A Single-Cell Level and Connectome-Derived Computational Model of the Drosophila Brain

Computer simulations play an important role in testing hypotheses, integrating knowledge, and providing predictions of neural circuit functions. While considerable effort has been dedicated into simulating primate or rodent brains, the fruit fly (Drosophila melanogaster) is becoming a promising model animal in computational neuroscience for its small brain size, complex cognitive behavior, and abundancy of data available from genes to circuits. Moreover, several Drosophila connectome projects have generated a large number of neuronal images that account for a significant portion of the brain, making a systematic investigation of the whole brain circuit possible. Supported by FlyCircuit (http://www.flycircuit.tw), one of the largest Drosophila neuron image databases, we began a long-term project with the goal to construct a whole-brain spiking network model of the Drosophila brain. In this paper, we report the outcome of the first phase of the project. We developed the Flysim platform, which (1) identifies the polarity of each neuron arbor, (2) predicts connections between neurons, (3) translates morphology data from the database into physiology parameters for computational modeling, (4) reconstructs a brain-wide network model, which consists of 20,089 neurons and 1,044,020 synapses, and (5) performs computer simulations of the resting state. We compared the reconstructed brain network with a randomized brain network by shuffling the connections of each neuron. We found that the reconstructed brain can be easily stabilized by implementing synaptic short-term depression, while the randomized one exhibited seizure-like firing activity under the same treatment. Furthermore, the reconstructed Drosophila brain was structurally and dynamically more diverse than the randomized one and exhibited both Poisson-like and patterned firing activities. Despite being at its early stage of development, this single-cell level brain model allows us to study some of the fundamental properties of neural networks including network balance, critical behavior, long-term stability, and plasticity

Circuit analysis of the <i>Drosophila</i> brain using connectivity-based neuronal classification reveals organization of key communication pathways

AbstractWe present a functionally relevant, quantitative characterization of the neural circuitry of Drosophila melanogaster at the mesoscopic level of neuron types as classified exclusively based on potential network connectivity. Starting from a large neuron-to-neuron brain-wide connectome of the fruit fly, we use stochastic block modeling and spectral graph clustering to group neurons together into a common “cell class” if they connect to neurons of other classes according to the same probability distributions. We then characterize the connectivity-based cell classes with standard neuronal biomarkers, including neurotransmitters, developmental birthtimes, morphological features, spatial embedding, and functional anatomy. Mutual information indicates that connectivity-based classification reveals aspects of neurons that are not adequately captured by traditional classification schemes. Next, using graph theoretic and random walk analyses to identify neuron classes as hubs, sources, or destinations, we detect pathways and patterns of directional connectivity that potentially underpin specific functional interactions in the Drosophila brain. We uncover a core of highly interconnected dopaminergic cell classes functioning as the backbone communication pathway for multisensory integration. Additional predicted pathways pertain to the facilitation of circadian rhythmic activity, spatial orientation, fight-or-flight response, and olfactory learning. Our analysis provides experimentally testable hypotheses critically deconstructing complex brain function from organized connectomic architecture

Teasing apart the interaction between HDAC4 and Ankyrin2 in Drosophila neuronal function : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry, School of Fundamental Sciences, Massey University, Manawatu, New Zealand

Histone deacetylase 4 (HDAC4) is a class IIa histone deacetylase that has previously been implicated in a range of neurodevelopmental and neurodegenerative diseases which involve deficits in memory and cognition. Overexpression of HDAC4 in the Drosophila brain impairs memory, therefore making Drosophila an ideal genetic model system to further investigate the molecular pathways through which HDAC4 acts. A recent genetic screen in Drosophila for genes that interact in the same molecular pathway as HDAC4 identified the cytoskeletal regulator Ankyrin2 (Ank2). The Ank2 protein plays a pivotal role in maintaining the stability and plasticity of the spectrin-actin cytoskeleton by organising the distribution of ion channels and cell adhesion molecules, which is essential to normal learning and memory formation. Both overexpression of HDAC4 and knockdown of Ank2 result in similar deficits in Drosophila brain development and long-term memory formation, suggesting that these two proteins may interact together in such processes. HDAC4 contains an N-terminal ankyrin repeat binding motif and it was hypothesised that HDAC4 interacts physically with the ankyrin repeat region at the N-terminus of Ank2, however, no physical interaction was detected via co-immunoprecipitation. Further investigation was then carried out to elucidate the nature of the genetic interaction proposed between HDAC4 and Ank2. In doing so, it was observed that nuclear accumulation of HDAC4 is required for this interaction, however, the presence of the HDAC4 ankyrin repeat binding motif is not required. This is consistent with the finding that HDAC4 does not bind Ank2 and indicates that the interaction between HDAC4 and Ank2 is indirect. It was also identified that Ank2 and HDAC4 are both required for Drosophila eye development as knockdown of Ank2 paired with overexpression of HDAC4 resulted in a severe novel "blueberry" phenotype that has not yet been characterised for these genes. Furthermore, it was observed that Ank2 was required for normal growth and morphogenesis of dendrites in the visual system, whereby both knockdown of Ank2 and overexpression of HDAC4 disrupt dendrite morphogenesis. These data provide further understanding of the roles of HDAC4 and Ank2 in Drosophila neuronal function, and the establishment of the molecular pathway in which HDAC4 and Ank2 act will be essential in unravelling additional mechanisms involved in the processes of learning and memory

A single-cell level and connectome-derived computational model of the drosophila brain

[[abstract]]Computer simulations play an important role in testing hypotheses, integrating knowledge, and providing predictions of neural circuit functions. While considerable effort has been dedicated into simulating primate or rodent brains, the fruit fly (Drosophila melanogaster) is becoming a promising model animal in computational neuroscience for its small brain size, complex cognitive behavior, and abundancy of data available from genes to circuits. Moreover, several Drosophila connectome projects have generated a large number of neuronal images that account for a significant portion of the brain, making a systematic investigation of the whole brain circuit possible. Supported by FlyCircuit (http://www.flycircuit.tw), one of the largest Drosophila neuron image databases, we began a long-term project with the goal to construct a whole-brain spiking network model of the Drosophila brain. In this paper, we report the outcome of the first phase of the project. We developed the Flysim platform, which (1) identifies the polarity of each neuron arbor, (2) predicts connections between neurons, (3) translates morphology data from the database into physiology parameters for computational modeling, (4) reconstructs a brain-wide network model, which consists of 20,089 neurons and 1,044,020 synapses, and (5) performs computer simulations of the resting state. We compared the reconstructed brain network with a randomized brain network by shuffling the connections of each neuron. We found that the reconstructed brain can be easily stabilized by implementing synaptic short-term depression, while the randomized one exhibited seizure-like firing activity under the same treatment. Furthermore, the reconstructed Drosophila brain was structurally and dynamically more diverse than the randomized one and exhibited both Poisson-like and patterned firing activities. Despite being at its early stage of development, this single-cell level brain model allows us to study some of the fundamental properties of neural networks including network balance, critical behavior, long-term stability, and plasticity

Investigating the expression of Topoisomerase II Beta in aged neurons: development of a Murine Cell Line and Drosophila model

The enzyme Topoisomerase II Beta (Top2B) has previously been shown to be a crucial component of neuronal differentiation and development in mammals. It is also expressed in adult neuronal tissue where it plays important roles in facilitating transcription of long genes and early response genes and may also be involved in DNA repair. To date, studies investigating age-related changes in Top2B expression in neuronal tissue are limited and the importance of Top2B in the maintenance of neuronal function and integrity during ageing has not yet been fully elucidated, thus this study aimed to further investigate Top2B during the ageing process. The development of an in vitro murine model of neuronal ageing was successfully achieved using the Cath.a-differentiated (CAD) cell line. A neuronal-like phenotype in CAD cells was achieved through serum starvation and cells were then chronologically aged. Levels of Top2B mRNA and protein were seen to decline significantly during ageing of the cells in RT-qPCR and western blotting experiments, respectively. Concomitant increases in protein levels of the tumour suppressor gene p21 were also observed as well as a significant accumulation of double strand breaks as shown by γH2AX assays. In addition, preliminary in vivo experiments also revealed age-related declines of Top2B in mouse hippocampus. The development of an equivalent human in vitro model using the human neuroblastoma cell line SH-SY5Y was unsuccessful. Further in vivo experiments using Drosophila brain tissue also revealed significant age-related declines in Topoisomerase II (Top2) protein levels with ageing in both males and females, which was accompanied by a decline in locomotor function and increases in advanced glycation end-products (AGEs) in females. Interestingly, in Drosophila this was not accompanied by a reduction in Top2 mRNA levels. Reduction in the levels of mouse Top2B and Drosophila Top2 with age may have profound effects on transcription and the ability of cells to repair DNA damage and may result in increased vulnerability to oxidative stress, ultimately having detrimental effects on longevity and normal ageing. Thus, these models offer an opportunity to further elucidate the functional effect of this loss, its causes and potential pharmaceutical interventions to reverse these effects. Importantly, they also illustrate the need for such research to be carried out in human neuronal cells and brain tissues