Biology subjects

Roy, S.

Publications and source records attributed to Roy, S..

334 records · Page 19Linked to original sources

bioRxiv2017

Formation of retinal direction-selective circuitry initiated by starburst amacrine cell homotypic contact

Impact statementSelective synapse formation in a retinal motion-sensitive circuit is orchestrated by starburst amacrine cells, which use homotypic interactions to initiate formation of a dendritic scaffold that recruits projections from circuit partners.\n\nSUMMARYA common strategy by which developing neurons locate their synaptic partners is through projections to circuit-specific neuropil sublayers. Once established, sublayers serve as a substrate for selective synapse formation, but how sublayers arise during neurodevelopment remains unknown. Here we identify the earliest events that initiate formation of the direction-selective circuit in the inner plexiform layer of mouse retina. We demonstrate that radially-migrating newborn starburst amacrine cells establish homotypic contacts on arrival at the inner retina. These contacts, mediated by the cell-surface protein MEGF10, trigger neuropil innervation resulting in generation of two sublayers comprising starburst-cell dendrites. This dendritic scaffold then recruits projections from circuit partners. Abolishing MEGF10-mediated contacts profoundly delays and ultimately disrupts sublayer formation, leading to broader direction tuning and weaker direction-selectivity in retinal ganglion cells. Our findings reveal a mechanism by which differentiating neurons transition from migratory to mature morphology, and highlight this mechanisms importance in forming circuit-specific sublayers.

neuroscience↗

bioRxiv2017

Processive movement of actin by biased polymerization: a new paradigm of axonal transport

Classic pulse-chase studies have shown that actin is conveyed in slow axonal transport, but the mechanistic basis for this movement is unknown. Recently, we reported that axonal actin was surprisingly dynamic, with focal assembly/dis-assembly events (\"hotspots\") and elongating polymers along the axon-shaft (\"trails\"). Using a combination of live imaging, super-resolution microscopy, and modeling, here we explore how these axonal actin dynamics can lead to processive transport. We found abundant actin nucleation, along with a slow, anterogradely-biased flow of actin in axon-shafts. Starting with first principles of monomer/filament assembly - and incorporating imaging data - we generated a quantitative model simulating axonal hotspots and trails. Our simulations predict that the axonal actin dynamics indeed lead to an anterogradely-biased flow of the population, at rates consistent with slow transport. Collectively, the data point to a surprising scenario where local assembly and biased polymerization generate the slow axonal transport of actin. This mechanism is distinct from polymer-sliding, and seems well suited to convey highly dynamic cytoskeletal cargoes.\n\nAcknowledgementsThis work was supported by an NIH grant to SR (R01NS075233). The authors thank Stephanie Gupton (UNC) for the Mena/Vasp constructs.

neuroscience↗

bioRxiv2017

Id proteins suppress E2A-driven innate-like T cell development prior to TCR selection

Id proteins have been shown to promote the differentiation of conventional {beta} and {gamma}{delta}T cells, and to suppress the expansion of invariant Natural Killer T (iNKT) cells and innate-like {gamma}{delta}NKT within their respective cell lineages. However, it remains to be determined whether Id proteins regulate lineage specification in developing T cells that give rise to these distinct cell fates. Here we report that in the absence of Id2 and Id3 proteins, E2A prematurely activates genes critical for the iNKT cell lineage prior to TCR expression. Enhanced iNKT development in Id3-deficient mice lacking {gamma}{delta} NKT cells suggests that Id3 regulates the lineage competition between these populations. RNA-Seq analysis establishes E2A as the transcriptional regulator of both iNKT and {gamma}{delta}NKT development. In the absence of pre-TCR signaling, Id2/Id3 deletion gives rise to a large population of iNKT cells and a unique innate-like DP population, despite the block in conventional {beta} T cell development. The transcriptional profile of these unique DP cells reflects enrichment of innate-like signature genes, including PLZF (Zbtb16) and Granzyme A (Gzma). Results from these genetic models and genome-wide analyses suggest that Id proteins suppress E2A-driven innate-like T cell programs prior to TCR selection to enforce predominance of conventional T cells.

immunology↗

bioRxiv2017

p53 suppresses mutagenic RAD52 and POLθ pathways by orchestrating DNA replication restart homeostasis

Classically, p53 tumor-suppressor acts in transcription, apoptosis, and cell-cycle arrest. Yet, replication-mediated genomic instability is integral to oncogenesis, and p53 mutations promote tumor progression and drug-resistance. By delineating human and murine separation-of-function p53 alleles, we find that p53 null and gain-of-function (GOF) mutations exhibit defects in restart of stalled or damaged DNA replication forks driving genomic instability independent of transcription activation. By assaying protein-DNA fork interactions in single cells, we unveil a p53-MLL3-enabled recruitment of MRE11 DNA replication restart nuclease. Importantly, p53 defects or depletion unexpectedly allow mutagenic RAD52 and POL{theta} pathways to hijack stalled forks, which we find reflected in p53 defective breast-cancer patient COSMIC mutational signatures. These data uncover p53 as a keystone regulator of replication homeostasis within a DNA restart network. Mechanistically, this has important implications for development of resistance in cancer therapy. Combined, these results define an unexpected role for p53 suppression of replication genome instability.

genetics↗

bioRxiv2017

Allosteric Activation of p300 Autoacetylation by the Tumor Suppressor p53

The transcriptional coactivator p300 is essential for p53 transactivation, although its precise mechanism remains unclear. We report that, p53 allosterically activates the acetyltransferase activity of p300 through the enhancement of p300 autoacetylation. Cryo-electron microscopy revealed that the domain organization of p300 is substantially altered upon binding of p53, suggesting that a structural switch may underpin the activation. Acetylated p300 accumulates near the transcription start sites accompanied by a similar enrichment of activating histone marks near those sites. Disruption of p53-p300 interaction by a site-directed peptide inhibitor abolished autoacetylated p300-mediated enhanced histone acetylation, suggesting a crucial role played by the allosteric activation in p53-mediated gene regulation. Gain-of-function mutant p53, known to impart aggressive proliferative properties in tumor cells, also activate p300 autoacetylation. The same peptide abolished many of the gain-of-functions of mutant p53 as well. We conclude that allosteric activation of p300 by p53 underpins gene regulation by p53. Reversal of gain-of-function properties of mutant p53 suggests that molecules targeting the p53-p300 interface may be good candidates for anti-tumor drugs.

molecular biology↗

bioRxiv2017

Heterologous expression of the immune receptor EFR in Medicago truncatula reduces pathogenic infection, but not rhizobial symbiosis

Interfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad-spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen-associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae-specific PRR ELONGATION FACTOR-THERMO UNSTABLE RECEPTOR (EFR) from Arabidopsis thaliana to the legume Medicago truncatula, conferring recognition of the bacterial EF-Tu protein. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF-Tu-derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR-Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling.\n\nSignificance StatementCrop engineering helps reducing the economic and environmental costs of plant disease. The genetic transfer of immune receptors across plant species is a promising biotechnological approach to increase disease resistance. Surface-localized pattern-recognition receptors (PRRs), which detect conserved characteristic microbial features, are functional in heterologous taxonomically-diverse plant species, and confer broad-spectrum disease resistance. It was unclear whether PRR transfer negatively impacts the association of the recipient plants with symbiotic microbes. Here, we show that a legume engineered with a novel PRR recognizing a conserved bacterial protein becomes more resistant to an important bacterial pathogen without significant impact on nitrogen-fixing symbiosis with rhizobia. This finding is of particular relevance as attempts to transfer this important symbiosis into non-legume plants are ongoing.

plant biology↗

bioRxiv2017

Bacterial Communication And Relevance Of Quantum Theory

The recent findings confirm that bacteria communicate each other through chemical and electrical signals. Bacteria use chemical signaling molecules which are called as quorum sensing molecules(QSMs) or autoinducers. Moreover, the ion channels in bacteria conduct a long-range electrical signaling within biofilm communities through propagated waves of potassium ions and biofilms attracts other bacterial species too. Both communication process are used by bacteria to make their own survival strategies. In this article, we model this bacterial communication mechanism by complex Ginzburg- Landau equation and discuss the formation of patterns depending on kinematic viscosity associated with internal noise. Again, the potassium wave propagation is described by the non-linear Schrodinger equation in a dissipative environment. By adding perturbation to non-linear Schrodinger equation one arrives at Complex Ginzburg-Landau equation. In this paper we emphasize that at the cellular level(bacteria) we use Complex Ginzburg - Landau equation as a perturbed Nonlinear Schrodinger equation to understand the bacterial communication as well as pattern formation in Biofilms for certain range of kinematic viscosity which can be tested in laboratory experiment. Here, the perturbation is due to the existence of non thermal fluctuations associated to the finite size of the bacteria. It sheds new light on the relevance of quantum formalism in understanding the cell to cell communication.

biophysics↗

bioRxiv2017

The role of coherence in bacterial communication

Bacteria within biofilms can coordinate their behavior through distinct from of communication mechanism1. The well-established cell - to - cell signaling process in bacteria is known as quorum sensing through chemical signaling molecules2-5. Recently, another cell- to - cell communication process based on ion channel mediated electrical signaling6 has also been observed. In this article, we propose a novel approach to explain the role of coherence and phase synchronization in the cell - to - cell bacterial communication. The observable long - range coherent electrical signaling is species independent and it is caused by membrane - potential - dependent modulation of tumbling frequency7-9. Moreover, noise can play a constructive role in enhancing the synchronization of chaotic bacterial communication systems and noise associated with the opening and closing the gate of ion channel induce small kinetic viscosity that make a wave-like pattern in concentration profile of quorum sensing.

biophysics↗

bioRxiv2017

Bacterial Conversations and Pattern Formation

It has long been recognized that certain bacterial groups exhibit cooperative behavioral patterns. Bacteria accomplish such communication via exchange of extracellular signaling molecules called pheromones(autoinducer or quorum sensing molecules). As the bacterial culture grows, signal molecules are released into extracellular milieu accumulate, changing water fluidity. Under such threshold conditions swimming bacterial suspensions impose a coordinated water movement on a length scale of the order 10 to 100 micrometers compared with a bacterial size of the order of 3 micrometers.Here, we investigate the non-local hydrodynamics of the quorum state and pattern formation using forced Burgers equation with Kwak transformation. Such approach resulted in the conversion of the Burgers equation paradigm into a reaction-diffusion system. The examination of the dynamics of the quorum sensing system, both analytically as well as numerically result in similar long-time dynamical behaviour.

biophysics↗

bioRxiv2016

Senescence gives insights into the morphogenetic evolution of anamniotes.

Summary statementWe report the presence of senescent cells in several transient structures in developing amphibian and teleost fish, suggesting novel mechanisms of morphogenesis that appeared early in vertebrate evolution.\n\nAbstractSenescence represents a mechanism to avoid undesired cell proliferation that plays a role in tumor suppression, wound healing and embryonic development. In order to gain insight on the evolution of senescence, we looked at its presence in developing axolotls (urodele amphibians) and in zebrafish (teleost fish), which are both anamniotes. Our data indicate that cellular senescence is present in various developing structures in axolotls (pronephros, olfactory nerve fascicles, lateral organs, gums) and in zebrafish (epithelium of the yolk sac and in the lower part of the gut). Senescence was particularly associated with transient structures (pronephros in axolotls & yolk sac in zebrafish) suggesting that it plays a role in the elimination of these tissues. Our data supports the notion that cellular senescence evolved early in vertebrate evolution to influence embryonic development.

developmental biology↗