Biology subjects

Boergens, K. M.

Publications and source records attributed to Boergens, K. M..

10 recordsLinked to original sources

bioRxiv2025

Ultrastructural changes at auditory nerve synapses following moderate noise exposure

Moderate noise exposure is a common experience, yet its impact on central auditory synapses remains poorly understood. We study this issue at the first synapses in the central auditory pathway formed by auditory nerve afferents onto bushy cells in the cochlear nucleus, called endbulbs of Held. Non-traumatic noise exposure alters endbulb properties, decreasing the probability of vesicle release and enlarging the pool of releasable vesicles as assessed using electrophysiological methods and immunolabelling. These changes appear homeostatic, to maintain synaptic efficacy during periods of high activity. To identify structural changes underlying the larger vesicle pool, we used serial blockface electron microscopy of endbulbs from control and noise-exposed mice to quantitatively assess synaptic morphology. We observed no differences in the juxtapositional area between endbulbs and bushy cells, nor in the number or density of active zones and postsynaptic densities. Images of endbulb terminals were significantly darker after noise exposure, indicating an increase in the density of synaptic vesicles. These results suggest that moderate noise exposure induces an activity-dependent increase in presynaptic vesicle numbers, consistent with the observed physiological changes in neurotransmitter release. This work sets the stage for high-resolution studies to quantify docked and reserve vesicles. Significance statementNoise exposure is a fact of everyday life, and it is important to understand how noise affects function in the auditory pathway in the brain to understand the full consequences of noise exposure. Electrophysiological experiments indicate that noise triggers a homeostatic increase in the releasable pool of vesicles at auditory nerve synapses. We examined the cellular basis for this change using serial blockface electron microscopy of auditory nerve synapses with and without noise exposure. We reconstructed a number of bushy cells and their presynaptic auditory nerve terminals. After noise exposure, there was no significant increase in the area of synaptic contact or the number or density of synaptic release sites. There was an increase in the number of vesicles near release sites, which may account for the physiological changes. These results emphasize the importance of detailed anatomical studies to study the effects of noise exposure and thus determine the best mechanistic approach for therapies and treatments of noise-induced hearing loss.

neuroscience↗

bioRxiv2023

A Pipeline for a Primate Projectome: mapping every individual myelinated axon across the whole brain

1We developed a pipeline to detail the morphology and complete trajectory of every long distance projecting neuron in large volumes of the non-human primate brain - a projectome. A projectome would organize how the hundreds of brain regions in a primate brain communicate with each other and provide a comprehensive classification of long distance neurons. The reason such projectomes do not exist already is that there is no single imaging technique with the resolution and sampling depth capable of producing one in primates. Here we address that gap by combining new ways to cut brains with minimal tissue loss, nanoscale x-ray microscopy imaging that reveals every individual myelinated axon (MA) and the location, size, and morphology of every neuron, and algorithms for tracing individual myelinated axons for millimeters to centimeters, across tissue gaps.

neuroscience↗

bioRxiv2023

Photoemission electron microscopy for connectomics

1Detailing the physical basis of neural circuits with large-volume serial electron microscopy (EM), connectomics, has emerged as an invaluable tool in the neuroscience armamentarium. However, imaging synaptic resolution connectomes is currently limited to either transmission electron microscopy (TEM) or scanning electron microscopy (SEM). Here, we describe a third way, using photoemission electron microscopy (PEEM) which illuminates ultra-thin brain slices collected on solid substrates with UV light and images the photoelectron emission pattern with a wide-field electron microscope. PEEM works with existing sample preparations for EM and routinely provides sufficient resolution and contrast to reveal myelinated axons, somata, dendrites, and sub-cellular organelles. Under optimized conditions, PEEM provides synaptic resolution; and simulation and experiments show that PEEM can be transformatively fast, at Gigahertz pixel rates. We conclude that PEEM imaging leverages attractive aspects of SEM and TEM, namely reliable sample collection on robust substrates combined with fast wide-field imaging, and could enable faster data acquisition for next-generation circuit mapping.

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bioRxiv2022

Connectomic Analysis of Thalamus-driven Disinhibition in Cortical Layer 4

In mammals, sensory signals are transmitted via the thalamus primarily to layer 4 of the primary sensory cortices. While information about average neuronal connectivity in this layer is available, the detailed and higher-order circuit structure is not known. Here, we used 3-dimensional electron microscopy for a connectomic analysis of the thalamus-driven inhibitory network in a layer 4 barrel. We find that thalamic input drives a subset of interneurons with high specificity. These interneurons in turn target spiny stellate and star pyramidal excitatory neurons with subtype specificity. In addition, they create a directed disinhibitory network directly driven by the thalamic input. Together, this circuit can create differential windows of opportunity for activation of the types of excitatory neurons in dependence of strength and timing of thalamic input. With this, we have identified a so-far unknown degree of specialization of the microcircuitry in the main thalamocortical recipient layer of the primary sensory cortex.

neuroscience↗

bioRxiv2020

Laser Ablation of the Pia Mater for Insertion of High-Density Microelectrode Arrays in a Translational Sheep Model

The safe insertion of high density intracortical electrode arrays has been a long-standing practical challenge for neural interface engineering and applications such as brain-computer interfaces (BCIs). Here we describe a surgical procedure, inspired by laser corneal ablation, that can be used in large mammals to thin the pia mater, the innermost meningeal layer encapsulating the brain. This procedure allows for microelectrode arrays to be inserted into the cortex with less force, thus reducing deformation of underlying tissue during placement of the microelectrodes. We demonstrate that controlled pia removal over a small area of cortex allows for insertion of high-density electrode arrays and subsequent acute recordings of spiking neuron activity in sheep cortex. We also show histological and electrophysiological evidence that laser removal of the pia does not acutely affect neuronal viability in the region. This approach suggests a promising new path for clinical BCI with high-density microelectrode arrays.

neuroscience↗

bioRxiv2020

The Argo: A 65,536 channel recording system for high density neural recording in vivo

Here we demonstrate the Argo System, a massively parallel neural recording system based on platinum-iridium microwire electrode arrays bonded to a CMOS voltage amplifier array. The Argo system is the highest channel count in vivo neural recording system built to date, supporting simultaneous recording from 65,536 channels, sampled at over 32 kHz and 12-bit resolution. This system is designed for cortical recordings, compatible with both penetrating and surface microelectrodes. We have validated this system by recording spiking activity from 791 neurons in rats and cortical surface Local Field Potential (LFP) activity from over 30,000 channels in sheep. While currently adapted for head-fixed recording, the microwire-CMOS architecture is well suited for clinical translation. Thus, this demonstration helps pave the way for a future high data rate intracortical implant.

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bioRxiv2019

Cell-type specific innervation of cortical pyramidal cells at their apical tufts

We investigated the synaptic innervation of apical tufts of cortical pyramidal cells in a region between layers 1 and 2 using 3-D electron microscopy (3D-EM) applied to four cortical regions in mouse. Across all cortices, we found the relative inhibitory input at the apical dendrites main bifurcation to be more than 3-fold stronger for layer 2 pyramidal cells than for all other pyramidal cells. Towards the distal tuft dendrites in upper layer 1, however, the relative inhibitory input was about 2-fold stronger for L5 pyramidal cells than for all others. Only L3 pyramidal cells showed homogeneous inhibitory input density. The inhibitory to excitatory synaptic balance is thus specific for the types of pyramidal cells. Inhibitory axons preferentially innervated either layer 2 or L3/5 apical dendrites, but not both. These findings describe connectomic principles for the control of pyramidal cells at their apical dendrites in the upper layers of the cerebral cortex and point to differential computational properties of layer 2, layer 3 and layer 5 pyramidal cells in cortex.

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bioRxiv2018

Dense connectomic reconstruction in layer 4 of the somatosensory cortex

The dense circuit structure of the mammalian cerebral cortex is still unknown. With developments in 3-dimensional (3D) electron microscopy, the imaging of sizeable volumes of neuropil has become possible, but dense reconstruction of connectomes from such image data is the limiting step. Here, we report the dense reconstruction of a volume of about 500,000 m3 from layer 4 of mouse barrel cortex, about 300 times larger than previous dense reconstructions from the mammalian cerebral cortex. Using a novel reconstruction technique, FocusEM, we were able to reconstruct a total of 0.9 meters of dendrites and about 1.8 meters of axons investing only about 4,000 human work hours, about 10-25 times more efficient than previous dense circuit reconstructions. We find that connectomic data alone allows the definition of inhibitory axon types that show established principles of synaptic specificity for subcellular postsynaptic compartments. We find that also a fraction of excitatory axons exhibit such subcellular target specificity. Only about 35% of inhibitory and 55% of excitatory synaptic subcellular innervation can be predicted from the geometrical availability of membrane surface, revoking coarser models of random wiring for synaptic connections in cortical layer 4. We furthermore find evidence for enhanced variability of synaptic input composition between neurons at the level of primary dendrites in cortical layer 4. Finally, we obtain evidence for Hebbian synaptic weight adaptation in at least 24% of connections; at least 35% of connections show no sign of such previous plasticity. Together, these results establish an approach to connectomic phenotyping of local dense neuronal circuitry in the mammalian cortex.

neuroscience↗

bioRxiv2018

FluoEM: Virtual labeling of axons in 3-dimensional electron microscopy data for long-range connectomics

Volume electron microscopy (3D EM) has enabled the dense reconstruction of neuronal circuits in datasets that are so far about a few hundred micrometers in extent. In mammalian brains, most neuronal circuits are however highly non-local, such that a large fraction of the synapses in such a volume of neuropil originates from distant projection sources. The labeling and identification of such long-range axonal inputs from multiple sources within a densely reconstructed EM dataset has been notoriously difficult because of the limited color label space of EM. Here, we present FluoEM, a set of experimental and computational methods that allows the identification of multi-color fluorescently labeled axons in dense EM data without the need for artificially introduced fiducial marks or direct label conversion for EM. The approach is based on correlated imaging of the tissue and computational matching of neurite reconstructions, amounting to a virtual color labeling of axons in dense EM circuit data. We show that the identification of fluorescent light-microscopically (LM) imaged axons in 3D EM data from mouse cortex is faithfully possible as soon as the EM dataset is about 40-50 m in extent, relying on the unique trajectories of axons in dense mammalian neuropil. The method is exemplified for the identification of longdistance axonal input into layer 1 of the mouse cerebral cortex.

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bioRxiv2017

SynEM: Automated synapse detection for connectomics

Nerve tissue contains a high density of chemical synapses, about 1 per {micro}m3 in the mammalian cerebral cortex. Thus, even for small blocks of nerve tissue, dense connectomic mapping requires the identification of millions to billions of synapses, of which about 80-90% are excitatory synapses. While the focus of connectomic data analysis has been on neurite reconstruction, synapse detection becomes limiting when datasets grow in size and dense mapping is required. Here, we report SynEM, a method for automated detection of excitatory synapses from conventionally en-bloc stained 3D electron microscopy image stacks. The approach is based on a segmentation of the image data and focuses on classifying borders between neuronal processes as synaptic or non-synaptic. SynEM yields 98% precision and recall in binary excitatory cortical connectomes with no user interaction. It scales to large volumes of cortical neuropil, plausibly even whole-brain datasets. SynEM removes the burden of manual synapse annotation for large densely mapped connectomes.

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