Biology subjects

Klug, A.

Publications and source records attributed to Klug, A..

16 recordsLinked to original sources

bioRxiv2026

High precision animal stereotaxis with 3D polychromic photogrammetry

Stereotaxic brain surgery is a foundational neurosurgical technique used to deliver chemical, pharmacological, or genetic material to specific brain regions, or to precisely implant electrodes and stimulators. Accurate targeting depends on reliable identification of skull landmarks, particularly bregma and lambda. Here we present a photogrammetry-based automated small animal stereotaxic platform that uses a single, freely handheld camera, such as a standard smartphone, to generate high-resolution, polychromatic 3D skull reconstructions. Because photogrammetry requires no fixed overhead hardware, the surgical field remains fully accessible for instruments, microscopes, and other equipment. The resulting color reconstructions substantially improve identification of bregma and lambda compared to monochromatic approaches, and the higher spatial resolution translates directly into improved targeting accuracy and surgical speed. The system operates by a user moving a handheld camera around the exposed skull. The platform automatically produces a detailed 3D mesh and computes stereotaxic coordinates without manual measurement. Together, these properties yield a practical, accessible yet accurate platform for automated small animal neurosurgery. We previously described a structured illumination approach in combination with a Steward platform; however, that system required a fixed projector and camera array that occupied critical surgical workspace and produced monochromatic meshes that complicated landmark identification. The photogrammetry-based method described here overcomes both limitations while retaining full compatibility with the Steward platform as a stereotaxic base.

neuroscience↗

bioRxiv2025

In-vivo optogenetic manipulation approach for gerbil medial nucleus of trapezoid body

PurposeThis study introduces an in-vivo optogenetic manipulation approach for the medial nucleus of the trapezoid body (MNTB) in Mongolian gerbils, a species with a hearing range similar to humans. The MNTB is crucial for sound localization, but traditional methods lack temporal precision and reversibility. The aim of this study is to develop a specific, reversible method for controlling MNTB activity with fast and precise temporal control, an approach vital for studying sound localization. MethodsWe stereotactically injected adeno-associated viral vectors encoding opsins into the gerbil MNTB. Precise targeting was achieved despite the MNTBs location in a deep, heavily myelinated area of the brainstem. Opsin expression was confirmed via confocal microscopy. In-vivo electrophysiology combined with optical stimulation was used to test optical activation and suppression of MNTB activity during sound stimuli. ResultsOpsin expression was strong and stable in MNTB neurons over weeks and months. Laser stimulation during in-vivo recordings successfully induced both activation and suppression of MNTB neurons, demonstrating fast and precise control over neural activity. ConclusionThis in-vivo optogenetic method provides specific, reversible control of MNTB activity in gerbils with rapid, real-time modulation. It offers a powerful tool for investigating sound localization and auditory processing with high temporal precision.

neuroscience↗

bioRxiv2025

Spatial hearing and temporal processing ability of the Mongolian gerbil (Meriones unguiculatus) measured using prepulse inhibition of acoustic startle

The Mongolian gerbil is a common model organism for studying the neural and behavioral mechanisms of binaural and spatial hearing, largely because of its ability to hear lower frequencies than other rodents and thus utilize both interaural time and level difference cues for sound localization. Prior spatial hearing studies in gerbils have relied on operant conditioning paradigms, requiring large amounts of time-consuming training and testing on multiple different tasks needed to make a comprehensive assessment of spatial hearing ability (including temporal processing, spatial acuity and spatial unmasking). This limits the ability of researchers to thoroughly assess behavioral performance in individual animals. In this study, we used the reflexive prepulse inhibition of the acoustic startle reflex (PPI) to extensively assess spatial hearing and temporal processing abilities in individual gerbils of both sexes. Results show that gerbils inhibit a startle response to a brief loud sound based on prepulse acoustical cues consisting of a 1) temporal gap in ongoing sounds, 2) change in sound source location, and 3) target sound in the presence of a masker. In each test, the magnitude of the suppression of startle increased monotonically as a function of the magnitude of the acoustical prepulse, not unlike a psychometric function, from which threshold performance could be measured. Thresholds in the gerbils in each task measured using PPI matched those acquired using operant conditioning methods.

animal behavior and cognition↗

bioRxiv2024

Sapphire-Based Optrode for Low Noise Neural Recording and Optogenetic Manipulation

Electrophysiological recordings of neurons in deep brain regions using optogenetic stimulation are essential to understanding and regulating the role of complex neural activity in biological behavior and cognitive function. Optogenetic techniques have significantly advanced neuroscience research by enabling the optical manipulation of neural activities. Because of the significance of the technique, constant advancements in implantable optrodes that integrate optical stimulation with low-noise, large-scale electrophysiological recording are in demand to improve the spatiotemporal resolution for various experimental designs and future clinical applications. However, robust and easy-to-use neural optrodes that integrate neural recording arrays with high-intensity light emitting diodes (LEDs) are still lacking. Here, we propose a neural optrode based on Gallium Nitride (GaN) on sapphire technology, which integrates a high-intensity blue LED with a 5x2 recording array monolithically for simultaneous neural recording and optogenetic manipulation. To reduce the noise interference between the recording electrodes and the LED, which is in close physical proximity, three metal grounding interlayers were incorporated within the optrode, and their ability to reduce LED-induced artifacts during neural recording was confirmed through both electromagnetic simulations and experimental demonstrations. The capability of the sapphire optrode to record action potentials has been demonstrated by recording the firing of mitral/tuft cells in the olfactory bulbs of mice in vivo. Additionally, the elevation of action potential firing due to optogenetic stimulation observed using the sapphire probe in medial superior olive (MSO) neurons of the gerbil auditory brainstem confirms the capability of this sapphire optrode to precisely access neural activities in deep brain regions under complex experimental designs.

neuroscience↗

bioRxiv2024

Computational model for synthesizing auditory brainstem responses to assess neuronal alterations in aging and autistic animal models

PurposeThe auditory brainstem response (ABR) is a widely used objective electrophysiology measure for non-invasively assessing auditory function and neural activity in the auditory brainstem, but its ability to reflect detailed neuronal processing is limited due to the averaging nature of the electroencephalogram-type recordings. MethodThis study addresses this limitation by developing a computational model of the auditory brainstem which is capable of synthesizing ABR traces based on a large, population scale neural extrapolation of a spiking neuronal network of auditory brainstem circuitry. The model was able to recapitulate alterations in ABR waveform morphology that have been shown to be present in two medical conditions: animal models of autism and aging. Moreover, in both of these conditions, these ABR alterations are caused by known distinct changes in auditory brainstem physiology, and the model could recapitulate these changes. ResultsIn the autism model, the simulation revealed myelin deficits and hyperexcitability, which caused a decreased wave III amplitude and a prolonged wave III-V interval, consistent with experimentally recorded ABRs in Fmr1-KO mice. For the aging condition, the model recapitulated ABRs recorded in aged gerbils and indicated a reduction in activity in the medial nucleus of the trapezoid body (MNTB), a finding validated by confocal imaging data. ConclusionThese results demonstrate not only the models accuracy but also its capability of linking features of ABR morphology to underlying neuronal properties and suggesting follow-up physiological experiments.

neuroscience↗

bioRxiv2024

Age-related myelin deficits in the auditory brain stem contribute to cocktail party-deficits

Age-related hearing loss consists of both peripheral and central components and is an increasing global health concern. While peripheral hearing loss is well understood, central hearing loss-- age-related changes in the central auditory pathways resulting in a listeners inability to process sound correctly --remains poorly understood. In this study, we focus on the pathway from the cochlear nucleus to the medial nucleus of the trapezoid body (MNTB), which depends on heavily myelinated axons for microsecond-level temporal precision required for sound localization. Using a combination of auditory brainstem response recordings (ABR), advanced light and electron microscopy, and behavioral testing with prepulse inhibition of the acoustic startle response (PPI) we identified a correlation between oligodendrocyte loss, abnormal myelination in MNTB afferents, altered ABR wave III morphology indicating MNTB dysfunction, and deficits in spatial hearing behaviors in aging Mongolian gerbils. These findings provide a mechanistic explanation of how demyelination contributes to age-related dysfunction in the auditory brainstems sound localization pathway.

neuroscience↗

bioRxiv2024

Degradation in Binaural and Spatial Hearing and Auditory Temporal Processing Abilities as a Function of Aging

ObjectivesSensorineural hearing loss is common with advancing age, but even with normal or near-normal hearing in older persons, performance deficits are often seen for suprathreshold listening tasks such as understanding speech in background noise or localizing sound direction. This suggests there is also a more central source of the problem. Objectives of this study were to examine as a function of age (young adult to septuagenarian) performance on: 1) a spatial acuity task examining localization ability, and a spatial speech-in-noise (SSIN) recognition task, both measured in a hemi-anechoic sound field using a circular horizontal-plane loudspeaker array, and 2) a suprathreshold auditory temporal processing task and a spectro-temporal processing task, both measured under headphones. Further, we examined any correlations between age, hearing thresholds including extended high frequency (EHF: >8000 Hz), and these measures. DesignSubjects were 48 adults, aged 21 to 78, with either normal hearing or only a mild sensorineural hearing loss through 4000 Hz. The localization task measured minimum audible angle (MAA) for 500 and 4000 Hz 1/3rd octave narrowband noise (NBN) in diffuse background noise for both an on-axis (reference source 0{degrees}) and off-axis (reference source 45{degrees}) listening condition at signal-to-noise ratios (SNRs) of -3, -6, -9, and -12 dB. SSIN testing was also completed for key word recognition in sentences in multi-talker babble noise; specifically, the separation between speech and noise loudspeakers was adaptively varied to determine the difference needed for 40% and 80% correct performance levels. Finally, auditory temporal processing ability was examined using the Temporal Fine Structure (TFS) test, and the Spectro-Temporal Modulation (STM) test. ResultsSpatial acuity was poorer (larger MAAs) in older compared to younger subjects, particularly in the more adverse listening conditions (off-axis, and poorer SNRs). The SSIN data also showed declining mean performance with age at both criterion levels, emerging in the middle age group (> 40 years), but was not correlated with standard audiometric hearing thresholds. Decreased performance on the TFS and STM tasks was dependent on age, emerging only in the older (> 60 years) and middle (>40 years) age groups, respectively; neither was dependent on hearing thresholds. Results of multiple regression analyses suggest that SSIN recognition scales with the ability of the subjects to use both low-frequency binaural temporal fine structure as well as higher-frequency binaural envelope cues, both of which are impacted by aging but not necessarily audiometric hearing thresholds. Finally, EHF range hearing thresholds significantly decreased with age, but performance on tasks remained significantly correlated with age when controlled for EHF hearing. ConclusionsParticularly for more adverse listening conditions, age-related deficits, but not hearing-threshold-related deficits, were found on both of the spatial hearing tasks and in temporal and spectro-temporal processing abilities. It may be that deficits in temporal processing ability contribute to poorer spatial hearing performance in older subjects due to inaccurate coding of binaural/interaural timing information sent from the periphery to the binaural brainstem. In addition, EHF hearing loss may be a coexisting factor in the reduced performance seen in older subjects.

neuroscience↗

bioRxiv2022

Multichannel neural spike sorting with spike reduction and positional feature

Sorting neural voltages measured from a multichannel neural probe to extract the single unit activities of neuronal firing, especially in real-time, remains a significant technical challenge, largely due to the large amount of acquired data and the technical difficulties involved in processing and classifying these neural spikes promptly. Most neural spike sorting algorithms focus on sorting neural spikes post hoc for high sorting accuracy, and reducing the processing time generally is not the chief concern. Here we report on two signal processing modifications to our previously developed single-channel real-time spike sorting (Enhanced Growing Neural Gas) algorithm, which is largely based on graph network. Duplicated neural spikes were eliminated and represented by the neural spike with the strongest signal profile, significantly reducing the amount of neural data to be processed. In addition, the channel from which the representing neural spike was recorded was used as an additional feature to differentiate between neural spikes recorded from different neurons having similar temporal features. With these two modifications, the Graph nEtwork Multichannel (GEMsort) neural spike sorting algorithm can rapidly sort neural spikes without requiring significant computer processing power and system memory storage. The parallel processing architecture of GEMsort is particularly suitable for digital hardware implementation to improve processing speed and recording channel scalability. Multichannel synthetic neural spikes and actual neural recordings with Neuropixels probes were used to evaluate the sorting accuracies of the GEMsort algorithm.

neuroscience↗

bioRxiv2022

Effects of recombination on the evolvability, genetic diversity and mutational robustness of neutrally evolving populations

Understanding the benefits and costs of recombination under different scenarios of evolutionary adaptation remains an open problem for theoretical and experimental research. In this study, we focus on finite populations evolving on neutral networks comprising viable and unfit genotypes. We provide a comprehensive overview of the effects of recombination by jointly considering different measures of evolvability and mutational robustness over a broad parameter range, such that many evolutionary regimes are covered. We find that several of these measures vary non-monotonically with the rates of mutation and recombination. Moreover, the presence of unfit genotypes that introduce inhomogeneities in the network of viable states qualitatively alters the effects of recombination. We conclude that conflicting trends induced by recombination can be explained by an emerging trade-off between evolvability on the one hand, and mutational robustness on the other. Finally, we discuss how different implementations of the recombination scheme in theoretical models can affect the observed dependence on recombination rate through a coupling between recombination and genetic drift. Author summaryMany genetic mechanisms have been invoked to explain the advantage of sex, but a coherent picture is still to emerge. Here we present a systematic theoretical and computational investigation of the effects of recombination in populations evolving on neutral fitness landscapes with unfit genotypes. We focus on populations that are large enough to be polymorphic, but nevertheless strongly affected by drift, which causes them to diffuse across the neutral network of viable genotypes. We identify a novel trade-off between evolvability, robustness and fitness that can lead to a dramatic reduction of the genetic diversity at large recombination rates. This disproves the common notion (often referred to as Weismanns hypothesis) that recombination generally increases diversity and evolvability, and instead highlights the interplay of recombination and mutational robustness.

evolutionary biology↗

bioRxiv2021

Predicting the Influence of Axon Myelination on Sound Localization Precision Using a Spiking Neural Network Model of Auditory Brainstem

Spatial hearing allows animals to rapidly detect and localize auditory events in the surrounding environment. The auditory brainstem plays a central role in processing and extracting binaural spatial cues through microsecond-precise binaural integration, especially for detecting interaural time differences (ITDs) of low-frequency sounds at the medial superior olive (MSO). A series of mechanisms exist in the underlying neural circuits for preserving accurate action potential timing across multiple fibers, synapses and nuclei along this pathway. One of these is the myelination of afferent fibers that ensures reliable and temporally precise action potential propagation in the axon. There are several reports of fine-tuned myelination patterns in the MSO circuit, but how specifically myelination influences the precision of sound localization remains incompletely understood. Here we present a spiking neural network model of the auditory brainstem with myelinated axons to investigate whether different axon myelination thicknesses alter the sound localization process. Our model demonstrates that axon myelin thickness along the contralateral pathways can substantially modulate ITD detection. Furthermore, optimal ITD sensitivity is reached when the MSO receives contralateral inhibition via thicker myelinated axons compared to contralateral excitation, a result that is consistent with previously reported experimental observations. Our results suggest specific roles of axon myelination for extracting temporal dynamics in ITD perception, especially in the pathway of the contralateral inhibition.

neuroscience↗

bioRxiv2021

Myelination deficits in the auditory brainstem of a mouse model of Fragile X Syndrome, a possible mechanism for auditory phenotypes

1Auditory symptoms are one of the most frequent sensory issues described in people with Fragile X Syndrome (FXS), the most common genetic form of intellectual disability. However, the mechanisms that lead to these symptoms are under explored. In this study, we examined whether alterations in myelination in auditory brainstem circuitry contribute to auditory impairments in FXS mice. Specifically, we studied myelinated fibers that terminate in the Calyx of Held, which encode temporally precise sound arrival time, and are some of the most heavily myelinated axons in the brain. We measured anatomical myelination characteristics using coherent anti-stokes Raman spectroscopy (CARS) and electron microscopy (EM) in a FXS mouse model in the medial nucleus of the trapezoid body (MNTB) where the Calyx of Held synapses. We measured number of mature oligodendrocytes (OL) and oligodendrocyte precursor cells (OPCs) to determine if changes in myelination were due to changes in the number of myelinating or immature glial cells. The two microscopy techniques (EM and CARS) showed a decrease in fiber diameter in FXS mice. Additionally, EM results indicated reductions in myelin thickness and axon diameter, and an increase in g-ratio, a measure of structural and functional myelination. Lastly, we showed an increase in both OL and OPCs in MNTB sections of FXS mice suggesting that the myelination phenotype is not due to an overall decrease in number of myelinating OLs. This is the first study to show that a potential myelination mechanism can explain alterations seen in FXS at the level of the auditory brainstem.

neuroscience↗

bioRxiv2020

S-nitrosylated and non-nitrosylated COX2 has differential expression and distinct subcellular localization in normal and breast cancer tissue

Immunohistochemical staining in breast cancer shows both gain and loss of COX2 expression with disease risk and progression. We investigated four common COX2 antibody clones and found high specificity for purified human COX2 for three clones; however, recognition of COX2 in cell lysates was clone dependent. Biochemical characterization revealed two distinct forms of COX2, with SP21 recognizing an S-nitrosylated form and CX229 and CX294 appearing to recognize the same non-nitrosylated COX2 antigen. We found S-nitrosylated and non-nitrosylated COX2 occupy different subcellular locations in normal and breast cancer tissue, implicating distinct synthetic/trafficking pathways and function. Dual stains of ~2000 breast cancer cases show early onset breast cancer has increased expression of both forms of COX2 compared to postmenopausal cases. Our results highlight the strengths of using multiple, highly characterized antibody clones for COX2 immunohistochemical studies and raise the prospect that S-nitrosylation of COX2 may play a role in breast cancer biology.

cancer biology↗

bioRxiv2020

Robotic Stereotaxic System based on 3D skull reconstruction to improve surgical accuracy and speed

Some experimental approaches in neuroscience research require the precise placement of a recording electrode, pipette or other tool into a specific brain area that can be quite small and/or located deep beneath the surface. This process is typically aided with stereotaxic methods but remains challenging due to a lack of advanced technology to aid the experimenter. Currently, procedures require a significant amount of skill, have a high failure rate, and take up a significant amount of time. We developed a next generation robotic stereotaxic platform for small rodents by combining a three-dimensional (3D) skull profiler sub-system and a full six degree-of-freedom (6DOF) robotic platform. The 3D skull profiler is based on structured illumination in which a series of horizontal and vertical line patterns are projected onto an animal skull. These patterns are captured by two two-dimensional (2D) CCD cameras which reconstruct an accurate 3D skull surface based on structured illumination and geometrical triangulation. Using the reconstructed 3D profile, the skull can repositioned using a 6DOF robotic platform to accurately align a surgical tool. The system was evaluated using mechanical measurement techniques, and the accuracy of the platform was demonstrated using brain phantoms. Additionally, small and deep brain nuclei were targeted in rodents for additional testing. The results indicate that this new stereotaxic system can improve the accuracy and speed of small-animal brain surgeries and reduce the failure rate of experiments.

bioengineering↗

bioRxiv2019

Auditory binaural and spatial hearing impairments in a Fragile X Syndrome mouse model

The auditory brainstem compares sound-evoked excitation and inhibition from both ears to compute sound source location. Although alterations to the anatomy and physiology of the auditory brainstem have been demonstrated in Fragile X Syndrome (FXS) it is not known whether these changes cause sound localization impairments in FXS. To test the hypothesis that FXS-related alterations to brainstem circuits impair spatial hearing abilities, a reflexive prepulse inhibition (PPI) task, with sound source location as the prepulse stimulus, was used to show that Fmr1 knockout mice have decreased inhibition of their startle responses. Specifically, Fmr1 mice show decreased PPI compared to wildtype during gap detection, changes in sound source location, and spatial release from masking with no alteration to their overall startle thresholds compared to wildtype. Lastly, Fmr1 mice have increased latency to respond in these tasks suggesting additional impairments in the pathway responsible for reacting to a startling sound.

neuroscience↗

bioRxiv2019

Recombination and mutational robustness in neutral fitness landscapes

Mutational robustness quantifies the effect of random mutations on fitness. When mutational robustness is high, most mutations do not change fitness or have only a minor effect on it. From the point of view of fitness landscapes, robust genotypes form neutral networks of almost equal fitness. Using deterministic population models it has been shown that selection favors genotypes inside such networks, which results in increased mutational robustness. Here we demonstrate that this effect is massively enhanced by recombination. Our results are based on a detailed analysis of mesa-shaped fitness landscapes, where we derive precise expressions for the dependence of the robustness on the landscape parameters for recombining and non-recombining populations. In addition, we carry out numerical simulations on different types of random holey landscapes as well as on an empirical fitness landscape. We show that the mutational robustness of a genotype generally correlates with its recombination weight, a new measure that quantifies the likelihood for the genotype to arise from recombination. We argue that the favorable effect of recombination on mutational robustness is a highly universal feature that may have played an important role in the emergence and maintenance of mechanisms of genetic exchange. Author summaryTwo long-standing and seemingly unrelated puzzles in evolutionary biology concern the ubiquity of sexual reproduction and the robustness of organisms against genetic perturbations. Using a theoretical approach based on the concept of a fitness landscape, in this article we argue that the two phenomena may in fact be closely related. In our setting the hereditary information of an organism is encoded in its genotype, which determines it to be either viable or non-viable, and robustness is defined as the fraction of mutations that maintain viability. Previous work has demonstrated that the purging of non-viable genotypes from the population by natural selection leads to a moderate increase in robustness. Here we show that genetic recombination acting in combination with selection massively enhances this effect, an observation that is largely independent of how genotypes are connected by mutations. This suggests that the increase of robustness may be a major driver underlying the evolution of sexual recombination and other forms of genetic exchange throughout the living world.

evolutionary biology↗

bioRxiv2019

De novo assembly of the Mongolian gerbil genome and transcriptome

BACKGROUNDThe Mongolian gerbil (Meriones unguiculatus) has historically been used as a model organism for the auditory and visual systems, stroke/ischemia, epilepsy and aging related research since 1935 when laboratory gerbils were separated from their wild counterparts. In this study we report genome sequencing, assembly, and annotation further supported by transcriptome data from 27 different tissues samples. FINDINGSThe genome was assembled using Illumina HiSeq 2000 and resulted in a final genome size of 2.54 Gbp with contig and scaffold N50 values of 31.4 Kbp and 500.0 Kbp, respectively. Based on the k-mer estimated genome size of 2.48 Gbp, the assembly appears to be complete. The genome annotation was supported by transcriptome data that identified 36 019 predicted protein-coding genes across 27 tissue samples. A BUSCO search of 3023 mammalian groups resulted in 86% of curated single copy orthologs present among predicted genes, indicating a high level of completeness of the genome. CONCLUSIONSWe report a de novo assembly of the Mongolian gerbil genome that was further enhanced by annotation of transcriptome data from several tissues. Sequencing of this genome increases the utility of the gerbil as a model organism, opening the availability of now widely used genetic tools. The data sets supporting the results of this article are available in the China National GeneBank CNSA repository, Accession id: CNP0000340.

genomics↗