Biology subjects

Bech, P.

Publications and source records attributed to Bech, P..

8 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

Dynamic interaction between tentacle-tethered microdomains in Integrator and NELF regulates the promoter-proximal pause checkpoint

Negative Elongation Factor (NELF) and Integrator are general regulators of transcriptional pausing and premature termination at the beginning of protein-coding genes. While NELF is a key pausing factor, Integrator triggers premature termination of dysfunctional RNAPII complexes. Here, we identify a direct interaction between the plant homeodomain (PHD) finger of Integrator subunit 12 (INTS12) and a previously unrecognized C-terminal domain (CTD) in the flexible tentacle of NELF-A. Mutation of either domain disrupts the interaction, and although RNAPII-associated pausing complexes still form, they are dysfunctional. Importantly, while deletion of the INTS12 PHD finger functionally mimics Integrator loss, a single point mutation in NELF-A CTD instead mimics loss of NELF, suggesting the presence of competitive interactions. Together, our findings uncover a novel mode of PHD finger binding and outline how an interaction between Integrator and NELF regulates transcriptional pausing and premature termination.

cell biology↗

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

Control of gene output by intron RNA structure

During mRNA biogenesis, RNA folding can promote or antagonize transcript processing. The effects of intron structure on mRNA and protein levels remain largely unexplored, although introns account for the bulk of nascent RNA. Here we systematically probe the effect of intron structure using massively parallel reporter assays. We show that base pairing modulates gene expression across orders of magnitude through inhibitory RNA structures at splice sites and at newly identified regions. Conversely, poor splicing of human {beta}-globin pre-mRNA could be improved by sequence alterations that reduce base pairing. For large libraries of RNA structures differing in stability, machine learning models could nearly fully explain observed gene output. Structure destabilizing mutations emerge rapidly under selective pressure. Thus, formation of RNA structures as dictated by intron sequence provides a simple, powerful means to adjust gene expression.

biochemistry↗

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

Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts

Gene expression requires DNA transcription and simultaneous RNA processing steps that transform the precursor RNA into fully mature RNA. In eukaryotes, the processing of protein-encoding messenger RNAs (mRNAs) includes 5 end capping, editing, splicing, RNA modification, poly-adenylation cleavage, and polyadenylation. Short-read sequencing of total or messenger RNA largely reveals the final output of transcription and processing because it utilizes 1) steady-state, mature RNA that is mostly processed and 2) sequencing reads that are too short to detect adjacent processing events (e.g. two adjacent introns). In contrast, long-read sequencing of nascent RNA allows the detection of rarer, full-length transcripts that are in the process of being transcribed and processed. The 3 end of each nascent RNA establishes the position of RNA polymerase II (Pol II) along the gene at the time of cell lysis, providing a timeline for RNA processing events. In addition, the density of 3 ends along genes or at gene landmarks reflects Pol II density, which is related to changes in transcription elongation rate. In organisms with complex gene architectures, information about splicing across multiple introns within the same transcript can be extracted, as well as the location of transcription start sites (TSSs) and polyA cleavage sites. Here, we describe the isolation of nascent RNA from the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, preparation of a cDNA library for long-read sequencing on Oxford Nanopore Technologies or Pacific Biosciences platforms, and initial data analysis steps. These methods comprise versatile and powerful tools for the investigation of coupled RNA synthesis and processing.

molecular biology↗

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↗

bioRxiv2019

A unified framework for dopamine signals across timescales

Rapid phasic activity of midbrain dopamine neurons are thought to signal reward prediction errors (RPEs), resembling temporal difference errors used in machine learning. Recent studies describing slowly increasing dopamine signals have instead proposed that they represent state values and arise independently from somatic spiking activity. Here, we developed novel experimental paradigms using virtual reality that disambiguate RPEs from values. We examined the dopamine circuit activity at various stages including somatic spiking, axonal calcium signals, and striatal dopamine concentrations. Our results demonstrate that ramping dopamine signals are consistent with RPEs rather than value, and this ramping is observed at all the stages examined. We further show that ramping dopamine signals can be driven by a dynamic stimulus that indicates a gradual approach to a reward. We provide a unified computational understanding of rapid phasic and slowly ramping dopamine signals: dopamine neurons perform a derivative-like computation over values on a moment-by-moment basis.

neuroscience↗