Biology subjects

Topcu, E.

Publications and source records attributed to Topcu, E..

3 recordsLinked to original sources

bioRxiv2025

Processing and sectioning of organ donor spinal cord tissue for electrophysiology on acute human spinal cord slices

Acute spinal cord slice electrophysiology is a powerful technique used in preclinical basic science research to investigate sensory and motor neuron function and pathophysiology. A major barrier that stands between implementing these findings into effective clinical treatments is the translational gap between rodent models and human patients. To date, no methods or protocols describe how to prepare viable human spinal cord slices for acute electrophysiological recordings. To bridge this translational divide, we describe here a protocol for the extraction of spinal cord tissue from consenting human organ donors and the preparation and sectioning of this tissue for acute spinal cord slice electrophysiology. With the collaboration of a transplant service and licensed surgeon, tissue can be extracted in 30-50 minutes. Acute spinal cord slices can then be prepared in the laboratory by trained graduate students in 2.5-5 hours, depending on the amount of tissue and scope of experiments. Using a viability stain to confirm that spinal slices are of sufficient quality to proceed, slices can then be used for either patch-clamp recordings to study the excitability of individual neurons or for high-density multielectrode array recordings to study intact sensory circuits. Slices remain viable for 4 to 8 hours, providing ample time for investigating synaptic and circuit-level signalling dynamics, including the use of pharmacological agents to probe the roles of specific molecular targets. The approaches described here can be implemented to improve translational physiological research and as a human tissue-based preclinical drug target identification and validation assay.

neuroscience↗

bioRxiv2023

Heterogeneity of synaptic NMDA receptor responses within individual lamina I pain processing neurons across sex in rats and humans

Excitatory glutamatergic NMDA receptors (NMDARs) are key regulators of spinal pain processing, and yet the biophysical properties of NMDARs in dorsal horn nociceptive neurons remain poorly understood. Despite the clinical implications, it is unknown whether the molecular and functional properties of NMDAR synaptic responses are conserved between males and females as well as from rodents to humans. To address these translational gaps, we systematically compared individual and averaged excitatory synaptic responses from lamina I pain-processing neurons of adult Sprague Dawley rats and human organ donors, including both sexes. By combining patch-clamp recordings of outward miniature excitatory postsynaptic currents with non-biased data analyses, we uncovered a wide range of decay constants of excitatory synaptic events within individual lamina I neurons. Decay constants of quantal synaptic responses were distributed in a continuum from 1-20 ms to greater than 1000 ms, suggesting that individual lamina I neurons contain AMPA receptor (AMPAR)-only as well as GluN2A-, GluN2B-, and GluN2D-NMDAR-dominated synaptic events. This intraneuronal heterogeneity in AMPAR- and NMDAR-mediated decay kinetics was observed across sex and species. However, we discovered a decreased relative contribution of GluN2B-dominated NMDAR responses as well as larger amplitude GluN2D-like events at human lamina I synapses compared to rodent synapses, suggesting species differences relevant to NMDAR subunit-targeting therapeutic approaches. The conserved heterogeneity in decay rates of excitatory synaptic events within individual lamina I pain-processing neurons may enable synapse-specific forms of plasticity and sensory integration within dorsal horn nociceptive networks.

neuroscience↗

bioRxiv2019

PeSA: A Software Tool for Peptide Specificity Analysis

The discovery of molecular interactions is crucial towards a better understanding of complex biological functions. Particularly protein-protein interactions (i.e., PPIs), which are responsible for a variety of cellular functions from epigenetic modifications to enzyme-substrate specificity, have been studied extensively over the past decades. Position-specific scoring matrices (PSSM) in particular are used extensively to help determine interaction specificity or candidate interaction motifs. However, not all studies successfully report their results as a candidate interaction motif. In many cases, this is the result of a lack of analysis tools for simple analysis and motif generation. Peptide Specificity Analyst (PeSA) is developed with the goal of filling this gap and providing an analysis software to aid peptide array analysis and subsequent motif generation. PeSA utilizes two models of motif creation: (1) frequency-based using a peptide list, and (2) weight-based using a quantified matrix. The ability to generate motifs effortlessly will make analyzing, interpreting and sharing peptide specificity study results in a simple and straightforward process.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC=\"FIGDIR/small/760140v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@1668389org.highwire.dtl.DTLVardef@145bbfeorg.highwire.dtl.DTLVardef@1392eaeorg.highwire.dtl.DTLVardef@127e2c3_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIBiological motifs are widely used representations for peptide specificity analysis.\nC_LIO_LIPeSA populates a list of peptides matching a set threshold from a quantified matrix.\nC_LIO_LIFrequency-based motif using a peptide list to spot residue patterns.\nC_LIO_LIUse of quantified matrices to create weight-based motifs using residue positions.\nC_LI

bioinformatics↗