Biology subjects

Gopalakrishnan, M.

Publications and source records attributed to Gopalakrishnan, M..

4 recordsLinked to original sources

bioRxiv2024

Pharmacological inhibition of macrophage triglyceride biosynthesis pathways does not improve Mycobacterium tuberculosis control in infected mice

Triglyceride rich macrophages (foam cells) are a hallmark of necrotic granulomas in tuberculosis, and multiple antimicrobial functions are down-regulated in these cells. In this study, we assessed the ability of two different compounds to reduce triglyceride content and intracellular burden in Mycobacterium tuberculosis (Mtb)-infected macrophages: A-922500 (DGATi), an inhibitor of diacylglycerol acyltransferase 1, an enzyme involved in triglyceride synthesis; and LY2584702 (p70S6Ki), an inhibitor of p70 S6 kinase, a serine/threonine kinase involved in mTORC-1dependent lipid biogenesis. Additionally, we evaluated the adjunctive activity of these inhibitors as host-directed therapies against chronic Mtb infection in C3HeB/FeJ mice. DGATi and p70S6Ki significantly reduced the lipid content and bacillary burden in Mtb-infected human monocyte-derived macrophages. In Mtb-infected mice, each inhibitor reduced the triglyceride content (P[≤] 0.0001) in cells from bronchoalveolar lavage samples. Adjunctive treatment of DGATi with isoniazid and p70S6Ki monotherapy reduced the lipid droplet content (P[≤] 0.05) within lung macrophages of Mtb-infected mice. However, neither inhibitor reduced the lung bacterial burden in Mtb-infected mice alone or in combination with isoniazid, and they did not alter lung inflammation. These findings provide further insights into the role of foam cells in tuberculosis pathogenesis and the utility of interventions targeting these cell populations as adjunctive host-directed therapies.

pharmacology and toxicology↗

bioRxiv2019

Spatio-temporal correlations between catastrophe events in a microtubule bundle: a computational study

We explore correlations between dynamics of different microtubules in a bundle, via numerical simulations, using a one-dimensional stochastic model of a microtubule. The GTP-bound tubulins undergo diffusion-limited binding to the tip. Random hydrolysis events take place along the filament, and converts GTP-tubulin to GDP-tubulin. The filament starts depolymerising when the monomer at the tip becomes GDP-bound; in this case, detachment of GDP-tubulin ensues and continues until either GTP-bound tubulin is exposed or complete depolymerisation is achieved. In the latter case, the filament is defined to have undergone a \"catastrophe\". Our results show that, in general, the dynamics of growth and catastrophe in different filaments are coupled to each other; closer the filaments are, the stronger the coupling. In particular, all filaments grow slower, on average, when brought closer together. The reduction in growth velocity also leads to more frequent catastrophes. More dramatically, catastrophe events in the different filaments forming a bundle are found to be correlated; a catastrophe event in one filament is more likely to be followed by a similar event in the same filament. This propensity of bunching disappears when the filaments move farther apart.

biophysics↗

bioRxiv2017

Force Generation By Polymerizing Filaments Revisited: Diffusive Interaction Leads To Nonlinear Force-Number Scaling

Polymers growing against a barrier generate force and push it forward. We study here force generation by a bundle of N rigid polymers growing in parallel against a diffusing, rigid, flat barrier, resembling a bundle of microtubules. To estimate the polymerization force, the barrier is subjected to a force f acting against the direction of growth of the polymers and the mean velocity VN (f) of the filament assembly is computed. The maximum polymerization force (alias stall force) [Formula] is deduced from the condition [Formula]. This problem has been studied in the literature earlier, but two important aspects have escaped attention: (a) free diffusion of monomers is hindered by the barrier, even when it is far from the growing tips and (b) parallel filaments could interact through the monomer density field (\"diffusive coupling\"), leading to negative interference between them. In our model, both these effects are investigated in detail. A mathematical treatment based on a set of continuum Fokker-Planck equations for combined filament-wall dynamics suggests that the barrier reduces the influx of monomers to the growing polymer tip, thereby reducing the growth velocity and also the stall force, but it doesnt affect the scaling of the stall force with number, i.e., [Formula]. However, Brownian dynamics simulations show that the linear scaling holds only when the filaments are far apart; when they are arranged close together, forming a bundle, sublinear scaling of force with number appears. We argue that the nonlinear scaling could be attributed to diffusive interaction between the growing tips which becomes significant when the tips are close together. These conclusions, initially established for simple flat-faced polymers, are also found to hold true for microtubules with their characteristic hollow cylindrical geometry and rugged tip structure. In particular, simulations show conclusively that the stall force of a single microtubule is a fraction of the combined stall force of the 13 protofilaments. This result is supported by a simple analytical estimate of the force using diffusive coupling theory, and is in agreement with earlier experimental observations.

biophysics↗

bioRxiv2017

Ultrasensitivity and Fluctuations in the Barkai-Leibler Model of Chemotaxis Receptors in Escherichia coli

A stochastic version of the Barkai-Leibler model of chemotaxis receptors in Escherichia coli is studied here with the goal of elucidating the effects of intrinsic network noise in their conformational dynamics. The model was originally proposed to explain the robust and near-perfect adaptation of E. coli observed across a wide range of spatially uniform attractant/repellent (ligand) concentrations. In the model, a receptor is either active or inactive and can stochastically switch between the two states. The enzyme CheR methylates inactive receptors while CheB demethylates active receptors and the probability for a receptor to be active depends on its level of methylation and ligand occupation. In a simple version of the model with two methylation sites per receptor (M = 2), we show rigorously, under a quasi-steady state approximation, that the mean active fraction of receptors is an ultrasensitive function of [CheR]/[CheB] in the limit of saturating receptor concentration. Hence the model shows zero-order ultrasensitivity (ZOU), similar to the classical two-state model of covalent modification studied by Goldbeter and Koshland (GK). We also find that in the limits of extremely small and extremely large ligand concentrations, the system reduces to two different two-state GK modules. A quantitative measure of the spontaneous fluctuations in activity is provided by the variance [Formula] in the active fraction, which is estimated mathematically under linear noise approximation (LNA). It is found that [Formula] peaks near the ZOU transition. The variance is a non-monotonic, but weak function of ligand concentration and a decreasing function of receptor concentration. Gillespie simulations are also performed in models with M = 2, 3 and 4. For M = 2, simulations show excellent agreement with analytical results obtained under LNA. Numerical results for M = 3 and M = 4 are qualitatively similar to our mathematical results in M = 2; while all the models show ZOU in mean activity, the variance is found to be smaller for larger M. The magnitude of receptor noise deduced from available experimental data is consistent with our predictions. A simple analysis of the downstream signaling pathway shows that this noise is large enough to affect the motility of the organism, and may have a beneficial effect on it. The response of mean receptor activity to small time-dependent changes in the external ligand concentration is computed within linear response theory, and found to have a bilobe form, in agreement with earlier experimental observations.

biophysics↗