Biology subjects

Stark, E.

Publications and source records attributed to Stark, E..

13 recordsLinked to original sources

bioRxiv2026

Sub-stoichiometric modifications of Aplysia californica tRNAs and tRNA fragments revealed by integrating intact and bottom-up mass spectrometry

Transfer RNA (tRNA) modifications regulate protein synthesis, yet their sequence positions and stoichiometries are known only for a subset of tRNAs in model organisms. Aplysia californica is a key neurobiological model in which neuronal modified ribonucleosides have been linked to changes in animal behavior. However, Aplysia tRNA modifications have not been mapped, obscuring their roles in modulating neuronal functions. To address this knowledge gap, we leveraged hybridization pulldowns and an integrated mass spectrometry (MS) strategy combining nucleoside profiling, intact tRNA measurements, and bottom-up tRNA modification mapping to determine the full sequences of Aplysia tRNAGluCUC and tRNALysUUU. Sub-stoichiometric modifications including dihydrouridine (D), 5-methylcytidine (m5C), 5,2'-O-dimethyluridine (m5Um) and 1-methyladenosine (m1A) on tRNAGluCUC varied across tissues, suggesting tRNA modifications are regulated to accommodate translational needs. In addition to conserved thio-modifications in the anticodon loop of tRNALysUUU, we report 2-thiocytidine (s2C) at position 32, representing the first detection of s2C in eukaryotes. We also developed a generalizable method to directly detect tRNA halves by intact LC-MS, revealing endogenous tRNA cleavage patterns. Our findings illustrate the advantages of combining intact and bottom-up MS, reveal s2C as an unexpected tRNA modification in a classical neurobiological model and offer new insights into post-transcriptional regulation of animal physiology.

biochemistry↗

bioRxiv2025

High-density extracellular recordings from the interior of intact brain organoids enable automated high-throughput functional assay

Bridging the gap between preclinical screening and clinical outcomes remains a major challenge in drug development for neurological disorders. Brain organoids, derived from human induced pluripotent stem cells, offer a scalable and physiologically relevant platform to model human neural circuits. We develop a fully automated system to record neural activity from the interior of intact human cortical organoids using a high-density microfabricated probe. The robotic system completes insertion within minutes while preserving organoid integrity and enables immediate recording of spontaneous spikes. We extract physiologically grounded and deterministic spike features, and train a long short-term memory classifier to distinguish between organoids derived from healthy individuals and those harboring familial Alzheimers disease (AD) mutations in the amyloid precursor protein. Despite intra-class variability, the classifier differentiates between organoid classes with 100% accuracy. The model classifies AD organoids treated with a drug candidate that reduces amyloid-{beta} levels as retaining an AD-like electrophysiological phenotype, demonstrating that functional readout can contradict molecular markers. The findings establish a high-throughput functional framework that may complement and extend existing drug screening assays.

neuroscience↗

bioRxiv2024

Dorsal CA1 silencing degrades tactile short-term memory

Previous studies in rodents showed that the hippocampus is involved in spatial short-term memory (STM), but hippocampal necessity for maintaining short-term sensory memories is unknown. Here, we develop tactile discrimination and STM tasks for freely-moving mice. Subjects learn to discriminate between textures after four shaping sessions and a single post-shaping session, and learn the STM task within a dozen sessions. Transient closed-loop silencing of dorsal hippocampal region CA1 during memory maintenance degrades task performance, compared to interleaved control blocks. Thus, uninterrupted hippocampal activity is required for acting upon tactile information maintained in STM. The findings suggest that the role of the hippocampus extends beyond spatial navigation, encoding memories, and long-term consolidation of experiences.

neuroscience↗

bioRxiv2023

The meditative brain: State and trait changes in harmonic complexity for long-term mindfulness meditators

Meditation is an ancient practice that is shown to yield benefits for cognition, emotion regulation and human flourishing. In the last two decades, there has been a surge of interest in extracting the neural correlates of meditation, in particular of mindfulness meditation. Yet, these efforts have been mostly limited to the analysis of certain regions or networks of interest and a clear understanding of meditation-induced changes in the whole-brain dynamics has been lacking. Here, we investigate meditation-induced changes in brain dynamics using a novel connectome-specific harmonic decomposition method. Specifically, utilising the connectome harmonics as brain states - elementary building blocks of complex brain dynamics - we study the immediate (state) and long-term (trait) effects of mindfulness meditation in terms of the energy, power and complexity of the repertoire of these harmonic brain states. Our results reveal increased power, energy and complexity of the connectome harmonic repertoire and demonstrate that meditation alters brain dynamics in a frequency selective manner. Remarkably, the frequency-specific alterations observed in meditation are reversed in resting state in group-wise comparison revealing for the first time the long-term (trait) changes induced by meditation. These findings also provide evidence for the entropic brain hypothesis in meditation and provide a novel understanding of state and trait changes in brain dynamics induced by mindfulness meditation revealing the unique connectome harmonic signatures of the meditative brain.

neuroscience↗

bioRxiv2023

Local activation of CA1 pyramidal cells induces theta phase precession

Hippocampal theta phase precession is involved in spatiotemporal coding and generating multineural spike sequences, but how precession originates remains unresolved. To determine whether precession can be generated directly in CA1 and disambiguate multiple competing mechanisms, we used optogenetic activation to impose artificial place fields in pyramidal cells of mice running on a linear track. More than a third of the CA1 artificial fields exhibited synthetic precession that persisted for a full cycle. In contrast, artificial fields in the parietal cortex did not exhibit synthetic precession. The findings are incompatible with precession models based on inheritance, spreading activation, dual-input, or inhibition-excitation summation. Thus, a precession generator resides locally within CA1.

neuroscience↗

bioRxiv2023

Wired together, change together: Spike timing modifies transmission in converging assemblies

Precise timing of neuronal spikes may lead to changes in synaptic connectivity and is thought to be crucial for learning and memory. However, the effect of spike timing on neuronal connectivity in the intact brain remains unknown. Using closed-loop optogenetic stimulation in CA1 of freely-moving mice, we generated new spike patterns between presynaptic pyramidal cells (PYRs) and postsynaptic parvalbumin-immunoreactive (PV) cells. This stimulation led to spike transmission changes which occurred together across all presynaptic PYRs connected to the same postsynaptic PV cell. The precise timing of all presynaptic and postsynaptic cells spikes impacted transmission changes. These findings reveal an unexpected plasticity mechanism, wherein spike timing of a whole cell assembly has a more substantial impact on effective connectivity than that of individual cell pairs.

neuroscience↗

bioRxiv2023

Short-term auditory priming in freely-moving mice

Priming, a change in the mental processing of a stimulus as a result of prior encounter with a related stimulus, has been observed repeatedly and studied extensively. Yet currently there is no behavioral model of short-term priming in lab animals, limiting the study of the neurobiological basis of priming. Here, we describe an auditory discrimination paradigm for studying response priming in freely-moving mice. We find a priming effect in success rate in all mice tested on the task. In contrast to humans, we do not find a priming effect in response times. Compared to non-primed discrimination trials, the addition of incongruent prime stimuli reduces success rate more than congruent prime stimuli, suggesting a cognitive mechanism based on differential interference. The results establish the short-term priming phenomenon in rodents, and the paradigm opens the door to studying the cellular-network basis of priming.

neuroscience↗

bioRxiv2023

Learning to learn: Single session acquisition of new rules by freely-moving mice

Learning from examples and adapting to new rules are fundamental attributes of human cognition. However, it is unclear what conditions allow for fast and successful learning, especially in non-human subjects. To determine how rapidly freely-moving mice can learn a new rule, we designed a two-alternative forced-choice visual discrimination paradigm in which the rules governing the task can change between sessions. We find that experienced animals can learn a new rule after being exposed to only five training and three testing trials. The propensity for single session learning improves over time and is accurately predicted based on animal experience and rule difficulty. After establishing procedural learning of a paradigm, mice continuously improve their performance on new rules. Thus, mice learn to learn.

neuroscience↗

bioRxiv2023

Positive and biphasic extracellular waveforms correspond to return currents and axonal spikes

Multiple biophysical mechanisms may generate non-negative extracellular waveforms during action potentials, but the origin and prevalence of positive spikes and biphasic spikes in the intact brain are unknown. Using extracellular recordings from densely-connected cortical networks in freely-moving mice, we find that a tenth of the waveforms are non-negative. Positive phases of non-negative spikes occur in synchrony or just before wider same-unit negative spikes. Narrow positive spikes occur in isolation in the white matter. Isolated biphasic spikes are narrower than negative spikes, occurring right after spikes of verified inhibitory units. In CA1, units with dominant non-negative spikes exhibit place fields, phase precession, and phase-locking to ripples. Thus, near-somatic narrow positive extracellular potentials correspond to return currents, and isolated non-negative spikes correspond to axonal potentials. Identifying non-negative extracellular waveforms that correspond to non-somatic compartments during spikes can enhance the understanding of physiological and pathological neural mechanisms in intact animals.

neuroscience↗

bioRxiv2022

Hybrid offspring of C57BL/6J mice exhibit improved properties for neurobehavioral research

C57BL/6 is the most commonly used mouse strain in neurobehavioral research, serving as a background for multiple transgenic lines. However, C57BL/6 exhibit behavioral and sensorimotor disadvantages that worsen with age. We bred FVB/NJ females and C57BL/6J males to generate first-generation hybrid offspring, (FVB/NJ x C57BL/6J)F1. The hybrid mice exhibit reduced anxiety-like behavior, improved learning, and enhanced long-term spatial memory. In contrast to both progenitors, older hybrids maintain sensorimotor performance and exhibit improved long-term memory. The hybrids are larger than C57BL/6J, exhibiting enhanced running behavior on a linear track during freely-moving electrophysiological recordings. Hybrids exhibit typical rate and phase coding of space by CA1 pyramidal cells. Hybrids generated by crossing FVB/NJ females with transgenic males of a C57BL/6 background support optogenetic neuronal control in neocortex and hippocampus. The hybrid mice provide an improved model for neurobehavioral studies combining complex behavior, electrophysiology, and genetic tools readily available in C57BL/6 mice.

neuroscience↗

bioRxiv2020

Neuronal resonance can be generated independently at distinct levels of organization

Neuronal resonance is defined as maximal amplification of the response of a system to a periodic input at a finite non-zero input frequency band. Resonance has been observed experimentally in the nervous system at the level of membrane potentials, spike times, post-synaptic potentials, and neuronal networks. It is often assumed that resonance at one level of organization endows resonance at another level, but how the various forms of neuronal resonances interact is unknown. Here we show that a direct link of the frequency response properties across neuronal levels of organization is not necessary. Using detailed biophysical modeling combined with numerical simulations, extracellular recordings, and optogenetic manipulations from behaving mice, we show how low-pass filtering, high-pass filtering, and amplification mechanisms can generate resonance at a single level of organization. Subthreshold resonance, synaptic resonance, and spiking resonance can each occur in the lack of resonance at any other level of organization. In contrast, frequencydependent mechanisms at several levels of organization are required to generate the more complex phenomenon of network resonance. Together, these results show that multiple independent mechanisms can generate resonance in neuronal systems.

neuroscience↗

bioRxiv2020

The dynamics of the improvising brain: a study of musical creativity using jazz improvisation

The neuroscience of jazz improvisation has shown promising results for understanding domain-specific and domain-general processes of creativity. Here, we used fMRI to measure for the first time the dynamic neural substrates of musical creativity in 16 skilled jazz pianists while they played by memory, improvised freely (iFreely) and by melody (iMelody), and during resting-state. We used the Leading Eigenvector Dynamics Analysis (LEiDA) to examine how different modes of improvisation (musical creativity) evolve over time, and which cognitive mechanisms are responsible for different stages of musical creation. Our results reveal that a substate comprising auditory, sensorimotor and posterior salience networks had a significantly higher probability of occurrence (POc) in both modes of improvisation than in resting-state and play by memory. Another substate comprising the default mode (DMN), executive control (ECN) and language networks had significantly lower POc in iFreely than in resting-state, with iMelody having a higher POc than iFreely. Such indicates that iMelody, a more constrained form of creativity involves a higher recurrence of subsystems responsible for goal-directed cognition and cognitive control processes. On the other hand, iFreely recruits brain networks responsible for generation of spontaneous musical creativity. Overall, this study brings new insights into the large-scale brain mechanisms supporting and promoting the complex process of creativity, specifically in the context of jazz improvisation, as well as the relevance of different improvisation modes in creativity research.

neuroscience↗

bioRxiv2020

Effective psychological treatment for PTSD changes the dynamics of specific large-scale brain networks

AO_SCPLOWBSTRACTC_SCPLOWVery little is known about the role of effective cognitive therapy in reversing imbalances in brain activity after trauma. We hypothesised that exaggerated threat perception characteristic of post-traumatic stress disorder (PTSD), and subsequent recovery from this disorder, are underpinned by changes in the dynamics of large-scale brain networks. Here, we use a novel data-driven approach with high temporal precision to find recurring brain networks from fMRI data and estimate when these networks become active during exposure to either trauma reminders or neutral pictures. We found that PTSD patients spend less time in two default mode sub-networks in contrast to trauma-exposed healthy controls, and that PTSD symptom severity correlates positively with time spent in the salience network during exposure to trauma reminders. The former are important for different aspects of self-referential processing and the latter for detection of threat. Importantly, the decreased time in the default mode sub-networks is rebalanced after successful cognitive therapy for PTSD. Our results show that remittance of PTSD through trauma-focused cognitive therapy is associated with the successful reinstatement of a healthy balance in self-referential and threat detection brain networks.

neuroscience↗