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Biology subjects

Dey, S.

Publications and source records attributed to Dey, S..

At least 91 records · Page 5Linked to original sources

Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring

Bacterial cell division begins with the formation of the Z-ring via polymerization of FtsZ and the localization of Z-ring beneath the inner membrane through membrane anchors. In Mycobacterium tuberculosis (Mtb), SepF is one such membrane anchor, but our understanding of the underlying mechanism is very limited. Here we used molecular dynamics simulations to characterize how SepF itself, a water-soluble protein, tethers to acidic membranes that mimic the Mtb inner membrane. In addition to an amphipathic helix (residues 1-12) at the N-terminus, membrane binding also occurs through two stretches of positively charged residues (Arg27-Arg 37 and Arg95-Arg107) in the long linker preceding the FtsZ-binding core domain (residues 128-218). The additional interactions via the disordered linker stabilize the membrane tethering of SepF, and keep the core domain of SepF and hence the attached Z-ring close to the membrane. The resulting membrane proximity of the Z-ring in turn enables its interactions with and thus recruitment of two membrane proteins, FtsW and CrgA, at the late stage of cell division.

biophysics↗

Novel genetic modules encoding high-level antibiotic-free protein expression in probiotic lactobacilli

Lactobacilli are ubiquitous in nature, often beneficially associated with animals as commensals and probiotics, and are extensively used in food fermentation. Due to this close-knit association, there is considerable interest to engineer them for healthcare applications in both humans and animals, for which high-performance and versatile genetic parts are greatly desired. For the first time, we describe two genetic modules in Lactiplantibacillus plantarum that achieve high-level gene expression using plasmids that can be retained without antibiotics, bacteriocins or genomic manipulations. These include (i) a promoter, PtlpA, from a phylogenetically distant bacterium, Salmonella typhimurium, that drives up to 5-fold higher level of gene expression compared to previously reported promoters and (ii) multiple toxin-antitoxin systems as a self-contained and easy-to-implement plasmid retention strategy that facilitates the engineering of tunable transient Genetically Modified Organisms. These modules and the fundamental factors underlying their functionality that are described in this work will greatly contribute to expanding the genetic programmability of lactobacilli for healthcare applications.

synthetic biology↗

Coupling of protein condensates to ordered lipid domains determines functional membrane organization

During T-cell activation, the transmembrane adaptor Linker of Activation of T-cells (LAT) forms biomolecular condensates with Grb2 and Sos1, facilitating signaling. LAT has also been associated with cholesterol-rich condensed lipid domains. However, the potential coupling between protein condensation and lipid phase separation and its role in organizing T-cell signaling were unknown. Here, we report that LAT/Grb2/Sos1 condensates reconstituted on model membranes can induce and template lipid domains, indicating strong coupling between lipid- and protein-based phase separation. Correspondingly, activation of T-cells induces protein condensates that associate with and stabilize raft-like membrane domains. Inversely, lipid domains nucleate and stabilize LAT protein condensates in both reconstituted and living systems. This coupling of lipid and protein assembly is functionally important, since uncoupling of lipid domains from cytoplasmic protein condensates abrogates T-cell activation. Thus, thermodynamic coupling between protein condensates and ordered lipid domains regulates the functional organization of living membranes. SUMMARYMembrane-associated protein condensates couple to ordered membrane domains to determine the functional organization of T-cell plasma membranes

cell biology↗

Ferric reductase-related proteins mediate fungal heme acquisition

Heme can serve as iron source in many environments, including the iron-poor animal host environment. The fungal pathobiont Candida albicans expresses a family of extracellular CFEM hemophores that capture heme from host proteins and transfer it across the cell wall to the cell membrane, to be endocytosed and utilized as heme or iron source. Here we identified Frp1 and Frp2, two ferric reductase (FRE)-related proteins that lack an extracellular N-terminal substrate-binding domain, as being required for hemoglobin heme utilization and for sensitivity to toxic heme analogs. Frp1/2 redistribute from the ER to the plasma membrane in the presence of hemoglobin, consistent with a direct role in heme trafficking. Expression of Frp1 with the CFEM hemophore Pga7 can promote heme utilization in Saccharomyces cerevisiae as well, confirming the functional interaction between these proteins. Sequence and structure comparison reveals that the CFEM hemophores are related to the FRE substrate-binding domain that is missing in Frp1/2. We conclude that Frp1/2 and the CFEM hemophores form a functional complex that evolved from ferric reductases to enable extracellular heme uptake.

microbiology↗

Modelling spatially autocorrelated detection probabilities in spatial capture-recapture using random effects

Spatial capture-recapture (SCR) models are now widely used for estimating density from repeated individual spatial encounters. SCR accounts for the inherent spatial autocorrelation in individual detections by modelling detection probabilities as a function of distance between the detectors and individual activity centres. However, additional spatial heterogeneity in detection probability may still creep in due to environmental or sampling characteristics. if unaccounted for, such variation can lead to pronounced bias in population size estimates. Using simulations, we describe and test three Bayesian SCR models that use generalized linear mixed models (GLMM) to account for latent heterogeneity in baseline detection probability across detectors using: independent random effects (RE), spatially autocorrelated random effects (SARE), and a twogroup finite mixture model (FM). Overall, SARE provided the least biased population size estimates (median RB: -9 - 6%). When spatial autocorrelation was high, SARE also performed best at predicting the spatial pattern of heterogeneity in detection probability. At intermediate levels of autocorrelation, spatially-explicit estimates of detection probability obtained with FM where more accurate than those generated by SARE and RE. In cases where the number of detections per detector is realistically low (at most 1), all GLMMs considered here may require dimension reduction of the random effects by pooling baseline detection probability parameters across neighboring detectors ("aggregation") to avoid over-parameterization. The added complexity and computational overhead associated with SCR-GLMMs may only be justified in extreme cases of spatial heterogeneity. However, even in less extreme cases, detecting and estimating spatially heterogeneous detection probability may assist in planning or adjusting monitoring schemes.

ecology↗

A cobB like protein in Oryza sativa indica regulates the mitochondrial machinery under stress conditions

Sirtuins are ubiquitous in nature and are known to play an important role as metabolic regulators. In plants, these NAD+ dependent deacetylases are not well characterized. In this study, we are reporting a new member of sirtuin in Oryza sativa indica. It shares approx. 89% sequence identity with bacterial sirtuin, a class III sirtuin member. This protein is mostly present in mitochondria with trace amounts in the nucleus. It can physically interact with histones H3 and H4 and can specifically deacetylate histone H3 at K9 and K18 positions. In mitochondria, acetyl coA synthetase (AcS) and isocitrate dehydrogenase (IDH2) are the targets for its deacetylation. This removal of acetyl group is the mode of regulation under certain stress conditions. Thus, this is the first mitochondrial cobB targeting important plant machinery under changing growth environment. The OscobB deacetylase activity is not majorly affected by its products, NAM & ADP ribose but are sensitive to certain metal ions like Fe2+ and Mg2+. In contrast to some class III members, it does not have any ADP ribosyl transferase activity. In response to abiotic stress conditions like dehydration and low temperature, this enzyme can also mobilize to the nucleus to regulate the plant metabolism. HighlightsO_LIA new class III member of the sirtuin family found in Oryza sativa indica. C_LIO_LIUnder normal conditions, this protein is localized mostly in mitochondria, with trace amounts in the nucleus. C_LIO_LIThis enzyme is capable of using both NAD+ and NADP+ as a substrate for catalysis. C_LIO_LIIt specifically deacetylates the nuclear histone H3 at K9 and K18 positions. C_LIO_LIMitochondrial proteins acetyl coA synthetase (AcS) and isocitrate dehydrogenase (IDH2) are the regulatory targets of OscobB. C_LIO_LIUnder certain stress conditions in plants like dehydration, pathogenesis and low temperature, there is localisation of OscobB from mitochondria to nucleus. C_LI

plant biology↗

Dynamic analysis of sequestration-based feedbacks in cellular and biomolecular circuits

Nonlinear feedback controllers are ubiquitous features of biological systems at different scales. A key motif arising in these systems is a sequestration-based feedback. As a physiological example of this type of feedback architecture, platelets (specialized cells involved in blood clotting) differentiate from stem cells, and this process is activated by a protein called Thrombopoietin (TPO). Platelets actively sequester and degrade TPO, creating negative feedback whereby any depletion of platelets increases the levels of freely available TPO that upregulates platelet production. We show similar examples of sequestration-based feedback in intracellular biomolecular circuits involved in heat-shock response and microRNA regulation. Our systematic analysis of this feedback motif reveals that platelets induced degradation of TPO is critical in enhancing system robustness to external disturbances. In contrast, reversible sequestration of TPO without degradation results in poor robustness to disturbances. We develop exact analytical results quantifying the limits to which the sensitivity to disturbances can be attenuated by sequestration-based feedback. Next, we consider the stochastic formulation of the circuit that takes into account low-copy number fluctuations in feedback components. Interestingly, our results show that the extent of random fluctuations are enhanced with increasing feedback strength, but can exhibit local maxima and minima across parameter regimes. In summary, our systematic analysis highlights design principles for enhancing the robustness of sequestration-based feedback mechanisms to external disturbances and inherent noise in molecular counts.

physiology↗

The effect of migration and variation on populations of Escherichia coli adapting to complex fluctuating environments

Migration, a critical evolutionary force, can have contrasting effects on adaptation. It can aid as well as impede adaptation. The effects of migration on microbial adaptation have been studied primarily in simple constant environments. Very little is known about the effects of migration on adaptation to complex, fluctuating environments. In our study, we subjected replicate populations of Escherichia coli, adapting to complex and unpredictably fluctuating environments to different proportions of clonal ancestral immigrants. Contrary to the results from simple/constant environments, the presence of clonal immigrants reduced all measured proxies of fitness. However, migration from a source population with a greater variance in fitness resulted in no change in fitness w.r.t the no-migration control, except at the highest level of migration. Thus, the presence of variation in the immigrants could counter the adverse effects of migration in complex and unpredictably fluctuating environments. Our study demonstrates that the effects of migration are strongly dependent on the nature of the destination environment and the genetic makeup of immigrants. These results enhance our understanding of the influences of migrating populations, which could help better predict the consequences of migration.

evolutionary biology↗

Estimating spatially variable and density-dependent survival using open-population spatial capture-recapture models

Open-population spatial capture-recapture (OPSCR) models use the spatial information contained in individual detections collected over multiple consecutive occasions to estimate occasion-specific density, but also demographic parameters. OPSCR models can also estimate spatial variation in vital rates, but such models are neither widely used nor thoroughly tested. We developed a Bayesian OSPCR model that not only accounts for spatial variation in survival using spatial covariates, but also estimates local density-dependent effects on survival within a unified framework. Using simulations, we show that OPSCR models provide sound inferences on the effect of spatial covariates on survival, including multiple competing sources of mortality, each with potentially different spatial determinants. Estimation of local density-dependent survival was possible but required more data due to the greater complexity of the model. Not accounting for spatial heterogeneity in survival led to positive bias in abundance estimates (up to 10% relative bias). We provide a set of features in R package nimbleSCR that allow computationally efficient fitting of Bayesian OPSCR models with spatially varying survival. The ability to make population-level inferences of spatial variation in survival is an essential step towards a fully spatially-explicit OPSCR model that can disentangle the role of multiple spatial drivers on population dynamics. Open Research statementcode to reproduce the analysis is available on github; https://github.com/Cyril-Milleret/Public/tree/master/SpatialSurvivalOPSCR

ecology↗

Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins

For intrinsically disordered proteins (IDPs), a pressing question is how sequence codes for function. Dynamics serves as a crucial link, reminiscent of the role of structure in sequence-function relations of structured proteins. To define general rules governing sequence-dependent backbone dynamics, we carried out long molecular dynamics simulations of eight IDPs. Blocks of residues exhibiting large amplitudes in slow dynamics are rigidified by local inter-residue interactions or secondary structures. A long region or an entire IDP can be slowed down by long-range contacts or secondary- structure packing. On the other hand, glycines promote fast dynamics and either demarcate rigid blocks or facilitate multiple modes of local and long-range inter-residue interactions. The sequence-dependent backbone dynamics endows IDPs with versatile response to binding partners, with some blocks recalcitrant while others readily adapting to intermolecular interactions.

biophysics↗

The interplay of active and passive mechanisms in slow axonal transport

A combination of intermittent active movement of transient aggregates and a paused state that intervenes between periods of active transport has been proposed to underly the slow, directed transport of soluble proteins in axons. A component of passive diffusion in the axoplasm may also contribute to slow axonal transport, although quantitative estimates of the relative contributions of diffusive and active movement in the slow transport of a soluble protein, and in particular how they might vary across developmental stages, are lacking. Here, we propose and study a model for slow axonal transport, addressing data from bleach-recovery measurements on a small, soluble, protein, Choline Acetyltransferase (ChAT), in thin axons of the lateral chordotonal (lch5) sensory neurons of Drosophila. ChAT is mainly present in soluble form in the axon and catalyses the acetylation of choline at the synapse. It does not form particulate structures in axons and moves at rates characteristic of slow component b ({approx} 1-10 mm/day or 0.01-0.1 m/s). Using our model, which incorporates active transport, paused and diffusive states, we predict bleach recovery and cargo trajectories obtained through kymographs, comparing these to experimental observations at different developmental stages. We show that changes in the diffusive fraction of cargo during these developmental stages dominate bleach recovery and that a combination of active motion with a paused state alone cannot reproduce the data. We compared predictions of the model with results from photoactivation experiments. The importance of the diffusive state in reproducing the bleach recovery signal in the slow axonal transport of small soluble proteins is our central result. STATEMENT OF SIGNIFICANCEWhile the fast axonal transport of cargo in axons is by now well-understood, the nature of slow transport remains controversial. A number of different models having been proposed for slow axonal transport, including models which allow for transitions between an intermittently moving molecular-motor driven state and a stalled state. How mechanisms for slow axonal transport are modulated during development is unexplored. We study a number of different models for slow axonal transport, comparing their predictions to data on transport of the enzyme Choline Acetyltransferase (ChAT) in thin lateral chordotonal (lch5) sensory neurons of Drosophila larva, across developmental stages where flux increases significantly. We show that accounting for changes in the diffusive fraction of cargo during these developmental stages is essential and diffusion cannot be neglected in the modelling of the slow axonal transport of small soluble proteins.

biophysics↗

Identifying potential key genes and existing drugs for Multiple sclerosis, Schizophrenia, and Autism- an in silico approach

Nowadays, neurological conditions are a major concern as it not only preys on a patients health but also is a huge economic burden that is placed on the patients family. The diagnosis and treatment of disease sometimes cause methodological limitations. This is mainly common for individuals who have the signs of MS and schizophrenia (SZ). Patients suffering from multiple sclerosis are more likely to develop schizophrenia. Besides, a significant portion of patients who have been diagnosed with Autism Spectrum Disorder (ASD) later acquire the symptoms of Schizophrenia. In this study, we used bioinformatics tools to determine differentially expressed genes (DEGs) in all these diseases, and then we created a protein-protein interaction network using the online software STRING and identified 15 significant genes with the help of Cytohubba a plug-in tool in Cytoscape, the offline software (version3.8.2). We then used a drug-gene interaction database to conduct a drug-gene interaction study of the 15 hub genes and from there we identified 37 FDA-approved drugs. These findings may provide a new and common therapeutic approach for MS, SZ, and ASD therapy.

neuroscience↗

Artificial Intelligence Guided Conformational Mining of Intrinsically Disordered Proteins

Artificial intelligence recently achieved the breakthrough of predicting the three-dimensional structures of proteins. The next frontier is presented by intrinsically disordered proteins (IDPs), which, representing 30% to 50% of proteomes, readily access vast conformational space. Molecular dynamics (MD) simulations are promising in sampling IDP conformations, but only at extremely high computational cost. Here, we developed generative autoencoders that learn from short MD simulations and generate full conformational ensembles. An encoder represents IDP conformations as vectors in a reduced-dimensional latent space. The mean vector and covariance matrix of the training dataset are calculated to define a multivariate Gaussian distribution, from which vectors are sampled and fed to a decoder to generate new conformations. The ensembles of generated conformations cover those sampled by long MD simulations and are validated by small-angle X-ray scattering profile and NMR chemical shifts. This work illustrates the vast potential of artificial intelligence in conformational mining of IDPs.

biophysics↗

Biochemical analysis of deacetylase activity of rice sirtuin OsSRT1, a class IV member in plants

The role of plant sirtuins is slowly unwinding. There are only reports of H3K9Ac deacetylation by OsSRT1. This belongs to class IV sirtuin family with a longer C-terminus. Here C-terminus is required for ligand binding and catalysis. OsSRT1 can deacetylate the lys residues at the N terminal tail of both H3 and H4. It can also target the non-histone target, OsPARP1 playing a role in DNA damage repair pathway. Changes in the extent of different histone deacetylation by OsSRT1 is also related with different abiotic stress conditions. NAM and ADP-ribose has negative effect on OsSRT1 deacetylation. HighlightsO_LIOsSRT1 is capable of deacetylating various lysine residues of histone H3 and H4 as well as OsPARP1. C_LIO_LIThe extra long C-terminus of OsSRT1 is required for its substrate binding and thus, its catalysis. C_LIO_LIOn plants exposure to H2O2 and Arsenic toxicity, there is a relationship between increased expression of OsSRT1 and increased deacetylation of H3 and H4. C_LI

plant biology↗

Transcriptomic analysis revealed reactive oxygen species scavenging mechanisms associated with ferrous iron toxicity in aromatic Keteki Joha rice

Lowland acidic soils with water-logged regions are often affected by ferrous iron (Fe2+) toxicity, a major yield-limiting factor of rice production. The Reactive Oxygen Species (ROS) was hypothesized to be crucial under severe Fe2+ toxicity conditions. However, molecular mechanisms and associated ROS homeostasis genes are still not well-explored. In this study, a comparative RNA-Seq based transcriptome analysis was conducted to understand the Fe2+ toxicity tolerance mechanism in aromatic Keteki Joha. About 69 Fe homeostasis related genes and their homologs were identified, where most of the genes were downregulated. Differentially expressed genes (DEGs) are associated with biological processes-response to stress, stimulus and abiotic stimulus. DEGs involved in the Biosynthesis of amino acids, RNA degradation, Glutathione metabolism etc. were induced, whereas, Phenylpropanoid biosynthesis, Photosynthesis, and Fatty acid elongation were inhibited. The Mitochondrial iron transporter (OsMIT), Vacuolar Iron Transporter 2 (OsVIT2), Ferritin (OsFER), Vacuolar Mugineic Acid Transporter (OsVMT), Phenolic Efflux Zero1 (OsPEZ1), Root Meander Curling (OsRMC), Nicotianamine synthase (OsNAS3), etc. were upregulated in different tissues suggesting the importance of Fe retention and sequestration for detoxification. However, several antioxidants, ROS scavenging genes and abiotic stress-responsive transcription factors indicate ROS homeostasis as one of the most important defense mechanisms under severe Fe2+ toxicity. The CAT, GSH, APX, MDHAR, DHAR, GR were upregulated. Moreover, abiotic stress-responsive transcription factors NAC, MYB, ARF, bZIP, WRKY, C2H2-ZFP were also upregulated. Accordingly, ROS homeostasis has been proposed to be an important defense mechanism under such conditions. Thus, our results will enrich the knowledge of understanding Fe-homeostasis in rice.

genomics↗

Mathematical modelling of activation-induced heterogeneity reveals cell state transitions underpinning macrophage responses to LPS

Despite extensive work on macrophage heterogeneity, the mechanisms driving activation induced heterogeneity (AIH) in macrophages remain poorly understood. Here, we use two in vitro cellular models of LPS-induced tolerance (bone marrow-derived macrophages or BMDMs and RAW 264.7 cells), single-cell protein measurements, and mathematical modelling to explore how AIH underpins primary and secondary responses to LPS. We measure expression of TNF, IL-6, pro-IL-1{beta}, and NOS2 and demonstrate that macrophage community AIH is dependent on LPS dose. We show that altered AIH kinetics in macrophages responding to a second LPS challenge underpin hypo-responsiveness to LPS. These empirical data can be explained by a mathematical 3-state model including negative, positive, and non-responsive states (NRS), but they are also compatible with a 4-state model that includes distinct reversibly NRS and non-responsive permanently states (NRPS). Our mathematical model, termed NoRM (Non-Responsive Macrophage) model identifies similarities and differences between BMDM and RAW 264.7 cell responses. In both cell types, transition rates between states in the NoRM model are distinct for each of the tested proteins and, crucially, macrophage hypo-responsiveness is underpinned by changes in transition rates to and from NRS. Overall, our findings provide support for a critical role for phenotypically negative macrophage populations as an active component of AIH and primary and secondary responses to LPS. This reveals unappreciated aspects of cellular ecology and community dynamics associated with LPS-driven training of macrophages.

immunology↗

Analysis of Gene Expression Profiles to study Malaria Vaccine Dose Efficacy & Immune Response Modulation.

Malaria is a life-threatening disease, and the Africa is still one of the most affected endemic regions despite years of policy to limit infection and transmission rates. Further, studies into the variable efficacy of the vaccine are needed to provide a better understanding of protective immunity. Thus, the current study is designed to delineate the effect of the different vaccination doses on the transcriptional profiles of subjects to determine its efficacy and understand the molecular mechanisms underlying the protection this vaccine provides. Here, we used gene expression profiles of pre and post-vaccination patients after various doses of RTS,S based on 275 and 583 samples collected from the GEO datasets. At first, exploratory data analysis based Principal component analysis (PCA) shown the distinct pattern of different doses. Subsequently, differential gene expression analysis using edgeR revealed the significantly (FDR <0.005) 158 down-regulated and 61 upregulated genes between control vs. Controlled Human Malaria Infection (CHMI) samples. Further, enrichment analysis of significant genes using Annotation and GAGE tools delineate the involvement of CCL8, CXCL10, CXCL11, XCR1, CSF3, IFNB1, IFNE, IL12B, IL22, IL6, IL27, etc.,genes which found to be upregulated after earlier doses but downregulated after the 3rd dose in cytokine-chemokine pathways. Notably, we identified 13 cytokine genes whose expression significantly varied during three doses. Eventually, these findings give insight to the dual role of cytokine responses in malaria pathogenesis and variations in their expression patterns after various doses of vaccination involved in protection.

bioinformatics↗

Dendrite regeneration in C. elegans is controlled by the RAC GTPase CED-10 and the RhoGEF TIAM-1

Neurons are vulnerable to physical insults which compromise the integrity of both dendrites and axons. Although several molecular pathways of axon regeneration are identified, our knowledge of dendrite regeneration is limited. To understand the mechanisms of dendrite regeneration, we used PVD neurons in C. elegans having stereotyped branched dendrites. Using femtosecond laser, we severed the primary dendrites and axon of this neuron. After severing the primary dendrites near the cell body, we observed sprouting of new branches from the proximal site within 6 hours, which regrew further with timein an unstereotyped manner.This was accompanied by reconnection between the proximal and distal dendrites as well as the fusion among the higher-order branches as reported before. We quantified the regeneration pattern in threeaspects -territory length, number of branchesand fusion phenomena.Axonal injury causes a retraction of the severed end followed by a Dual leucine zipper kinase-1 (DLK-1) dependent regrowth from the severed end.We tested the roles of the major axon regenerationsignaling hubs such as DLK-1-RPM-1, cAMP elevation, let-7 miRNA, AKT-1, Phosphatidyl serine exposure/PS in dendrite regeneration. We found that neither regrowth nor fusionis affected by the axon injury pathway molecules. Surprisingly, we found that the RAC GTPase CED-10and its upstream GEF TIAM-1 play a cell-autonomous role in dendrite regeneration. Additionally, function of CED-10 in epidermal cell is critical for post-dendrotomy fusion phenomena. This work describes a novel regulatory mechanism of dendrite regeneration andprovides a framework for understanding the cellular mechanism of dendrite regeneration using PVD neuron as a model system.

neuroscience↗