Biology subjects

Sirmpilatze, N.

Publications and source records attributed to Sirmpilatze, N..

9 recordsLinked to original sources

bioRxiv2026

Absence of the Earths magnetic field activates stress-related brain circuits in a mammal

The Earths magnetic field is a constantly available cue for animals with a magnetic sense. While magnetic navigation is best studied in migratory birds, a magnetic sense is also found in some mammals. Among these, it is most thoroughly studied in African mole-rats of the genus Fukomys, subterranean mammals that navigate in kilometre-long dark tunnel systems. Our understanding of the neural pathways involved in magnetoreception remains incomplete. To address this, we here performed an unbiased whole-brain screen for magnetically induced neuronal activity in the mole-rat brain. We set up MoBI-DisC (Mole-rat Brain Imaging with iDISCO and ClearMap), an experimental pipeline that combines global c-Fos immunolabelling, tissue clearing, light-sheet microscopy, and mapping to a novel 3D brain atlas. To identify brain areas involved in magnetosensation, we exposed mole-rats to a changing magnetic field and compared their brain activity to that of control animals exposed to a near-zero magnetic field. Unexpectedly, we found that the near-zero magnetic field exposure activated many brain areas, predominantly those involved in stress and anxiety responses. These included the amygdala, the bed nucleus of the stria terminalis, the substantia innominata, and the periaqueductal grey. This suggests that magnetic field deprivation acts as a physiological stressor in mole-rats. To test this, we conducted a place-preference test and found that mole-rats avoid entering a zone with a near-zero magnetic field, consistent with the hypothesis that this condition is not neutral for these animals. In summary, we present a novel pipeline for unbiased mapping of neural activity in subterranean mole-rats and uncover evidence of stress and avoidance responses to the absence of an Earth-strength magnetic field.

neuroscience↗

bioRxiv2025

Mapping the magnetoreceptive brain: A 3D digital atlas of the migratory bird Eurasian blackcap (Sylvia atricapilla)

Birds undisputedly range amongst natures foremost navigators. To successfully navigate between breeding and wintering quarters, they, in addition to other natural orientation cues, rely on their ability to sense the Earths magnetic field. For this reason, migratory birds have become key model species for studying the sensory mechanisms underlying magnetic field-guided navigation, as evidenced by the identification of several brain regions believed to be involved in processing magnetic field information. However, there is as yet no readily accessible, high-resolution three-dimensional (3D) brain atlas to serve as a common reference within and across studies. Here we provide the neuroscience research community with the first freely available, digital, high-resolution (25 {micro}m), 3D bird brain atlas. It is based on light microscopy images from ten Eurasian blackcaps (Sylvia atricapilla), a night-migratory songbird widely used model species in magnetoreception and navigation research. We outline the individual steps for the creation of a brain atlas, from whole-brain imaging using serial-section, two-photon tomography, to the creation of an average template at an isotropic 25-{micro}m voxel size, and finally to brain area segmentation and annotation. In this first version of the atlas, we have mapped a total of 24 brain areas, including 6 principal compartments, 13 conspicuous anatomical subdivisions common to all bird species and 5 functionally defined areas of the visual and trigeminal sensory systems involved in processing magnetic field information. This atlas is accessible via the standardised BrainGlobe Atlas API, making it compatible with a growing suite of computational neuroanatomy tools provided by the BrainGlobe Initiative. This integration enables precise alignment of future experimental data to a common coordinate space, facilitating collaboration, data visualization and sharing. Furthermore, this resource enables the accurate localization and comparison of implanted devices, injection sites, and/or cell populations across individual brains, both within and across studies.

neuroscience↗

bioRxiv2024

Activation mapping in multi-center rat sensory-evoked functional MRI datasets using a unified pipeline.

Functional Magnetic Resonance Imaging (fMRI) in rodents is pivotal for understanding the mechanisms underlying Blood Oxygen Level-Dependent (BOLD) signals and phenotyping animal models of disorders, amongst other applications. Despite its growing use, comparing rodent fMRI results across different research sites remains challenging due to variations in experimental protocols. Here, we aggregated and analyzed 22 sensory-evoked rat fMRI datasets from 12 imaging centers, totaling scans from 220 rats, to assess the consistency of results across diverse protocols. We applied a standardized preprocessing pipeline and evaluated the impact of different hemodynamic response function models on group and individual level activity patterns. Our analysis revealed inter-dataset variability attributed to differences in experimental design, anesthesia protocols, and imaging parameters. We identified robust activation clusters in all (22/22) datasets. The comparison between stock human models implemented in software and rat-specific models showed significant variations in the resulting statistical maps. Our findings emphasize the necessity for standardized protocols and collaborative efforts to improve the reproducibility and reliability of rodent fMRI studies. We provide open access to all datasets and analysis code to foster transparency and further research in the field.

neuroscience↗

bioRxiv2024

NeuralPlayground: A Standardised Environment for Evaluating Models of Hippocampus and Entorhinal Cortex

Neural processes in the hippocampus and entorhinal cortex are thought to be crucial for spatial cognition. A growing variety of theoretical models have been proposed to capture the rich neural and behavioral phenomena associated with these circuits. However, systematic comparison of these theories, both against each other and against empirical data, remains challenging. To address this gap, we present NeuralPlayground, an open-source standardised software framework for comparisons between theory and experiment in the domain of spatial cognition. This Python software package offers a reproducible way to compare models against a centralised library of published experimental results, including neural recordings and animal behavior. The framework implements three Agents embodying different computational models; three Experiments comprising publicly available neural and behavioral datasets; a customisable 2-dimensional Arena (continuous and discrete) able to generate common and novel spatial layouts; and a Comparison tool that facilitates systematic comparisons between models and data. Each module can also be used separately, allowing standardised and flexible access to influential models and data sets. We hope NeuralPlayground, available on GitHub3, provides a starting point for a shared, standardized, open, and reproducible computational understanding of the role of the hippocampus and entorhinal cortex in spatial cognition.

neuroscience↗

bioRxiv2023

Preserving functional network structure under anesthesia in the marmoset monkey brain

Initiatives towards acquiring large-scale neuroimaging data in non-human primates promise improving translational neuroscience and cross-species comparisons. Crucial among these efforts is the need to expand sample sizes while reducing the impact of anesthesia on the functional properties of brain networks. Yet, the effects of anesthesia on non-human primate brain networks remains unclear. Here, we demonstrate that isoflurane anesthesia induces a variety of brain states in the marmoset brain with dramatically altered functional connectivity profiles. As an alternative, we recommend using a continuous infusion of the sedative medetomidine, supplemented with a low concentration of isoflurane. With this protocol, we observed robust visual activation during flickering light stimulation and identified resting-state networks similar to the awake state. In contrast, isoflurane alone led to a suppressed visual activation and the absence of awake-like network patterns. Comparing states using a graph-theoretical approach, we confirmed that the structure of functional networks is preserved under our proposed anesthesia protocol but is lost using isoflurane alone. We believe that the widespread adoption of this protocol will be a step towards advancing translational neuroscience initiatives in non-human primate neuroimaging. To promote the shared use of neuroimaging resources, we share our datasets on the Marmoset connectome project. HighlightsO_LIMedetomidine combined with isoflurane is an effective protocol for driving visual BOLD responses compared to isoflurane-only anesthesia. C_LIO_LIIndependent component analysis revealed similar resting-state networks for medetomidine-isoflurane anesthesia and awake states. C_LIO_LIThe structure of resting-state networks was maintained under medetomidine-isoflurane but lost under isoflurane-only anesthesia. C_LI

neuroscience↗

bioRxiv2021

Spatial signatures of anesthesia-induced burst-suppression differ between primates and rodents

During deep anesthesia, the electroencephalographic (EEG) signal of the brain alternates between bursts of activity and periods of relative silence (suppressions). The origin of burst-suppression and its distribution across the brain remain matters of debate. In this work, we used functional magnetic resonance imaging (fMRI) to map the brain areas involved in anesthesia-induced burst-suppression across four mammalian species: humans, long-tailed macaques, common marmosets, and rats. At first, we determined the fMRI signatures of burst-suppression in human EEG-fMRI data. Applying this method to animal fMRI datasets, we found distinct burst-suppression signatures in all species. The burst-suppression maps revealed a marked inter-species difference: in rats the entire neocortex engaged in burst-suppression, while in primates most sensory areas were excluded--predominantly the primary visual cortex. We anticipate that the identified species-specific fMRI signatures and whole-brain maps will guide future targeted studies investigating the cellular and molecular mechanisms of burst-suppression in unconscious states.

neuroscience↗

bioRxiv2020

A collaborative resource platform for non-human primate neuroimaging

Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field.

neuroscience↗

bioRxiv2020

Circuits in the absence of cortical layers: increased callosal connectivity in reeler mice revealed by brain-wide input mapping of VIP neurons in barrel cortex

The neocortex is composed of layers. Whether layers constitute an essential framework for the formation of functional circuits is not well understood. We investigated if neurons require the layer organization to be embedded into brain-wide circuits using the reeler mouse. This mutant is characterized by a migration deficit of cortical neurons so that no layers are formed. Still, neurons retain their properties and reeler mice show little cognitive impairment. We focused on VIP neurons because they are known to receive strong long-range inputs and have a typical laminar bias towards upper layers. In reeler these neurons are more distributed across the cortex. We mapped the brain-wide inputs of VIP neurons in barrel cortex of wildtype and reeler mice with rabies virus tracing. Innervation by subcortical inputs was not altered in reeler, in contrast to the cortical circuitry. Numbers of long-range ipsilateral cortical inputs were reduced in reeler, while contralateral inputs were strongly increased. Reeler mice had more callosal projection neurons. Hence, the corpus callosum was larger in reeler as shown by structural imaging. We argue that in the absence of cortical layers, circuits with subcortical structures are maintained but cortical neurons establish a different network capable to preserve cognitive functions.

neuroscience↗

bioRxiv2019

Temporal stability of fMRI in medetomidine-anesthetized rats

Medetomidine has become a popular choice for anesthetizing rats during long-lasting sessions of blood-oxygen-level dependent (BOLD) functional magnetic resonance imaging (fMRI). Despite this, it has not yet been established how commonly reported fMRI readouts evolve over several hours of medetomidine anesthesia and how they are affected by the precise timing, dose, and route of administration. We used four different protocols of medetomidine administration to anesthetize rats for up to six hours and repeatedly evaluated somatosensory stimulus-evoked BOLD responses and resting state functional connectivity throughout. We found that the temporal evolution of fMRI readouts strongly depended on the method of administration. Protocols that combined an initial medetomidine bolus (0.05 mg/kg) together with a subsequent continuous infusion (0.1 mg/kg/h) led to temporally stable measures of stimulus-evoked activity and functional connectivity. However, when the bolus was omitted, or the dose of medetomidine lowered, the measures attenuated in a time-dependent manner. We conclude that medetomidine can sustain consistent fMRI readouts for up to six hours of anesthesia, but only with an appropriate administration protocol. This factor should be considered for the design and interpretation of future preclinical fMRI studies in rats.

neuroscience↗