Biology subjects

Sachdev, R.

Publications and source records attributed to Sachdev, R..

14 recordsLinked to original sources

bioRxiv2026

Coordinated orienting behavior emerges following unilateral optogenetic activation of Superior Colliculus GABAergic neurons

Orienting coordinates movements of the eyes, whiskers, nose, and other effectors, but how the superior colliculus (SC) recruits these components over time remains unclear. We combined unilateral optogenetic activation of SC GABAergic neurons with high-speed tracking of facial movements and Neuropixels recordings to examine SC-evoked orienting in head-fixed mice. Stimulation recruited movements of the whiskers, nose, eyes, and pupil. Horizontal eye and nose movements were directed contralateral to the stimulated hemisphere, whereas vertical eye movements, pupil dilation, and whisker protraction did not differ significantly between stimulation sides. Nose and whisker movements generally preceded eye movements, followed by slower pupil dilation, revealing a temporally organized response. Recordings from the SC contralateral to the stimulated hemisphere revealed heterogeneous neuronal responses comprising short-latency excitation and delayed excitation or inhibition. Short-latency excitation was similar on trials with and without evoked movements, whereas delayed excitation was greater on trials that evoked eye or nose movements. Neurons modulated during spontaneous nose movements showed corresponding optogenetically evoked responses, linking stimulation-induced activity to endogenous movement-related activity. Thus, activation of SC GABAergic neurons initiates evolving population activity that recruits a coordinated sequence of orienting movements.

neuroscience↗

bioRxiv2026

Cortex-wide representational drift of different layers

Representational drift, the gradual evolution of neural population codes over days, has been widely documented at the level of single neurons. However, whether drift is organized across larger cortical populations and spatial scales remains unclear. Here, we examined cortex-wide population dynamics under tightly controlled sensory input and behavior. Using widefield calcium imaging, we longitudinally recorded excitatory activity in Layers 2/3 (L2/3) or Layer 5 (L5) across 25 cortical areas while mice performed a whisker-based texture discrimination task. Sensory-evoked activity was tracked over five consecutive days during stable task performance. Population activity patterns reorganized over days, across the cortex, in both layers. This reorganization followed distinct laminar motifs: notably L5 responses exhibited a widespread, monotonic decrease in activity across most cortical areas, whereas L2/3 responses showed spatially localized and heterogeneous changes that were strongest during the sensory period. These laminar differences extended beyond the stimulus period, with L5 exhibiting more prolonged temporal engagement than L2/3. Together, these findings indicate that representational drift can unfold as a process that is coordinated across cortex with distinct laminar profiles. Thus, drift may reflect a structured feature of cortex-wide circuit dynamics.

neuroscience↗

bioRxiv2025

mTORC1-Dependent Signaling in Layer 5b Neurons Is Required for Memory Consolidation

Memory consolidation relies on activity-dependent neuronal plasticity, particularly in deep-layer cortical neurons that integrate long-range inputs from medial temporal lobe (MTL) structures. In the neocortex, apical tuft dendrites of layer 5b pyramidal neurons receive direct input from the MTL within cortical layer 1, and their activation is critical for associative learning. However, the molecular mechanisms that enable learning-induced plasticity in these neurons remain poorly understood. Here, we demonstrate that activity-dependent, mTORC1-regulated translation in layer 5b neurons contributes to learning and memory. Using in vivo paradigms such as exposure to an enriched environment (EE) and in vitro models of network activation by chemical long-term potentiation (cLTP), combined with cell type-specific translational profiling (RiboTag), we identify candidate mRNAs associated with experience-dependent plasticity. We further show that pharmacological inhibition of canonical mTORC1 signaling during memory-relevant tasks abrogated memory consolidation. Our findings identify the mTORC1 pathway as a central regulator of learning-induced protein translation and cortical plasticity.

neuroscience↗

bioRxiv2025

Cortex-wide laminar dynamics diverge during learning

Learning to link sensory information to motor actions involves dynamic coordination across cortical layers and regions. However, the involvement of a particular layer in learning, especially from a cortex-wide perspective, is relatively unknown. Using wide-field calcium imaging in mice as they learn a whisker-based go/no-go task, we tracked activity in layers 2/3 or 5 (L2/3 or L5) across 25 cortical areas. A surprising initial effect of learning was that activity in L5 but not in L2/3 was globally suppressed at auditory cue onset. As the texture comes into touch, we found that L2/3 displayed learning-related enhancements in higher order association areas rostrolateral (RL) and secondary somatosensory (S2), whereas L5 in these areas oppositely decreased. During texture touch, the barrel cortex (BC) displayed similar learning-related enhancement in both layers. As sensory information is transformed into a motor action, there was a frontal/posterior divergence that emerges after learning, in which L5 was enhanced in the frontal cortex and L2/3 was suppressed in the posterior cortex. In general, learning related correlations were often stronger between distant cortical layers than within the same column, suggesting that learning drives laminar interactions that transcend traditional columnar organization. Together, these results reveal that learning orchestrates a dynamic interplay of activity across space, time and cortical layers. Our findings emphasize the critical role of laminar architecture in shaping cortical plasticity and support the view that layer-specific circuits are fundamental to sensorimotor learning.

neuroscience↗

bioRxiv2025

Contextual modulation and blunted defensive responses to predators in head-fixed and freely moving mice

Behavioral responses to threat -- such as fleeing, freezing, or fighting--can be innate, learned, and strongly shaped by context or competing goals. Here, we asked whether exposure to an ecologically relevant predator obligatorily elicits canonical defensive behaviors across behavioral contexts. We examined predator responses in mice across four experimental conditions: one novel head-fixed reward-driven foraging task and three established paradigms in freely moving animals. In the head-fixed condition, water-deprived mice were trained to walk on a treadmill controlling a virtual environment and water reward delivery and were subsequently exposed to a live rat positioned above the lick spout. Despite the presence of the predator, most mice (5 of 7) maintained foraging performance at baseline levels. However, individual mice exhibited significant, coordinated changes in running speed, pupil diameter, eye movements, and posture, indicating engagement with the threat. To assess how context influences predator responses, we exposed 36 naive, freely moving mice to fear-inducing stimuli, including looming visual cues, rat odor, and a live rat. Even under these conditions, defensive behaviors were variable: only a subset of mice displayed avoidance or escape, and when presented with a freely moving rat, approximately half of the mice avoided the predator. Together, these findings show that predator threat does not elicit a uniform or obligatory defensive repertoire in mice. Instead, defensive responses are expressed flexibly, and are shaped by environmental constraints, task demands, and individual variability. These results challenge the assumption that innate fear behaviors are automatically triggered by predator encounters. Graphical AbstractUsing a head-fixed, reward-based foraging task and complementary freely moving paradigms, we show that mouse responses to predator-related stimuli are variable and context dependent, with limited expression of canonical defensive behaviors such as freezing or flight. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/658679v3_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@a05a31org.highwire.dtl.DTLVardef@1815084org.highwire.dtl.DTLVardef@cd3a11org.highwire.dtl.DTLVardef@19f5d95_HPS_FORMAT_FIGEXP M_FIG C_FIG

animal behavior and cognition↗

bioRxiv2025

Tuft dendrites in frontal motor cortex enable flexible learning

Flexible learning relies on integrating sensory and contextual information to adjust behavioral output in different environments. The anterolateral motor cortex (ALM) is a frontal area critical for action selection in rodents. Here we show that inputs critical to decision-making converge on the apical tuft dendrites of L5b pyramidal neurons in ALM. We therefore investigated the role of these dendrites in a rule-switching paradigm. Activation of dendrite-inhibiting layer 1 interneurons impaired relearning, without affecting previously learned behavior. Remarkably, this inhibition profoundly suppressed calcium activity selectively in dendritic shafts but not spines while reducing burst firing. Moreover, excitatory synaptic inputs to tuft dendrites exhibited rule-dependent clustering. We conclude that active dendritic integration is a key computational component of flexible learning.

neuroscience↗

bioRxiv2024

LRRK2 G2019S variant is associated with transcriptional changes in Parkinson's disease human myeloid cells under proinflammatory environment

The G2019S mutation in the leucine-rich repeat kinase 2 (LRRK2) gene is a major risk factor for the development of Parkinsons disease (PD). LRRK2, although ubiquitously expressed, is highly abundant in cells of the innate immune system. Given the importance of central and peripheral immune cells in the development of PD, we sought to investigate the consequences of the G2019S mutation on microglial and monocyte transcriptome and function. We have generated large-scale transcriptomic profiles of isogenic human induced microglial cells (iMGLs) and patient derived monocytes carrying the G2019S mutation under baseline culture conditions and following exposure to the proinflammatory factors IFN{gamma} and LPS. We demonstrate that the G2019S mutation exerts a profound impact on the transcriptomic profile of these myeloid cells, and describe corresponding functional differences in iMGLs. The G2019S mutation led to an upregulation in lipid metabolism and phagolysosomal pathway genes in untreated and LPS/IFN{gamma} stimulated iMGLs, which was accompanied by an increased phagocytic capacity of myelin debris. We also identified dysregulation of cell cycle genes, with a downregulation of the E2F4 regulon. Transcriptomic characterization of human-derived monocytes carrying the G2019S mutation confirmed alteration in lipid metabolism associated genes. Altogether, these findings reveal the influence of G2019S on the dysregulation of the myeloid cell transcriptome under proinflammatory conditions.

genetics↗

bioRxiv2023

Refined movement analysis in the Staircase test reveals differential motor deficits in mouse models of stroke

Accurate assessment of post-stroke deficits is vital in translational research. Recent advances in machine learning provide unprecedented precision in quantifying rodent motor behavior post-stroke. However, the extent to which these tools can detect lesion-specific upper extremity deficits remains unclear. Using proximal middle cerebral artery occlusion (MCAO) and cortical photothrombosis (PT), we assessed post-stroke impairments in mice through the Staircase test. Lesion locations were identified using 7T-MRI. Machine learning was applied to reconstruct kinematic trajectories using MouseReach, a data-processing toolbox. This yielded 30 refined outcome parameters effectively capturing motor deficits. Lesion reconstructions located ischemic centers in the striatum (MCAO) and sensorimotor cortex (PT). Pellet retrieval was altered in both cases but did not correlate with stroke volume or ischemia extent. Instead, cortical ischemia was characterized by increased hand slips and modified reaching success. Striatal ischemia led to progressively prolonged reach durations, mirroring delayed symptom onset in basal ganglia strokes. In summary, refined machine learning-based movement analysis revealed specific deficits in mice after cortical and striatal ischemia. These findings emphasize the importance of thorough behavioral profiling in preclinical stroke research to increase translational validity of behavioral assessments.

neuroscience↗

bioRxiv2022

What moves when mice move a single whisker to touch? Individuality and stereotypy in behavior

A key function of the brain is to move the body through a rich, complex environment. When rodents engage with their environment, they move their whiskers as they extract tactile information. Even though the study of whisking has a long history, the details of individual whisker movements bilaterally, of nose movement, of stereotypy and variability in an active whisking to touch task are unknown. Here we trained head fixed mice in a simple go-cue task to move a whisker on one side of the face to touch a sensor and tracked facial movements. Our analysis shows that mice specifically control movement of the whisker they use to touch and that as they move their whiskers, they move their nose and apply forces on the head-post in a manner that reflects the behavioral epoch, i.e. whether go cue triggered movement had begun, or a whisker was touching the sensor. Importantly, mice control the setpoint, amplitude and frequency of movement of whiskers bilaterally and individually. Additionally, even though mice achieved the goal of the task -- to touch the sensor within 2 seconds -- how they coordinated movement of the nose and forces on head post with movement of individual whiskers was stereotyped and related to the distance they needed to move a whisker to touch the sensor. Our work shows how stereotyped mouse behavior can be, and it emphasizes both the level of fine motor control mice can exert over individual whiskers and the extent of facial movements in a goal-directed whisking-to-touch task. SignificanceRecent work shows that facial movements are reflected in the activity of a surprisingly large number of brain areas. But what aspects of the face do mice move when they move a whisker to actively touch an object? Our work shows that while mice control the movement of a whisker they use to touch, they also move their nose, apply forces on the head-post and move adjacent whiskers and whiskers on the other side of the face. Additionally, our analysis shows that from day-to-day, this behavior can be surprisingly stereotyped, and that small changes in how far mice move a whisker during tactile behavior fundamentally changes the relationship between the movement of a single whisker and other facial movements.

neuroscience↗

bioRxiv2021

Input to layer 1 of somatosensory cortex: Local input outweighs long-range and can modulate the activity of layer 1 interneurons

Neocortical Layer (L) 1 has been proposed to be at the center for top-down and bottom-up integration. It is a locus for interactions between long-range inputs, L1 interneurons and apical tuft dendrites of pyramidal neurons. While input to L1 has been studied intensively, the level and effect of input to this layer has still not been completely characterized. Here we examined the input to L1 of mouse somatosensory cortex with retrograde tracing and optogenetics. Our assays reveal that local input to L1 is predominantly from L2/3 and L5 pyramidal neurons and interneurons, and that subtypes of local L5 and L6b neurons project to L1 with different probabilities. Long-range input from sensory-motor cortices to L1 of S1 arose predominantly from L2/3 neurons. Our optogenetic experiments showed that intra-telencephalic L5 pyramidal neurons drive L1 interneurons but have no effect locally on L5 apical tuft dendrites. Dual retrograde tracing revealed that a fraction of local and long-range neurons were both presynaptic to L5 neurons and projected to L1. Our work highlights the prominent role of local inputs to L1 and shows the potential for complex interactions between long-range and local inputs which are both in position to modify the output of somatosensory cortex.

neuroscience↗

bioRxiv2021

The impact of phosphorylated Pten at threonine 366 on cortical connectivity and behaviour

The lipid phosphatase Pten (phosphatase and tensin homologue on chromosome 10) is a key tumour suppressor gene and an important regulator of neuronal signalling. Pten mutations have been identified in patients with autism spectrum disorders, characterized by macrocephaly, impaired social interactions and communication, repetitive behaviour, intellectual disability, and epilepsy. Pten enzymatic activity is regulated by a cluster of phosphorylation sites at the C-terminus of the protein. Here we specifically focussed on the role of Pten T366 phosphorylation and generated a knock-in mouse line in which Pten T366 was substituted with alanine (PtenT366A/T366A). We identify that phosphorylation of Pten at T366 controls neuron size and connectivity of brain circuits involved in sensory processing. We show in behavioural tests that PtenT366/T366A mice exhibit cognitive deficits and selective sensory impairments, with significant differences in male individuals. We identify restricted cellular overgrowth of cortical neurons in PtenT366A/T366A brains, linked to increases in both dendritic arborization and soma size. In a combinatorial approach of anterograde and retrograde monosynaptic tracing using rabies virus, we characterize differences in connectivity to the primary somatosensory cortex of PtenT366A/T366A brains, with imbalances in long-range cortico-cortical input to neurons. We conclude that phosphorylation of Pten at T366 controls neuron size and connectivity of brain circuits involved in sensory processing and propose that PTEN T366 signalling may account for a subset of autism-related functions of Pten.

neuroscience↗

bioRxiv2021

The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote mitotic NPC assembly

During mitotic exit, thousands of nuclear pore complexes (NPCs) assemble concomitant with the nuclear envelope to build a transport-competent nucleus. We show here that Nup50 plays a crucial role in NPC assembly that is independent of its well-established function in nuclear transport. RNAi-mediated downregulation in cells or immunodepletion of the protein in Xenopus egg extracts interferes with NPC assembly. We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and NPC interaction. Surprisingly, neither NPC interaction nor binding of Nup50 to importin , {beta}, the GTPase Ran or chromatin is crucial for its function in the assembly process. Instead, we discovered that an N-terminal fragment of Nup50 can stimulate the Ran guanine exchange factor RCC1 and NPC assembly, indicating that Nup50 acts via the Ran system in mitotic NPC reformation. In support of this conclusion, Nup50 mutants defective in RCC1 binding and stimulation cannot replace the wild type protein in in vitro NPC assembly assays.

cell biology↗

bioRxiv2021

Predicting behavior from eye movement and whisking asymmetry

Navigation through complex environments requires motor planning, motor preparation and the coordination between multiple sensory motor modalities. For example, the stepping motion when we walk is coordinated with motion of the torso, arms, head and eyes. In rodents, movement of the animal through the environment is often coordinated with whisking. Here we trained head fixed mice, navigating a floating Airtrack plus maze, to overcome their directional preference and use cues indicating the direction of movement expected in each trial. Once cued, mice had to move backward out of a lane, then turn in the correct direction, and enter a new lane. In this simple paradigm, as mice begin to move backward, they position their whiskers asymmetrically: whiskers on one side of the face protract, and on the other side they retract. This asymmetry reflected the turn direction. Additionally, on each trial, mice move their eyes conjugately in the direction of the upcoming turn. Not only do they move their eyes, but saccadic eye movement is coordinated with the asymmetric positioning of the whiskers. Our analysis shows that the asymmetric positioning of the whiskers predicts the direction of turn that mice will make at an earlier stage than eye movement does. We conclude that, when mice move or plan to move in complex real-world environments, their motor plan and behavioral state can be read out in the movement of both their whiskers and eyes.

neuroscience↗

bioRxiv2018

Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA

Processing bodies (PBs) are cytoplasmic mRNP granules that assemble via liquid-liquid phase separation and are implicated in the decay or storage of mRNAs. How PB assembly is regulated in cells remains unclear. We recently identified the ATPase activity of the DEAD-box protein Dhh1 as a key regulator of PB dynamics and demonstrated that Not1, an activator of the Dhh1 ATPase and member of the CCR4-NOT deadenylase complex inhibits PB assembly in vivo [Mugler et al., 2016]. Here, we show that the PB component Pat1 antagonizes Not1 and promotes PB assembly via its direct interaction with Dhh1. Intriguingly, in vivo PB dynamics can be recapitulated in vitro, since Pat1 enhances the phase separation of Dhh1 and RNA into liquid droplets, whereas Not1 reverses Pat1-Dhh1-RNA condensation. Overall, our results uncover a function of Pat1 in promoting the multimerization of Dhh1 on mRNA, thereby aiding the assembly of large multivalent mRNP granules that are PBs.

biochemistry↗