A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain

Published: 23 March 2018The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fninf.2018.00013/full#supplementary-material Supplementary Figure 1. 3D renderings of the 14 regions used for quantitative evaluation of atlas performances in segmentation and registration tasks. The 14 regions shown here were extracted from the atlas of Ito et al. (2014) that has been registered onto the group-wise inter-sex atlas (available from http://fruitfly.tefor.net). Supplementary Figure 2. Selected lines from the Janelia Farm collection showing an overlap value with the search pattern ranking among the first 50 for at least three of the five PDF profiles. (Left) GAL4-driven GFP profile registered on the standard brain. (Right) overlap between the first PDF profile and the GAL4-driven GFP profile. Numbers refer to Janelia Farm lines with associated gene names. Scale bar: 20 μm. Supplementary Table 1. Results of the 3D space query for each of the five PDF profiles. Overlap values are indicated for each Janelia Farm line and the corresponding gene name (FlyBase nomenclature) is indicated for the overlap values ranking among the first 50 for at least three of the five PDF profiles (blue). Bold names correspond to the three lines shown in Figure 10. Supplementary Movie 1. Animated rendering of the group-wise inter-sex atlas. Successively: nc82 template image (2D sections then 3D volume rendering, opaque then transparent); label image (3D surface rendering of anatomical regions, defined following Ito et al. 2014); six registered patterns of GAL4-GFP expression (3D surface rendering of intensity-thresholded pattern images); same patterns (left half of the brain) with the anatomical regions (right half of the brain).Imaging the expression patterns of reporter constructs is a powerful tool to dissect the neuronal circuits of perception and behavior in the adult brain of Drosophila, one of the major models for studying brain functions. To date, several Drosophila brain templates and digital atlases have been built to automatically analyze and compare collections of expression pattern images. However, there has been no systematic comparison of performances between alternative atlasing strategies and registration algorithms. Here, we objectively evaluated the performance of different strategies for building adult Drosophila brain templates and atlases. In addition, we used state-of-the-art registration algorithms to generate a new group-wise inter-sex atlas. Our results highlight the benefit of statistical atlases over individual ones and show that the newly proposed inter-sex atlas outperformed existing solutions for automated registration and annotation of expression patterns. Over 3,000 images from the Janelia Farm FlyLight collection were registered using the proposed strategy. These registered expression patterns can be searched and compared with a new version of the BrainBaseWeb system and BrainGazer software. We illustrate the validity of our methodology and brain atlas with registration-based predictions of expression patterns in a subset of clock neurons. The described registration framework should benefit to brain studies in Drosophila and other insect species.IA-C, TM, NM, FS, and AJ were funded by the Tefor Infrastructure under the Investments for the Future program of the French National Research Agency (Grant #ANR-11-INBS-0014). FR was supported by INSERM. Work at Institut des Neurosciences Paris-Saclay was supported by ANR Infrastructure Tefor and by ANR ClockEye(#ANR-14-CE13-0034-01). JI was supported by the Spanish Ministry of Economy and Competitiveness (TEC2014-51882-P), the European Union's Horizon 2020 research and innovation programme (Marie Sklodowska-Curie grant 654911, project THALAMODEL), and the European Research Council (ERC Starting Grant no. 677697 BUNGEE-TOOLS). VRVis (KB, FS) is funded by BMVIT, BMWFW, Styria, SFG and Vienna Business Agency in the scope of COMET - Competence Centers for Excellent Technologies (854174) which is managed by FFG. The Institut Jean-Pierre Bourgin benefits from the support of the LabEx Saclay Plant Sciences-SPS (#ANR-10-LABX-0040-SPS)

Mapping Functional Connectivity between Neuronal Ensembles with Larval Zebrafish Transgenic for a Ratiometric Calcium Indicator

The ability to map functional connectivity is necessary for the study of the flow of activity in neuronal circuits. Optical imaging of calcium indicators, including FRET- based genetically encoded indicators and extrinsic dyes, is an important adjunct to electrophysiology and is widely used to visualize neuronal activity. However, techniques for mapping functional connectivities with calcium imaging data have been lacking. We present a procedure to compute reduced functional couplings between neuronal ensembles undergoing seizure activity from ratiometric calcium imaging data in three steps: 1) calculation of calcium concentrations and neuronal firing rates from ratiometric data; 2) identification of putative neuronal populations from spatio-temporal timeseries of neural bursting activity; and then, 3) derivation of reduced connectivity matrices that represent neuronal population interactions. We apply our method to the larval zebrafish central nervous system undergoing chemoconvulsant induced seizures. These seizures generate propagating, central nervous system-wide neural activity from which population connectivities may be calculated. This automatic functional connectivity mapping procedure provides a practical and user-independent means for summarizing the flow of activity between neuronal ensembles

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

Visualizing anatomically registered data with Brainrender

Three-dimensional (3D) digital brain atlases and high-throughput brain wide imaging techniques generate large multidimensional datasets that can be registered to a common reference frame. Generating insights from such datasets depends critically on visualization and interactive data exploration, but this a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. Here, we present brainrender: an open-source Python package for interactive visualization of multidimensional datasets registered to brain atlases. Brainrender facilitates the creation of complex renderings with different data types in the same visualization and enables seamless use of different atlas sources. High-quality visualizations can be used interactively and exported as high-resolution figures and animated videos. By facilitating the visualization of anatomically registered data, brainrender should accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data

MODULATORY ACTIONS OF SEROTONERGIC SYSTEM IN CARDIAC FUNCTION, BEHAVIOR, AND SENSORIMOTOR CIRCUIT ACTIVITY IN DROSOPHILA MELANOGASTER

In this dissertation, I have focused on the role of serotonin (5-HT) as a modulator in heart rate, feeding and locomotion behaviors as well as sensorimotor circuit activity in Drosophila melanogaster. A general overview in the actions of the serotonergic (5-HTergic) system on the larval heart and nervous system in larvae and adults is reviewed in Chapter One. I sought to further study the actions of serotonergic system to provide additional insights into cellular and molecular underpinnings in the actions of 5-HT.In Chapter two, I present studies on mechanisms of action by 5-HT in larvae cardiac system. For this purpose, genetic and pharmacological approaches were used. The transgenic flies used expressed hM4Di receptors (designer receptors exclusively activated by designer drugs (DREADDs)) which were employed to manipulate the activity of Gαi heterotrimeric protein through activation of engineered G-protein coupled receptors hM4Di DREADD. The activation of hM4Di DREADD receptors by clozapine-N-oxide (CNO) arrested the heart beat; however, pharmacological manipulation of adenylyl cyclase activity and cAMP levels had no significant effect on heart rate. In Chapter Three the role of various 5-HT receptor subtypes that mediate 5-HT action in larval cardiac tissue is addressed. In this study, various 5-HT agonists and antagonists were employed. The pharmacological results demonstrate that a 5-HT2 agonist significantly increases the heart rate. Furthermore, 5-HT2 antagonist, markedly reduces the effect of 5-HT. In addition, I employed genetic approaches to corroborate the pharmacological results. In addition, I investigated the role of the 5-HTergic system in locomotion and feeding behaviors as well as in modulation of sensorimotor circuits. This study is delineated in Chapter Four. The 5-HT biosynthesis was dysregulated by feeding Drosophila larvae various pharmacological agents. 5-HT receptor subtypes were manipulated using RNA interference mediated knockdown and 5-HT receptor insertional mutations. Moreover, synaptic transmission at 5-HT neurons was blocked or induced in both larvae and adult flies. The results demonstrate that disruption of components within the 5-HT system significantly impairs locomotor activity and feeding behavior in larvae. In addition, acute activation of 5-HT neurons disrupts normal locomotor activity in adult flies. In Chapter Five, I addressed direct actions of fluoxetine on synaptic transmission at neuromuscular junctions (NMJs), neural properties, and cardiac function unrelated to fluoxetine’s action as a selective 5-HT reuptake inhibitor using Drosophila, crayfish and primary neurons in mouse model system. Fluoxetine application blocked action potentials in crayfish axons, enhanced occurrences of spontaneous synaptic vesicle fusion events at NMJs of both Drosophila and crayfish. In rodent primary neurons, fluoxetine application resulted in increase of cytoplasmic Ca2+. I also developed teaching modules, which are presented in Chapter Seven, to guide students how to exploit a vast array of genetic tools, such as optogenetics in Drosophila to manipulate various neural circuits and to observe their effects on behavior and sensorimotor circuit activity. I also developed a module to teach college level students a hands-on experiment regarding proprioception and tension receptors in crab limb, which is detailed in Chapter Eight

Brain connectivity inversely scales with developmental temperature in Drosophila

Variability of synapse numbers and partners despite identical genes reveals the limits of genetic determinism. Here, we use developmental temperature as a non-genetic perturbation to study variability of brain wiring and behavior in Drosophila. Unexpectedly, slower development at lower temperatures increases axo-dendritic branching, synapse numbers, and non-canonical synaptic partnerships of various neurons, while maintaining robust ratios of canonical synapses. Using R7 photoreceptors as a model, we show that changing the relative availability of synaptic partners using a DIPγ mutant that ablates R7’s preferred partner leads to temperature-dependent recruitment of non-canonical partners to reach normal synapse numbers. Hence, R7 synaptic specificity is not absolute but based on the relative availability of postsynaptic partners and presynaptic control of synapse numbers. Behaviorally, movement precision is temperature robust, while movement activity is optimized for the developmentally encountered temperature. These findings suggest genetically encoded relative and scalable synapse formation to develop functional, but not identical, brains and behaviors

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

Representations of Reward and Movement in Drosophila Dopaminergic Neurons

The neuromodulator dopamine is known to influence both immediate and future behavior, motivating and invigorating an animal’s ongoing movement but also serving as a reinforcement signal to instruct learning. Yet it remains unclear whether this dual role of dopamine involves the same dopaminergic pathways. Although reward-responsive dopaminergic neurons display movement-related activity, debate continues as to what features of an individual’s experience these motor-correlates correspond and how they influence concurrent behavior. The mushroom body, a prominent neuropil in the brain of the fruit fly Drosophila melanogaster, is richly innervated by dopaminergic neurons that play an essential role in the formation of olfactory associations. While dopaminergic neurons respond to reward and punishment to drive associative learning, they have also been implicated in a number of adaptive behaviors and their activity correlates with the behavioral state of an animal and its coarse motor actions. Here, we take advantage of the concise circuit architecture of the Drosophila mushroom body to investigate the nature of motor-related signals in dopaminergic neurons that drive associative learning. In vivo functional imaging during naturalistic tethered locomotion reveals that the activity of different subsets of mushroom body dopaminergic neurons reflects distinct aspects of movement. To gain insight into what facets of an animal’s experience are represented by these movement-related signals, we employed a closed loop virtual reality paradigm to monitor neural activity as animals track an olfactory stimulus and are actively engaged in a goal-directed and sensory-motivated behavior. We discover that odor responses in dopaminergic neurons correlate with the extent to which an animal tracks upwind towards the fictive odor source. In different experimental contexts where distinct motor actions were required to track the odor, dopaminergic neurons become emergently linked to the behavioral metric most relevant for effective olfactory navigation. Subsets of dopaminergic neurons were correlated with the strength of upwind tracking regardless of the identity of the odor and remained so even after the satiety state of an animal was altered. We proceed to demonstrate that transient inhibition of dopaminergic neurons that are positively correlated with upwind tracking significantly diminishes the normal approach responses to an appetitive olfactory cue. Accordingly, activation of those same dopaminergic neurons enhances approach to an odor and even drives upwind tracking in clean air alone. Together, these results reveal that the same dopaminergic pathways that convey reinforcements to instruct learning also carry representations of an animal’s moment-by-moment movements and actively influence behavior. The complex activity patterns of mushroom body dopaminergic neurons therefore represent neither purely sensory nor motor variables but rather reflect the goal or motivation underlying an animal’s movements. Our data suggest a fundamental coupling between reinforcement signals and motivation-related locomotor representations within dopaminergic circuitry, drawing a striking parallel between the mushroom body dopaminergic neurons described here and the emerging understanding of mammalian dopaminergic pathways. The apparent conservation in dopaminergic neuromodulatory networks between mammals and insects suggests a shared logic for how neural circuits assign meaning to both sensory stimuli and motor actions to generate flexible and adaptive behavior

Deconstructing Spinal Interneurons, one cell type at a time

Documenting the extent of cellular diversity is a critical step in defining the functional organization of the nervous system. In this context, we sought to develop statistical methods capable of revealing underlying cellular diversity given incomplete data sampling - a common problem in biological systems, where complete descriptions of cellular characteristics are rarely available. We devised a sparse Bayesian framework that infers cell type diversity from partial or incomplete transcription factor expression data. This framework appropriately handles estimation uncertainty, can incorporate multiple cellular characteristics, and can be used to optimize experimental design. We applied this framework to characterize a cardinal inhibitory population in the spinal cord. Animals generate movement by engaging spinal circuits that direct precise sequences of muscle contraction, but the identity and organizational logic of local interneurons that lie at the core of these circuits remain unresolved. By using our Sparse Bayesian approach, we showed that V1 interneurons, a major inhibitory population that controls motor output, fractionate into diverse subsets on the basis of the expression of nineteen transcription factors. Transcriptionally defined subsets exhibit highly structured spatial distributions with mediolateral and dorsoventral positional biases. These distinctions in settling position are largely predictive of patterns of input from sensory and motor neurons, arguing that settling position is a determinant of inhibitory microcircuit organization. Finally, we extensively validated inferred cell types by direct experimental measurement and then, extend our Bayesian framework to full transcriptome technologies. Together, these findings provide insight into the diversity and organizational logic through which inhibitory microcircuits shape motor output