Biology subjects

Petersen, C. C.

Publications and source records attributed to Petersen, C. C..

11 recordsLinked to original sources

bioRxiv2026

CICADA: A unified framework for NWB-based neurophysiological data analysis

Neurophysiology datasets are becoming increasingly complex, combining behavioral measurements with high-dimensional neuronal activity recordings coming from optical and/or electrophysiological measurements. The Neurodata Without Borders (NWB) standard has emerged in the community as the format of record. While standardized and widely used preprocessing tools generating NWB files have been developed, extensible frameworks for scientific analysis downstream of the NWB ecosystem are still under-represented. We present CICADA, a Python framework dedicated to analysis of neurophysiological data in the standardized NWB format. The toolbox is built as three hierarchically-organized packages: cicada-nwb (NWB access layer), cicada-analysis (plugin-based analysis engine and tool library), and cicada-gui (PyQt5 desktop application at the head of the pipeline). Beyond this architectural separation, CICADA is built around a central design principle: supporting a continuum from turnkey use to full modularity. Researchers can use the complete GUI-driven cicada-gui workflow without writing code, programmatically use existing analysis plugins from cicada-analysis, contribute to new analysis plugins, reuse utilities from cicada-tools, or build entirely custom pipelines on top of the cicada-nwb access layer alone. The same analysis plugin runs identically in interactive GUI and parameter-configured headless modes, enabling reproducible multi-session, multi-animal group analyses. We illustrate the versatility of CICADA with example analyses of behavioral, calcium imaging (two-photon and widefield) and extracellular electrophysiology datasets from rodent laboratories. CICADA is open source, actively maintained, and designed so that any laboratory can contribute at any level of the stack without modifying the core framework.

neuroscience↗

bioRxiv2026

Rapid cortical reorganization tracks goal-directed sensorimotor learning in real time

Sensorimotor associations are typically thought to require days of training to consolidate in sensory cortex, yet adaptive behavior can emerge within minutes. Here, we developed a barrel cortex-dependent whisker-based detection task in which mice learned to associate a novel tactile whisker stimulus with reward within a single behavioral session. Longitudinal two-photon calcium imaging of layer 2/3 barrel cortex neurons revealed that reward-driven learning rapidly reorganized the neuronal representation of the whisker deflection within a single session. Population decoding tracked this transition trial-by-trial during learning with neuronal trajectories mirroring behavior. Critically, neurons that gained stimulus responsiveness across training preferentially took part in spontaneous reactivation events during learning, suggesting that online reactivations could act as a potential upstream selection mechanism. Our results suggest that reward-based learning evokes rapid sensory cortical reorganization on the timescale of minutes, which could be mediated by a concurrent reactivation-based mechanism driving plasticity.

neuroscience↗

bioRxiv2025

Inter-Instrument Quantification of Fluorescence Read-out Signal Using DNA Origami Calibrator Beads

Comparing experimental results across different instruments and laboratories is challenging due to variations in instrument sensitivity and resolution, particularly for analyzing nano-sized and dimly fluorescing particles like viruses and extracellular vesicles. To address this challenge, we conducted a study using fluorescent DNA calibrator beads to test, calibrate, and compare the sensitivity of five different flow cytometers. Our approach involves DNA beads produced through a bottom-up DNA origami method. These beads contain a defined number of fluorophores (0-220) and exhibit no autofluorescence. Fluorophores are precisely conjugated onto the beads in a controlled array, minimizing dye interactions. This allows triggering on one fluorophore and calibration based on another, facilitating precise and accurate calibration in absolute fluorophore numbers. We tested five flow cytometers--FACSAria III, NovoCyte 3000YBG, NovoCyte Quanteon 4500, LSRFortessa, and CytoFlex S--using Cy5 and FAM DNA calibrator beads. We investigated various instrument parameters, including count rate, trigger and calibration gain, gain amplification linearity, and fluorescence trigger sensitivity. Using fluorescent triggering, we demonstrated the capability to detect dimly fluorescent particles, enabling instrument calibration and fluorescence sensitivity comparison using DNA calibrators. In conclusion, our study offers a robust method for addressing instrument fluorescence channel resolution in absolute fluorophore numbers in the analysis of nano-sized and dimly fluorescent particles.

biophysics↗

bioRxiv2025

Retrosplenial cortex enables context-dependent goal-directed sensorimotor transformation

The ability to dynamically adjust a behavioral response to a stimulus depending on context is of critical importance for animals. To investigate the neural basis supporting context-dependent sensory processing we developed a behavioral task in which mice changed their response to a single whisker deflection according to a continuously present contextual cue. Through unbiased optogenetic inactivation mapping, we found that neuronal activity in sensory and motor cortices contributed to task execution and, interestingly, we uncovered an unexpected role of retrosplenial cortex for contextual integration. Widefield calcium imaging revealed that retrosplenial cortex was the first dorsal cortical area to show context discrimination in response to whisker stimulation, followed by whisker motor cortex. Finally, we combined optogenetic inactivation with calcium imaging to define causal context-dependent changes in sensorimotor processing. Our cortex-wide mapping experiments thus begin to define key cortical nodes for context-dependent sensorimotor transformation and highlight an important contribution of retrosplenial cortex.

neuroscience↗

bioRxiv2025

Single-cell proteomics: a powerful new tool to study kidney cell heterogeneity

BackgroundTechnological advancements in protein mass spectrometry have significantly enhanced analytical sensitivity and throughput, enabling single-cell proteomics by mass spectrometry (SCP-MS) to become reality. SCP-MS allows high-resolution analysis of cellular heterogeneity and function, bypassing bulk analysis limitations. Here, we used SCP-MS to document at the protein level the cellular diversity of mouse kidney cells. We further focused SCP-MS on low abundance distal convoluted tubule (DCT) cells that are essential for body electrolyte homeostasis and blood pressure control. MethodsMouse kidney cells were isolated via enzymic digestion and single-cells isolated using fluorescence- activated cell sorting (FACS). DCT cells were isolated from mice with GFP expression specifically in the DCT (parvalbumin-GFP) using a similar workflow. SCP-MS analyses was performed using an Orbitrap Ascend Mass Spectrometer with a FAIMS Pro Duo interface coupled with Wide ISolation window High-resolution MS1 Data Independent Acquisition (WISH-DIA). Spectronaut was used for protein identification and quantification, and cell-type annotation and clustering were performed in Python by scanpy implementation. ResultsWorkflow benchmarking using Hela cells confirmed a successful SCP-MS setup. From 768 single mouse kidney cells, SCP-MS identified 2626 unique proteins. Computational approaches resolved various nephron segments, including distinct DCT populations. From enriched DCT cells, 1912 proteins were identified, enabling classification of three populations - DCT1, DCT2, and a proliferative subset (ProLIF) that represented a transient state between DCT1 and DCT2. ProLIF cells had elevated abundance of the sodium-chloride cotransporter NCC and represented approximately 33% of DCT cells, substantially exceeding previous transcriptomic estimates of ProLIF cell frequency (~0.1%). High proliferation (~39%) of DCT cells was confirmed using immunohistochemistry. ConclusionsThis SCP-MS analysis of mouse kidney uncovered significant cellular heterogeneity not captured effectively using transcriptomics. Despite imitations in proteome depth and throughput, SCP-MS provides a powerful approach for investigating kidney cellular dynamics at the protein level. Key pointsO_LIWe developed a single-cell proteomics by mass spectrometry (SCP-MS) workflow identifying up to ~2,000 proteins in a single mouse kidney cell C_LIO_LISCP-MS identified a substantial proliferative subset of cells in the DCT underestimated by transcriptomics C_LIO_LISCP-MS could inform on clinical strategies for kidney disease monitoring, offering robust indicators of tubular injury or regeneration. C_LI

biochemistry↗

bioRxiv2024

Biologically informed cortical models predict optogenetic perturbations

A recurrent neural network fitted to large electrophysiological datasets may help us understand the chain of cortical information transmission. In particular, successful network reconstruction methods should enable a model to predict the response to optogenetic perturbations. We test recurrent neural networks (RNNs) fitted to electrophysiological datasets on unseen optogenetic interventions, and measure that generic RNNs used predominantly in the field generalize poorly on these perturbations. Our alternative RNN model adds biologically informed inductive biases like structured connectivity of excitatory and inhibitory neurons, and spiking neuron dynamics. We measure that some biological inductive biases improve the model prediction on perturbed trials in a simulated dataset, and a dataset recorded in mice in vivo. Furthermore, we show in theory and simulations that gradients of the fitted RNN can be used to target micro-perturbations in the recorded circuits, and discuss the potential utility to bias an animals behavior and study cortical circuit mechanisms.

neuroscience↗

bioRxiv2024

Cell class-specific long-range axonal projections of neurons in mouse whisker-related somatosensory cortices

The extensive long-range axonal projections of diverse classes of neocortical excitatory neurons are thought to contribute importantly to the highly integrative brain-wide interactions underlying the processing of sensory, cognitive and motor signals. Here, we investigated the long-range axonal output of various classes of genetically-defined projection neurons with cell bodies located in the whisker-related somatosensory cortices of the mouse through brain-wide light-sheet imaging of fluorescently-labeled axons segmented by specifically-trained convolutional networks quantified within the Allen Mouse Brain Atlas Common Coordinate Framework. We injected Cre-dependent virus to express GFP or tdTomato in the posterior primary somatosensory barrel cortex and the posterior supplemental somatosensory cortex, which contain the representations of the large posterior mystacial whiskers. We investigated the six following transgenic mouse lines which preferentially express Cre in different glutamatergic neocortical cell classes: Rasgrf2-dCre for layer 2/3 intratelencephalic projection neurons, Scnn1a-Cre for layer 4 intratelencephalic projection neurons, Tlx3-Cre for layer 5 intratelencephalic projection neurons, Sim1-Cre for layer 5 pyramidal tract projection neurons, Rbp4-Cre for layer 5 projection neurons and Ntsr1-Cre for layer 6 corticothalamic neurons. We found long-range axonal projections in many diverse downstream brain areas with largely similar output from primary and secondary cortices, but with genetically-defined cell classes showing distinct innervation patterns, with Rbp4-Cre mice showing the broadest innervation targets, subsets of which were innervated in the other mouse lines. To test whether the revealed axonal projections might underpin functional circuits, we compared the spatial organization of the axonal innervation with functional connectivity maps obtained from optogenetic stimulation of sensory cortex and wide-field imaging of the activity propagation to frontal cortices. Both methods indicated that neurons located more laterally in somatosensory cortex topographically signaled to more anteriorly located regions in motor cortex. The current methodology therefore appears to quantify brain-wide axonal innervation patterns supporting brain-wide signaling, and, together with further technological advances, this will help provide increasingly detailed connectivity information of the mouse brain, essential for understanding the complex neuronal circuitry underlying even simple goal-directed behaviors.

neuroscience↗

bioRxiv2022

Primary motor cortex drives expressive facial movements related to reward processing in mice

During reward-based learning tasks, animals make orofacial movements that globally influence brain activity at the timings of reward expectation and acquisition. These orofacial movements are not explicitly instructed and typically appear along with goal-directed behaviors. Here we show that reinforcing optogenetic stimulation of midbrain dopamine neurons (oDAS) in mice is sufficient to induce orofacial movements in the whiskers and nose without accompanying goal-directed behaviors. Pavlovian conditioning with a sensory cue and oDAS elicited cue-locked and oDAS aligned orofacial movements, which were distinguishable by a machine learning model. Inhibition or knock-out of dopamine D1 receptors in the nucleus accumbens inhibited oDAS-induced motion but spared cue-locked motion, suggesting differential neural regulation of these two types of orofacial motions. In contrast, inactivation of the whisker primary motor cortex (wM1) abolished both types of orofacial movements. We found specific neuronal populations in wM1 representing either oDAS-aligned or cue-locked whisker movements. Notably, optogenetic stimulation of wM1 neurons successfully replicated these two types of movements. Our results thus suggest that accumbal D1 receptor-dependent and -independent neuronal signals converge in the wM1 for facilitating uninstructed orofacial movements during a reward-based learning task.

neuroscience↗

bioRxiv2022

Membrane potential dynamics of excitatory and inhibitory neurons in mouse barrel cortex during active whisker sensing

Neocortical neurons can increasingly be divided into well-defined classes, but their activity patterns during quantified behavior remain to be fully determined. Here, we obtained membrane potential recordings from various classes of excitatory and inhibitory neurons located across different cortical depths in the primary whisker somatosensory barrel cortex of awake head-restrained mice during quiet wakefulness, free whisking and active touch. Excitatory neurons, especially those located superficially, were hyperpolarized with low action potential firing rates relative to inhibitory neurons. Parvalbumin-expressing inhibitory neurons on average fired at the highest rates, responding strongly and rapidly to whisker touch. Vasoactive intestinal peptide-expressing inhibitory neurons were excited during whisking, but responded to active touch only after a delay. Somatostatin-expressing inhibitory neurons had the smallest membrane potential fluctuations and exhibited hyperpolarising responses at whisking onset for superficial, but not deep, neurons. Interestingly, rapid repetitive whisker touch evoked excitatory responses in somatostatin-expressing inhibitory neurons, but not when the intercontact interval was long. Our analyses suggest that distinct genetically-defined classes of neurons at different subpial depths have differential activity patterns depending upon behavioral state providing an important basis for constraining future computational models of neocortical function.

neuroscience↗

bioRxiv2022

Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas

Excitatory and inhibitory neurons in diverse cortical regions are likely to contribute differentially to the transformation of sensory information into goal-directed motor plans. Here, we investigate the relative changes across mouse sensorimotor cortex in the activity of putative excitatory and inhibitory neurons - categorized as regular or fast spiking according to their action potential waveform - comparing before and after learning of a whisker detection task with delayed licking as perceptual report. Surprisingly, we found that the whisker-evoked activity of regular versus fast spiking neurons changed in opposite directions after learning in primary and secondary whisker motor cortices, while it changed similarly in primary and secondary orofacial motor cortices. Our results suggest that changes in the balance of excitation and inhibition in local circuits concurrent with changes in the long-range synaptic inputs in distinct cortical regions might contribute to performance of delayed sensory-to-motor transformation.

neuroscience↗

bioRxiv2020

Ultrastructural comparison of dendritic spine morphology preserved with cryo and chemical fixation

Previously we showed that cryo fixation of brain tissue gave a truer representation of brain ultrastructure in comparison with a standard chemical fixation method (Korogod et al 2005). Extracellular space matched physiological measurements, there were larger numbers of docked vesicles and less glial coverage of synapses and blood capillaries. Here, using the same preservation approaches we compared the morphology of dendritic spines. We show that the length of the spine and the volume of its head is unchanged, however, the spine neck width is thinner by more than 30 % after cryo fixation. In addition, the weak correlation between spine neck width and head volume seen after chemical fixation was not present in cryo-fixed spines. Our data suggest that spine neck geometry is independent of the spine head volume, with cryo fixation showing enhanced spine head compartmentalization and a higher predicted electrical resistance between spine head and parent dendrite.

neuroscience↗