Biology subjects

Kulkarni, A. S.

Publications and source records attributed to Kulkarni, A. S..

9 recordsLinked to original sources

bioRxiv2026

Corticospinal neuron subpopulations with opposing dynamics converge to shape spinal interneuron computations

Corticospinal neuron (CSN) activation plays a crucial role in orchestrating goal-directed actions, but the functional role of reduced CSN output, a feature conserved across species, remains unknown. By combining population imaging, projection mapping, and modelling in mice performing a Go/NoGo lever push task, we reveal that distinct corticospinal neuron subpopulations with opposing dynamics (i.e. increased or decreased activity) are selectively associated with skilled movement execution. Both activity profiles are observed throughout CSN somatodendritic compartments and are spatially organized, with increased activity concentrated in upper layer 5B and decreased activity localized to deeper subregions. Notably, single neuron projection mapping revealed that opposing CSN signals converge onto shared spinal interneurons, while modelling showed that reduced CSN output drives subtractive modulation of spinal interneuron input-output transformations, avoiding output saturation and enabling flexible scaling of output firing rates. These findings redefine corticospinal function by demonstrating that reduced output in a subpopulation of CSNs is critical for shaping spinal cord computations during skilled movement execution.

neuroscience↗

bioRxiv2026

An aptamer targeting TfR1 enhances ASO delivery to muscle tissue

Oligonucleotide based therapeutics continue to rise as a significant class of medicines for the treatment of human disease. However, achieving delivery to non-hepatic tissues remains a challenge in the field. While substantial advances have been realized, largely through the use of antibody or protein based targeting agents to tissues including muscle and the CNS, these large protein agents present complications in synthesis and carry the potential for immune responses. In an effort to identify a simpler, smaller and robust means of delivery, we have generated and evaluated aptamers targeting the human transferrin receptor (hTfR) for the delivery of both ASO and siRNA cargoes to muscle. Using a fully backbone modified anti-TfR aptamer, 36 nt in length, that binds hTfR and does not compete for binding with the natural ligand, transferrin, we evaluated the ability to deliver ASOs to skeletal muscle following systemic delivery. Using optimized linker chemistry, aptamer-ASO conjugates led to >50% target gene knockdown in muscle tissue for up to 42 days following a single dose at 3 mg/kg ASO ([~]11 mg/kg total drug) in mice. Taken as a whole, these results offer significant promise for the use of aptamers in the development of future therapeutics.

pharmacology and toxicology↗

bioRxiv2026

Organoids reveal niche-specific mechanotransduction-guided human cortical patterning and cell fate acquisition

The highly dynamic mechanical environment of the developing cerebral cortex has the potential to encode information vital for neuronal differentiation. Changes in local biophysical properties have been implicated in processes ranging from the maintenance of neural progenitors to long-range axon guidance. However, whether cortical mechanics influence cellular organisation and specification during neurogenesis remains largely unexplored. Here, we leverage a 3D mosaic organoid model of human cortical development, in which we selectively disrupt a key component of nuclear mechanosensing, the LINC complex, decoupling cells from their mechanical environment. We show that LINC-decoupling alters nuclear morphology in a compartment-specific manner, driving preferential exclusion from the germinal zone and concomitant premature differentiation. Excluded cells exhibit a biased spatial distribution in the cortical plate and altered fate allocation, with loss of intermediate progenitors and upper-layer neuron populations. Combining this approach with single-cell transcriptomic profiling, we reveal a signature of impaired ERK activation and density sensing in LINC-decoupled cells. Furthermore, we show that altered density sensing contributes to mislocalisation of the nuclear envelope protein emerin and disruption of histone mark deposition during differentiation. Taken together, our findings illustrate how the dynamic mechanical environment of a complex tissue can dictate cell fate and pattern formation during development.

developmental biology↗

bioRxiv2024

The transcriptomic landscape of spinal V1 interneurons reveals a role for En1 in specific elements of motor output

Neural circuits in the spinal cord are composed of diverse sets of interneurons that play crucial roles in shaping motor output. Despite progress in revealing the cellular architecture of the spinal cord, the extent of cell type heterogeneity within interneuron populations remains unclear. Here, we present a single-nucleus transcriptomic atlas of spinal V1 interneurons across postnatal development. We find that the core molecular taxonomy distinguishing neonatal V1 interneurons perdures into adulthood, suggesting conservation of function across development. Moreover, we identify a key role for En1, a transcription factor that marks the V1 population, in specifying one unique subset of V1Pou6f2 interneurons. Loss of En1 selectively disrupts the frequency of rhythmic locomotor output but does not disrupt flexion/extension limb movement. Beyond serving as a molecular resource for this neuronal population, our study highlights how deep neuronal profiling provides an entry point for functional studies of specialized cell types in motor output.

neuroscience↗

bioRxiv2024

Highly conserved brain vascular receptor ALPL mediates transport of engineered viral vectors across the blood-brain barrier

Delivery of systemically administered therapeutics to the central nervous system (CNS) is restricted by the blood-brain barrier (BBB). Bioengineered Adeno-Associated Virus (AAV) capsids have been shown to penetrate the BBB with great efficacy in mouse and non-human primate models, but their translational potential is often limited by species selectivity and undefined mechanisms of action. Here, we apply our RNA-guided TRACER AAV capsid evolution platform to generate VCAP-102, an AAV9 variant with markedly increased brain tropism following intravenous delivery in both rodents and primates. VCAP-102 demonstrates a similar CNS tropism in cynomolgus macaque, african green monkey, marmoset and mouse, showing 20- to 400-fold increased transgene expression across multiple brain regions relative to AAV9. We demonstrate that the enhanced CNS tropism of VCAP-102 results from direct interaction with alkaline phosphatase (ALPL), a highly conserved membrane-associated protein expressed on the brain vasculature. VCAP-102 interacts with human, primate and murine ALPL isoforms, and ectopic expression of ALPL is sufficient to initiate receptor-mediated transcytosis of VCAP-102 in an in vitro transwell model. Our work identifies VCAP-102 as a cross-species CNS gene delivery vector with a strong potential for clinical translation and establishes ALPL as a brain delivery shuttle capable of efficient BBB transport to maximize CNS delivery of biotherapeutics.

neuroscience↗

bioRxiv2022

Glucagon-like peptide-1 receptors in the gustatory cortex influence food intake

The gustatory region of the insular cortex (GC) processes taste information in manners important for taste-guided behaviors, including food intake itself. In addition to oral gustatory stimuli, GC activity is also influenced by physiological states including hunger. The specific cell-types and molecular mechanisms that afford with GC with such influences on food intake are unclear. Glucagon-like peptide 1 (GLP-1) is produced by neurons in the brain whereafter it can act upon GLP-1 receptor-expressing (GLP-1R+) neurons found in several brain regions. In these brain regions, GLP-1R agonism suppresses homeostatic food intake and dampens the hedonic value of food. Here, we report in mice of both sexes that cells within the GC express GLP-1R mRNA and further, by ex vivo brain slice recordings, that GC GLP-1R+ neurons are depolarized by the selective GLP-1R agonist, exendin-4 (Ex-4). Next we found that chemogenetic stimulation of GLP-1R+ neurons, and also pharmacological stimulation of GC-GLP-1Rs themselves, both reduced homeostatic food intake. When maintained on a high-fat diet, obese mice exhibited impaired food intake responses when Ex-4 was administered into the GC. Yet, when obese mice were switched to a low-fat diet, the effect of GC Ex-4 was restored - indicating that GC GLP-1R influences may depend upon palatability of the food. Together, these results provide evidence for a specific cell population in the GC which may hold roles in both homeostatic and hedonic food intake.

neuroscience↗

bioRxiv2022

scShapes: A statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

BackgroundSingle cell RNA sequencing (scRNA-seq) methods have been advantageous for quantifying cell-to-cell variation by profiling the transcriptomes of individual cells. For scRNA-seq data, variability in gene expression reflects the degree of variation in gene expression from one cell to another. Analyses that focus on cell-cell variability therefore are useful for going beyond changes based on average expression and instead, identifying genes with homogenous expression versus those that vary widely from cell to cell. ResultsWe present a novel statistical framework scShapes for identifying differential distributions in single-cell RNA-sequencing data using generalized linear models. Most approaches for differential gene expression detect shifts in the mean value. However, as single cell data are driven by over-dispersion and dropouts, moving beyond means and using distributions that can handle excess zeros is critical. scShapes quantifies gene-specific cell-to-cell variability by testing for differences in the expression distribution while flexibly adjusting for covariates if required. We demonstrate that scShapes identifies subtle variations that are independent of altered mean expression and detects biologically-relevant genes that were not discovered through standard approaches. ConclusionsThis analysis also draws attention to genes that switch distribution shapes from a unimodal distribution to a zero-inflated distribution and raises open questions about the plausible biological mechanisms that may give rise to this, such as transcriptional bursting. Overall, the results from scShapes helps to expand our understanding of the role that gene expression plays in the transcriptional regulation of a specific perturbation or cellular phenotype. Our framework scShapes is incorporated into Bioconductor R package (https://github.com/Malindrie/scShapes).

bioinformatics↗

bioRxiv2020

α-Synuclein perturbs in vivo neural activity following seeding in the olfactory bulb

BACKGROUNDParkinsons disease (PD) neuropathology is characterized by intraneuronal protein aggregates composed of misfolded -Synuclein (-Syn), as well as degeneration of substantia nigra dopamine neurons. Deficits in olfactory perception and aggregation of -Syn in the olfactory bulb (OB) are observed during early stages of PD, and have been associated with the PD prodrome, before onset of the classic motor deficits. -Syn fibrils injected into the OB of mice cause progressive propagation of -Syn pathology throughout the olfactory system and are coupled to olfactory perceptual deficits. OBJECTIVEWe hypothesized that accumulation of pathogenic -Syn in the OB impairs neural activity in the olfactory system. METHODSTo address this, we monitored spontaneous and odor-evoked local field potential dynamics in awake wild type mice simultaneously in the OB and piriform cortex (PCX) one, two, and three months following injection of pathogenic preformed -Syn fibrils in the OB. RESULTSWe detected -Syn pathology in both the OB and PCX. We also observed that -Syn fibril injections influenced odor-evoked activity in the OB. In particular, -Syn fibril-injected mice displayed aberrantly high odor-evoked power in the beta spectral range. A similar change in activity was not detected in the PCX, despite high levels of -Syn pathology. CONCLUSIONSTogether, this work provides evidence that synucleinopathy impacts in vivo neural activity in the olfactory system at the network-level.

neuroscience↗

bioRxiv2020

Optimal spectral templates for triggered feedback experiments

In the field of songbird neuroscience, researchers have used playback of aversive noise bursts to drive changes in song behavior for specific syllables within a birds song. Typically, a short (~5-10 msec) slice of the syllable is selected for targeting and the average spectrum of the slice is used as a template. Sounds that are sufficiently close to the template are considered a match. If other syllables have portions that are spectrally similar to the target, false positive errors will weaken the operant contingency. We present a gradient descent method for template optimization that increases the separation in distance between target and distractors slices, greatly improving targeting accuracy. Applied to songs from five adult Bengalese finches, the fractional reduction in errors for sub-syllabic slices was 51.54{+/-}22.92%. At the level of song syllables, we use an error metric that controls for the vastly greater number of distractors vs. target syllables. Setting 5% average error (misses + false positives) as a minimal performance criterion, the number of targetable syllables increased from 3 to 16 out of 61 syllables. At 10% error, targetable syllables increased from 11 to 26. By using simple and robust linear discriminant methods, the algorithm reaches near asymptotic performance when using 10 songs as training data, and the error increases by <2.3% on average when using only a single song for training. Targeting is temporally precise, with average jitter of 3.33 msec for the 16 accurately targeted syllables. Because the algorithm is concerned only with the problem of template selection, it can be used as a simple and robust front end for existing hardware and software implementations for triggered feedback.

neuroscience↗