Biology subjects

Claridge-Chang, A.

Publications and source records attributed to Claridge-Chang, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Contextualized phenovectors reveal a Drosophila serotonergic circuit controlling satiety

Distinguishing whether a neural circuit genuinely controls a holistic behavioral state, rather than merely producing isolated effects, is a central challenge in neuroscience. Feeding research illustrates the problem: decades of work have reached conflicting conclusions partly because individual behavioral features are assessed in isolation. Here we establish a contextualized ethomics approach that benchmarks optogenetic circuit manipulations against natural hunger-satiety transitions, using high-dimensional behavioral tracking in Drosophila and starvation as a ground-truth intervention. Applying this framework, we find that serotonergic neurons marked by the Tryptophan hydroxylase neuronal (Trhn) enhancer are both required for and instructive of a satiety-like state, whereas other feeding-related circuits produce only fragmentary behavioral changes. Intersectional dissection localized this control to Trhn neurons of the ventral nerve cord, which act through the sugar transporter Sut2 to sense nutrient state. This work strengthens our understanding of serotonergic feeding control and provides a generalizable framework for validating circuit-state relationships.

neuroscience↗

bioRxiv2026

Brief illumination of an optoGPCR elicits prolonged inhibition of Drosophila behavior

Light-actuated G protein-coupled receptors (optoGPCRs) are a class of opsins that act through intracellular signaling cascades. As optogenetic tools, bistable inhibitory optoGPCRs are attractive as they decouple the duration of silencing from the duration of illumination: brief light pulses drive prolonged signaling. Opsin3 from the mosquito Anopheles stephensi (MosOPN3) is a bistable Gi/o-coupled opsin that produces sustained inhibition in mammalian neurons and C. elegans, but its utility in vinegar flies, Drosophila melanogaster, remains untested. Here we tested three optoGPCRs in adult flies; MosOPN3 emerged as the most effective and was benchmarked against an established inhibitor, Guillardia theta anion channelrhodopsin 1 (GtACR1), in walking and memory assays. MosOPN3 inhibitory potency was comparable to that of GtACR1 across most neuronal classes tested, with substantially lower developmental toxicity. Rearing flies on all-trans-retinal-supplemented food throughout development improved both viability and inhibitory efficacy for both opsins. A single pulse of green light (as brief as 5 s) inhibited behavior for minutes, and was sufficient to ablate aversive olfactory learning over a one-minute training epoch. For flies, MosOPN3 is a low-toxicity optogenetic inhibitor for flies that yields minutes of silencing from brief light pulses--especially useful where continuous actuating light would be confounding. Key pointsO_LITo our knowledge, Anopheles stephensi Opsin3 (OPN3) is the first GPCR opsin that inhibits behavior in adult Drosophila melanogaster. C_LIO_LIOPN3 has inhibitory efficacy close to that of GtACR1, with superior viability. C_LIO_LIBrief light pulses drive sustained inhibition lasting minutes, eliminating the need for continuous illumination. C_LIO_LIFor both GtACR1 and OPN3, rearing flies on ATR-supplemented food enhances inhibition efficacy and improves developmental viability. C_LI

neuroscience↗

bioRxiv2026

Long-Stokes-Shift mScarlet3 as a Structural Marker for Two-Photon Imaging

Two-photon imaging with genetically encoded sensors is widely used to monitor neurophysiology. An additional fluorescent protein can provide anatomical landmarks for cell-type identification and motion detection. However, monomeric red fluorescent proteins often require a dedicated excitation laser. We made transgenic Drosophila with a long-Stokes-shift mScarlet variant (LSSmScarlet3) to image alongside green sensors with a single 920-nm laser. We describe excitation and emission spectra of the expressed protein and show robust fluorescence at 920 nm in vitro and in vivo with minimal channel crosstalk. This approach can reduce equipment complexity and cost while placing functional calcium dynamics in their anatomical context.

neuroscience↗

bioRxiv2026

A mushroom-body output neuron that mediates octopamine-driven and hunger-motivated feeding in Drosophila

Feeding behavior requires the integration of environmental cues, metabolic signals, and internal states through neuromodulatory networks, yet the role of specific neuromodulatory neurons and how they are coordinated in controlling feeding remains unclear. Using automated feed-tracking and optogenetics in Drosophila melanogaster, we found that activation of two octopaminergic neurons (VPM3/4) increases food consumption. Both VPM neurons form direct synapses with a mushroom-body output neuron MBON11, which, through opto-activation and opto-inhibition, can exert bidirectional control over food intake, with sexually dimorphic effects. Epistasis experiments demonstrated that octopamine-driven feeding requires functional MBON11 output. Additionally, we found that the dopaminergic PPL101 neurons, which also synapse with MBON11, are required for hunger-driven feeding. Ethomic analysis contextualized with natural hunger and satiety provided a holistic view of how different neuron types linked to the mushroom-body influence feeding behaviors. This analysis revealed that MBON11 interventions best recapitulate natural hunger-satiety transitions. These findings revealed a circuit where two neuromodulatory neuron types with distinct unidirectional feeding effects--octopaminergic VPM3/4 (instructive but not required) and dopaminergic PPL101 (required but not instructive)--converge onto MBON11, a neuron whose activity is both required for and instructive of hunger-related feeding. This circuit arrangement may represent an architecture for integrating multiple motivational signals in feeding regulation. Key pointsO_LIWhen activated, octopaminergic VPM3 and VPM4 cells drive increased food consumption, effects that require octopamine signaling and are dependent on MBON11 function. C_LIO_LIOctopaminergic neuronal activity is not required for hunger-driven feeding. C_LIO_LIReceiving direct synaptic inputs from VPM3 and 4, MBON11 neurons bidirectionally control feeding, and broadly phenocopy natural hunger-satiety transitions. C_LIO_LIDopaminergic PPL101 neurons that synapse onto MBON11 are required for hunger-motivated feeding. C_LIO_LIMBON11 appears to integrate octopaminergic and dopaminergic signals, and regulate the feeding behavioral state. C_LI

neuroscience↗

bioRxiv2026

Getting over ANOVA: Estimation graphics for multi-group comparisons

Data analysis in experimental science mainly relies on null-hypothesis significance testing, despite its well-known limitations. A powerful alternative is estimation statistics, which focuses on effect-size quantification. However, current estimation tools struggle with the complex, multi-group comparisons common in biological research. Here we introduce DABEST 2.0, an estimation framework for complex experimental designs, including shared-control, repeated-measures, two-way factorial experiments, and meta-analysis of replicates.

bioinformatics↗

bioRxiv2025

Two-photon characterisation of long-Stokes-shift dye ATTO 490LS for single-laser multicolour imaging

Long-Stokes-shift fluorophores enable high sensitivity and multiplexed imaging with single-wavelength excitation. Under single-photon illumination ATTO 490LS exhibits a 165-nm Stokes shift, but its two-photon properties remain uncharacterised. Emission and excitation spectral analyses of ATTO 490LS in ex vivo Drosophila melanogaster brains identified two-photon excitation sensitivity at 940 nm, with peak emission at 640 nm. We demonstrate successful duplexed imaging of ATTO 490LS alongside Alexa Fluor 488 using a single 920-nm fibre laser and dual photomultiplier tubes, enabling distinct measurement of red and green fluorescence signals. These findings establish ATTO 490LS as suitable for multicolour two-photon microscopy with single-laser systems.

neuroscience↗

bioRxiv2025

Entirely synthetic memory inception via dual optogenetic activation of sensory and dopaminergic neurons

Associative conditioning is a fundamental learning paradigm that links salient stimuli to appropriate behavior. The vinegar fly is an important memory model that can associate odors with rewarding or punishing reinforcement stimuli via distinct sets of dopaminergic neurons. While much is known about learning, a crucial question remains: is the simple co-activation of sensory and neuromodulatory dopaminergic neurons sufficient to induce memory formation? To address this, we systematically replaced natural stimuli, namely odor-evoked activity, punishment, and reward signals, with optogenetic activation of corresponding neurons, both individually and in combination. In all cases, including a full-substitution paradigm where both olfactory activity and reinforcement dopamine signals were replaced, optogenetic activation successfully implanted synthetic memories. These findings provide a clear answer: simple coincident, rectangular-pulse sensory and neuromodulatory stimulation can instruct associative memory formation. We conclude that associative memory does not have strict requirements for temporal or ensemble activity patterns in olfactory or dopaminergic neurons that are specific to natural stimuli (e.g. odorants, sugar, or pain); rather, simple coincidence is an effective driver of memory inception. These findings open new avenues for manipulating and studying memory formation with all-optical control.

animal behavior and cognition↗

bioRxiv2025

Stabilized ion selectivity corrects activation drift in kalium channelrhodopsins

Effective optogenetic inhibition of neuronal activity requires tools that can reliably silence neurons across diverse conditions and cell types. Potassium-selective channelrhodopsins (KCRs) have emerged as promising alternatives to chloride-conducting channels for optogenetic inhibition of cellular excitability, but they exhibit dynamic ion selectivity shift under prolonged or intense illumination, causing activation. This inhibition to activation transition limits their utility for silencing circuits. Through behavioral and electrophysiological analyses in Drosophila, and C. elegans, we found that the C29D variant of KCR1 maintains the most stable potassium selectivity among tested variants. While other KCR variants showed excitation defects, KCR1-C29D consistently provided robust in vivo inhibition across cell types, illumination conditions, and species. Electrophysiological recordings revealed that while most KCRs show declining PK/PNa ratios during illumination, KCR1-C29D maintains stable ion selectivity, consistent with its robust silencing capability. This work resolves a key limitation of KCR optogenetics and shows that KCR1-C29D is a superior tool for reliable inhibition. Our findings offer valuable mechanistic and practical insights for the design of next generation optogenetic inhibitors.

neuroscience↗

bioRxiv2024

Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelid Alvinella pompejana yield insight into animal evolution in extreme environments

The types of genomic change needed for environmental adaptation are of great interest. Annelid worms are a large phylum found in a rich diversity of habitats, giving opportunities to explore this issue. We report the chromosome level genome sequence of the Pompeii worm, the annelid Alvinella pompejana, an inhabitant of an extreme deep-sea hydrothermal vent environment. We find strong but heterogeneously distributed genetic divergence between populations taken from either side of the equator. Using transcript data, we produced a set of gene models and analysed the predicted protein set in the light of past hypotheses about the thermotolerance of Alvinella, and compared it to other recently sequenced annelid vent worms. We do not find evidence of a more extreme genome wide amino acid composition than other species, neither do we find evidence for rapid genome evolution in the form of disrupted synteny. We discount the hypothesis of loss of amino acid biosynthesis genes associated with obligate symbioses reported in siboglinid annelids. We do find evidence of a parallel increase in the number of globin encoding genes and loss of light sensitive opsins and cryptochromes. Alvinella encodes several respiratory enzymes unusual for bilaterian animals, suggesting an ability to better tolerate hypoxic environments.

genomics↗

bioRxiv2024

Kalium channelrhodopsins effectively inhibit neurons in the small model animals

The analysis of neural circuits has been revolutionized by optogenetic methods. Light-gated chloride-conducting anion channelrhodopsins (ACRs)--recently emerged as powerful neuron inhibitors. For cells or sub-neuronal compartments with high intracellular chloride concentrations, however, a chloride conductance can have instead an activating effect. The recently discovered light-gated, potassium-conducting, kalium channelrhodopsins (KCRs) might serve as an alternative in these situations, with potentially broad application. As yet, KCRs have not been shown to confer potent inhibitory effects in the small genetically tractable animals. Here, we evaluated the utility of KCRs to suppress behavior and inhibit neural activity in Drosophila, C. elegans, and zebrafish. In direct comparisons with ACR1, a KCR1 variant with enhanced plasma-membrane trafficking displayed comparable potency, but with improved properties that include reduced toxicity and superior efficacy in putative high-chloride cells. This comparative analysis of behavioral inhibition between chloride- and potassium-selective silencing tools establishes KCRs as next-generation optogenetic inhibitors for in vivo circuit analysis in behaving animals.

neuroscience↗

bioRxiv2022

A dopaminergic memory circuit controls acute valence

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 two 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 dopamines 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.

animal behavior and cognition↗

bioRxiv2022

Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella.

BackgroundThe transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to the separation of vent populations, local adaptation and is likely to promote bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution. ResultsIn the present study, we explored genomic patterns of divergence in the early and late steps of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement. ConclusionOur analyses pointed out the non-negligible role of natural selection on both the early and late stages of speciation in the emblematic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed ligth on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time.

evolutionary biology↗

bioRxiv2021

Most primary olfactory neurons have individually neutral effects on behavior

Animals use olfactory receptors to navigate mates, food, and danger. However, for complex olfactory systems, it is unknown what proportion of primary olfactory sensory neurons can individually drive avoidance or attraction. Similarly, the rules that govern behavioral responses to receptor combinations are unclear. We used optogenetic analysis in Drosophila to map the behavior elicited by olfactory-receptor neuron (ORN) classes: just one-fifth of ORN-types drove either avoidance or attraction. Although wind and hunger are closely linked to olfaction, neither had much effect on single-class responses. Several pooling rules have been invoked to explain how ORN types combine their behavioral influences; we activated two-way combinations and compared patterns of single- and double-ORN responses: these comparisons were inconsistent with simple pooling. We infer that the majority of primary olfactory sensory neurons have neutral behavioral effects individually, but participate in broad, odor-elicited ensembles with potent behavioral effects arising from complex interactions.

animal behavior and cognition↗

bioRxiv2021

Contingent-behavior assay shows zebrafish preference for alcohol is biphasic

Alcohol use disorders are complex, multifactorial phenomena with a large footprint within the global burden of diseases. Here, we report the development of an accessible, two-choice self-administration zebrafish assay (SAZA) to study the neurobiology of addiction. Using this assay, we first demonstrated that, while zebrafish avoid higher concentrations of alcohol, they are attracted to low concentrations. Pre-exposure to alcohol did not change this relative preference, but acute exposure to an alcohol deterrent approved for human use decreased alcohol self-administration. A pigment mutant used in whole-brain imaging studies displayed a similar relative alcohol preference profile, however, mutants in CCSER1, a gene associated with alcohol dependence in human genetic studies, showed a reversal in relative preference. The presence of a biphasic response (hormesis) in zebrafish validated a key aspect of vertebrate responses to alcohol. SAZA adds a new dimension for discovering novel alcohol deterrents, and studying the neurogenetics of addiction using the zebrafish.

neuroscience↗

bioRxiv2021

Characterization of induction methods for Drosophila seizure mutations

Epilepsy is one of the most common neurological disorders. Around one third of patients do not respond to current medications. This lack of treatment indicates a need for better understanding of the underlying mechanisms and, importantly, the identification of novel targets for drug manipulation. The fruitfly Drosophila melanogaster has a fast reproduction time, powerful genetics, and facilitates large sample sizes, making it a strong model of seizure mechanisms. However, there has not yet been a systematic analysis of the wide range of behavioral and physiological phenotypes observed across major fly seizure genotypes. To understand this, we systematically measured seizure severity and secondary behavioral phenotypes at both the larval and adult stage. Comparison of several seizure-induction methods; specifically electrical, mechanical and heat-induction, show that larval electroshock is the most effective at inducing seizures across a wide range of seizure-prone mutants. Locomotion in adults and larvae was found to be non-predictive of seizure susceptibility. Recording activity in identified larval motor neurons revealed variations in action potential patterns, across different genotypes, but these patterns did not correlate with seizure susceptibility. To conclude, while there is wide variation in mechanical induction, heat induction, and secondary phenotypes, electroshock is the most consistent method of seizure induction across known major seizure genotypes in Drosophila. Significance StatementEpilepsy is a neurological disorder affecting 1 in 130 people globally, with a significant impact on patients, families, and society. Approximately one third of epileptics do not respond to currently available medication. Thus, better insights into underlying disease mechanisms and identification of new drugs are needed. Fruit flies (Drosophila melanogaster) are a powerful genetic model: a number of single gene mutant flies exhibit seizures, phenotypes that have been shown to respond to established antiepileptic drugs. We compare methods of seizure induction and their utility, to establish which induction method is the most consistent across a range of different seizure-inducing genetic backgrounds. Adopting a common method for seizure analysis in this model will, we predict, speed identification of novel anti-convulsive treatments.

neuroscience↗

bioRxiv2020

A neural m6A/YTHDF pathway is required for learning and memory in Drosophila

The roles of epitranscriptomic modifications in mRNA regulation have recently received substantial attention, with appreciation growing for their phenotypically selective impacts within the animal. We adopted Drosophila melanogaster as a model system to study m6A, the most abundant internal modification of mRNA. Here, we report proteomic and functional analyses of fly m6A-binding proteins, confirming nuclear (YTHDC) and cytoplasmic (YTHDF) YTH domain proteins as the major m6A binders. Since all core m6A pathway mutants are viable, we assessed in vivo requirements of the m6A pathway in cognitive processes. Assays of short term memory revealed an age-dependent requirement of m6A writers working via YTHDF, but not YTHDC, comprising the first phenotypes assigned to Drosophila mutants of the cytoplasmic m6A reader. These factors promote memory via neural-autonomous activities, and are required in the mushroom body, the center for associative learning. To inform their basis, we mapped m6A from wild-type and mettl3 null mutant heads, allowing robust discrimination of Mettl3-dependent m6A sites. In contrast to mammalian m6A, which is predominant in 3 UTRs, Drosophila m6A is highly enriched in 5 UTRs and occurs in an adenosine-rich context. Genomic analyses demonstrate that Drosophila m6A does not directionally affect RNA stability, but is preferentially deposited on genes with low translational efficiency. However, functional tests indicate a role for m6A in translational activation, since we observe reduced nascent protein synthesis in mettl3-KO cells. Finally, we show that ectopic YTHDF can increase m6A target reporter output in an m6A-binding dependent manner, and that this activity is required for in vivo neural function of YTHDF in memory. Altogether, we provide the first tissue-specific m6A maps in this model organism and reveal selective behavioral and translational defects for m6A/YTHDF mutants.

animal behavior and cognition↗

bioRxiv2019

NEURONS THAT FUNCTION WITHIN AN INTEGRATOR TO PROMOTE A PERSISTENT BEHAVIORAL STATE IN DROSOPHILA

Innate behaviors involve both reflexive motor programs and internal states. In Drosophila, optogenetic activation of male-specific P1 interneurons triggers courtship song, as well as a persistent behavioral state that prolongs courtship and enhances aggressiveness. Here we identify pCd neurons as persistently activated by repeated P1 stimulation. pCd neurons are required for P1-evoked persistent courtship and aggression, as well as for normal social behavior. Activation of pCd neurons alone is inefficacious, but enhances and prolongs courtship or aggression promoted by female cues. Transient female exposure induced persistent increases in male aggressiveness, an effect suppressed by transiently silencing pCd neurons. Transient silencing of pCd also disrupted P1-induced persistent physiological activity, implying a requisite role in persistence. Finally, P1 activation of pCd neurons enhanced their responsiveness to cVA, an aggression-promoting pheromone. Thus, pCd neurons function within a circuit that integrates P1 input, to promote a persistent internal state that enhances multiple social behaviors.

neuroscience↗

bioRxiv2019

Motor context coordinates visually guided walking in Drosophila

Course control is critical for the acquisition of spatial information during exploration and navigation, and it is thought to rely on neural circuits that process locomotive-related multimodal signals. However, which circuits underlie this control, and how multimodal information contributes to the control system are questions poorly understood. We used Virtual Reality to examine the role of self-generated visual signals (visual feedback) on the control of exploratory walking in flies. Exploratory flies display two distinct motor contexts, characterized by low speed and fast rotations, or by high speed and slow rotations, respectively. Flies use visual feedback to control body rotations, but in a motor-context specific manner, primarily when walking at high speed. Different populations of visual motion-sensitive cells estimate body rotations via congruent, multimodal inputs, and drive compensatory rotations. However, their effective contribution to course control is dynamically tuned by a speed-related signal. Our data identifies visual networks with a multimodal circuit mechanism for adaptive course control and suggests models for how visual feedback is combined with internal signals to guide exploratory course control.

neuroscience↗