Biology subjects

Banerjee, S.

Publications and source records attributed to Banerjee, S..

16 recordsLinked to original sources

bioRxiv2018

Tissue Fluidity Promotes Epithelial Wound Healing

Epithelial tissues are inevitably damaged from time to time and must therefore have robust repair mechanisms. The behaviour of tissues depends on their mechanical properties and those of the surrounding environment1. However, it remains poorly understood how tissue mechanics regulates wound healing, particularly in in vivo animal tissues. Here we show that by tuning epithelial cell junctional tension, we can alter the rate of wound healing. We observe cells moving past each other at the wound edge by intercalating, like molecules in a fluid, resulting in seamless wound closure. Using a computational model, we counterintuitively predict that an increase in tissue fluidity, via a reduction in junctional tension, can accelerate the rate of wound healing. This is contrary to previous evidence that actomyosin tensile structures are important for wound closure2-6. When we experimentally reduce tissue tension, cells intercalate faster and wounds close in less time. The role we describe for tissue fluidity in wound healing, in addition to its known roles in developing7,8 and mature tissues9, reinforces the importance of the fluid state of a tissue.

biophysics↗

bioRxiv2018

An Extreme Value Theory Model of Cross-Modal Sensory Information Integration in Modulation of Vertebrate Visual System Functions

We propose a computational model of vision that describes the integration of cross-modal sensory information between the olfactory and visual systems in zebrafish based on the principles of the statistical extreme value theory. The integration of olfacto-retinal information is mediated by the centrifugal pathway that originates from the olfactory bulb and terminates in the neural retina. Motivation for using extreme value theory stems from physiological evidence suggesting that extremes and not the mean of the cell responses direct cellular activity in the vertebrate brain. We argue that the visual system, as measured by retinal ganglion cell responses in spikes/sec, follows an extreme value process for sensory integration and the increase in visual sensitivity from the olfactory input can be better modeled using extreme value distributions. As zebrafish maintains high evolutionary proximity to mammals, our model can be extended to other vertebrates as well.

neuroscience↗

bioRxiv2018

A molecular model of the surface-assisted protein aggregation process

The importance of cell surfaces in the self-assembly of proteins is widely accepted. One biologically significant event is the assembly of amyloidogenic proteins into aggregates, which leads to neurodegenerative disorders like Alzheimers and Parkinsons. The interaction of amyloidogenic proteins with cellular membranes appears to dramatically facilitate the aggregation process. Recent findings indicate that, in the presence of surfaces, aggregation occurs at physiologically low concentrations, suggesting interaction with surfaces plays a critical role in the disease-prone aggregation process. However, the molecular mechanisms behind on-surface aggregation remain unclear. Here we provide a theoretical model that offers a molecular explanation. According to this model, monomers transiently immobilized to surfaces increase the local monomer protein concentration and thus work as nuclei to dramatically accelerate the entire aggregation process. This theory was verified by experimental studies, using mica surfaces, to examine the aggregation kinetics of amyloidogenic-synuclein protein (-Syn) and non-amyloidogenic cytosine deaminase APOBEC3G (A3G).

biophysics↗

bioRxiv2018

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences network complexity of microbial communities. We investigated the impact of conventional, no-till and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harboured a much more complex fungal network than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiota.

microbiology↗

bioRxiv2018

O-GlcNAc modification of oncogenic transcription factor Sox2 promotes protein stability and regulates self-renewal in pancreatic cancer

Pancreatic cancer is among the 3rd leading cause of cancer related deaths in the United States along with a 5-year survival rate of 7%. The aggressive biology of the disease is responsible for such dismal outcome and is manifested by an increase in self-renewal capacity of the cancer cells, which leads to an increased rate of tumor-recurrence, contributing to poor prognosis. Transcription factor SOX2 maintains a critical balance between differentiation and \"stemness\" and is thus tightly regulated within a cell. In cancer, SOX2 is aberrantly \"turned-on\" leading to activation of self-renewal pathways in cancer. Regulation of Sox2 in cancer is poorly understood. In the current study, we show for the first time that in pancreatic cancer, Sox2 is modified by addition of O-GlcNAc moiety, catalyzed by OGT (O-GlcNAc Transferase) at S246. This activates Sox2 transcriptional activity by stabilizing the protein in the nucleus. A CRISPR-OGT knockout in pancreatic cancer cell line S2VP10 resulted in a delayed tumor initiation. We further showed that mutation of this site (S246A) prevents the modification of Sox2 and its downstream activity. Our study also demonstrated that targeting OGT in vivo with a small molecule inhibitor OSMI, results in decreased tumor burden, delayed tumor progression and a decreased expression of SOX2 in pancreatic cancer cells. Our study highlights for the first time that that the O-GlcNAc transferase dependent SOX2 glycosylation has a profound effect on the transcriptional activity of SOX2 and is instrumental in determining self-renewal in pancreatic cancer.\n\nSignificanceOur study highlights for the first time that that the O-GlcNAc transferase dependent SOX2 glycosylation determines self-renewal in pancreatic cancer which is responsible for tumor initiation.

cancer biology↗

bioRxiv2018

Microbial Dysbiosis and polyamine metabolism as predictive markers for early detection during progression of pancreatic adenocarcinoma in spontaneous mouse model

PurposeThe lack of tools for early detection of pancreatic ductal adenocarcinoma (PDAC) is directly correlated to the abysmal survival rate in patients. In addition to several potential detection tools under active investigation, we tested the gut microbiome and its metabolic complement as one of the earliest detection tools that could be useful in patients at high-risk for PDAC.\n\nExperimental DesignA combination of 16s pyrosequencing and whole-genome sequencing of gut microbiota was used in a spontaneous genetically engineered PDAC murine model (KRASG12DTP53R172HPdxCre or KPC). Metabolic reconstruction of microbiome was done using the HUmanN2 pipeline. Serum polyamine levels were measured from murine and patient samples using standard methods.\n\nResultsResults showed a progressive Proteobacterial and Firmicutes dominance in gut microbiota in early stages of PDAC development. Upon in silico reconstruction of active metabolic pathways within the altered microbial flora, polyamine and nucleotide biosynthetic pathways were significantly elevated. These metabolic products are known to be actively assimilated by the host and eventually utilized by rapidly dividing cells for proliferation validating their importance in the context of tumorigenesis. In KPC mice, as well as PDAC patients, we show significantly elevated serum polyamine concentration. Therefore, at the early stages of tumorigenesis, the gut microbial composition changes in a way to release metabolites that foster host tumorigenesis, thereby fulfilling the vicious cycle hypothesis of the role of the microbiome in health and disease states.\n\nConclusionsOur results provide a potential, precise, non-invasive tool for early detection of PDAC, which will result in improved outcomes.\n\nSynopsisGut microbiota changes during early stages of pancreatic ductal adenocarcinoma (PDAC) progression and contributes towards host polyamine pool. Both changes can be used as an early predictive marker for PDAC.\n\nTranslational RelevancePancreatic carcinogenesis progresses through pre-cancerous PanIN lesions to invasive cancer. Even though these morphological changes are histologically distinct, imaging techniques are not able to distinguish the pre-invasive PanINs from normal pancreas, making detection of a tumor at a precancerous stage impossible. Thus, majority of cases (85-90%) present with advanced pancreatic cancer at the time of diagnosis. This contributes to the dismal survival rate in this disease. Our study of gut microbiome analysis on KPC mice during tumor progression followed by metabolic reconstruction and experimental validation in human samples indicate that gut-microbiome analysis along with an analysis of the microbial metabolites can be developed as potential biomarkers for detection of PDAC at early stages when histological changes are not yet grossly apparent.

cancer biology↗

bioRxiv2018

Force localization modes in dynamic epithelial colonies

Collective cell behaviors, including tissue remodeling, morphogenesis and cancer metastasis rely on dynamics between cells, their neighbors and the extracellular matrix. The lack of quantitative models precludes understanding of how cell-cell and cell-matrix interactions regulate tissue-scale force transmission to guide morphogenic processes. We integrate biophysical measurements on model epithelial tissues and computational modelling to explore how cell-level dynamics alter mechanical stress organization at multicellular scales. We show that traction stress distribution in epithelial colonies can vary widely for identical geometries. For colonies with peripheral localization of traction stresses, we recapitulate previously described mechanical behavior of cohesive tissues with a continuum model. By contrast, highly motile cells within colonies produce traction stresses that fluctuate in space and time. To predict the traction force dynamics, we introduce an Active Adherent Vertex Model (AAVM) for epithelial monolayers. AAVM predicts that increased cellular motility and reduced intercellular mechanical coupling localize traction stresses in the colony interior, in agreement with our experimental data. Furthermore, the model captures a wide spectrum of localized stress production modes that arise from individual cell activities including cell division, rotation, and polarized migration. This approach provides a robust quantitative framework to study how cell-scale dynamics influence force transmission in epithelial tissues.

biophysics↗

bioRxiv2018

Phospholipid membranes promote the early stage assembly of α-synuclein aggregates

Development of Parkinsons disease is associated with spontaneous self-assembly of -synuclein (-syn). Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive. We report a novel effect of phospholipid bilayers on the catalysis of -syn aggregation from monomers. We directly visualized -syn aggregation on supported lipid bilayers using time-lapse atomic force microscopy. We discovered that -syn assemble in aggregates on bilayer surfaces even at the nanomolar concentration of monomers in solution. The efficiency of the aggregation process depends on the membrane composition, being highest for a negatively charged bilayer. Furthermore, assembled aggregates can dissociate from the surface, suggesting that on-surface aggregation can be a mechanism by which pathological aggregates are produced. Computational modeling revealed that interaction of -syn with bilayer surface changes the protein conformation and its affinity to assemble into dimers, and these properties depend on the bilayer composition. A model of the membrane-mediated aggregation triggering the assembly of neurotoxic aggregates is proposed.

neuroscience↗

bioRxiv2017

Sensory and decisional components of endogenous attention are dissociable.

Endogenously cueing a stimulus for attention enhances sensory processing of the attended stimulus, and efficiently selects information from the attended stimulus for guiding behavioral decisions. Yet, it is unknown if these sensory and decisional components of endogenous attention are under the control of common, overlapping or distinct mechanisms. Here, we tested human observers in a multi-alternative visuospatial attention task with probabilistic spatial cues, whose predictive validity varied across spatial locations. Observers behavioral choices were analyzed with a multidimensional signal detection model, derived from Bayesian decision theory. The model effectively decoupled attentions effects on perceptual sensitivity from those on decisional thresholds (bias), and revealed striking dissociations between them. Sensitivity was highest at the cued location, and not significantly different among uncued locations, suggesting a spotlight-like allocation of sensory resources at the cued location. On the other hand, bias varied systematically with endogenous cue validity, suggesting a graded distribution of decision thresholds across all locations. Cueing-induced modulations of sensitivity and bias were uncorrelated within and across subjects. Finally, bias selectively correlated with key measures of decision-making: reaction times were strongly correlated with bias, cueing-induced benefits in reaction times were correlated with bias changes independently of sensitivity changes, and subjects who exhibited higher bias, rather than higher sensitivity, toward the cued location produced more optimal behavioral decisions. Our model and findings demonstrate that endogenous cueing of attention does not engage a unitary selection mechanism, but rather involves the operation of dissociable sensory enhancement and decisional selection processes.\n\nSignificance statementThe capacity for selective attention allows us to engage efficiently with the most important objects in the world around us. Attention affects the way we perceive important stimuli and also affects how we make behavioral decisions about these stimuli. In this study, we test human observers on a multiple alternative attention task and show that attentions effects on perceptual processing and decision-making can be dissociated. Specifically, attentions sensory effects alone are in line with the conventional notion of an attentional \"spotlight\". These insights are obtained with a novel Bayesian decision model, which we propose as a powerful tool for teasing apart component processes of cognitive phenomena, and could aid the search for the neural correlates of these phenomena.

neuroscience↗

bioRxiv2017

Hijacking of Multiple Phospholipid Biosynthetic Pathways and Induction of Membrane Biogenesis by a Picornaviral 3CD Protein

RNA viruses induce specialized membranous structures for use in genome replication. These structures are often referred to as replication organelles (ROs). ROs exhibit distinct lipid composition relative to other cellular membranes. In many picornaviruses, phosphatidylinositol-4-phosphate (PI4P) is a marker of the RO. Studies to date indicate that the viral 3A protein hijacks a PI4 kinase to induce PI4P by a mechanism unrelated to the cellular pathway, which requires Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1, GBF1, and ADP ribosylation factor 1, Arf1. Here we show that a picornaviral 3CD protein is sufficient to induce synthesis of not only PI4P but also phosphatidylinositol-4,5-bisphosphate (PIP2) and phosphatidylcholine (PC). Synthesis of PI4P requires GBF1 and Arf1. We identified 3CD derivatives: 3CDm and 3CmD, that we used to show that distinct domains of 3CD function upstream of GBF1 and downstream of Arf1 activation. These same 3CD derivatives still supported induction of PIP2 and PC, suggesting that pathways and corresponding mechanisms used to induce these phospholipids are distinct. Phospholipid induction by 3CD is localized to the perinuclear membrane, the outcome of which is the proliferation of membranes in this area of the cell. We conclude that a single viral protein can serve as a master regulator of cellular phospholipid and membrane biogenesis, likely by commandeering normal cellular pathways.\n\nAUTHOR SUMMARYPicornaviruses replicate their genomes in association with host membranes. Early during infection, existing membranes are used but remodeled to contain a repertoire of lipids best suited for virus multiplication. Later, new membrane synthesis occurs, which requires biosynthesis of phosphatidylcholine in addition to the other more specialized lipids. We have learned that a single picornaviral protein is able to induce membrane biogenesis and decorate these membranes with some of the specialized lipids induced by the virus. A detailed mechanism of induction has been elucidated for one of these lipids. The ability of a single viral protein to commandeer host pathways that lead to membrane biogenesis was unexpected. This discovery reveals a new target for antiviral therapy with the potential to completely derail all aspects of the viral lifecycle requiring membrane biogenesis.

biochemistry↗

bioRxiv2017

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by a RNA-Mediated Dimerization Mechanism

Human APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA editing enzymes function in innate immunity by restricting the replication of viruses and transposons. Misregulated APOBEC3H also contributes to cancer mutagenesis. Here we address the role of RNA in APOBEC3H regulation. APOBEC3H co-purifies with RNA as an inactive protein, and RNase A treatment yields enzyme preparations with stronger DNA deaminase activity. RNA binding-defective mutants are DNA hypermutators. Chromatography profiles and crystallographic data demonstrate a mechanism in which double-stranded RNA mediates enzyme dimerization. RNA binding is required for APOBEC3H cytoplasmic localization and for packaging into HIV-1 particles and antiviral activity. Related DNA deaminases including other APOBEC3 family members and the antibody gene diversification enzyme AID also bind RNA and are predicted to have a similar RNA binding motif suggesting mechanistic conservation and relevance to innate and adaptive immunity and to multiple diseases.\n\nHIGHLIGHTSRNA inhibits human APOBEC3H DNA cytosine deaminase activity\n\nRNA binding mutants are DNA hypermutators\n\nX-ray structure demonstrates an RNA duplex-mediated APOBEC3H dimerization mechanism\n\nRNA binding is required for packaging into HIV-1 particles and antiviral activity

microbiology↗

bioRxiv2017

Bayesian multiple logistic regression for meta-analyses of GWAS

Genetic variants in genome-wide association studies (GWAS) are tested for disease association mostly using simple regression, one variant at a time. Standard approaches to improve power in detecting disease-associated SNPs use multiple regression with Bayesian variable selection in which a sparsity-enforcing prior on effect sizes is used to avoid overtraining and all effect sizes are integrated out for posterior inference. For binary traits, the logistic model has not yielded clear improvements over the linear model. For multi-SNP analysis, the logistic model required costly and technically challenging MCMC sampling to perform the integration.\n\nHere, we introduce the quasi-Laplace approximation to solve the integral and avoid MCMC sampling. We expect the logistic model to perform much better than multiple linear regression except when predicted disease risks are spread closely around 0.5, because only close to its inflection point can the logistic function be well approximated by a linear function. Indeed, in extensive benchmarks with simulated phenotypes and real genotypes, our Bayesian multiple LOgistic REgression method (B-LORE) showed considerable improvements (1) when regressing on many variants in multiple loci at heritabilities [≥] 0.4 and (2) for unbalanced case-control ratios.\n\nB-LORE also enables meta-analysis by approximating the likelihood functions of individual studies by multivariate normal distributions, using their means and covariance matrices as summary statistics. Our work should make sparse multiple logistic regression attractive also for other applications with binary target variables. B-LORE is freely available from: https://github.com/soedinglab/b-lore.

genetics↗

bioRxiv2017

Filament Rigidity And Connectivity Tune The Deformation Modes Of Active Biopolymer Networks

Molecular motors embedded within collections of actin and microtubule filaments underlie the dynamic behaviors of cytoskeletal assemblies. Understanding the physics of such motor-filament materials is critical to developing a physical model of the cytoskeleton and the design of biomimetic active materials. Here, we demonstrate through experiments and simulations that the rigidity and connectivity of filaments in active biopolymer networks regulates the anisotropy and the length scale of the underlying deformations, yielding materials with varying contractility. Semi-flexible filaments that can be compressed and bent by motor stresses undergo deformations that are predominantly biaxial. By contrast, rigid filament bundles contract via actomyosin sliding deformations that are predominantly uniaxial. Networks dominated by filament buckling are robustly contractile under a wide range of connectivities, while networks dominated by actomyosin sliding can be tuned from contractile to extensile through reduced connectivity via cross-linking. These results identify physical parameters that control the forces generated within motor-filament arrays, and provide insight into the self-organization and mechanics of cytoskeletal assemblies.

biophysics↗

bioRxiv2017

Multiple Poliovirus-Induced Organelles Suggested By Comparison Of Spatiotemporal Dynamics Of Membranous Structures And Phosphoinositides

Poliovirus (PV) infection induces membranes with elevated levels of phosphatidylinositol-4-phosphate (PI4P) and invaginated, tubular structures that appear as vesicular clusters in cross section. Here, we characterize PV mutants, termed EG and GG, which exhibit aberrant proteolytic processing of the P3 precursor that can delay the onset of genome replication and/or impair virus assembly. For WT PV, changes to the PI4P pool were observed as early as 30 min post-infection. PI4P remodeling occurred even in the presence of guanidine hydrochloride, a replication inhibitor. Vesicular clusters were not apparent until 3 h post-infection, a time too slow for these structures to be responsible for genome replication. Delays in the onset of genome replication observed for EG and GG PVs were explained completely by the reduced kinetics of virus-induced remodeling of PI4P pools, consistent with PI4P serving as a marker of the genome-replication organelle. Infectious virus produced by GG PV is known to be reduced nearly 5 logs. We show that GG PV was unable to make virus-induced vesicular clusters. Instead, GG PV-infected cells accumulated elongated tubules. Our results are consistent with the existence of distinct organelles for genome-replication and virus assembly. We suggest that the pace of formation and spatiotemporal dynamics of PV induced organelles may be set by the rate of P3 precursor processing to form 3AB and/or 3CD proteins.\n\nAUTHOR SUMMARYAll positive-strand RNA viruses replicate their genomes in association with host cell membranes. PV does not just remodel existing membranes, but induces membranes with unique structure and lipid composition. There has been some suggestion that the functions of the PV induced structures observed during infection may not be those that perform genome-replication. This study uses kinetic analysis of virus-induced membrane formation and PI4P induction by two PV mutants to provide evidence for the existence of a virus-induced genome-replication organelle distinct from a second organelle, the absence of which impairs virus assembly. In addition, our studies suggest that formation of both organelles may require participation of viral proteins, 3AB and/or 3CD. Therefore, this study provides a new perspective on the cell biology of PV infection and should inspire a fresh look at picornavirus-induced organelles, their functions and the role of P3 proteins in their formation.

molecular biology↗

bioRxiv2017

Nanoscale Dynamics of Centromere Nucleosomes and the Critical Roles of CENP-A

In the absence of a functioning centromere, chromosome segregation becomes aberrant, leading to an increased rate of aneuploidy. The highly specific recognition of centromeres by kinetochores suggests that specific structural characteristics define this region, however, the structural details and mechanism underlying this recognition remains a matter of intense investigation. To address this, High speed atomic force microscopy was used for direct visualization of the spontaneous dynamics of CENP-A nucleosomes at the sub-second time scale. We report that CENP-A nucleosomes change conformation spontaneously and reversibly, utilizing two major pathways: unwrapping, and looping of the DNA; enabling core transfer between neighboring DNA substrates. Along with these nucleosome dynamics we observed that CENP-A stabilizes the histone core against dissociating to histone subunits, unique from H3 cores which are only capable of such plasticity in the presence of remodeling factors. These findings have implications for the dynamics and integrity of nucleosomes at the centromere.

biophysics↗

bioRxiv2017

Structure-based analysis of CysZ-mediated cellular uptake of sulfate

Sulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. Current understanding of the cellular delivery of SO42- at the molecular level is limited however. CysZ has been described as a SO42- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42- binding and uptake experiments in cells and proteoliposomes, and single-channel conductance measurements, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42- across membranes. CysZ properties differ markedly from those of known transporters and ion channels. The structures display a hitherto unknown fold with dual topology, assembling in CysZ from Pseudomonas denitrificans as a trimer of antiparallel dimers in the membrane. CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues.

biophysics↗