Biology subjects

Maresca, D.

Publications and source records attributed to Maresca, D..

13 recordsLinked to original sources

bioRxiv2026

Modeling behavior to disentangle motion-related effects in functional ultrasound imaging in awake, head-fixed mice

Functional ultrasound imaging (fUSI) enables brain-wide mapping of hemodynamic activity in awake rodents, offering a powerful bridge between systems neuroscience in animals and human neuroimaging. However, extending fUSI beyond tightly controlled sensory paradigms to more naturalistic behaviors is limited by motion-related confounds arising from locomotion, physiological arousal, and movement-linked neural activity. Here, we introduce a behavior-informed modeling framework that explicitly incorporates continuous measurements of running speed and head motion into a general linear model to account for motion-related variance while preserving interpretable task-related signals. We validate this approach in two head-fixed paradigms with distinct motion profiles: a visual stimulation task with minimal stimulus-driven movement, and a noxious stimulation task in which locomotion and arousal are intrinsic to the behavioral response. In both cases, explicit behavioral modeling recovers neural response patterns that more closely resemble low-motion reference conditions than blind, model-free denoising approaches. Critically, during noxious stimulation, behavior-informed modeling preserves shock-intensity-dependent activity in the primary somatosensory cortex that is attenuated by global component removal. These findings demonstrate that explicit modeling of behavior enables reliable interpretation of brain-wide fUSI signals during naturalistic, high-motion conditions, opening the door to studying affective and cognitive processes that were previously difficult to access with functional ultrasound imaging.

neuroscience↗

bioRxiv2025

Ultrasound Transparent Neural Interfaces for Multimodal Interaction

Neural interfaces that unify diagnostic and therapeutic functionalities hold particular promise for advancing both fundamental neuroscience and clinical neurotechnology. Functional ultrasound imaging (fUSI) has recently emerged as a powerful modality for high-resolution, non-invasive monitoring of brain function and structure. However, conventional metal-based microelectrodes typically impede ultrasound propagation, limiting compatibility with fUSI. Here, we present flexible, ultrasound-transparent neural interfaces that retain practical metal thicknesses while achieving high acoustic transparency. We introduce a theoretical and simulation-based framework to investigate the conditions under which commonly used polymers and metals in neural interfaces can become acoustically transparent. Based on these insights, we propose design guidelines that maximize ultrasound transmission through soft neural interfaces. We experimentally validate our approach through immersion experiments and by demonstrating the acoustic transparency of a suitably engineered interface using fUSI in phantom and in vivo experiments. Finally, we discuss the potential extension of this approach to therapeutic focused ultrasound (FUS). This work establishes a foundation for the development of multimodal neural interfaces with enhanced diagnostic and therapeutic capabilities, enabling both scientific discovery and translational impact.

bioengineering↗

bioRxiv2025

Selective-plane Functional Ultrasound Neuroimaging

Functional ultrasound (fUS) is a sensitive neuroimaging technique that uses high frame rate ultrasound to monitor brain hemo-dynamics as a proxy for neural activity. Recent studies have demonstrated its potential for brain-machine interfaces (BMIs) in both primates and humans. However, current 2D fUS approaches are limited to a single brain slice, restricting the ability to decode widespread neural activity. While 3D fUS could overcome this, it demands high data throughput, increased computation, and higher temperature increases due to the requirement of a higher number of transmitted waves. To address this, we present selective-plane fUS, a method that leverages the wide field of view of row-column addressed (RCA) transducer arrays to capture activity in targeted brain regions without moving the probe. By electronically selecting imaging planes, this approach achieves higher spatio-temporal resolution with lower data and pulse repetition rate compared to 3D fUS, while preserving sensitivity to neurovascular signals. Our pipeline begins with a 3D functional activation scan to guide plane selection, followed by high frame rate focused wave (FW) imaging in coronal or sagittal slices. This method offers robust detection of visually evoked responses in rodents and reduces signal variability compared to 3D fUS. By imaging only functional regions of interest, selective-plane fUS cuts computational load by an order of magnitude, enables continuous 1000 Hz recordings, and reduces functional signal variability fivefold. We envision that this method will allow tailored continuous functional imaging of widespread neuronal activity in the human brain in a BMI context.

neuroscience↗

bioRxiv2025

Adaptive transcranial ultrasound Doppler imaging of the brain

The development of fully noninvasive, transcranial functional ultrasound (fUS) would increase the translatability and clinical potential of this neuroimaging modality. Unfortunately, transcranial fUS is hindered by skull-induced aberrations which degrade power Doppler image quality and lower sensitivity. As a result, a majority of fUS imaging studies rely on craniotomies or acoustically transparent cranial windows. To advance fUS technology further, we present an adaptive aberration correction method based on ray-tracing through 4 tissue layers (transducer lens, gel & skin, bone and brain tissue). Our method segments these layers, and estimates ultrasound wave speeds in each layer iteratively. Once a velocity model of the imaging plane of interest is retrieved, ultrafast power Doppler imaging of the brain is performed using a ray-tracing beamformer that accounts for wave refraction. We tested our method in three adult rats, and estimated wave speeds for the skin/gel layer (1628 {+/-} 7 m/s), skull bone (3247 {+/-} 110 m/s), and brain tissue (1526 {+/-} 55 m/s). After aberration correction, we measured an average adult rat skull thickness of 388 {+/-} 41 m in agreement with anatomical records. The largest improvements in Doppler imaging quality were observed in cortical brain layers adjacent to the skull, specifically lateral spatial resolution was improved by 32%. Our method consistently outperformed Doppler imaging based on traditional delay-and-sum (DAS) beamforming, which assumes a uniform sound speed.

neuroscience↗

bioRxiv2025

Acoustic pH sensor for dynamic ultrasound imaging of cellular acidification

Genetically encoded pH sensors based on fluorescent proteins enable dynamic optical imaging of cellular processes such as endocytosis and exocytosis. To date, light scattering in thick tissue as well as photobleaching of fluorescent proteins prevent deep cellular imaging over sustained periods of time. To visualize intracellular pH variations across opaque organs, we introduce a genetically encoded acoustic pH sensor dubbed pHonon. We modified the outer gas vesicle protein (GvpC) of echogenic protein nanostructures via histidine point mutations. At low pH, engineered gas vesicles exhibit an increased shell stiffness which switched their acoustic response from nonlinear to linear. By combining pHonons with nonlinear ultrasound imaging, we captured dynamic deep tissue images of lysosomal acidification by macrophages in murine liver. The combination of pHonon with nonlinear ultrasound creates the possibility for basic studies of endo- and exocytic activity in deep tissue of living opaque organisms.

bioengineering↗

bioRxiv2024

Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale

Light-sheet fluorescence microscopy has revolutionized biology by visualizing dynamic cellular processes in three dimensions. However, light scattering in thick tissue and photobleaching of fluorescent reporters limit this method to studying thin or translucent specimens. Here we show that non-diffractive ultrasonic beams used in conjunction with a cross-amplitude modulation sequence and nonlinear acoustic reporters enable fast and volumetric imaging of targeted biological functions. We report volumetric imaging of tumor gene expression at the cm3 scale using genetically encoded gas vesicles, and localization microscopy of currently uncharted cerebral capillary networks using intravascular microbubble contrast agents. Nonlinear sound-sheet microscopy provides a [~]64x acceleration in imaging speed, [~]35x increase in imaged volume and [~]4x increase in classical imaging resolution compared to the state-of-the-art in biomolecular ultrasound.

bioengineering↗

bioRxiv2022

Cryo-EM structure of gas vesicles for buoyancy-controlled motility

Gas vesicles allow a diverse group of bacteria and archaea to move in the water column by controlling their buoyancy (1). These gas-filled cellular nanocompartments are formed by up to micrometers long protein shells that are permeable only to gas. The molecular basis of their unique properties and mechanism of assembly remains unknown. Here, we solve the 3.2 [A] cryo-EM structure of the B.megaterium gas vesicle shell made from the structural protein GvpA that self-assembles into hollow helical cylinders closed off by cone-shaped tips. Remarkably, the unique fold adopted by GvpA generates a corrugated cylinder surface typically found in force-bearing thin-walled structures. We identified pores in the vesicle wall that enable gas molecules to freely diffuse in and out of the GV shell, while the exceptionally hydrophobic interior surface effectively repels water. Our results show that gas vesicles consist of two helical half-shells connected through a unique arrangement of GvpA monomers, suggesting a mechanism of gas vesicle biogenesis. Comparative structural analysis confirms the evolutionary conservation of gas vesicle assemblies and reveals molecular details of how the secondary structural protein GvpC reinforces the GvpA shell. Our findings provide a structural framework that will further research into the biology of gas vesicles, and enable rational molecular engineering to harness their unique properties for acoustic imaging (2, 3).

biophysics↗

bioRxiv2021

Doppler Slicing for Ultrasound Super-Resolution Without Contrast Agents

Much of the information needed for diagnosis and treatment monitoring of diseases like cancer and cardiovascular disease is found at scales below the resolution limit of classic ultrasound imaging. Recently introduced vascular super-localization methods provide more than a ten-fold improvement in spatial resolution by precisely estimating the positions of microbubble contrast agents. However, most vascular ultrasound scans are currently performed without contrast agents due to the associated cost, training, and post-scan monitoring. Here we show that super-resolution ultrasound imaging of dense vascular structures can be achieved using the natural contrast of flowing blood cells. Instead of relying on separable targets, we used Fourier-based decomposition to separate signals arising from the different scales of vascular structures while removing speckle noise using multi-ensemble processing. This approach enabled the use of compressed sensing for super-resolution imaging of the underlying vascular structures, improving resolution by a factor of four. Reconstruction of ultrafast mouse brain scans revealed details that could not be resolved in regular Doppler images, agreeing closely with bubble-based super-localization microscopy of the same fields of view. By combining multi-ensemble Doppler acquisitions with narrowband Fourier decomposition and computational super-resolution imaging, this approach opens new opportunities for affordable and scalable super-resolution ultrasound imaging.

bioengineering↗

bioRxiv2021

Volumetric ultrasound localization microscopy of the whole brain microvasculature

Technologies to visualize whole organs across scales in vivo are essential for our understanding of biology in health and disease. To date, only post-mortem techniques such as perfused computed tomography scanning or optical microscopy of cleared tissues achieve cellular resolution across entire organs and imaging methods with equal performance in living mammalian organs have yet to be developed. Recently, 2D ultrasound localization microscopy has successfully mapped the fine-scale vasculature of various organs down to a 10 m precision. However, reprojection issues and out-of-plane motion prevent complex blood flow quantification and fast volumetric imaging of whole organs. Here, we demonstrate for the first time in vivo volumetric ultrasound localization microscopy mapping of the rodent brain vasculature. We developed a complete methodological pipeline that includes specific surgery, a dedicated 3D ultrasound acquisition sequence, localization and tracking algorithms, motion correction and realignment, as well as the post-processing quantification of cerebral blood flow. We illustrate the power of this approach, by mapping the whole rat brain vasculature at a resolution of 12 m, revealing mesoscopic to macroscopic vascular architectures and cerebral blood flows ranging from 1 to 100 mm/s. Our results pave the way to the investigation of in vivo vascular processes across the mammalian brain in health and disease, in a wide range of contexts and models.

bioengineering↗

bioRxiv2020

Single Trial Decoding of Movement Intentions Using Functional Ultrasound Neuroimaging

Brain-machine interfaces (BMI) are powerful devices for restoring function to people living with paralysis. Leveraging significant advances in neurorecording technology, computational power, and understanding of the underlying neural signals, BMI have enabled severely paralyzed patients to control external devices, such as computers and robotic limbs. However, high-performance BMI currently require highly invasive recording techniques, and are thus only available to niche populations. Here, we show that a minimally invasive neuroimaging approach based on functional ultrasound (fUS) imaging can be used to detect and decode movement intention signals usable for BMI. We trained non-human primates to perform memory-guided movements while using epidural fUS imaging to record changes in cerebral blood volume from the posterior parietal cortex - a brain area important for spatial perception, multisensory integration, and movement planning. Using hemodynamic signals acquired during movement planning, we classified left-cued vs. right-cued movements, establishing the feasibility of ultrasonic BMI. These results demonstrate the ability of fUS-based neural interfaces to take advantage of the excellent spatiotemporal resolution, sensitivity, and field of view of ultrasound without breaching the dura or physically penetrating brain tissue.

neuroscience↗

bioRxiv2019

Acoustic biomolecules enhance hemodynamic functional ultrasound imaging of neural activity

Hemodynamic functional ultrasound imaging (fUS) of neural activity provides a unique combination of spatial coverage, spatiotemporal resolution and compatibility with freely moving animals. However, deep and transcranial monitoring of brain activity and the imaging of dynamics in slow-flowing blood vessels remains challenging. To enhance fUS capabilities, we introduce biomolecular hemodynamic enhancers based on gas vesicles (GVs), genetically encodable ultrasound contrast agents derived from buoyant photosynthetic microorganisms. We show that intravenously infused GVs enhance ultrafast Doppler ultrasound contrast and visually-evoked hemodynamic contrast in transcranial fUS of the mouse brain. This hemodynamic contrast enhancement is smoother than that provided by conventional microbubbles, allowing GVs to more reliably amplify neuroimaging signals.

neuroscience↗

bioRxiv2019

Genetically encoded nanostructures enable acoustic manipulation of engineered cells

The ability to mechanically manipulate and control the spatial arrangement of biological materials is a critical capability in biomedicine and synthetic biology. Ultrasound has the ability to manipulate objects with high spatial and temporal precision via acoustic radiation force, but has not been used to directly control biomolecules or genetically defined cells. Here, we show that gas vesicles (GVs), a unique class of genetically encoded gas-filled protein nanostructures, can be directly manipulated and patterned by ultrasound and enable acoustic control of genetically engineered GV-expressing cells. Due to their differential density and compressibility relative to water, GVs experience sufficient acoustic radiation force to allow these biomolecules to be moved with acoustic standing waves, as demonstrated within microfluidic devices. Engineered variants of GVs differing in their mechanical properties enable multiplexed actuation and act as sensors of acoustic pressure. Furthermore, when expressed inside genetically engineered bacterial cells, GVs enable these cells to be selectively manipulated with sound waves, allowing patterning, focal trapping and translation with acoustic fields. This work establishes the first genetically encoded nanomaterial compatible with acoustic manipulation, enabling molecular and cellular control in a broad range of contexts.

bioengineering↗

bioRxiv2019

Acoustically Detonated Biomolecules for Genetically Encodable Inertial Cavitation

Recent advances in molecular engineering and synthetic biology have made it possible for biomolecular and cell-based therapies to provide highly specific disease treatment. However, both the ability to spatially target the action of such therapies, and their range of effects on the target tissue remain limited. Here we show that biomolecules and cells can be engineered to deliver potent mechanical effects at specific locations inside the body under the direction of focused ultrasound. This capability is based on gas vesicles, a unique class of air-filled protein nanostructures derived from buoyant photosynthetic microbes. We show that low-frequency ultrasound can convert these nanoscale biomolecules into micron-scale cavitating bubbles, as demonstrated with acoustic measurements and ultrafast optical microscopy. This allows gas vesicles targeted to cell-surface receptors to serve as remotely detonated cell-killing agents. In addition, it allows cells genetically engineered to express gas vesicles to be triggered with ultrasound to lyse and release therapeutic payloads. We demonstrate these capabilities in vitro, in cellulo, and in vivo. This technology equips biomolecular and cellular therapeutics with unique capabilities for spatiotemporal control and mechanical action.

bioengineering↗