Biology subjects

Zeidler, M.

Publications and source records attributed to Zeidler, M..

6 recordsLinked to original sources

bioRxiv2024

Biophysical Essentials - A Full Stack Open-Source Software Framework for Conserved and Advanced Analysis of Patch-Clamp Recordings

Patch-Clamp recordings allow for in depth electrophysiological characterization of single cells, their general biophysical properties as well as characteristics of voltage- and ligand-gated ionic currents. Different acquisition modes, such as whole-cell patch-clamp recordings in the current or voltage clamp configuration, capacitance measurements or single channel recordings from cultured cells as well as acute brain slices are routinely performed for these purposes. Nevertheless, multipurpose transparent and adaptable software tools to perform reproducible state-of-the-art analysis of multiple experiment types and to manage larger sets of experimental data are currently unavailable. We therefore developed Biophysical Essentials (BPE) as an open-source python software for transparent and reproducible analysis of electrophysiological recordings. While initially designed to improve time consuming and repetitive analysis steps, BPE was optimized to cover entire workflows from data acquisition, preprocessing, visualization and normalization of single recordings up to stacked calculations and statistics of multiple experiments. BPE can operate with different file formats from different amplifier systems and producers. An in-process database logs all analysis steps for later review and serves as a central storage point for recordings. Statistical testing as well as advanced analysis functions like Boltzmann-fitting and dimensional reduction methods further support the researchers needs in projects involving electrophysiology techniques. Impact statementBiophysical Essentials provides fundamental support for transparent patch-clamp analysis to improve reproducibility in electrophysiology research.

neuroscience↗

bioRxiv2023

IL-4 shaping glutamatergic synapse like structures for more mature iPSC derived neuron phenotypes

The prototypical pleiotropic anti-inflammatory cytokine IL-4 not only acts on immune cells but also has important roles in the nervous system mediating antinociception and neuroregeneration. Therefore, we explored the expression of IL-4, its receptors IL4RA and IL13RA1 and downstream signaling components together with morphological and functional assays as well as transcriptomic profiling in human nociceptors differentiating from induced pluripotent stem cells (iNocs). IL-4 induced de novo formation of synaptic boutons immunoreactive for vesicular glutamate transporter vGLUT1 in iNocs which express both, components of the IL-4 receptor complex (IL-4RA and IL-13RA1) and signaling machinery (Jak1/2, STAT6, PKC isoforms, translation factor EiF4E) during differentiation. Pharmacological inhibition of these translational or cellular signaling components reduced the synaptogenic effect. IL-4 induced distinct transcriptomic changes associated with biological process ontologies for "neuron projection development", "axonogenesis" and "synapse", "cellular process involved in reproduction in multicellular organism", "regulation of membrane potential" and "calcium ion transmembrane transport". This partially reflected injury-induced transcriptional changes of mouse nerve injury models which contribute to regenerative processes in peripheral nerve but possibly also to reconnecting primary afferent neurons to their projections in the spinal dorsal horn and indicates a critical role for IL-4 in the control of developing and established neuronal networks.

neuroscience↗

bioRxiv2023

NOCICEPTRA2.0 - a comprehensive ncRNA atlas of human native and iPSC-derived sensory neurons

Non-coding RNAs (ncRNAs) play a critical role in regulating gene expression during development and in the pathogenesis of diseases. In particular, microRNAs have been extensively studied in the context of neurogenesis, the differentiation of pain sensing nociceptive neurons and the pathogenesis of pain disorder, however, little is known about the developmental signatures of other ncRNA species throughout sensory neuron differentiation. Moreover, there is currently no information available about the general expression signatures of ncRNAs in human dorsal root ganglia (DRGs) harboring the cell bodies of primary afferent nociceptors. To bridge this knowledge gap, we developed a comprehensive atlas of small ncRNA species signatures during the differentiation of human induced pluripotent stem cell (iPSC)-derived nociceptive neurons. By employing a combination of iPSC-derived sensory neuron and human DRG long and short RNA co-sequencing, we identified specific signatures that describe the developmental processes and the signatures of all currently known small ncRNA species in detail. Our analysis revealed that different ncRNA species, including tRNAs, snoRNAs, lncRNAs, and piRNAs, are associated with different stages of sensory neuron differentiation and maturation. We retrieved pronounced similarities in ncRNA expression between human DRG and late-stage iPSC-derived sensory neurons, which further supports the use of iPSC-derived sensory neurons to uncover functional and regulatory changes in ncRNAs and their suitability as a as a human model system to bridge the translational gap between preclinical findings mostly from rodent models and our understanding of human disorders for the development of mechanism-based treatments. In summary, our findings provide important insights into the role of ncRNA species other than microRNAs in human nociceptors. The updated NOCICEPTRA2.0 Tool will be the first fully comprehensive searchable ncRNA database for human sensory neurons enabling researchers to investigate important hub ncRNA regulators in nociceptors in full detail.

neuroscience↗

bioRxiv2021

The plant-specific SCL30a SR protein regulates ABA-dependent seed traits and salt stress tolerance during germination

SR (serine/arginine-rich) proteins are conserved RNA-binding proteins best known as key regulators of splicing, which have also been implicated in other steps of gene expression. Despite mounting evidence for their role in plant development and stress responses, the molecular pathways underlying SR protein regulation of these processes remain elusive. Here we show that the plant-specific SCL30a SR protein negatively regulates abscisic acid (ABA) signaling to control important seed traits and salt stress responses during germination in Arabidopsis. The SCL30a gene is upregulated during seed imbibition and germination, and its loss of function results in smaller seeds displaying enhanced dormancy and elevated expression of ABA-responsive genes as well as of genes repressed during the germination process. Moreover, the knockout mutant is hypersensitive to ABA and high salinity, while transgenic plants overexpressing SCL30a exhibit reduced ABA sensitivity and enhanced tolerance to salt stress during seed germination. An ABA biosynthesis inhibitor rescues the mutants enhanced sensitivity to stress, and epistatic analyses confirm that this hypersensitivity requires a functional ABA pathway. Finally, seed ABA levels are unchanged by altered SCL30a expression, indicating that the SR protein positively regulates stress tolerance during seed germination by reducing sensitivity to the phytohormone. Our results reveal a new key player in ABA-mediated control of early development and stress response, and underscore the role of plant SR proteins as important regulators of the ABA signaling pathway. Author SummarySeed germination is a critical step in plant development determining the transition to aerial growth and exposure to a more challenging environment. As such, seeds have evolved mechanisms that prevent germination under adverse conditions, thereby increasing the chances of plant survival. As a general regulator of plant development and a key mediator of stress responses, the hormone abscisic acid (ABA) promotes a prolonged non-germinating state called dormancy, influences seed size and represses germination under environmental stress. Here, we show that an RNA-binding protein, SCL30a, controls seed size, dormancy, germination and tolerance to high salinity in the model plant Arabidopsis thaliana. Loss of SCL30a gene function results in smaller and more dormant seeds with reduced ability to germinate in a high-salt environment; by contrast, SCL30a overexpression produces larger seeds that germinate faster under salt stress. Using a large-scale gene expression analysis, we identify the ABA hormonal pathway as a putative target of SCL30a. We then use genetic and pharmacological tools to unequivocally demonstrate that the uncovered biological functions of SCL30a are achieved through modulation of the ABA pathway. Our study reveals a novel regulator of key seed traits and has biotechnological implications for crop improvement under adverse environments.

plant biology↗

bioRxiv2021

NOCICEPTRA: Gene and microRNA signatures and their trajectories characterizing human iPSC-derived nociceptor maturation

Nociceptors are primary afferent neurons serving the reception of acute pain but also the transit into maladaptive pain disorders. Since native human nociceptors are hardly available for mechanistic functional research, and rodent models do not necessarily mirror human pathologies in all aspects, human iPSC-derived nociceptors (iDN) offer superior advantages as a human model system. Unbiased mRNA::microRNA co-sequencing, immunofluorescence staining and qPCR validations, revealed expression trajectories as well as miRNA target spaces throughout the transition of pluripotent cells into iDNs. mRNA and miRNA candidates emerged as regulatory hubs for neurite outgrowth, synapse development and ion channel expression. The exploratory data analysis tool NOCICEPTRA is provided as a containerized platform to retrieve experimentally determined expression trajectories, and to query custom gene sets for pathway and disease enrichments. Querying NOCICEPTRA for marker genes of cortical neurogenesis revealed distinct similarities and differences for cortical and peripheral neurons. The platform provides a public domain neuroresource to exploit the entire data sets and explore miRNA and mRNA as hubs regulating human nociceptor differentiation and function.

neuroscience↗

bioRxiv2018

Knock-in rats expressing Cre and Flp recombinases at the Parvalbumin locus.

Rats have the ability to learn and perform sophisticated behavioral tasks, making them very useful for investigating neural circuit functions. In contrast to the extensive mouse genetic toolkit, the paucity of recombinase-expressing rat models has limited the ability to monitor and manipulate molecularly-defined neural populations in this species. Here we report the generation and validation of two knock-in rat strains expressing either Cre or Flp recombinase under the control of Parvalbumin (Pvalb), a gene expressed in the critical \"fast-spiking\" subset of inhibitory interneurons (FSIs). These strains were generated with CRISPR-Cas9 gene editing and show highly specific and penetrant labeling of Pvalb-expressing neurons, as demonstrated by in situ hybridization and immunohistochemistry. We validated these models in both prefrontal cortex and striatum using both ex vivo and in vivo approaches, including whole-cell recording, optogenetics, extracellular physiology and photometry. Our results demonstrate the utility of these new transgenic models for a wide range of neuroscience experiments.

neuroscience↗