Biology subjects

Kilic, K.

Publications and source records attributed to Kilic, K..

14 recordsLinked to original sources

bioRxiv2026

Insulin fails to mitigate amyloid pathology but modulates intestinal morphology in the 5xFAD model revealed by synchrotron-based XPCT

Intranasal insulin has been investigated as a metabolic intervention in Alzheimers disease (AD), but its effects across the brain-gut axis remain unclear. We combined multiscale synchrotron X-ray phase-contrast tomography (XPCT), amyloid-{beta} immunofluorescence, and fecal metaproteomics to examine structural and molecular responses in 5xFAD mice. Twenty-four mice representing wild-type and 5xFAD genotypes, saline and insulin conditions, and terminal ages of 2 and 6 months received insulin at 1 U/mouse/day for 5 weeks. Micro-XPCT visualized plaque-like deposits, nanoXPCT revealed their heterogeneous internal organization, and MOAB-2 labeling provided qualitative support for amyloid pathology. Detectable plaque burden was not lower after treatment: deposits occurred in two of three treated versus none of three untreated 5xFAD mice at 2 months, and treated animals had higher descriptive regional means at 6 months. In the ileum, insulin was associated with lower villus length and crypt depth in 6-month-old 5xFAD mice, whereas no significant differences were detected at 2 months. Fecal profiles retained broad taxonomic overlap but differed in functional annotations, with hydrolase-associated fractions of 81%, 92%, 96%, and 93% across untreated wild-type, treated wild-type, untreated 5xFAD, and treated 5xFAD conditions, respectively, within the selected peptide subset. Thus, lower ileal dimensions coexisted with non-reduced detectable brain plaque burden and a fecal protein profile distinct from untreated wild type. Together, these findings reveal contrasting central and peripheral patterns following intranasal insulin treatment in 5xFAD mice: no detectable reduction in cerebral plaque burden, alongside attenuation of selected ileal structural alterations and distinct fecal metaproteomic profiles. Although exploratory, the findings raise the possibility that intranasal insulin alters amyloid compartmentalization or plaque detectability rather than promoting amyloid clearance, while producing distinct peripheral remodeling.

biophysics↗

bioRxiv2026

Brain-resident myeloid cells promote rapid leukocyte adhesion in leptomeningeal vessels after anti-Aβ immunotherapy

Anti-amyloid {beta} (A{beta}) immunotherapy improves cognitive outcomes in Alzheimer's disease (AD) but is associated with amyloid-related imaging abnormalities (ARIA), through poorly understood mechanisms. To define how anti-A{beta} antibodies acutely engage brain immune and vascular compartments, we developed a longitudinal in vivo two-photon imaging platform to track microglial dynamics, peripheral immune cell recruitment, and vascular responses in APP/PS1 mice. Anti-A{beta} antibodies, including aducanumab and lecanemab, rapidly initiated microglial activation and spatial reorganization within 24 hours of dosing, with recruitment to plaque-associated regions, stabilizing plaque growth. Aducanumab and lecanemab also triggered a rapid and transient cerebrovascular immune response characterized by rolling and adhesion of peripheral immune cells along leptomeningeal vessels, accompanied by endothelial activation. Immune cell characterization revealed recruitment of innate immune cells (Iba1Ki67 monocytes and Ly6G neutrophils) and proliferative CD3 T cells into the vascular compartment following treatment. Prophylactic treatment with high-dose dexamethasone reduced the number of adherent cells without affecting microglial activation. Depletion of brain-resident immune cells similarly reduced peripheral immune cell recruitment, supporting their contribution to leukocyte recruitment. Postmortem brain tissue from an AD patient treated with lecanemab showed higher proliferation-associated monocyte signature scores, suggesting translational relevance to the proliferative myeloid response observed in our mouse models. These findings demonstrate that anti-A{beta} immunotherapy rapidly initiates a coordinated central and peripheral immune response at the leptomeningeal interface. These early immune-vascular interactions represent a plausible initiating mechanism for ARIA and provide a mechanistic framework to guide strategies for mitigating ARIA risk

neuroscience↗

bioRxiv2026

Blood-Mediated Opto-Acoustic Stimulation of Brain Cortex at Sub-millimeter Precision

Direct modulation of neural activity with high spatiotemporal precision is a cornerstone in experimental neuroscience. Here, we present a blood-mediated optoacoustic stimulation (BOAS) approach that utilizes blood as an endogenous transducer for brain stimulation. By delivering 532-nm nanosecond pulsed laser to the cortex, we demonstrate that the absorption of hemoglobin generates sufficient acoustic pressure to trigger neuronal activity. By integrating BOAS with calcium imaging in GCaMP6f-expressing mice, localized neuronal responses were observed. Quantitative analysis reveals that BOAS produces responses comparable to natural visual stimulation and is significantly more efficient than the photothermal stimulation. Furthermore, we show that the response is dose-dependent. At high energy doses, BOAS induces cortical spreading depression. Histological evaluation confirmed that the brain maintains tissue integrity even under these stimulation parameters. Together, this work establishes a versatile method for precise brain stimulation as an alternative method for stimulating neuron at cortex.

bioengineering↗

bioRxiv2026

Visual gamma stimulation causes prolonged enhancement of low-frequency blood flow oscillations across cortical regions in mice

IntroductionGamma entrainment using sensory stimuli (GENUS) uses 40Hz-pulsed sensory stimuli to entrain neural activity in the gamma band (30-150Hz). However, the effect of GENUS on low-frequency vascular oscillations has not been fully explored. ObjectivesThe objective of this study is to elucidate the effect of GENUS on vasomotion in healthy mice and potential confounds for future application in disease studies. MethodsHead-fixed, awake C57Bl/6 mice (n=18; 9M 9F) aged between 18 to 60 weeks were subjected to white light of either 40Hz visual flicker (GENUS), or constant stimulus (control). Blood flow was imaged using laser speckle contrast imaging (LSCI) before, during, immediately after 1 hour of stimulus, and 30min after the stimulus termination. ResultsA linear mixed-effects model showed that GENUS enhanced the magnitude of 0.2-0.4Hz blood flow oscillations by 38% during stimulation and by 30% at 30 minutes after stimulation compared to control when controlled for age, sex, and other factors. The effect on vasomotion was distributed across many cortical regions not limited to visual areas and lasted beyond 24 hours post-stimulus. ConclusionThese results support the exploration of GENUS for increasing vasomotion in therapeutic contexts. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/729102v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@1deee2eorg.highwire.dtl.DTLVardef@e71833org.highwire.dtl.DTLVardef@1e5c4f0org.highwire.dtl.DTLVardef@1e4832e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Widefield in vivo imaging system with two fluorescence and two reflectance channels, a single sCMOS detector, and shielded illumination

SignificanceWidefield microscopy of the entire dorsal part of mouse cerebral cortex enables large-scale ("mesoscopic") imaging of different aspects of neuronal activity with spectrally compatible fluorescent indicators as well as hemodynamics via oxy- and deoxyhemoglobin absorption. Versatile and cost-effective imaging systems are needed for large-scale, color-multiplexed imaging of multiple fluorescent and intrinsic contrasts. AimDevelop a system for mesoscopic imaging of two fluorescent and two reflectance channels. ApproachExcitation of red and green fluorescence is achieved through epi-illumination. Hemoglobin absorption imaging is achieved using 525- and 625-nm LEDs positioned around the objective lens. An aluminum hemisphere placed between objective and cranial window provides diffuse illumination of the brain. Signals are recorded sequentially by a single sCMOS detector. ResultsWe demonstrate performance of our imaging system by recording large-scale spontaneous and stimulus-evoked neuronal, cholinergic, and hemodynamic activity in awake head-fixed mice with a curved "crystal skull" window expressing the red calcium indicator jRGECO1a and the green acetylcholine sensor GRABACh3.0. Shielding of illumination light through the aluminum hemisphere enables concurrent recording of pupil diameter changes. ConclusionsOur widefield microscope design with single camera can be used to acquire multiple aspects of brain physiology and is compatible with behavioral readouts of pupil diameter.

neuroscience↗

bioRxiv2022

Measuring Capillary Flow Dynamics using Interlaced Two-Photon Volumetric Scanning

Two photon microscopy and optical coherence tomography (OCT) are two standard methods for measuring flow speeds of red blood cells in microvessels, particularly in animal models. However, traditional two photon microscopy lacks the depth of field to adequately capture the full volumetric complexity of the cerebral microvasculature and OCT lacks the specificity offered by fluorescent labeling. In addition, the traditional raster scanning technique utilized in both modalities requires a balance of image frame rate and field of view, which severely limits the study of RBC velocities in the microvascular network. Here, we overcome this by using a custom two photon system with an axicon based Bessel beam to obtain volumetric images of the microvascular network with fluorescent specificity. We combine this with a novel scan pattern that generates pairs of frames with short time delay sufficient for tracking red blood cell flow in capillaries. We track flow speed in 10 or more capillaries simultaneously at 1 Hz in a 237 m x 237m x 120 m volume and quantify both spatial and temporal variability in speed. We also demonstrate the ability to track flow speed changes around stalls in capillary flow.

bioengineering↗

bioRxiv2022

EDoF-Miniscope: pupil engineering for extended depth-of-field imaging in a fluorescence miniscope

Extended depth of field (EDoF) microscopy has emerged as a powerful solution to greatly increase the access into neuronal populations in table-top imaging platforms. Here, we present EDoF-Miniscope, which integrates an optimized thin and lightweight binary diffractive optical element (DOE) onto the gradient refractive index (GRIN) lens of a head-mounted fluorescence miniature microscope, i.e. "miniscope". We achieve an alignment accuracy of 70 m to allow a 2.8X depth-of-field extension between the twin foci. We optimize the phase profile across the whole back aperture through a genetic algorithm that considers the primary GRIN lens aberrations, optical property of the submersion media, and axial intensity loss from tissue scattering in a Fourier optics forward model. Compared to other computational miniscopes, our EDoF-Miniscope produces high-contrast signals that can be recovered by a simple algorithm and can successfully capture volumetrically distributed neuronal signals without significantly compromising the speed, signal-to-noise, signal-to-background, and maintain a comparable 0.9-m lateral spatial resolution and the size and weight of the miniature platform. We demonstrate the robustness of EDoF-Miniscope against scattering by characterizing its performance in 5-m and 10-m beads embedded in scattering phantoms. We demonstrate that EDoF-Miniscope facilitates deeper interrogations of neuronal populations in a 100-m thick mouse brain sample, as well as vessels in a mouse brain. Built from off-the-shelf components augmented by a customizable DOE, we expect that this low-cost EDoF-Miniscope may find utility in a wide range of neural recording applications.

bioengineering↗

bioRxiv2022

Targeted photothrombotic stroke leads to disruptions in neurovascular coupling

Functional neuroimaging, which measures hemodynamic responses to brain activity, has great potential for monitoring stroke patients. However, the neurophysiological interpretations of these hemodynamic signals remain a challenge as the stroke is likely to alter both neural activity and neurovascular coupling. To address this challenge, we simultaneously captured neural activity, through fluorescence calcium imaging, and hemodynamics, through intrinsic optical signal imaging, during longitudinal stroke recovery. We found that photothrombotic stroke to somatosensory forelimb region altered neurovascular coupling in the acute phase (2 days and 1 week post-stroke) within the affected forelimb and peri-infarct regions. Neurovascular coupling was reestablished in the chronic phase (4 weeks post-stroke), and acute recovery of neurovascular coupling predicted sensorimotor function. Stroke also resulted in increases in the power of global brain oscillations, which showed distinct patterns between calcium and hemodynamics. Increased calcium excitability in the contralesional hemisphere was associated with increased intrahemispheric connectivity. Additionally, acute increases in hemodynamic oscillations were associated with improved sensorimotor outcomes. TeaserAcute ischemic stroke leads to neurovascular uncoupling and the extent of early recoupling predicts sensorimotor recovery.

physiology↗

bioRxiv2021

Large-scale cellular-resolution imaging of neural activity in freely behaving mice

Miniaturized microscopes for head-mounted fluorescence imaging are powerful tools for visualizing neural activity during naturalistic behaviors, but the restricted field of view of first-generation miniscopes limits the size of neural populations accessible for imaging. Here we describe a novel miniaturized mesoscope offering cellular-resolution imaging over areas spanning several millimeters in freely moving mice. This system enables comprehensive visualization of activity across entire brain regions or interactions across areas.

neuroscience↗

bioRxiv2020

Wide field-of-view volumetric imaging by a mesoscopic scanning oblique plane microscopy with switchable objective lens

Conventional light sheet fluorescence microscopy (LSFM), or selective plane illumination microscopy (SPIM), enables high resolution 3D imaging over a large volume by using two orthogonally aligned objective lenses to decouple excitation and emission. The recent development of oblique plane microscopy (OPM) simplifies LSFM design with only one single objective lens, by using off-axis excitation and remote focusing. However, most reports on OPM has a limited microscopic field of view (FOV), typically within 1×1 mm2. Our goal is to overcome the limitation with a new variant of OPM to achieve mesoscopic FOV. We implemented an optical design of mesoscopic scanning OPM to allow using low numerical aperture (NA) objective lens. The angle of the intermediate image before the remote focusing system was increased by a demagnification under Scheimpflug condition such that the light collecting efficiency in the remote focusing system was significantly improved. We characterized the 3D resolutions and FOV by imaging fluorescence microspheres, and demonstrated the volumetric imaging on intact whole zebrafish larvae, mouse cortex, and multiple Caenorhabditis elegans (C. elegans). We demonstrate a mesoscopic FOV up to ~6× 5×0.6 mm3 volumetric imaging, the largest reported FOV by OPM so far. The angle of the intermediate image plane is independent of the magnification. As a result, the system is highly versatile, allowing simple switching between different objective lenses with low (10x, NA 0.3) and median NA (20x, NA 0.5). Detailed microvasculature in zebrafish larvae, mouse cortex, and neurons in C. elegans are clearly visualized in 3D. The proposed mesoscopic scanning OPM allows using low NA objective such that centimeter-level FOV volumetric imaging can be achieved. With the extended FOV, simple sample mounting protocol, and the versatility of changeable FOVs/resolutions, our system will be ready for the varieties of applications requiring in vivo volumetric imaging over large length scales.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

bioRxiv2019

Neutrophil-mediated dynamic capillary stalls in ischemic penumbra: persistent traffic jams after reperfusion contribute to injury

Ever since the introduction of thrombolysis and the subsequent expansion of endovascular treatments for acute ischemic stroke, it remains to be identified why the actual outcomes are less favorable despite recanalization. Here, by high spatio-temporal resolution imaging of capillary circulation in mice, we introduce the pathological phenomenon of dynamic flow stalls in cerebral capillaries, occurring persistently in the salvageable penumbra after recanalization. These stalls, which are distinct from permanent cellular plugs that can lead to no-flow, were temporarily and repetitively occurring in the capillary network, impairing the overall circulation like small focal traffic jams. In vivo microscopy in the ischemic penumbra revealed leukocytes traveling through capillary lumen or getting stuck, while red blood cell flow was being disturbed in the neighboring segments, within 3 hours after stroke onset. Stall dynamics could be modulated, by injection of an anti-Ly6G antibody specifically targeting neutrophils. By decreasing the number and duration of stalls, we were able to improve the blood flow in the penumbra within 2-24 hours after reperfusion, increase capillary oxygenation, decrease cellular damage and improve functional outcome. Thereby the dynamic microcirculatory stall phenomenon contributes to the ongoing penumbral injury and is a potential hyperacute stage mechanism adding on previous observations of detrimental effects of activated neutrophils in ischemic stroke.\n\nSignificanceThis work provides in vivo evidence that, even in perfused capillaries, abnormal capillary flow patterns in the form of dynamic stalls can contribute to ongoing tissue injury in the salvageable penumbra in very early hours of cerebral ischemia. These events resembling micro traffic jams in a complex road network, are mediated by passage of neutrophils through the microcirculation and persist despite recanalization of the occluded artery.

neuroscience↗

bioRxiv2019

Microscale physiological events on the human cortical surface detected with PEDOT:PSS Electrodes

Despite ongoing advancements in our understanding of the local single-cellular and network-level activity of neuronal populations in the human brain, extraordinarily little is known about their intermediate microscale local circuit dynamics. Here, we utilized ultrahigh density microelectrode arrays and a rare opportunity to perform intracranial recordings across multiple cortical areas in human participants to discover three distinct classes of cortical activity that are not locked to ongoing natural brain rhythmic activity. The first included fast waveforms similar to extracellular single unit activity. The other two types were discrete events with slower waveform dynamics and were found preferentially in upper layers of the grey matter. They were also observed in rodents, non-human primates, and semi-chronic recordings in humans via laminar and Utah array microelectrodes. The rates of all three events were selectively modulated by auditory and electrical stimuli, pharmacological manipulation, and cold saline application and had small causal co-occurrences. These results suggest that with the proper combination of high resolution microelectrodes and analytic techniques it is possible to capture neuronal dynamics that lay between somatic action potentials and aggregate population activity and that understanding these intermediate microscale dynamics may reveal important details of the full circuit behavior in human cognition.

neuroscience↗

bioRxiv2019

Functional ultrasound speckle decorrelation-based velocimetry of the brain

A high-speed, contrast free, quantitative ultrasound velocimetry (vUS) for blood flow velocity imaging throughout the rodent brain is developed based on the normalized first order temporal autocorrelation function of the ultrasound field signal. vUS is able to quantify blood flow velocity in both transverse and axial directions, and is validated with numerical simulation, phantom experiments, and in vivo measurements. The functional imaging ability of vUS is demonstrated by monitoring blood flow velocity changes during whisker stimulation in awake mice. Compared to existing power Doppler and color Doppler-based functional ultrasound imaging techniques, vUS shows quantitative accuracy in estimating both axial and transverse flow speeds and resistance to acoustic attenuation and high frequency noise.

bioengineering↗

bioRxiv2019

Dynamic Laser Speckle Imaging

Utilizing a high-speed camera and recording back-scattered laser light at more than 20,000 frames per second, we introduce the first wide-field dynamic laser speckle imaging (DLSI) in which we are able to quantify the laser speckleintensity temporal auto-correlation function g2({tau}) for every pixel individually to obtain a quantitative image of the dynamics of the light scattering particles in the sample. The ability to directly and quantitatively measure the intensity auto-correlation function allows us to solve the problem of how to quantitatively interpret data measured by laser speckle contrast imaging (LSCI), multi-exposure laser speckle imaging (MESI) and laser Doppler flowmetry (LDF). The intensity auto-correlation function is related to the field temporal auto-correlation function g1({tau}), which has been quantitatively related to the dynamics of the light scattering particles including flowing red blood cells. The form of g1({tau}) depends on the amount of light scattering (i.e. single or multiple scattering) and the type of particle motion (i.e. ordered or unordered). Although these forms of the field correlation functions have been established for over 30 years, there is no agreement nor experimental support on what scattering and motion regimes are relevant for the varied biomedical applications. We thus apply DLSI to image cerebral blood flow in mouse through a cranial window and show that the generally accepted form of g1({tau}), is applicable only to visible surface vessels of a specific size (20 - 200m). We demonstrate that for flow in smaller vessels and in parenchymal regions that the proper g1({tau}) form corresponds with multiple scattering light and unordered motion which was never considered to be relevant for these techniques. We show that the wrong assumption for the field auto-correlation model results in a severe underestimation of flow changes when measuring blood flow changes during ischemic stroke. Finally, we describe how DLSI can be integrated with other laser speckle methods to guide model selection, or how it can be used by itself as a quantitative blood flow imaging technique.

bioengineering↗