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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 217 records · Page 12Linked to original sources

bioRxiv2021

Petascale neural circuit reconstruction: automated methods

3D electron microscopy (EM) has been successful at mapping invertebrate nervous systems, but the approach has been limited to small chunks of mammalian brains. To scale up to larger volumes, we have built a computational pipeline for processing petascale image datasets acquired by serial section EM, a popular form of 3D EM. The pipeline employs convolutional nets to compute the nonsmooth transformations required to align images of serial sections containing numerous cracks and folds, detect neuronal boundaries, label voxels as axon, dendrite, soma, and other semantic categories, and detect synapses and assign them to presynaptic and postsynaptic segments. The output of neuronal boundary detection is segmented by mean affinity agglomeration with semantic and size constraints. Pipeline operations are implemented by leveraging distributed and cloud computing. Intermediate results of the pipeline are held in cloud storage, and can be effortlessly viewed as images, which aids debugging. We applied the pipeline to create an automated reconstruction of an EM image volume spanning four visual cortical areas of a mouse brain. Code for the pipeline is publicly available, as is the reconstructed volume.

neuroscience↗

bioRxiv2021

Strip1 regulates retinal ganglion cell survival by suppressing Jun-mediated apoptosis to promote retinal neural circuit formation

In the vertebrate retina, an interplay between retinal ganglion cells (RGCs), amacrine, and bipolar cells establishes a synaptic layer called the inner plexiform layer (IPL). This circuit conveys signals from photoreceptors to visual centers in the brain. However, the molecular mechanisms involved in its development remain poorly understood. Striatin-interacting protein 1 (Strip1) is a core component of the STRIPAK complex, and it has shown emerging roles in embryonic morphogenesis. Here, we uncover the importance of Strip1 in inner retina development. Using zebrafish, we show that loss of Strip1 causes defects in IPL formation. In strip1 mutants, RGCs undergo dramatic cell death shortly after birth. Amacrine and bipolar cells subsequently invade the degenerating RGC layer, leading to a disorganized IPL. Mechanistically, zebrafish Strip1 interacts with its STRIPAK partner, Striatin3, and both show overlapping functions in RGC survival. Furthermore, loss of Strip1 or Striatin 3, leads to activation of the pro-apoptotic marker, Jun, within RGCs, and Jun knockdown rescues RGC survival in strip1 mutants. In addition to its function in RGC maintenance, Strip1 is required for RGC dendritic patterning, which likely contributes to proper IPL formation. Taken together, we propose that a series of Strip1-mediated regulatory events coordinates inner retinal circuit formation by maintaining RGCs during development, which ensures proper positioning and neurite patterning of inner retinal neurons.

developmental biology↗

bioRxiv2022

Signal denoising through topographic modularity of neural circuits

Information from the sensory periphery is conveyed to the cortex via structured projection pathways that spatially segregate stimulus features, providing a robust and efficient encoding strategy. Beyond sensory encoding, this prominent anatomical feature extends throughout the neocortex. However, the extent to which it influences cortical processing is unclear. In this study, we combine cortical circuit modeling with network theory to demonstrate that the sharpness of topographic projections acts as a bifurcation parameter, controlling the macroscopic dynamics and representational precision across a modular network. By shifting the balance of excitation and inhibition, topographic modularity gradually increases task performance and improves the signal-to-noise ratio across the system. We demonstrate that in biologically constrained networks, such a denoising behavior is contingent on recurrent inhibition. We show that this is a robust and generic structural feature that enables a broad range of behaviorally-relevant operating regimes, and provide an in-depth theoretical analysis unravelling the dynamical principles underlying the mechanism.

neuroscience↗

bioRxiv2022

Neuronal membrane proteasomes homeostatically regulate neural circuit activity in vivo and are required for learning-induced behavioral plasticity

Protein degradation is critical for brain function through processes that remain poorly understood. Here we investigated the in vivo function of a recently reported neuronal membrane-associated proteasome (NMP) in the brain of Xenopus laevis tadpoles. We demonstrated that NMPs are present in the tadpole brain with biochemistry and electron microscopy, and showed that they actively degrade neuronal activity-induced nascent proteins. Using in vivo calcium imaging in the optic tectum, we showed that acute inhibition of NMP function rapidly increased spontaneous neuronal activity, resulting in hyper-synchronization among tectal neurons. At the circuit level, inhibiting NMPs abolished learning-dependent improvement in a visuomotor behavior paradigm in live animals. Our data provide the first in vivo characterization of NMP functions in the vertebrate nervous system and suggest that NMP-mediated degradation of activity-induced nascent proteins may serve as a homeostatic modulatory mechanism in neurons that is critical for regulating neuronal activity and experience-dependent circuit plasticity.

neuroscience↗

bioRxiv2022

Ghrelin receptor signaling contributes to fasting-induced suppression of conditioned avoidance behavior and neural circuit activation in male rats

Interoceptive feedback to the brain regarding the bodys physiological state plays an important role in guiding motivated behaviors. For example, a state of negative energy balance tends to increase exploratory/food-seeking behaviors while reducing avoidance behaviors. We recently reported that overnight food deprivation reduces conditioned passive avoidance behavior in male (but not female) rats. Since fasting increases circulating levels of ghrelin, we hypothesized that ghrelin signaling contributes to the ability of fasting to reduce conditioned avoidance. To test this, ad libitum-fed male rats were trained in a passive avoidance procedure using mild footshock. Later, following overnight food deprivation, the same rats were pretreated with ghrelin receptor antagonist (GRA) or saline vehicle 30 min before avoidance testing. GRA restored passive avoidance in fasted rats as measured both by latency to enter and time spent in the shock-paired context. In addition, compared to vehicle-injected fasted rats, fasted rats that received GRA before re-exposure to the shock-paired context displayed more activation of prolactin-releasing peptide (PrRP)-positive noradrenergic neurons in the caudal nucleus of the solitary tract, accompanied by more activation of downstream neurons in the bed nucleus of the stria terminalis and paraventricular nucleus of the hypothalamus. These results support the view that ghrelin signaling contributes to the inhibitory effect of fasting on learned passive avoidance behavior, perhaps by suppressing recruitment of PrRP-positive noradrenergic neurons and their downstream hypothalamic and limbic forebrain targets.

neuroscience↗

bioRxiv2022

A critical developmental interval of coupling axon branching to synaptic degradation during neural circuit formation

The emergence of neuronal wiring specificity requires stabilization of dynamic axonal branches at sites of selective synapse formation. Models that explain how axonal branching is coupled to synaptogenesis postulate molecular regulators acting in a spatiotemporally restricted fashion. We report that Epidermal Growth Factor Receptor (EGFR) activity is required in presynaptic axonal branches during two distinct temporal intervals to regulate circuit wiring in the developing Drosophila visual system. EGFR is required early to regulate primary axonal branching and independently again later to prevent autophagic degradation of the synaptic active zone protein Bruchpilot (Brp). The protection of synaptic material during this later interval of wiring ensures the stabilization of terminal branches, circuit connectivity and appropriate visual behavior. Phenotypes of EGFR inactivation were rescued by increasing Brp levels or downregulating autophagic genes. We identify a temporally restricted molecular mechanism required for coupling axonal branching and synaptic stabilization that contributes to the emergence of neuronal wiring specificity.

neuroscience↗

bioRxiv2022

Boosting of neural circuit chaos at the onset of collective oscillations

Neuronal spiking activity in cortical circuits is often temporally structured by collective rhythms. Rhythmic activity has been hypothesized to regulate temporal coding and to mediate the flexible routing of information flow across the cortex. Spiking neuronal circuits, however, are non-linear systems that, through chaotic dynamics, can amplify insignificant microscopic fluctuations into network-scale response variability. In nonlinear systems in general, rhythmic oscillatory drive can induce chaotic behavior or boost the intensity of chaos. Thus, neuronal oscillations could rather disrupt than facilitate cortical coding functions by flooding the finite population bandwidth with chaotically-boosted noise. Here we tackle a fundamental mathematical challenge to characterize the dynamics on the attractor of effectively delayed network models. We find that delays introduce a transition to collective oscillations, below which ergodic theory measures have a stereotypical dependence on the delay so far only described in scalar systems and low-dimensional maps. We demonstrate that the emergence of internally generated oscillations induces a complete dynamical reconfiguration, by increasing the dimensionality of the chaotic attractor, the speed at which nearby trajectories separate from one another, and the rate at which the network produces entropy. We find that periodic input drive leads to a dramatic increase of chaotic measures at a the resonance frequency of the recurrent network. However, transient oscillatory input only has a moderate role on the collective dynamics. Our results suggest that simple temporal dynamics of the mean activity can have a profound effect on the structure of the spiking patterns and therefore on the information processing capability of neuronal networks.

neuroscience↗

bioRxiv2022

Neural circuit mechanisms for transforming learned olfactory valences into wind-oriented movement

How memories are used by the brain to guide future action is poorly understood. In olfactory associative learning in Drosophila, multiple compartments of the mushroom body act in parallel to assign valence to a stimulus. Here, we show that appetitive memories stored in different compartments induce different levels of upwind locomotion. Using a photoactivation screen of a new collection of split-GAL4 drivers and EM connectomics, we identified a cluster of neurons postsynaptic to the mushroom body output neurons (MBONs) that can trigger robust upwind steering. These UpWind Neurons (UpWiNs) integrate inhibitory and excitatory synaptic inputs from MBONs of appetitive and aversive memory compartments, respectively. After training, disinhibition from the appetitive-memory MBONs enhances the response of UpWiNs to reward-predicting odors. Blocking UpWiNs impaired appetitive memory and reduced upwind locomotion during retrieval. Photoactivation of UpWiNs also increased the chance of returning to a location where activation was initiated, suggesting an additional role in olfactory navigation. Thus, our results provide insight into how learned abstract valences are gradually transformed into concrete memory-driven actions through divergent and convergent networks, a neuronal architecture that is commonly found in the vertebrate and invertebrate brains.

neuroscience↗

bioRxiv2023

A Prefrontal Neural Circuit for Maternal Behavioural Leaning in Mice

Maternal behaviors, which are crucial for the survival of mammalian infants, require the coordinated operation of multiple brain regions to process infant cues, make decisions, and execute motor plans. Although these processes likely demand higher cognitive functions, the prefrontal areas that regulate limbic parental programs remains poorly understood. Here, we show that the orbitofrontal cortex (OFC) excitatory projection neurons promote alloparental caregiving behaviors in female mice. By chronic microendoscopy, we observed robust yet adaptable representations of pup-directed anticipatory and motor-related activities within the OFC. Some of these plastic responses were significantly overlapped with those related to nonsocial reward signals. The inactivation of OFC output reduced the phasic activities of midbrain dopamine (DA) neurons specifically tied to pup retrieval and impaired the modulation of DA release to the ventral striatum during the acquisition of alloparental behaviors. These findings suggest that the OFC transiently boosts DA activity during the acquisition phase, thereby facilitating the manifestation of alloparental behaviors.

neuroscience↗

bioRxiv2023

A bistable inhibitory OptoGPCR for multiplexed optogenetic control of neural circuits

Information is transmitted between brain regions through the release of neurotransmitters from long-range projecting axons. Understanding how the activity of such long-range connections contributes to behavior requires efficient methods for reversibly manipulating their function. Chemogenetic and optogenetic tools, acting through endogenous G-protein coupled receptor (GPCRs) pathways, can be used to modulate synaptic transmission, but existing tools are limited in sensitivity, spatiotemporal precision, or spectral multiplexing capabilities. Here we systematically evaluated multiple bistable opsins for optogenetic applications and found that the Platynereis dumerilii ciliary opsin (PdCO) is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precision in-vivo. PdCO has superior biophysical properties that enable spectral multiplexing with other optogenetic actuators and reporters. We demonstrate that PdCO can be used to conduct reversible loss-of-function experiments in long-range projections of behaving animals, thereby enabling detailed synapse-specific functional circuit mapping.

neuroscience↗

bioRxiv2023

Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior

Programmed cell death (PCD) is a common feature of animal development. During development of the C. elegans hermaphrodite, programmed cell death eliminates 131 cells in stereotyped positions in the cell lineage, mostly in neuronal lineages. Blocking cell death results in supernumerary "undead" neurons. We find that undead neurons can be wired into circuits, can display activity, and can modify specific behaviors. The two undead RIM-like neurons participate in the RIM-containing circuit that computes movement. The presence of these two extra neurons results in animals that initiate fewer reversals and lengthens the duration of those reversals that do occur. We describe additional behavioral alterations of cell-death mutants, including in locomotory turning angle and pharyngeal pumping. These findings indicate that physiological or evolutionary variations in PCD might reveal latent neuronal elements that the nervous system can incorporate to modify nervous system function and animal behavior.

neuroscience↗

bioRxiv2023

Employing a honeybee olfactory neural circuit as a novel gas sensor for the detection of human lung cancer biomarkers

Human breath contains biomarkers (odorants) that can be targeted for early disease detection. It is well known that honeybees have a keen sense of smell and can detect a wide variety of odors at low concentrations. Here, for the first time, we employ honeybee olfactory neuronal circuitry to classify human lung cancer volatile biomarkers and their mixtures at concentration ranges relevant to human breath, parts-per-billion to parts-per-trillion. Different lung cancer biomarkers evoked distinct spiking response dynamics in the honeybee antennal lobe neurons indicating that those neurons encoded biomarker-specific information. By investigating lung cancer biomarker-evoked population neuronal responses from the honeybee antennal lobe, we could classify individual human lung cancer biomarkers successfully (88% success rate). When we mixed six lung cancer biomarkers at different concentrations to create synthetic lung cancer vs. synthetic healthy breath, honeybee population neuronal responses were also able to classify those complex breath mixtures successfully (100% success rate with a leave-one-trial-out method). Finally, we used separate training and testing datasets containing responses to the synthetic lung cancer and healthy breath mixtures. We identified a simple metric, the peak response of the neuronal ensemble, with the ability to distinguish synthetic lung cancer breath from the healthy breath with 86.7% success rate. This study provides proof-of-concept results that a powerful biological gas sensor, the honeybee olfactory system, can be used to detect human lung cancer biomarkers and their complex mixtures at biological concentrations.

bioengineering↗

bioRxiv2023

Molecular Connectomics Reveals a Glucagon-Like Peptide 1 Sensitive Neural Circuit for Satiety

Liraglutide and other agonists of the glucagon-like peptide 1 receptor (GLP-1RAs) are effective weight loss drugs, but how they suppress appetite remains unclear. One potential mechanism is by activating neurons which inhibit hunger-promoting Agouti-related peptide (AgRP) neurons of the arcuate hypothalamus (Arc). To identify these afferents, we developed a method combining rabies-based connectomics with single-nuclei transcriptomics. Applying this method to AgRP neurons predicted at least 21 afferent subtypes in the mouse mediobasal and paraventricular hypothalamus. Among these are Trh+ Arc neurons (TrhArc), inhibitory neurons which express the Glp1r gene and are activated by the GLP-1RA liraglutide. Activating TrhArc neurons inhibits AgRP neurons and feeding in an AgRP neuron-dependent manner. Silencing TrhArc neurons causes over-eating and weight gain and attenuates liraglutides effect on body weight. Our results demonstrate a widely applicable method for molecular connectomics, comprehensively identify local inputs to AgRP neurons, and reveal a circuit through which GLP-1RAs suppress appetite.

neuroscience↗

bioRxiv2023

A Photoactivatable Norepinephrine for Probing Adrenergic Neural Circuits

Norepinephrine (NE) is a critical neuromodulator that mediates a wide range of behavior and neurophysiology, including attention, arousal, plasticity, and memory consolidation. A major source of NE is the brainstem nucleus the locus coeruleus (LC), which sends widespread projections throughout the central nervous system (CNS). Efforts to dissect this complex noradrenergic circuitry have driven the development of many tools that detect endogenous NE or modulate widespread NE release via LC activation and inhibition. While these tools have enabled research that elucidates physiological roles of NE, additional tools to probe these circuits with a higher degree of spatial precision could enable a finer delineation of function. Here, we describe the synthesis and chemical properties of a photo-activatable NE, [Ru(bpy)2(PMe3)(NE)]PF6 (RuBi-NE). We validate the one-photon (1P) release of NE using whole-cell patch clamp electrophysiology in acute mouse brain slices containing the LC. We show that a 10 ms pulse of blue light, in the presence of RuBi-NE, briefly modulates the firing rate of LC neurons via -2 adrenergic receptors. The development of a photo-activatable NE that can be released with light in the visible spectrum provides a new tool for fine-grained mapping of complex noradrenergic circuits, as well as the ability to probe how NE acts on non-neuronal cells in the CNS.

neuroscience↗

bioRxiv2024

Neural Circuit Revision in Retinal Remodeling, A Pathoconnectomics Approach

Retinitis pigmentosa (RP), a retinal degenerative disease, is characterized by progressive photoreceptor loss and ongoing remodeling and rewiring of the inner retina. This study investigates rod network rewiring through pathoconnectomic evaluation and its impacts on signaling patterns. The glycinergic Aii amacrine cell (Aii) plays a central role in the healthy retina bridging rod and cone pathways, enabling an increased dynamic range of vision. Pathoconnectomics reveals altered connectivity in both the excitatory drive and gap junctional coupling of Aiis in retinal degeneration. A computational model of the rewired network was developed to assess the functional consequences of these structural changes by simulating light-evoked responses and changes in excitatory postsynaptic potentials (EPSPs). The model predicts significant changes in bipolar and Aii EPSPs between active and baseline conditions, driven by newly formed gap junctions in the degenerate retina. Notably, the aberrant circuitry induces rhythmic firing of up to 10 Hz in retinal ganglion cells, consistent with network depolarization relative to the healthy baseline state. These findings align with patch-clamp observations in rd1 and rd10 mouse models of RP, suggesting that Aii-mediated network alterations may underlie early clinical symptoms, including impaired adaptation between photopic and scotopic vision. More broadly, this work demonstrates that integrating computational modeling with pathoconnectomics enables predictive analysis of signaling in early-stage retinal degeneration and may help identify windows for therapeutic intervention. Such models could be further extended with multi-scale bioelectromagnetic simulations to optimize neurostimulation strategies aimed at slowing disease progression. Author summaryUnderstanding how retinal degeneration alters wiring topologies of the inner retina is important for the success of multiple therapeutic interventions, including cell replacement strategies, optogenetics, and electrode implants. Here, we continue our evaluation of retinal pathoconnectome 1 (RPC1), describing additional network-level changes occurring early in retinal degeneration. This analysis extends our previous findings on the emergence of gap junctions in rod bipolar cells in retinal degeneration to include the effects of these changes on the synaptic strength of inputs to the Aii. We then model how these network changes overall effect retinal processing through the creation of a more complete degenerate retina model. From these results we propose the emergence of aberrant gap junctions in the rod pathway as the network cause of atypical retinal ganglion cell firing and provide the field with a realistic network model for evaluating and optimizing therapeutic strategies.

neuroscience↗

bioRxiv2024

Neural circuit basis of adolescent THC-induced potentiation of opioid responses in adult mice

Use of one drug of abuse typically influences the behavioral response to other drugs, either administered at the same time or a subsequent time point. The nature of the drugs being used, as well as the timing and dosing, also influence how these drugs interact. Here, we tested the effects of adolescent THC exposure on the development of morphine-induced behavioral adaptations following repeated morphine exposure during adulthood. We found that adolescent THC administration potentiated reward, and paradoxically impaired the development of morphine reward. Following a forced abstinence period, we then mapped the whole-brain response to a moderate dose of morphine, and found that adolescent THC administration led to increased morphine-induced activity in the basal ganglia and increased functional connectivity between frontal cortical regions and the ventral tegmental area. Last, we show using rabies virus-based circuit mapping that adolescent THC exposure triggers a long-lasting elevation in connectivity from the frontal cortex regions onto ventral tegmental dopamine cells. Our study adds to the rich literature on the interaction between drugs of abuse, including THC and opioids, and provides potential circuit substates by which adolescent THC exposure influences responses to morphine later in life.

neuroscience↗

bioRxiv2025

Audiovisual gamma stimulation enhances hippocampal neurogenesis and neural circuit plasticity in aging mice

Gamma oscillations are disrupted in various neurological disorders, including Alzheimers disease (AD). In AD mouse models, non-invasive audiovisual stimulation (AuViS) at 40 Hz enhances gamma oscillations, clears amyloid-beta, and improves cognition. We investigated mechanisms of circuit remodeling underlying these restorative effects by leveraging the sensitivity of hippocampal neurogenesis to activity in middle-aged wild-type mice. AuViS increased progenitor cell proliferation, neuronal differentiation and morphological maturation of newborn granule cells, promoting their synaptic integration. While visual or auditory stimuli alone induced dendritic growth, axonal changes required combined audiovisual stimulation. The actions of AuViS involved neurotrophin pathways, as shown by the lack of effect upon TrkB signaling blockade. These results reveal widespread plasticity mechanisms triggered by AuViS, a therapeutic approach currently proposed for treating neurological disorders in humans.

neuroscience↗

bioRxiv2025

A formal model of anxiety disorders based on the neural circuit dynamics of the fear and extinction circuits

The pathophysiology of anxiety disorders is the outcome of an imbalance of the fear-anxiety circuit and the extinction circuit. We present a formal model using nonlinear dynamics and network theory, which captures the dynamic interactions of the key nodes of the anxiety and extinction networks. This rudimentary model can be modified by newer data. These core nodes consist of the cells of the paraventricular nucleus of the thalamus coding negative valence, the neurons of the basal-lateral amygdala coding negative valence (Rspo2+), the anterior cingulate cortex, the ventral hippocampus neurons coding fear memories, the somatostatin expressing cells of the lateral segment of the central amygdala, the medial segment of the central nucleus of the amygdala-bed nucleus of the stria terminalis and their target nodes. The extinction network consists primarily of the paraventricular thalamic cells coding positive valence, (Ppp1r1b+) cells of the basolateral amygdala coding positive valence, the ventromedial prefrontal cortex, the PKC{delta} cells of the lateral segment of the central amygdala, and the intercalated cells. Human and non-human animal genetic and epigenetic studies point to deficiencies in brain-derived neurotrophic factor and neurotrophic receptor kinase tyrosine 2 production in key nodes causing reduced plasticity extinction network plasticity and leading to a weakened extinction response. We rely primarily on the neurophysiological studies of non-human animal models since nodes generating fear/anxiety and extinction responses are highly conserved across species and equivalent nodes are present within analogous circuits of the human brain. The results are confirmed, where possible by human functional magnetic resonance imaging studies. We believe this simplified model is of heurist value and can lead to a more consistent focus on physiologically based pathophysiology. This would lead to treatments to reverse the pathologic physiology produced by genetic and epigenetic abnormalities, and greater efforts to directly correct pathologic circuit activity through direct interventions such as transcranial magnetic stimulation. SignificanceWe believe this simplified model is of heurist value and can lead to a more consistent focus on physiologically based pathophysiology. This would lead to treatments to reverse the pathologic physiology produced by genetic and epigenetic abnormalities, and greater efforts to directly correct pathologic circuit activity through direct interventions such as transcranial magnetic stimulation.

neuroscience↗