Biology subjects

Hay, E.

Publications and source records attributed to Hay, E..

At least 19 recordsLinked to original sources

bioRxiv2026

A global signature of microbiome resilience to climate stress

As climate change accelerates, the microbial communities sustaining organisms and ecosystems worldwide face an uncertain future, with some proving resilient to stress while others collapse, yet no generalizable framework exists to distinguish the two beforehand. Using amplicon sequencing data from ~29,000 microbiomes, we constructed over 440 matched network pairs spanning three of the most pressing stressors: drought, warming, and salinity. We show that keystone microbes with high connectivity, functional redundancy, and metabolic flexibility, are disproportionately likely to survive stress, and that baseline network and functional properties predict community-level structural and functional stability even as taxonomic composition shifts stochastically. These relationships held across the diverse hosts, ecosystems, and regions we tested. Because these properties can be derived from standard, low-cost sequencing collected before disturbance occurs, our findings turn baseline microbiome data into an early-warning system for identifying which communities are most vulnerable to climate stress.

systems biology↗

bioRxiv2026

Preserving spiking and EEG in detailed models of human cortical microcircuits with morphological reductions

Biophysically detailed models of human cortical microcircuit provide key insights into brain function and disease biomarkers, yet their computational cost lengthens simulation runtime and limits scalability. To address this, we systematically evaluated recent simplification methods for morphological reduction and synapse merging in terms of preserving spiking and electroencephalographic (EEG) properties of human cortical microcircuit models. At the single- cell level, reduced compartmental models accurately reproduced spiking behaviors. However, at the microcircuit level, while achieving a 5-fold speed-up, morphological reduction failed to preserve spectral dynamics of spiking and EEG despite maintaining average baseline and response firing rates. Conversely, applying synapse merging alone on the full morphology successfully reproduced both spiking activity and EEG dynamics, when constrained to [≤] 50 m spatial intervals, and yielded a 2-fold speed-up. These results were consistent across both cortical layer 2/3 and layer 5 models, and in depression models with reduced somatostatin interneuron inhibition. Our study identifies model simplification methods that speed up cortical microcircuit simulations while preserving the accuracy of the simulated brain signals.

neuroscience↗

bioRxiv2025

Linking age changes in human cortical microcircuits to impaired brain function and EEG biomarkers

Human brain aging involves a variety of cellular and synaptic changes, but how these changes affect brain function and signals remains poorly understood due to experimental limitations in humans, meriting the use of detailed computational models. We identified key human cellular and synaptic changes occurring with age from previous studies, including a loss of inhibitory cells, NMDA receptors, and spines. We integrated these changes into our detailed human cortical microcircuit models and simulated activity in middle-age ([~]50 yrs) and older ([~]70 yrs) microcircuits, and linked the altered mechanisms to reduced spike rates and impaired signal detection. We then simulated EEG potentials arising from the microcircuit activity and found that the emergent power spectral changes due to these aging cellular mechanisms reproduced most of the resting-state EEG biomarkers seen in human aging, including reduced aperiodic offset, exponent, and periodic peak center frequency. Using machine learning, we demonstrated that the changes to the cellular and synaptic aging mechanisms can be estimated accurately from the simulated EEG aging biomarkers. Our results link cellular and synaptic mechanisms of aging with impaired cortical function and physiological biomarkers in clinically-relevant brain signals.

neuroscience↗

bioRxiv2024

The Regulation of MAGI2 and its Diagnostic Application in Podocytopathies

Podocyte dysfunction is central to various glomerular diseases, necessitating reliable biomarkers for early detection and diagnosis. This study investigates the regulatory mechanisms of membrane-associated guanylate kinase inverted 2 (MAGI2) and its potential as a biomarker for podocytopathies. The expression of the gene coding for the scaffolding protein MAGI2 was examined across four species and demonstrated to be conserved within the podocyte filtration slit. In vitro and in vivo studies using isolated glomeruli and mammalian animal models of glomerular disease, including DOCA-salt hypertension, nephrotoxic serum nephritis, and puromycin aminonucleoside nephropathy, demonstrated significant downregulation of MAGI2 in injured podocytes. This downregulation was also conserved in a zebrafish model of focal and segmental glomerulosclerosis (FSGS), and the podocyte-specific MAGI2 ortholog Magi2a was reduced post podocyte injury. CRISPR/Cas9-generated zebrafish mutants for magi2a exhibited marked glomerular filtration barrier defects and downregulation of nephrin, underscoring MAGI2s critical role in podocyte function. Human biopsy analyses revealed differential MAGI2 expression: it was increased in minimal change disease (MCD) patients but significantly decreased in primary, but not secondary FSGS cases. As MAGI2 localization did not change in disease states it is an alternative marker for super-resolution microscopy-based morphometry of the filtration slit, correlating with nephrin-based measurements. These findings highlight the potential of MAGI2 as a sensitive biomarker for podocyte injury and its diagnostic utility in differentiating between primary FSGS and MCD.

cell biology↗

bioRxiv2024

Spine loss in depression impairs dendritic signal integration in human cortical microcircuit models

Major depressive disorder (depression) is associated with altered dendritic structure and function in excitatory cortical pyramidal neurons, due to decreased inhibition from somatostatin interneurons and loss of spines and associated synapses, as indicated in postmortem human studies. Dendrites play an important role in signal processing as they receive the majority of synaptic inputs and exhibit nonlinear properties including backpropagating action potentials and dendritic Na+ spikes that enhance the computational power of the neuron. However, it is currently unclear how depression-related dendritic changes impact the integration of signals. Here, we expanded our previous data-driven detailed computational models of human cortical microcircuits in health and depression to include active dendritic properties that enable backpropagating action potentials as measured in human neurons, and spine loss in depression in terms of synapse loss and altered intrinsic property. We show that spine loss dampens signal response and thus results in a larger impairment of cortical function such as signal detection than due to reduced somatostatin interneuron inhibition alone. We further show that the altered intrinsic properties due to spine loss abolish nonlinear dendritic integration of signals and impair recurrent microcircuit activity. Our study thus mechanistically links cellular changes in depression to impaired dendritic processing in human cortical microcircuits.

neuroscience↗

bioRxiv2024

A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence.

The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control.

microbiology↗

bioRxiv2024

Deriving connectivity from spiking activity in biophysical cortical microcircuits

Inferring detailed cortical microcircuit connectivity is essential for uncovering how information is processed in the brain. A common method in vivo uses short-lag spike cross-correlations to derive putative monosynaptic connections, but inactive neurons and correlated firing can hinder the derivation accuracy. Previous computational studies that developed methods to derive connectivity from cross-correlations employed simplified or small network models and thus did not address the above key confounds of physiological large-scale networks. We tested connectivity derivation using simulated ground-truth spiking from detailed models of human cortical microcircuits in different layers and between key neuron types. While derivation accuracy was high for cortical layer 5 microcircuits, we showed that low-firing and inactive neurons in layer 2/3 microcircuits resulted in poor performance. We then showed that general activation paradigms for layer 2/3 microcircuits led to only a moderate improvement in derivation performance, due to a trade-off between reducing the proportion of inactive neurons and increasing correlated overactive neurons. We further improved the connection derivation performance using a more refined activation paradigm leading to jittered moderate spiking, which decreased inactive neurons without incurring unwanted correlations. Our results address key physiological challenges and provide methods to improve performance in deriving connections from spiking activity in large-scale neuronal microcircuits.

neuroscience↗

bioRxiv2024

Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity

Treatment for major depressive disorder (depression) often has partial efficacy and a large portion of patients are treatment resistant. Recent studies implicate reduced somatostatin (SST) interneuron inhibition in depression, and new pharmacology boosting this inhibition via positive allosteric modulators of 5-GABAA receptors (5-PAM) offers a promising effective treatment. However, testing the effect of 5-PAM on human brain activity is limited, meriting the use of detailed simulations. We utilized our previous detailed computational models of human depression microcircuits with reduced SST interneuron inhibition and 5-PAM effects, to simulate EEG of virtual subjects across depression severity and 5-PAM doses. We developed machine learning models that predicted optimal dose from EEG with high accuracy and recovered microcircuit activity and EEG. This study provides dose prediction models for 5-PAM administration based on EEG biomarkers of depression severity. Given limitations in doing the above in the living human brain, the results and tools we developed will facilitate translation of 5-PAM treatment to clinical use.

neuroscience↗

bioRxiv2024

EEG biomarkers of GABA α5 positive allosteric modulators in rodents

Reduced cortical inhibition mediated by gamma-aminobutyric acid (GABA) is reported in depression, anxiety disorders, and aging. Novel positive allosteric modulator that specifically target 5-GABAA receptor subunit (5-PAM), ligand GL-II-73, shows anxiolytic, antidepressant, and pro-cognitive effects without the common side effects associated with non-specific modulation by benzodiazepines such as diazepam (DZP), thus suggesting novel therapeutic potential. However, it is unknown if 5-PAM has detectable signatures in clinically-relevant brain electroencephalography (EEG). We analyzed EEG in freely moving rats at baseline and following injections of 5-PAM and DZP. We showed that 5-PAM specifically decreased theta peak power whereas DZP shifted peak power from high to low theta, while increasing beta and gamma power. EEG decomposition showed that these effects were periodic and corresponded to changes in theta oscillation event duration. Our study thus shows that 5-PAM has robust and distinct EEG biomarkers in rodents, indicating that EEG could enable non-invasive monitoring of 5-PAM treatment efficacy.

neuroscience↗

bioRxiv2023

Implications of reduced inhibition in schizophrenia on simulated human prefrontal microcircuit activity and EEG

Reduced cortical inhibition by parvalbumin-expressing (PV) interneurons in schizophrenia is thought to be associated with impaired cortical processing in the prefrontal cortex and altered EEG signals such as oddball mismatch negativity (MMN). Recent studies also suggest loss of somatostatin (SST) interneuron inhibition. However, establishing the link between reduced interneuron inhibition and reduced MMN experimentally in humans is currently not possible. To overcome these challenges, we simulated spiking activity and EEG during baseline and oddball response in detailed models of human prefrontal microcircuits in health and schizophrenia, with reduced PV and SST interneuron inhibition as constrained by postmortem patient data. We showed that reduced PV interneuron inhibition can account for the decreased MMN amplitude seen in schizophrenia, with a threshold below which the amplitude effect was low as seen in at-risk patients. In contrast, reduced SST interneuron inhibition did not affect the MMN amplitude. We further showed that both types of inhibition loss were necessary to account for changes in resting EEG in schizophrenia, with reduced SST interneuron inhibition increasing theta power, and reduced PV interneuron inhibition leading to a right shift from alpha to beta frequencies. Our study thus links reduced PV and SST interneuron inhibition in schizophrenia to distinct EEG biomarkers that can serve to improve stratification and early detection using non-invasive brain signals.

neuroscience↗

bioRxiv2023

In-silico testing of new pharmacology for restoring inhibition and human cortical function in depression

Reduced inhibition by somatostatin-expressing interneurons is associated with depression. Administration of positive allosteric modulators of 5 subunit-containing GABAA receptor (5-PAM) that selectively target this lost inhibition exhibit antidepressant and pro-cognitive effects in rodent models of chronic stress. However, the functional effects of 5-PAM on the human brain in vivo are unknown, and currently cannot be assessed experimentally. We modeled the effects of 5-PAM on tonic inhibition as measured in human neurons, and tested in silico 5-PAM effects on detailed models of human cortical microcircuits in health and depression. We found that 5-PAM effectively recovered impaired cortical processing as quantified by stimulus detection metrics, and also recovered the power spectral density profile of the microcircuit EEG signals. We performed an 5-PAM dose response and identified simulated EEG biomarker candidates. Our results serve to de-risk and facilitate 5-PAM translation and provide biomarkers in non-invasive brain signals for monitoring target engagement and drug efficacy.

neuroscience↗

bioRxiv2022

The PREGCARE study: Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation

Next-generation sequencing has led to a dramatic improvement in molecular diagnoses of serious pediatric disorders caused by apparently de novo mutations (DNMs); by contrast, clinicians ability to counsel the parents about the risk of recurrence in a future child has lagged behind. Owing to the possibility that one of the parents could be mosaic in their germline, a recurrence risk of 1-2% is frequently quoted, but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk stratification, by combining deep-sequencing of multiple tissues in the mother-father-child trio with haplotyping to determine the parental origin of the DNM. In the first 58 couples analysed (total of 59 DNMs in 49 different genes), the risk for 35 (59%) DNMs was decreased below 0.1% but for 6 (10%) couples it was increased owing to parental mosaicism - that could be quantified in semen (recurrence risks of 5.6-12.1%) for the paternal cases. Deep-sequencing of the DNM efficiently identifies couples at greatest risk for recurrence and may qualify them for additional reproductive technologies. Haplotyping can further reassure many other couples that their recurrence risk is very low, but its implementation is more technically challenging and will require better understanding of how couples respond to information that reduces their risks.

genetics↗

bioRxiv2022

Adipocyte differentiation of 3T3-L1 cells under TAF, TDF and INSTIs selective challenge: an in vitro model.

Integrase strand transfer inhibitors (INSTI) are a recently available class of antiretroviral therapy (ART) medications with a good tolerability profile and a high genetic barrier to HIV drug resistance. However, several studies report more significant weight gain among persons receiving INSTI-based ART regimens for initial therapy compared to protease inhibitors (PIs) and nucleoside reverse transcriptase inhibitors (NNRTI)-based regimens. In our experimental setting, we used the in vitro model of adipogenesis of 3T3-L1 cells to investigate the effects of the NRTIs tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide (TAF), alone or in combination with four integrase strand transfer inhibitors: raltegravir (RAL), elvitegravir (ELV), dolutegravir (DTG) and bictegravir (BIC) on adipose differentiation. In addition, protein expression levels of PPAR{gamma} and C/EBP, and the intracellular lipid accumulation by Red Oil staining, were used to monitor adipocyte differentiation. Compared to control, RAL, ELV, DTG, and BIC were all able to increase adipogenesis, being in this, RAL and ELV more efficient. On the other hand, TAF and TDF inhibited adipogenesis. Moreover, when used in combination with the other INSTI molecules, TAF and TDF were able to reduce the adipogenic effects of all four drugs. This ability was more evident when TAF was used in combination with DTG and BIC. All these data suggest that TAF and TDF have an inhibitory effect on adipogenesis in vitro and that they could also effectively counteract the increased adipogenesis caused by the treatment with INSTIs. Finally, to evaluate if the 3T3-L1 cell could express fibroblast-like features following INSTIs treatment, we evaluated the immunohistochemical expression of ER-TR7, a well-known fibroblastic marker. This last assay showed that treatment with INSTIs increased the expression of ER-TR7 compared to control and to cells treated with TAF o TDF. In conclusion, our experimental data support the evidence that in vitro challenge of 3T3-L1 cells with INSTIs is able to increase adipocytic differentiation and to drive a number of these cells toward the expression of fibroblastic features, with a different degree according to the various drugs used, while TAF and TDF have an antagonistic role on this phenomenon.

pharmacology and toxicology↗

bioRxiv2021

Age-dependent increased sag current in human pyramidal neurons dampens baseline cortical activity

Aging involves various neurobiological changes, although their effect on brain function in humans remains poorly understood. The growing availability of human neuronal and circuit data provides opportunities for uncovering age-dependent changes of brain networks and for constraining models to predict consequences on brain activity. Here we found increased sag voltage amplitude in human middle temporal gyrus layer 5 pyramidal neurons from older subjects, and captured this effect in biophysical models of younger and older pyramidal neurons. We used these models to simulate detailed layer 5 microcircuits and found lower baseline firing in older pyramidal neuron microcircuits, with minimal effect on response. We then validated the predicted reduced baseline firing using extracellular multi-electrode recordings from human brain slices of different ages. Our results thus report changes in human pyramidal neuron input integration properties and provide fundamental insights on the neuronal mechanisms of altered cortical excitability and resting state activity in human aging.

neuroscience↗

bioRxiv2021

scoMorphoFISH: A Deep-Learning enabled toolbox for single-cell single-mRNA quantification and correlative (ultra-)morphometry

Increasing the information depth of single kidney biopsies can improve diagnostic precision, personalized medicine and accelerate basic kidney research. Until now, information on mRNA abundance and morphologic analysis has been obtained from different samples, missing out on the spatial context and single-cell correlation of findings. Herein, we present scoMorphoFISH, a modular toolbox to get spatial single-cell single-mRNA expression data optimized for routinely generated kidney biopsies. Deep-Learning was used to virtually dissect tissue sections in tissue compartments and cell types to which single-cell expression data was assigned. Furthermore, we show correlative and spatial single-cell expression quantification with super-resolved podocyte foot process morphometry on the same histological section. In contrast to bulk analysis methods, this approach will help to identify local transcription changes even in less frequent kidney cell types on a spatial single-cell level with single-mRNA resolution. As this method performs well with standard formalin-fixed paraffin-embedded samples and we provide pretrained DL-networks embedded in a comprehensive image analysis workflow, this method can be applied immediately in a variety of settings.

pathology↗

bioRxiv2021

EEG Biomarkers of reduced inhibition in human cortical microcircuits in depression

Reduced cortical inhibition by somatostatin-expressing (SST) interneurons has been strongly associated with treatment-resistant depression. However, whether the effects of reduced SST interneuron inhibition on microcircuit activity have signatures detectible in electroencephalography (EEG) signals remains unknown. We simulated resting-state activity and EEG using detailed models of human cortical microcircuits with normal (healthy) or reduced SST interneuron inhibition (depression). Healthy microcircuit models showed emergent key features of resting-state EEG, and depression microcircuits exhibited increased theta, alpha and low beta power (4 - 15 Hz). The changes in depression involved a combination of an aperiodic broadband, and periodic theta components. We then demonstrated the specificity of the EEG signatures of reduced SST interneuron inhibition by showing they were distinct from those corresponding to reduced parvalbumin-expressing (PV) interneuron inhibition. Our study thus links SST interneuron inhibition level to distinct features in EEG simulated from detailed human microcircuits, which can serve to better identify mechanistic subtypes of depression using EEG, and non-invasively monitor modulation of cortical inhibition.

neuroscience↗

bioRxiv2021

Reduced inhibition in depression impairs stimulus processing in human cortical microcircuits

Cortical processing depends on finely-tuned excitatory and inhibitory connections in neuronal microcircuits. Reduced inhibition by somatostatin-expressing interneurons is a key component of altered inhibition associated with treatment-resistant major depressive disorder (depression), which is implicated in cognitive deficits and rumination, but the link remains to be better established mechanistically in humans. Here, we tested the impact of reduced somatostatin interneuron mediated inhibition on cortical processing in human neuronal microcircuits using a data-driven computational approach. We integrated human cellular, circuit and gene-expression data to generate detailed models of human cortical microcircuits in health and depression. We simulated microcircuit baseline and response activity and found reduced signal-to-noise ratio and increased false/failed detection of stimuli due to a higher baseline activity in depression. Our results thus applied novel models of human cortical microcircuits to demonstrate mechanistically how reduced inhibition impairs cortical processing in depression, providing quantitative links between altered inhibition and cognitive deficits.

neuroscience↗

bioRxiv2021

Super-resolved local recruitment of CLDN5 to filtration slits implicates a direct relationship with podocyte foot process effacement

Under healthy conditions, foot processes of neighboring podocytes are interdigitating and connected by an electron-dense slit diaphragm. Beside slit diaphragm proteins, typical adherens junction proteins are also found to be expressed at this cell-cell junction. It is therefore considered as a highly specialized type of adherens junction. During podocyte injury, podocyte foot processes lose their characteristic 3D structure and the filtration slits typical meandering structure gets linearized. It is still under debate how this change of structure leads to the phenomenon of proteinuria. Using super-resolution 3D structured illumination microscopy, we observed a spatially restricted up-regulation of the tight junction protein claudin 5 (CLDN5) in areas where podocyte processes of patients suffering from minimal change disease (MCD), focal and segmental glomerulosclerosis (FSGS) as well as in murine nephrotoxic serum (NTS) nephritis and uninephrectomy DOCA-salt hypertension models, were locally injured. CLDN5/nephrin ratios in human glomerulopathies and NTS-treated mice were significantly higher compared to controls. In patients, the CLDN5/nephrin ratio is significantly correlated with the filtration slit density as a foot process effacement marker, confirming a direct association of local CLDN5 up-regulation in injured foot processes. Moreover, CLDN5 up-regulation was observed in some areas of high filtration slit density, suggesting that CLND5 up-regulation preceded the changes of foot processes. Therefore, CLDN5 could serve as a biomarker predicting early foot process effacement. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/429338v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d05e3aorg.highwire.dtl.DTLVardef@da61f4org.highwire.dtl.DTLVardef@154e7f1org.highwire.dtl.DTLVardef@147bc6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗