Biology subjects

Gerber, B.

Publications and source records attributed to Gerber, B..

At least 19 recordsLinked to original sources

bioRxiv2026

High temperature ligation enables in vitro assembly of eukaryotic genes

Our ability to efficiently construct synthetic DNA products is essential to studying and engineering biology. There is an abundance of widely adopted DNA assembly technologies suitable for generating synthetic constructs from diverse DNA inputs, but these techniques suffer from low specificity of connection during assembly, which decreases the accuracy, efficiency, and throughput of construction. Here we propose a broadly applicable paradigm for DNA assembly, High Temperature (HighT) assembly, that lowers misconnection rates by ligating complementary single strand DNA overhangs at reaction temperatures significantly higher than their predicted melting temperatures. By expanding the concept of melting temperature to demarcate smaller association fractions of DNA duplexes, we characterize HighT and demonstrate 40 percentage points increase in accuracy, and 4 orders of magnitude increase in yield of transformants when applying the technique to conventional assembly technologies. HighT is then applied to develop cloning pipelines for the development of efficient assembly-to-integration protocols, the construction of specific low-abundance isoforms of medically relevant proteins from human gDNA and oligos, and the de novo construction of a 10 kb, GC rich genomic region from the functionally extinct Northern White Rhinoceros created entirely in vitro.

molecular biology↗

bioRxiv2026

Distinct associative learning abilities for colour and odour in the flower-feeding Drosophila elegans and the fruit-feeding Drosophila melanogaster

Animal behaviour is both innately constrained and shaped by learning. This mosaic organization has evolved in response to species-specific ecological demands and may differ between sensory modalities. Flower-visiting animals are a particularly useful system for investigating the relationship between sensory ecology and learning because they rely on multiple floral cues, particularly odour and colour, to locate food sources. However, it remains largely unexplored whether specialization on floral resources entails divergence in learning abilities across sensory modalities. Drosophila elegans is a flower-feeding species that depends heavily on floral resources throughout its life; adults spend much of their time on flowers and larvae develop on fallen flower leaves. Here, we compared odour-reward and colour-reward associative learning between the flower-feeding D. elegans and the fruit-feeding D. melanogaster. We found that, under conditions of equilibrated motivation, odour- and colour-preference, and using the same sugar reward, D. elegans exhibited poorer odour-reward learning performance but better colour-reward learning performance than D. melanogaster. These results suggest that the modality-specific eligibility of sensory information to enter into associations, known as the 'Garcia-effect' in experimental psychology, can evolve oppositely between species. This highlights the relationship between ecological specialization and mnemonic processing, and shows that biological 'intelligence' is not general.

evolutionary biology↗

bioRxiv2026

Ferulic acid eicosyl ester enhances cognitive flexibility and modulates arousal-related neural circuits in mice

Cognitive deficits are a major contributor to disability in numerous neuropsychiatric and neurodegenerative disorders, yet effective pharmacological treatments remain limited. Ferulic acid eicosyl ester (FAE-20), a natural constituent of the plant Rhodiola rosea, has previously been identified as an enhancer of simple forms of Pavlovian conditioning in flies, bees, and mice. Here, we investigated whether FAE-20 has further potential to enhance cognitive flexibility, working memory, or spatial learning in mice, and explored potential neurobiological mechanisms underlying such enhancement. Cognitive flexibility was assessed using the attentional set-shifting task (ASST). Subchronic FAE-20 treatment significantly improved ASST performance in both male and female young adult mice, indicating enhanced cognitive flexibility. In contrast, no effects were observed on spatial working memory, assessed by spontaneous alternations in the Y-maze, or on spatial learning in the Barnes maze in either young or aged mice. Notably, FAE-20 enabled spatial learning in the Barnes maze in a subgroup of aged mice that failed to learn the task under vehicle treatment. Histological analyses using c-Fos immunohistochemistry as a marker of neural activity and doublecortin expression and spine density as markers of hippocampal plasticity revealed sex-specific effects on components of the ascending arousal system. FAE-20 increased the activation of orexinergic neurons in the lateral hypothalamus of male mice, whereas it reduced the activity of cholinergic neurons in the laterodorsal tegmental nucleus of females. No effects were detected on hippocampal neurogenesis or dendritic spine density. These findings suggest that the cognitive effects of FAE-20 are selective, depending on the cognitive demands of the task and the baseline cognitive abilities of the animals, and may be mediated, at least in part, by modulation of arousal-related neural circuits. HighlightsO_LIFAE-20 enhanced cognitive flexibility in young adult mice C_LIO_LIEffects of FAE-20 were strongest in demanding cognitive tasks C_LIO_LIAged poor learners benefited from FAE-20 treatment C_LIO_LIFAE-20 activated hypothalamic orexin neurons in male mice C_LIO_LIFAE-20 modulated ascending arousal systems in a sex-specific manner C_LI

neuroscience↗

bioRxiv2026

Starvation modulates associative short-term memory of Drosophila in a task-dependent manner

It is widely believed that starvation favours the processing of food-related cues, a notion here called the adaptive specificity hypothesis. Indeed, in Drosophila melanogaster starvation is required for appetitive odour-sugar but not for aversive odour-shock memory. Results from Gruber et al. (2013) and Meschi et al. (2024), however, suggest that starvation improves aversive short-term memory, too, challenging this hypothesis. We survey how starvation affects Drosophila associative olfactory short-term memory across 26 learning tasks. These tasks differ in the reinforcers and the amount of training, the life stage of the animals, in the predictive structure and associative timing of the task, in whether memory is expressed as an increase or decrease in odour preference, and in whether the learned behaviour is motivated by obtaining reward or avoiding/ escaping punishment. In adult flies, an improvement was observed for appetitive odour-sugar memories, whereas all tasks yielding aversive memory were unaffected. Strikingly, appetitive tasks that are not sugar-related, namely odour-shock extinction learning and punishment-relief associations, were either unaffected or even impaired, supporting the adaptive specificity hypothesis. In contrast, in 5-day-old larvae sugar-related appetitive associations were compromised, and the same was observed, to varying degrees, in larvae starved one day earlier and for aversive quinine associations, challenging the adaptive specificity hypothesis. Furthermore, we observed starvation-induced changes in locomotion and preference for a subset of the cues used in our study. Our results defy a simplistic interpretation in terms of the adaptive specificity hypothesis and call for case-by-case analyses of how starvation affects learning and behaviour.

neuroscience↗

bioRxiv2025

Avoidance engages dopaminergic punishment in Drosophila

It was classically suggested that behaviour can cause emotions (Darwin 1872). For example, smiling can make us feel happier, and in rodents the induced patterns of cardiac activity and breathing that are indicative of fear can in turn evoke it (Coles et al. 2022, Hsueh et al. 2023, Jhang et al. 2024). However, the adaptive significance of such feedback is unclear. We show that inducing backward movement, an element of avoidance behaviour in Drosophila, engages negative valence signals in these animals, and reveal the neuronal mechanisms and adaptive significance of this effect. We develop a paradigm with odours as conditioned stimuli paired with optogenetically induced backward movement instead of a punishing unconditioned stimulus, and combined these experiments with pharmacology, high-resolution video tracking, functional imaging, connectome analyses, and modelling. Our results show that backward movement engages dopaminergic punishment neurons and supports aversive memories. Such avoidance-to-punishment feedback counterbalances extinction learning and maintains learned avoidance, reducing the risk of further punishment. This can explain the long-standing "avoidance paradox", the observation that avoidance adaptively persists even when it is successful and no punishment is received (Bolles 1972). Our results provide a neurobiologically grounded argument for an integrated view of behaviour organization and valence processing.

neuroscience↗

bioRxiv2024

Compromising tyrosine hydroxylase function establishes a delusion-like temporal profile of reinforcement by dopamine neurons in Drosophila

For a proper representation of the causal structure of the world, one must consider both evidence for and evidence against causality. To take punishment as an example, the causality of a stimulus is reasonable if the stimulus precedes punishment, whereas causality can be ruled out if the punishment occurred first. This is reflected in the associative principle of timing-dependent valence reversal: aversive memories are formed when a stimulus occurs before the punishment, whereas memories of appetitive valence are observed when a stimulus is presented upon its relieving termination. We map the temporal profile of punishment induced by optogenetic activation of the PPL1-01 neuron in the fly Drosophila melanogaster, and find that impairment of tyrosine hydroxylase function, either acutely by pharmacological methods or by cell-specific RNAi, i) enhances learning with a time gap between stimulus and PPL1-01 punishment (trace conditioning), ii) impairs learning when the stimulus immediately precedes PPL1-01 punishment (delay conditioning), and iii) prevents learning about a stimulus presented after PPL1-01 punishment has ceased (relief conditioning). This implies a delusion-like state in which causality is attributed to cues that do not merit it (better trace conditioning), whereas both credible evidence for and credible evidence against causality is not properly appreciated (worse delay and relief conditioning). Under conditions of low dopamine, we furthermore observe a compensatory role for serotonin that is pronounced in trace conditioning, weaker in delay conditioning, and absent in relief conditioning. We discuss a disturbed dopamine-serotonin balance as an endophenotype for the positive and cognitive symptoms in schizophrenia.

animal behavior and cognition↗

bioRxiv2023

Cognitive limits of larval Drosophila: Testing for conditioned inhibition, sensory preconditioning and second-order conditioning

Drosophila larvae are an established model system for studying the mechanisms of innate and simple forms of learned behaviour. They have about 10 times fewer neurons than adult flies, and it was the low total number of their neurons that allowed for an electron microscopic reconstruction of their brain at synaptic resolution. Regarding the mushroom body, a central brain structure for associative learning in insects, it turned out that more than half of the classes of synaptic connection had previously escaped attention. Understanding the function of these circuit motifs, subsequently confirmed in adult flies, is an important current research topic. In this context, we test larval Drosophila for their cognitive abilities in three tasks that are characteristically more complex than those previously studied. Our data provide evidence for (i) conditioned inhibition, as has previously been reported for adult flies and honeybees. Unlike what is described for adult flies and honeybees, however, our data do not provide evidence for (ii) sensory preconditioning or (iii) second-order conditioning in Drosophila larvae. We discuss methodological features of our experiments as well as four specific aspects of the organisation of the larval brain that may explain why these two forms of learning are observed in honeybees and adult flies, but not in larval Drosophila.

animal behavior and cognition↗

bioRxiv2022

Prediction error drives associative olfactory learning and conditioned behavior in a spiking model of Drosophila larva

Predicting reinforcement from the presence of environmental clues is an essential component of guiding goal-directed behavior. In insect brains, the mushroom body is central to learning the necessary associations between sensory signals and reinforcement. We propose a biologically realistic spiking network model of the Drosophila larva olfactory pathway for the association of odors and reinforcement to bias behavior towards approach or avoidance. We demonstrate that prediction error coding through the integration of currently present and expected reinforcement in dopaminergic neurons can serve as a driving force in learning that can, combined with a synaptic homeostasis mechanism, account for experimentally observed features of acquisition and loss of associations in the larva that depend on the intensity of odor and reinforcement and temporal features of their pairing. To allow direct comparisons of our simulations with behavioral data [1], we model learning-induced plasticity over the complete time course of behavioral experiments and simulate the locomotion of individual larvae towards or away from odor sources in a virtual environment.

neuroscience↗

bioRxiv2022

Rewarding capacity of optogenetically activating a giant GABAergic central-brain interneuron in larval Drosophila

Larvae of the fruit fly Drosophila melanogaster are a powerful study case for understanding the neural circuits underlying behavior. Indeed, the numerical simplicity of the larval brain has permitted the reconstruction of its synaptic connectome, and genetic tools for manipulating single, identified neurons allow neural circuit function to be investigated with relative ease and precision. We focus on one of the most complex neurons in the brain of the larva (of either sex), the GABAergic anterior paired lateral neuron (APL). Using behavioral and connectomic analyses, optogenetics, Ca2+ imaging and pharmacology, we study how APL affects associative olfactory memory. We first provide a detailed account of the structure, regional polarity, connectivity, and metamorphic development of APL, and further confirm that optogenetic activation of APL has an inhibiting effect on its main targets, the mushroom body Kenyon cells. All these findings are consistent with the previously identified function of APL in the sparsening of sensory representations. To our surprise, however, we found that optogenetically activating APL can also have a strong rewarding effect. Specifically, APL activation together with odor presentation establishes an odor-specific, appetitive, associative short-term memory, whereas naive olfactory behavior remains unaffected. An acute, systemic inhibition of dopamine synthesis as well as an ablation of the dopaminergic pPAM neurons impair reward learning through APL activation. Our findings provide a study case of complex circuit function in a numerically simple brain, and suggest a previously unrecognized capacity of central-brain GABAergic neurons to engage in dopaminergic reinforcement. Significance statementThe single, identified giant anterior paired lateral (APL) neuron is one of the most complex neurons in the insect brain. It is GABAergic and contributes to the sparsening of neuronal activity in the mushroom body, the memory center of insects. We provide the most detailed account yet of the structure of APL in larval Drosophila as a neurogenetically accessible study case. We further reveal that, contrary to expectations, the experimental activation of APL can exert a rewarding effect, likely via dopaminergic reward pathways. The present study both provides an example of unexpected circuit complexity in a numerically simple brain, and reports an unexpected effect of activity in central-brain GABAergic circuits.

neuroscience↗

bioRxiv2022

High-resolution analysis of individual Drosophila melanogaster larvae within groups uncovers inter- and intra-individual variability in locomotion and its neurogenetic modulation

Neuronally orchestrated muscular movement and locomotion are defining faculties of multicellular animals. Due to its numerically simple brain and neuromuscular system and its genetic accessibility, the larva of the fruit fly Drosophila melanogaster is an established model to study these processes at tractable levels of complexity. However, although the faculty of locomotion clearly pertains to the individual animal, present studies of locomotion in larval Drosophila mostly use group assays and measurements aggregated across individual animals. The alternative is to measure animals one at a time, an extravagance for larger-scale analyses. In principle or in practice, this in particular rules out grasping the inter- and intra-individual variability in locomotion and its genetic and neuronal determinants. Here we present the IMBA (Individual Maggot Behaviour Analyser) for tracking and analysing the behaviour of individual larvae within groups. Using a combination of computational modelling and statistical approaches, the IMBA reliably resolves individual identity across collisions. It does not require specific hardware and can therefore be used in non-expert labs. We take advantage of the IMBA first to systematically describe the inter- and intra-individual variability in free, unconstrained locomotion in wild-type animals. We then report the discovery of a novel, complex locomotion phenotype of a mutant lacking an adhesion-type GPCR. The IMBA further allows us to determine, at the level of individual animals, the modulation of locomotion across repeated activations of dopamine neurons. Strikingly, IMBA can also be used to analyse silly walks, that is patterns of locomotion it was not originally designed to investigate. This is shown for the transient backward locomotion induced by brief optogenetic activation of the brain-descending mooncrawler neurons, and the variability in this behaviour. Thus, the IMBA is an easy-to-use toolbox allowing an unprecedentedly rich view of the behaviour and behavioural variability of individual Drosophila larvae, with utility in multiple biomedical research contexts.

neuroscience↗

bioRxiv2022

Age-related decrease in appetitive associative memory in fruit flies

Memory scores are dynamic across developmental stages. In particular, memory scores typically decrease from late adolescence into old age, reflecting complex changes in mnemonic and sensory-motor faculties, metabolic and motivational changes, and changes in cognitive strategy as well. In Drosophila melanogaster, such age-related decreases in memory scores have been studied intensely for the association of odours with electric shock punishment. We report that odour-sucrose reward memory scores likewise decrease as the flies age. This was observed after one-trial and after two-trial conditioning, and for both immediate testing and for recall tests one day later. This decrease was already particularly pronounced in relatively young animals, in the first 2-3 weeks after adult hatching, and was more pronounced in female than in male flies.

animal behavior and cognition↗

bioRxiv2022

Optogenetically induced reward and 'frustration' memory in larval Drosophila

Humans and animals alike form oppositely valenced memories for stimuli that predict the occurrence versus the termination of a reward: appetitive reward memory for stimuli associated with the occurrence of a reward and aversive frustration memory for stimuli that are associated with its termination. We characterize these memories in larval Drosophila using a combination of Pavlovian conditioning, optogenetic activation of the dopaminergic central-brain DAN-i1864 neuron, and high-resolution video-tracking. This reveals their dependency on the number of training trials and the duration of DAN-i1864 activation, their temporal stability, and the parameters of locomotion that are modulated during memory expression. Together with previous results on punishment versus relief learning by DAN-f1 neuron activation, this reveals a 2x2 matrix of timing-dependent memory valence for the occurrence/ termination of reward/ punishment. These findings should aid the understanding and modelling of how brains decipher the predictive, causal structure of events around a target reinforcing occurrence.

neuroscience↗

bioRxiv2021

Mammals adjust diel activity across gradients of urbanization

Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator-prey dynamics. Yet, changes in animal behavior within the shorter 24-hour light-dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify the diel behavior of eight mammal species across ten U.S. cities. We found high variability in diel activity patterns within and among species and species-specific correlations between diel activity and human population density, impervious land cover, available greenspace, vegetation cover, and mean daily temperature. We also found that some species may modulate temporal behaviors to manage both natural and anthropogenic risks. Our results highlight the complexity with which temporal activity patterns interact with local environmental characteristics, and suggest that urban mammals may use time along the 24-hour cycle to reduce risk, adapt, and therefore persist in human-dominated ecosystems.

ecology↗

bioRxiv2021

Rethinking habitat occupancy modeling and the role of diel activity in an anthropogenic world

Current methods to model species habitat use through space and diel time are limited. Development of such models is critical when considering rapidly changing habitats where species are forced to adapt to anthropogenic change, often by shifting their diel activity across space. We use an occupancy modeling framework to develop a new model, the multi-state diel occupancy model (MSDOM), which can evaluate species diel activity against continuous response variables which may impact diel activity within and across seasons or years. We used two case studies, fosa in Madagascar and coyote in Chicago, USA, to conceptualize the application of this model and to quantify the impacts of human activity on species spatial use in diel time. We found support that both species varied their habitat use by diel states--in and across years, and by human disturbance. Our results exemplify the importance of understanding animal diel activity patterns and how human disturbance can lead to temporal habitat loss. The MSDOM will allow more focused attention in ecology and evolution studies on the importance of the short temporal scale of diel time in animal-habitat relationships and lead to improved habitat conservation and management.

ecology↗

bioRxiv2021

A quick and versatile protocol for the 3D visualization of transgene expression across the whole body of larval Drosophila

Larval Drosophila are used as a genetically accessible study case in many areas of biological research. Here we report a fast, robust and user-friendly procedure for the whole-body multifluorescence imaging of Drosophila larvae; the protocol has been optimized specifically for larvae by systematically tackling the pitfalls associated with clearing this small but cuticularized organism. Tests on various fluorescent proteins reveal that the recently introduced monomeric infrared fluorescent protein (mIFP) is particularly suitable for our approach. This approach comprises an effective, low-cost clearing protocol with minimal handling time and reduced toxicity in the reagents employed. It combines a success rate high enough to allow for small-scale screening approaches and a resolution sufficient for cellular-resolution analyses with light sheet and confocal microscopy. Given that publications and database documentations typically specify expression patterns of transgenic driver lines only within a given organ system of interest, the present procedure should be versatile enough to extend such documentation systematically to the whole body. As examples, the expression patterns of transgenic driver lines covering the majority of neurons, or subsets of chemosensory, central brain or motor neurons, are documented in the context of whole larval body volumes (using nsyb-Gal4, IR76b-Gal4, APL-Gal4 and mushroom body Kenyon cells, or OK371-Gal4, respectively). Notably, the presented protocol allows for triple-color fluorescence imaging with near-infrared, red and yellow fluorescent proteins.

neuroscience↗

bioRxiv2020

Molecular basis for recognition of Listeria cell wall teichoic acid by the pseudo-symmetric SH3b-like repeats of a bacteriophage endolysin

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3 O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. The multidisciplinary approach described here delineates a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

biophysics↗

bioRxiv2019

Multilevel feedback architecture for adaptive regulation of learning in the insect brain

Modulatory (e.g. dopaminergic) neurons provide \"teaching signals\" that drive associative learning across the animal kingdom, but the circuits that regulate their activity and compute teaching signals are still poorly understood. We provide the first synaptic-resolution connectome of the circuitry upstream of all modulatory neurons in a brain center for associative learning, the mushroom body (MB) of the Drosophila larva. We discovered afferent pathways from sensory neurons, as well as an unexpected large population of 61 feedback neuron pairs that provide one- and two-step feedback from MB output neurons. The majority of these feedback pathways link distinct memory systems (e.g. aversive and appetitive). We functionally confirmed some of the structural pathways and found that some modulatory neurons compare inhibitory input from their own compartment and excitatory input from compartments of opposite valence, enabling them to compute integrated common-currency predicted values across aversive and appetitive memory systems. This architecture suggests that the MB functions as an interconnected ensemble during learning and that distinct types of previously formed memories can regulate future learning about a stimulus. We developed a model of the circuit constrained by the connectome and by the functional data which revealed that the newly discovered architectural motifs, namely the multilevel feedback architecture and the extensive cross-compartment connections, increase the computational performance and flexibility on learning tasks. Together our study provides the most detailed view to date of a recurrent brain circuit that computes teaching signals and provides insights into the architectural motifs that support reinforcement learning in a biological system.

neuroscience↗

bioRxiv2018

Accounting for location uncertainty in azimuthal telemetry data improves ecological inference

Characterizing animal space use is critical to understand ecological relationships. Despite many decades of using radio-telemetry to track animals and make spatial inference, there are few statistical options to handle these unique data and no synthetic framework for modeling animal location uncertainty and accounting for it in ecological models. We describe a novel azimuthal telemetry model (ATM) to account for azimuthal uncertainty with covariates and propagate location uncertainty into ecological models. We evaluate the ATM with commonly used estimators in several study design scenarios using simulation. We also provide illustra-tive empirical examples, demonstrating the impact of ignoring location uncertainty within home range and resource selection analyses. We found the ATM to have good performance and the only model that has appropriate measures of coverage. Ignoring animal location un-certainty when estimating resource selection or home ranges can have pernicious effects on ecological inference. We demonstrate that home range estimates can be overly confident and conservative when ignoring location uncertainty and resource selection coefficients can lead to incorrect inference and over confidence in the magnitude of selection. Our findings and model development have important implications for interpreting historical analyses using this type of data and the future design of radio-telemetry studies.

ecology↗