Biology subjects

Grodem, S.

Publications and source records attributed to Grodem, S..

9 recordsLinked to original sources

bioRxiv2026

Large-scale volumetric two-photon calcium imaging enables cellular-resolution mesoscopic mapping of marmoset cortical areas

Primate neocortex is organized into functionally defined domains. Understanding how the functional organization within each domain emerges from single-cell tuning properties has been hampered by the lack of imaging tools that can capture large-scale activity at different depths of the scattering primate brain at cellular resolution and physiological timescales. Here, we demonstrate mesoscopic and volumetric cellular-resolution calcium imaging of entire cortical areas in the marmoset brain at multi-Hertz rates by combining fluorescence lifetime-limited temporally multiplexed two-photon recording based on Light Beads Microscopy (LBM) with optimized calcium indicator targeting. Using this approach, we perform volumetric recording of neuronal population activity within cortical volumes spanning up to 4 x 4 x 0.3 mm3 capturing the simultaneous activity of over 96,000 cells, including more than 46,000 stimulus-responsive neurons. In auditory cortex, we found fine-grain heterogeneous tuning of individual neurons to frequencies within broader tonotopic gradients. In the middle temporal area (MT) we found direction tuning along functional continua rather than discrete categories, encompassing uni-, bi-, and pandirectional tuning, where cells with similar tuning tend to cluster. Tuning direction follows a columnar organization with a lateral periodicity of [~]500 {micro}m and low variability across depth. Columns are organized by a pinwheel structure. Noise correlations between cells, revealing functional interactions, decay isotropically and monotonically with distance but remain significant even at lateral distances exceeding 3 mm and thus the scale of multiple columns. Together, these discoveries reveal the need for neurotechnologies bridging scales from single cells to multi-columnar systems. The technological advancements open the door for future large-scale, cellular-resolution investigations of functional organization and population dynamics across entire cortical areas in the primate brain.

neuroscience↗

bioRxiv2026

Raster photostimulation of large-scale neural populations

Neural computations are implemented by distributed neural populations that typically span multiple brain areas. Simultaneous recording and photo-activation experiments can reveal the structure and logic of these neural computations, but such methods are typically limited to small subsets of neurons in restricted fields of view. Here we describe a new system called raster photostimulation for activating and recording thousands of neurons, over a short 300 ms time window and over a large 5 mm field-of-view on a two-photon mesoscope. The photo-activation is precisely matched to the neural recording configuration, as it uses the same optical path, although with a different laser that is independently gated. We demonstrate pixel-level precision, frame-by-frame mask updating, and single-frame photostimulation of thousands of neurons. While this method lacks the precise temporal control of alternative methods, it compensates with ease-of-use, spatial precision, cost of implementation and by pushing the limits on the number of near-simultaneously stimulated neurons.

neuroscience↗

bioRxiv2025

Spatial predictive coding in visual cortical neurons

Predictive coding is a theoretical framework that can explain how animals build internal models of their sensory environments by predicting sensory inputs. Predictive coding may capture either spatial or temporal relationships between sensory objects. While the original theory by Rao and Ballard, 1999 described spatial predictive coding, much of the recent experimental data has been interpreted as evidence for temporal predictive coding. Here we directly tested whether the "mismatch" neural responses in sensory cortex are due to a spatial or a temporal internal model. We adopted two common paradigms to study predictive coding: one based on virtual-reality and one based on static images. After training mice with repeated visual stimulation for several days, we performed multiple manipulations, including: 1) we introduced a novel stimulus, 2) we replaced a stimulus with a novel gray wall, 3) we duplicated a trained stimulus, or 4) we altered the order of the stimuli. The first two manipulations induced a substantial mismatch response in neural populations of up to 20,000 neurons recorded across primary and higher-order visual cortex, while the third and fourth ones did not. Thus, a mismatch response only occurred if a new spatial - not temporal - pattern was introduced.

neuroscience↗

bioRxiv2025

Brainstem sensing of multiple body signals during food consumption

Studies of body-to-brain communication often examine one stimulus or organ at a time, yet the brain must integrate many body signals during behavior. For example, food consumption generates diverse oral and post-oral chemical and mechanical signals transduced by well-characterized peripheral neuronal pathways. Far less is known about how these and other bodily signals are integrated and organized in the brainstem lateral parabrachial nucleus (LPBN), a key interoceptive sensory hub. We established methods to image the activity of 1000s of neurons throughout a large region of mouse LPBN. Food consumption drove a seconds-long wave of activity across LPBN, with dynamics mirroring the movement of food through the upper gastrointestinal tract observed using X-ray fluoroscopy. By imaging the same neurons across days, we found that spatially clustered subsets of neurons encoded oral signals, stomach filling, visceral malaise, arousal, and/or body movement. Moreover, only certain subsets were modulated by cortical input. Together, these experiments reveal a functional specialization in the LPBN that integrates contextual information from the body to guide behavior.

neuroscience↗

bioRxiv2024

Task and Behavior-Related Variables Are Encoded by the Postrhinal and Medial Entorhinal Cortex During Non-Spatial Associative Learning

The medial entorhinal cortex (MEC) is pivotal in spatial computations and episodic memory. In particular, an animals position can be decoded from the activity of entorhinal grid cells. However, it remains elusive whether MEC could play a more general role in different types of associative learning and how the representations develop during the learning process. It has been shown that the postrhinal cortex (POR), which is directly connected to MEC, integrates visual stimuli with salient outcomes. Here, we use a non-spatial visual association task to investigate whether MEC neurons represent low-level visual cues during learning. Using a Go/NoGo visual association task, we recorded neural activity in MEC and POR throughout the learning phase as mice associated drifting gratings with rewarded, aversive, or neutral outcomes. Our findings reveal that the neural tuning curves in both the POR and MEC change with the learning of the task. From the start of training, the POR neurons exhibited response tuning to the visual cues, and the tuning was stable to cue orientations during learning. In contrast, MEC neurons did not initially respond very strongly to visual cues but developed a robust tuning toward the rewarded trials. While the MECs representation of visual information was limited, it encoded other task elements. A large fraction of the neurons formed distinct functional clusters that were either activated or suppressed by reward-related behavior. Remarkably, these clusters segregated anatomically in MEC and maintained strong within-cluster correlations before and after training. Notably, although the same functional clusters were apparent in the POR, they did not show any anatomical structure as in the MEC. Task reversal induced significant changes in network responses across both regions, with a decrease in overall task-responsive neurons but a slight increase in stimulus representation. Strikingly, information about the choice to lick emerged with learning in both brain areas, and most significantly within the functional cell clusters representing reward consumption and plus-cue stimulus. Our results demonstrate that although neurons in MEC and POR develop behavior-modulated tuning during learning of a non-spatial visual association task, the MEC exhibits stronger within-cluster correlations and anatomical organization. Conversely, the POR population exhibits less structural organization and more specific stimulus-tuning, which is reflective of being a higher visual association area. Our findings reveal that the MEC can encode task- and behavior-related variables beyond spatial information.

neuroscience↗

bioRxiv2024

Cortical Reactivations Modulated by Local InhibitoryCircuits Mediate Memory Consolidation

Highly salient events activate neurons across various brain regions. During subsequent rest or sleep, the activity patterns of these neurons often correlate with those observed during the preceding experience. Growing evidence suggests that these reactivations play a crucial role in memory consolidation, the process by which experiences are solidified in cortical networks for long-term storage. Here, we demonstrate that reactivations in the lateral visual cortex are vital for the consolidation of visual association learning. By employing longitudinal two-photon Ca2+ imaging alongside paired LFP recordings in the hippocampus and cortex, we show that targeted manipulation of PV+ inhibitory neurons in the lateral visual cortex after daily training selectively attenuated cue-specific reactivations and learning, with no apparent effect on normal network function during training. In contrast, reactivations in the control group were biased towards salient cues, aligned with learning process and persisted for hours after training had ended. Overall, our results underscore a crucial role for cortical reactivations in memory consolidation.

neuroscience↗

bioRxiv2024

Deciphering the Role of Aggrecan in Parvalbumin Interneurons: Unexpected Outcomes from a Conditional ACAN Knockout That Eliminates WFA+ Perineuronal Nets

The transition from juvenile to adult is accompanied by the maturation of inhibitory parvalbumin-positive (PV+) neurons and reduced plasticity. This transition involves the formation of perineuronal nets (PNNs), a dense configuration of the extracellular matrix that predominantly envelops parvalbumin-positive (PV+) neurons. Aggrecan, a proteoglycan encoded by the ACAN gene, has been shown to have a key role in the PNNs as knock-out of ACAN in the adult brain reactivates juvenile plasticity, but the contribution of different cell populations is unknown Here, we establish and characterize a mouse model in which ACAN is selectively knocked out (KO) in PV+ neurons (ACANflx/PVcre). Moreover, we develop a viral tool to perform similar cell-type directed KO in adult mice. Both models are compared with the traditional method of PNN removal, namely enzymatic degradation of PNNs with Chondroitinase ABC (chABC). We show that PV+ neurons in adult ACANflx/PVcre mice do not produce PNNs that are labeled by Wisteria floribunda agglutinin (WFA), the most commonly used PNN marker. Surprisingly, electrophysiological properties of PV+ interneurons in the visual cortex (V1) and ocular dominance plasticity of adult ACANflx/PVcre mice were similar to controls. In contrast, AAV-mediated ACAN knockout in adult mice increased ocular dominance plasticity. Moreover, in vivo chABC treatment of KO mice resulted in reduced firing rate of PV+ cells and increased frequency of spontaneous excitatory postsynaptic currents (sEPSC), a phenotype associated with chABC treatment of WT animals. This suggests compensatory mechanisms in the germline KO. Indeed, qPCR of bulk tissue indicates that other PNN components are expressed at higher levels in the KO animals. Finally, we perform memory-and behavioral testing to see if the lack of ACAN from PV+ neurons throughout development affected stereotypic behaviors and memory processing. ACANflx/PVcre mice have learning and memory abilities similar to controls, but use bold search strategies during navigation in the Morris water maze. The low level of anxiety-related behavior is confirmed in an open field and zero maze, where they spent nearly twice the time in open areas.

neuroscience↗

bioRxiv2021

An updated suite of viral vectors for in vivo calcium imaging using local and retro-orbital injections

Calcium imaging using genetically encoded Ca2+ indicators (GECIs) is a widely adopted method to measure neural activity in modern neuroscience. Here, we explore the use of systemically administered viral vectors for brain-wide expression of GECIs, and adapt novel GECIs to optimize signal-to-noise. We show that systemic injections of PHP.eB AAVs to express GECIs is a highly promising technique for imaging neural activity and circumvent the need for transgenic GECI expressing mouse lines. We also establish the use of soma-targeted GECIs that outperform current Ca2+ indicators using both systemic and local virus injections.

neuroscience↗

bioRxiv2019

Molecular determinants of Arc oligomerization and formation of virus-like capsids

Expression of activity-regulated cytoskeleton-associated protein (Arc) is critical for long-term synaptic plasticity, memory formation, and cognitive flexibility. The ability of Arc to self-associate and form virus-like capsid structures implies functionally distinct oligomeric states. However, the molecular mechanism of Arc oligomerization is unknown. Here, we identified a 28-amino-acid region necessary and sufficient for Arc oligomerization. This oligomerization region is located within the second coil of a predicted anti-parallel coiled-coil in the N-terminal domain (NTD). Using alanine scanning mutagenesis, we found a 7-amino-acid motif critical for oligomerization and Arc-mediated transferrin endocytosis in HEK cells. Intermolecular fluorescence lifetime imaging in hippocampal neurons confirmed self-association mediated by the motif. To quantify oligomeric size, we performed a single-molecule photobleaching analysis of purified Arc wild-type and mutant. This analysis revealed a critical role for the NTD motif in the formation of higher-order Arc oligomers (30-170 molecules). Moreover, assembly of higher-order wild-type Arc oligomers was significantly enhanced by addition of GFP RNA. Purified wild-type Arc formed virus-like capsids, as visualized by negative-stain EM, and was estimated by light scattering analysis to contain 40-55 Arc units. In contrast, mutant Arc formed a homogenous dimer population as demonstrated by single-molecule TIRF imaging, size-exclusion chromatography with multi-angle light scattering analysis, small-angle X-ray scattering analysis, and single-particle 3D EM reconstruction. Thus, the dimer appears to be the basic building block for assembly. Herein, we show that the NTD motif is essential for higher-order Arc oligomerization, assembly of virus-like capsid particles, and facilitation of oligomerization by exogenous RNA. SIGNIFICANCEArc protein is rapidly expressed in neurons in response to synaptic activity and plays critical roles in synaptic plasticity, postnatal cortical developmental, and memory. Arc has diverse molecular functions, which may be related to distinct oligomeric states of the protein. Arc has homology to retroviral Gag protein and self-assembles into retrovirus-like capsid structures that are capable of intercellular transfer of RNA. Here, we identified a motif in the N-terminal coiled-coil domain of mammalian Arc that mediates higher-order oligomerization and formation of virus-like capsids. The basic building block is the Arc dimer and exogenous RNA facilitates further assembly. The identified molecular determinants of Arc oligomerization will help to elucidate the functional modalities of Arc in the mammalian brain.

biochemistry↗