Biology subjects

Herz, A.

Publications and source records attributed to Herz, A..

7 recordsLinked to original sources

bioRxiv2026

Next-generation insect digitization: combining phenomics and genomics by subsequent synchrotron X-ray imaging and DNA sequencing

Recent technological advances allow for the large-scale acquisition of genetic and morphological data: high-throughput sequencing has transformed the field of genomics while synchrotron X-ray microtomography enables rapid, noninvasive 3D imaging. However, integrating these approaches for the same specimens is challenging because X-rays can fragment DNA, and DNA extraction damages internal morphology, particularly relevant for small bodied organisms, such as insects. We systematically tested multiple extraction protocols and irradiation conditions across three model insect species. We irradiated more than 1,000 specimens under varying conditions and tested DNA quality through DNA barcoding and UCE sequencing. Our results demonstrate that high-quality DNA and high-resolution tomograms can be obtained from the same individuals, provided that the parameters are carefully optimized and rapid SR-CT scanning precedes DNA extraction. In this respect, our findings establish practical guidelines for combining genomics and phenomics, paving the way for comprehensive integrative digitization of biodiversity.

genetics↗

bioRxiv2024

Grid cells anticipate the animal's future movement

Grid cells in the rodent medial entorhinal cortex preferentially fire spikes when the animal is within certain regions of space. When experimental data are averaged over time, spatial firing fields become apparent. If these firing fields represented only the current position of the animal, a grid cells firing should not depend on whether the animal is running into or out of a firing field. Yet many grid cells are sensitive to the animals direction of motion relative to the firing-field center. Such apparent egocentric "inbound-outbound tuning" could be a sign of prospective encoding of future position, but it is unclear whether grid cells code ahead in space or in time. To investigate this question, we decided to undo the inbound-outbound modulation by shifting all spikes within a given firing field by a fixed distance in space or in time. For grid-cell data recorded in mice, optimizing in space requires a forward shift of around 2.5 cm, whereas optimizing in time yielded a forward shift of about 170 ms. In either case the firing-field sizes decrease. Minimizing just the field size yields somewhat smaller shifts (roughly 1.8 cm and around 115 ms ahead). Jointly optimizing along the temporal and spatial dimension reveals a continuum of flat inbound-outbound tuning curves and a shallow minimum for field sizes, located at about 2.3 cm and 35 ms. These findings call into question a purely spatial or purely temporal interpretation of grid-cell firing fields and inbound-outbound tuning.

neuroscience↗

bioRxiv2023

Insect Detect: An open-source DIY camera trap for automated insect monitoring

Insect monitoring is essential to design effective conservation strategies, which are indispensable to mitigate worldwide declines and biodiversity loss. For this purpose, traditional monitoring methods are widely established and can provide data with a high taxonomic resolution. However, processing of captured insect samples is often time-consuming and expensive, which limits the number of potential replicates. Automated monitoring methods can facilitate data collection at a higher spatiotemporal resolution with a comparatively lower effort and cost. Here, we present the Insect Detect DIY (do-it-yourself) camera trap for non-invasive automated monitoring of flower-visiting insects, which is based on low-cost off-the-shelf hardware components combined with open-source software. Custom trained deep learning models detect and track insects landing on an artificial flower platform in real time on-device and subsequently classify the cropped detections on a local computer. Field deployment of the solar-powered camera trap confirmed its resistance to high temperatures and humidity, which enables autonomous deployment during a whole season. On-device detection and tracking reliably estimated insect activity/abundance after metadata post-processing. Our insect classification model achieved a high top-1 accuracy on the test dataset and generalized well on a real-world dataset with captured insect images. The camera trap design and open-source software are highly customizable and can be adapted to different use cases. With custom trained detection and classification models, as well as accessible software programming, many possible applications surpassing our proposed deployment method can be realized.

bioinformatics↗

bioRxiv2019

Spike afterpotentials shape the in-vivo burst activity of principal cells in medial entorhinal cortex

Principal neurons in rodent medial entorhinal cortex (MEC) generate high-frequency bursts during natural behavior. While in vitro studies point to potential mechanisms that could support such burst sequences, it remains unclear whether these mechanisms are effective under in-vivo conditions. In this study, we focused on the membrane-potential dynamics immediately following action potentials, as measured in whole-cell recordings from male mice running in virtual corridors (Domnisoru et al., 2013). These afterpotentials consisted either of a hyperpolarization, an extended ramp-like shoulder, or a depolarization reminiscent of depolarizing afterpotentials (DAPs) recorded in vitro in MEC stellate and pyramidal neurons. Next, we correlated the afterpotentials with the cells propensity to fire bursts. All DAP cells with known location resided in Layer II, generated bursts, and their inter-spike intervals (ISIs) were typically between five and fifteen milliseconds. The ISI distributions of Layer-II cells without DAPs peaked sharply at around four milliseconds and varied only minimally across that group. This dichotomy in burst behavior is explained by cell-group-specific DAP dynamics. The same two groups of bursting neurons also emerged when we clustered extracellular spike-train autocorrelations measured in real two-dimensional arenas (Latuske et al., 2015). No difference in the spatial coding properties of the grid cells across all three groups was discernible. Layer III neurons were only sparsely bursting and had no DAPs. As various mechanisms for modulating the ion-channels underlying DAPs exist, our results suggest that the temporal features of MEC activity can be altered while maintaining the cells spatial tuning characteristics. Significance StatementDepolarizing afterpotentials (DAPs) are frequently observed in principal neurons from slice preparations of rodent medial entorhinal cortex (MEC), but their functional role in vivo is unknown. Analyzing whole-cell data from mice running on virtual tracks, we show that DAPs do occur during behavior. Cells with prominent DAPs are found in Layer II; their inter-spike intervals reflect DAP time-scales. In contrast, neither the rarely bursting cells in Layer III, nor the high-frequency bursters in Layer II, have a DAP. Extracellular recordings from mice exploring real two-dimensional arenas demonstrate that grid cells within these three groups have rather similar spatial coding properties. We conclude that DAPs shape the temporal but not the spatial response characteristics of principal neurons in MEC. Author contributionsAll authors designed research. DEC, CF, and JN performed research and analyzed data (equal contribution). AVMH wrote and edited the paper with support from MS and the other authors.

neuroscience↗

bioRxiv2019

Zebrafish use visual cues and geometric relationships to form a spatial memory

Animals use salient cues to navigate in their environment, but their specific cognitive strategies are largely unknown. We developed a conditioned place avoidance paradigm to discover whether and how zebrafish form spatial memories in a Y-shaped maze. Juvenile zebrafish, older than three weeks, learned to avoid the arm of the maze that was cued with a mild electric shock. We found that the fish required distinct visual patterns to develop a conditioned response. Interestingly, individual fish solve this task in different ways: by staying in the safe center of the maze, by preference for one, or both, of the safe patterns, or by mixed strategies. In experiments in which the learned patterns were swapped, rotated or replaced, the animals could transfer the association of safety to a different arm or to a different pattern using either visual cues or location as the conditioned stimulus. These findings show that juvenile zebrafish exhibit several complementary spatial learning modes and pave the way for neurobiological studies of navigational mechanisms in this model species.

neuroscience↗

bioRxiv2018

Anticipatory neural activity improves the decoding accuracy for dynamic head-direction signals

Insects and vertebrates harbor specific neurons that encode the animals head direction (HD) and provide an internal compass for spatial navigation. Each HD cell fires most strongly in one preferred direction. As the animal turns its head, however, HD cells in rat anterodorsal thalamic nucleus (ADN) and other brain areas fire already before their preferred direction is reached, as if the neurons anticipated the future head direction. This phenomenon has been explained at a mechanistic level but a functional interpretation is still missing. To close this gap, we use a computational approach based on the animals movement statistics and a simple model for the behavior of the ADN head-direction network. Network activity is read out using population vectors in a biologically plausible manner, so that only past spikes are taken into account. We find that anticipatory firing improves the representation of the present HD by reducing the motion-induced temporal bias inherent in causal decoding. The amount of anticipation observed in ADN enhances the precision of the HD compass read-out by up to 40%. In addition, our framework predicts that neural integration times not only reflect biophysical constraints, but also the statistics of natural stimuli; anticipatory tuning should be found whenever neurons encode sensory signals that change gradually in time.\n\nSignificance statementAcross different brain regions, populations of noisy neurons encode dynamically changing stimuli. Decoding a time-varying stimulus from the population response involves a trade-off: For short read-out times, stimulus estimates are unreliable as the number of stochastic spikes will be small; for long read-out times, estimates are biased because they lag behind the true stimulus. We show that optimal decoding relies not only on finding the right read-out time window, but requires neurons to anticipate future stimulus values. We apply this framework to the rodent head-direction system and show that the experimentally observed anticipation of future head directions can be explained at a quantitative level from the neuronal tuning properties, the network size, and the animals head-movement statistics.

neuroscience↗

bioRxiv2017

GABA regulates resonance and spike rate encoding via a universal mechanism that underlies the modulation of action potential generation

Different mechanisms for action potential (AP) generation exist that shape neuronal coding and network dynamics. The neuro-transmitter GABA regulates neuronal activity but its role in modulating AP dynamics itself is unclear. Here we show that GABA indeed changes the AP mechanism: it causes regularly firing hippocampal CA3 neurons to bistably switch between spiking and quiescence, converts graded discharge-to-current relationships to have abrupt onsets, and induces resonance. Modeling reveals that A-currents enable these GABA-induced transitions. Mathematically, we prove that this transition sequence originates from a single universal principle that generically underlies the modulation of AP dynamics in any conductance-based neuron model. Conductance clamp experiments in hippocampal and brainstem neurons show the same transitions, confirming the universal theory. In simulated networks, synaptically controlled AP dynamics, permits dynamic gating of signals and targeted synchronization of neuronal sub-ensembles. These results advance the systematic understanding of AP modulation and its role in neuronal and network function.

neuroscience↗