available connectomics, and unparalleled genetics, offers the opportunity to interrogate individual sleep-regulating centers. In Drosophila, neurons projecting to the dorsal fan-shaped body (dFB) have been proposed to be key regulators of sleep, particularly sleep homeostasis. We recently demonstrated that the most widely used genetic tool to manipulate dFB neurons, the 23E10-GAL4 driver, expresses in 2 sleep-regulating neurons (VNC-SP neurons) located in the ventral nerve cord (VNC), the fly analog of the vertebrate spinal cord. Since most data supporting a role for the dFB in sleep regulation have been obtained using 23E10-GAL4, it is unclear whether the sleep phenotypes reported in these studies are caused by dFB neurons or VNC-SP cells. A recent publication replicated our finding that 23E10-GAL4 contains sleep-promoting neurons in the VNC. However, it also proposed that the dFB is not involved in sleep regulation at all, but this suggestion was made using genetic tools that are not dFB-specific and a very mild sleep deprivation protocol. In this study, using a newly created dFB-specific genetic driver line, we demonstrate that optogenetic activation of the majority of 23E10-GAL4 dFB neurons promotes sleep and that these neurons are involved in sleep homeostasis. We also show that dFB neurons require stronger stimulation than VNC-SP cells to promote sleep. In addition, we demonstrate that dFB-induced sleep can consolidate short-term memory (STM) into long-term memory (LTM), suggesting that the benefit of sleep on memory is not circuit-specific. Finally, we show that dFB neurons are neurochemically heterogeneous and can be divided in 3 populations. Most dFB neurons express both glutamate and acetylcholine, while a minority of cells expresses only one of these 2 neurotransmitters. Importantly, dFB neurons do not express GABA, as previously suggested. Using neurotransmitter-specific dFB tools, our data also points at cholinergic dFB neurons as particularly potent at regulating sleep and sleep homeostasis.

Single-cell type analysis of wing premotor circuits in the ventral nerve cord of Drosophila melanogaster

To perform most behaviors, animals must send commands from higher-order processing centers in the brain to premotor circuits that reside in ganglia distinct from the brain, such as the mammalian spinal cord or insect ventral nerve cord. How these circuits are functionally organized to generate the great diversity of animal behavior remains unclear. An important first step in unraveling the organization of premotor circuits is to identify their constituent cell types and create tools to monitor and manipulate these with high specificity to assess their functions. This is possible in the tractable ventral nerve cord of the fly. To generate such a toolkit, we used a combinatorial genetic technique (split-GAL4) to create 195 sparse transgenic driver lines targeting 196 individual cell types in the ventral nerve cord. These included wing and haltere motoneurons, modulatory neurons, and interneurons. Using a combination of behavioral, developmental, and anatomical analyses, we systematically characterized the cell types targeted in our collection. In addition, we identified correspondences between the cells in this collection and a recent connectomic data set of the ventral nerve cord. Taken together, the resources and results presented here form a powerful toolkit for future investigations of neuronal circuits and connectivity of premotor circuits while linking them to behavioral outputs.

Inhibitory circuits generate rhythms for leg movements during Drosophila grooming

Limbs execute diverse actions coordinated by the nervous system through multiple motor programs. The basic architecture of motor neurons that activate muscles which articulate joints for antagonistic flexion and extension movements is conserved from flies to vertebrates. While excitatory premotor circuits are expected to establish sets of leg motor neurons that work together, our study uncovered an instructive role for inhibitory circuits - including their ability to generate rhythmic leg movements. Using electron microscopy data in the Drosophila nerve cord, we categorized ~120 GABAergic inhibitory neurons from the 13A and 13B hemilineages into classes based on similarities in morphology and connectivity. By mapping their connections, we uncovered pathways for inhibiting specific groups of motor neurons, disinhibiting antagonistic counterparts, and inducing alternation between flexion and extension. We tested the function of specific inhibitory neurons through optogenetic activation and silencing, using high resolution quantitative analysis of leg movements during grooming. We combined findings from anatomical and behavioral analyses to construct a computational model that can reproduce major aspects of the observed behavior, confirming sufficiency of these premotor inhibitory circuits to generate rhythms.

Metaxin-2 tunes mitochondrial transportation and neuronal function in Drosophila

Metaxins are a family of evolutionarily conserved proteins that reside on the mitochondria outer membrane (MOM) and participate in the protein import into the mitochondria. Metaxin-2 (Mtx2), a member of this family, has been identified as a key component in the machinery for mitochondrial transport in both C. elegans and human neurons. To deepen our understanding of Mtx2's role in neurons, we examined the homologous genes CG5662 and CG8004 in Drosophila. The CG5662 is a non-essential gene while CG8004 null mutants die at late pupal stages. The CG8004 protein is widely expressed throughout the Drosophila nervous system and is targeted to mitochondria. However, neuronal CG8004 is dispensable for animal survival and is partially required for mitochondrial distribution in certain neuropil regions. Conditional knockout of CG8004 in adult gustatory receptor neurons (GRNs) impairs mitochondrial trafficking along GRN axons and diminishes the mitochondrial quantities in axon terminals. The absence of CG8004 also leads to mitochondrial fragmentation within GRN axons, a phenomenon that may be linked to mitochondrial transport through its genetic interaction with the fusion proteins Marf and Opa1. While the removal of neuronal CG8004 is not lethal during the developmental stage, it does have consequences for the lifespan and healthspan of adult Drosophila. At last, double knockout (KO) of CG5662 and CG8004 shows similar phenotypes as the CG8004 single KO, suggesting that CG5662 does not compensate for the loss of CG8004. In summary, our findings suggest that CG8004 plays a conserved and context-dependent role in axonal mitochondrial transport, as well it is important for sustaining neuronal function. Therefore, we refer to CG8004 as the Drosophila Metaxin-2 (dMtx2).

Ca2+ excitability of glia to neuromodulator octopamine in Drosophila living brain is greater than that of neurons

AIM

Octopamine in the Drosophila brain has a neuromodulatory role similar to that of noradrenaline in mammals. After release from Tdc2 neurons, octopamine/tyramine may trigger intracellular Ca2+ signaling via adrenoceptor-like receptors on neural cells, modulating neurotransmission. Octopamine/tyramine receptors are expressed in neurons and glia, but how each of these cell types responds to octopamine remains elusive. This study aimed to characterize Ca2+ responses of neurons and astrocytes to neuromodulatory octopamine signals.

METHODS

We expressed Ca2+ indicator jGCaMP7b in specific cell type in adult Drosophila brains and performed intracellular Ca2+ imaging in the brain optic lobes upon bath application of octopamine by confocal microscopy.

RESULTS

Octopamine-stimulated Ca2+ responses in neurons were different from those of glial cells. The amplitude of octopamine-mediated Ca2+ signals in neurons was 3.4-fold greater than in astrocytes. However, astrocytes were more sensitive to octopamine; the median effective concentration that triggered Ca2+ responses was nearly 6-fold lower in astrocytes than in neurons. In both cell types, Ca2+ transients are shaped by Gq and Gs protein-coupled octopamine/tyramine receptors. Our snRNA-seq database screening uncovered differential expression patterns of these receptors between brain cell types, which may explain the difference in Ca2+ signaling.

CONCLUSION

In the brain optic lobes, astrocytes, not neurons, appear to be the sole responders to low concentration octopamine signals, and therefore likely drive synaptic plasticity and visual processing. Given the interconnectivity of the optic lobes with other brain regions, octopaminergic signals acting through the optic lobe astrocytes may also influence higher-order brain functions including learning and memory.

Synaptic enrichment and dynamic regulation of the two opposing dopamine receptors within the same neurons

Dopamine can play opposing physiological roles depending on the receptor subtype. In the fruit fly Drosophila melanogaster, Dop1R1 and Dop2R encode the D1- and D2-like receptors, respectively, and are reported to oppositely regulate intracellular cAMP levels. Here, we profiled the expression and subcellular localization of endogenous Dop1R1 and Dop2R in specific cell types in the mushroom body circuit. For cell-type-specific visualization of endogenous proteins, we employed reconstitution of split-GFP tagged to the receptor proteins. We detected dopamine receptors at both presynaptic and postsynaptic sites in multiple cell types. Quantitative analysis revealed enrichment of both receptors at the presynaptic sites, with Dop2R showing a greater degree of localization than Dop1R1. The presynaptic localization of Dop1R1 and Dop2R in dopamine neurons suggests dual feedback regulation as autoreceptors. Furthermore, we discovered a starvation-dependent, bidirectional modulation of the presynaptic receptor expression in the protocerebral anterior medial (PAM) and posterior lateral 1 (PPL1) clusters, two distinct subsets of dopamine neurons, suggesting their roles in regulating appetitive behaviors. Our results highlight the significance of the co-expression of the two opposing dopamine receptors in the spatial and conditional regulation of dopamine responses in neurons.

Driver lines for studying associative learning in Drosophila

The mushroom body (MB) is the center for associative learning in insects. In Drosophila, intersectional split-GAL4 drivers and electron microscopy (EM) connectomes have laid the foundation for precise interrogation of the MB neural circuits. However, investigation of many cell types upstream and downstream of the MB has been hindered due to lack of specific driver lines. Here we describe a new collection of over 800 split-GAL4 and split-LexA drivers that cover approximately 300 cell types, including sugar sensory neurons, putative nociceptive ascending neurons, olfactory and thermo-/hygro-sensory projection neurons, interneurons connected with the MB-extrinsic neurons, and various other cell types. We characterized activation phenotypes for a subset of these lines and identified a sugar sensory neuron line most suitable for reward substitution. Leveraging the thousands of confocal microscopy images associated with the collection, we analyzed neuronal morphological stereotypy and discovered that one set of mushroom body output neurons, MBON08/MBON09, exhibits striking individuality and asymmetry across animals. In conjunction with the EM connectome maps, the driver lines reported here offer a powerful resource for functional dissection of neural circuits for associative learning in adult Drosophila.

A carnitine transporter at the blood-brain barrier modulates sleep via glial lipid metabolism in Drosophila

To regulate brain function, peripheral compounds must traverse the blood-brain barrier (BBB), an interface between the brain and the circulatory system. To determine whether specific transport mechanisms are relevant for sleep, we conducted a BBB-specific inducible RNAi knockdown (iKD) screen for genes affecting sleep in Drosophila. We observed reduced sleep with knockdown of solute carrier CG6126, a carnitine transporter, as determined by isotope flux. Our findings suggest that CG6126 regulation of sleep is through the role of the carnitine shuttle in regulating fatty acid metabolism as lipid droplets accumulate in the brains of CG6126 BBB iKD flies. Knocking down mitochondrial carnitine transferases in non-BBB glial cells mimicked the reduced sleep of the CG6126 BBB iKD flies, while bypassing the necessity of carnitine transport with dietary medium-chain fatty acids or palmitoylcarnitine rescued sleep. We propose that carnitine transport via CG6126 promotes brain fatty acid metabolism necessary for maintaining sleep.

Neural substrates of cold nociception in Drosophila larva

Metazoans detect and differentiate between innocuous (non-painful) and/or noxious (harmful) environmental cues using primary sensory neurons, which serve as the first node in a neural network that computes stimulus specific behaviors to either navigate away from injury-causing conditions or to perform protective behaviors that mitigate extensive injury. The ability of an animal to detect and respond to various sensory stimuli depends upon molecular diversity in the primary sensors and the underlying neural circuitry responsible for the relevant behavioral action selection. Recent studies in Drosophila larvae have revealed that somatosensory class III multidendritic (CIII md) neurons function as multimodal sensors regulating distinct behavioral responses to innocuous mechanical and nociceptive thermal stimuli. Recent advances in circuit bases of behavior have identified and functionally validated Drosophila larval somatosensory circuitry involved in innocuous (mechanical) and noxious (heat and mechanical) cues. However, central processing of cold nociceptive cues remained unexplored. We implicate multisensory integrators (Basins), premotor (Down-and-Back) and projection (A09e and TePns) neurons as neural substrates required for cold-evoked behavioral and calcium responses. Neural silencing of cell types downstream of CIII md neurons led to significant reductions in cold-evoked behaviors and neural co-activation of CIII md neurons plus additional cell types facilitated larval contraction (CT) responses. Further, we demonstrate that optogenetic activation of CIII md neurons evokes calcium increases in these neurons. Finally, we characterize the premotor to motor neuron network underlying cold-evoked CT and delineate the muscular basis of CT response. Collectively, we demonstrate how Drosophila larvae process cold stimuli through functionally diverse somatosensory circuitry responsible for generating stimulus-specific behaviors.

A split-GAL4 driver line resource for Drosophila neuron types

Techniques that enable precise manipulations of subsets of neurons in the fly central nervous system (CNS) have greatly facilitated our understanding of the neural basis of behavior. Split-GAL4 driver lines allow specific targeting of cell types in Drosophila melanogaster and other species. We describe here a collection of 3060 lines targeting a range of cell types in the adult Drosophila CNS and 1373 lines characterized in third-instar larvae. These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. NeuronBridge and other search tools relate light microscopy images of these split-GAL4 lines to connectomes reconstructed from electron microscopy images. The collections are the result of screening over 77,000 split hemidriver combinations. Previously published and new lines are included, all validated for driver expression and curated for optimal cell-type specificity across diverse cell types. In addition to images and fly stocks for these well-characterized lines, we make available 300,000 new 3D images of other split-GAL4 lines.

Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, and knowledge of what neurotransmitters and neuromodulators they express, will be required to gain mechanistic understanding of how these functions are implemented. We generated and characterized split-GAL4 driver lines that express in individual or small subsets of about half of CX cell types. We surveyed neuropeptide and neuropeptide receptor expression in the central brain using fluorescent in situ hybridization. About half of the neuropeptides we examined were expressed in only a few cells, while the rest were expressed in dozens to hundreds of cells. Neuropeptide receptors were expressed more broadly and at lower levels. Using our GAL4 drivers to mark individual cell types, we found that 51 of the 85 CX cell types we examined expressed at least one neuropeptide and 21 expressed multiple neuropeptides. Surprisingly, all co-expressed a small neurotransmitter. Finally, we used our driver lines to identify CX cell types whose activation affects sleep, and identified other central brain cell types that link the circadian clock to the CX. The well-characterized genetic tools and information on neuropeptide and neurotransmitter expression we provide should enhance studies of the CX.

Morphological and functional convergence of visual projection neurons from diverse neurogenic origins in Drosophila

The Drosophila visual system is a powerful model to study the development of neural circuits. Lobula columnar neurons-LCNs are visual output neurons that encode visual features relevant to natural behavior. There are ~20 classes of LCNs forming non-overlapping synaptic optic glomeruli in the brain. To address their origin, we used single-cell mRNA sequencing to define the transcriptome of LCN subtypes and identified lines that are expressed throughout their development. We show that LCNs originate from stem cells in four distinct brain regions exhibiting different modes of neurogenesis, including the ventral and dorsal tips of the outer proliferation center, the ventral superficial inner proliferation center and the central brain. We show that this convergence of similar neurons illustrates the complexity of generating neuronal diversity, and likely reflects the evolutionary origin of each subtype that detects a specific visual feature and might influence behaviors specific to each species.

Developmental and age-related synapse elimination is mediated by glial Croquemort

Neurons and glia work together to dynamically regulate neural circuit assembly and maintenance. In this study, we show Drosophila exhibit large-scale synapse formation and elimination as part of normal CNS circuit maturation, and that glia use conserved molecules to regulate these processes. Using a high throughput ELISA-based in vivo screening assay, we identify new glial genes that regulate synapse numbers in Drosophila in vivo, including the scavenger receptor ortholog Croquemort (Crq). Crq acts as an essential regulator of glial-dependent synapse elimination during development, with glial Crq loss leading to excess CNS synapses and progressive seizure susceptibility in adults. Loss of Crq in glia also prevents age-related synaptic loss in the adult brain. This work provides new insights into the cellular and molecular mechanisms that underlie synapse development and maintenance across the lifespan, and identifies glial Crq as a key regulator of these processes.

Astrocyte-dependent local neurite pruning in Beat-Va neurons

Developmental neuronal remodeling is extensive and mechanistically diverse across the nervous system. We sought to identify Drosophila pupal neurons that underwent mechanistically new types of neuronal remodeling and describe remodeling Beat-VaM and Beat-VaL neurons. We show that Beat-VaM neurons produce highly branched neurites in the CNS during larval stages that undergo extensive local pruning. Surprisingly, although the ecdysone receptor (EcR) is essential for pruning in all other cell types studied, Beat-VaM neurons remodel their branches extensively despite cell autonomous blockade EcR or caspase signaling. Proper execution of local remodeling in Beat-VaM neurons instead depends on extrinsic signaling from astrocytes converging with intrinsic and less dominant EcR-regulated mechanisms. In contrast, Beat-VaL neurons undergo steroid hormone-dependent, apoptotic cell death, which we show relies on the segment-specific expression of the Hox gene Abd-B. Our work provides new cell types in which to study neuronal remodeling, highlights an important role for astrocytes in activating local pruning in Drosophila independent of steroid signaling, and defines a Hox gene-mediated mechanism for segment-specific cell elimination.

Temporal and Notch identity determine layer targeting and synapse location of medulla neurons

How specification mechanisms that generate neural diversity translate into specific neuronal targeting, connectivity, and function in the adult brain is not understood. In the medulla region of the Drosophila optic lobe, neural progenitors generate different neurons in a fixed order by sequentially expressing a series of temporal transcription factors as they age. Then, Notch signaling in intermediate progenitors further diversifies neuronal progeny. By establishing the birth order of medulla neurons, we found that their temporal identity correlates with the depth of neuropil targeting in the adult brain, for both local interneurons and projection neurons. We show that this temporal identity-dependent targeting of projection neurons unfolds early in development and is genetically determined. By leveraging the Electron Microscopy reconstruction of the adult fly brain, we determined the synapse location of medulla neurons in the different optic lobe neuropils and find that it is significantly associated with both their temporal identity and Notch status. Moreover, we show that all the putative medulla neurons with the same predicted function share similar neuropil synapse location, indicating that ensembles of neuropil layers encode specific visual functions. In conclusion, we show that temporal identity and Notch status of medulla neurons can predict their neuropil synapse location and visual function, linking their developmental patterning with their specific connectivity and functional features in the adult brain.

Trithorax regulates long-term memory in Drosophila through epigenetic maintenance of mushroom body metabolic state and translation capacity

The role of epigenetics and chromatin in the maintenance of postmitotic neuronal cell identities is not well understood. Here, we show that the histone methyltransferase Trithorax (Trx) is required in postmitotic memory neurons of the Drosophila mushroom body (MB) to enable their capacity for long-term memory (LTM), but not short-term memory (STM). Using MB-specific RNA-, ChIP-, and ATAC-sequencing, we find that Trx maintains homeostatic expression of several non-canonical MB-enriched transcripts, including the orphan nuclear receptor Hr51, and the metabolic enzyme lactate dehydrogenase (Ldh). Through these key targets, Trx facilitates a metabolic state characterized by high lactate levels in MBγ neurons. This metabolic state supports a high capacity for protein translation, a process that is essential for LTM, but not STM. These data suggest that Trx, a classic regulator of cell type specification during development, has additional functions in maintaining underappreciated aspects of postmitotic neuron identity, such as metabolic state. Our work supports a body of evidence suggesting that a high capacity for energy metabolism is an essential cell identity characteristic for neurons that mediate LTM.

Adaptation to visual sparsity enhances responses to isolated stimuli

Sensory systems adapt their response properties to the statistics of their inputs. For instance, visual systems adapt to low-order statistics like mean and variance to encode stimuli efficiently or to facilitate specific downstream computations. However, it remains unclear how other statistical features affect sensory adaptation. Here, we explore how Drosophila's visual motion circuits adapt to stimulus sparsity, a measure of the signal's intermittency not captured by low-order statistics alone. Early visual neurons in both ON and OFF pathways alter their responses dramatically with stimulus sparsity, responding positively to both light and dark sparse stimuli but linearly to dense stimuli. These changes extend to downstream ON and OFF direction-selective neurons, which are activated by sparse stimuli of both polarities but respond with opposite signs to light and dark regions of dense stimuli. Thus, sparse stimuli activate both ON and OFF pathways, recruiting a larger fraction of the circuit and potentially enhancing the salience of isolated stimuli. Overall, our results reveal visual response properties that increase the fraction of the circuit responding to sparse, isolated stimuli.

Accelerated protein retention expansion microscopy using microwave radiation

Protein retention expansion microscopy (ExM) retains fluorescent signals in fixed tissue and isotropically expands the tissue to allow nanoscale (<70 nm) resolution on diffraction-limited confocal microscopes. Despite the numerous advantages of ExM, the protocol is time-consuming. Here, we adapted an ExM protocol to vibratome-sectioned brain tissue of Xenopus laevis tadpoles and implemented a microwave (M/W)-assisted protocol (M/WExM) to reduce the workflow from days to hours. Our M/WExM protocol maintains the superior resolution of the original ExM protocol and yields a higher magnitude of expansion, suggesting that M/W radiation may also facilitate the expansion process. We then adapted the M/W protocol to the whole-mount brain of Drosophila melanogaster fruit flies, and successfully reduced the processing time of a widely used Drosophila IHC-ExM protocol from 6 to 2 days. This demonstrates that with appropriate adjustment of M/W parameters, this protocol can be readily adapted to different organisms and tissue types to greatly increase the efficiency of ExM experiments.

The sparse driver system for in vivo single-cell labeling and manipulation in Drosophila

In this protocol, we introduce a sparse driver system for cell-type specific single-cell labeling and manipulation in Drosophila, enabling complete and simultaneous expression of multiple transgenes in the same cells. The system precisely controls expression probability and sparsity via mutant FRT sites with reduced recombination efficiency and tunable FLP levels adjusted by heat-shock durations. We demonstrate that this generalizable toolkit enables tunable sparsity, multi-color staining, single-cell trans-synaptic tracing, single-cell manipulation, and in vivo analysis of cell-autonomous gene function. For details on the use and execution of this protocol, please refer to Xu et al. 2024.

The astrocyte-enriched gene deathstar plays a crucial role in the development, locomotion, and lifespan of D. melanogaster

The Drosophila melanogaster brain is a complex organ with various cell types, orchestrating the development, physiology, and behaviors of the fly. While each cell type in Drosophila brain is known to express a unique gene set, their complete genetic profile is still unknown. Advances in the RNA sequencing techniques at single-cell resolution facilitate identifying novel cell type markers and/or re-examining the specificity of the available ones. In this study, exploiting a single-cell RNA sequencing data of Drosophila optic lobe, we categorized the cells based on their expression pattern for known markers, then the genes with enriched expression in astrocytes were identified. CG11000 was identified as a gene with a comparable expression profile to the Eaat1 gene, an astrocyte marker, in every individual cell inside the Drosophila optic lobe and midbrain, as well as in the entire Drosophila brain throughout its development. Consistent with our bioinformatics data, immunostaining of the brains dissected from transgenic adult flies showed co-expression of CG11000 with Eaat1 in a set of single cells corresponding to the astrocytes in the Drosophila brain. Physiologically, inhibiting CG11000 through RNA interference disrupted the normal development of male D. melanogaster, while having no impact on females. Expression suppression of CG11000 in adult flies led to decreased locomotion activity and also shortened lifespan specifically in astrocytes, indicating the gene's significance in astrocytes. We designated this gene as 'deathstar' due to its crucial role in maintaining the star-like shape of glial cells, astrocytes, throughout their development into adult stage.

NeuroMechFly v2: simulating embodied sensorimotor control in adult Drosophila

Discovering principles underlying the control of animal behavior requires a tight dialogue between experiments and neuromechanical models. Such models have primarily been used to investigate motor control with less emphasis on how the brain and motor systems work together during hierarchical sensorimotor control. NeuroMechFly v2 expands Drosophila neuromechanical modeling by enabling vision, olfaction, ascending motor feedback and complex terrains that can be navigated using leg adhesion. We illustrate its capabilities by constructing biologically inspired controllers that use ascending feedback to perform path integration and head stabilization. After adding vision and olfaction, we train a controller using reinforcement learning to perform a multimodal navigation task. Finally, we illustrate more bio-realistic modeling involving complex odor plume navigation, and fly-fly following using a connectome-constrained visual network. NeuroMechFly can be used to accelerate the discovery of explanatory models of the nervous system and to develop machine learning-based controllers for autonomous artificial agents and robots.

Whole-brain in situ mapping of neuronal activation in Drosophila during social behaviors and optogenetic stimulation

Monitoring neuronal activity at single-cell resolution in freely moving Drosophila engaged in social behaviors is challenging because of their small size and lack of transparency. Extant methods, such as Flyception, are highly invasive. Whole-brain calcium imaging in head-fixed, walking flies is feasible but the animals cannot perform the consummatory phases of social behaviors like aggression or mating under these conditions. This has left open the fundamental question of whether neurons identified as functionally important for such behaviors using loss- or gain-of-function screens are actually active during the natural performance of such behaviors, and if so during which phase(s). Here, we perform brain-wide mapping of active cells expressing the Immediate Early Gene hr38 using a high-sensitivity/low background fluorescence in situ hybridization (FISH) amplification method called HCR-3.0. Using double-labeling for hr38 mRNA and for GFP, we describe the activity of several classes of aggression-promoting neurons during courtship and aggression, including P1a cells, an intensively studied population of male-specific interneurons. Using HI-FISH in combination with optogenetic activation of aggression-promoting neurons (opto-HI-FISH), we identify candidate downstream functional targets of these cells in a brain-wide, unbiased manner. Finally, we compare the activity of P1a neurons during sequential performance of courtship and aggression, using intronic vs. exonic hr38 probes to differentiate newly synthesized nuclear transcripts from cytoplasmic transcripts synthesized at an earlier time. These data provide evidence suggesting that different subsets of P1a neurons may be active during courtship vs. aggression. HI-FISH and associated methods may help to fill an important lacuna in the armamentarium of tools for neural circuit analysis in Drosophila.

BIFROST: A method for registering diverse imaging datasets of the Drosophila brain

Imaging methods that span both functional measures in living tissue and anatomical measures in fixed tissue have played critical roles in advancing our understanding of the brain. However, making direct comparisons between different imaging modalities, particularly spanning living and fixed tissue, has remained challenging. For example, comparing brain-wide neural dynamics across experiments and aligning such data to anatomical resources, such as gene expression patterns or connectomes, requires precise alignment to a common set of anatomical coordinates. However, reaching this goal is difficult because registering in vivo functional imaging data to ex vivo reference atlases requires accommodating differences in imaging modality, microscope specification, and sample preparation. We overcome these challenges in Drosophila by building an in vivo reference atlas from multiphoton-imaged brains, called the Functional Drosophila Atlas. We then develop a registration pipeline, BrIdge For Registering Over Statistical Templates (BIFROST), for transforming neural imaging data into this common space and for importing ex vivo resources such as connectomes. Using genetically labeled cell types as ground truth, we demonstrate registration with a precision of less than 10 microns. Overall, BIFROST provides a pipeline for registering functional imaging datasets in the fly, both within and across experiments.

Dopamine neurons that inform Drosophila olfactory memory have distinct, acute functions driving attraction and aversion

The brain must guide immediate responses to beneficial and harmful stimuli while simultaneously writing memories for future reference. While both immediate actions and reinforcement learning are instructed by dopamine, how dopaminergic systems maintain coherence between these 2 reward functions is unknown. Through optogenetic activation experiments, we showed that the dopamine neurons that inform olfactory memory in Drosophila have a distinct, parallel function driving attraction and aversion (valence). Sensory neurons required for olfactory memory were dispensable to dopaminergic valence. A broadly projecting set of dopaminergic cells had valence that was dependent on dopamine, glutamate, and octopamine. Similarly, a more restricted dopaminergic cluster with attractive valence was reliant on dopamine and glutamate; flies avoided opto-inhibition of this narrow subset, indicating the role of this cluster in controlling ongoing behavior. Dopamine valence was distinct from output-neuron opto-valence in locomotor pattern, strength, and polarity. Overall, our data suggest that dopamine's acute effect on valence provides a mechanism by which a dopaminergic system can coherently write memories to influence future responses while guiding immediate attraction and aversion.

Serotonin acts through multiple cellular targets during an olfactory critical period

Serotonin (5-HT) modulates early development during critical periods when experience drives heightened levels of plasticity in neurons. Here, we investigate the cellular mechanisms by which 5-HT modulates critical period plasticity (CPP) in the olfactory system of Drosophila. We first demonstrate that 5-HT is necessary for experience-dependent structural plasticity in response to chronic CO2 exposure and can re-open the critical period long after it normally closes. Knocking down 5-HT7 receptors in a subset of GABAergic local interneurons was sufficient to block CPP, as was knocking down GABA receptors expressed by CO2-sensing olfactory sensory neurons (OSNs). Furthermore, direct modulation of OSNs via 5-HT2B receptors in CO2-sensing OSNs and autoreceptor expression by serotonergic neurons was also required for CPP. Thus, 5-HT targets individual neuron types in the olfactory system via distinct receptors to enable sensory driven plasticity.

Slit regulates compartment-specific targeting of dendrites and axons in the Drosophila brain

Proper functioning of the nervous system requires precise neuronal connections at subcellular domains, which can be achieved by projection of axons or dendrites to subcellular domains of target neurons. Here we studied subcellular-specific targeting of dendrites and axons in the Drosophila mushroom body (MB), where mushroom body output neurons (MBONs) and local dopaminergic neurons (DAN) project their dendrites and axons, respectively, to specific compartments of MB axons. Through genetic ablation, we demonstrate that compartment-specific targeting of MBON dendrites and DAN axons involves mutual repulsion of MBON dendrites and/or DAN axons between neighboring compartments. We further show that Slit expressed in subset of DANs mediates such repulsion by acting through different Robo receptors in different neurons. Loss of Slit-mediated repulsion leads to projection of MBON dendrites and DAN axons into neighboring compartments, resulting formation of ectopic synaptic contacts between MBONs and DANs and changes in olfactory-associative learning. Together, our findings suggest that Slit-mediated repulsion controls compartment-specific targeting of MBON dendrites and DAN axons, which ensures precise connections between MBON dendrites and DAN axons and proper learning and memory formation.

Identification of a novel downstream single-minded midline regulatory element in Drosophila melanogaster

Development of the Drosophila melanogaster central nervous system midline depends on the gene single-minded ( sim ). Although sim regulation has been studied extensively, the fact that an enhancer mediating late embryonic sim transcription has not been identified suggests that additional regulatory sequences remain unknown. We tested several evolutionarily conserved sequences in the sim downstream region and isolated sim_3pB , whose midline activity in a reporter gene assay begins later than previously characterized sim enhancers. Its activity shares several key similarities with the Aedes aegypti sim _ 5P3 enhancer, though is sufficiently different to warrant further investigation into how sim_3pB functions in its native context.

Neural pathways and computations that achieve stable contrast processing tuned to natural scenes

Natural scenes are highly dynamic, challenging the reliability of visual processing. Yet, humans and many animals perform accurate visual behaviors, whereas computer vision devices struggle with rapidly changing background luminance. How does animal vision achieve this? Here, we reveal the algorithms and mechanisms of rapid luminance gain control in Drosophila, resulting in stable visual processing. We identify specific transmedullary neurons as the site of luminance gain control, which pass this property to direction-selective cells. The circuitry further involves wide-field neurons, matching computational predictions that local spatial pooling drive optimal contrast processing in natural scenes when light conditions change rapidly. Experiments and theory argue that a spatially pooled luminance signal achieves luminance gain control via divisive normalization. This process relies on shunting inhibition using the glutamate-gated chloride channel GluClα. Our work describes how the fly robustly processes visual information in dynamically changing natural scenes, a common challenge of all visual systems.

Connectomic reconstruction predicts visual features used for navigation

Many animals use visual information to navigate1-4, but how such information is encoded and integrated by the navigation system remains incompletely understood. In Drosophila melanogaster, EPG neurons in the central complex compute the heading direction5 by integrating visual input from ER neurons6-12, which are part of the anterior visual pathway (AVP)10,13-16. Here we densely reconstruct all neurons in the AVP using electron-microscopy data17. The AVP comprises four neuropils, sequentially linked by three major classes of neurons: MeTu neurons10,14,15, which connect the medulla in the optic lobe to the small unit of the anterior optic tubercle (AOTUsu) in the central brain; TuBu neurons9,16, which connect the AOTUsu to the bulb neuropil; and ER neurons6-12, which connect the bulb to the EPG neurons. On the basis of morphologies, connectivity between neural classes and the locations of synapses, we identify distinct information channels that originate from four types of MeTu neurons, and we further divide these into ten subtypes according to the presynaptic connections in the medulla and the postsynaptic connections in the AOTUsu. Using the connectivity of the entire AVP and the dendritic fields of the MeTu neurons in the optic lobes, we infer potential visual features and the visual area from which any ER neuron receives input. We confirm some of these predictions physiologically. These results provide a strong foundation for understanding how distinct sensory features can be extracted and transformed across multiple processing stages to construct higher-order cognitive representations.

Brain bilateral asymmetry - insights from nematodes, zebrafish, and Drosophila

Chirality is a fundamental trait of living organisms, encompassing the homochirality of biological molecules and the left-right (LR) asymmetry of visceral organs and the brain. The nervous system in bilaterian organisms displays a lateralized organization characterized by the presence of asymmetrical neuronal circuits and brain functions that are predominantly localized within one hemisphere. Although body asymmetry is relatively well understood, and exhibits robust phenotypic expression and regulation via conserved molecular mechanisms across phyla, current findings indicate that the asymmetry of the nervous system displays greater phenotypic, genetic, and evolutionary variability. In this review we explore the use of nematode, zebrafish, and Drosophila genetic models to investigate neuronal circuit asymmetry. We discuss recent discoveries in the context of body-brain concordance and highlight the distinct characteristics of nervous system asymmetry and its cognitive correlates.

A Detailed Re-Examination of the Period Gene Rescue Experiments Shows That Four to Six Cryptochrome-Positive Posterior Dorsal Clock Neurons (DN1p) of Drosophila melanogaster Can Control Morning and Evening Activity

Animal circadian clocks play a crucial role in regulating behavioral adaptations to daily environmental changes. The fruit fly Drosophila melanogaster exhibits 2 prominent peaks of activity in the morning and evening, known as morning (M) and evening (E) peaks. These peaks are controlled by 2 distinct circadian oscillators located in separate groups of clock neurons in the brain. To investigate the clock neurons responsible for the M and E peaks, a cell-specific gene expression system, the GAL4-UAS system, has been commonly employed. In this study, we re-examined the two-oscillator model for the M and E peaks of Drosophila by utilizing more than 50 Gal4 lines in conjunction with the UAS-period16 line, which enables the restoration of the clock function in specific cells in the period (per) null mutant background. Previous studies have indicated that the group of small ventrolateral neurons (s-LNv) is responsible for controlling the M peak, while the other group, consisting of the 5th ventrolateral neuron (5th LNv) and the three cryptochrome (CRY)-positive dorsolateral neurons (LNd), is responsible for the E peak. Furthermore, the group of posterior dorsal neurons 1 (DN1p) is thought to also contain M and E oscillators. In this study, we found that Gal4 lines directed at the same clock neuron groups can lead to different results, underscoring the fact that activity patterns are influenced by many factors. Nevertheless, we were able to confirm previous findings that the entire network of circadian clock neurons controls M and E peaks, with the lateral neurons playing a dominant role. In addition, we demonstrate that 4 to 6 CRY-positive DN1p cells are sufficient to generate M and E peaks in light-dark cycles and complex free-running rhythms in constant darkness. Ultimately, our detailed screening could serve as a catalog to choose the best Gal4 lines that can be used to rescue per in specific clock neurons.