Biology subjects

Hart, G.

Publications and source records attributed to Hart, G..

5 recordsLinked to original sources

bioRxiv2025

MembraneBuilder: High-speed membrane construction for large molecular dynamics simulations

1Membrane building and embedding of proteins into a membrane is a crucial step in preparing a simulation for Molecular Dynamics (MD). When an MD simulation contains several million atoms, embedding the protein into a membrane becomes computationally expensive. MembraneBuilder [1] speeds up the generation of these membranes by simplifying the lipid insertion process, which allows membranes to be generated for these larger systems. Realistic lipid densities and elimination of infinite forces caused by overlapping atoms are achieved at a low computational cost. See Figure 1 for specific time comparisons. The comparisons emphasize that not only does MembraneBuilder run orders of magnitude faster than state-of-the-art programs [2, 3, 4], it enables generation of systems several orders of magnitude larger. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/689436v1_fig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1ebfd2aorg.highwire.dtl.DTLVardef@39e8faorg.highwire.dtl.DTLVardef@1ee8ccborg.highwire.dtl.DTLVardef@5d9294_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Speed Analysis: Comparison between the amount of time taken to run MembraneBuilder and CHARMM-GUI with varying protein sizes and their requisite amount of lipids. Note that the x and y scales are on a log scale, which further emphasizes the efficiency of MembraneBuilder. C_FIG MembraneBuilder enables customizable embedding of proteins into a membrane. Users can modify lipid types and their ratios, the location to insert the membrane, the size of the membrane box, as well as the lipid density. The program reduces the computational time required to perform a membrane embedding by bypassing many of the computationally expensive steps, such as identification of polar/non-polar sections of the protein and exhaustive packing of the lipids into the membrane with the intent to avoid steric clashes. Efficient packing begins with constricting the lipid bonds by a given factor in x, y, and z directions before inserting them on a grid. Grid spacing is determined by the width of the constricted lipids. The grid spacing is smaller than in other lipid-generation tools due to the constriction process. The constricted bonds will relax and the lipids will assume realistic interweaving during energy minimization and equilibration.

biophysics↗

bioRxiv2024

Rare and novel RELA variants are common in systemic autoimmunity

ObjectivePhenotypic diversity of autoimmune diseases presents an ongoing diagnostic and drug development challenge for clinicians and scientists. Recent discovery of mutations in RELA (encoding RELA) in patients with different diagnoses has highlighted that different pathogenic molecular mechanisms are at play and may explain the observed phenotypic diversity. We identified seven novel/rare RELA variants in patients with autoimmune diseases and examine the functional consequences on immune signalling. MethodsWild type and mutant RELA proteins were ectopically expressed in HEK293 cells. Western blot and NF-{kappa}B/IFN{beta} luciferase reporter assays were used to determine RELA expression and transcriptional activity, respectively. In patients (n=3), B and T cell populations were examined via flow cytometry and NF-{kappa}B and interferon stimulated genes in PBMCs were assessed via qPCR following toll-like receptor activation. ResultsRELAI250V, RELAR295H and RELAE3* displayed a loss in NF-{kappa}B transcriptional activity. Comparative to RELAWT, RELAI250V protein expression was reduced. Two variants, RELAI250V and RELAR295H, induced hyperactivation of the IFN{beta} promoter. An elevated IFN gene signature was not detected in patient PBMCs following toll-like receptor activation, however the patient heterozygous for I250V had elevated IFN{beta} transcripts at baseline and after TLR7/8 activation. A reduction in transitional, unswitched memory and memory B cell and cTfh (CCR6-CXCR3-) T cell subsets was shared by the patient group. ConclusionWe expand upon the clinical syndromes linked to RELA dysfunction and uncover rare and novel variants that have distinct functional effects on gene transcription downstream of NF-{kappa}B and IFN{beta} promoter elements. These findings reinforce an important role for RELA in a range of autoimmune and autoinflammatory diseases.

immunology↗

bioRxiv2022

Striatal dopamine encodes the relationship between actions and reward

Although the role of striatal dopamine in Pavlovian conditioning and in habits has been reasonably well described, relatively little is known about its function in goal-directed action. In this study we trained hungry rats on two lever press actions for distinct food outcomes and recorded dopamine release in the dorsomedial striatum as these action-outcome associations were encoded and subsequently degraded. During initial training the lever press actions generated bilateral dopamine release that was found to reflect the predicted action value. This value was updated by the prediction error generated by the feedback produced by contact with the outcome, or its absence, after the press. Importantly, hemispheric dopamine release became increasingly lateralized across the course of training, with greater release in the hemisphere contralateral to the press. Using video analysis and multiple different measures, we could find no evidence that the degree of lateralized release was associated with movement; rather, we found that it tracked the strength of the action-outcome association, increasing and decreasing with increments and decrements in the contingency between specific actions and their consequences. Similar results emerged whether the rewards were delivered on ratio or interval schedules of reinforcement and whether we used unpaired outcome delivery or outcome-identity reversal to modify the specific contingencies. These findings suggest that, whereas moment-to-moment fluctuations in action value are reflected in bilateral dopamine release, a second signal broadcasts the overall strength of specific action-outcome relationships via the difference between contralateral and ipsilateral release during actions.

neuroscience↗

bioRxiv2020

Striatal direct and indirect pathway neurons differentially control the encoding and updating of goal-directed learning.

The posterior dorsomedial striatum (pDMS) is necessary for goal-directed action, however the role of the direct (dSPN) and indirect (iSPN) spiny projection neurons in the pDMS in such action remains unclear. In this series of experiments, we examined the role of pDMS SPNs in goal-directed action and found that, whereas dSPNs were critical for goal-directed learning and for energizing the learned response, iSPNs were involved in updating that learning to support response flexibility. Instrumental training elevated expression of the plasticity marker Zif268 in dSPNs only, and chemogenetic suppression of dSPN activity during training prevented goal-directed learning. Unilateral optogenetic inhibition of dSPNs induced an ipsilateral response bias in goal-directed action performance. In contrast, although initial goal-directed learning was unaffected by iSPN manipulations, optogenetic inhibition of iSPNs, but not dSPNs, impaired the updating of this learning and attenuated response flexibility after changes in the action-outcome contingency.

neuroscience↗

bioRxiv2019

Circadian control of intrinsic heart rate via a sinus node clock and the pacemaker channel

In the human, there is a circadian rhythm in the resting heart rate and it is higher during the day in preparation for physical activity. Conversely, slow heart rhythms (bradyarrhythmias) occur primarily at night. Although the lower heart rate at night is widely assumed to be neural in origin (the result of high vagal tone), the objective of the study was to test whether there is an intrinsic change in heart rate driven by a local circadian clock. In the mouse, there was a circadian rhythm in the heart rate in vivo in the conscious telemetrized animal, but there was also a circadian rhythm in the intrinsic heart rate in denervated preparations: the Langendorff-perfused heart and isolated sinus node. In the sinus node, experiments (qPCR and bioluminescence recordings in mice with a Per1 luciferase reporter) revealed functioning canonical clock genes, e.g. Bmal1 and Per1. We identified a circadian rhythm in the expression of key ion channels, notably the pacemaker channel Hcn4 (mRNA and protein) and the corresponding ionic current (funny current, measured by whole cell patch clamp in isolated sinus node cells). Block of funny current in the isolated sinus node abolished the circadian rhythm in the intrinsic heart rate. Incapacitating the local clock (by cardiac-specific knockout of Bmal1) abolished the normal circadian rhythm of Hcn4, funny current and the intrinsic heart rate. Chromatin immunoprecipitation demonstrated that Hcn4 is a transcriptional target of BMAL1 establishing a pathway by which the local clock can regulate heart rate. In conclusion, there is a circadian rhythm in the intrinsic heart rate as a result of a local circadian clock in the sinus node that drives rhythmic expression of Hcn4. The data reveal a novel regulator of heart rate and mechanistic insight into the occurrence of bradyarrhythmias at night.

physiology↗