Biology subjects

Caudal, L. C.

Publications and source records attributed to Caudal, L. C..

3 recordsLinked to original sources

bioRxiv2022

Novel algorithms for improved detection and analysis of fluorescent signal fluctuations

Fluorescent dyes and genetically encoded fluorescence indicators (GEFI) are common tools for visualizing concentration changes of specific ions and messenger molecules during intra-as well as intercellular communication. Using advanced imaging technologies, fluorescence indicators are a prerequisite for the analysis of physiological molecular signaling. Automated detection and avnalysis of fluorescence signals requires to overcome several challenges, including correct estimation of fluorescence fluctuations at basal concentrations of messenger molecules, detection and extraction of events themselves as well as proper segmentation of neighboring events. Moreover, event detection algorithms need to be sensitive enough to accurately capture localized and low amplitude events exhibiting a limited spatial extent. Here, we present two algorithms (PBasE and CoRoDe) for accurate baseline estimation of fluorescent detection of messenger molecules and automated detection of fluorescence fluctuations. Author summaryAnalyzing molecular signalling is crucial in understanding intra- and intercellular communication. These signals are visualized using fluorescent dyes or genetically encoded fluorescence indicators. In the brain, Ca2+ signals of glial cells are essential in deciphering complex regulatory functions in health and disease. Due to signal heterogeneity, detection and analysis are highly challenging. They can be stationary, with low amplitude and localized in cell processes, occur as prominent somatic signals or propagate as waves across cellular networks. We have developed two algorithms to analyze fluorescence transients, each tackling a specific problem. PBasE performs automatic and adaptive background correction, removing basal fluorescence fluctuations. CoRoDe automatically extracts regions of interest, explicitly including temporal information to obtain a precise segmentation, which is essential for accurate transient extraction. Combined, these algorithms are able to detect regions exhibiting low amplitude transients with small spatial extent as well as large, high amplitude signals. Extracted transients are categorized based on their peak amplitude, allowing detailed analyses by comparing changes of specific properties. In order to make these algorithms accessible, an interactive application, called Msparkles, has been designed.

neuroscience↗

bioRxiv2020

Deciphering spatio-temporal fluorescence changes using multi-threshold event detection (MTED)

Recent achievements in indicator optimization and imaging techniques promote the exploration of Ca2+ activity patterns as a main second messenger in many organs. Astrocytes are important regulators of brain activity and well known for their Ca2+-dependent modulation of neurons. However, standardized methods to analyze and interpret Ca2+ activity recordings are missing and hindering global comparisons. Here, we present a biophysics-based concept to analyze Ca2+signals, which includes multiple thresholds and provides the experimenter with a comprehensive toolbox for a differentiated and in-depth characterization of Ca2+ signals. We analyzed various ex vivo and in vivo imaging datasets and verify the validity of our multi-threshold event detection (MTED) algorithm across Ca2+ indicators, imaging setups, and model systems from primary cell culture to awake, head-fixed mice. Applying our MTED concept enables standardized analysis and advances research using optical readouts of cellular activity to decrypt brain function. It allowed us to obtain new insights into the complex dependence of Ca2+activity patterns on temperature and neuronal activity. Highlights[->] We present a robust pixel-based algorithm to analyze multidimensional fluorescence data. [->]Automated multiple-threshold analysis accurately quantifies changes in fluorescence across magnitudes. [->]It characterizes the complexity of dynamic and overlapping activity patterns of Ca2+ activity of astrocytes in vitro, in situ, and in vivo. [->]Its application provides quantitative parameters how temperature and neuronal activity determine astrocytic Ca2+ activity.

neuroscience↗

bioRxiv2020

ALG-2 interacting protein-X (Alix) is required for activity-dependent bulk endocytosis at brain synapses

In chemical synapses undergoing high frequency stimulation, vesicle components can be retrieved from the plasma membrane via a clathrin-independent process called activity dependent bulk endocytosis (ADBE). Alix (ALG-2 interacting protein X)/ PDCD6IP) is an adaptor protein binding to ESCRT and endophilin-A proteins which is required for clathrin-independent endocytosis in fibroblasts. Alix is expressed in neurons and concentrates at synapses during epileptic seizures. Here, we used cultured neurons to show that Alix is recruited to presynapses where it interacts with, and concentrates endophilin-A during conditions triggering ADBE. Using Alix knockout (ko) neurons we showed that this recruitment, which requires interaction with the calcium-binding protein ALG-2, is necessary for ABDE. We also found that presynaptic compartments of Alix ko hippocampi display subtle morphological defects compatible with flawed synaptic activity and plasticity detected electrophysiologically. Furthermore, mice lacking Alix in the forebrain undergo less seizures during kainate-induced status epilepticus and reduced propagation of the epileptiform activity. These results thus show that impairment of ADBE due to the lack of neuronal Alix alters synaptic recovery during physiological or pathological repeated stimulations.

neuroscience↗