Biology subjects

Cooper, B. G.

Publications and source records attributed to Cooper, B. G..

4 recordsLinked to original sources

bioRxiv2026

Automated inference of respiratory and syringeal biomechanical trajectories from birdsong acoustics

Songbirds, in particular zebra finches (Taeniopygia guttata), provide a powerful model for investigating the neural mechanisms of learned vocal behavior. Researchers typically rely on the acoustic structure of birdsong to quantify vocal behavior. As a more direct measure of motor control, we present VIBE: Vocal acoustic Inversion to Biomechanical Estimates, an open-source pipeline that recovers the biomechanical control parameters of song production directly from the acoustic waveform. Biomechanical models of the songbird syrinx describe vocal production with two continuously varying parameters: and {beta}, representing subsyringeal air sac pressure and syringeal muscle tension, respectively. Recovering these parameters from song acoustics provides a motor-based coordinate system against which neural activity or other dependent variables can be directly compared. Because and {beta} are the coupled control parameters of a nonlinear oscillator, their joint recovery is non-trivial. VIBE addresses this through iterative optimization of the governing normal-form equations. We validate VIBE against recorded air sac pressure across 44 songs from twelve birds, showing that the recovered corresponds to empirically measured air sac pressure. Pairing VIBE with Neuropixels recordings from RA in five birds, we find that RA activity is well predicted by the recovered parameters, and that and {beta} add predictive power beyond the acoustic features of song. By recovering biomechanical control parameters from the acoustic signal, VIBE makes the biomechanical coordinate system of song production accessible to the broader songbird research community. New & NoteworthyVIBE provides a novel, fully automated pipeline to recover the biomechanical control parameters of the avian vocal organ, and {beta}, as continuously varying quantities from the raw acoustic waveform, making the full biomechanical model of song production accessible at the scale of modern datasets.

neuroscience↗

bioRxiv2025

Holistic Motor Control of Zebra Finch Song Syllable Sequences

How brain circuits are organized to skillfully produce learned sequences of behaviors is still poorly understood. Here, we functionally examine how the cortical song premotor region HVC, which is necessary for zebra finch song, controls the sequential production of learned song syllables. We find that HVC can generate the complete sequence of learned song syllables independently of its main synaptic input pathways. Thalamic input to HVC is permissive for song initiation but it is not required for transitions between syllables or completing song. We show that excitation of HVC neurons during song reliably causes vocalizations to skip back to the beginning of song, reminiscent of a skipping record. This restarting of syllable sequences can be induced at any moment in song and depends on local circuits within HVC. We identify and computationally model a synaptic network including intratelencephalic premotor and corticostriatal neurons within HVC that are essential for completing song syllable sequences. Together, our results show that the learned zebra finch song is controlled by a cortical sequence-generating network in HVC that, once started, can sustain production of all song syllables independent of major extrinsic input pathways. Thus, sequential neuronal activity can be organized to fuse well-learned vocal-motor sequences, ultimately achieving holistic control of this naturally learned behavior.

neuroscience↗

bioRxiv2022

Motile Living Biobots Self-Construct from Adult Human Somatic Progenitor Seed Cells

Fundamental knowledge gaps exist with respect to the plasticity of cells from adult soma and the potential diversity of body shape and behavior in living constructs derived from such genetically wild-type cells. Here we introduce Anthrobots, a spheroid-shaped multicellular biological robot (biobot) platform with diameters ranging from 30 to 500 microns. Anthrobots have an inherent capacity for motility in aqueous environments, via cilia covering their surface. Each Anthrobot starts out as a single cell, derived from the adult human lung, and self-constructs into a multicellular motile biobot after having been cultured in extra cellular matrix for 2 weeks and transferred into a minimally viscous habitat. Anthrobots exhibit a wide range of behaviors with motility patterns ranging from tight loops to straight lines and speeds ranging from 5-50 microns/second. Our anatomical investigations reveal that this behavioral diversity is significantly correlated with their morphological diversity. Anthrobots can assume diverse morphologies from fully polarized to wholly ciliated bodies with spherical or ellipsoidal shapes, each correlating with a distinct movement type. Remarkably, as a function of these different movement types, Anthrobots were found to be capable of traversing live human tissues in various ways. Furthermore, Anthrobots were able to induce rapid repair of wounds in human neural cell sheets in vitro. By controlling microenvironmental cues in bulk, entirely novel structure, behavior, and biomedically-relevant capabilities can be discovered in morphogenetic processes without direct genetic editing or manual sculpting. Significance StatementWe demonstrate that normal, non-genetically-modified human tracheal cells can be induced to form a new proto-organism - Anthrobots - which exhibit spontaneous behavior, swimming around in one of several patterns, demonstrating plasticity for novel form and function inherent in even elderly human somatic cells. Moreover, Anthrobots are able to traverse over cultured neurons, settling down and causing repair under them: the nerves knit together across the wound gap due to the presence of the Anthrobot. A patients own cells can be harnessed to make a motile biological robot that can traverse human tissue and induce repair. In the future, this platform can deliver pro-regenerative therapeutics for a range of biomedical applications that will not trigger rejection or require immune suppression.

bioengineering↗

bioRxiv2018

Transitioning between preparatory and precisely sequenced neuronal activity in production of a skilled behavior

Precise neural sequences are associated with the production of well-learned skilled behaviors. Yet, how neural sequences arise in the brain remains unclear. In songbirds, premotor projection neurons in the cortical song nucleus HVC are necessary for producing learned song and exhibit precise sequential activity during singing. Using cell-type specific calcium imaging we identify populations of HVC premotor neurons associated with the beginning and ending of singing-related neural sequences. We discovered neurons that bookend singing-related sequences and neuronal populations that transition from sparse preparatory activity prior to song to precise neural sequences during singing. Recordings from downstream premotor neurons or the respiratory system suggest that pre-song activity may be involved in motor preparation to sing. These findings reveal population mechanisms associated with moving from non-vocal to vocal behavioral states and suggest that precise neural sequences begin and end as part of orchestrated activity across functionally diverse populations of cortical premotor neurons.

neuroscience↗