Biology subjects

Wagenaar, D. A.

Publications and source records attributed to Wagenaar, D. A..

11 recordsLinked to original sources

bioRxiv2025

Mapping function in the tree shrew visual system using functional ultrasound imaging.

We adapted functional ultrasound imaging (fUSI) for awake, head-fixed northern tree shrews and used it to produce functional maps of visual processing at [~]100 {micro}m spatial resolution and [~]100 ms temporal resolution. Using classical retinotopic stimuli, full-field noise, motion localizers, and object versus scrambled object contrasts, we demonstrate robust, spatially specific hemodynamic responses across primary and extrastriate visual cortex, superior colliculus and subcortical structures. fUSI reliably reveals retinotopic reversals, laterality, and stimulus-selective modules, and yields high signal-to-noise %CBV changes that enable single-session mapping and targeting of electrophysiology or perturbations. These mesoscale maps provide a systems-level complement to recent high-density electrophysiological surveys of tree shrew visual cortex, which reported a compressed ventral-stream hierarchy and surprisingly early emergence of object coding in V2 (Lanfranchi et al., 2025). Together, our results establish fUSI as a powerful, scalable tool for functional mapping in the tree shrew, bridging large-scale circuit measurement and single-neuron electrophysiology and accelerating this species utility as a bridge between rodent genetics and primate vision.

neuroscience↗

bioRxiv2024

Hydrogel encapsulation of a designed fluorescent protein biosensor for continuous measurements of sub-100 nanomolar nicotine

The reinforcing and addictive properties of nicotine result from concentration- and time-dependent activation, desensitization, and upregulation of nicotinic acetylcholine receptors. However, time-resolved [nicotine] measurement in people who consume nicotine is challenging, as current approaches are expensive, invasive, tedious, and discontinuous. To address the challenge of continuous nicotine monitoring in human biofluids, we report the encapsulation of a purified, previously developed fluorescent biosensor protein, iNicSnFR12, into acrylamide hydrogels and polyethylene glycol diacrylate (PEGDA) hydrogels. We optimized the hydrogels for optical clarity and straightforward slicing. With fluorescence photometry of the hydrogels in a microscope and an integrated miniscope, [nicotine] is detected within a few min at the smoking- and vaping-relevant level of 10 - 100 nM (1.62 - 16.2 ng/ml), even in a 250 {micro}m thick hydrogel at the end of 400 {micro}m dia multimode fiber optic. Concentration-response relations are consistent with previous measurements on isolated iNicSnFR12. Leaching of iN-icSnFR12 from the hydrogel and inactivation of iNicSnFR12 are minimal for several days, and nicotine can be detected for at least 10 months after casting. This work provides the molecular, photophysical, and mechanical bases for personal, wearable continuous [nicotine] monitoring, with straightforward extensions to existing, homologous "iDrugSnFR" proteins for other abused and prescribed drugs.

neuroscience↗

bioRxiv2024

Kilohertz volumetric imaging of in-vivo dynamics using squeezed light field microscopy

Volumetric functional imaging of transient cellular signaling and motion dynamics poses a significant challenge to current microscopy techniques, primarily due to limitations in hardware bandwidth and the restricted photon budget within short exposure times. In response to this challenge, we present squeezed light field microscopy (SLIM), a computational imaging method that enables rapid detection of high-resolution three-dimensional (3D) light signals using only a single, low-format camera sensor area. SLIM pushes the boundaries of 3D optical microscopy, achieving over one thousand volumes per second across a large field of view of 550 m in diameter and 300 m in depth with a spatial resolution of 3.6 m laterally and 6 m axially. Using SLIM, we demonstrated blood cell velocimetry across the embryonic zebrafish brain and in a free-moving tail exhibiting high-frequency swinging motion. The millisecond temporal resolution also enables accurate voltage imaging of neural membrane potentials in the leech ganglion, and in the hippocampus of behaving mice. These results collectively establish SLIM as a versatile and robust imaging tool for high-speed microscopy applications.

bioengineering↗

bioRxiv2023

Large-scale brain-wide neural recording in nonhuman primates

High-density, integrated silicon electrodes have begun to transform systems neuroscience, by enabling large-scale neural population recordings with single cell resolution. Existing technologies, however, have provided limited functionality in nonhuman primate species such as macaques, which offer close models of human cognition and behavior. Here, we report the design, fabrication, and performance of Neuropixels 1.0-NHP, a high channel count linear electrode array designed to enable large-scale simultaneous recording in superficial and deep structures within the macaque or other large animal brain. These devices were fabricated in two versions: 4416 electrodes along a 45 mm shank, and 2496 along a 25 mm shank. For both versions, users can programmatically select 384 channels, enabling simultaneous multi-area recording with a single probe. We demonstrate recording from over 3000 single neurons within a session, and simultaneous recordings from over 1000 neurons using multiple probes. This technology represents a significant increase in recording access and scalability relative to existing technologies, and enables new classes of experiments involving fine-grained electrophysiological characterization of brain areas, functional connectivity between cells, and simultaneous brain-wide recording at scale.

neuroscience↗

bioRxiv2021

Open-Source Thermometer, Temperature Controller, and Light Meter for Use in Animal Facilities and During Experiments

Experiments with biological samples require precise control of environmental conditions. In our work we use zebrafish (Danio rerio) to understand the neurobiology of sleep, which requires precise control of temperature and lighting. Like many labs, lighting and temperature in the animal facility are centrally controlled in the building. During behavioral experiments and microscopy sessions, we use custom-built heating systems and perform occasional manual checks of conditions. However, without a system to precisely record conditions, gradual changes in temperature can go unnoticed for a long time, and temporary failures may be missed entirely. Here we present the design and characterization of affordable open-source tools to record temperature and light conditions during animal experiments using an Arduino microcontroller or a Raspberry Pi compact computer. The waterproof temperature sensor has high stability over 50 days of recording and is precise to 0.1{degrees}C. The Arduino device can be used through a common serial port interface for which we present code in Python and MATLAB. The Raspberry Pi version can be accessed through a web interface, for which we provide an installation guide. We use the device to record and review temperature and lighting conditions in two zebrafish animal facilities. We use our platform to add a water heating system to maintain temperature at 28{degrees}C during in vivo light-sheet imaging of larval zebrafish. We show that a change in temperature from 28{degrees}C to 32{degrees}C affects resting heart rate of the animal, highlighting the importance of maintaining and recording conditions. The protocols presented here do not require advanced engineering, fabrication, or software skills, and provide an approach to accurately record and report experimental conditions.

bioengineering↗

bioRxiv2020

Dorsal raphe dopamine neurons signal motivational salience dependent on internal and external states

The ability to recognize motivationally salient events and respond to them adaptively is critical for survival. Here we tested whether dopamine (DA) neurons in the dorsal raphe nucleus (DRN) contribute to this process. Population recordings of DRNDA neurons during associative learning tasks showed that their activity dynamically tracks salience, developing excitation to both reward- and punishment-paired cues. The DRNDA response to reward-predicting cues was diminished after satiety, suggesting modulation by internal states. DRNDA activity was also greater for unexpected outcomes than for expected outcomes. Two-photon imaging of DRNDA neurons demonstrated that the majority of individual neurons developed activation to reward-predicting cues but not to punishment-predicting cues, which was surprising and qualitatively distinct from the population results. Head-fixation during fear learning abolished the neural response to aversive cues, indicating modulation by behavioral context. Overall, these results suggest that DRNDA neurons encode motivational salience, dependent on internal and external factors.

neuroscience↗

bioRxiv2020

Combined membrane potential imaging and connectome of behavioral circuits in an annelid worm

Dorsal Excitor motor neuron DE-3 in the medicinal leech plays three very different dynamical roles in three different behaviors. Without rewiring its anatomical connectivity, how can a motor neuron dynamically switch roles to play appropriate roles in various behaviors? We previously used voltage-sensitive dye imaging to record from DE-3 and most other neurons in the leech segmental ganglion during (fictive) swimming, crawling, and local-bend escape (Tomina and Wagenaar, 2017). Here, we repeated that experiment, then re-imaged the same ganglion using serial blockface electron microscopy and traced all of DE-3s processes. Further, we traced back the processes of all of DE-3s presynaptic partners to their respective somata. This allowed us to analyze the relationship between circuit anatomy and the activity patterns it sustains. We found that input synapses important for all of the behaviors were widely distributed over DE-3s branches, yet that functional clusters were different during (fictive) swimming vs. crawling.

neuroscience↗

bioRxiv2019

Stimulus-specific neural encoding of a persistent, internal defensive state in the hypothalamus

Persistent neural activity has been described in cortical, hippocampal, and motor networks as mediating short-term working memory of transiently encountered stimuli1-4. Internal emotion states such as fear also exhibit persistence following exposure to an inciting stimulus5,6, but such persistence is typically attributed to circulating stress hormones7-9; whether persistent neural activity also plays a role has not been established. SF1+/Nr5a1+ neurons in the dorsomedial and central subdivision of the ventromedial hypothalamus (VMHdm/c) are necessary for innate and learned defensive responses to predators10-13. Optogenetic activation of VMHdmSF1 neurons elicits defensive behaviors that can outlast stimulation11,14, suggesting it induces a persistent internal state of fear or anxiety. Here we show that VMHdmSF1 neurons exhibit persistent activity lasting tens of seconds, in response to naturalistic threatening stimuli. This persistent activity was correlated with, and required for, persistent thigmotaxic (anxiety-like) behavior in an open-field assay. Microendoscopic imaging of VMHdmSF1 neurons revealed that persistence reflects dynamic temporal changes in population activity, rather than simply synchronous, slow decay of simultaneously activated neurons. Unexpectedly, distinct but overlapping VMHdmSF1 subpopulations were persistently activated by different classes of threatening stimuli. Computational modeling suggested that recurrent neural networks (RNNs) incorporating slow excitation and a modest degree of neurochemical or spatial bias can account for persistent activity that maintains stimulus identity, without invoking genetically determined \"labeled lines\"15. Our results provide causal evidence that persistent neural activity, in addition to well-established neuroendocrine mechanisms, can contribute to the ability of emotion states to outlast their inciting stimuli, and suggest a mechanism that could prevent over-generalization of defensive responses without the need to evolve hardwired circuits specific for each type of threat.

neuroscience↗

bioRxiv2019

Electrophysiology and transcriptomics reveal two photoreceptor classes and complex visual integration in Hirudo verbana

Among animals with complex visual processing mechanisms, the leech Hirudo verbana is a rare example in which all neurons can be identified. However, little is known about its visual system, which is composed of several pigmented head eyes and photosensitive non-pigmented sensilla that are distributed across its entire body. Although several interneurons are known to respond to visual stimuli, their response properties are poorly understood. Among these, the S cell system is especially intriguing: It is multimodal, spans the entire body of the leech, and is thought to be involved in complex sensory integration. To improve our understanding of the role of this system, we tested its spectral sensitivity, spatial integration, and adaptation properties. The response of the S cell system to visual stimuli was found to be strongly dependent on the size of the area stimulated, and adaptation was local. Furthermore, a "bleaching experiment" demonstrated that at least two color channels contributed to the response, and that their contribution was dependent on the adaptation to the background. The existence of at least two color channels was further supported by transcriptomic evidence, which indicated the existence of at least two distinct groups of putative opsins for leeches. Taken together, our results show that the S cell system has highly sophisticated response properties, and could be involved in the processing of complex visual stimuli. We propose the leech as a novel system to understand visual processing mechanisms with many practical advantages. Summary statementDetailed quantitative analysis of light responses in the medicinal leech Hirudo verbana unequivocally demonstrates the existence of parallel visual pathways processing visual and UV stimuli. Responses to spatially complex stimuli indicate relatively sophisticated information processing.

neuroscience↗

bioRxiv2017

Whole-Ganglion Imaging Of Voltage In The Medicinal Leech Using A Double-Sided Microscope

Studies of neuronal network emergence during sensory processing and motor control are greatly promoted by technologies that allow us to simultaneously record the membrane potential dynamics of a large population of neurons in single cell resolution. To achieve whole-brain recording with the ability to detect both small synaptic potentials and action potentials, we developed a voltage-sensitive dye (VSD) imaging technique based on a double-sided microscope that can image two sides of a nervous system simultaneously. We applied this system to the segmental ganglia of the medicinal leech. Double-sided VSD imaging enabled simultaneous recording of membrane potential events from almost all of the identifiable neurons. Using data obtained from double-sided VSD imaging we analyzed neuronal dynamics in both sensory processing and generation of behavior and constructed functional maps for identification of neurons contributing to these processes.

neuroscience↗

bioRxiv2017

Responses To Mechanically And Visually Cued Water Waves In The Nervous System Of The Medicinal Leech

Summary statementCues from water movement help aquatic predators find their prey. We study how the nervous system of the medicinal leech processes visual and mechanical information derived from surface waves.\n\nAbstractSensitivity to water waves is a key modality by which aquatic predators can detect and localize their prey. For one such predator, the medicinal leech, Hirudo verbana, behavioral responses to visual and mechanical cues from water waves are well documented. Here, we quantitatively characterized the response patterns of a multisensory interneuron, the S cell, to mechanically and visually cued water waves. The frequency dependence of the S-cell response matched the behavioral response well, in that sensitivity was higher for low frequencies in the visual modality and for high frequencies in the mechanical modality. We demonstrated that neither the cephalic ganglia nor the tail brain is required for the S cell to respond to visually cued water waves. The direction of spike propagation within the S- cell system did follow the direction of wave propagation under certain circumstances, but it is unlikely that downstream neuronal targets can use this information. In terms of overall firing rate, the S cell response was not direction selective. Accordingly we propose a role for the S cell in the detection of waves but not in the localization of their source.

neuroscience↗