Biology subjects

John, T.

Publications and source records attributed to John, T..

8 recordsLinked to original sources

bioRxiv2025

Representation of visual sequences in the tuning and topology of neuronal activity in the human hippocampus

Time is a critical component of memory and yet how the hippocampus incorporates temporal information with the sensory contents of memories remains unclear. We hypothesized that the hippocampus can learn arbitrary sequences through rapid changes in the tuning and population geometry of individual neurons to mirror the sequence structure. We recorded single-unit activity from 134 neurons in the hippocampus of 17 patients with epilepsy while they viewed sequences of visual scenes that were presented repeatedly in the same order by looping from the end to start. As the sequence repeated, hippocampal neurons that were initially responsive to one scene in the sequence began responding to the other scenes proportional to their temporal proximity. The population vectors of spiking activity across recorded hippocampal neurons for each scene came to form a high-dimensional ring topology that encoded the circular structure of the sequence in a manner that preserved the serial order of the scenes. These effects were not observed when sequences were scrambled upon each repetition to destroy temporal structure, nor in brain regions outside of the hippocampus for both structured and random sequences. These findings suggest that temporal structure governs the representation of sensory stimuli in human hippocampal neurons.

neuroscience↗

bioRxiv2022

Red blood cell lingering modulates hematocrit distribution in the microcirculation

The distribution of red blood cells (RBCs) in the microcirculation determines the oxygen delivery and solute transport to tissues. This process relies on the partitioning of RBCs at successive bifurcations throughout the microvascular network and it is known since the last century that RBCs partition disproportionately to the fractional blood flow rate, therefore leading to heterogeneity of the hematocrit (i.e. volume fraction of RBCs in blood) in microvessels. Usually, downstream of a microvascular bifurcation, the vessel branch with a higher fraction of blood flow receives an even higher fraction of RBC flux. However, both temporal and time-average deviations from this phaseseparation law have been observed in recent works. Here, we quantify how the microscopic behavior of RBCs lingering (i.e. RBCs temporarily residing near the bifurcation apex with diminished velocity) influences their partitioning, through combined in vivo experiments and in silico simulations. We developed an approach to quantify the cell lingering at highly-confined capillary-level bifurcations and demonstrate that it correlates with deviations of the phase-separation process from established empirical predictions by Pries et al. Furthermore, we shed light on how the bifurcation geometry and cell membrane rigidity can affect the lingering behavior of RBCs, e.g. rigid cells tend to linger less than softer ones. Taken together, RBC lingering is an important mechanism that should be considered when studying how abnormal RBC rigidity in diseases such as malaria and sickle-cell disease could hinder the microcirculatory blood flow or how the vascular networks are altered under pathological conditions (e.g. thrombosis, aneurysm).

biophysics↗

bioRxiv2022

Lipid Oxidation Controls Peptide Self-Assembly near Membranes

The self-assembly of peptides into supramolecular fibril structures has been linked to neurodegenerative diseases such as Alzheimers disease but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly membrane lipids, within a cellular milieu. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of biomimetic membranes that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid {beta} (1-40) peptide (A{beta}40), linked to Alzheimers disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While A{beta}40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an -helical conformation compared to A{beta}40. Different peptide-to-lipid ratios resulted in different effects. Molecular dynamics simulations provided detailed mechanistic insights into the peptide-lipid interactions and secondary structure stability. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predictions how cellular changes might impact peptide self-assembly in vivo, and potentially impact related diseases.

biophysics↗

bioRxiv2021

Imaging erythrocyte sedimentation in whole blood

The erythrocyte sedimentation rate (ESR) is one of the oldest medical diagnostic tools. However, currently there is some debate on the structure formed by the cells during the sedimentation process. While the conventional view is that erythrocytes sediment as separate aggregates, others have suggested that they form a percolating gel, similar to other colloidal suspensions. A direct probing of the structures formed by erythrocytes in blood at stasis is then required to settle these discrepancies. Here, we report observations performed with three different optical imaging techniques: direct light transmission through thin samples, two-photon microscopy and light-sheet microscopy. All techniques revealed a dynamic structure of a channeling gel but with differences in the resolved details. A quantitative analysis of the erythrocyte related processes and interactions during the sedimentation need a further refinement of the experimental set-ups.

biophysics↗

bioRxiv2021

Size Matters: A Mechanistic Model of Nanoparticle Curvature Effects on Amyloid Fibril Formation

The aggregation of peptides into amyloid fibrils is linked to ageing-related diseases, such as Alzheimers disease and type 2 diabetes. Interfaces, particularly those with large nanostructured surface areas, can affect the kinetics of peptide aggregation, ranging from a complete inhibition to strong acceleration. While a number of physiochemical parameters determine interface effects, we here focus on the role of nanoparticle curvature for the aggregation of the amyloidogenic peptides A{beta}40, NNFGAIL, GNNQQNY and VQIYVK. Nanoparticles (NPs) provided a surface for peptide monomers to adsorb, enabling the nucleation into oligomers and fibril formation. High surface curvature, however, destabilized prefibrillar structures, providing an explanation for inhibitory effects on fibril growth. Thioflavin T (ThT) fluorescence assays as well as dynamic light scattering (DLS), atomic force microscopy (AFM) and electron microscopy experiments revealed NP size-dependent effects on amyloid fibril formation, with differences between the peptides. While 5 nm gold NPs (AuNP-5) retarded or inhibited the aggregation of most peptides, larger 20 nm gold NPs (AuNP-20) tended to accelerate peptide aggregation. Molecular dynamics (MD) studies demonstrated that NPs ability to catalyze or inhibit oligomer formation was influenced by the oligomer stability at curved interfaces which was lower at more highly curved surfaces. Differences in the NP effects for the peptides resulted from the peptide properties (size, aggregation propensity) and concomitant surface binding affinities. The results can be applied to the design of future nanostructured materials for defined applications.

biochemistry↗

bioRxiv2021

Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding

The main protease (Mpro) of SARS-CoV-2 is central to its viral lifecycle and is a promising drug target, but little is known concerning structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of classical molecular mechanics and quantum mechanical techniques, including automated docking, molecular dynamics (MD) simulations, linear-scaling DFT, QM/MM, and interactive MD in virtual reality, to investigate the molecular features underlying recognition of the natural Mpro substrates. Analyses of the subsite interactions of modelled 11-residue cleavage site peptides, ligands from high-throughput crystallography, and designed covalently binding inhibitors were performed. Modelling studies reveal remarkable conservation of hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular at the P2/S2 sites. The binding modes of the natural substrates, together with extensive interaction analyses of inhibitor and fragment binding to Mpro, reveal new opportunities for inhibition. Building on our initial Mpro-substrate models, computational mutagenesis scanning was employed to design peptides with improved affinity and which inhibit Mpro competitively. The combined results provide new insight useful for the development of Mpro inhibitors.

bioinformatics↗

bioRxiv2020

Allosteric inhibition of the SARS-CoV-2 main protease - insights from mass spectrometry-based assays

Following translation of the SARS-CoV-2 RNA genome into two viral polypeptides, the main protease Mpro cleaves at eleven sites to release non-structural proteins required for viral replication. MPro is an attractive target for antiviral therapies to combat the coronavirus-2019 disease (COVID-19). Here, we have used native mass spectrometry (MS) to characterize the functional unit of Mpro. Analysis of the monomer-dimer equilibria reveals a dissociation constant of Kd = 0.14 {+/-} 0.03 M, revealing MPro has a strong preference to dimerize in solution. Developing an MS-based kinetic assay we then characterized substrate turnover rates by following temporal changes in the enzyme-substrate complexes, which are effectively "flash-frozen" as they transition from solution to the gas phase. We screened small molecules, that bind distant from the active site, for their ability to modulate activity. These compounds, including one proposed to disrupt the catalytically active dimer, slow the rate of substrate processing by ~35%. This information was readily obtained and, together with analysis of the x-ray crystal structures of these enzyme-small molecule complexes, provides a starting point for the development of more potent molecules that allosterically regulate MPro activity.

biophysics↗

bioRxiv2017

Comparing neurotransmitter metabolism in the brain of patients with symptomatic and aysmptomatic Alzheimer’s disease and healthy individuals

INTRODUCTIONThree of the four treatments for Alzheimers disease are cholinesterase inhibitors targeting the pathological reduction of acetylcholine levels. Here we aimed to determine the role of other neurotransmitter pathways in AD pathology.\n\nMETHODSTissue samples were obtained from three groups, controls, AD and asymptomatic AD i.e. cognitively normal individuals that had significant AD neuropathology. Three brain areas were studied, the middle frontal gyrus (MFG) the inferior temporal gyrus (ITG) and the cerebellum.\n\nRESULTS11 of 15 measured metabolites were shown to be associated with disease. Decreases in dopamine were seen in the ASYMAD group in the MFG when compared to control and AD patients (FC=0.78, p=4.1x10-3). In AD patients changes were mainly seen in the ITGs inhibitory GABAergic system.\n\nDISCUSSIONThese results indicate that dopamine could be depleted in brains with Alzheimers pathology but intact cognition, while and imbalance of several neurotransmitters is evident in the brain of AD patients.

neuroscience↗