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1. Whole-brain, all-optical interrogation of neuronal dynamics underlying gut interoception in zebrafish

   https://doi.org/10.1101/2025.03.26.645305  

   Chen, Weiyu; James, Ben; Ruetten, Virginia_M S; Banala, Sambashiva; Wei, Ziqiang; Fleishman, Greg; Rubinov, Mikail; Fishman, Mark C; Engert, Florian; Lavis, Luke D; et al (March 2025, bioRxiv)

   Abstract Internal signals from the body and external signals from the environment are processed by brain-wide circuits to guide behavior. However, the complete brain-wide circuit activity underlying interoception—the perception of bodily signals—and its interactions with sensorimotor circuits remain unclear due to technical barriers to accessing whole-brain activity at the cellular level during organ physiology perturbations. We developed an all-optical system for whole-brain neuronal imaging in behaving larval zebrafish during optical uncaging of gut-targeted nutrients and visuo-motor stimulation. Widespread neural activity throughout the brain encoded nutrient delivery, unfolding on multiple timescales across many specific peripheral and central regions. Evoked activity depended on delivery location and occurred with amino acids and D-glucose, but not L-glucose. Many gut-sensitive neurons also responded to swimming and visual stimuli, with brainstem areas primarily integrating gut and motor signals and midbrain regions integrating gut and visual signals. This platform links body-brain communication studies to brain-wide neural computation in awake, behaving vertebrates. 

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2. Neuromodulation of Neural Oscillations in Health and Disease

   https://doi.org/10.3390/biology12030371  

   Weiss, Evan; Kann, Michael; Wang, Qi (March 2023, Biology)

   Using EEG and local field potentials (LFPs) as an index of large-scale neural activities, research has been able to associate neural oscillations in different frequency bands with markers of cognitive functions, goal-directed behavior, and various neurological disorders. While this gives us a glimpse into how neurons communicate throughout the brain, the causality of these synchronized network activities remains poorly understood. Moreover, the effect of the major neuromodulatory systems (e.g., noradrenergic, cholinergic, and dopaminergic) on brain oscillations has drawn much attention. More recent studies have suggested that cross-frequency coupling (CFC) is heavily responsible for mediating network-wide communication across subcortical and cortical brain structures, implicating the importance of neurotransmitters in shaping coordinated actions. By bringing to light the role each neuromodulatory system plays in regulating brain-wide neural oscillations, we hope to paint a clearer picture of the pivotal role neural oscillations play in a variety of cognitive functions and neurological disorders, and how neuromodulation techniques can be optimized as a means of controlling neural network dynamics. The aim of this review is to showcase the important role that neuromodulatory systems play in large-scale neural network dynamics, informing future studies to pay close attention to their involvement in specific features of neural oscillations and associated behaviors. 

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3. CREIMBO: Cross-Regional Ensemble Interactions in Multi-view Brain Observations

   Mudrik, Noga; Ly, Ryan; Ruebel, Oliver; Charles, Adam S (January 2025, The International Conference on Learning Representations)

   Modern recordings of neural activity provide diverse observations of neurons across brain areas, behavioral conditions, and subjects; presenting an exciting opportunity to reveal the fundamentals of brain-wide dynamics. Current analysis methods, however, often fail to fully harness the richness of such data, as they provide either uninterpretable representations (e.g., via deep networks) or oversimplify models (e.g., by assuming stationary dynamics or analyzing each session independently). Here, instead of regarding asynchronous neural recordings that lack alignment in neural identity or brain areas as a limitation, we leverage these diverse views into the brain to learn a unified model of neural dynamics. Specifically, we assume that brain activity is driven by multiple hidden global sub-circuits. These sub-circuits represent global basis interactions between neural ensembles—functional groups of neurons—such that the time-varying decomposition of these sub-circuits defines how the ensembles’ interactions evolve over time non-stationarily and non-linearly. We discover the neural ensembles underlying non-simultaneous observations, along with their non-stationary evolving interactions, with our new model, CREIMBO (Cross-Regional Ensemble Interactions in Multi-view Brain Observations). CREIMBO identifies the hidden composition of per-session neural ensembles through novel graph-driven dictionary learning and models the ensemble dynamics on a low-dimensional manifold spanned by a sparse time-varying composition of the global sub-circuits. Thus, CREIMBO disentangles overlapping temporal neural processes while preserving interpretability due to the use of a shared underlying sub-circuit basis. Moreover, CREIMBO distinguishes session-specific computations from global (session-invariant) ones by identifying session covariates and variations in sub-circuit activations. We demonstrate CREIMBO’s ability to recover true components in synthetic data, and uncover meaningful brain dynamics in human high-density electrode recordings, including cross-subject neural mechanisms as well as inter- vs. intra-region dynamical motifs. Furthermore, using mouse whole-brain recordings, we show CREIMBO’s ability to discover dynamical interactions that capture task and behavioral variables and meaningfully align with the biological importance of the brain areas they represent 

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4. A Framework to Control Functional Connectivity in the Human Brain

   https://doi.org/10.1109/CDC40024.2019.9029223  

   Menara, Tommaso; Baggio, Giacomo; Bassett, Danielle S.; Pasqualetti, Fabio (December 2019, IEEE Conference on Decision and Control)

   In this paper, we propose a framework to control brain-wide functional connectivity by selectively acting on the brain's structure and parameters. Functional connectivity, which measures the degree of correlation between neural activities in different brain regions, can be used to distinguish between healthy and certain diseased brain dynamics and, possibly, as a control parameter to restore healthy functions. In this work, we use a collection of interconnected Kuramoto oscillators to model oscillatory neural activity, and show that functional connectivity is essentially regulated by the degree of synchronization between different clusters of oscillators. Then, we propose a minimally invasive method to correct the oscillators' interconnections and frequencies to enforce arbitrary and stable synchronization patterns among the oscillators and, consequently, a desired pattern of functional connectivity. Additionally, we show that our synchronization-based framework is robust to parameter mismatches and numerical inaccuracies, and validate it using a realistic neurovascular model to simulate neural activity and functional connectivity in the human brain. 

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5. Cavefish brain atlases reveal functional and anatomical convergence across independently evolved populations

   https://doi.org/10.1126/sciadv.aba3126  

   Jaggard, James B.; Lloyd, Evan; Yuiska, Anders; Patch, Adam; Fily, Yaouen; Kowalko, Johanna E.; Appelbaum, Lior; Duboue, Erik R.; Keene, Alex C. (September 2020, Science Advances)

   null (Ed.)

   Environmental perturbation can drive behavioral evolution and associated changes in brain structure and function. The Mexican fish species, Astyanax mexicanus , includes eyed river-dwelling surface populations and multiple independently evolved populations of blind cavefish. We used whole-brain imaging and neuronal mapping of 684 larval fish to generate neuroanatomical atlases of surface fish and three different cave populations. Analyses of brain region volume and neural circuits associated with cavefish behavior identified evolutionary convergence in hindbrain and hypothalamic expansion, and changes in neurotransmitter systems, including increased numbers of catecholamine and hypocretin/orexin neurons. To define evolutionary changes in brain function, we performed whole-brain activity mapping associated with behavior. Hunting behavior evoked activity in sensory processing centers, while sleep-associated activity differed in the rostral zone of the hypothalamus and tegmentum. These atlases represent a comparative brain-wide study of intraspecies variation in vertebrates and provide a resource for studying the neural basis of behavioral evolution. 

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