Learning and Memory: How memories are encoded in the brain of the fruit fly

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How memories are encoded by the brain is a fantastically complicated process. Professor André Fiala at the University of Göttingen in Germany has developed a highly specific transgenic model of the fruit fly to progress our understanding of learning and memory. By utilising fluorescent imaging while the flies undergo associative learning, Prof Fiala’s team investigates how odour memories are encoded in the insect brain. This research contributes to our understanding of how learned information is acquired and stored by brain circuits in general.

Strong smells have always had the power to evoke vivid memory recall. For some, the smell of vodka can bring a shudder-inducing memory of a night spent sleeping on the bathroom floor after one too many. For others, cinnamon can bring back childhood memories of Christmas baking. These strong associations are a form of learning and memory that is essential for our survival. They teach us which sensory stimuli have been good to us in the past, and which have not. In a rudimentary sense, this would have aided our survival as we would have learnt to avoid eating the sweet-smelling poisonous berries again.


The processing of odours in the brain occurs in much the same way as the processing of other sensory stimuli. The brain is mainly composed of specialised cells called neurons that communicate with each other via electrical pulses called action potentials. Action potentials cause the release of transmitter substances at terminals of neurons called synapses. The synaptic connections between neurons determine which neurons act together as neuronal circuits. Information about sensory stimuli like smell is transmitted in a hierarchical manner between circuits within different brain regions wherein the further up you go, the better the neurons and circuits are able to extract important information. For instance, in the human brain, odour information is detected by sensory neurons in the nose and transmitted to the olfactory bulb of the brain, and from there via mitral cells to higher brain regions such as the cerebral cortex.

Measuring activity in mushroom body cells allowed the researchers to elucidate the neuronal activity at the integration point of the conditioned and unconditioned stimulus.

Interestingly, there are very similar neuronal connections and circuits in the much smaller brains of insects. In Drosophila melanogaster, or the fruit fly, odour information is first passed from sensory neurons to olfactory projection neurons to so-called Kenyon cells in the mushroom bodies (higher-order structures of arthropod brains that integrate incoming sensory information with positive or negative experiences). The different brain regions in which these neurons are located act as stations for encoding different aspects of odours. One aspect is that odours can be learned as positive or negative, and that information can be stored as a memory. But how exactly do these circuits change if an odour is learned, e.g. as attractive or repulsive?

Mushroom bodies are visible in a Drosophila brain as two stalks.

Neurons that are part of a network will become activated in a specific pattern if a stimulus like an odour is perceived. This pattern will be modified if the odour has been learned as positive or negative, and this modified activity pattern represents a “memory trace”. It is believed that reactivation of the pattern that can occur in the future, e.g. through smelling of an odour that has previously been learned as positive or negative, informs the learner such that they react in an appropriate way. It is the plasticity of synapses that underlies the formation of such memories: during learning, physical changes at the implicated neuronal synapses occur, such that the activity patterns of neurons are changed to represent a memory trace that is accessible at a later date.

In humans, odour information is detected by sensory neurons in the nose and transmitted to the olfactory bulb of the brain. From there, the information travels to higher brain regions. Axel_Kock/Shutterstock.com

When flies were trained to learn an odour as repulsive, different synaptic boutons on the same Kenyon cells would change their concerted activity and desynchronise.

However, learning and memory are not quite so simple. It turns out that the myriads of neurons and synapses involved are hard to follow and visualise experimentally. Therefore, the fruit fly represents an excellent tool for investigating the principles of learning and memory. As an organism, their brains are complex enough to extract information meaningful to neuroscience, while at the same time representing a system that is simple enough to be experimentally measured. The fruit fly also has a manipulatable genome allowing complex experimental techniques to be developed. In this way, the fruit fly can be used to address this key issue in learning and memory research: how do the many synapses of a neuronal circuit change in the course of learning?

During learning, synapses of a neuronal circuit change to form a “memory trace”. Designua/Shutterstock.com

Using fruit flies as a model of learning and memory
Professor André Fiala and his colleagues at the University of Göttingen, Germany, have utilised the insect brain to enhance our knowledge of learning and memory. The group have taken advantage of the fruit fly to generate a highly specific genetically altered model. To put it simply, they have generated flies that express a green fluorescence calcium indicator in a few Kenyon cells of the mushroom body. This calcium indicator is valuable because calcium levels increase when neurons are active. Monitoring the indicator’s fluorescence using high-resolution microscopy (which is called calcium imaging) allows researchers to have a readout of neuronal activity that can be used to infer functional properties. This allowed Prof Fiala and his colleagues to open the heads of the tiny fruit flies and to monitor the activity of single Kenyon cell synaptic boutons in the brains of the living fruit flies in real time.

Mushroom bodies (yellow) in the brain of Drosophila melanogaster.

Synaptic boutons are small, specialised structures of some neurons that contain synapses. The cells within the mushroom body were targeted as this brain structure is well-characterised as the site of associative learning. Importantly, the synaptic boutons in the brains of living flies were fluorescently imaged while the flies were subjected to training called olfactory conditioning. The flies were presented with a particular odour (conditioned stimulus) and an electric shock as a negative signal (unconditioned stimulus). Typically, the flies learn to avoid this odour in the future. The group wanted to understand how these cells and synaptic boutons are differentially responsive, and how their responses are modified to form memory traces.

The results
The research team was able to demonstrate that when odours are presented to the flies, different synaptic boutons on the same Kenyon cells would respond. This was shown by light emission of the green, fluorescent calcium indicator from the synaptic boutons. But pairing of the odour with a negative experience resulted in a complex alteration of calcium signalling at the boutons. They changed their concerted, coherent pattern of activity and became more desynchronised in their activity, rendering the “code” for the perceived odour unique, and more distinct from the code for other odours that have not been learned. This may be how different odour association memories are encoded as relevant. These results are significant as they indicate that the concerted and orchestrated actions of numerous, widely distributed synapses of many neurons contribute to the formation of memories. In the future, these experiments can be progressed further to investigate the precise molecular processes underlying memory trace formation.

Do you believe that individualisation of synapses underlies memory formation in other brain regions of other animals implicated in memory, such as the hippocampus of mammals?

Our work provides a novel concept, which can be tested by other researchers also in other animals. It will be interesting to see whether the principle of changing the coherence between synapses during learning holds true for other brains and neuronal circuits as well, including those of mammals.


  • Bilz, F., Geurten, B.R.H., Hancock, C.E., Widmann, A., and Fiala, A. (2020). Visualisation of a distributed synaptic memory code in the Drosophila brain. Neuron, 106, 1–14.
  • Mohamed, A.A.A. and Sachse, S. (2020). Everyone on their own! Individualisation of synaptic boutons. Neuron Reviews, 106, 875–878.
  • Hancock, C.E., Bilz, F., and Fiala, A. (2019). In Vivo optical calcium imaging of a learning-induced synaptic plasticity in Drosophila melanogaster. Journal of Visualised Experiments, 152, e60288. Available at: https://www.doi.org/10.3791/60288
  • Pech, U., Revelo, N.H., Rizzoli, S.O., and Fiala, A. (2015). Optical dissection of experience-dependent pre and postsynaptic plasticity in the Drosophila brain. Cell Reports, 10, 2083–95. Available at: https://doi.org/10.1016/j.celrep.2015.02.065
  • Barth, J., Dipt, S., Pech, U., Hermann, M., Riemensperger, T., and Fiala, A. (2014). Differential Associative Training Enhances Olfactory Acuity in Drosophila melanogaster. The Journal of Neuroscience, 34, 1819–1837. Available at: https://doi.org/10.1523/JNEUROSCI.2598-13.2014

Research Objectives
Prof Fiala studies the learning behaviour of fruit flies, aiming to dig deeper into the computational principles underlying the encoding of learned information.


  • German Research Foundation (DFG)


  • Martin P. Nawrot
  • Bertram Gerber
  • Oren Schuldiner
  • Gaia Tavosanis
  • Ilona Grunwald Kadow
  • Stephan J. Sigrist
  • David Owald

After graduating from the Free University of Berlin with a Diploma in Biology in 1996, Dr André Fiala achieved his doctoral degree in 1999 for work on molecular mechanisms underlying learning and memory in honeybees. Dr Fiala worked as a post-doc at the Memorial Sloan-Kettering Institute in New York and at the University of Würzburg until 2008, when the University of Göttingen hired him as professor.

André Fiala
University of Göttingen
Schwann-Schleiden Research Center
Julia-Lermontowa-Weg 3
37077 Göttingen

E: afiala@gwdg.de
T: +49 551 39 177920
W: https://www.uni-goettingen.de/en/94792.html
W: https://twitter.com/FialaLab

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